OGI School of 03/04 Science & Engineering Catalog

www.ogi.edu/catalog OGI School of Science & Engineering

20000 N.W. Walker Road • Beaverton, OR • 97006-8921 phone (503) 748-1027 toll free (800) 685-2423 fax (503) 748-1285 e-mail [email protected] URL www.ogi.edu www.ogi.edu/catalog

0803 TABLE OF CONTENTS | OGI

WELCOME TO THE OGI SCHOOL OF SCIENCE & ENGINEERING LETTER FROM THE DEAN ...... 4 HISTORICAL BACKGROUND ...... 4 MISSION...... 5 EQUAL OPPORTUNITY ...... 5 ACADEMIC CALENDAR ...... 5 ABOUT THIS CATALOG ...... 6 OVERVIEW ACADEMIC DEPARTMENTS ...... 6 DEGREE PROGRAMS...... 6 CERTIFICATE PROGRAMS ...... 6 STUDENTS NOT SEEKING DEGREES ...... 6

ACCREDITATION...... 6

ADMISSIONS ...... 6

TUITION & FINANCES ...... 7

COURSE NUMBERS ...... 7

ACADEMIC POLICIES...... 8

THE CAMPUS...... 10

OVERVIEW OF OGI ACADEMIC PROGRAMS BIOCHEMISTRY AND MOLECULAR BIOLOGY PROGRAM...... 13 BIOMEDICAL ENGINEERING PROGRAM...... 13 COMPUTER SCIENCE AND ENGINEERING PROGRAM...... 13 ELECTRICAL ENGINEERING PROGRAM ...... 13 ENVIRONMENTAL SCIENCE AND ENGINEERING PROGRAM ...... 14 MANAGEMENT IN SCIENCE AND TECHNOLOGY PROGRAM...... 14

ACADEMIC DEPARTMENTS/PROGRAMS/RESEARCH/FACULTY BIOMEDICAL ENGINEERING ...... 15 COMPUTER SCIENCE AND ENGINEERING...... 23 ELECTRICAL ENGINEERING PROGRAM IN SEMICONDUCTOR ENGINEERING...... 41 ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS...... 45 MANAGEMENT IN SCIENCE AND TECHNOLOGY ...... 61

CROSS-INSTITUTIONAL PROGRAMS AND COURSES PROGRAMS OF STUDY IN SPOKEN LANGUAGE UNDERSTANDING ...... 67 APPLIED COMPUTING COURSES...... 67 APPLIED MATHEMATICS COURSES ...... 67 GENERAL EDUCATION COURSES...... 67

COURSE DESCRIPTIONS APPLIED COMPUTING...... 69 BIOMEDICAL ENGINEERING...... 69 COMPUTER SCIENCE AND ENGINEERING...... 71 ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS...... 76 ELECTRICAL ENGINEERING COURSES ...... 79 APPLIED MATHEMATICS...... 84 MANAGEMENT IN SCIENCE AND TECHNOLOGY ...... 85 OREGON MASTER OF SOFTWARE ENGINEERING ...... 88

Photography by Jerome Hart, David Moore, Rick Rappaport, Anne Rybak and Jeff Schilling. 3 OGI | LETTER FROM THE DEAN

research support each year from government and industrial sources. In WELCOME fact, our Department of Computer Science and Engineering ranks an impressive HISTORICAL BACKGROUND 15th in the nation, based on federal research grants. OGI is small enough to The OGI School traces its origins to the early remain responsive to changing needs in 1960s, when Mark Hatfield, then Oregon’s the fields we serve, and to foster governor, and an advisory committee of collaborative, interdisciplinary research industrial and educational leaders across a broad — yet synergistic — range recommended creating an independent of scientific endeavors. institution for graduate education and research in the Portland area. In 1963 they Accredited M.S. degrees are offered established the Oregon Graduate Center for A LETTER FROM THE DEAN through four academic departments: Study and Research. In 1989, the center was It’s about the connections between a Biomedical Engineering (BME), Computer renamed the Oregon Graduate Institute of healthy environment and a healthy Science and Engineering (CSE), Science and Technology. population. It’s about computers that think Environmental and Biomolecular Systems Over the next decade, OGI awarded more like people do, and are reliable enough to (EBS) and Management in Science and than 1,000 graduate degrees, offered trust with the safety of our communities. Technology (MST). Students can earn hundreds of continuing education classes and It’s about helping our seniors live longer, accredited doctoral degrees through the workshops, and pursued more than $100 more satisfying lives. It’s about cultivating BME, CSE and EBS departments. Students million in research, most of it federally business leaders who can guide Oregon’s can also obtain an electrical engineering funded. Now in its third year as a school of high-technology companies through today’s M.S. or Ph.D. degree by selecting EE Oregon Health & Science University, OGI tough markets. At the OGI School of specialization areas within the BME or CSE continues as a premier provider of high- Science & Engineering, it’s all about departments. These specialization areas quality graduate science and engineering building healthier, better-informed and include computer engineering, signal education, with more than 500 students more secure communities in Oregon and processing, medical optics and sensors. working full- or part-time toward master’s or beyond. Virtually everything we do - be it OGI also offers graduate-level certificates Ph.D. degrees, and more than $18 million in graduate education, research, industrial in Management in Science and Technology research annually. collaboration, or community outreach - is and Health Care Management. We are aimed at solving important societal proud of our diverse population of full- and OHSU is a health and research university problems, and at putting these solutions part-time students, who learn in an dedicated to graduate education, research into the hands of those that need them environment where fundamental knowledge and health care. The university educates most. Are you interested in expanding your is balanced with a focus on practical some 3,000 students each year and in 2001 science and engineering knowledge in this problem solving. OGI is committed to brought in more than $212 million in type of environment? As a component of following discoveries from concept all the research dollars - a figure that is expected to Oregon Health & Science University, our way through to fruition, leveraging the grow by 15 to 20 percent annually. About school welcomes high-caliber students who commercial potential of our technologies 1,500 scientists are working on basic and seek to apply advanced technologies in wherever possible to serve the broadest applied research projects throughout OHSU. real-world situations. This electronic possible cross-section of the public. Its merger with OGI has broadened the catalog is designed to tell you everything At OGI, it’s all about making a difference. mission of the institution to encompass new you need to know about pursuing a I’ve tried to give you an idea of how we research frontiers where technology and graduate degree at OGI. make a difference in our region and beyond. engineering converge with health care and biomedicine. As you scroll through the catalog, you may Now, I invite you to read for yourself how be surprised at the wide range of programs OGI can make a difference to you. The OGI School of Science & Engineering offered through such a small school. Since remains committed to its historical purpose: OGI’s inception 40 years ago, the school’s to educate students and conduct high-quality small size has been one of its key strengths. research in science and engineering and to We offer an enviable faculty/student ratio of serve as a resource for Oregon’s high- 1/1.9 for Ph.D. students. Despite our size, technology industry. The merger both OGI awards a significant percentage of Ed Thompson, Ph.D. strengthens OGI’s traditional research-based Oregon’s graduate degrees in high- OHSU Vice-President and Dean programs and enables the school to expand in technology fields, and our highly productive OGI School of Science & Engineering new directions. In 2002, with a $4 million faculty attract approximately $18 million in grant from the M.J. Murdock Charitable Trust, the school established a Department of

4 ACADEMIC CALENDAR | OGI

Biomedical Engineering, the new curriculum ACADEMIC CALENDAR 2003 2004 of which is published here for the first time. | The merger also facilitates cross- FALL QUARTER 2003 disciplinary collaboration, especially in the August 11 Registration begins for Fall Quarter biosciences, environmental sciences and September 22-26 New student orientation week information technology. September 28* Last day to register without late fees OGI is part of OHSU’s West Campus, which September 29 Fall Quarter instruction begins also includes the Vaccine and Gene Therapy October 6 Student account balances due Institute, the Neurological Sciences Institute October 24* Last day to add/drop classes and the Oregon National Primate Research November 10 Registration begins for Winter Quarter Center. The West Campus is about 12 miles November 27-28 Thanksgiving holiday (no classes, OGI offices closed) from OHSU’s central campus on Portland’s December 8-12 Final exams Marquam Hill. December 25 Christmas holiday (OGI offices closed)

MISSION WINTER QUARTER 2004 The mission of the OGI School of Science & November 10 Registration begins for Winter Quarter Engineering is to carry out advanced January 1 New Year’s holiday (OGI offices closed) research in science, engineering and January 4* Last day to register without late fees management that responds to important January 5 Winter Quarter instruction begins social, environmental and industry needs; to January 12 Student account balances due offer outstanding graduate and professional January 19 Martin Luther King Jr.’s Birthday educational opportunities; and, by so doing, (no classes, OGI offices closed) to contribute to the region’s economy and January 30* Last day to add/drop classes well-being. February 9 Registration begins for Spring Quarter February 16 President’s Day (no classes, OGI offices closed) TO ACCOMPLISH THIS MISSION, March 16-19 Final exams (Monday, March 15th will be a regular class day THE OGI SCHOOL: to account for two Monday holidays earlier this quarter) • provides students with the necessary knowledge, skills and breadth for leader- SPRING QUARTER 2004 ship in a technological society; February 9 Registration begins for Spring Quarter * • supports, through research, education and March 28 Last day to register without late fees training, the people, industries and organi- March 29 Spring Quarter instruction begins zations that drive the economic growth of April 5 Student account balances due the Pacific Northwest; April 23* Last day to add/drop classes May 3 Registration begins for Summer Quarter • attracts and develops high-quality faculty, May 31 Memorial Day holiday (no classes, OGI offices closed) students and staff. June 6 Commencement EQUAL OPPORTUNITY June 7-11 Final exams

Oregon Health & Science University and the SUMMER QUARTER 2004 OGI School of Science & Engineering are May 3 Registration begins for Summer Quarter firmly committed to a policy of affirmative June 20* Last day to register without late fees action and equal opportunity. This June 21 Summer Quarter instruction begins encompasses all employment, education and patient service activities connected with June 28 Student account balances due OHSU. No patient, employee, student, July 5 Independence Day holiday (no classes, OGI offices closed) trainee, beneficiary or potential beneficiary July 16* Last day to add/drop classes of the hospitals and clinics or the university August 30- Final exams shall be unlawfully discriminated against on September 3 the basis of race, color, sex, sexual September 6 Labor Day holiday (no classes, OGI offices closed) orientation, religion, creed, national origin, age, marital status, disability, veteran status *Management in Science and Technology weekend and Distance Learning courses have or another applicable basis in law. unique late registration and add/drop deadlines. Please refer to OGI’s quarterly course schedule for the specific MST registration information.

5 OGI | OGI SCHOOL OF SCIENCE & ENGINEERING

ABOUT THIS CATALOG STUDENTS NOT SEEKING DEGREES • Three original letters of recommendation. The letters should attest to the student’s Any qualified student may take courses at This catalog is as accurate as possible as of ability to succeed in a graduate program. OGI, in a part-time capacity, without September 1, 2003. Information contained Recommendation letters must be signed enrolling in a degree program. Students may in the catalog may be changed during the and preferably mailed directly from the take a full-time course load for only one course of any academic year, including but author. If sent in by the student, the quarter while waiting for a decision not limited to changes in policies, fees, recommendation letter must be in a sealed regarding admission to a degree program. course offerings and requirements. This envelope. Alternatively, a recommendation Up to 21 credits completed prior to document should not be construed as form is available to use (see www.ogi.edu/ matriculation (enrollment in a degree forming the basis of a contract. grad-ed/pdf/recommendation_letter.pdf). program), either taken at OGI or transferred Additional student and academic policies from another institution, may be accepted ADDITIONAL REQUIREMENTS FOR are listed in the OGI Student Handbook toward degree requirements. Departmental INTERNATIONAL STUDENTS located at www.ogi.edu/students/ regulations may be more restrictive. studenthandbook.pdf. To be considered for admission to the ACCREDITATION OGI School for a full course of study, OVERVIEW international students must also provide Oregon Health & Science University and the documentation to show that they meet the ACADEMIC DEPARTMENTS OGI School of Science & Engineering are following requirements: accredited by the Commission on Colleges of The OGI School of Science & Engineering • Evidence of adequate financial resources the Northwest Association of Schools and has four academic departments: Biomedical to pay for their OGI education and their Colleges, an institutional accrediting body Engineering (BME), Computer Science and cost of living. Engineering (CSE), Environmental and recognized by the Council for Higher Biomolecular Systems (EBS) and Education Accreditation and/or the U.S. •Written TOEFL scores for all applicants Management in Science and Technology Department of Education. The address whose native language is not English, (MST). Students benefit from cross- is: Commission on Colleges, NWASC, except for those who have earned a degree disciplinary research and education as 8060 165th Avenue NE, Suite 100, from a U.S. institution. The OGI School will faculty members take part in research Redmond, WA 98052. accept both the paper-based test and the projects outside their main department. This computer-based test. Required scores for encourages the exchange of ideas across ADMISSIONS individual programs are discussed in the related research areas and provides the department sections of this catalog. For fullest use of the wide range of ADMISSIONS REQUIREMENTS more information on the TOEFL please visit www.toefl.org. instrumentation available at the school. Individual academic programs have specific requirements in addition to those shown APPLICATION PROCEDURES DEGREE PROGRAMS below. These are found in the department The OGI School of Science & Engineering sections of the catalog. For degree programs, the following items must be submitted: offers M.S. and Ph.D. degrees in: • To enroll in any degree program at the •Biochemistry and Molecular Biology OGI School, an applicant must have pre- • Completed OGI School of Science & •Biomedical Engineering viously earned a four-year bachelor’s, or Engineering application form. equivalent, degree, although a student • Computer Science and Engineering • $65 nonrefundable application fee, which may be provisionally admitted prior to •Electrical Engineering is valid for one year and cannot be waived that time. An international applicant with or deferred. • Environmental Science and Engineering a three-year bachelor’s degree from a for- • Management in Science and Technology eign country should have his/her •Official transcripts from each college or (M.S. degree only) academic credentials evaluated by an university attended. The transcripts must external evaluation company in order to arrive in a sealed envelope and should be CERTIFICATE PROGRAMS determine equivalency to a four-year, mailed directly to the Department of U.S. bachelor’s degree. Graduate Education (see address below). Certificate programs are available through our Department of Management in Science • The Graduate Record Examination • Three letters of recommendation. and Technology in: (GRE) may be required. See Department •Official GRE scores (if applicable, see section for specific requirements. • Health Care Management Department). The institutional code for • Management in Science and Technology • Official transcripts from each college or OGI is 4592. university attended. • TOEFL scores (if applicable, see above).

6 OGI SCHOOL OF SCIENCE & ENGINEERING | OGI

For certificate programs, the following items must includes OHSU’s activity fee, building fee, financial aid may also be found on OHSU’s be submitted: technology fee and incidental fee. Web site, www.ohsu.edu/finaid/. • Completed OGI certificate program appli- The “Free Application for Student Aid” • Environmental and Biomolecular Systems cation form. (FAFSA) forms may be found at students pay tuition on an annual basis, www.fafsa.ed.gov/. Hard-copy forms are • $25 nonrefundable application fee, which which may be paid in full at the beginning available from the OHSU Financial Aid is valid for one year and cannot be waived of the year or in quarterly installments. Office. Use Federal School Code 004883 or deferred. • Deposits. Upon admission as a master’s when completing the FAFSA form. Completed applications, transcripts and student, applicants in the Environmental other application materials should be and Biomolecular Systems department COURSE NUMBERS sent to: must deposit $100 to reserve a place in Department of Graduate Education the program. Deposits will be applied Effective Fall Quarter 2003, the OGI School OGI School of Science and Engineering toward tuition and are nonrefundable. has renumbered many of its courses to 20000 N.W. Walker Road better align course numbers with the Beaverton, Oregon 97006-8921 HEALTH INSURANCE Oregon Health & Science University standard numbering scheme. To assist in Phone: 503 748-1382 Full-time, matriculated students enrolled in relating the new course numbers to courses Toll-free: 800 685-2423 an OGI degree program are eligible for offered in the past, a course number Fax: 503 748-1285 group student medical insurance through “crosswalk” is available online at E-mail to: [email protected] the school. In fact, eligible students must www.ogi.edu/schedule/crosswalk.shtml. either enroll in OGI’s insurance plan or Due dates: Applications are considered on a Additionally, the following guidelines will provide proof of other medical insurance year-round basis. It is highly recommended help you understand the standardized coverage. OGI pays the entire premium for that domestic students submit their features of our new numbering system. applications 10 weeks prior to the quarter full-time Ph.D. students and two-thirds of 5xx Graduate courses offered primarily in which they would like to begin, 15 weeks the premium for full-time master’s students. in support of master’s programs. for international students. NOTE: priority is Insurance for family members may be May be used towards a doctoral given in the admission and financial support purchased for an additional charge. Contact program as appropriate. processes to those applications received by the Graduate Education Department for March 1. current premium rates. 6xx Graduate courses offered primarily in support of doctoral programs. Start date: The academic year formally begins FINANCIAL AID May be used towards a master’s in September and students are encouraged program as appropriate. to start the academic program at that time. Entering full-time Ph.D. students may be However, mid-year admissions may be offer- eligible for financial support through a Courses listed as 5xx/6xx are applicable to ed. Generally, Ph.D. students are admitted combination of tuition scholarships, OGI both a master’s program as well as a for Fall quarter and as full-time students. fellowships, named fellowships and graduate doctoral program. Master’s and certificate research assistantships. Offers of support students should register for the 5xx class STUDENT VISAS are initiated by the individual academic and doctoral students should register for the departments. Part-time Ph.D. students may 6xx class when available. Information on student visas and other be eligible for some of the above. Partial immigration services can be found on the Web The following standard course numbers tuition scholarships may be awarded by the site for OGI’s Office of International Students may be included in each program’s course school or individual academic departments and Scholars, www.ogi.edu/immigration. offerings. Refer to the individual program to entering full-time M.S. students. No for further details. additional application is required. TUITION AND FINANCES 501/601 Master’s Non-Thesis Research/PhD Subsidized and Unsubsidized Federal Pre-qualifying Research TUITION AND FEES Stafford Loans are available to eligible 502/602 Independent Study students who are formally admitted to a For the 2003-2004 academic year, tuition master’s or Ph.D. program at the OGI School 503/603 Master’s Thesis Research/PhD for full-time matriculated students (defined of Science & Engineering. Students must be Dissertation Research as nine or more credit hours per quarter) is enrolled for at least five credits each 504/604 Internship $5,355. Part-time tuition for regular OGI quarter, and must be either U.S. citizens or School of Science & Engineering courses is 505/605 Reading and Conference eligible non-citizens. For application $595 per credit hour or audit unit. Please 506/606 Special Topics Courses materials and additional information, note that there is no full-time tuition rate contact the Financial Aid Office at OHSU at 507/607 Seminar for non-matriculated students, except when 503 494-7800 or 800 775-5460 or 508/608 Workshop an admission decision is pending. Tuition [email protected]. Information about 509/609 Practicum 7 OGI | OGI SCHOOL OF SCIENCE & ENGINEERING

ACADEMIC POLICIES limits directory information to the student’s although nine or more is considered full- full name, address(es) — including but not time status. A student may not register for The following is a summary of selected OGI limited to e-mail address, telephone more than 12 credits in a quarter without School of Science & Engineering academic number(s), major field of study, date(s) of his or her academic department’s approval. policies. A more comprehensive listing can attendance, degrees and dates received, and Up to 18 credits plus four audit units may be found in the OGI School Student the fact of enrollment, including whether the be taken with the approval of the student’s Handbook at www.ogi.edu/students/ student is enrolled full- or part-time. The academic department. Registering for more studenthandbook.pdf. school does not make this information than 18 credits plus four audit units available to vendors. requires Educational Policy Committee AUDITING A COURSE (EPC) permission and will incur an Each student has the right to designate additional tuition cost. OGI courses are offered for graded graduate directory information as not being subject credit hours or ungraded audit units. to release without his or her consent, GRADING/SATISFACTORY ACADEMIC PROGRESS Students may register to audit a course on a except as otherwise permitted by law. space available basis. Students taking a The University Registrar’s Office shall Most OGI School courses are graded with a course for credit have priority over students provide to each student a form entitled letter grade. Research work may be graded auditing a course. Audits are recorded on “Request to Restrict Directory Information” with either a Pass/No Pass or letter grade as the student’s transcript at the discretion of to be used by the student to designate determined by each academic department. the instructor, based upon a reasonable that directory information may not be Transfer credits and Pass/No Pass grades expectation of attendance and minimal released without the student’s consent. If are not counted in students’ Grade Point participation determined by the instructor. the student does not submit the completed Averages (GPAs). The GPA is a weighted Audits are charged at the standard tuition form by the date indicated, the University average of all eligible credits and grade rate. Audit units do not count toward a may release directory information value points. student’s full-time status. Instructors pertaining to that student. have final discretion over allowing audits The following value point scale is employed of their classes and defining their CONTINUOUS ENROLLMENT at the OGI School: academic expectations. A Ph.D. or M.S. student who has begun work A=4.00 B = 3.00 C = 2.00 CONFIDENTIALITY OF STUDENT RECORDS on their dissertation or thesis must register A- = 3.67 B- = 2.67 C- = 1.67 and pay for at least one credit hour of B+= 3.33 C+ = 2.33 F = 0.00 With the passage of the Federal Family research per quarter in order to maintain Educational Rights and Privacy Act matriculated status. If all requirements have The grading system is defined as: (FERPA) of 1974, Oregon Health & Science not been satisfied at the end of four A=Excellent University adopted rules to govern the consecutive academic quarters of collection, use and disclosure of student registering for only one credit per quarter, B=Satisfactory records with the goal of ensuring their or if an alternate plan of completion has not C=Below graduate standard privacy. Students have the right to inspect been approved by the department and the F=Failure their educational records that are Educational Policy Committee, matriculated maintained by OGI/OHSU, the right to a status may be terminated. If the student The following marks are also used: hearing to challenge the contents of those wishes to return to his/her program at a AU = Audit, no credit records when they allege the records later date, it will be necessary to reapply for P=Satisfactory completion contain misleading or inaccurate admission. Continuous enrollment is not information, and the right to give their required of master’s students not pursuing a NP = No credit, unsatisfactory written consent before their records are thesis, nor of master’s or Ph.D. students I=Incomplete released to any person, agency or who have not yet begun working on their PI = Permanent Incomplete organization other than OGI/OHSU thesis or dissertation. However, all W=Withdrawn (after the add/drop period) officials and certain authorized federal matriculated students are required to and state authorities. register for classes or to indicate temporary Matriculated students must maintain a Directory Information. OGI/OHSU can release inactive status by filing a Temporary cumulative GPA of 3.0. Failure to do so will certain public domain information, known as Inactive Status form with the Department of result in academic probation, and if the GPA directory information, unless a student files Graduate Education Department. is not improved, may lead to dismissal. a written request in the OGI Graduate Incompletes. An Incomplete must be completed CREDIT LOAD PER QUARTER Education Department or the OHSU by the end of the quarter following the Registrar’s Office to restrict the disclosure Twelve credits per quarter are considered a quarter in which the Incomplete was of all directory information. The school normal course load for full-time students, awarded. In cases where the Incomplete is

8 OGI SCHOOL OF SCIENCE & ENGINEERING | OGI not completed, the instructor has the choice MEASLES IMMUNIZATION POLICY REGISTRATION of assigning a grade or converting the Every full-time student who was born on or Any qualified student may take courses at Incomplete into a Permanent Incomplete. after January 1, 1957, must provide the OGI the OGI School of Science & Engineering, in The grade may be an “F” but instructors School with evidence of having received a a part-time capacity, without enrolling in a have the option of assigning another grade if sufficient measles vaccination (Rubeola). degree program. Non-matriculated students they feel quality and quantity of work Students are expected to submit a may take a full-time course load for only one accomplished warrants it. If a student completed Immunization Form when they quarter, while waiting for a decision wants an extension of this one quarter first register for classes at OGI. Students regarding admission to a degree program. deadline, the student may petition the who do not provide the needed evidence on Educational Policy Committee (EPC) Each quarter a class schedule is published this form will not be allowed to register for showing the instructor’s support of the with the specific courses being offered with classes for the second or succeeding extension (a separate letter, e-mail or the dates, times and locations. To access a quarters following their initial registration. signature on the petition will suffice). The current class schedule online, visit The complete Measles Immunization Policy petition should be specific, include a date by www.ogi.edu/schedule/. All students and Immunization Form are available from which the grade will be assigned and attending a class must be registered for that the of Graduate Education Department. submitted to the Graduate Education class. A student will not earn a grade or Department in writing. credits for the class if s/he is not registered ON-SITE (RESIDENCY) PH.D. REQUIREMENTS for that class. LEAVE OF ABSENCE The OGI School has a two-year on-site A student may register for classes online residency requirement for Ph.D. programs. In special circumstances, leaves of absence at www.ogi.edu/studentaccounts/. Online Full-time Ph.D. students usually meet this from a graduate program may be allowed. registration is available seven days a week requirement by an on-site dissertation A student considering a leave should first during established registration times. project under the advisement of an OGI discuss the issue with his/her advisor or Alternatively, if a student prefers to register faculty member. Part-time Ph.D. students department academic coordinator. If the in person, he or she may do so at the OGI can satisfy the first year of the on-site department supports the leave of absence, Graduate Education Department. requirement by attendance in classes on the the student then submits a petition to the OGI campus. Because part-time Ph.D. school’s Educational Policy Committee TIME LIMITS TO COMPLETE A DEGREE students, by definition, are not on campus (EPC) for approval. International students full time, the student’s academic department An M.S. degree must be completed should consult with OGI’s Manager of will determine residency requirements for within seven years from the quarter of International Students and Scholars before the second year. matriculation. A Ph.D. degree must be considering a leave of absence. completed within five years from the time In exceptional circumstances (e.g., the student passes the Ph.D. qualifying MATRICULATED VS. NON-MATRICULATED dissertation topics requiring access to exam. Petitions for extensions to the special facilities only available elsewhere), A matriculated student is admitted and time limit must first be approved by other arrangements may be proposed to the enrolled in a degree program. A non- the department and then submitted to student’s academic department for written matriculated student has not applied and the Educational Policy Committee for approval. There is no on-site program been admitted to a degree program. final approval. requirement for M.S. or certificate Full-time matriculated students carry a programs at OGI. minimum of nine credits per quarter. Audit TRANSCRIPTS units do not count toward the nine-credit PRE-MATRICULATION CREDITS APPLIED An official transcript is a formal, written minimum. Academic departments may TOWARD A DEGREE record of a student’s OGI School of Science require students to carry more than nine & Engineering educational experience. All credits per quarter as a condition of A maximum of 21 credits earned before courses taken at the OGI School and other eligibility for a stipend and/or tuition matriculation at OGI may be applied toward OHSU schools are recorded on it, as are all scholarship. Part-time matriculated degree requirements. This maximum may grades and degrees earned while at students are admitted to a degree program, include a combination of up to 12 (up to 18 OGI/OHSU. Requests for transcripts must be carry fewer than nine credits per quarter from Portland State University, the in writing with a signature, submitted either and pay tuition at the per-credit rate. University of Oregon and Oregon State by fax, mail or in person to the OHSU Non-matriculated students pay tuition at University) transfer credits and credits Registrar’s office. Official transcripts are on the per-credit rate and must register for taken at OGI. Individual departmental special paper and have the official OHSU fewer than nine credits unless they have regulations may be more restrictive. If seal. Official transcripts cost $8 per copy n application under review during necessary, a student may petition the when ordered 48 hours in advance. For that quarter. Educational Policy Committee (EPC) for an quicker service or a faxed official transcript exception to this policy.

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the fee is $10. A request form for an and Gene Therapy Institute. The OGI Oregon, Oregon State University, Portland official transcript can be found at campus consists of modern buildings that State University and the six baccalaureate www.ohsu.edu/registrar/transcriptreq.pdf. provide spacious laboratories, faculty and institutions in Washington, e.g., University administrative offices and a research library. of Washington and Washington State TRANSFER CREDIT University. The PORTALS consortium Providing a striking setting for collaborative, includes libraries in the Portland The OGI School of Science & Engineering interdisciplinary research and education, metropolitan area such as Portland State accepts transfer credits from accredited the 80,000 square-foot Bronson Creek University and Reed College. institutions that have not previously been Building is the newest addition to OGI’s applied toward another degree. Up to 12 campus landscape. Acquired by OHSU in The library’s public workstations not only credits may be transferred to OGI (up to 18 2002, the modern three-story brick provide for searching the catalog and the from Portland State University, University of structure is the new home of the OGI library’s databases but also provide entry to Oregon and Oregon State University). administration, members of the West Web resources for faculty, staff and Credits transferred to OGI must typically Campus Services team, and OGI’s students. The librarians will perform come from courses completed before departments of Biomedical Engineering and searches on the systems and databases that matriculation at OGI. The specific credits, Computer Science and Engineering. Taking are not available directly to students. if any, which will be accepted as transfer its name from a scenic stream nearby, the Library orientation is part of the credits into OGI and applied toward degree new building serves as a physical focal point introduction to OGI for new students, and requirements are determined solely by the of the entire West Campus. classes on library research methods are academic department. Only courses with a offered throughout the year. B or better grade may be transferred to a LIBRARY student’s OGI academic record. Transfer COMPUTER FACILITIES The Samuel L. Diack Library’s collection credit grades are not calculated in the OGI includes more than 21,000 monographic The OGI School of Science & Engineering’s grade point average. Credits graded on a titles (including 4,000 electronic books in computing environment gives members of Pass/No Pass basis may not be transferred. computer science and business) and over the community access to a rich array of 500 current print and electronic journal technologies and information resources. THE CAMPUS subscriptions. These support the teaching Many of these resources, including and research efforts at the OGI School by networks and telecommunications, are GEOGRAPHIC SETTING providing texts, conference proceedings, the responsibility of OHSU’s central reference materials, journals and research Information Technology Group (ITG). In The greater-Portland metropolitan area has monographs in the subject areas of addition, many OGI departments and a population of about 1 million, nearly half computer science, electrical engineering, laboratories maintain their own computing the population of Oregon. It provides diverse environmental science, biochemistry, facilities. Most OGI computers connect to a cultural activities including art, music, molecular biology and management as school-wide local area network and to the entertainment and sports. Portland has an related to science and technology. These Internet, providing convenient access to the extensive park system, including the largest resources are supplemented by the OHSU World Wide Web. The local area network is wilderness park within the limits of any city Library’s holdings of more than 74,000 connected to the Internet through two high- in the United States. The OGI School of monographs and 1,200 print and electronic speed data paths. In addition, it is also Science & Engineering is located 12 miles journal subscriptions. OGI students can connected to the Internet 2 (Internet2.edu) west of downtown Portland, in an area access the OHSU Library’s electronic resources. The Internet 2 connection was known as the “Silicon Forest”. OGI’s collections from OGI and can use the print made possible through an alliance of local neighbors include Intel’s largest research collections by visiting the hill campus or academic institutions. and development facility, Tektronix, IBM, requesting materials be sent to OGI. A proxy Hewlett-Packard, Mentor Graphics, Nike, server allows access to the libraries’ HOUSING Adidas and hundreds of other technology- electronic collections from off campus. based companies. Although the OGI School has no on-campus Materials unavailable from the OHSU housing, it is situated amid a very large We are the newest school within Oregon libraries are obtained on interlibrary loan residential area. There are numerous Health & Science University (OHSU), joining for faculty, staff and students at no cost. An apartment complexes, rental houses, bus the Schools of Medicine, Dentistry and online catalog, acquisitions and circulation and light-rail lines and shopping areas Nursing, which are located on the Marquam system is in place. The library is a member nearby. The Graduate Education Hill Campus in downtown Portland. OGI is of two consortia that provide access to other Department maintains a list of local part of OHSU’s 300-acre West Campus, college and university collections. The Orbis apartment buildings, available at which also includes the Neurological Cascade Alliance allows for direct-request http://www.ogi.edu/students/ housing.shtml. Sciences Institute, the Oregon National borrowing from 26 institutions in Oregon Additionally, the Student Council has a Primate Research Center and the Vaccine and Washington, including the University of Web site for current, new and prospective

10 OGI SCHOOL OF SCIENCE & ENGINEERING | OGI

OGI students who are looking for housing pets and pet owners. Following is a information,roommates, etc. This service summary of the policy: Anyone with a is found at http://cse.ogi.edu/council/ medical condition, fear of animals or related forums.html. condition is responsible for notifying the pet owner and the owner is obligated to respect STUDENT COUNCIL the individual’s concerns and requests. Pets are not allowed in specified areas of the The OGI Student Council serves as the campus, including eating areas, classrooms, liaison between the student body and the laboratories, restrooms and the library; they faculty and administration, and strives to must be leashed outside a private office. improve the quality of life for OGI students. Pets are allowed in private offices only Student representatives make themselves available to students in their department to forward comments, ideas and concerns to the Student Council and to promote involvement in student-body activities. Representatives also disseminate pertinent information to other students in their departments. As liaisons, members of the Student Council represent the student body and student interests on a variety of school task forces and committees, including the Educational Policy Committee and the Safety Committee. Two Student Council members are also representatives on OHSU’s All-Hill Council to represent OGI’s student body to the larger institution. This when the owner posts a notice alerting year, one of OGI’s own students, Dan people to the presence of a pet; the pet does Gareau, is president of the All-Hill Council. not bark, hiss or otherwise annoy others; The Student Council sponsors and the pet is caged, on a leash or behind a gate coordinates at least one major social event whenever left unsupervised; and the owner each quarter, open to everyone at the accommodates any individual who is not school. These events have included a comfortable with the pet. In addition, coffeehouse with live music performed by owners must clean up after their pet, pets people from the school community, an must be in good health with current annual International Food and Cultural Fair, immunizations, and animals in heat are not the fall orientation picnic and numerous allowed. Students, faculty, staff or visitors educational forums. Periodic skiing and who violate the policy are notified that their rafting trips have also been arranged. pet can no longer be brought to any part of Many student events throughout OHSU the campus. Our policy does not apply to are open to all students at the four OHSU seeing/hearing or personal assistant schools. More information on Student animals for individuals with disabilities. Council is available on their Web site, http://cse.ogi.edu/concil or by e-mail at [email protected].

PETS ON CAMPUS

The school enjoys the presence of well- behaved pets on our campus and has a detailed pet policy that can be found at www.ogi.edu/policies/pets.html. We consider it a privilege, and not a right, to bring pets onto the campus with certain restrictions. The rights of students, employees and visitors of the school are primary to those of

11 OVERVIEW OF OGI ACADEMIC PROGRAMS | OGI

OVERVIEW OF OGI BIOCHEMISTRY AND MOLECULAR BIOLOGY PROGRAM ACADEMIC PROGRAMS See Department of Environmental and Biomolecular Systems, page 45 Doctor of Philosophy in Biochemistry and Molecular Biology OGI prepares its graduates to Master of Science in Biochemistry and Molecular Biology become leaders in knowledge- driven professions by providing a learning environment strongly BIOMEDICAL ENGINEERING PROGRAM focused on collaborative, See Department of Biomedical Engineering, page 15 interdisciplinary research. OGI Doctor of Philosophy in Biomedical Engineering students learn to reach across Master of Science in Biomedical Engineering traditional academic boundaries Biomaterials Track to seek the knowledge and Biomedical Optics Track resources needed to solve Neuroengineering Track Speech and Language Engineering Track important technological problems. Our curriculum is organized to facilitate this type of educational COMPUTER SCIENCE AND ENGINEERING PROGRAM experience, where students may See Department of Computer Science and Engineering, page 23 choose from a number of Doctor of Philosophy in Computer Science and Engineering challenging paths to reach their Master of Science in Computer Science and Engineering goal of a degree in a particular Adaptive Systems Track discipline. This program-focused Computer Security Track Data-Intensive Systems Track curriculum encourages students Human-Computer Interfaces Track to work closely with their Networking Track Software Engineering Track advisors to select a course of Software Engineering for Industry Professionals Track study that matches their specific Spoken Language Systems Track needs, strengths and career Systems Software Track objectives. The following listing summarizes OGI’s current ELECTRICAL ENGINEERING PROGRAM academic programs and directs Doctor of Philosophy in Electrical Engineering the reader to the corresponding See Department of Biomedical Engineering, page 15 academic department(s) offering See Department of Computer Science and Engineering, page 23 that program. See Electrical Engineering Program in Semiconductor Engineering, page 41 Master of Science in Electrical Engineering BIOMEDICAL ENGINEERING CONCENTRATION: See Department of Biomedical Engineering, page 15 Biomaterials Track Biomedical Optics Track Neuroengineering Track Speech and Language Engineering Track

COMPUTER ENGINEERING AND DESIGN CONCENTRATION:

OGI’s annual Open House provides students See Department of Computer Science and Engineering, page 23 with a friendly introduction to the school’s Computer Architecture Track numerous graduate degree options. Circuit Design Track Signal Processing Track 131 OGI | OVERVIEW OF OGI ACADEMIC PROGRAMS

Master of Science in Electrical Engineering (cont’d) SEMICONDUCTOR ENGINEERING CONCENTRATION: See Electrical Engineering Program in Semiconductor Engineering, page 41 MEMS and Sensors Track Semiconductor Devices and Circuits Track Semiconductor Materials and Device Characterization Track Semiconductor Processing and Materials Track

SIGNALS AND SYSTEMS CONCENTRATION: See Department of Computer Science and Engineering, page 23 Signal and Image Processing Track Machine Learning Track Speech Processing Track

ENVIRONMENTAL SCIENCE AND ENGINEERING PROGRAM See Department of Environmental and Biomolecular Systems, page 45

Doctor of Philosophy in Environmental Science and Engineering Master of Science in Environmental Science and Engineering Environmental Information Technology Track Environmental Health Systems Track

MANAGEMENT IN SCIENCE AND TECHNOLOGY PROGRAM See Department of Management in Science and Technology, page 61

Master of Science in Management in Science and Technology Managing the Technology Company Track Managing in the Software Industries Track

14 THE DEPARTMENT OF BIOMEDICAL approved by the OHSU Faculty Senate. Full Department of ENGINEERING integrates the accreditation from the Oregon University System and the Commission on Colleges of disciplines of engineering, basic the Northwest Association of Schools and Biomedical Engineering biomedical science and clinical Colleges is pending and is expected during science. Our graduate educational the 2003–2004 academic year. Accepted applicants will be initially admitted to the www.bme.ogi.edu/ program is designed to provide a Electrical Engineering program in the DEPARTMENT HEAD broad education across these Department of Biomedical Engineering until Stephen Hanson, Ph.D. disciplines as well as knowledge the BME program is fully accredited, with 503 748-1435 the understanding that they will be E-mail: [email protected] and in-depth research training in reassigned to the BME program once full a specialty field. In our rigorous accreditation is obtained. ASSOCIATE DEPARTMENT HEAD William Roberts, Ph.D. curriculum, a quantitative 503 748-1082 engineering approach is applied ADMISSIONS REQUIREMENTS E-mail: [email protected] to the study of medically related In addition to the general requirements of DEPARTMENT ADMINISTRATOR systems and topics. Our OGI, admission to the BME Department Melanie Erskine requires the following: program prepares students for 503 748-1435 • A B.S. degree or M.S. degree in physics, E-mail: [email protected] careers in academia, industry, mathematics, engineering or other GENERAL INQUIRIES and government. quantitative science discipline is required. 503 748-1082 Highly qualified individuals with degrees The OGI/OHSU Department of Biomedical E-mail: [email protected] in biology may be considered if they have Engineering offers students both didactic demonstrated adequate quantitative skills. education and nontraditional learning modes. Students can do advanced basic research in • The GRE test is required for both M.S. leading laboratories and they can do and Ph.D. applicants unless a waiver is research projects that relate directly to specifically authorized. Additionally, the patients, working under medical supervision TOEFL is required of all applicants whose to develop and apply new technology in the native language is not English. However, clinics or in laboratories that study patients. students who have earned a prior degree in the United States are exempt from this Four degrees are offered: requirement. The preferred minimum • Master of Science in TOEFL score is 620 paper/250 computer. Biomedical Engineering Biomaterials Track Suggested preparatory prerequisites to Biomedical Optics Track the biomedical engineering program Neuroengineering Track include: courses in anatomy/physiology, Speech and Language Engineering Track one year of college biology, organic chemistry, calculus through differential • Master of Science in equations and linear algebra, one year of Electrical Engineering calculus-based physics, basic Biomaterials Track programming skills in a higher-level Biomedical Optics Track language and some experience with Neuroengineering Track numerical analysis software. Speech and Language Engineering Track • Doctor of Philosophy in Biomedical Engineering DEGREE REQUIREMENTS • Doctor of Philosophy in The basic degree requirements for both the Electrical Engineering Biomedical Engineering and the Electrical Engineering programs within the Department ACCREDITATION of Biomedical Engineering are the same. The two programs are differentiated by the OGI is home to Oregon’s first BME department, The curriculum of the Biomedical chosen electives, research project and/or which explores the use of technology to solve Engineering (BME) program has been dissertation topic. medical and healthcare problems. BME | BIOMEDICAL ENGINEERING

During the first year, students will focus part will test knowledge in the student’s BIOMATERIALS TRACK (suggested electives) on the core courses (listed below) chosen specialty. After successful BME 507b Current Topics in ...... 1 credit required for both the Biomedical completion of the Qualifying Exam, the /607b Tissue Engineering Engineering program and the Electrical SPC will work with the student to BME 525/625 Optical Nondestructive ...... 3 credits Evaluation Engineering program. During the student’s develop a research plan and schedule BME 541/641 Biomaterials I ...... 3 credits first year, a Student Program Committee for the dissertation. The dissertation BME 542/642 Biomaterials II ...... 3 credits (SPC) composed of three to five faculty must constitute significant, original BME 543/643 Advanced Tissue ...... 3 credits members, including one from another research resulting in a written Engineering Techniques department, will be formed for each document of publishable quality and BME 544/644 Advanced Biomaterials ...... 3 credits student. This committee will work with must be successfully defended in an BME 545/645 Biocompatibility — ...... 3 credits Host-Implant Interactions the student to advise a course of study oral presentation. EE 511/611 Analytical Scanning ...... 3 credits consistent with both the student’s Electron Microscopy interests and the need for broad CORE CURRICULUM (28 credits) EE 512/612 Focused Ion Beam Technology . . 3 credits knowledge in biomedical engineering BME 507a Biomedical Engineering Seminar . . . 1 credit EE 513/613 Transmission Electron ...... 3 credits and knowledge in the student’s /607a (miinimum 3 terms required) Microscopy CSE 569/669 Scholarship Skills ...... 3 credits ME 555 (PSU) Finite Element Modeling ...... 4 credits chosen specialty. and Analysis (Portland MINF 515 Ethical, Legal, and Social . . . . . 2 credits State University) Issues in Medical Informatics MASTER OF SCIENCE (M.S.) DEGREE Other appropriate Biomaterials courses as approved by LIFE SCIENCES your SPC The M.S. degree requires a total of 61 BME 511/611 Biochemistry for ...... 3 credits NEUROENGINEERING TRACK (suggested electives) credits, comprised of 28 credits of core Biolomedical Engineering courses, 21 credits from elective courses NEUS 627 Systems Neuroscience ...... 5 credits BME 507c Readings in Neurology ...... 1 credit /607c and Neuroscience and 12 or more research credits on an MATHEMATICS AND STATISTICS BME 561/661 Neuronal Control Systems . . . . . 3 credits original research project. A written MATH 510/610 Multivariate Calculus and . . . . . 3 credits BME 562/662 Motor Control ...... 3 credits summary of the research project must be Differential Equations BME 563/663 Mathematical and ...... 3 credits submitted and defended in an oral MATH 517/617 Probability and Statistics ...... 3 credits Computational Modeling of presentation. A student’s SPC should Neuronal Systems SIGNALS AND SYSTEMS approve the selection of elective courses BME 564/664 Methods in Neuromedicine . . . . 3 credits BME 513/613 Biomedical Signal Processing I . . 3 credits BME 565/665 Introduction to ...... 3 credits and research project prior to beginning BME 514/614 Biomedical Instrumentation . . . 3 credits Computational Neurophysiology the class or project. – Signals and Sensors BME 566/666 Biomedical Signal Processing II . . 3 credits BME 567/667 Visual Sensory Systems ...... 3 credits The M.S. degree may be earned as a non- The following specialized tracks are available BME 568/668 Auditory and Visual Processing . 3 credits thesis or thesis option. The non-thesis to students or they may consult with their by Human and Machine option requires an original research SPC to define a custom program. EE 582/682 Introduction to Digital ...... 3 credits project resulting in a written report. The Signal Processing thesis option requires original thesis BIOMEDICAL OPTICS TRACK (suggested electives) EE 584/684 Introduction to Image ...... 3 credits Processing research resulting in a written thesis and BME 522/622 Biomedical Optics I: ...... 3 credits NEUS 623 Introduction to Neuroanatomy . . 3 credits oral defense. Tissue Optics BME 523/623 Biomedical Optics II: ...... 3 credits NEUS 624 Cellular Neurophysiology ...... 4 credits Laser-Tissue Interactions Other appropriate Neuroengineering courses as DOCTOR OF PHILOSOPHY (PH.D.) DEGREE BME 524/624 Biomedical Optics III: ...... 3 credits approved by your SPC Engineering Design The Ph.D. degree requires 28 credits from SPEECH AND LANGUAGE ENGINEERING TRACK BME 525/625 Optical Nondestructive ...... 4 credits the core courses, 27 credits from elective Evaluation TRACK CORE (select 9 credits from the following) courses and a minimum of 36 credits BME 526/626 Computational Approaches . . . . 3 credits BME 568/668 Auditory and Visual Processing . . 3 credits from dissertation research. A Ph.D. to Laser Interaction with by Human and Machine student’s SPC committee may petition to Biological Tissues BME 572/672 Speech Synthesis ...... 3 credits BME 527/627 Computational Approaches . . . . 3 credits CSE 551/651 Structure of Spoken Language . . 3 credits have some of the course requirements to Light Transport with waived if the student demonstrates CSE 552/652 Hidden Markov Models for . . . . . 3 credits Biological Tissues Speech Recognition sufficient graduate-level knowledge of BME 528/628 Physical and Geometrical Optics . . 3 credits TRACK ELECTIVES required subjects. EE 525/625 Introduction to ...... 4 credits Electromagnetics for (select 12 credits for M.S. and 18 credits for Ph.D.) A Ph.D. student is required to pass a Modern Applications BME 571/671 Speech Systems ...... 3 credits Ph.D. Qualifying Exam. The two-part EE 526/626 Electromagnetics for ...... 4 credits CSE 540 /640 Neural Network Algorithms . . . . . 3 credits Modern Applications II and Architectures examination is normally taken 12 to 24 EE 582/682 Introduction to Digital ...... 3 credits CSE 547/647 Statistical Pattern Recognition . . 3 credits months after initial enrollment. The first Signal Processing CSE 550/650 Spoken Language Systems . . . . 3 credits part tests the student’s knowledge of the EE 584/684 Introduction to ...... 3 credits CSE 561/661 Dialogue ...... 3 credits biological sciences, engineering and Image Processing CSE 562/662 Natural Language Processing . . . 3 credits mathematics as they relate to the field Other appropriate Biomedical Optics courses as EE 580/680 Linear Systems ...... 3 credits approved by your SPC of biomedical engineering. The second EE 581/681 Intro to Signals, Systems, . . . . . 3 credits 16 and Information Processing BIOMEDICAL ENGINEERING | BME

EE 582/682 Introduction to Digital ...... 3 credits hired in biomedical engineering with research foci Rehabilitation and Biomechanics Research Signal Processing in medical imaging. In addition, a wide range of Many diseases and disorders of muscle, bone and EE 586/686 Adaptive and Statistical ...... 3 credits faculty across the OHSU campus use imaging in the nervous system result in treatment, Signal Processing their basic and clinical research. Thus, students immobilization, healing and then rehabilitation. MATH 519/619 Engineering Optimization ...... 3 credits will have an opportunity to implement imaging Basic and applied research in the Department of SySc 545 (PSU) Information Theory ...... 4 credits engineering research in a variety of biomedical Biomedical Engineering focuses on the normal and (Portland State University) research settings. Particular areas of abnormal control of movement and musculoskeletal Other appropriate Spoken Language Engineering concentration at OHSU are Neuroimaging, biology. This research is multidisciplinary and courses as approved by your SPC Cardiac Imaging and Cancer Imaging. Anderson, highly collaborative with both clinical and basic Bebo, Beer, Buist, Burnell, Cowley, Fletcher, science departments at OHSU. Currently active OTHER ELECTIVES – ALL TRACKS Hitzeman, Janowsky, Lutsep, Neuwelt, Pavel, research by our faculty has resulted in the BME 502/602 Independent Study Quinn, Raber, Rosenbaum, Sahn, Spencer, development of novel therapeutic devices and BME 504/604 Professional Internship Szumowski, Wang procedures that are tested on patient groups BME 505/605 Readings in Biomedical ...... 1 credit Informatics Research provided by collaborating clinicians. Cordo, Hart, Engineering Herzberg, Horak, Jabri, Klein, Macpherson, Nutt, BME 506/606 Special Topics Courses Informatics activities at OHSU are wide ranging; Orwoll, Peterka, P. Roberts, Shea, Welsh BME 566/666 Biomedical Signal Processing II . . 3 credits currently they include: managing and analyzing BME 581/681 Fourier Analysis ...... 3 credits gene expression data; programs in medical Tissue Engineering and Biomaterials Research informatics and outcomes research; basic research Research in tissue engineering and biomaterials is in databases; networks and embedded systems; and represented by a multi-disciplinary group of RESEARCH PROGRAMS techniques for 3-D visualization. The BME materials scientists, biomedical and tissue department serves as a focus for developing Biomedical Optics engineers, chemists, physiologists, dentists and technologies that leverages this expertise, in such physicians. Faculty projects include the following Research in biomedical optics is focused on the areas as computational bioengineering, medical research: physical biomechanics of dental and development of uses for lasers and light in visualization, integration of genomic and medical orthopedic implants, computational biomechanics medicine and biology. Examples of ongoing information, home health networking and hybrid of dental implants, dental restorations, dissolution applications in this well-established research instrumentation. BME will also contribute to and volatilization from dental alloys; non-invasive program include the use of lasers in clinical existing curricula in bioinformatics. Baptista, and non-destructive evaluation of engineered diagnosis, nondestructive evaluation of tissues, Cohen, Cowan, Delcambre, Dubay, Wu Chang Feng, tissues; laser welding of tissues; natural, optical imaging of disease, and light-activated Wu Chi Feng, Hersh, Hook, Hosom, Jones, Kiebertz, protein-based biomaterials; polymer mechanics; chemotherapy for cancer. Facilities include those Kramer, Launchbury, Logan, Pentacost, Price, micromechanics of biocomposites; thermal analysis; for both clinical application and basic research. Retzer, Roberts, Searles, Sheard, Walpole tribology; collagen and other biocomposites; skin Holmes, Jacques, Kirkpatrick, Prahl, Song Neuroengineering Research scaffolds; bone healing; blood vessel substitutes, Cardiovascular Bioengineering vascular grafts, and endovascular stents. Basic neuroscience research, clinical neurology Descriptions of specific projects are linked to the Cardiovascular bioengineering (CBE) is a growing and neurosurgery are strong programs within topics listed below. Dawson, Ferracane, Gregory, area of interest at OHSU. The CBE program will OHSU. The existence of a department of biomedical Hanson, Herzberg, Hinds, Kirkpatrick, McCarthy, encompass major areas of interest using engineer- engineering in this center of neuroscience research Sakaguchi, Shea, Winn ing tools for investigation. These areas will include and clinical medicine creates rich opportunities for cardiac and vessel mechanics, computational fluid biomedical engineers. They can work with dynamics, electrocardiography and electrical signal neuroscientists and clinicians to apply emerging FACILITIES processing, 4-D embryo modeling, functional scientific knowledge in the development of The Department of Biomedical Engineering magnetic resonance imaging, ultrasound tech- processes and devices needed for the diagnosis, occupies approximately 25,000 square feet on the nology, cellular mechano-transduction and gene assessment and treatment of neurological third floor of the Bronson Creek building, a modern expression, blood-material interactions, thromb- disorders and diseases. Ongoing research building on the OHSU/OGI West Campus, and osis, laser thrombolysis, and hemostasis. Baptista, opportunities range from very basic molecular additional space in the Murdock and Vollum Chugh, Ellenby, Faber, Goldstein, Gregory, Hanson, biophysics and modeling to systems analysis to buildings and the Oregon National Primate McNames, Sahn, Thong, Thornburg drug delivery systems, neuroprosthetics, and Research Center on that campus. The department’s neurosurgical devices. Baumann, Burchiel, Cohen, Genetic Engineering space accommodates “wet” labs with biosafety Cordo, Hammerstrom, Hayes, Hermansky, Hinds, hoods as well as other lab space. The department Genetic engineering is a branch of biology that Hitzeman, Hosom, Huber, Jabri, Larsson, involves the manipulation and modification of DNA, is equipped with a modern computer network Macpherson, Neuwelt, Nuttall, Pavel, Peterka, system, serviced by OGI’s and OHSU’s Information in particular the introduction of a foreign DNA P. Roberts, W. Roberts, Song, Welsh, Westbrook fragment into a DNA sequence. DNA is the Technology Groups. Most student work stations are blueprint for the individuality of an organism. The Point-of-Care Biomedical Engineering equipped with high-speed network connections. Special facilities, such as a simulated residential organism relies upon the information stored in its Research in this area is focused on the health care facility are also available. Video DNA for the management of every biochemical development of health care delivery systems teleconferencing facilities are available to allow process. The life, growth, and unique features of suitable for use in homes, assisted-living facilities students and faculty to interact with others at the organism depend on its DNA. Genes are the and other residential settings. Application areas seminars and other events on OHSU’s Marquam segments of DNA that are associated with specific include processes and technologies for the Hill Campus. features or functions of an organism. Duvoisin, monitoring, evaluation and treatment of people Some students’ research projects are carried out in Frueh, Harrington, Reddy disabled by aging, chronic disease, or disability. laboratories in other OHSU departments or in local Research challenges include the development of industries. Available facilities in which students Imaging Research unobtrusive sensors, wireless communication of may do research projects include: Oregon Medical Imaging technology is now central to the diagnosis multi-rate signals, processing and fusion of signals Laser Center, Advanced Imaging Center, Oregon and treatment of nearly all diseases and is critical from multitudes of noisy sensors, and ubiquitous Hearing Research Center, Neurological Sciences for drug development, evaluation of treatment perceptual interfaces. Fried-Oken, Hammerstrom, Institute, and Heart Research Center, as well as effects as basic science on the biology of normal Hayes, Hermansky, Horak, Huber, Krohn, Maier, the many labs in the basic science departments and abnormal tissue function. Core faculty will be Pavel, Peterka and institutes of OHSU. 17 BME | BIOMEDICAL ENGINEERING | F ACULTY FACULTY

STEPHEN HANSON WILLIAM J. ROBERTS TAMARA HAYES MONICA THACKER HINDS Professor and Department Head Assistant Professor and Assistant Professor Assistant Professor Ph.D., Chemical Engineering Associate Department Head Ph.D., Behavioral Neuroscience Ph.D., Mechanical Engineering University of Washington, 1977 Ph.D., Physiology University of Pittsburgh, 1994 Johns Hopkins University, 1998 [email protected] University of Minnesota, 1970 [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Thrombosis and vascular healing RESEARCH INTERESTS Algorithms and technologies for Relationship between fluid responses are being evaluated in Neuroengineering. Neuronal improving speech and language dynamics and extracellular matrix animal models to identify key mechanisms of pain. Influence of processing in patient and elderly production by cells, vascular hemostatic mechanisms, blood sympathetic nervous system on populations (augmentative tissue engineering, role of component interactions with sensory functions. Electrical communication). Attentional mechanical stimulation in tissue natural and synthetic surfaces and stimulation for pain relief. processes in human language engineered constructs, elastin the effects of blood-flow Motor systems. processing. Adaptive computer based biomaterials. phenomena. Our ultimate goals interfaces for improving human are to develop more effective anti- REPRESENTATIVE PUBLICATIONS task performance (augmented REPRESENTATIVE PUBLICATIONS thrombotic and anti- Bon, K., Wilson, S.G., Mogil, J.S., cognition). Unobtrusive monitoring M.T. Hinds, D.W. Courtman, T. Goodell, arteriosclerotic drug therapies, Roberts, W.J., “Genetic Evidence for technologies for remote care of M. Kwong, H. Brant-Zawadzki, A. and to improve the performance of the Correlation of Deep Dorsal Horn elderly populations (point-of-care Burke, B. Fox, and K.W. Gregory, prosthetic cardiovascular devices. fos Protein Immunoreactivity with engineering). “Development of a Xenogenic Elastin- Tonic Formalin Pain Behavior Journal based Biomaterial: Calcification and of Pain. 3,181–189, 2002. Inflammatory Effects of Aluminum REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS Chloride Treatment,” Journal of Gillette, R.G., Kramis, R.C., Roberts, Hanson, S.R., “Blood Coagulation and A.M. Adami, T. L. Hayes, and Biomedical Materials Research W.J., “Suppression of Activity in Spinal Blood-Materials Interactions,” in M. Pavel, “Unobtrusive Monitoring (accepted), 2003. Nocireceptive ‘Low Back’ Neurons Biomaterials Science, 2nd Edition of Sleep Patterns,” 25th Annual by Paravertebral Somatic Stimuli S.J. Kirkpatrick, M.T. Hinds, and (Ratner, B.D., Hoffman, A.S., Schoen, International Conference of the IEEE in the Cat,” Neurosci Lett. 1998 Jan D.D. Duncan, “Acousto-optical F.J., Lemons, J.E., Eds.), Academic Engineering In Medicine And Biology 23;241(1), 45–8. Characterization of the Viscoelastic Press, New York, in press, 2003. Society, Cancun, September 2003. Nature of a Nuchal Elastin Tissue Kramis, R.C., Roberts, W.J., Gillette, Gruber, A., Cantwell, A., DiCera, T.L. Hayes, K. Li, and M. Pavel, Scaffold,” Tiss. Eng. (accepted), 2003. R.G., “Non-nociceptive Aspects of E., Hanson, S.R., “The W215A/E217A “Augmenting Search Performance by Persistent Musculoskeletal Pain,” M.T. Hinds and S.J. Kirkpatrick, Mutant of Thrombin Shows Safe Improving Attention Allocation,” J Orthop Sports Phys Ther. 1996 “Material Properties of Engineered and Potent Anticoagulant and Bio-Bionics: DARPA Augmenting Oct;24(4), 255–67. Tissues Evaluated with Nondestructive Antithrombotic Effects in vivo. J Biol Cognition Workshop, Kona, Hawaii, Methods,” Proceedings SPIE Chem 277(31), 27581–4, 2002. Kramis, R.C., Roberts, W.J., Gillette, January 2003. 4617:275–283, 2002. R.G., “Post-sympathectomy Neuralgia: Verheye, S., Markou, C.P., Salame, T.L. Hayes, “Harness the Internet for Hypotheses on Peripheral and Central M. Kajitani, Y. Wadia, M.T. Hinds, M.Y., Wan, B., King, S.B., Robinson, Telemedicine Programs,” invited Neuronal Mechanisms,” Pain, 1996 J. Teach, K.R. Swartz, and K.W. K.A., Chronos, N.A., Hanson, S.R., workshop at Develop and Maintain Jan;64(1), 1–9. Gregory, “Successful Repair of “Reduced Thrombus Formation by Profitable Telemedicine Programs, Esophageal Injury Using an Elastin- Hyaluronic Acid Coating of Fine, P.G., Roberts, W.J., Gillette, Conference, Boston, MA, April 1996. based Biomaterial Patch,” Asaio J, Endovascular Devices,” Arterioscler R.G., Child, T.R., “Slowly Developing T.L. Hayes and D.A. Lewis, 47(4), 342–5, 2001. Thromb Vasc Biol 20, 1168–1172, Placebo Responses Confound Tests of “Anatomical Specialization of the 2000. Intravenous Phentolamine to Determine M.T. Hinds, Y.J. Park, S.A. Jones, Anterior Motor Speech Area: Mechanisms Underlying Idiopathic D.P. Giddens, and B.R. Alevriadou, Markou, C.P., Lutostansky, E.M., Ku, Hemispheric Differences in Chronic Low Back Pain,” Pain, 1994 “Local Hemodynamics Affect Monocytic D.N., Hanson, S.R., “A Novel Method for Magnopyramidal Neurons,” Brain and Feb;56(2), 235–42. Cell Adhesion to a Three-Dimensional Efficient Drug Delivery,” Ann Biomed Language 49, 289–308, 1995. Flow Model Coated with E-selectin,” Eng 26, 502–511, 1998. Gillette, R.G., Kramis, R.C., Roberts, T.L. Hayes and D.A. Lewis, Journal of Biomechanical Engineering, W.J., “Sympathetic Activation of Cat Hanson, S.R. and Sakariassen, K.S., “Hemispheric Differences in Layer III 34(1), 95-103, 2001. Spinal Neurons Responsive to Noxious “Blood Flow and Antithrombotic Drug Pyramidal Neurons of the Anterior Stimulation of Deep Tissues in the Low M. Kajitani, Y. Wadia, H. Xie, M. Hinds, Effects,” Am Heart Journal 135, Language Areas,” Archives of Neurology Back,” Pain, 1994 Jan;56(1), 31–42. S. Shalaby, K. Schwartz, and K.W. S132–S145, 1998. 50, 501–505, 1993. Gregory, “Use of New Elastin Patch and Glue,” ASAIO J, 46(4), 409–414, 2000.

18 F ACULTY | BIOMEDICAL ENGINEERING | BME

JOHN-PAUL HOSOM STANLEY J. HUBER MARWAN JABRI STEVEN L. JACQUES Assistant Professor Assistant Professor Gordon and Betty Moore Professor Ph.D., Computer Science M.D., School of Medicine Professor of Microelectronics Ph.D., Biophysics and and Engineering, Oregon Health & Ph.D., Electrical Engineering Medical Physics Oregon Graduate Institute of Science University, 1965 University of Sydney, 1988 University of California, Science & Technology, 2000 [email protected] [email protected] Berkeley, 1984 [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Blood chemistry by ophthalmic Artificial intelligence and RESEARCH INTERESTS Automatic speech recognition spectroscopy; instrumentation; intelligent signal processing. The Biomedical optics and laser-tissue (ASR). Time alignment of neuroengineering; point-of-care understanding of the principles by interactions. Development of phonemes. Acoustic-phonetic biomedical engineering which humans and/or other diagnostic and therapeutic devices analysis of speech. Assistive organisms perceive the for medicine and biology using technology. REPRESENTATIVE PUBLICATIONS environment, process sensory optical technologies. S.J. Huber, “Photic Pulse Stimulator signals, reason, make decisions REPRESENTATIVE PUBLICATIONS for ERG Analysis,” Sloan Foundation and learn. The development and REPRESENTATIVE PUBLICATIONS J. P. Hosom, “Automatic Speech S.J. Huber, “Battlefield application of biologically inspired S.L. Jacques, J.C. Ramella-Roman and Recognition,” in Encyclopedia of Management of Ocular Injuries,” information engineering. The K. Lee, “Imaging Skin Pathology with Information Systems, H. Bidgoli (ed.)., ICMM, Interlochen, Switzerland design of integrated systems for Polarized Light,” J. Biomed. Opt., in vol. 4, pp. 155-169, Academic Press, press, 2002. S.J. Huber, “Biological Effects of intelligent signal processing. San Francisco, 2003 (invited chapter). Space Radiation Fields,” Classified J.A. Viator, G. Au, G. Paltauf, J. P. Hosom, A. B. Kain, T. Mishra, Report, USAF MOL Project REPRESENTATIVE PUBLICATIONS S.L. Jacques, S.A. Prahl, H. Ren, J. P. H. van Santen, M. Fried-Oken Z. Chen and J.S. Nelson, “Clinical S.J. Huber, “Triage and O. J.-M. D. Coenen,.M.P. Arnold, and J. Staehely, “Intelligibility of Testing of a Photoacoustic Probe for Management of Ocular Injuries,” T.J. Sejnowski and M.A. Jabri, “Parallel Modifications to Dysarthric Speech,” Port Wine Stain Depth Determination,” CIOMR, Brussels, Belgium Fiber Coding in the Cerebellum for The 2003 International Conference Lasers Surg. Med., 30 (2), 141–8, Lifelong Learning,” Autonomous Robots, on Acoustics, Speech, and Signal S.J. Huber, “Hazards of Military 2002. 11(3), 291–7, Kluwer Academic Processing (ICASSP 2003), Hong Kong, Lasers,” CIOMR, Brussels, Belgium Publishers, The Netherlands, 2001. S.L. Jacques, N. Ramanujam, April 2003. S.J. Huber, “Radiation Induced Eye G. Vishnoi, R. Choe and B. Chance, B. Zhang, R. Coggins, M.A. Jabri, D. J. P. Hosom, “Automatic Phoneme Injuries,” CIOMR, Brussels, Belgium “Modeling Photon Transport in D. Dersch, and B. Flower, “Multiresolution Alignment Based on Acoustic-Phonetic Transabdominal Fetal Oximetry,” S.J. Huber, “TacStar, A New Concept Forecasting for Futures Trading Using Modeling.” The 2002 International J. Biomed. Optics, 5, 277–282, 2000. in Military Medical Training,” CIOMR, Wavelet Decompositions,” IEEE Conference on Spoken Language Wurzburg, Germany Transactions on Neural Networks, V.V. Vaidyanathan, S. Rastegar, Processing (ICSLP 2002), Boulder, Co., 12(4), 767–775, July 2001. T.W. Fossum, P. Flores, E.W. van der vol. I, pp. 357–360, September 2002. Breggan, N.G. Egger, S.L. Jacques M.A. Jabri and R. Coggins, J.P. Hosom and R.A. Cole, “Burst and M. Motamedi, “A Study of “Micro Power Adaptive Circuits for Detection Based on Measurements of Aminolevulenic Acid-induced Implantable Devices,” in Low Power- Intensity Discrimination.” The 2000 Protoporphyrin IX Fluorescence Low Voltage Circuits and System, International Conference on Spoken Kinetics in the Canine Oral Cavity,” E. Sanchez-Sinencio and Andreas Language Processing (ICSLP 2000), Lasers Surg. Med., 26, 405–414, 2000. Andreou, eds., IEEE Press, pp. 500- Beijing, vol. IV, pp. 564-567, Oct. 2000. 518, 1999. S.L. Jacques, J. Roman and K. Lee, J.P. Hosom, R.A. Cole and P. Cosi, “Imaging Superficial Tissues with R. Coggins and M.A. Jabri, “A Low “Improvements in Neural-Network Polarized Light,” Lasers Surg. Med., Complexity Intracardiac Electrogram Training and Search Techniques for 26, 119–129, 2000. Compression Algorithm,” IEEE Continuous Digit Recognition,” Transactions on Biomedical Engineering, L.V. Wang, and S.L. Jacques, “Source Australian Journal of Intelligent 46(1), 82–91, January 1999. of Error in Calculation of Optical Information Processing Systems, 5(4), Diffuse Reflectance from Turbid Media 277–284, Summer 1999. J. Raymond, W. Wang and M.A. Jabri, Using Diffusion Theory,” Comput. “A Computational Model of the Auditory J.P. Hosom and M.Yamaguchi, Methods Programs Biomed., 61(3), Pathway to the Superior Colliculus,” in “Proposal and Evaluation of a Method 163–70, 2000. Brain-like Computation and Intelligent for Accurate Analysis of Glottal Source Information Systems, Shun-ichi Amari Parameters,” The Institute of and Nikola Kasabov, eds., Springer Electronics, Information and Verlag, pp. 81-104, 1998. Communication Engineers (IEICE) Transactions on Information and X.Q. Li and M.A. Jabri, “Machine Systems, E77-D (10), pp. 1130-1141, Learning-based VLSI Cells Shape October 1994. Function Estimation,” IEEE Transactions on CAD for Integrated Circuits and Systems, 17(7), 613–623, 1998.

19 BME | BIOMEDICAL ENGINEERING | F ACULTY

SEAN J. KIRKPATRICK JACK MCCARTHY MISHA PAVEL TRAN THONG Associate Professor Assistant Professor Professor Assistant Professor Ph.D., Biomechanics Ph.D., Materials Science Ph.D., Experimental Psychology Ph.D., Electrical Engineering Unversity of Miami, 1992 and Engineering New York University, 1980 Princeton University, 1975 [email protected] Oregon Graduate Institute of [email protected] [email protected] Science & Technology, 1996 RESEARCH INTERESTS [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Development and application of Analysis and modeling of complex Cardiovascular engineering in the coherent light techniques to RESEARCH INTERESTS behaviors of biological systems, area of cardiac tachyarrhythmia address issues in biomaterials Ongoing research includes including visual and auditory prediction and prevention both in science and tissue mechanics. multibeam electron processing, pattern recognition, atria and ventricles, heart rate Laser speckle techniques are of nanolithography, control of information fusion and decision- variability as an indicator of particular interest. Recent nanoscale hillocks in sputtered Au making. Development of parasympathetic (vagal) tone investigations have focused on the metallizations for use in GaAs engineering systems mimicking during relaxed states such as evaluation of the micromechanical devices and the fabrication and these abilities to support meditation and sleep and as a long behavior of vascular, development of sensor-chip multimodal communication term indicator of health in mind- dermatological and skeletal tissues hybrids for monitoring the between humans and machines body exercise programs like yoga using novel laser speckle strain electrical activity of the heart, (speech and video), machine and tai-chi, effect of measurement methods. Other pathogens, organic and inorganic vision, visually guided vehicular parasympathetic tone on interests include experimental gases in the environment. This control and virtual reality. tachyarrhythmia, in-vivo micro- investigations into the research requires fabrication and Applications of these techniques to recording of cardiac cell micromechanics of synthetic characterization on the micron, the development of future depolarization. biomaterials used to replace or sub-micron and nano-scales. The biomedical and healthcare augment damaged or pathological primary fabrication tool in this systems, in particular point-of Biomedical signal processing using tissue. research is the focused ion beam care biomedical engineering. discrete time modeling and system workstation (FIB), which permits design. REPRESENTATIVE PUBLICATIONS seeing, machining and REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS S.J. Kirkpatrick and D.D. Duncan, microforming on the micron and Adami, A., Yang, K., Song, X., “Acousto-optical Assessment of Skin nanoscales. The characterization and Pavel M., “Model-Base Image T. Thong and J. McNames, Viscoelasticity,” Proc. SPIE, 2003 Processing and Analysis for Fracture “Transforms for Continuous Time is provided by scanning and System Modeling,” Proceedings 45th (in press). transmission electron microscopy Classification,” Proceedings of the Second Joint Engineering in Medicine IEEE Midwest Symposium on Circuits S.J. Kirkpatrick, M.T. Hinds, and (SEM, TEM) and atomic force and Biology Conference, October 2002, and Systems, August 4–7, 2002, Tulsa, D.D. Duncan, “Acousto-optical microscopy (AFM). FIB fabrication Houston, TX, pp. 2525–2527. Oklahoma, pp. II-408–II-411. Characterization of the Viscoelastic techniques and SEM, AFM and Nature of a Nuchal Elastin Tissue McGee, D.R., Pavel, M. and Cohen, T. Thong and J. McNames, “Nonlinear Scaffold,” Tissue Engineering TEM characterization and in-situ P.R. (2001) “Context Shifts: Representation of Over-sampled (accepted), 2002. experimentation feedback are used Extending the Meanings of Physical Coarsely Quantized Signals,” Objects with Language,” Human Proceedings 45th IEEE Midwest S.J. Kirkpatrick and D.D. Duncan, to accelerate research on Computer Interaction, 16, Context- Symposium on Circuits and Systems, “Optical Assessment of Tissue nanofabrication, biomimetic aware computing. August 4–7, 2002, Tulsa, Oklahoma, Mechanics,” in Optical Biomedical sensors, biomaterials and pp. II-416–II-417. Diagnostics, V.V. Tuchin, ed., SPIE microelectronic thin films. J. Palmer, P. Verghese and M. Pavel, Press, Bellingham, WA, 2002. “The Psychophysics of Visual Search,” T. Thong, B. Goldstein, “Prediction Vision Research, 40, 1227–1268, 2000. of Tachyarrhythmia Episodes,” S.J. Kirkpatrick, D.A. Baker and REPRESENTATIVE PUBLICATIONS Proceedings of the Second Joint D.D. Duncan, “Speckle Tracking of S. Gosavi, J.M. McCarthy, J.L. House, T. Arai, M. Pavel, H. Hermansky EMBS/BMES Conference, Houston, TX, Low-frequency Surface Acoustic Waves B. Scholte van Mast, G. Janaway and and C. Avendano, “Syllable October 23–26, 2002, pp. 1445–1446. for Mechanical Characterization of C.N. Berglund, “Stability Improvement Intelligibility for Temporally Filtered T. Thong, B. Goldstein, “Prediction of Tissues,” Proceedings SPIE, p. 461, at High Emission Densities for Gold LPC Cepstral Trajectories,” Journal of Ventricular Tachyarrhythmia Episodes 2002. Thin Film Photocathodes Used in the Acoustical Society of America, 105, from Heart Rhythm Data by a Vagal Advanced Electron Beam 2783–2791, 1999. S.J. Kirkpatrick, M.T. Hinds and Fatigue Index,” Abstract 435, Lithographies,” 45th International D.D. Duncan, “Laser Speckle Method R.K. Sharma, T.K. Leen and M.Pavel, Circulation, 106(19), II-86. for Measurement of Cell and Cell Sheet Conference on Electron, Ion and Photon “Probabilistic Image Sensor Fusion,” Mechanics,” Proceedings SPIE, Beam Technology and Nanofabrication, in Advances in Neural Information T. Thong, B. Goldstein, “Sustained p. 4617, 2002. accepted for publication in JVSTB, Processing Systems 11, M.S. Kearns, Ventricular Tachyarrhythmia Prediction Nov.-Dec. 2001. S.A. Solla and D.A. Cohn, eds., MIT from Heart Rhythm Data,” Abstract M.T. Hinds and S.J. Kirkpatrick, 333, PACE, Vol. 26, No. 4, Part II, J.M. McCarthy, Z. Pei, M. Becker and Press, Cambridge, Mass., 1999. “Material Properties of Engineered p. 1012. Tissues Evaluated with Nondestructive D. Atteridge, “FIB Micromachined Methods,” Proceedings SPIE, Submicron Thickness Cantilevers for p. 4617, 2002. the Study of Thin Film Properties,” Thin Solid Films 358, 146–151, 2000.

20 F ACULTY | BIOMEDICAL ENGINEERING | BME

JOINT FACULTY ROBERT PETERKA RICHARD FAIRLEY Associate Scientist Associate Dean of Academic THOMAS BAUMANN Neurological Sciences Institute Affairs and Professor Associated Professor Oregon Health & Science University Department of Computer Science Department of and Engineering SCOTT PRAHL Neurological Surgery OGI School of Science Oregon Health & Science University Assistant Professor & Engineering Oregon Medical Laser Center PHIL COHEN BRAHM N. GOLDSTEIN PATRICK ROBERTS Professor Professor JAN P. H. VAN SANTEN Department of Computer Science Assistant Scientist Director of Medical Services & Engineering Neurological Sciences Institute Professor and Center Doernbecher Children’s Hospital OGI School of Science Oregon Health & Science University Director of CSLU & Engineering JAMES HOOK Ph.D., Mathematical Psychology RON SAKAGUCHI Professor and Department Head University of Michigan, 1979 PAUL CORDO Professor Department of Computer Science [email protected] Scientist and Director Department of Biomaterials and Engineering Neurological Sciences Institute & Biomechanics OGI School of Science RESEARCH INTERESTS Oregon Health & Science University OHSU School of Dentistry & Engineering Speech timing, intonation, signal JACK FERRACANE XUBO SONG JERI JANOWSKY processing, statistical analysis of Professor and Chair Assistant Professor text and speech corpora, and text- Associate Professor Department of Biomaterials Department of Computer Science to-speech (TTS) system evaluation. Department of Neurology & Biomechanics & Engineering OHSU School of Medicine Oregon Health & Science University OGI School of Science REPRESENTATIVE PUBLICATIONS & Engineering DAVID MAIER J. van Santen and B. Möbius, MELANIE FRIED-OKEN Professor “A Model of Fundamental Frequency Associate Professor KENT THORNBURG Contour Alignment,” in Intonation: Department of Computer Science Professor Analysis, Modelling and Technology, Department of Neurology and Engineering Cambridge University Press, Oregon Health & Science University Department of Physiology OGI School of Science and Pharmacology Cambridge, United Kingdom, 2000. DAN HAMMERSTROM & Engineering J. van Santen and C. Shih, OHSU School of Medicine Professor “Segmental and Suprasegmental Timing EDWARD NEWELT in American English and Manadarin Department of Computer Science Professor Chinese,” Journal of the Acoustical & Engineering AFFILIATE FACULTY Department of Neurology Society of America, 1012–1026, 2000. OGI School of Science OHSU School of Medicine ANTÓNIO BAPTISTA J. van Santen and R. Sproat, & Engineering “Highaccuracy Automatic Professor and Head SUSAN PRICE Segmentation,” Proceedings of FAY HORAK Department of Environmental Assistant Professor EUROSPEECH 99, Budapest, Senior Scientist and Biomolecular Systems Department of Medical Informatics Hungary, 1999. Neurological Sciences Institute OGI School of Science and Outcomes Research J. van Santen, “Combinatorial Issues Oregon Health & Science University & Engineering OHSU School of Medicine in Text-to-speech Synthesis,” Proceedings of EUROSPEECH 97, TODD LEEN NINIAN J. BLACKBURN P. HEMACHANDRA REDDY Rhodes, Greece, 1997. Professor Professor Assistant Scientist J. van Santen and A.L. Buchsbaum, Department of Computer Science Department of Environmental Neurological Sciences Institute “Methods for Optimal Text Selection,” & Engineering and Biomolecular Systems Oregon Health & Science University in Proceedings Eurospeech 1997, OGI School of Science OGI School of Science Rhodes, Greece, 1997. DAVID J. SAHN & Engineering & Engineering J. van Santen, “Prosodic Modelling in Professor Text-to-speech Synthesis,” in MELANIE MITCHELL KIM BURCHIEL Departments of Pediatrics, Proceedings Eurospeech, 1997, Associate Professor Chief Diagnostic Radiology, and Rhodes, Greece, 1997. Department of Computer Science Department of Obstetrics and Gynecology; J. van Santen, “Segmental Duration & Engineering Neurological Surgery Director, Clinical Care Center and Speech Timing,” in Y. Sagisaka, OGI School of Science & Oregon Health & Science University for Congenital Heart Disease; W.N. Campbell and N., Higuchi, eds., Engineering and Director, Interdisciplinary Computing Prosody, New York, DAVID DAWSON Springer, 1996. GERMAN NUNEZ Program for Cardiac Imaging Professor and Chair Oregon Health & Science University J. van Santen, R.W. Sproat, J. Olive Vice Provost Department of Physiology and J. Hirschberg, eds., Progress in Office of Diversity MARIE SHEA Speech Synthesis, New York, Springer- and Pharmacology & Multicultural Affairs Verlag, 1996 OHSU School of Medicine Assistant Professor Oregon Health & Science University Department of Orthopedics J. JOB FABER ALFRED NUTTAL and Rehabilitation Professor OHSU School of Medicine Professor Department of Physiology Department of Otolaryngology and Pharmacology GARY WESTBROOK Oregon Health & Science University OHSU School of Medicine Senior Scientist, Vollum Institute Professor, Department of Neurology OHSU School of Medicine 21 THE DEPARTMENT OF COMPUTER *APC 515, Data Structures and Discrete Department of SCIENCE AND ENGINEERING has an Mathematics, may be taken to meet this prerequisite internationally acclaimed Computer Science To be considered for admission to an EE research program. The breadth degree program, a candidate must hold a and Engineering and depth of the research is bachelor’s degree in physics, applied apparent in the research projects physics, engineering physics, electrical engineering or equivalent. Candidates with www.cse.ogi.edu and research centers listed below, undergraduate degrees in applied and in the educational program. mathematics as well as other branches of DEPARTMENT HEAD Four degrees are offered: Master engineering will also be considered. James Hook, Ph.D. 503 748-1169 of Science in Computer Science ADVANCED PLACEMENT ADMISSIONS E-mail: [email protected] FOR M.S. STUDENTS and Engineering, Master of ASSOCIATE CHAIR FOR EDUCATION Science in Electrical Engineering, Students who have completed at least four IN COMPUTER SCIENCE Doctor of Philosophy in Computer OGI courses may be eligible to apply for Lois Delcambre, Ph.D. admission under the Advanced Placement 503 748-1689 Science and Engineering option. Under this option, applicants are E-mail: [email protected] and Doctor of Philosophy in exempt from the GRE and TOEFL ASSOCIATE CHAIR FOR EDUCATION requirements and are required to provide Electrical Engineering. IN ELECTRICAL ENGINEERING only two letters of recommendation. All other Daniel Hammerstrom, Ph.D. admissions requirements remain the same. ADMISSION REQUIREMENTS 503 503-4037 For students applying to the M.S. CSE degree E-mail: [email protected] In addition to the general OGI admission program through Advanced Placement, the ACADEMIC COORDINATOR FOR requirements, the CSE Department requires four courses must include at least two, COMPUTER SCIENCE the general aptitude GRE scores, except in preferably three, courses from the M.S. CSE Shirley Kapsch the case of advanced placement admission Core listed below. The remaining credits must 503 748-1255 for M.S. students (see below). be CSE, EE or MATH courses. E-mail: [email protected] The Test of English as a Foreign Language M.S. CSE CORE ACADEMIC COORDINATOR FOR (TOEFL) is required of all M.S. applicants CSE 511 Principles of Compiler Design ELECTRICAL ENGINEERING whose native language is not English unless CSE 513 Introduction to Operating Systems Melissa Kretz CSE 514 Introduction to Database Systems the applicant earned an undergraduate 503 748-1266 degree in the United States. Desirable CSE 516 Introduction to Software Engineering E-mail: [email protected] score is 650. An applicant whose score is CSE 521 Introduction to Computer Architecture CSE 532 Analysis and Design of Algorithms between 580 and 650 may be admitted if DEPARTMENT SECRETARY CSE 533 Automata and Formal Languages special mitigating factors exist, e.g., excellent Barbara Mosher GRE scores. For students applying to the M.S. EE 503 748-1151 program through Advanced Placement, the E-mail: [email protected] Candidates for the CSE degree program four courses must include at least two typically hold a bachelor’s degree in CSE AND EE GENERAL INQUIRIES courses from the Computer Engineering and computer science, mathematics, engineering, 503 748-1151 Design Concentration Core or the Signals one of the biological or physical sciences, E-mail: [email protected] and Systems Concentration Core listed below. or one of the quantitative social sciences. The remaining courses must be EE, CSE or However, candidates from nontraditional MATH courses. backgrounds are encouraged to apply as well. All candidates are expected to M.S. EE COMPUTER ENGINEERING AND DESIGN CONCENTRATION CORE have completed courses in the following EE 560 Introduction to Electronics subject areas: and Instrumentation • An introduction to programming in a EE 570 Advanced Logic Design high-level language EE 571 System On a Chip (SOC) Design with • Data structures* Programmable Logic EE 572 Advanced Digital Design-Timing Analysis •Discrete mathematics* and Test CSE professor Phil Cohen demonstrates his • Logic design and computer organization EE 573 Computer Organization and Design intelligent map technology, one of many • Calculus or other college- EE 574 CMOS Digital VLSI Design I projects under development at the Center for level mathematics EE 575 CMOS Digital VLSI Design II Human-Computer Communication CSE | COMPUTER SCIENCE AND ENGINEERING

M.S. EE SIGNALS AND SYSTEMS advisor. The department does not assign CSE 527 Principles and Practices of ...... 3 credits CONCENTRATION CORE thesis advisors. System Security CSE 528 Cryptography ...... 3 credits CSE 547 Statistical Pattern Recognition •M.S. CSE CORE (listed above) CSE 506 Building Secure Systems ...... 3 credits EE 580 Linear Systems • CSE 503 M.S. THESIS RESEARCH (maximum 12 credits) EE 581 Introduction to Signals, Systems and •ELECTIVES (12 credits), as directed by the thesis • SUGGESTED ELECTIVES (9 credits) Information Processing advisor or SPC CSE 515 Distributed Computing Systems . . . 3 credits EE 582 Introduction to Digital Signal Processing Please note: Students may not receive credit for both Any CSE class not already taken. MATH 510 Multivariate Calculus and CSE 519 and OMSE 533. Please note: Students may not receive credit for both CSE Differential Equations 519 and OMSE 533. MATH 517 Probability and Statistics M.S. CSE NON-THESIS OPTION DATA-INTENSIVE SYSTEMS TRACK MATH 519 Engineering Optimization Students choosing the non-thesis M.S. CSE •M.S. CSE CORE (listed above) Students must earn an overall grade point option must complete a minimum of 15 •DATA-INTENSIVE SYSTEMS CORE (12 credits) average of 3.0 in their course work at OGI and courses and a minimum of 45 credits. Up to a “B” or better in each M.S. core class to be six credits of non-thesis research (CSE 501) Choose four: may be included with the approval of the CSE 506 Special Topics: ...... 3 credits eligible to apply through Advanced Placement. Web Data Management student’s Student Program Committee (SPC). CSE 506 Special Topics: ...... 3 credits The first three credits of research may be Information Integration DEGREE REQUIREMENTS counted as one class; an additional three CSE 506 Special Topics: Informational . . . . . 3 credits For M.S. students in CSE and for Ph.D. credits may be counted as a second class Retrieval and the Internet toward the 15-class requirement. CSE 506 Any special topics course in the students in CSE and EE, a Student database area Program Committee (SPC) that provides TRACKS CSE 515 Distributed Computing Systems . . . . 3 credits academic advising is assigned for each Students pursuing the non-thesis option CSE 526 Advanced Topics in ...... 3 credits Operating Systems matriculated student. The SPC approves must choose one of the nine tracks defined CSE 541 Database Implementation ...... 3 credits the application of courses toward the below or consult their SPC to define a student’s degree requirements. CSE 542 Object Data Management ...... 3 credits custom program. One course from the System Software Core For master’s students in EE, a single faculty ADAPTIVE SYSTEMS TRACK One course from the Software Engineering Core or the member will serve as an advisor. Software Engineering for Industry Professionals Core •M.S. CSE CORE (listed above) • SUGGESTED ELECTIVES (12 credits) The program of study for each M.S. student •ADAPTIVE SYSTEMS CORE (12 credits) Any CSE class not already taken. may be tailored to meet individual needs by Required: Please note: Students may not receive credit for both CSE the SPC or advisor. Students are particularly CSE 547 Statistical Pattern Recognition . . . . 3 credits 519 and OMSE 533. encouraged to include special-topic courses CSE 559 Machine Learning ...... 3 credits HUMAN-COMPUTER INTERACTION TRACK relevant to their interests. Choose two: CSE 540 Neural Network Algorithms ...... 3 credits •M.S. CSE CORE (listed above) M.S. CSE PROFESSIONAL INTERNSHIP OPTION and Architecture • HUMAN-COMPUTER INTERACTION CORE (18 credits) Participation is limited by available industrial CSE 545 Advanced Neural and ...... 3 credits Required: Adaptive Algorithms internships. Students declaring this option CSE 560 Artificial Intelligence ...... 3 credits CSE 546 Data and Signal Compression . . . . 3 credits must complete 45 credits of course work and CSE 564 Introduction to Human- ...... 3 credits up to an additional three credits of a CSE 550 Spoken Language Systems ...... 3 credits Computer Interactions CSE 558 Evolutionary Computation ...... 3 credits professional internship (CSE504). Choose three: CSE 560 Artificial Intelligence ...... 3 credits CSE 506 Special Topics: 3D Graphics . . . . . 3 credits CSE 562 Natural Language Processing . . . . . 3 credits CSE 550 Spoken Language Systems ...... 3 credits CSE 564 Introduction to Human- ...... 3 credits MASTER OF SCIENCE IN COMPUTER CSE 559 Machine Learning ...... 3 credits Computer Interaction SCIENCE AND ENGINEERING CSE 561 Dialogue ...... 3 credits CSE 568 Empirical Research Methods . . . . . 3 credits All M.S. CSE students must complete the CSE 562 Natural Language Processing . . . . . 3 credits EE 586 Adaptive and Statistical ...... 3 credits M.S. CSE core of 21 credits: Signal Processing CSE 563 Multi-Agent Systems ...... 3 credits CSE 565 Advanced Topics in Human- ...... 3 credits • SUGGESTED ELECTIVES (12 credits) M.S. CSE CORE COURSES Computer Interaction CSE 511 Principles of Compiler Design . . . . 3 credits CSE 506 Appropriate special topics course CSE 567 Developing User-Oriented Systems . . 3 credits CSE 513 Introduction to Operating Systems . . 3 credits CSE 563 Multiagent Systems ...... 3 credits CSE 568 Empirical Research Methods . . . . . 3 credits CSE 514 Introduction to Database Systems . . 3 credits CSE 569 Scholarship Skills ...... 3 credits CSE 516 Introduction to ...... 3 credits Any CSE class not already taken • SUGGESTED ELECTIVES (6 credits) Software Engineering Please note: Students may not receive credit for both CSE CSE 506 Special Topics: Real-time ...... 3 credits CSE 521 Introduction to ...... 3 credits 519 and OMSE 533. Rendering using Modern Graphics Computer Architecture CSE 515 Distributed Computing Systems . . . . 3 credits COMPUTER SECURITY TRACK CSE 532 Analysis and Design of Algorithms . . 3 credits CSE 540 Neural Network Algorithms ...... 3 credits CSE 533 Automata and Formal Languages . . 3 credits •M.S. CSE CORE (listed above) & Architecture • COMPUTER SECURITY CORE (15 credits) CSE 547 Statistical Pattern Recognition . . . . 3 credits M.S. CSE THESIS OPTION Required: CSE 551 Structure of Spoken Language . . . . 3 credits Students choosing the thesis option must find CSE 517 Software Engineering Processes . . . . 3 credits CSE 552 Hidden Markov Models for ...... 3 credits a faculty member willing to serve as a thesis CSE 524 TCP/IP Internetworking Protocols . . 3 credits Speech Recognition Architecture 24 COMPUTER SCIENCE AND ENGINEERING | CSE

CSE 569 Scholarship Skills ...... 3 credits Choose one: MASTER OF SCIENCE IN Any CSE class not already taken. CSE 564 Introduction to Human- ...... 3 credits ELECTRIAL ENGINEERING Please note: Students may not receive credit for both CSE Computer Interaction 519 and OMSE 533. CSE 567 Developing User-Oriented Systems . . 3 credits M.S. EE students may pursue either a NETWORKING TRACK • SUGGESTED ELECTIVES (9 credits) Computer Engineering and Design Any CSE class not already taken. Concentration or Signals and Systems •M.S. CSE CORE (listed above) Please note: Students may not receive credit for both Concentration. • NETWORKING CORE: (18 credits) CSE 519 and OMSE 533. Required: SPOKEN LANGUAGE SYSTEMS TRACK M.S. EE COMPUTER ENGINEERING AND DESIGN CSE 524 TCP/IP Internetworking Protocols . . 3 credits (CE) CONCENTRATION CSE 525 Advanced Networking ...... 3 credits •M.S. CSE CORE (listed above) EE 590 Digital Communication I ...... 3 credits • SOFTWARE ENGINEERING CORE (15 credits) All M.S. EE students pursuing the Computer Three of: Required: Engineering and Design Concentration CSE 515 Distributed Computing Systems . . . 3 credits CSE 550 Spoken Language Systems ...... 3 credits must complete the CE Concentration Core CSE 526 Advanced Topics in ...... 3 credits CSE 551 Structure of Spoken Language . . . . 3 credits of 28 credits: Operating Systems CSE 552 Hidden Markov Models for ...... 3 credits CSE 527 Principles and Practices of ...... 3 credits Speech Recognition M.S. EE COMPUTER ENGINEERING AND DESIGN System Security CONCENTRATION CORE Any two: EE 582 Introduction to Digital ...... 3 credits EE 560 Introduction to Electronics ...... 4 credits BME 568 Auditory & Visual Processing by . . . 3 credits Signal Processing and Instrumentation Human & Machine EE 591 Digital Communication II ...... 3 credits EE 570 Advanced Logic Design ...... 4 credits BME 571 Speech Systems ...... 3 credits EE 592 Digital Communication Systems . . . 3 credits EE 571 System On a Chip (SOC) Design . . . 4 credits BME 572 Speech Synthesis ...... 3 credits with Programmable Logic Special Topics in Systems Software or Networking CSE 547 Statistical Pattern Recognition . . . . 3 credits or Communication such as: EE 572 Advanced Digital Design-Timing . . . 4 credits CSE 559 Machine Learning ...... 3 credits CSE 506 Special Topics: ...... 3 credits Analysis and Test Multi-Media Networking CSE 560 Artificial Intelligence ...... 3 credits EE 573 Computer Organization and Design . . 4 credits CSE 506 Special Topics: ...... 3 credits CSE 561 Dialogue ...... 3 credits EE 574 CMOS Digital VLSI Design I ...... 4 credits Advanced Distributed Systems CSE 562 Natural Language Processing . . . . . 3 credits EE 575 CMOS Digital VLSI Design II ...... 4 credits CSE 506 Special Topics: ...... 3 credits CSE 564 Introduction to Human- ...... 3 credits Networking Practicum Computer Interaction M.S. EE THESIS OPTION IN THE COMPUTER ENGINEERING AND DESIGN CONCENTRATION Please note: Students may not receive credit for both EE 581 Introduction to Signals, Systems both CSE 519 and OMSE 533. and Information Processing ...... 3 credits Students choosing the thesis option must find EE 582 Introduction to Digital ...... 3 credits a faculty member willing to serve as a thesis SOFTWARE ENGINEERING TRACK Signal Processing advisor. The department does not assign •M.S. CSE CORE (listed above) • SUGGESTED ELECTIVES (9 credits) thesis advisors. • SOFTWARE ENGINEERING CORE (15 credits) Courses in the Spoken Language Systems core •M.S. EE CE CONCENTRATION CORE (listed above) Any CSE class not already taken Required: • EE 503 M.S. THESIS RESEARCH (maximum 12 credits) CSE 517 Software Engineering Processes . . 3 credits Please note: Students may not receive credit for both CSE 519 and OMSE 533. • ELECTIVES (8 credits) from the CE Concentration CSE 519 Object-Oriented Analysis ...... 3 credits electives listed below and Design SYSTEMS SOFTWARE TRACK CSE 520 Software Architecture ...... 3 credits M.S. EE NON-THESIS OPTION IN THE COMPUTER CSE 529 Object-Oriented Programming . . . . . 3 credits •M.S. CSE CORE (listed above) ENGINEERING AND DESIGN CONCENTRATION One of: • SYSTEMS SOFTWARE CORE (12 credits) All M.S. EE students in the Computer CSE 564 Introduction to Human- ...... 3 credits Choose four: Engineering and Design Concentration must Computer Interaction CSE 515 Distributed Computing Systems . . . 3 credits complete the concentration core of 28 credits CSE 567 Developing User-Oriented Systems . . 3 credits CSE 524 TCP/IP Internetworking Protocols . . 3 credits (listed above), one of the following track • SUGGESTED ELECTIVES (9 credits) CSE 525 Advanced Networking ...... 3 credits cores, and remaining elective credits to total MST 512 Project Management ...... 4 credits CSE 526 Advanced Topics in ...... 3 credits 48 credits. Any course in software engineering, data-intensive systems, Operating Systems systems software, systems security or human-computer CSE 527 Principles and Practices of ...... 3 credits CIRCUIT DESIGN TRACK interfaces or any CSE course not already taken. System Security Please note: Students may not receive credit for both CSE CSE 541 Database Implementation ...... 3 credits •M.S. EE CE CORE (listed above) 519 and OMSE 533. Special Topics in Systems Software or Networking such as: •CIRCUIT DESIGN CORE (16 credits): SOFTWARE ENGINEERING FOR INDUSTRY CSE 506 Special Topics: Advanced ...... 3 credits Required: PROFESSIONALS TRACK Distributed Systems EE 536 Operation of Semiconductor Devices 4 credits CSE 506 Special Topics: ...... 3 credits EE 561 Analog Integrated Circuit Design . . 4 credits •M.S. CSE CORE (listed above) Networking Practicum EE 562 Digital Integrated Circuit Design . . . 4 credits • SOFTWARE ENGINEERING FOR INDUSTRY CSE 506 Special Topics: ...... 3 credits PROFESSIONALS CORE (15 credits) EE 563 Analog CMOS Integrated ...... 4 credits Multi-Media Networking Circuit Design Required: • SUGGESTED ELECTIVES (12 credits) • SUGGESTED CE ELECTIVES (4 credits - listed below) OMSE 511 Managing Software Development . . 3 credits Any course in the Systems Software area core OMSE 521 Using Metrics and Models ...... 3 credits Any CSE class not already taken. COMPUTER ARCHITECTURE TRACK OMSE 531 Software Requirements ...... 3 credits Engineering Please note: Students may not receive credit for both CSE •M.S. EE CE CORE (listed above) 519 and OMSE 533. OMSE 533 Software Design Techniques . . . . . 3 credits • COMPUTER ARCHITECTURE CORE (6 credits) 25 CSE | COMPUTER SCIENCE AND ENGINEERING

Required: EE 581 Introduction to Signals, Systems . . . 3 credits SUGGESTED ELECTIVES FOR SIGNALS CSE 521 Introduction to ...... 3 credits and Information Processing AND SYSTEMS CONCENTRATION Computer Architecture EE 582 Introduction to Digital ...... 3 credits (to total 45 required credits for M.S. EE degree in the CSE 522 Advanced Computer Architecture . . 3 credits Signal Processing SAS Concentration) • SUGGESTED CE ELECTIVES (14 credits - listed below) MATH 510 Multivariate Calculus and ...... 3 credits Differential Equations BME 513 Biomedical Signal Processing . . . . 3 credits BME 568 Auditory & Visual Processing by . . . 3 credits SIGNAL PROCESSING TRACK MATH 517 Probability and Statistics ...... 3 credits Human & Machine MATH 519 Engineering Optimization ...... 3 credits •M.S. EE CE CORE (listed above) BME 571 Speech Systems ...... 3 credits •SIGNAL PROCESSING CORE (9 credits) M.S. EE THESIS OPTION IN THE SIGNALS CSE 506 Special Topics: Real-Time ...... 3 credits AND SYSTEMS CONCENTRATION Rendering using Modern Required: Students choosing the thesis option must find Graphic Architecture EE 581 Introduction to Signals, Systems, . . 3 credits CSE 532 Analysis and Design of Algorithms . . 3 credits & Information Processing a faculty member willing to serve as a thesis CSE 540 Neural Networks Algorithims . . . . . 3 credits EE 582 Introduction to Digital ...... 3 credits advisor. The department does not assign and Architectures Signal Processing thesis advisors. CSE 546 Data and Signal Compression . . . . 3 credits EE 584 Introduction to Image Processing . . 3 credits •M.S. EE SAS CONCENTRATION CORE (listed above) CSE 552 Hidden Markov Models for ...... 3 credits • SUGGESTED CE ELECTIVES (11 credits - listed below) • EE 503 M.S. THESIS RESEARCH (maximum 12 credits) Speech Recognition CSE 559 Machine Learning ...... 3 credits SUGGESTED ELECTIVES FOR COMPUTER ENGINEERING •ELECTIVES (15 credits) from the SAS Concentration AND DESIGN CONCENTRATION electives listed below CSE 560 Artificial Intelligence ...... 3 credits CSE 562 Natural Language Processing . . . . . 3 credits (to total 48 required credits for M.S. EE degree in the CE M.S. EE NON-THESIS OPTION IN THE SIGNALS EE 584 Introduction to Image Processing . . 3 credits Concentration) AND SYSTEMS CONCENTRATION Any EE or CSE course not already taken BME 513 Biomedical Signal Processing I . . . 3 credits All M.S. EE students in the Signals and Additionally, students may consider the following courses BME 566 Biomedical Signal Processing II . . . 3 credits Systems Concentration must complete the from other universities: EE 525 Introduction to Electromagnetics . . 4 credits concentration core of 21 credits (listed SySc 545 Information Theory (Portland State University) for Modern Applications EE 526 Electromagnetics for Modern . . . . . 4 credits above), one of the following track cores and COOPERATIVE COMPUTER Applications II remaining elective credits to total 45 credits. SCIENCE PROGRAMS EE 531 Introduction to Quantum Mechanics . . 4 credits The OGI School has established for Electrical & Computer Engineering SIGNAL AND IMAGE PROCESSING TRACK EE 535 MOSFET Modeling for VLSI ...... 4 credits •M.S. EE SAS CORE (listed above) undergraduate/graduate cooperative Circuit Design •SIGNAL AND IMAGE PROCESSING CORE (12 credits) programs with Lewis & Clark College, Pacific EE 560 Introduction to Electronics ...... 4 credits Required: University, Reed College and Willamette & Instrumentation BME 568 Auditory & Visual Processing by . . . 3 credits University. These programs allow selected EE 565 Introduction to Wireless ...... 4 credits Human & Machinex Integrated Circuit Design undergraduate students to enter the master’s EE 584 Introduction to Image Processing . . 3 credits EE 576 Algorithms for VLSI Design & Test . . 4 credits program in computer science and engineering EE 585 Introduction to Digital ...... 3 credits at the beginning of their senior year. In two EE 583 Digital Signal Processing II ...... 3 credits Video Processing EE 590 Digital Communication I ...... 3 credits EE 586 Adaptive & Statistical ...... 3 credits years of residence at OGI, the student can EE 591 Digital Communication II ...... 3 credits Signal Processing simultaneously fulfill requirements for the EE 592 Digital Communication Systems . . . 3 credits • SUGGESTED SAS ELECTIVES (12 credits – listed below) bachelor’s degree at the undergraduate EE 593 Analytical Techniques in ...... 3 credits institution and the master’s degree at OGI. Statistical Signal Processing MACHINE LEARNING TRACK & Communications •M.S. EE SAS CORE (listed above) Any EE or CSE course not already taken COMPUTER SCIENCE AND Additionally, students may consider the following courses •SIGNAL MACHINE LEARNING CORE (12 credits) from other universities: Required: ENGINEERING PH.D. PROGRAM ECE 527 VLSI System Design (Oregon State University) CSE 540 Neural Networks Algorithms ...... 3 credits In addition to the general OGI requirements ECE 570 High Performance Computer Architecture and Architectures (Oregon State University) CSE 558 Evolutionary Computation ...... 3 credits for a Ph.D., candidacy in CSE is satisfied in ECE 675 Introduction to Integrated Circuit Test CSE 559 Machine Learning ...... 3 credits three parts: (Portland State University) EE 586 Adaptive & Statistical ...... 3 credits FOUNDATION REQUIREMENTS: Students are ECE 699 Digital Design Using Hardware Description Signal Processing Languages (Portland State University) • SUGGESTED SAS ELECTIVES (12 credits - listed below) required to take six foundation courses. Particularly well-prepared students can M.S. EE SIGNALS AND SYSTEMS SPEECH PROCESSING TRACK waive some of these courses by passing an (SAS) CONCENTRATION •M.S. EE SAS CORE (listed above) examination on the course material. •SPEECH PROCESSING CORE (12 credits) All M.S. EE students pursuing the Signal and AREA REQUIREMENTS: Students choose Required: Systems Concentration must complete the BME 572 Speech Synthesis ...... 3 credits three courses within one area and three SAS Concentration Core of 21 credits: CSE 550 Spoken Language Systems ...... 3 credits courses out of that area, as outlined below. CSE 551 Structure of Spoken Language . . . . 3 credits M.S. EE SIGNALS AND SYSTEMS CONCENTRATION CORE RESEARCH SKILLS ASSESSMENT: CSE 547 Statistical Pattern Recognition . . . . 3 credits CSE 552 Hidden Markov Models for ...... 3 credits Speech Recognition Students are required to take CSE 669, EE 580 Linear Systems ...... 3 credits • SUGGESTED SAS ELECTIVES (12 credits - listed below) Scholarship Skills, and to pass the research

26 COMPUTER SCIENCE AND ENGINEERING | CSE proficiency examination (RPE), which RESEARCH SKILLS REQUIREMENT (3 credits) CSE 631 Foundations of Semantics ...... 3 credits requires a written and oral presentation of CSE 669 Scholarship Skills ...... 3 credits CSE 636 Functional Programming ...... 3 credits SYSTEMS SOFTWARE a research paper. The RPE usually takes AREA REQUIREMENTS (18 credits) place in the spring quarter of the second CSE 606 Special Topics: Building ...... 3 credits Secure Systems year of residence. Three courses from one of the following five areas, and three other courses not from that CSE 606 Special Topics: ...... 3 credits Ph.D. students must obtain a grade of “B” Web Distribution Architecture area and not already taken: CSE 606 Special Topics: Security Protocols . . 3 credits or better in each required course. The ADAPTIVE SYSTEMS AND APPLICATIONS CSE 614 Introduction to Database Systems . . 3 credits doctoral dissertation will document a BME 668 Auditory and Visual Processing . . . 3 credits CSE 615 Distributed Computing Systems . . . 3 credits significant, original research contribution by Human and Machine CSE 622 Advanced Computer Architecture . . 3 credits and must be of publishable quality in both CSE 606 Special topics in Cognitive Science CSE 624 TCP/IP Internetworking Protocols . . 3 credits content and presentation. CSE 640 Neural Network Algorithms ...... 3 credits CSE 625 Advanced Networking ...... 3 credits and Architectures CSE 626 Advanced Topics in ...... 3 credits The faculty strongly recommends that CSE 645 Advanced Neural and ...... 3 credits Operating Systems Adaptive Algorithms students prepare a formal thesis proposal CSE 627 Principles and Practices of ...... 3 credits CSE 646 Data and Signal Compression . . . . 3 credits between 9 and 18 months before the Ph.D. System Security CSE 647 Statistical Pattern Recognition . . . . 3 credits defense. The proposal is not a candidate CSE 628 Cryptography ...... 3 credits CSE 658 Evolutionary Computation ...... 3 credits screening tool, but instead a means to CSE 629 Object-Oriented Programming . . . . . 3 credits CSE 659 Machine Learning ...... 3 credits CSE 641 Database Implementation ...... 3 credits ensure an acceptable level of intellectual CSE 668 Empirical Research Methods . . . . . 3 credits CSE 642 Object Data Management ...... 3 credits vigor and maturity. Starting in the second EE 686 Adaptive and Statistical ...... 3 credits THEORY year, the faculty strongly recommends that Signal Processing CSE 606 Special Topics: Principles of . . . . . 3 credits students deliver yearly research talks. The HUMAN-COMPUTER INTERACTIVE SYSTEMS Database Systems RPE, presentation at the student research BME 668 Auditory and Visual Processing . . . 3 credits by Human and Machine symposium, the thesis proposal and talks CSE 628 Cryptography ...... 3 credits CSE 606 Special Topics: ...... 3 credits CSE 630 Introduction to Mathematical Logic . . 3 credits at refereed conferences satisfy this Computer Graphics CSE 631 Foundations of Semantics ...... 3 credits requirement. Practice talks for conference CSE 606 Special Topics: ...... 3 credits CSE 634 Computability and Intractability . . . 3 credits papers should be open for commentary. Scientific Visualization CSE 606 Special Topics: Real-time ...... 3 credits CSE 635 Categories in Computer Science . . 3 credits The program of study for each Ph.D. Rendering using Modern Graphics Architecture student is tailored to meet individual needs ELECTRICAL ENGINEERING and interests. Each student’s Student CSE 650 Spoken Language Systems ...... 3 credits CSE 651 Structure of Spoken Language . . . . 3 credits PH.D. PROGRAM Program Committee provides academic CSE 652 Hidden Markov Models for ...... 3 credits advising and is in direct control of the Speech Recognition A Ph.D. program in Electrical Engineering student’s program of study. The SPC will CSE 660 Artificial Intelligence ...... 3 credits with emphasis in Computer Engineering and work with the student to set and review CSE 661 Dialogue ...... 3 credits Design or Signals and Systems is offered goals on a twice-yearly basis. Students CSE 663 Multiagent Systems ...... 3 credits through the Department of Computer Science must write a progress report for all SPC CSE 664 Introduction to Human- ...... 3 credits and Engineering. Upon entry into the Computer Interaction meetings except the first one. The entire program a Student Program Committee (SPC) CSE 665 Advanced Topics in Human- ...... 3 credits faculty reviews each Ph.D. student’s Computer Interaction of three faculty members is formed. The academic progress annually. CSE 667 Developing User-Oriented Systems . . 3 credits student discusses feasible research areas CSE 668 Empirical Research Methods . . . . . 3 credits and eventual research directions with the FOUNDATION REQUIREMENTS (18 credits) PROGRAMMING LANGUAGES AND SOFTWARE ENGINEERING committee and together they chart an Required: CSE 606 Special Topics: High Assurance . . . 3 credits individualized course of study to prepare the CSE 613 Introduction to Operating Systems . . 3 credits Software Engineering student for the qualifying exam. CSE 621 Introduction to Computer ...... 3 credits CSE 606 Special Topics: Model Checking . . . 3 credits Architecture for Bug Discovery The qualifying exam may be written or oral or CSE 632 Analysis and Design of Algorithms . . 3 credits CSE 606 Special Topics: Domain ...... 3 credits both, at the discretion of the SPC, and may CSE 633 Automata and Formal Languages . . 3 credits Specific Languages additionally involve a formal research Choose one programming language course: CSE 611 Principles of Compiler Design . . . . 3 credits proposal. It is usually taken within 12 months CSE 629 Object-Oriented Programming . . . . . 3 credits CSE 612 Compiling Functional Languages . . 3 credits CSE 631 Foundations of Semantics ...... 3 credits CSE 616 Introduction to ...... 3 credits of enrolling in the program, and may be CSE 636 Functional Programming ...... 3 credits Software Engineering scheduled at any time of year. The amount of CSE 617 Software Engineering Processes . . 3 credits Choose one interactive and adaptive systems course: course work to be completed before taking CSE 618 Software Design and Development . . 3 credits CSE 640 Neural Network Algorithms the qualifying exam depends on the and Architectures ...... 3 credits CSE 619 Object-Oriented Analysis ...... 3 credits individual’s level of preparation at entry. At and Design CSE 659 Machine Learning ...... 3 credits CSE 620 Software Architecture ...... 3 credits minimum, three graded Electrical CSE 660 Artificial Intelligence ...... 3 credits CSE 629 Object-Oriented Programming . . . . . 3 credits Engineering courses from OGI must be CSE 664 Introduction to Human- ...... 3 credits completed before taking the exam. Computer Interaction CSE 630 Introduction to Mathematical Logic . . 3 credits

27 CSE | COMPUTER SCIENCE AND ENGINEERING

After passing the qualifying exam, the student architecture, gaining a more robust capability for the system requires two machines: a potentially works with the SPC to develop a research supporting human-human collaboration, insecure “front-line” machine, and a known secure plan specifically for the dissertation. Ph.D. multimedia and dynamic adaptation to processing back-end. Information about system calls is stored environments. Cohen in a MySQL database on the back-end. 4N6 is built students are required to make annual reports on top of SNARE. Feng, Feng, Walpole, Maier to the SPC on the status of their research, and may be called upon to deliver timely Digital Government Infopipes research presentations as the work DOT is collaborating with the U.S. Forest Service, Bureau of Land Management, Fish and Wildlife The Infopipes project is building tools to aid in the progresses. The dissertation itself must Service and other government agencies to build a development of timing-sensitive distributed constitute a significant research contribution forest information portal for the Adaptive applications, such as streaming video and real- and must be of publishable quality. The Ph.D. Management Area (AMA) program. The AMAs time sensor networks. degree is granted following the presentation develop and test innovative approaches to forest The goal of most existing communications of an acceptable dissertation and successful management. We are developing an information model called Metadata++ to locate documents and middleware is Communication Transparency: oral defense. document fragments along several dimensions and communication is hidden behind a conventional to search for documents based on “similarity invocation interface and, as far as possible, the programmer is unaware that communication is RESEARCH PROGRAMS search” between locations. The forest project also includes participants from the MST and ESE taking place. The property that makes this possible is Blocking Transparency: the idea that an The specific research projects under way at departments at OGI, from Portland State University, the University of Nevada, Las Vegas invocation that performs some computation and any given time depend upon current interests and from the private sector. immediately returns can be transparently replaced and obligations of faculty, students and Delcambre and Maier (CSE), Toccalino (ESE), by an invocation that blocks for an arbitrary time. research sponsors. Phillips, Steckler, and Koch (MST), Tolle (Forest In effect, Blocking Transparency disconnects Service), Landis (consultant), Palmer (UNLV), “application time” from “real time.” Hence, neither and Shapiro (PSU) Communication Transparency nor Blocking Transparency is appropriate for distributed RESEARCH PROGRAMS streaming applications that require control over Efficient Intrusion Detection and Response Systems timing. In addition, streaming applications may (Intel and ETIC) require control over other aspects of Adaptive Systems This project is focused on studying the perfor- communication, such as bandwidth, reliability, Our work on adaptive systems includes theoretical, mance of full-packet classification algorithms and ordering and topology. algorithmic, scientific and practical aspects. packet classification caching algorithms. By Research on theory and algorithms for machine Infopipes are a powerful communications understanding emerging network traffic patterns learning includes supervised, unsupervised and abstraction that have been designed to meet the and leveraging hardware support provided by reinforcement learning; neural networks; genetic needs of streaming applications. Current work the IXP network processor platform, we plan on algorithms; generalization theory (model selection includes creating appropriate Middleware libraries systematically studying alternative architectures and pruning, invariant learning and theoretical for Infopipes, and developing a domain-specific for providing high-speed classifiers. characterization); stochastic optimization; local language to describe Infopipe components and Wu-chang Feng and mixture models; time series; control; and Infopiplines at a high enough level of abstraction context-sensitive learning. Research on biological that tools can automatically check the properties of and cognitive modeling includes the effect of noise Environmental Observation and Forecasting Systems proposed Infopipelines before they are constructed, on learning in neural circuits, cognitive models of (EOFS) and then generate the code that manages many of visual pattern recognition and analogy-making, and the low-level details such as thread management, The goal of this research is to develop software modeling of evolutionary systems. Practical synchronization, deadlock avoidance and thread technology to enable EOFS to evolve efficiently and applications of our research in these areas include latency. Black, Walpole, Pu to deliver quantifiably reliable information about speech and image processing, medical screening the environment. Our focus is on EOFS for technology, environmental forecasting and estuarine and coastal regions. The project includes Image, Video Processing and Analysis observation systems, anomaly detection for developing quality-scalable information processing, aeronautics, aircraft control, sensor fusion and Both low-level processing and high-level analysis storage and access; developing machine learning optimization, and automatic programming. are studied. Special emphasis is on the interface technology to improve sensor reliability, to Hammerstrom, Hayes, Leen, Mitchell, Pavel, of machine learning and computer vision, where categorize and detect different estuarine dynamics, Song, Wan insights from probability theory, stochastic systems and to fuse sensor data with numerical models; and information theory are used to produce new improving data product generation and algorithms that are robust, accurate and efficient. Agent-Based Systems management; applying parallelism to simulation Current projects include information fusion, the and data manipulation, improving sensor This project is designing a new agent incorporation of context for image recognition, networking technology; and developing new communication language (AGENTTALK) and model-based image segmentation, enhancement visualization techniques. multiagent architecture. Unlike DARPA’s current and 3-D reconstruction, and motion analysis for Baptista, Feng, Feng, Leen, Maier, Silva, Walpole language (KQML), the language offers a true autonomous navigation. Song, Pavel semantics, and provably correct dialogue protocols, based on joint intention theory. The Adaptive Agent Forensix: Large-scale Tamper-Resistant Computer Model-Relative Control of Autonomous Vehicles Architecture, a successor to our earlier Open Forensic Systems (NSF) Agent Architecture, offers platform and application This multidisciplinary project is exploring the The goal of the Forensix (“4N6”) Project is to allow interoperability, facilitated communication, proper design and implementation of nonlinear a system to be monitored so that, in the event of a concurrent operation, dynamic reconfigurability of reconfigurable controllers that exploit the coupled security compromise, it is easy to track the facilitators and separation of data and control. dynamics between a model of a flight vehicle, compromise back to its source. To facilitate this, Quickset has been reimplemented to use this such as a helicopter, and adaptive models of the 28 COMPUTER SCIENCE AND ENGINEERING | CSE

environment. New model-predictive techniques are synapses, the relevant signals are the small These are the problems that we are tackling in the developed to perform on-line optimization of variable electrophysiological events called synaptic Perspectives project at OGI. Our work to date has vehicle control trajectories under dynamic and potentials. When learning occurs, there is a change been focused in three areas. situational constraints. This resulting in the relative weighted value of these synaptic • The search for new, high-level representations environmentally informed control approach will potentials. At the macroscopic level of a functional of program source code - which we refer to as enable aircraft operations under all-weather region of the brain, the relevant variables are an “abstract program structure” or APS - that is conditions, as well as increased automation for systems properties of the response to large able to capture program semantics fully while modeless control and extreme maneuvers at numbers of cellular inputs. The system needs to simultaneously abstracting away from specific levels not realizable with conventional control optimize the trade-off between accuracy, which details of syntax and physical structure. Instead, approaches. Kieburtz, Wan, Baptista may take some time to establish, and adaptability, which often requires rapid adjustment to changes common representations of a program - such as in the sensory environment. This collaborative the one- or two-dimensional syntax of a linear Multimodal Systems project combines statistical adaptive system source text, the underlying abstract syntax Multimodal interfaces enable more natural and approaches with tools from computational biology trees, or the class diagrams that describe its efficient interaction between humans and machines and experimental neurophysiology. The present architecture — should be obtained as different by supporting multiple coordinated channels focus is on modeling adaptation in a sensory-motor views on a rich APS. through which input and output can pass. The system in weakly electric mormyrid fish. The • The design and implementation of a practical Center for Human-Computer Communication is modeling forms a bridge between microscopic tool called Sweet that permits considerably engaged in empirical investigation of multimodal dynamics and macroscopic system behavior. This more flexible decomposition and construction of interaction. This informs our research and project involves a novel aspect of modeling Java programs than do conventional Java development of architectures for multimodal emphasizing statistical properties of then-synaptic compilers. In the input to Sweet, a programmer language processing, work which draws on a range adaptation in the presence of noise, and making blends definitions of parts of the program of fields such as cognitive science, natural testable predictions about how noise can affect the structure, for example, packages, class language processing, multimedia, user interface accuracy of the fish’s stored signal memories. hierarchies, or methods, with descriptions of design, speech recognition, gesture recognition and Leen, Roberts the executable content that should be placed visual parsing. The Quickset system developed at within that structure. CHCC supports multimodal pen/voice interaction with complex visual/spatial displays, such as maps. Operating Systems • The integration and experimentation with these The Rasa system allows users to engage Our operating systems-related research focuses ideas in the context of a practical, interactive multimodally with tangible tools, such as paper and primarily on adaptive systems software and its development system. This work is based on the Post-it notes. Finally, work is ongoing to develop application in distributed, mobile and multimedia Eclipse IDE and is sponsored by Object techniques for 3-D multimodal interaction in computing environments. Several large projects Technology International. Black, Jones augmented and virtual reality environments. are currently under way in the areas of quality of Cohen, Oviatt service control, defining abstractions that support Programatica adaptive resource management and dynamic specialization for enhanced performance of “Programming as if properties mattered.” We are Natural Language Dialogue streaming applications. Black, Walpole developing a new kind of program development The performance of speech recognition systems environment that actively supports and encourages improves significantly when the spoken language its users in thinking about, stating and validating understanding system can predict the next Perspectives correctness properties of software as an integral utterance. Accordingly, we are performing The Perspectives project aims to produce part of the programming process. The perceptual studies of dialogue and building models foundational results and practical tools for Programatica framework allows programmers to of human and human-computer dialogue in order representing and manipulating software from assert precise properties of program elements as to develop computational models of conversation multiple viewpoints. Our ability to build complex part of their source code. Assertions can then be that can be used to track and predict spoken software systems relies on composition techniques annotated with one or more “certificates” that language. This work is based on speech-act and programming language mechanisms that provide evidence of their validity. The certificate theory, multiagent architectures and models of enable us to construct complete programs from interface is generic; certificate servers can range spontaneous speech. Cohen, Heeman, Oviatt smaller pieces. A particular decomposition imposes from “pencil and paper” proofs, randomized test a structure that makes it possible to manage the suites, all the way to formal proofs checked by a complexity of a large system, provided that each theorem prover. Changes to the original program Net Data Management component can be developed and maintained with are tracked by the framework, requiring only those We believe that data management systems of the some degree of independence, and that each certificates that depend on the changed code to be future must stress data movement over data feature can be localized in one or two components. reverified. Property-oriented development storage. NIAGARA is an initial effort, conducted Unfortunately, the same decomposition makes it environments such as Programatica are a key with the University of Wisconsin, to move beyond harder to add or change features that cut across technology in helping developers build more robust disk-centric data management to net-centric that structure. and secure software systems. systems. Current work includes algebras and Hook, Jones, Kieburtz, Matthews special operators for XML, exploiting stream We believe that the design, evolution, maintenance semantics for efficient processing, data-query and comprehension of software can be better Project Timber hybrids for distributed query evaluation, and supported by tools that allow programmers to peer-to-peer catalog management. examine and work with multiple perspectives on a Project Timber (“Time as a basis for embedded Maier, DeWitt, Naughton program instead of constraining them to a single real-time systems”) is exploring new techniques for decomposition. That is, programmers should be building more reliable software for embedded empowered to think of programs not as linear texts systems. One of the project’s goals is to investigate Neurobiological Modeling but as equivalence classes of concrete views, each the role that advanced programming languages can The brain handles a continuous temporal flow of of which is useful for certain tasks, but none of play in this area. We have designed a new sensory information. At the microscopic level of the which is more definitive than any other. programming language, also called Timber, that we

29 CSE | COMPUTER SCIENCE AND ENGINEERING

are using, as a proof-of-concept demonstration, to interfaces is growing as computing gradually in operation and quantum effects become the rule develop control algorithms for a small robotic moves off of the desktop and into mobile devices. rather than the exception. It is unlikely that vehicle called Timbot. The language offers a high- Spoken language engineering is an interdisciplinary existing computational models will be an optimal level, declarative approach to key aspects of field that draws elements from digital signal mapping to these new devices and technologies. embedded systems development such as real-time processing, computer science, linguistics, machine One source of inspiration for new kinds of control, event handling, and concurrency. Another learning, and human perception. The Center for computing structures is coming from goal is to develop techniques for building systems Spoken Language Understanding (CSLU) has Computational Neuroscience. Biology uses loosely that adapt dynamically to changes in their unique breadth and depth of experience in all coupled, relatively slow, globally asynchronous, environment or in the way that they are being components of spoken language engineering, distributed computing with unreliable (and used. One of our motivating examples in this area including text-to-speech synthesis, speech occasionally failing) components. Furthermore, is a video pipeline that relays live video across a recognition, dialogue modeling, and signal even simple biological systems perform highly wireless network from a camera on Timbot to a processing. Research efforts at CSLU include sophisticated pattern recognition and control. remote viewer. When other tasks leave Timbot assistive technology, speech as an information Biological systems are self-organizing, tolerant of without the CPU power or network bandwidth that source for medical diagnosis, universal access to manufacturing defects, and they adapt, rather than it needs to send a full quality video signal, the computers, small-footprint speech recognition and being programmed, to their environments. The software adapts automatically and according to text-to-speech synthesis, and basic research on all problems they solve are important, involving the user preferences, for example by sending fewer aspects of spoken-language processing. interaction of an organism/system with the real frames or less detailed images, to maximize quality Heeman, Hosom, van Santen, Wan world. An important aspect of this is the efficient of service. Jones, Black, Kieburtz, Walpole representation of knowledge or contextual information. In this project a variety of highly Spoken Language Systems parallel algorithms are being studied, including Query Optimization Spoken language systems make it possible for neuromorphic structures, with the intent of Our work on query optimization and evaluation people to interact with computers using speech, enhancing the representation and manipulation of deals with both general frameworks and specific the most natural mode of communication. A spoken knowledge in silicon. Borrowing from techniques for different data model and query language system combines speech recognition, Computational Neuroscience is very difficult, but it language features. Columbia is a C++-based, top- natural language understanding and human does promise a new way to look at computation down framework for construction of cost-based interface technology. It functions by recognizing the and insight into new solutions to important query optimizers. We are currently examining person’s words, interpreting the words in terms of problems. These models will be massively parallel pruning techniques for searching, transforms for the context and goals of the task, and providing an and require massively parallel silicon architectures collection-valued attributes and nested queries, appropriate response to the user. We are involved for efficient execution. Hammerstrom, Jabri and “multiplex” query optimization for efficiently in the analysis and development of various optimizing groups of queries. Columbia is a joint components of such systems, ranging from project with Portland State University. empirical studies of human dialogues through the Maier, Shapiro construction of interactive systems to the RESEARCH CENTERS development of abstract models of behavior. Cohen, Oviatt, Heeman, van Santen CENTER FOR HUMAN-COMPUTER COMMUNICATION Speech Recognition DEBBIE DESHAIS, Financial/Business Manager The goal of Large Vocabulary Continuous Speech Phone: 503 748-1248 Recognition research is to enable normal human Superimposed Information and Superimposed E-mail: [email protected] speech as an input device in next-generation Applications computers alongside today’s keyboard and mouse We are interested in providing typical database The Center for Human-Computer Communication is input. This technology can be used by itself for system capabilities in an environment where we do dedicated to realizing a vision of transparent dictation and command control applications. not own or manage the underlying, base information and service access. Research projects It can also form part of a powerful information information. We seek to develop a superimposed are broadly interdisciplinary, and include processing system when used together with layer of information that can reference selected collaborations with numerous universities, federal information retrieval and natural language information from the base layer and can also add research laboratories, and the Data-Intensive understanding systems. The research focuses new information to highlight, interconnect, Systems Center at the OGI School of Science & include accurate acoustic modeling, speaker elaborate or annotate the selected information. We Engineering. Research activities focus on: adaptation, confidence measure and rejection, have defined an architecture for building and modeling spontaneous speech. superimposed applications and have implemented • Multimodal human-computer interaction that our first tool: SLIMPad, a scratchpad application allows people to state their needs using speech, The goal for language and speaker recognition is to that allows users to easily create “scraps” that writing and gestures, and that provides identify which language is being used in a reference selected items from the base layer and multimedia output. conversation and who is talking by using signal organize scraps into bundles. The tendency to use processing, pattern recognition and computer • User-centered design of next-generation scraps and bundles to organize our thoughts is science technology. The technology can be used to interface technology, including spoken language common practice, as confirmed by our increase security and customer services. Our and multimodal interfaces, and interfaces for observational research team that is studying how research in this area includes how to analyze, mobile and multimedia technology. clinicians seek and use information in a hospital identify and capture these nuances and how to intensive-care unit. Observational team (OHSU • Intelligent agent technologies-software systems model these specific acoustics landmarks and Divison of Medical Informatics and Outcomes that help users accomplish tasks and can reason phonotactic constraints contained in the targeted Research): Gorman, Ash, Lavelle; computer science about how and where to carry out users’ language and speakers. Yan, Heeman team: Delcambre, Maier requests in a worldwide distributed information environment.

Spoken Language Engineering VLSI Architecture for Intelligent Computing • Collaboration technologies to support human- Speech is the most natural and efficient means by human communication, and collaborative Moore’s law is pushing VLSI design down to the which individuals may access a wide variety of decision making among groups of people. molecular scale where devices are more stochastic information, and the need for speech-based 30 COMPUTER SCIENCE AND ENGINEERING | CSE

CHCC organizes an annual Distinguished Lecture DATABASE AND OBJECT FACILITIES Series on the Future of Human-Computer TECHNOLOGY LABORATORY Interaction. World-class researchers are invited to The Department of Computer Science and JO ANN BINKERD, Center Administrator share current topics. Engineering provides a state-of-the-art computing Phone: 503 748-1112 environment designed to support the needs of Dr. Philip Cohen and Dr. Sharon Oviatt are co- E-mail: [email protected] research and education. The computing facilities directors of the center. Other center faculty include staff has a wide range of skills that allow the The Database and Object Technology Lab (DOT) Dr. Peter Heeman and Dr. Misha Pavel. For more computing environment at CSE to be flexible conducts theoretical and applied research related to information, visit CHCC’s Web pages at and responsive in meeting the department’s database management and object-oriented systems. www.cse.ogi.edu/CHCC/. 39 changing needs. Query processing is a long-term focus, particularly query optimization frameworks as well as query Support for central services such as mail, dial-up PACIFIC SOFTWARE RESEARCH CENTER processing over Internet data sources, particularly access, video conferencing, database access and KELLY ATKINSON, Center Administrator those containing XML. DOT research also considers file- and printer-sharing, as well as access to and develops conceptual models, including models Internet and Internet2 services, is distributed Phone: 503 748-1336 for superimposed information and data across a group of Sun computers and a Network E-mail: [email protected] transformation. DOT has a history of involvement Appliance file server that make up the core with database support for scientific applications, support environment. SHERI DHUYVETTER, Center Administrator including forest canopy research, and more Phone: 503 748-1476 recently, data product management for scientific Although Sun computers are highly visible at CSE, E-mail: [email protected] observation and simulation. Web data management both Intel- and Alpha-based machines running is another area of research carried out at DOT, Windows or Linux are mainstays of our research The Pacific Software Research Center (PacSoft) is activities. The generous support of our industry a team of faculty, students and professional particularly management of semi-structured data and XML, Web information integration and and government research partners allows CSE to research staff who study mathematically based maintain a high-quality computing infrastructure techniques for the specification, development and ubiquitous access to Web data and services. Dr. David Maier of the OGI School of Science & capable of supporting a high degree of validation of complex computer software. Our goals heterogeneity as required for high-quality research. are to explore and test new techniques that can Engineering is the director of DOT. Additional DOT- support the development of software products in affiliated faculty members are Dr. Lois Delcambre The department also has facilities for research and which clients can have high confidence. and Dr. Juliana Freire, all with OGI, and Dr. teaching in computer hardware design and Leonard Shapiro of Portland State University. electrical engineering. Mentor Graphics IC Design PacSoft’s approach to software specification and Station is used for VLSI design. Chips are development is grounded in functional program- SYSTEMS SOFTWARE LABORATORY fabricated at the Mosis foundry and can be tested ming, type theory, meta-programming, formal on our IMS XL60 chip tester. Mentor and Altera methods, and programming language semantics. CYNTHIA PFALTZGRAFF, Center Administrator CAD tools are provided for FPGA programmable Our research methods extend from theoretical Phone: 503 748-7109 logic design. The computer design lab is equipped investigation, through prototype software tool E-mail: [email protected] with PC workstations, Tektronix digital development, to experimental validation. oscilloscopes, FPGA development boards and TI The Systems Software Lab (SySL) is a center for DSP boards. We have test equipment and facilities Much of our work during the past decade has research spanning the areas of distributed and focused on techniques for the design and for analog and mixed signal design along with mobile computing, operating systems, networking simulation support with Cadence PSpice. A digital implementation of domain-specific languages. and wide-area-network-based information A domain-specific language is able to express the television lab is available for video signal management systems. SySL focuses on the processing projects. abstractions and operations used in a particular development of adaptive systems that utilize engineering domain in terms familiar to domain techniques such as feedback control, specialization, In all, a facilities staff of eight supports almost experts. This allows non-programmers, who are domain-specific languages, and quality of service 400 computer systems, X terminals and domain experts, to create significant software management to enable them to operate effectively peripheral devices spanning multiple networks artifacts that meet their own needs. Construction in today’s rapidly evolving and widely using a variety of automated techniques, many of domain specific languages requires experts in heterogeneous distributed environments. We developed internally, to cope with the high both the domain and language design. Domains in emphasize the real-world applicability of our degree of complexity inherent in such a which this work has demonstrated considerable research results and we continue to build heterogeneous environment. success are the design of complex microarchi- distributed and scalable prototype systems for tectures for high performance microprocessors, application areas such as multimedia computing the construction of encryption algorithms, and and communications, active networks, Internet- languages where time plays a central role. based information management and survivable Dr. Tim Sheard is the director of the Center. distributed systems. We collaborate closely with Dr. Richard Kieburtz is the founding director. Other industry sponsors such as Intel and IBM, and have faculty members of PacSoft are Dr. Andrew Black, strong federal funding from DARPA and NSF. Dr. Dr. James Hook, Dr. Mark Jones, Dr. John Jonathan Walpole is the director of SySL. Launchbury, and Dr. John Matthews of the OGI Additional SySL-affiliated faculty are Drs. Wu-chi School of Science & Engineering, and Dr. Andrew Feng, Wu-chang Feng, and Andrew Black of OGI, Tolmach of Portland State University. The Center and Dr. Molly Shor of Oregon State University. employs six postdoctoral researchers and has numerous visitors each year. Research by PacSoft scientists is supported by grants and contracts from the National Science Foundation, DARPA, DOD, Intel Corp. and OTI. For additional information, visit the PacSoft Web site, http://www.cse.ogi.edu/PacSoft/. 31 CSE | COMPUTER SCIENCE AND ENGINEERING | F ACULTY FACULTY

JAMES HOOK ANDREW P. BLACK NIRUPAMA BULUSU PHIL COHEN Associate Professor Professor Assistant Professor Professor, Co-Director Center for and Department Head D. Phil. University of Oxford Ph.D., Computer Science Human-Computer Communication Ph.D., Computer Science (Balliol College), England University of California at Ph.D., Computer Science Cornell University, 1988 [email protected] Los Angeles, 2002 University of Toronto, 1978 [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Programming languages; Embedded Networked Sensing RESEARCH INTERESTS Domain-specific languages, formal distributed systems; streaming (ENS) systems; computer Multimodal interfaces; human- methods and functional infrastructure for wide-area networks; mobile and wireless computer interaction; natural programming. networks; object-oriented networks; network applications language processing; dialogue; languages and systems; and security; large-scale delegation technology; cooperating REPRESENTATIVE PUBLICATIONS programming environments; and distributed systems. agents; communicative action; W. Harrison, T. Sheard and J. Hook, the ways in which all of these applications to mobile computing; “Fine Control of Demand in Haskell,” areas interrelate. REPRESENTATIVE PUBLICATIONS information management; network Proceedings of the Sixth International N. Bulusu, J. Heidemann, D. Estrin management; manufacturing. Conference on the Mathematics of REPRESENTATIVE PUBLICATIONS and T. Tran, “Self-configuring Program Construction, Dagstuh, Nathanael Schärli, Stéphane Ducasse, Localization Systems: Design and REPRESENTATIVE PUBLICATIONS Germany, July 2002. Experimental Evaluation,” ACM Oscar Nierstrasz and Andrew Black, S. Kumar, P. Cohen and H. Levesque, Transactions on Embedded Computing J. Hook, E. Meijer and D. Leijen, “Traits: Composable Units of Behavior,” “The Adaptive Agent Architecture: Systems (TECS), Special Issue on “Client-side Web Scripting in European Conference on Object-Orinted Achieving Fault-Tolerance Using Networked Embedded Systems. May Haskell,” in proceedings of Practical Programming, Springer Lecture Notes Persistent Broker Teams,” in the 2003. To appear. Applications of Declarative Languages, in Computer Science, July 2003. Fourth International Conference on January 1999. A.P. Black, J. Huang, R. Koster, N. Bulusu, J. Heidemann and D. Multiagent Systems (ICMAS 2000), J. Hook, E. Meijer and D. Leijen, J. Walpole, and C. Pu, “Infopipes: an Estrin, “Adaptive Beacon Placement,” Boston, July 2000. in Proceedings of 21st International “Haskell as an Automation Controller,” Abstraction for Multimedia Streaming,” S. Kumar and P. Cohen, “Towards Conference on Distributed Computing in Advanced Functional Programming, Multimedia Systems (special issue on a Fault-Tolerant Multiagent System Systems (ICDCS-21), Phoenix, Arizona, Swierstra, Henriques and Oliveira, eds., Multimedia Middleware) 8(5), 406-419, Architecture,” in the Fourth April 2001. Springer Verlag, LNCS, Vol.1608. 2002. International Conference on T. Widen and J. Hook, “Software Johan Nordlander, Mark P. Jones, N. Bulusu, J. Heidemann and D. Autonomous Agents (Agents 2000), Design Automation: Language Design Magnus Carlsson, Richard B. Kieburtz Estrin, “GPS-less Low Cost Outdoor Barcelona, June 2000. Localization for Very Small Devices,” in the Context of Domain Engineering,” and Andrew Black, “Reactive Objects,” D. McGee, P. Cohen and L. Wu, IEEE Personal Communications, 7(5), Sere 98, June 1998. 5th IEEE International Symposium on “Something from Nothing: Augmenting 28-34, October 2000. J. Bell, F. Bellegarde and J. Hook, Object-oriented Real-time Distributed a Paper-based Work Practice with “Type-driven Defunctionalization,” Computing, Crystal City, Virginia, USA, Multimodal Interaction,” Proceedings ICFP 97, June 1997. April 2002. of the Designing Augmented Reality Environments Conference, ACM Press, R. Kieburtz, F. Bellegarde et al., C. Pu, T. Autrey, A.P. Black, C. Consel, 71-80, Copenhagen, April 2000. “Calculating Software Generators from C. Cowan, J. Inouye, L. Kethana, J. Solution Specifications,” TAPSOFT 95, Walpole and K. Zhang, “Optimistic S. Oviatt and P. Cohen, “Multimodal Springer-Verlag, LNCS, May 1995. Incremental Specialization: Interfaces That Process What Comes Streamlining in a Commercial Naturally,” Communications of the F. Bellegarde and J. Hook, Operating System,” Proceedings of the ACM, 43( 3), 45-53, March 2000. “Substitution: A Formal Methods 15th ACM Symposium on Operating Case Study using Monads and Systems Principles, December 1995. L. Wu, S.L. Oviatt and P. Cohen, Transformations,” Science of Computer “Multimodal Integration — A Programming, 22 (2-3), 287, 1994. R.K. Raj, E.D. Tempero, H.M. Levy, Statistical View,” IEEE Transactions A.P. Black, N.C. Hutchinson and E. Jul, on Multimedia, 1( 4), 334-341, J. Bell, J. Hook et al., “Software “Emerald, A General Purpose December 1999. Design for Reliability and Reuse: Programming Language,” Software A Proof-of-Concept Demonstration,” Practice & Experience, 21 (1), 91, P. Cohen, D. McGee, S.L. Oviatt, TRI-Ada 94 Proceedings, ACM Press, January 1991. L. Wu, J. Clow, R. King, S. Julier and November 1994. L. Rosenblum, “Multimodal Interactions A.P. Black and Y. Artsy, Digital for 2-D and 3-D Environments,” IEEE Equipment Corp., “Implementing Computer Graphics and Applications, Location Independent Invocation,” IEEE pp.10-13, July-August 1999. Trans. on Parallel and Distributed Systems, B 1(1), 107, January 1990.

32 F ACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

CRISPIN COWAN LOIS DELCAMBRE RICHARD E. (DICK) FAIRLEY WU-CHANG FENG Assistant Research Professor Professor Professor and Associate Dean Assistant Professor Ph.D., Computer Science Ph.D., Computer Science for Academic Affairs Ph.D., Computer Science University of Western Ontario, University of Southwestern Ph.D., Computer Science University of Michigan, 1999 1995 Louisiana, 1982 UCLA, 1971 [email protected] [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Scalable Internet systems; System security and survivability; Superimposed information; All aspects of software Internet congestion control and operating systems; distributed database system data models; engineering, including but not queue management; wireless systems; computer architecture; scientific data management. limited to systems engineering of networking; programmable optimism; programming languages. software-intensive systems; network infrastructure. REPRESENTATIVE PUBLICATIONS software process modeling and REPRESENTATIVE PUBLICATIONS M. Weaver, L. Delcambre and process improvement; software REPRESENTATIVE PUBLICATIONS C. Wright, C. Cowan, S. Smalley, D. Maier, “A Superimposed requirements engineering; W. Feng, F. Chang, W. Feng and J. Morris and G. Kroah-Hartman, Architecture for Enhanced Metadata,” software design; software quality J. Walpole, “Provisioning On-line “Linux Security Modules: General DELOS Workshop on Interoperability engineering; software metrics; Games: A Traffic Analysis of a in Digital Libraries, held in conjunction Security Support for the Linux software project management; Busy Counter-Strike Server,” Kernel,” Eleventh USENIX Security with European Conference on Digital Internet Measurement Workshop, Conference, 2002. Libraries (ECDL 2001), Darmstadt, software cost and schedule November 2002. Germany, September 2001. estimation; software risk C. Cowan, S. Beattie, C. Wright W. Feng, D. Kandlur, D. Saha and management; and software and G. Kroah-Hartman, “RaceGuard: S. Bowers and L. Delcambre, “A K. Shin, “Adaptive Packet Marking for Automatic Adaptive Detection and Generic Representation for Exploiting engineering policies, procedures, Maintaining End-to-End Throughput Prevention of Buffer-Overflow Model-Based Information,” ETAI standards and guidelines. in a Differentiated Services Internet,” Attacks,” Tenth USENIX Security Journal, Linköping Electronic Articles IEEE/ACM Transactions on Networking, Conference, 2001. in Computer and Information Science, REPRESENTATIVE PUBLICATIONS 7(5), October 2001. ISSN 1401-9841, Vol. 6, nr 006, 2001, C. Cowan, M. Barringer, S. Beattie, www.ep.liu.se/ea/cis/2001/006/. “Software Project Management,” W. Feng, D. Kandlur, D. Saha and G. Kroah-Hartman, M. Frantzen and Encyclopedia of Computer Science, K. Shin, “Blue: An Alternative Approach J. Lokier, “FormatGuard: Automatic L. Delcambre, D. Maier, S. Bowers, Groves Dictionaries, 2001. to Active Queue Management,” Adaptive Detection and Prevention of L. Deng, M. Weaver, P. Gorman, NOSSDAV 2001, June 2001. “Software Estimation Risk,” Buffer-Overflow Attacks,” Tenth USENIX J. Ash, M. Lavelle and J. Lyman, Encyclopedia of Software Engineering, W. Feng, D. Kandlur, D. Saha and Security Conference, 2001. “Bundles in Captivity: An Application of Superimposed Information,” Vol. 2, John Wiley and Sons, 2000. K. Shin, “Stochastic Fair Blue: A Queue D. McNamee, J. Walpole, C. Cowan, Management Algorithm for Enforcing Proceedings of the IEEE International R. Fairley, “A Process-Oriented C. Pu, C. Krasic, P. Wagle, C. Consel, Fairness,” INFOCOM 2001, April 2001. Conference on Data Engineering, Approach to Software Product G. Muller and R. Marlet, “Specialization Heidelberg, Germany, April 2001. Improvement,” PROFES’99 Conference W. Feng, D. Kandlur, D. Saha and Tools and Techniques for Systematic Proceedings, Oulu, Finland, June 1999. K. Shin, “A Self-Configuring RED Optimization of Systems Software,” S. Bowers and L. Delcambre. Gateway,” INFOCOM 1999, May 1999. ACM Transactions on Computer “Representing and Transforming R. Fairley, “The Concept of Systems, 19(2), May 2001. Modelbased Information,” in Operations – The Bridge from W. Feng, D. Kandlur, D. Saha and Proceedings of the International Operational Requirements to Technical K. Shin, “Understanding and Improving C. Cowan, C. Pu, D. Maier, H. Hinton, Workshop on the Semantic Web, in Specifications,” Annals of Software TCP Performance over Networks with J. Walpole, P. Bakke, S. Beattie, conjunction with ECDL 2000, Lisbon, Engineering, Vol. 3, Amsterdam, Minimum Rate Guarantees,” IEEE/ACM A. Grier, P. Wagle and Q. Zhang, September 2000. September 1997. Transactions on Networking, 7(2), “Stackguard: Automatic Adaptive 173-187, April 1999. Detection and Prevention of Buffer- P. Gorman, J. Ash, M. Lavelle, R. Fairley, “Standard for Concept Overflow Attacks,” Seventh USENIX J. Lyman, L. Delcambre, D. Maier, of Operations Documents,” IEEE Security Conference, 1998. S. Bowers and M. Weaver, “Bundles Standard, Vol. 1362, IEEE Computer in the Wild: Tools for Managing Society, 1997. C. Cowan and H. Lutfiyya, “A Information to Solve Problems and R. Fairley, “Standard for Software Wait-Free Algorithm for Optimistic Maintain Situation Awareness,” Project Management Plans,” IEEE Programming: HOPE Realized,” 16th Library Trends 49 (2), Fall 2000. International Conference on Distributed Standard, Vol. 1058, IEEE Computer Computing Systems (ICDCS’96), D. Maier and L. Delcambre, Society, 1997. “Superimposed Information for the Hong Kong, 1996. R. Fairley, “Risk-Based Cost Internet,” in Proc. of the ACM SIGMOD Estimation,” Proceedings of the 11th C. Cowan, T. Autrey, C. Krasic, C. Pu Workshop on the Web and Databases COCOMO Users Group, Los Angeles, and J. Walpole, “Fast Concurrent (WebDB ‘99), pp. 1-9, June 1999. Dynamic Linking for an Adaptive November 1996. L. Delcambre and D. Maier, “Models Operating System,” in the International R. Fairley, “Some Hard Questions for Superimposed Information,” in Conference on Configurable Distributed for Software Engineering Educators,” Advances in Conceptual Modeling Systems (ICCDS’96), Annapolis, 1996. keynote presentation, CSEE 95 (ER ‘99), Vol. 1727, Lecture Notes Proceedings, ACM Conference on in Computer Science, pp. 264-280, Software Engineering Education, November 1999. New Orleans, March 1995. 33 CSE | COMPUTER SCIENCE AND ENGINEERING | F ACULTY

WU-CHI FENG JULIANA FREIRE DAN HAMMERSTROM PETER A. HEEMAN Associate Professor Assistant Professor Doug Strain Professor Assistant Professor Ph.D., Computer Science Ph.D., Computer Science Ph.D., Electrical Engineering Ph.D., Computer Science University of Michigan, 1996 State University of New York University of Illinois, 1977 University of Rochester, 1997 [email protected] at Stony Brook, 1997 [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Networking; multimedia RESEARCH INTERESTS Biologically inspired computation; Spontaneous speech recognition; systems; multimedia networking; Databases and knowledge-base VLSI chip design for image modeling disfluencies and video coding; middleware systems; information integration; processing, digital video, intonation; dialogue services; and massively scalable management of semi-stuctured signal processing and intelligent management; collaboration; streaming infrastructures. data; Web information systems and signal processing; molecular spoken dialogue systems; Internet applications. and nanoscale architecture; natural language processing. REPRESENTATIVE PUBLICATIONS technology transfer. A.S. Tosun and W. Feng, “On Error REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS Preserving Video Encryption Algorithms M. Benedikt, C-Y. Chan, W. Fan, S. Strayer and P. Heeman, “Dialogue for Wireless Transmission,” in J. Freire, and R. Rastogi. “Capturing J.R. Kerr, C. H. Luk, D. Hammerstrom, Structure and Mixed Initiative,’’ second Proceedings of the ACM Multimedia both Types and Constraints in M. Pavel, “Advanced Integrated workshop of the Special Interest Group 2001, October 2001. Data Integration,” ACM SIGMOD Enhanced Vision Systems,” Proceedings on Dialogue, Aalborg, Denmark, SPIE, April 2003. W. Feng and M. Liu, “Extending International Conference on September 2001. Management of Data, 2003. Critical Bandwidth Allocation C. Gao, D. Hammerstrom, S. Zhu, P. Heeman and J. Allen, “Improving Techniques for Stored Video P. Bohannon, J. Freire, J.R. Haritsa, M. Butts, “FPGA Implementation Of Robustness by Modeling Spontaneous Delivery Across Best-Effort M. Ramanath, P. Roy and J. Siméon, Very Large Associative Memories – Speech Events,” in Robustness in Networks,” International Journal “Bridging the XML-Relational Divide Scaling Issues,” chapter submitted for Language and Speech Technology, of Communication Systems, 14, with LegoDB: A Demonstration,” IEEE book, FPGA Implementations of Neural J. Junqua and G. van Noord, eds., 925-940, September 2001. International Conference on Data Networks, Amos Omondi (ed.), Kluwer Kluwer Academic Publishers, 2000. Engineering (ICDE), 2003. Academic Publishers, Boston, 2003. A.S. Tosun and W. Feng, “Lightweight K. Ward and P. Heeman, Security Mechanisms for Wireless Video J. Freire, J.R. Haritsa, M. Ramanath, C. Gao and D. Hammerstrom, “Acknowledgments in Human-Computer Transmission,” in Proceedings of the P. Roy and J. Siméon, “StatiX: “Platform Performance Comparison Interaction,” in Proceedings of the IEEE International Conference on Making XML Count,” ACM SIGMOD of PALM Network on Pentium 4 and 1st Conference of the North American Information Technology: Coding and International Conference on FPGA,” IJCNN 03, July 2003. Chapter of the Association for Computing 2001, Las Vegas, April 2001. Management of Data, pp. 181-192, S. Zhu and D. Hammerstrom, Computational Linguistics, Seattle, A.S. Tosun and W. Feng, “On 2002. “Reinforcement Learning in Associative May 2000. Improving Quality of Video for H.263 J. Freire and J. Simeon, “Adaptive Memory,” Proceedings of the IJCNN, P. Heeman, “Modeling Speech Repairs over Wireless CDMA Networks,” in XML Shredding: Architecture, July 2003. and Intonational Phrasing to Improve Proceedings of the IEEE Wireless Implementation, and Challenges,” G. Zeng and D. Hammerstrom, Speech Recognition,” in IEEE Workshop Communications and Networking Efficiency and Effectiveness of XML “Distributed Associative Neural on Automatic Speech Recognition and Conference, Chicago, September 2000. Tools, and Techniques (EEXTT), Network Model Approximates Bayesian Understanding, Keystone, Colorado, A. Agarwal, W. Feng and C. Wolfe, pp. 104-116, 2002. Inference,” Proceedings of ANNIE 2003, December 1999. “A Multi-Differential Video Coding P. Bohannon, J. Freire, J.R. Haritsa, St. Louis Mo., December 2002. P. Heeman and J. Allen, “Speech Algorithm for Robust Video M. Ramanath, P. Roy and J. Siméon, S. Zhu and D. Hammerstrom, Repairs, Intonational Phrases and Conferencing,” in Proceedings of “LegoDB: Customizing Relational “Simulation of Associative Neural Discourse Markers: Modeling the SPIE Voice, Video and Data Storage for XML Documents,” Very Networks,” Proceedings of the Speakers’ Utterances in Spoken Communications Conference, Boston, Large Databases Conference (VLDB), International Conference on Neural Dialog,” Computational Linguistics, November 2000. pp. 1091-1094, 2002. Information Processing, Singapore, Vol. 25-4, 1999. A.S. Tosun, A. Agarwal and W. Feng, M. Benedikt, J. Freire and November 2002. P. Heeman, “POS Tags and Decision “Providing Efficient Support for P. Godefroid, “VeriWeb: Automatically D. Hammerstrom, “Digital VLSI for Trees for Language Modeling,” in Lossless Video Transmission and Testing Dynamic Web Sites,” Neural Networks,” in The Handbook Proceedings of the Joint SIGDAT Playback,” in 10th International International World Wide Web of Brain Theory and Neural Networks, Conference on Empirical Methods in Workshop on Network and Operating Conference (WWW), 2002. 2nd Ed., Michael Arbib (ed.), MIT Natural Language Processing and Very Systems Support for Digital Audio and Large Corpora, College Park, Maryland, P. Bohannon, J. Freire, P. Roy and Press, 2003. Video, Chapel Hill, North Carolina, June 1999. June 2000. J. Siméon, “From XML Schema to D. Hammerstrom and D. Lulich, Relations: A Cost-based Approach to “Image Processing Using One- P. Heeman, M. Johnston, J. Denney XML Storage,” IEEE International Dimensional Processor Arrays,” and E. Kaiser, “Beyond Structured Conference on Data Engineering The Proceedings of the IEEE, 84(7), Dialogues: Factoring Out Grounding,” (ICDE), pp. 64-75, 2002. 27-43, July 1996. in Proceedings of the International Conference on Spoken Language J. Freire, D.F. Lieuwen and Processing ICSLP-98, Sydney, J.J. Ordille, “Integrating Network December 1998. Devices in a Metadirectory: The MetaComm experience,” Information Systems 27(3), 193-217, 2002. 34 F ACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE FACULTY

MARK P. JONES RICHARD B. KIEBURTZ JOHN LAUNCHBURY TODD K. LEEN Associate Professor Professor Professor Professor D.Phil., Computation Ph.D., Electrical Engineering Ph.D., Computing Science Ph.D., Physics University of Oxford, 1992 University of Washington, 1961 University of Glasgow, 1990 University of Wisconsin, 1982 [email protected] [email protected] [email protected] [email protected]

RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Programming language design and Functional programming; program Functional programming Machine learning, local and implementation; programming transformation; domain-specific languages; semantics-based mixture models, invariance, paradigms; module and component languages; program verification; program analysis; program stochastic learning, with systems; type theory; semantics; high-confidence software. transformation and partial applications to anomaly detection, program transformation and evaluation. environmental systems monitoring, analysis. REPRESENTATIVE PUBLICATIONS and data coding. Modeling R.B. Kieburtz, “Real-time Reactive REPRESENTATIVE PUBLICATIONS neurobiological systems. REPRESENTATIVE PUBLICATIONS Programming for Embedded J. Lewis, M. Shields, E. Maijer and Mark P. Jones, “Type Classes with Controllers,” QAPL 2001, J. Launchbury, “Implicit Parameters,” REPRESENTATIVE PUBLICATIONS September 2001. Functional Dependencies,” in Implicit Parameters, ACM Principles of R. Sharma, T.K. Leen and M. Pavel, Proceedings of the 9th European R.B. Kieburtz, “A Logic for Rewriting Programming Languages, 2000. “Bayesian Image Sensor Fusion Using Symposium on Programming, ESOP Strategies,” Strategies ‘01, June 2001. J. Matthews and J. Launchbury, Local Linear Generative Models,” 2000, Berlin, Germany, Springer-Verlag R.B. Kieburtz, “Defining and “Elementary Microarchitecture Optical Engineering, 40, 1364, 2001. LNCS 1782, March 2000. Implementing Closed Domain-Specific Algebra,” Computer Aided C. Archer and T.K. Leen, “The Coding M.P. Jones, “First-class Polymorphism Languages,” SAIG ‘00, September 2000. Verification, 1999. Optimal Transform,” in Proceedings of with Type Inference,” in Proceedings R.B. Kieburtz, “Taming Effects J. Launchbury, J. Lewis and B. Cook. the Data Compression Conference of the 24th Annual ACM SIGPLAN- with Monadic Typing,” in Proc. 3rd “On Embedding a Microarchitecture 2001, IEEE Computer Press, 2001. SIGACT Symposium on Principles of International Conf. on Functional Design Language within Haskell,” Programming Languages, Paris, C. Archer and T.K. Leen, “From Programming, ACM Press, April 1998. International Conference on Functional Mixtures of Mixtures to Adaptive January 1997. Programming, ACM, 1999. R.B. Kieburtz, “Reactive Functional Transform Coding,” in Advances in M.P. Jones, “Using Parameterized Programming,” in PROCOMET’98, J. Launchbury and A. Sabry, Neural Information Processing Systems, Signatures to Express Modular pp. 263-284, Chapman and Hall, “Axiomatization and Type Safety T. Leen, T. Dietterich, V. Tresp, eds., Structure,” in Proceedings of the June 1998. of Monadic State,” Proc. ACM 13, MIT Press, 2001. 23rd Annual ACM SIGPLAN-SIGACT International Conference on Functional W. Wei, T.K. Leen and E. Barnard, “A Symposium on Principles of R.B. Kieburtz, L. McKinney, J. Bell, Programming, 1997. Programming Languages, St. J. Hook, A. Kotov, J. Lewis, D. Oliva, Fast Histogram-Based Postprocessor Petersburg Beach, Fla., January 1996. T. Sheard, I. Smith and L.Walton, “A J. Launchbury and R. Paterson, that Improves Posterior Probability Software Engineering Experiment in “Parametricity and Unboxing with Estimates,” Neural Computation, 11, M.P. Jones, “Simplifying and Software Component Generation,” in Unpointed Types,” Proc. European 1235, 1999. Improving Qualified Types,” in Proceedings of the 18th International Symposium on Programming, Proceedings of FPCA ‘95: Conference T.K. Leen, B. Schottky and D. Saad, Conference on Software Engineering, Linkoping, 1996. on Functional Programming Languages “Optimal Symptotic Learning: Berlin, March 1996. and Computer Architecture, La Jolla, J. Launchbury and S.P. Jones, “State Macroscopic Versus Microscopic Calif., June 1995. R.B. Kieburtz, F. Bellegarde, J. Bell, in Haskell,” J. of Lisp and Symbolic Dynamics,” Physical Review E, 59, J. Hook, J. Lewis, D. Oliva, T. Sheard, Computation, December 1995. 985, 1999. M.P. Jones, “A System of Constructor L. Walton and T. Zhou, “Calculating Classes: Overloading and Implicit J. Launchbury and S.P. Jones, “Lazy T.K. Leen and J.E. Moody, “Stochastic Software Generators from Solution Higher-order Polymorphism,” Journal Functional State Threads,” in Proc. Manhattan Learning: Time-Evolution Specifications,” TAPSOFT ‘95, Springer- of Functional Programming, 5(1), SIGPLAN Programming Languages Operator for the Ensemble Dynamics,” Verlag, series LNCS, 915, 546, 1995. Cambridge University Press, January Design and Implementation, Orlando, Physical Review E, 56, 1262, 1997. 1995. R.B. Kieburtz, “Programming with Fla., 1994. N. Kambhatla and T.K. Leen, Algebras,” in Advanced Functional S. Liang, P. Hudak and M.P. Jones, A. Gill, J. Launchbury and S.P. Jones, “Dimension Reduction by Local Programming, E. Meijer and J.Jeuring, “Monad Transformers and Modular “A Short Cut to Deforestation,” in Principal Component Analysis,” eds., Springer-Verlag, Series LNCS, Interpreters,” in Conference Record of Proc. SIGPLAN/SIGARCH Functional Neural Computation, 9, 1493, 1997. Vol. 925, 1995. POPL’95: 22nd ACM SIGPLANSIGACT Programming and Computer T.K. Leen, “From Data Distribution to Symposium on Principles of R.B. Kieburtz, “Results of the SDRR Architecture, Copenhagen, 1993. Regularization in Invariant Learning,” Programming Languages, San Validation Experiment,” Pacific J. Launchbury, “A Natural Semantics Neural Computation, 7, 974, 1995. Francisco, January 1995. Software Research Center Software for Lazy Evaluation,” in Proc. SIGPLAN T.K. Leen, “A Coordinate-Independent Design for Reliability and Reuse: M.P. Jones, Qualified Types: Theory Principles of Programming Languages, Center Manifold Reduction,” Physics Phase I Final Scientific and Technical and Practice, Cambridge University Charleston, S.C., 1993. Letters, A 174, 89, 1993. Report, Vol. VI, CDRL No. 0002.11, Press, November 1994. February 1995 J. Hughes and J. Launchbury, “Projections for Polymorphic First- Order Strictness Analysis,” in Mathematical Structures in Computer Science, 2, 301, C.U.P., 1992.

35 CSE | COMPUTER SCIENCE AND ENGINEERING | F ACULTY

DAVID MAIER JOHN MATTHEWS MELANIE MITCHELL SHARON L. OVIATT Professor Assistant Professor Associate Professor Professor Ph.D., Electrical Engineering Ph.D., Computer Science Ph.D., Computer Science Co-Director for Center for and Computer Science Oregon Graduate Institute, 2000 University of Michigan, 1990 Human Computer Communication Princeton University, 1978 [email protected] [email protected] Ph.D., Experimental Psychology [email protected] University of Toronto, 1979 RESEARCH INTERESTS RESEARCH INTERESTS [email protected] RESEARCH INTERESTS Formal verification; theorem Artificial intelligence; machine Database systems (including proving; model checking; learning; cognitive science and RESEARCH INTERESTS object-oriented database specification languages; functional complex systems;. computer Multimodal and spoken language management systems, query and constraint logic programming modeling of perception and interfaces; conversational processing, scientific information languages. analogy-making; theory and interfaces; ubiquitous and management, superimposed applications of evolutionary perceptive interfaces; modality information and net data REPRESENTATIVE PUBLICATIONS computation; collective effects in communication and management); object-oriented and L. Lamport, J. Matthews, M. Tuttle computation in spatially extended communication models; tele- logic programming languages; and Y. Yu, “Specifying and Verifying systems such as cellular automata communication and technology- algorithms; bioinformatics and Systems With TLA+,” Tenth ACM and neural models; history of mediated communication; health information technology. SIGOPS European Workshop: Can we science and technology. mobile and interactive interfaces; really depend on an OS?, Saint-Emilion, France, September 2002 (to appear). human-computer interaction; REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS empirically based design and S. Krstic and J. Matthews, “Verifying P. Tucker, D. Maier, T. Sheard and L. Pagie and M. Mitchell, “A evaluation of human-computer BDD Algorithms through Monadic L. Fegaras. “Exploiting Punctuation Comparison of Evolutionary and Interpretation,” Proceedings of the interfaces; cognitive science and Semantics in Continuous Data Coevolutionary Search,” to appear in Third International Workshop on research methodology. Streams,” IEEE Transactions on International Journal of Computational Verification, Model Checking and Knowledge and Data Engineering, Intelligence and Applications, in press. Abstract Interpretation, Venice, Italy, 15(3), May/June 2003. REPRESENTATIVE PUBLICATIONS January 2002. M. Mitchell, “Analogy-making as a S.L. Oviatt, “Breaking the Robustness V. Papadimos, D. Maier and K. Tufte. Complex Adaptive System,” in Design J. Matthews, “Recursive Function Barrier: Recent Progress on the Design “Distributed Query Processing and Principles for the Immune System and Definition over Coinductive Types,” of Robust Multimodal Systems,” Catalogs for Peer-to-Peer Systems,” Other Distributed Autonomous Systems, Proceedings of the 12th International Advances in Computers (ed. by Proceedings CIDR 2003: First Biennial L. Segel and I. Cohen, eds., Oxford Conference on Theorem Proving in M. Zelkowitz) Academic Press, 2002, Conference on Database Systems University Press, 2001. Higher Order Logics, Nice, France, vol. 56, pp. 305-341. Research, Asilomar, CA, January 2003. LNCS Vol. 1690, September 1999. M. Mitchell, “Can Evolution Explain S.L. Oviatt, “Multimodal Interfaces,” L. Shapiro, D. Maier, P. Benninghoff, How the Mind Works? A Review of the J. Matthews and J. Launchbury, in J. Jacko and A. Sears, eds., Handbook K. Billings, Y. Fan, K. Hatawal, B.Vance Evolutionary Psychology Debates,” “Elementary Microarchitecture of Human-Computer Interaction, and Q.Wang, “Exploiting Upper and Complexity, 3 (3), 17-24, 1999. Algebra,” Proceedings of the 11th Lawrence Erlbaum Assoc., Mahwah, Lower Bounds in Top-down Query International Conference on Computer E. van Nimwegen, J.P. Crutchfield and N.J., 2002, ch. 14, pp. 286-304. Optimization,” Proceedings of IDEAS Aided Verification, Trento, Italy, LNCS M. Mitchell, “Statistical Dynamics of 2001, Grenoble, France, July 2001. S.L. Oviatt, P.R. Cohen, L. Wu, Vol. 1633, July, 1999. the Royal Road Genetic Algorithm,” J. Vergo, L. Duncan, B. Suhm, J. Bers, J. Shanmugasundaram, K. Tufte, Theoretical Computer Science, 229 (1), B. Cook, J. Launchbury and J. T. Holzman, T. Winograd, J. Landay, D. DeWitt, J. Naughton and D. Maier. 41-102, 1999. Matthews, “Specifying Superscalar J. Larson and D. Ferro. “Designing “Architecting a Network Query Engine Microprocessors in Hawk,” Workshop M. Mitchell, “A Complex-Systems the User Interface for Multimodal for Producing Partial Results,” in The on Formal Techniques for Hardware Perspective on the ‘Computation vs. Speech and Gesture Applications: World Wide Web and Databases (Third and Hardware-like Systems, Marstrand, Dynamics’ Debate in Cognitive State-of-theart Systems and Research International Workshop WebDB 2000), Sweden, June 1998. Science,” in M. A. Gernsbacher and Directions,” Human Computer Lecture Notes in Computer Science, S. J. Derry, eds., Proceedings of the Interaction, 15 (4), 263-322, Vol. 1997, Springer-Verlag, 2001. J. Matthews, J. Launchbury and B. 20th Annual Conference of the 2000. Reprinted in J. Carroll, ed., Cook, “Microprocessor Specification in L. Delcambre, D. Maier, S. Bowers, Cognitive Science Society-Cogsci98, Human-Computer Interaction in the Hawk,” Proceedings of the IEEE L. Deng, M. Weaver, P. Gorman, J. Ash, pp. 710-715, 1998. New Millennium, Addison-Wesley International Conference on Computer M. Lavelle and J. Lyman, “Bundles Press, 2001. Languages 1998, Chicago, May 1998. J.P. Crutchfield and M. Mitchell, “The in Captivity: An Application of Evolution of Emergent Computation,” S.L. Oviatt, “Multimodal System Superimposed Information,” Proceedings of the National Academy of Processing in Mobile Environments,” Proceedings of the IEEE International Sciences, USA, 92 (23), 10742, 1995. Proceedings of the 13th Annual ACM Conference on Data Engineering, Symposium on User Interface Software M. Mitchell, J.P. Crutchfield and P.T. Heidelberg, Germany, April 2001. Technology UIST’2000, pp. 21-30, 2000. Hraber, “Dynamics, Computation, and L. Fegaras and D. Maier, the ‘Edge of Chaos’: A Re-examination,” S.L. Oviatt, “Taming Recognition “Optimizing Object Queries Using in Complexity: Metaphors, Models, and Errors with a Multimodal an Effective Calculus,” ACM Reality, G. Cowan, D. Pines and D. Architecture,” Communications of Transactions on Database Systems Melzner, eds., Addison-Wesley, 1994. the ACM, 43 (9), 45-51, (special 25 (4), December 2000. issue on “Conversational Interfaces”), September 2000. 36 F ACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

CALTON PU TIM SHEARD CLÁUDIO T. SILVA XUBO SONG Professor Associate Professor, Associate Professor Assistant Professor Ph.D., Computer Science Director Pacific Software Ph.D., Computer Science Ph.D. Electrical Engineering University of Washington, 1986 Research Center State University of New York California Institute of Technology, [email protected] Ph.D., Computer at Stony Brook, 1996 1999 and Information Science [email protected] [email protected] RESEARCH INTERESTS University of Massachusetts at Amherst, 1985 Transaction processing, RESEARCH INTERESTS RESEARCH INTERESTS [email protected] distributed databases, scientific Computer graphics; scientific Digital image and video databases, parallel and visualization; applied processing; statistical pattern distributed operating systems. RESEARCH INTERESTS computational geometry; high recognition; machine learning; Functional programming; software performance computing. sensor fusion; computer vision; REPRESENTATIVE PUBLICATIONS specification; program generation; information theory; biomedical L. Liu and C. Pu, “An Adaptive Object- meta-programming and staging. REPRESENTATIVE PUBLICATIONS engineering. Oriented Approach to Integration and S. Fleishman, M. Alexa, D. Cohen-Or Access of Heterogeneous Information REPRESENTATIVE PUBLICATIONS and C. Silva, “Progressive Point Set REPRESENTATIVE PUBLICATIONS Sources,” International Journal on T. Sheard, “Accomplishments and Surfaces,” ACM Transactions on G. Wang, M. Pavel, X. Song, “Robust Distributed and Parallel Databases, Research Challenges in Meta- Graphics (to appear). Recognition Based on Combination of 5 (2), April 1997. Programming,” Second International W. Corrêa, J. Klosowski and C. Silva, Weak Classifiers,” International Joint K.L. Wu, P.S. Yu and C. Pu, Workshop on Semantics, Applications “Out-Of-Core Sort-First Parallel Conference of Neural Networks, “Divergence Control for Epsilon- and Implementation of Program Rendering for Cluster-Based Tiled July 2003. Serializability,” IEEE Transactions on Generation (SAIG 2001), LNCS 2196, Displays,” Parallel Computing, 29, X. Song, Y.S. Abu-Mostafa, J. Sill, Knowledge and Data Engineering, 9 Florence, Italy, September 2001. 325-338, 2003. H.L. Kasdan and M. Pavel, “Image (2), March-April 1997. T. Sheard, “Generic Unification via M. Alexa, J. Behr, D. Cohen-Or, Recognition by Fusion of Contextual J. Biggs, C. Pu, A. Groeninger and Two-Level Types and Parameterized S. Fleishman, C. Silva and D. Levin, Information,” Information Fusion P.E. Bourne, “pdbtool: An Interactive Modules,” Sixth ACM SIGPLAN “Computing and Rendering Point Set Journal 3, 277-287, 2002. Browser and Geometry Checker for International Conference on Functional Surfaces,” IEEE Transactions on A. Adami, K. Yang, X. Song, M. Pavel Protein Structures,” Journal of Applied Programming (ICFP’01), ACM Press, Visualization and Computer Graphics, and D. Dirschl, “Model-based Image Crystallography, 29 (4), 1996. Florence, Italy, September 2001. 9(1), 3-15, 2003. Processing and Analysis for Fracture L. Liu, C. Pu, R. Barga and T. Zhou, T. Sheard, Z. Benaissa and E. Pasalic, R. Farias and C. Silva, “Out-Of-Core Classification,” The Second Joint “Differential Evaluation of Continual “DSL Implementation Using Staging and Rendering of Large Unstructured Meeting of the IEEE Engineering in Queries,” Proceedings of the 16th Monads,” Usenix, Second Conference on Grids,” IEEE Computer Graphics and Medicine and Biology Society (EMBS) International Conference on Distributed Domain Specific Languages. Austin, Applications, 21(4), 42-50, 2001. and the Biomedical Engineering Society Computing Systems, Hong Kong, May Texas. October 1999. (BMES), 2002. 1996. P. Lindstrom and C. Silva, “A Memory W. Taha, Z. Benaissa and T. Sheard, Insensitive Technique for Large Model X. Song, Y. Abu-Mostafa, J. Sill and K. Ramamrithan and C. Pu, “A Formal “Multi-Stage Programming: Simplification,” IEEE Visualization H. Kasdan, “Image Recognition in Characterization of Epsilon Axiomatization and Type Safety,” 25th 2001, pp. 121-126. Context: Application to Microscopic Serializability,” IEEE Transactions on International Colloquium on Automata, Urinalysis,” in Advances in Neural J. El-Sana, N. Sokolovsky and C. Silva, Knowledge and Data Engineering, 7 (6), Languages and Programming, July 1998. Information Processing Systems, S.A. “Integrating Occlusion Culling with December 1995. Solla, T.K. Leen, and K.R. Muller (eds.), M. Shields, T. Sheard and S. Peyton View-Dependent Rendering,” IEEE MIT Press, pp. 963-969, 2000. C. Pu, T. Autrey, A.P. Black, C. Consel, Jones, “Dynamic Typing as Staged Type Visualization 2001, pp. 371-378. C. Cowan, J. Inouye, L. Kethana, J. Inference,” ACM-SIGPLAN-SIGACT X. Song, Y. Abu-Mostafa, J. Sill and J. Klosowski and C. Silva, “The Walpole and K. Zhang, “Optimistic Symposium on Principles of H. Kasdan, “Incorporating Contextual Prioritized-Layered Projection Incremental Specialization: Programming Languages (POPL ‘98), Information into White Blood Cell Image Algorithm for Visible Set Estimation,” Streamlining a Commercial Operating San Diego, January 1998. Recognition,” in Advances in Neural IEEE Transactions on Visualization and System,” Proceedings of the 15th Information Processing Systems, T. Sheard, “A Type-Directed, On-Line, Computer Graphics, 6(2), 108-123, Symposium on Operating Systems M.I. Jordan, M.J. Kearns, and S.A. Solla Partial Evaluator for a Polymorphic 2000. Principles, December 1995. (eds.), MIT Press, pp. 950-956, 1998. Language,” ACM-SIGPLAN Conference B. Wei, C. Silva, E. Koutsofios, R. Barga and C. Pu, “A Practical and on Partial Evaluation and Semantics- Y. Abu-Mostafa, and X. Song, “Bin S. Krishnan and S. North. “Visualization Modular Implementation Technique of Based Program Manipulation, Model for Neural Networks,” in Research with Large Displays,” IEEE Extended Transaction Models,” Amsterdam, June 1997. Proceedings of the International Computer Graphics and Applications, Proceedings of the 21st International Conference on Neural Information W. Taha and T. Sheard, “Multi-Stage 20(4), 50-54, 2000. Conference on Very Large Data Bases, Processing, S. Amari, L. Xu, L. Chan, Programming with Explicit Zurich, September 1995. F. Bernardini, J. Mittleman, H. I. King, and K. Leung (eds.), Springer, Annotations,” ACM-SIGPLAN Rushmeier, C. Silva and G. Taubin, “The pp. 169-173, 1996. K. Ramamrithan and C. Pu, “A Formal Conference on Partial Evaluation and Ball-Pivoting Algorithm for Surface Characterization of Epsilon Semantics-Based Program Reconstruction,” IEEE Transactions on Serializability,” IEEE Transactions on Manipulation, Amsterdam, June 1997. Knowledge and Data Engineering, 7 (3), Visualization and Computer Graphics, June 1995. 5(4), 349-359, 1999.

37 CSE | COMPUTER SCIENCE AND ENGINEERING | F ACULTY

JONATHAN WALPOLE ERIC A. WAN YONGHONG YAN Professor Associate Professor Associate Professor Ph.D., Computer Science Ph.D., Electrical Engineering Ph.D., Computer Science University of Lancaster, 1987 Stanford University, 1994 & Engineering, [email protected] [email protected] Oregon Graduate Institute, 1995. [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Adaptive systems software Learning algorithms and RESEARCH INTERESTS and its application in distributed, architectures for neural Human computer interface design; mobile and multimedia networks and adaptive signal spoken language systems; large computing environments and processing; applications to vocabulary speech recognition; environmental observation and time-series prediction, speech computer vision; real-time forecasting systems; quality of enhancement, adaptive control embedded system and speech service specification, adaptive and telecommunications. signal processing. resource management and dynamic specialization for REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS enhanced performance, E.A. Wan, A.A. Bogdanov, R. Kieburtz, X. Wu, and Y. Yan, “Linear Regression survivability and evolvability A. Baptista, M. Carlsson, Y. Zhang and Under Maximum a Posteriori Criterion of large software systems. M. Zulauf, “Model Predictive Neural with Markov Random Field Prior,” Control for Aggressive Helicopter in Proceedings IEEE ICASSP2000, Maneuvers,” IEEE volume on Software- June, 2000. REPRESENTATIVE PUBLICATIONS Enabled Control, T. Samad and G. Balas C. Liu, and Y. Yan, “Speaker Change A. Goel, B. Krasic, K. Li and (eds.), 2003. J. Walpole, “Supporting Low-Latency Detection Using Minimum Message TCP-Based Media Streams,” in E.A. Wan and R. van der Merwe, Length Criterion,” in Proceedings 6th Proceedings International Workshop “The Unscented Kalman Filter,” in International Conference on Spoken on Quality of Service (IWQoS), 2002. Kalman Filtering and Neural Language Processing, October, 2000. Networks, S. Haykin (ed.), John Wiley C. Zheng, and Y. Yan, “Efficiently A. Black, R. Koster, J. Huang, & Sons, 2001. J. Walpole and C. Pu, “Infopipes: An Using Speaker Adaptation Data,” in Abstraction for Multimedia Streaming,” E. Wan, and A. Nelson, “Networks Proceedings 6th International to appear in ACM / Springer-Verlag for Speech Enhancement,” in Conference on Spoken Language Multimedia Systems Journal, 2002. Handbook of Neural Networks for Processing, October, 2000 Speech Processing, S. Katagiri (ed.), Y. Yan, “Speech Recognition Using K. Li, C. Krasic, J. Walpole, M. Shor Artech House, Boston, 1999. and C. Pu, “The Minimal Buffering Correlation Generated Neural Network Requirements of Congestion-Controlled E. Wan and F. Beaufays, Target,” IEEE Trans. on Speech and Interactive Multimedia Applications,” “Diagrammatic Methods for Deriving Audio Processing, May 1999. and Relating Temporal Neural Networks in Proceedings of the 8th International E. Barnard, and Y. Yan, “Toward New Algorithms,” in Adaptive Processing Workshop on Interactive Distributed Language Adaptation for Language of Sequences and Data Structures,” Multimedia Systems - iDMS 2001, Identification,” Speech Communication, Lecture Notes in Artificial Intelligence, Lancaster, UK, September 2001. Also 21(4), 245-254, May 1997. published in Springer-Verlag’s Lecture M. Gori, and C.L. Giles (eds.), Springer Y. Yan, E. Barnard, R.A. Cole, Notes in Computer Science Series Verlag, 1998. “Development of an Approach to LNCS 2158, pp. 181-192. E. Wan, and A. Nelson, “Neural Automatic Language Identification Dual Extended Kalman Filtering: R. Koster, A. Black, J. Huang, based on Phone Recognition,” in Applications in Speech Enhancement J. Walpole and C. Pu, “Thread Computer, Speech Language, 10(1), and Monaural Blind Signal Separation,” Transparency in Information Flow 37-54, January, 1996. Middleware,” in Proceedings IEEE Workshop on Neural Networks Middleware 2001-IFIP/ACM and Signal Processing, 1997. International Conference on E. Wan, “Adjoint LMS: An Alternative zDistributed Systems Platforms, to Filtered-X LMS and Multiple Error Heidelberg, Germany, November 2001. LMS,” ICASSP96, 3, 1842-1845, 1996. Also appears as OGI Technical Report E. Wan, “Time Series Prediction Using CSE-01-004. a Neural Network with Embedded D. McNamee, J. Walpole, C. Cowan, Tapped Delay-Lines,” in Predicting the C. Pu, C. Krasic, P. Wagle, C. Consel, Future and Understanding the Past, G. Muller and R. Marlet, “Specialization A. Weigend, and N. Gershenfeld (eds.), Tools and Techniques for Systematic SFI Studies in the Science of Complexity, Optimization of Systems Software,” Proc., 17, Addison-Wesley, 1993. ACM Transactions on Computer E. Wan, “Discrete Time Neural Systems, 19(2), 217-251, May 2001. Networks,” Journal of Applied Intelligence, 3(1), 91-105, 1993. 38 F ACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

INSTRUCTORS JOINT FACULTY PART-TIME FACULTY ADJUNCT FACULTY ROBERT JAFFE, PH.D. DR. ANTÓNIO BAPTISTA DR. CHARLES CONSEL MR. MARK ANDERS (electrical and computer Environmental & University of Bordeaux Intel Corporation engineering), Biomolecular Systems DR. DAVID G. NOVICK MR. CHEDLEY AORIRI Portland State University, 1988. OGI School of Science Signals and applied systems; & Engineering University of Texas, El Paso Consultant applied mathematics; DR. FRANCOISE BELLEGARDE MR. ROBERT BAUER mathematical systems theory; Rational Software Corp. linear systems; robust control. University of Franche Comte, France DR. C. MIC BOWMAN SAVA KRSTIC, PH.D. (mathematics) DR. TAMARA HAYES Intel Corporation Belgrade University, 1986. Biomedical Engineering MR. SHEKHAR BORKAR OGI School of Science Theoretical computer science; Intel Corporation hardware and software & Engineering MR. BRENT CAPPS verification; cryptography; DR. SHANNON K. MCWEENEY group theory. Oregon Master of Public Health and Software Engineering JOHN D. LYNCH, B.S. Preventive Medicine (electrical engineering), Oregon Health & DR. CHRISTOPHER DUBAY University of Utah, 1979. Science University Oregon Health & System-on-Chip design; DR. MISHA PAVEL Science University electronic design automation; Biomedical Engineering self-timed logic design; logic DR. ANREW GILL OGI School of Science synthesis and timing analysis. Galois & Engineering Has 23-year industry career MR. ROY HALL in designing digital systems. DR. LEONARD SHAPIRO Crisis in Perspective Department of Computer Science Portland State University DR. DAVID HANSEN George Fox University DR. ANDREW TOLMACH Department of Computer Science MR. ROY KRAVITZ Portland State University RadiSys Corporation DR. JAMES LARSON Intel Corporation DR. WAYNE MUSIC Lattice Semiconductor DR. GIL NEIGER Intel Corporation MR. SANJEEV QAZI Intel Corporation DR. RICHARD SPROAT AT&T Labs, New Jersey MS. ELISABETH SULLIVAN TruSec Solutions MR. JAMES TSCHANZ Intel Corporation MR. STEWART TAYLOR Maxim DR. PAUL THADIKARAN Intel Corporation MR. PERRY WAGLE Computer Science and Engineering OGI School of Science & Engineering MS. REBECCA WIRFS-BROCK Consultant DR. MAZIN YOUSIF Intel Corporation 39 The academic and research progress at a rate determined by the Electrical Engineering programs in Electrical and student’s ability and effort. Computer Engineering (ECE) have The major fields of research activity in the Program in EESE Program are: been realigned within the • Atmospheric Optics Computer Science and Semiconductor Engineering •Display Technology including Thin Film Engineering (CSE) and Biomedical Transistors and Phosphors Engineering (BME) departments. •Electro-Optic Systems www.ece.ogi.edu OGI will continue to offer M.S. •Micro-Electrical-Mechanical Analysis PROGRAM DIRECTOR and Ph.D. degrees in electrical (MEMS) Don Johansen • Processing for Ultra Shallow Device 503 748-1315 engineering with program Technology E-mail: [email protected] emphasis in computer • Semiconductor Electronic Devices ADMINISTRATIVE COORDINATOR engineering; signals and systems • Semiconductor Materials, Characterization Joan Sims processing; and biomedical and Processing 503 748-1130 E-mail: [email protected] engineering, as well as pursuing • Sensors research in these three areas. • Systems Dynamics EESE GENERAL INQUIRIES • Thermal Processing 503 748-1130 Students interested in these E-mail: [email protected] • Nanotechnology applications for areas should refer to the CSE electronics and/or BME departments for additional information. Program Seminars The EESE Program and other local The academic program in semiconductor- educational and corporate organizations may related topics is being phased out. OGI is no host invited talks and seminars on topics of longer accepting M.S. and Ph.D. applicants in interest in the field of semiconductor this area of emphasis. During the academic engineering. Although not required for year 2003 - 2004, the Electrical Engineering graduate credit, we recommend that all Program in Semiconductor Engineering EESE students attend these informative (EESE) will offer as many semiconductor- meetings. Seminar schedules are generally related courses as possible for students posted in the program each quarter. These interested in a curriculum concentration in seminars are free of charge and offer an this area while assisting matriculated opportunity to meet leading local and students to complete their degree programs. nationally recognized EE professionals and The research activities of the EESE Program learn about the latest technical advance- create a number of opportunities for students ments in the high-technology industry. to participate, via M.S. and Ph.D. thesis research or non-thesis student projects, in DEGREE REQUIREMENTS the research of the EESE faculty. Students may become involved in relatively MASTER OF SCIENCE (M.S.) AND fundamental investigations such as PH.D. PROGRAMS semiconductor materials characterization Those students admitted into the Electrical and processing. In all cases, the emphasis is and Computer Engineering Department (ECE) on scientific and engineering investigations prior to July 1, 2003 for a matriculated EE having well-defined goals and real utility in degree should follow the degree requirements an atmosphere resembling that of a working as stated in the OGI catalog effective their research development laboratory. The EESE year of matriculations. Program has close ties to local industry, particularly Intel. The academic program, Independent Study credits may be taken only Eric Thompson, a Ph.D. student, studies the while rigorous, is innovative and individually during a student’s final quarter of graduate electron work function of various photocathode planned to meet each student’s needs. The program for a maximum of 3 credits. Refer to materials. OGI offers numerous ways for limited number of students in residence the 2002/2003 OGI catalog (page 58) for students to pursue M.S. and Ph.D. degrees in assures close attention to each student and additional details. electrical engineering. EESE | ELECTRICAL ENGINEERING PROGRAM IN SEMICONDUCTOR ENGINEERING

CURRICULUM FOCUS AREA EE 554/654 Reliability and Failure of Electronic A possible solution for overcoming this barrier is Devices, Packages, and Assemblies to make devices with nanoscale structures that Students should refer to EESE Program’s EE 555/655 Simulation & Modeling of VLSI Interconnect can take advantage of quantum mechanical effects. 12-month Curriculum Planner to learn what EE 557/657 Technology of Photoresists The objective of this research is to address fundamental problems related to integration of courses may be offered in the 2003-2004 SEMICONDUCTOR MATERIALS AND nanowires and nanotubes for development of academic year. The following are DEVICE CHARACTERIZATION nanoelectronic devices. Freeouf, Hammerstrom, recommended core courses and tracks for EE 511/611 Analytical Scanning Electron Microscopy Rananavare, Solanki the semiconductor focus areas. EE 512/612 Focused Ion Beam Technology EE 513/613 Transmission Electron Microscopy Electronic Materials and Devices SEMICONDUCTOR DEVICES, MATERIALS, EE 514/614 Failure and Reliability in Microelectronics AND PROCESSING EE 545/645 Electronic Materials and An active research program in electronic materials Device Characterization growth and characterization focused on demands of EESE offers a broad spectrum of courses in the ever-shrinking microelectronic devices. The semiconductor synthesis, processing, device MEMS AND SENSORS main materials growth technique investigated is physics and integrated circuits. Courses are EE 548/648 Fundamentals of Sensors and atomic layer deposition, which allows growth of highly conformal thin films, one atomic layer at a designed to prepare the student for growth MEMS Fabrication time. Materials investigated using this approach areas in semiconductor-based technology. EE 550/650 Introduction to Sensor Microfabrication EE 552/652 Micro-electro-mechanical Systems include thin gate dielectrics, including Specific groups of courses are designed to EE 556/656 Semiconductor Sensors nanolaminates and metallic films which include provide a strong, cohesive, and marketable copper seed layers and barrier metals. Another body of knowledge in device processing, The following classes are required for Ph.D. area of research involves electrodeposition of copper films for microelectronic device device physics and design, and integrated students and are electives for M.S. students. interconnect applications. The focus of this circuit design. Students may tailor course However, these are recommended for M.S. investigation is to determine the correlation selections to create unique specializations in students planning to continue with our between the bath chemistry to the physical preparation for careers in this important Ph.D. program. properties of the films and their electromigration lifetimes. Freeouf, Solanki technology field. EE 525/625 Introduction to Electromagnetics for Modern Applications RECOMMENDED CORE CLASSES EE 526/626 Electromagnetics for Modern Applications II Optical Remote Sensing 1. EE 528/628 Introduction to Electronic Materials EE 527/627 Electromagnetics for Modern Applications III 2. EE 547/647 Statistical Process Control and DOE Analytical and experimental studies are exploring EE 531/631 Introduction to Quantum Mechanics for the use of the interaction of electromagnetic 3. Choose one device class from: Electrical and Computer Engineers radiation and turbulence to measure winds and EE 529/629 Fundamentals of Semiconductor EE 532/632 Advanced Quantum Mechanics for turbulence. Recent efforts include analytical, Device Structures Electrical and Computer Engineers numerical and experimental work on a CO2, optical EE 533/633 Advanced MOSFET Analysis I: DC Models heterodyne system for remote measurement of The following course tracks are recom- RESEARCH PROGRAMS atmospheric cross winds and strength of turbulence. Holmes mended for anyone who wishes to specialize in a particular area of microelectronics. Atmospheric Optics The use of laser systems to transmit signals SEMICONDUCTOR DEVICES/CIRCUITS through the atmosphere for purposes of RESEARCH FACILITIES EE 529/629 Fundamentals of Semiconductor communication, radar, recognition, and designation The EESE program has access to a complete Device Structures is severely limited by scattering due to turbulence complement of electronic measuring, recording, EE 530/630 Advanced Semiconductor Device and particulates such as water droplets or dust. Structures and Materials amplifying, signal generating, data processing, and Turbulence, which causes shimmer on a hot day servicing gear with associated power supplies and EE 533/633 Advanced MOSFET Analysis I: DC Models and makes stars seem to twinkle, results in the component stocks. Additional facilities and EE 534/634 Advanced MOSFET Analysis II: random steering, spreading and breaking-up equipment include: Dynamic Models (scintillation) of a laser beam. Particulate EE 535/635 MOSFET Modeling for VLSI Circuit Design scattering that severely attenuates the received COMPUTING RESOURCES EE 561/661 Analog Integrated Circuit Design signal also causes depolarization and multiple path EE 562/662 Digital Integrated Circuit Design effects such as pulse stretching and scrambling of •Windows 2000 computer lab with workstations and server EE 574/674 CMOS Digital VLSI Design I the signal. Experimental studies, in conjunction • Sun Enterprise 3500 departmental computer server EE 575/675 CMOS Digital VLSI Design II with concurrent theoretical work, are contributing • Unix lab with Solaris workstations and X-terminals significantly to fundamental understanding of the •8 Node Beowulf Computer Cluster SEMICONDUCTOR PROCESSING AND MATERIALS effects of atmospheric turbulence on laser beam, EE 514/614 Failure and Reliability in Microelectronics speckle propagation and its application to optical CIRCUIT DESIGN EE 537/637 Thin Film Deposition and Applications remote sensing. Holmes in Semiconductor Fabrication • Computer design lab with eight stations, each consisting EE 540/640 Microelectronic Device Fabrication I Nanoelectronics of a PC workstation an Altera UP1 board, Altera Nios EE 541/641 Microelectronic Device Fabrication II development board, TI DSP development board EE 542/642 Microelectronic Device Fabrication III The current microelectronics revolution has been • VLSI and FPGA circuit design software driven by miniaturization of the sillicon transistor. EE 543/643 Plasma Processing of Semiconductors • Digital television lab This trend is fast approaching fundamental limits EE 553/653 Modern Photolithographic Engineering that will create barriers to further downscaling.

42 ELECTRICAL ENGINEERING PROGRAM IN SEMICONDUCTOR ENGINEERING | EESE

MATERIALS AND ELECTRONIC CHARACTERIZATION • Far-infrared Fourier spectrometer • Parallel field-vibrating sample magnetometer •X-ray diffraction generator and cameras • Facility for electronic transport and luminescence measurements as a function of temperature •Visible, ultraviolet, and infrared gas, solid state and dye lasers • C-V, I-V measurement facilities •Electrical characterization (Hall) • Recombination Lifetime system suitable for bulk and thin film studies •Two spectroscopic ellipsometry systems: 250-750 nm and 140-300 nm •Process and device two-dimensional simulators, three- dimensional simulators, Monte Carlo simulators •Work function and high intensity photo-current stability measurement equipment • Atomic force microscope •Deep-UV spectroscopic ellipsometer

MICROSCOPY •Inverted and upright optical photomicroscopes •Field electron and ion micro–copes • Focused Ion Beam micromachining and microforming capabilities • Analytical scanning electron microscope – Heating, straining specimen stage • Analytical scanning/transmission electron microscopes — Heating specimen stage • High-resolution electron and ion microprobes • Scanning Auger microprobe microscopy • Scanning confocal microscopy •Ion mill, chemical jet-milling, sample preparation facilities, microtome • Complete JCPDF x-ray and electron powder diffraction database •Electron diffraction and image simulation program •Digital video capture for in-situ microscopy experiments

SEMICONDUCTOR AND LCD FABRICATION TECHNOLOGY • Photolithography mask generation and exposure systems • Semiconductor metallization •Sputter etching •Wet etching facilities • Sputter deposition systems • Pulsed UV-laser processing system •Atomic layer epitaxy deposition system •Liquid crystal display lab with pre-tilt, rubbing and single-cell electro-optic characterization facilities •Electrochemical deposition •Process simulators

43 EESE | ELECTRICAL ENGINEERING PROGRAM IN SEMICONDUCTOR ENGINEERING | F ACULTY FACULTY JOINT FACULTY ADJUNCT FACULTY YONGHONG YAN ANTHONY BELL Associate Professor, Consultant Department of Computer Science STEVE BRAINERD & Engineering Ph.D., Computer Science Maxim Integrated Products & Engineering YOUSSEF A. EL-MANSY Oregon Graduate Institute, 1995 Intel Corp. J. FRED HOLMES RAJ SOLANKI REINHART ENGLEMANN Professor Emeritus Professor Consultant Ph.D., Electrical Engineering Ph.D., Physics DAVID EVANS University of Washington, 1968 Colorado State University, 1982 [email protected] [email protected] Sharp Microelectronics Technology Inc. RESEARCH INTERESTS RESEARCH INTERESTS WAYNE K. FORD Speckle propagation through Atomic layer deposition of Intel Corp. turbulence, optical remote nanoscale films, copper electro- JOHN FREEOUF sensing of wind and turbulence, deposition and electropolishing electro-optic systems, instru- for multilevel interconnects, Interface Studies, Inc. mentation signal processing high-k gate dielectrics, polysilicon JODY HOUSE and biomedical optics. thin film transistors (TFTs), iSense Corp. silicon nanowires. REPRESENTATIVE PUBLICATIONS HARISH MUTHALI Holmes, J.F., Jacques, S.L., and REPRESENTATIVE PUBLICATIONS Intel Corp. Hunt, J.M., “Adapting Atmospheric J. Huo, J. McAndrew, and R. Solanki, Lidar Techniques to Imaging “Electropolishing of Copper for SHANKAR RANANAVARE Biological Tissue,” SPIE, Bios 2000 Microelectronics Applications,” Portland State University Conference, San Jose, California, J. Surface Engineering 19, 1 2003. January 22-28, 2000. R. Solanki, J. Huo, J. F. Freeouf, and KARTIK RAOL Becker, M., Holmes, J.F., and B. Miner, “Atomic layer Deposition of Intel Corp. Meekisho, L., “Interdisciplinary ZnSe/CdSe Superlattice Nanowires,” Curriculum Development in Electronics Appl. Phys. Lett., 81, 3864, 2002. EDWARD F. RITZ, JR. Packaging Using Course Segmentation,” J. Huo, R. Solanki, and J. McAndrew, Consultant ASEE 1998 Frontiers in Education “Characteristics of Copper Films Conference, Tempe, Arizona, November Produced via Atomic Layer Deposition,” MILTON SCHOLL 4-7, 1998. J. Mat. Research. 17, 2394 2002. Consultant Homes, J.F., and Rask, B.J., A. Y. Kang, P. M. Lenahan, “Range Resolved, 3-D Optical Remote J. F. Conley, and R. Solanki, “An THOMAS THOMAS Sensing of Atmospheric Winds Electron Spin Resonance Study of Using a CW Lidar,” Advances in Intel Corp. Interface Defects in ALCVD Hafnium Atmospheric Remote Sensing with Oxide on Si,” Appl. Phys. Lett. 81, Lidar, A. Amsmann, R. Neuber, 1128 2002. P. Rairoux, and U. Wandinger, eds., Springer-Verlag, Berlin, 1997. J. F. Conley, Y. Ono, W, Zhuang, D. J. Tweet, S. K. Mohammed, and Holmes, J.F., and Zhou, C., R.Solanki, “Atomic Layer Deposition of “Path Resolved, Optical Remote Hafnium Oxide Using Anhydrous Sensing of the Strength of Turbulence Hafnium Nitrate,” Electrochem. and Using a Pseudo Random Code Solid-State Lett., 5 , C57 2002. Modulated CW Lidar and Coherent Optical Processing,” 9th Conference A.T. Voutsas, H. Kisdarjono, and on Coherent Laser Radar, Linkoping, R.Solanki, “Numerical Simulation of Sweden, June, 1997. Non-Equilibrium, Ultra-Rapid Heating of Si Thin Films by Nanosecond Pulsed Holmes, J.F., and Rask, B.J., Excimer Lasers,” Simulation of “The Effect of Aerosol Speckle Phase Semiconductor Processes and Devices, Decorrelation on the Allowable Signal D. Tsoukalas and C. Tsamis, eds., Averaging Time for Coherent Optical Spinger Wien, New York, 2001. Receivers,” SPIE Annual Meeting, August 1996. H. Zhang and R. Solanki, “Atomic Layer Deposition of High Holmes, J.F., and Rask, B.J., Dielectric Constant Nanolaminates,” “Range Resolved, 3-D, Optical Remote J. Electrochem. Soc., 148, 63 2001. Sensing of Atmospheric Winds Using a CW Lidar,” 18th International Laser (Invited) B. Pathangey and R. Solanki, Radar Conference, Berlin, Germany, “Atomic Layer Deposition for Nanoscale July 1996. Thin Films,” Vacuum Technology and Coatings, 1, 32 2000. Holmes, J.F., and & B.J. Rask, “Optimum, Optical Local Oscillator R. Engelmann, J. Ferguson, and R. Levels for Coherent Detection Using Solanki, “Quantum Well Activated Photodiodes,” Appl. Opt., 34, Phosphors — A New Concept for February 1995. Electroluminescent Displays, Appl. Phys. Lett. 70, 411 1997. 44 The mission of the DEPARTMENT OF M.S. degrees are available in the thesis or non-thesis options. The thesis option Department of ENVIRONMENTAL AND BIOMOLECULAR generally requires up to eight academic SYSTEMS is to study physical, quarters, and the non-thesis option can be Environmental and chemical and biological processes completed in four academic quarters. Biomolecular Systems that occur naturally or result For students entering during the 2004-2005 from the interaction of humans academic year, the department expects to offer the following degrees only: with the environment, www.ebs.ogi.edu Master of Science in Environmental and DEPARTMENT HEAD emphasizing approaches that are Biomolecular Systems possible through novel advances Antónia M. Baptista, Ph.D. Doctor of Philosophy in Environmental and 503 748-1147 in biomolecular, genetic, Biomolecular Systems E-mail: [email protected] computational and information Special tracks in Environmental Science ASSOCIATE DEPARTMENT HEAD FOR EDUCATION sciences and technology. and Engineering, Environmental Information James J. Huntzicker, Ph.D. Technology, Environmental Health Systems, 503 748-1072 Three over-arching goals characterize our and Biochemistry and Molecular Biology E-mail: [email protected] research and education programs: will be available. ACADEMIC ADMINISTRATOR • Fundamental understanding of processes M.S. AND PH.D., ENVIRONMENTAL SCIENCE Therese Young at molecular, cellular and particle levels AND ENGINEERING 503 748-1247 • Integrative, process-based understanding The ESE program balances practical E-mail: [email protected] of ecosystems and other complex applications with fundamental investigations environmental and biological systems EBS GENERAL INQUIRIES of the physical, chemical and biological 503 748-1196 •Effective integration of science in society’s processes underlying environmental E-mail: [email protected] approaches to ecosystem health, human phenomena. The M.S. in Environmental health, and economic development Science and Engineering prepares students Prospective students are asked to carefully for careers in environmental management, examine faculty research interests and practice, or research. The curriculum is departmental research programs to highly interdisciplinary and is built on a solid determine whether their specific professional foundation of fundamental science and goals can be fulfilled at OGI in the engineering. For more information, see Department of Environmental and www.ese.ogi.edu/curriculum.html. Biomolecular Systems. Communication with • Environmental Information Technology Track – individual faculty members is encouraged EIT (M.S. and Ph.D.) before applying or enrolling. The EIT track combines the expertise and course work found in EBS and in the DEGREES OFFERED Department of Computer Science and Engineering (CSE). The goal of the EIT For students entering during the 2003-2004 track is to combine a deep understanding academic year, the department offers the of environmental processes with mastery following degrees: of sensing, modeling and information Master of Science in Environmental Science technology. Requirements for the EIT and Engineering track are the same as for the M.S. thesis Doctor of Philosophy in Environmental and non-thesis options described above, Science and Engineering except that students in the EIT track complete approximately 20 percent of Master of Science in Biochemistry and their course work in the CSE department. Molecular Biology The EIT curriculum includes fundamental Doctor of Philosophy in Biochemistry and courses, science courses, technology Molecular Biology courses, electives and capstone Special tracks in Environmental Information integrative courses. For more information Technology and Environmental Health on the EIT track and its curriculum, see Systems are available in the Environmental http://www.ese.ogi.edu/eit/. Science & Engineering degree programs. Coastal research in EBS department. EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS

• Environmental Health Systems Track – EHS APPLICATION DEADLINES DEGREE REQUIREMENTS (M.S. only) Applications for fall quarter received ENVIRONMENTAL SCIENCE AND ENGINEERING The EHS track focuses on how environ- by March 1 receive priority review for mental factors combine with genetics to Students may pursue the Ph.D. program admission and financial support. M.S. affect the well-being of humans, other or M.S. program (non-thesis or thesis applications are accepted year-round, species and ecosystems, as well as the options) in ESE, EIT or EHS. EIT and and applicants are encouraged to methods used to manage environmental EHS are educational tracks within the complete the application process by health in its broadest sense — with equal ESE program. Students who complete the July 31 for fall quarter admission. emphasis on human and ecological risk EIT or EHS tracks receive their degree in Ph.D. applications for admission in assessments, recognizing the complex Environmental Science and Engineering. quarters other than fall are considered interdependencies. The EHS track will on the basis of available space and M.S. IN ENVIRONMENTAL SCIENCE prepare students to take on leadership, financial assistance. AND ENGINEERING management and research roles in M.S. NON-THESIS OPTION the broad domain of environmental health systems. CREDITS FROM OTHER Students pursuing the M.S. non-thesis OHSU DEPARTMENTS option must complete at least 45 credit M.S. AND PH.D., BIOCHEMISTRY AND hours. These credits include the distribution MOLECULAR BIOLOGY Up to eight credits from courses taken requirements as outlined below and in other OHSU departments may be The BMB program offers students additional courses selected with the approval applied to an EBS program. The student’s immediate participation in research upon of the SPC. Up to eight credit hours may be program committee (SPC) must first entering. This early exposure to research granted for approved participation in non- approve the appropriateness of credits allows each student to become familiar with thesis research or approved work as an from other OHSU departments. the variety of activities represented in the intern with a local company or government department and aids the student in thesis agency. Comprehensive examinations are research selection. DEPOSIT not required.

Upon acceptance, applicants to the M.S. M.S. THESIS OPTION ADMISSION REQUIREMENTS program are reequired to pay a non- Students pursuing the M.S. thesis option refundable deposit of $100 to guarantee In addition to the general OGI admissions must complete at least 45 credits. These their places in the program. For those requirements, the EBS Department requires credits include the distribution requirements students who receive less than a full the following: outlined below, additional courses selected tuition scholarship, this fee will be with the approval of the SPC, and research M.S. AND PH.D. IN ENVIRONMENTAL SCIENCE applied to the tuition payment for the credits. M.S. thesis research (EBS 503) is AND ENGINEERING first quarter of residence. usually no more than nine credits. A written GRE general scores are required. GRE M.S. dissertation with an oral defense is subject scores are not required. TOEFL TUITION required. Comprehensive examinations are minimum score is 600 for the paper-based not required. Tuition for full-time students in the test or 250 for the computer-based test. Department of Environmental and PH.D. IN ENVIRONMENTAL SCIENCE M.S. IN BIOCHEMISTRY Biomolecular Systems department is AND ENGINEERING AND MOLECULAR BIOLOGY charged on an annual (four-quarter) basis Ph.D. students must complete at least 52 for the first academic year and quarterly GRE scores are not required. TOEFL credit hours of coursework. These credits thereafter. Completing the program in minimum score is 550 for the paper-based include the distribution requirements less than four quarters still incurs the test or 213 for the computer-based test. outlined below and additional courses annual tuition charge ($21,420 for 2003- selected with the approval of the SPC. PH.D. IN BIOCHEMISTRY 2004, exclusive of any scholarship Ph.D. candidates must pass a two-part AND MOLECULAR BIOLOGY award). Transferring credits from another comprehensive examination. The first part is institution can reduce the time to GRE general scores and GRE subject a written examination covering four subject complete a degree but does not reduce scores for one of the following tests: (a) areas selected by the department. The the annual first year tuition charged. biology, (b) chemistry or (c) biochemistry, second part is the preparation and oral The first year tuition can be paid in cell and molecular biology are required. defense of a proposal that defines the quarterly installments corresponding to TOEFL minimum score is 550 for the student’s Ph.D. dissertation research. the academic quarters. paper-based test or 213 for the computer- A written Ph.D. dissertation with an oral based test. defense is required.

46 ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | EBS

M.S. AND PH.D. IN ENVIRONMENTAL SCIENCE contribution to a larger project, providing Columbia River and its near-shore plume are AND ENGINEERING DISTRIBUTION REQUIREMENTS the student with extensive hands-on a dominant oceanographic feature of the experience in biochemical and molecular northeastern Pacific Ocean and the focus of To achieve the necessary breadth in training, controversial ecosystem management issues. M.S. and Ph.D. students take courses that biological techniques. CORIE represents a novel, promising and cover a range of scientific disciplines and M.S. THESIS OPTION much-needed infrastructure for physical and ecological research in this system. Second, we environ-mental media. Five courses must be The M.S. thesis option is a research degree envision that multipurpose observation and taken that satisfy the following distribution that requires satisfactory completion of 44 forecasting systems will become central to the requirements. No course can satisfy more management of coasts and estuaries worldwide. credits, 20 of which are in graded courses than one requirement. The Columbia River estuary is a challenging (12 credits in EBS 512, 513 and 514, plus natural laboratory to test concepts and tools, and At least one course must be taken from three eight or more credits in advanced courses), CORIE is a pilot system developed to anchor our of the following four discipline groups: and a written thesis based on independent environmental information technology and our research (EBS 503). coastal observation and prediction research. 1. Applied Mathematics - EBS 545/645; EBS Baptista, Chawla, Zhang, Zulauf 547/547; EBS 550/650; EBS 555/655 M.S. students in the BMB program are 2. Chemistry - EBS 510/610; EBS 535/635; encouraged to take the EBS Department Quality-Scalable Information Flow Systems for EBS 537/637 Seminar (EBS 507A). This course does not Environmental Observation and Forecasting 3. Fluid Dynamics - EBS 560/660; EBS count toward degree credit requirements. Recent advances in computer power and connectivity have fueled the development of real- 575/675; EBS 578/678 PH.D. IN BIOCHEMISTRY time Environmental Observation and Forecasting 4. Biology - EBS 590/690; EBS 593/693 AND MOLECULAR BIOLOGY Systems (EOFS). These systems will revolutionize the way scientists share information about the At least one course must be taken from each Ph.D. students are required to take the EBS environment and represent an unprecedented of the following environmental media groups: 612, 613, 614 biochemistry sequence and opportunity to break traditional information 1. Surface Waters - EBS 560/660; EBS three of the following core courses: barriers separating scientists from society at large. 575/675; EBS 578/678 EBS 625 Bioenergetics and ...... 4 credits Incipient forms of EOFS are already in use in areas Membrane Transport of strong social relevance, but they tend to be 2. Groundwater - EBS 570/670; EBS EBS 628 Enzyme Structure, Function small-scale, application- and domain specific, 571/671; EBS 572/672; EBS 573/673 and Mechanisms ...... 4 credits stand-alone systems. There is a need to evolve EBS 640 Instrumental Methods toward multipurpose, shared systems designed to Students in the EIT and EHS tracks have in Biophysics ...... I-4 credits adapt flexibly to evolving needs of information customized requirements defined by the SPC. EBS 685 Advanced Molecular Biology . . . . 4 credits consumers. To meet this need, we have assembled EBS 687 Molecular Cell Biology ...... 4 credits an interdisciplinary team, including computer M.S. and Ph.D. students in the ESE program Courses in other departments and schools within OHSU science and environmental science researchers are required to take the EBS Department may be substituted for the core course requirements with and a heterogeneous base of pilot users. Our goals Seminar (EBS 507A/607A) each academic permission of the SPC. The SPC may also advise additional include (a) developing missing integration concepts and technologies for EOFS, (b) closing the loop quarter, except summer. This course does not courses based upon the particular research interests and needs of the student. between environmental models and sensors, (c) count toward degree credit requirements. using, evaluating and refining the CORIE coastal Ph.D. Students must register for 12 credits observatory (www.ccalmr.ogi.edu /CORIE) as a BIOCHEMISTRY AND MOLECULAR BIOLOGY per quarter. These credits typically include pilot EOFS and (d) developing pilot multilevel Students may pursue the Ph.D. program or Student Seminars (EBS 607B or 607C), educational programs (http://www.ese.ogi.edu/eit/). Baptista, Walpole, Maier, Leen, Feng and Feng M.S. program (non-thesis or thesis options) Department Seminar (EBS 607A; required in BMB. each quarter, except summer), and Research (EBS 601 or 603). The qualifying Ocean Survival of Salmonids Relative to Migrational M.S. IN BIOCHEMISTRY AND MOLECULAR BIOLOGY examination for the Ph.D. is a Timing, Fish Health and Oceanographic Conditions. M.S. NON-THESIS OPTION comprehensive examination in biochemistry. Interannual variation in ocean recruitment of It must be completed within two years of salmon is high and thought to be associated with Students pursuing the M.S. non-thesis variation in nearshore ocean conditions. The option must satisfactorily complete a entering the school. An oral defense of the nearshore ocean environment, particularly that minimum of 44 credits, 28 in graded Ph.D. dissertation is required. associated with the Columbia River plume, is a courses and 16 derived from an critical habitat to outmigrating juvenile salmon. Several investigators have suggested that survival experimental research project (EBS 501), RESEARCH PROGRAMS during the first year of ocean life is a key to as well as a written report on the research. (alphabetically by faculty name) establishing year-class strength. In the case of Graded courses include 12 credits in EBS salmonids originating in the Columbia River Basin, 512, 513, 514, and 16 or more credits in CORIE: A Multipurpose Coastal Observatory survival success hinges on the complex interaction advanced courses (EBS 525 - 598), Student Operating since 1996, CORIE is a multipurpose of smolt quality and the abiotic and biotic ocean conditions at the time of entry and during their Seminars (EBS 507B or 507C), and Special coastal observatory for the Columbia River first year of ocean existence. This research Topics (EBS 506). Research for the M.S. (http://www.ccalmr.ogi.edu/ CORIE). The motivation of this research program is twofold. First, the hypothesizes that variation in the physical and non-thesis option is typically a specific biological conditions of the nearshore environment,

47 EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS

particularly that associated with the Columbia molecular mechanism of oxygen binding and 300 years, raising concerns about the protection River plume, affects overall survival of Columbia utilization by these oxidase and oxygenase of coastal communities in Oregon, Washington, River stocks. Further, the research hypothesizes enzymes. In our laboratory we overexpress wild- California and British Columbia. The coastal impact that primary factors driving the variation in the type and mutant proteins in mammalian cell of potential CSZ tsunamis is being investigated nearshore environment include (a) food availability culture using large-scale hollow fiber bioreactors, through numerical modeling. The need to use and habits, (b) time of entry, smolt quality and purified them to homogeneity and study them using geological evidence on paleotsunamis as the sole, growth and bioenergetic status at the time of entry a variety of physical and kinetic methods which loose reference for model validation makes this an and during the first growing season in the ocean include high pressure liquid chromatography unusually interesting and challenging problem. The and (c) predation (a companion study on predation (HPLC), mass spectrometry (MS), electron Oregon Department of Geology and Mineral on juvenile salmon is ongoing). This project, will paramagnetic resonance (EPR), Fourier transform- Industry (DOGAMI) has incorporated our joint characterize, over a 10-year period, the physical infrared (FT-IR) and X-ray absorption spectroscopy research results into the development of tsunami and biological features of the nearshore ocean (XAS). The XAS technique is performed at the inundation maps for the Oregon coast. environment with real-time and modeling Stanford Synchrotron Radiation Laboratory Chawla, Baptista, external collaborators projections of the Columbia River plume as it http://www-ssrl.slac.stanford.edu/, which is a interacts with the coastal circulation regime, and national user facility. Funded by grant R01 will relate these features, both spatially and NS27583 (Chemistry and Spectroscopy of Collaborative Research: Productivity, Biogeochemical temporally, to variation in salmon health, condition Copper Monooxygenases) from the National Transformations and Cross-Margin Transport in an and survival. Baptista, Jay, and multi-institutional Institutes of Neurological Disorders and Stroke Eastern Boundary Buoyant Plume Region (A.K.A. RISE- collaborators (PI: E. Casillas, NOAA Fisheries) http://crisp.cit.nih.gov/ Blackburn River Influences on Shelf Ecosystems) River plumes significantly alter nutrient supply, plankton growth rates and standing stocks as well Estuarine Habitat and Juvenile Salmon — Cellular Transport and Regulation of Metal Ions as enhance material export from productive Current and Historic Linkages in the Lower Metal ions such as iron and copper play an coastal areas across the continental margin. Columbia River and Estuary essential role in many cellular processes including Because the typical (upwelling-favorable) wind Estuaries are considered important to rearing of energy production, biosynthesis and antioxidation. stress and ambient currents act to move plumes juvenile salmon and represent an integral The key to their usefulness as enzyme cofactors away from the coast during high production component of the continuum of habitats that lies in their ability to catalyze redox reactions, but periods, cross margin export is extremely effective salmon occupy for significant periods of time. this very chemistry introduces the need to tightly on eastern boundaries. In this proposal we focus There is, however, a general lack of science-based regulate the speciation, concentration and on a highly productive Eastern Boundary river information concerning attributes of these tidal transport of cellular metal ions, since the free ions plume, the Columbia — a plume sufficiently large freshwater and oligohaline transition zones needed are themselves cytotoxic. Our lab is involved in to be of regional importance, yet small enough to to support juvenile salmon, particularly in the deducing the molecular mechanism of metal ion allow determination of dominant processes Columbia River estuary. Further, recent evidence transport. Copper enters the cell through the affecting river plumes, and to facilitate rate supports the concern that flow in the Columbia transporter CTR1 and is then partitioned between a comparisons with regions outside the plume. River significantly affects the availability of number of small molecule metallochaperone Available data suggest that the Columbia affects estuarine habitats, that flow is much reduced molecules (CCS, COX17, SCO1, HAH1) which regional productivity from phytoplankton up the compared to historic levels, and that seasonal flow selectively metallate target copper enzymes (e.g., food chain to juvenile fish (e.g., salmon). Prior patterns are much different now than a century SOD1, cytochrome c oxidase), or P-type ATPases measurements provide a framework for a new ago. The long history of wetland loss in the (MNK, WND) which provide further transport collaborative study that uses the Columbia to Columbia River estuary coupled with change in machinery for metallation of secreted proteins. examine plume effects on a productive eastern flow patterns suggests that restoration of the Through application of advanced spectroscopic margin. This study will integrate results from a habitats may benefit recovery of depressed salmon techniques such as X-ray absorption and mass nearby wind-driven CoOP study as well as salmon- stocks. The need to develop effective restoration spectrometry we are studying the mode of copper related regional studies to provide definitive new strategies led us to propose empirically identifying binding and transport within a number of these information on alteration of rates of the benefit of these habitats to juvenile salmon by chaperone-target systems. Part of this research biogeochemical processes by the unique evaluating habitat-salmon linkages in the lower involves developing semisynthetic methods for stratification, turbidity, mixing environment and Columbia River and estuary. We are conducting a incorporation of Se as selenocysteine into the nutrients of a river plume. Because the Columbia monitoring approach to identify associations metallochaperones which will provide us with a River provides no significant terrigenous nitrate to between salmon and habitat in the lower Columbia unique probe of metal coordination via Se- and the plume in the growing season, our study allows River and estuary. Baptista, Jay, and multi- Cu-K absorption edge spectroscopy. These studies plume-endemic processes to be isolated and hence institutional collaborators (PI: D. Bottom, NOAA will lead to a better understanding of the molecular process results can be directly applied to other Fisheries) mechanisms of metal-ion homeostasis and will aid plumes. Results can also be contrasted with in combating diseases (Menkes, Wilson, ALS) contrasted with more eutrophic, buoyancy believed to be associated with aberrant metal influenced coasts. Chemistry of Copper-Containing Enzymes ion regulation. Funded by a Program Project Our study is designed to address the following Increasing numbers of important enzymes are grant from the National Institute of General three hypotheses: known to contain copper at their active sites. Of Medical Studies (Mechanisms of Metal Ion particular interest are enzymes involved in Regulation in Human Cells), P01GM067166% • During upwelling the growth rate of neurotransmitter biosynthesis and metabolism www.crisp.cit.nih.gov/) Blackburn phytoplankton within the plume exceeds that in (including important neuroactive amines such as nearby areas outside the plume being fueled by nor-adrenaline and amphetamine); enzymes the same upwelling macronutrients. protecting against oxidative cellular damage Cascadia Subduction Zone Tsunamis • The plume enhances cross-margin transport of caused by reactive oxygen metabolites; and Large tsunamis are believed to be locally plankton and nutrients. enzymes catalyzing the biosynthesis of generated in the Cascadia Subduction Zone (CSZ) • Plume-specific nutrients (iron and silicate) alter neuropeptide hormones. A major goal is to every 200 to 600 years, based on geological and enhance productivity on nearby shelves. understand the catalytic role of copper and the records. The last large tsunami dates back about Jay, Baptista, and multi-institutional collaborators (PI: B. Hickey, University of Washington)

48 ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | EBS

Remediation of Explosives in Groundwater Using conducted to determine diffusion rates of a variety active sites. Our laboratory has a sensitive, state- Passive In Situ Permeable Reactive Barriers of organic compounds in porous media and the of-the-art Raman instrument: a fast spectrograph kinetics of adsorption and desorption for a variety with a liquid N -cooled CCD detector. We also use Groundwater contamination associated with the 2 use of explosives (e.g., TNT) is widespread at many of soil types and a range of water contents. a combined FT-IR/FT-Raman instrument for protein Department of Defense sites. Research in our Johnson and model compound studies. Our research focuses laboratories has shown that explosives can be on heme (iron porphyrin), nonheme-iron and copper enzymes and the roles of their metal ions rapidly destroyed in situ using zero-valent iron Multiphase Monitoring of Gasoline Movement (ZVI). When ZVI is placed in the subsurface as part in enzymatic catalysis. Of particular interest is the Using a Very Large Physical Model (OGI/LEAP) biochemistry of O . Metalloproteins are involved in of a permeable reactive barrier, it can prevent the 2 Leaks from underground storage tanks (UST) O binding (e.g., hemoglobin or hemocyanin) and migration of explosives in groundwater for decades 2 represent a major ongoing source of groundwater in oxidative chemistry whereby O is reduced in a manner that is completely passive. 2 contamination. The rapid detection of leaks is, Johnson and Tratnyek and substrates are oxygenated or oxidized. The therefore, a major goal of UST legislation. The investigation of trapped reaction intermediates OGI/LEAP facility is used to study the movement of and model compounds helps us to unravel these Simulation of Subsurface Processes Using Very gasoline components in the vapor, aqueous and complex processes and to define reaction Large Scale Experimental Aquifers pure-product phases. This work will help establish mechanisms. The availability of site-directed Many important chemical, physical and biological which of a variety of leak-detection technologies is mutants permits the alterations in structures and processes are difficult to study in the laboratory best suited to detect leaks under a range of reactivities to be studied. Loehr because of problems of scaling. Many of these environmental conditions. Johnson processes are also difficult to characterize in the Heme Oxygenase field, because of the complex and uncontrolled Statistical Pattern Recognition in Environmental nature of environmental systems. For these Heme oxygenase is a fascinating system that uses Observation and Forecasting Systems the O -binding affinity of its heme substrate in the reasons, OGI has established the Large 2 Environmental observation and forecasting systems Experimental Aquifer Program (OGI/LEAP). At cellular degradation of heme to open-chain (EOFS) are emerging new technologies with present, the facility consists of five large aquifers biliverdin. These studies are carried out with Paul unparalleled potential to impact sustainable used to examine the movements of organic solvents R. Ortiz de Montellano’s group at U.C. San development. EOFS are expected to foster and and petroleum compounds in the unsaturated and Francisco. The resting heme-heme oxygenase support new paradigms for generation, transfer saturated porous media. Future LEAP aquifers will enzyme substrate complex is much like myoglobin: and social application of knowledge in domains that examine inorganic geochemistry and the The heme is linked to the enzyme by an range from the global earth to its regional and interactions between chemical, biological and ironhistidine bond and the iron exists mainly in a local subsystems. At the core of EOFS is the timely physical processes in contaminated aquifers. six-coordinate, high-spin state with an additional and customized acquisition, generation, processing Johnson and other faculty water ligand. The Fe-NHis bond was identified from and delivery of reliable, relevant information to its resonance Raman vibration at 216 cm-1 in the many and very diverse audiences. Multiple Fe(II)-heme complex. The absence of this Gas-Phase Transport in Unsaturated Porous Media challenges need to be met to implement this fingerprint frequency in the H25A mutant clearly Gas-phase transport is important in controlling concept. A critical challenge is the development of identified His25 as the axial ligand. Remarkably, many subsurface processes, including respiration, automated procedures to verify the quality of the when imidazole was added to the inactive H25A pesticide behavior and contaminant volatilization huge amounts of observational and simulation data preparation, activity was fully restored. Our and movement. Laboratory experiments have been that are generated by EOFS both in real time and current efforts, in collaboration with Angela Wilks conducted to determine diffusion rates of a variety off-line. Processing based strategies for quality at University of Maryland, examine the structure of organic compounds in porous media and the control of scientific data, while effective for and activity of several bacterial heme oxygenases. kinetics of adsorption and desorption for a variety moderate-sized archival data, are too labor- Loehr and Moënne-Loccoz of soil types and a range of water contents. intensive to map well into EOFS-scale data sets. Johnson Strategies based on pattern recognition and machine learning hold significant promise as an Oxygen Activation by Iron Proteins alternative or complement. Under the proposed Several diiron enzymes react with molecular Watershed Hydrology and Transport Modeling project, we are developing approaches based on oxygen to form powerful oxidizing agents important Water and chemical movement through watersheds statistical pattern recognition and signal in biology. Examples include (i) ribonucleotide has an important impact on surface- and ground- processing, on-line adaptive systems, data mining reductase protein R2, which oxidizes tyrosine 122 water quality. The processes that control that and advanced search to address critical quality to its catalytically important neutral radical form; movement are, in turn, impacted by a range of land control issues including: 1) Detecting sensor (ii) methane monooxygenase, whose hydroxylase use and water use issues. These complex systems corruption in non-stationary, spatial-temporal component oxidizes hydrocarbons to alcohols; (iii) are frequently difficult to model because of their systems, 2) Estimating true signals from corrupted plant desaturases, which oxidize fatty acids to large scales and the level of detailed understanding sensor data, and 3) Detecting and characterizing olefins, e.g., stearoyl to oleoyl; and (iv) ferroxidase 2+ 3+ necessary to represent the important processes. regimes where model anomalies are likely. These reactions, in which Fe is oxidized to Fe . A We have developed new mathematical tools for quality control techniques will be developed and common feature of these enzymes appears to be addressing these problems and providing near- exercised on CORIE, a pilot coastal observatory for the formation of an initial peroxo intermediate the Columbia River estuary and adjacent coastal upon exposure of the reduced enzyme to O . In the real-time modeling of flow and transport in 2 waters (www.ccalmr.ogi.edu/CORIE/). respiratory protein, hemerythrin, O binding is watersheds. Johnson 2 Leen and Baptista accomplished by reduction to peroxide, and this reaction is readily reversible. However, in Gas-Phase Transport in Unsaturated Porous Media ribonucleotide reductase, peroxide is similarly Vibrational Spectroscopy of Metalloprotein Active Sites Gas-phase transport is important in controlling formed but decomposes irreversibly to a ferryl many subsurface processes, including respiration, We are interested in the structural and functional intermediate that is capable of carrying out pesticide behavior and contaminant volatilization properties of metal ions in enzymes and proteins, oxidative chemistry. This dichotomy of behavior is and movement. Laboratory experiments have been and we use electronic, vibrational (especially rR) reminiscent of the respiratory vs. peroxidase and EPR spectroscopy to characterize metal-ion

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functions of different heme-containing proteins. the protein has similarity to hemoglobin and the MTBE infiltration to the groundwater, laboratory We are interested in determining common C-terminus is homologous to reductase with a studies of MTBE biodegradation, and field studies principles that influence the pathways of oxygen flavin-binding domain. Recent studies showed that of several contaminated sites for MTBE and its utilization. This problem is being approached by flavohemoglobin is involved in detoxification of possible breakdown products. For more informa- structural elucidation of the iron sites in the nitric oxide. B. subtilis hmp was identified among tion on this work, see www.cgr.ese.ogi.edu/mtbe/. proteins themselves and in model complexes, genes, expression of which is induced by oxygen Pankow, Tratnyek, Johnson as well as by studying mechanisms of their limitation. The anaerobic induction of hmp reactions with oxygen-containing substrates. requires the ResD-ResE signal transduction pairs Loehr and Moënne-Loccoz and nitrite. The expression is also induced by Mechanisms of Mammalian Chemical Communication exogenous nitric oxide through ResDE-dependent and Vomeronasal Olfaction and -independent mechanisms. The detailed Chemical communication plays a significant role in Anaerobiosis of Bacillus subtilis regulatory mechanism of ç expression and its life strategies for many mammals. Our research A gram-positive soil bacterium, B. subtilis, is functional role in anaerobiosis are under focuses on chemical identification of pheromones highly amenable to genetic analysis and has been investigation. Nakano functioning during reproductive events in the Asian used as a model system to study fundamental elephant, Elephas maximus. A female-to-male microbiological research. In addition, B. subtilis is preovulatory urinary sex pheromone, (Z)-7- medically and industrially important since it Distribution of Organic Compounds Between the dodecen-1-yl acetate, has been identified and produces a variety of antibiotics and extracellular Gas and Urban Aerosol Particulate Phases demonstrated to be robust in its synthetic form. enzymes. Although the organism has been widely The behavior of organic compounds in the This compound is also bioactive in many used, it has been mistakenly referred to as a strict atmosphere depends in large part on the extent Lepidoptera, making it a good example of aerobe until recently. Our studies, together with to which they partition from the gas phase to convergent evolution of structure and function. others, have shown that B. subtilis is able to grow aerosol particulate matter. Processes that are Biochemical studies have established the presence under anaerobic conditions by utilizing nitrate or affected by this partitioning process include of the pheromone in the serum, and future studies nitrite as an alternative electron acceptor. In the precipitation scavenging of gases and particles will investigate its biosynthetic pathways. absence of terminal electron acceptors, it as well as dry deposition of gases and particles. Considerable progress has been made on undergoes fermentative growth. Our research aims Fundamental gas/solid sorption theory is being establishing the proteins functioning as pheromone include elucidation of the regulatory mechanisms used to investigate important aspects of transporters prior to signal transduction in the through which the cells adapt to oxygen limitation. atmosphericgas/particle partitioning. The study neuroreceptive cells of the vomeronasal organ. Molecular genetic and biochemical approaches are involves the investigation of basic partitioning Radiolabeled analogs, competition experiments and applied. Nakano behavior of a wide range of representative molecular biological studies have established atmospheric compounds (including alkanes and unusual roles for elephant albumin and olfactory polycyclic aromatic hydrocarbons) on a variety of binding protein. A second pheromonal system is ResD-ResE Two-Component Signal Transduction System representative model particulate substrates, actively being investigated. The facial temporal Bacteria often encounter sudden environmental including elemental carbon, organic carbon, silica gland, breath and urine exude unusual chemical changes. Cells cope with such changes by an and clay. Pankow compounds during musth in Asian male elephants. elaborate network of adaptive responses. The two- These signals have a role in mate choice by female component signal transduction system senses and elephants, spatial distribution by male elephants then processes information derived from Thermodynamics of Inorganic Solid Solutions and other reactions by conspecifics. Utilizing environmental changes so that the cell can choose The manner in which inorganic solid solutions several state-of-the-art gas chromatographic/mass the appropriate adaptive response. This simple behave is one of the last major research frontiers spectrometric techniques, we are identifying signal transduction system is widespread in in ambient temperature aqueous geochemistry. specific compounds that have a chemical bacteria and also found in plants and lower Coprecipitation of metal ions is well known in communication function, i.e., elicit behavioral eukaryotes. ResE is a histidine kinase and ResD is nature, e.g., Sr2+ can form a solid solution in responses, and correlating the release of such

a response regulator of this large protein family. calcium carbonate (CaCO3[s]). Unfortunately, little compounds with serum androgen levels. We have shown that ResD and ResE are is known about the thermodynamics of such solid L. Rasmussen indispensable for anaerobic respiration in B. solutions. That is, little is known about how the subtilis. A specific signal derived by oxygen activity coefficients of metal ions vary as a function limitation is recognized by the N-terminal input of composition in solid solutions of various types. Global Distributions and Mass Balances of domain of the ResE kinase leading to The values of the activity coefficients are of Halocarbons, Nitrous Oxide and Other Trace Gases

autophosphorylation of a conserved histidine interest because they control the extent to which Gases such as CCl3F (F-11), CCl2F2 (F-12) CHClF2

residue in the C-terminal transmitter domain. This the constituents in the solid solutions will be (F-22), CF4 (F-14), C2Cl3F3 (F-113), CH3CCl3, CH3Cl

phosphoryl group is then transferred to aspartate soluble in water, e.g., the extent to which a toxic and N2O are being added to the atmosphere by in the conserved N-terminal domain of ResD, metal ion like Cd2+ that is present in calcium various industrial processes and the public’s use altering the activity of its C-terminal domain as a carbonate will be soluble in water. In this work, of high-technology products. Such chlorine- transcriptional activator. The ResD-ResE signal activity coefficient values for a variety of containing compounds are believed to threaten transduction system is activated by oxygen environmentally important divalent metal ions are the Earth’s natural ozone layer high in the limitation or by addition of nitric oxide generators. being sought as a function of composition in atmosphere (stratosphere). This research will The objectives of our studies are to determine how calcium carbonate. Pankow systematically obtain a long-time series of ResE senses oxygen limitation or nitric oxide and concentration measurements by a flask sampling how anaerobically induced genes are activated system. The results are then interpreted with by ResD. Nakano Fate and Effects of Fuel Oxygenates global mass balance models and sophisticated The recent realization that oxygenated fuel statistical techniques to quantify the sources and additives such as MTBE are becoming widely lifetimes of these gases in the environment. Such Flavohemoglobin (Hmp) distributed groundwater contaminants has created data are now obtained from sites all over the world Flavohemoglobin is a ubiquitous protein present in a sudden and pressing demand for data on the extending from the Arctic Circle to the South Pole. organisms ranging from Escherichia coli to processes that control their environmental fate. R. Rasmussen Saccharomyces cerevisiae. The N-terminal part of Ongoing work in this area includes modeling of

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Studies of Past Atmospheres on the CO, O3, and OH cycles and its role in the Translational Control in Fungal Amino Acid Biosynthesis future of the environment. R. Rasmussen Atmospheric gases such as N2O, CO2, CO, CH3Cl, A greater understanding of many human health carbonyl sulfide (OCS) and CH4 are primarily issues relies on increased knowledge of how cells produced by natural processes, but over the past Development of Experimental Methods for Trace express genetic information. Gene expression can century human activities have been adding growing Gas Measurements be controlled by regulating the synthesis and amounts to their natural abundance. This process stability of functional RNA and protein. The goal of At present, some 50 atmospheric gases can be can upset the cycles of these gases and lead to our research is to obtain a greater understanding measured at the Trace Gas Laboratory. Still, new possibly adverse environmental effects such as the of how these mechanisms work using the methods are needed to improve the accuracy and warming of the Earth’s surface (N O, CO , CH ). Neurospora crassa arg-2 and Saccharomyces 2 2 4 precision of measurements and to satisfy the When both natural and anthropogenic processes cerevisiae CPA1 genes as models. These stringent demands of ultra-clean background air contribute to the current atmospheric abundance homologous genes encode the first enzyme in sampling. New methods are also being developed of a trace gas, it is of interest to determine the arginine biosynthesis and they are negatively for automated real-time analysis of many trace amount which existed before human activities had regulated at both transcriptional and translational gases. Research programs include development of any effect. Perhaps the only realistic method to levels in response to the availability of arginine. An gas chromatographic and mass spectrometric determine the composition of the ancient evolutionarily conserved upstream open reading methods for the analysis of trace gases. At present, atmosphere is to analyze the air in bubbles buried frame (uORF) present in the 5’ leader regions of GC/MS systems in the laboratory are being used to deep in polar ice. The depth of the ice indicates the these transcripts is responsible for translational routinely measure C -C nonmethane hydrocarbons age of the air in the bubbles. By going far enough 2 12 control. Synthesis of the uORF-encoded peptide at tens of parts-per-trillion levels. Techniques for back in time, the relationship between past causes ribosomes to stall when the level of collecting and storing air and water samples also atmospheric composition and climate might be arginine is high, blocking access of ribosomes to are being developed. R. Rasmussen found. The novel and simple method of studying the the translation initiation site for the polypeptide old atmosphere of the earth is beset by many encoding the arginine biosynthetic enzyme. Our problems that complicate the relationship between Biogenic Sources of Atmospheric Gases current work is focused on developing a molecular the gases in the bubbles and the composition of the understanding of how synthesis of this uORF- Living organisms produce and consume a variety of old atmosphere. Theoretical and experimental encoded peptide causes ribosomes to stall, since gases and may therefore form an integral part of research for resolving these problems as well as this will provide important insights into the the global cycle of a trace gas. Selected plants and the measurement of trace gases are the major fundamental cellular process of protein synthesis. animals, living in the sea or on land, are being goals of this project. R. Rasmussen Sachs studied to determine their role in the cycles of CH4,

N2O, CH3CI, CH3I, isoprene and other hydrocarbons. Ocean-Air Exchange of Gases R. Rasmussen Genome Organization in Fungi Some atmospheric gases are greatly influenced by The N. crassa genome and the genomes of other the Earth’s oceans. For instance, a large amount of The Global Cycle of Carbon Monoxide (CO) filamentous fungi are being sequenced, enabling the atmospheric methyl chloride (CH Cl) and comparisons of how these fungi differ from each 3 Based on 15 years of global sampling and the methyl iodide (CH I) are produced in the oceans, other and from the yeasts. We are focusing on the 3 application of modern trend analysis techniques, possibly by biogenic processes. It has also been characterization of the sub-telomeric regions of N. our data have shown that CO increased in the shown recently that carbonyl sulfide (OCS) is crassa, since genes in sub-telomeric regions are atmosphere until around 1987 and has since produced in the oceans and subsequently emitted implicated in environmental sensing and in declined. These changes in CO have major to the atmosphere. On the other hand, manmade interactions with host species. Sachs implications for atmospheric chemistry and the gases such as CCl F (F-11) can dissolve in the 3 role of biomass burning in causing global increases oceans and thus be removed from the atmosphere. of trace gases. Present research includes modeling This research project is devoted to determining the Human-Health Assessment of Water Quality of the global budgets, seasonal cycles and potential solubility of such gases in water and to modeling Since 1991, U.S. Geological Survey (USGS) environmental effects. R. Rasmussen the flux of gases into or out of the oceans. The scientists with the National Water-Quality results obtained are essential ingredients in Assessment (NAWQA) program have been determining the sources and fates of atmospheric Methane Emissions from Rice Fields collecting and analyzing data and information in trace gases and in estimating the effects of human more than 50 major river basins and aquifers Methane concentrations have nearly tripled activities on the future warming of the Earth or across the nation. Their goal is to develop long- compared to the natural atmosphere of 300 years depletion of the ozone layer. R. Rasmussen term consistent and comparable information on ago (based on ice core analyses). The increase of streams, groundwater, and aquatic ecosystems to rice agriculture to sustain an increasing support sound management and policy decisions. population may be a major contributor to the Studies of Atmospheric Methane State and national pilot efforts are underway with increase of methane during the last century. This Considerable evidence has been accumulated the USGS, in collaboration with the U.S. research program is designed to determine the showing that methane (CH ) is increasing in the Environmental Protection Agency (USEPA) and 4 role of rice agriculture in the global methane atmosphere, most likely as an indirect result of state agencies to develop, test and refine concepts cycle. Field experiments are being conducted in growing human population. In the future, such an to more effectively communicate water-quality China, Indonesia and the United States. increase of CH can lead to a global warming by information in a human-health context. Toccalino 4 Laboratory experiments and theoretical research enhancing the Earth’s natural greenhouse effect are being done at the Global Change Research and create more ozone and carbon monoxide in Center (Portland State University) in a the atmosphere. However, it might also prevent Harvesting Forest Information comprehensive research program. This work some of the destruction of the stratospheric ozone We are collaborating with the U.S. Forest includes modeling the production, oxidation and layer by the manmade fluorocarbons 11 and 12. Service, Bureau of Land Management, Fish and transport of methane in the rice paddy ecosystem In this project, experimental and theoretical Wildlife Service and other government agencies and measuring the controlling parameters. R. research is focused on statistical trend analyses to build a forest information portal for the Rasmussen for the global increase of CH4, its seasonal Adaptive Management Area (AMA) program. variation, sources and sinks, models of its effect The AMAs develop and test innovative

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approaches to forest management. We are such as hydroxyl radical. We are studying the exogenous ligands tune the redox potential and developing an information model to locate kinetics, mechanisms and products of these chemistry of these complexes? We are combining documents and document fragments and to reactions with a wide variety of contaminants. The the powerful tools of molecular biology with search for documents based on similarity aim of this work is to help assess the suitability of advanced spectroscopic and computational searches between locations. The Forest project various advanced oxidation technologies (AOTs) for approaches to explore the structure and dynamics is primarily housed in the CSE department at remediation of groundwater, as well as to better of Mn active sites. For MnSD, we find an OGI, and also includes participants from the MST understand the fate of contaminants in natural unexpected temperature dependence for the department, from UNLV, and from the private waters that are exposed to sunlight. Tratnyek structures of anion complexes, which change sector. Delcambre, Maier, Toccalino, Phillips, coordination as the temperature is raised. This Steckler, Koch, Tolle, Landis, Palmer thermal transition implies that the stability of the Correlation Analysis of Contaminant Reactivity active site structure is determined by dynamical Quantitative Structure-Activity Relationships features of the complex and that dynamical Remediation of Halocarbon-Contaminated Groundwater (QSARs) are of enormous importance in excitation may play an important role in controlling There is enormous demand for improved ways to environmental chemistry and toxicology because of the energetics of ligand binding and redox. A wide clean up aquifers that have been contaminated their predictive power, but they also reveal a great range of projects relating to the chemistry and with halogenated hydrocarbon solvents like deal about reaction mechanisms and the nature of biology of Mn are in progress. Whittaker carbon tetrachloride and TCE. Recent field-scale substituent effects. We are involved in the tests have shown that technologies based on development of QSARs for a wide range of redox dechlorination with granular iron may have reactions involving organic contaminants. This Electronic Spectroscopy of Biological Metal Complexes substantial value. The goal of our research in work involves the use of computational chemistry Electronic spectroscopy extends structural studies this area is to provide a sound scientific basis methods as well as advanced statistical techniques of biomolecules beyond the atomic resolution of for designing and operating such technologies by in exploratory data analysis. Tratnyek X-ray crystallography to a level of structural detail determining the mechanisms of dechlorination by that directly relates to chemistry. The techniques iron and the geochemical and microbiological used in these studies span five decades of the processes that affect the performance of this Radical Copper Oxidases electromagnetic spectrum, from microwaves to the technique in the field. For more information on Radical copper oxidases are a new class of redox ultraviolet and beyond. At the lowest energy, this work, see www.cgr.ese.ogi.edu/iron. Tratnyek metalloenzymes (including the fungal enzymes electron paramagnetic resonance (EPR) galactose oxidase and glyoxal oxidase) containing a spectroscopy gives information on the electronic protein free radical directly coordinated to a ground state, defining the molecular orbital that Remediation of Explosives-Contaminated Groundwater copper center. This free radical-coupled Cu contains the unpaired electron in a paramagnetic There are numerous facilities where military complex catalyzes the two-electron oxidation of complex. At higher energy, UV-visible absorption operations have resulted in contamination of simple alcohols and aldehydes and the reduction of spectroscopy excites orbital transitions between groundwater with explosives such as TNT and O2 to hydrogen peroxide, fueling extracellular electronic states, giving information on RDX. Both TNT and RDX react rapidly with zero- peroxidases involved in lignin degradation. In these characteristic metal-ligand interaction energies valent iron, suggesting that permeable reactive proteins, the free radical is localized on a tyrosine that can be understood in terms of a ligand barriers of zero-valent iron might be useful in residue covalently crosslinked to a cysteinyl side field or molecular orbital analysis. Polarization remediation of these sites. However, the chain (a Tyr-Cys dimer). The catalytically active spectroscopy (linear dichroism, circular dichroism products of these reactions with zero-valent iron enzyme is an intense green color, the result of and magnetic circular dichroism) can give more may not present a satisfactory remediation end- unusual optical spectra arising from electronic detailed information on ground and excited state point. Therefore, we are investigating the transitions within the copper radical complex. Low electronic wave functions using geometric features kinetics and mechanisms of this reaction in the energy transitions in the near IR result from of light to probe the active site. These experimental experiments performed in the laboratory and in interligand redox in this metal complex, ligand-to- approaches can be complemented by spectroscopic the field. See www.cgr.ese.ogi.edu/iron/. ligand charge transfer (LLCT) processes that are modeling and computational biology methods to Tratnyek and Johnson closely related to the electron transfer coordinate provide a detailed description of a metalloprotein for substrate oxidation. The active site metal complex and its interactions. Whittaker complex is surprisingly flexible, twisting through a Reduction Reactions of Organic Pollutants in pseudorotation distortion when exogenous ligands Anaerobic Environments bind, thereby modulating the basicity of a second Regulation of Long Chain Fatty Acid Transport and Some organic pollutants undergo rapid reduction tyrosine ligand that serves as a general base in Oxidation in Mammalian Heart and Liver in anaerobic sediments, soils and groundwaters. catalysis. Many of these aspects of electronic The rate-limiting step in ß-oxidation is the Despite the potential importance of this process, structure and dynamics of the radical copper conversion of long-chain acyl-CoA to acylcarnitine, little is known about the natural reducing agents oxidases are the focus of active research. a reaction catalyzed by the outer mitochondrial that are responsible for these reactions. In this Whittaker membrane enzyme carnitine palmitoyltransferase project, assays are being developed to identify I (CPTI) and inhibited by malonyl-CoA. The and quantify environmental reducing agents in acylcarnitine is then translocated across the situ. These assays will be used in kinetic studies Manganese Metalloenzymes inner mitochondrial membrane by the carnitine/ of important pollutant reduction reactions. Manganese is an essential element for life, acylcarnitine translocase and converted back Tratnyek forming the active site for a large number of to acyl-CoA by CPTII. This reaction in intact metalloenzymes catalyzing hydrolytic or redox mitochondria is inhibited by malonyl-CoA, the first reactions, including the photosynthetic oxygen intermediate in fatty acid synthesis, suggesting Oxidation Reactions of Organic Pollutants evolving complex. We are interested in the Mn coordinated regulation of fatty acid oxidation and Some organic pollutants undergo rapid oxidation in redox sites in Mn superoxide dismutase (MnSD, synthesis. Although CPTII has been examined in natural waters, when catalyzed by sunlight, and in mononuclear Mn) and Mn catalase (MnC, dinuclear detail, studies on CPTI have been hampered by an technological systems, when chemical oxidants are Mn), enzymes that provide protection from toxic inability to purify CPTI in an active form from added to effect remediation. These reactions are oxygen metabolites. The key question is: How do CPTII. In particular, it has not been conclusively usually mediated by “activated oxygen species” interactions between the protein, metal ion and demonstrated that CPTI is even catalytically active,

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or whether sensitivity of CPTI to malonyl-CoA is an establishment of genetic competence is coregulated CENTER FACULTY AND RESEARCH SCIENTISTS intrinsic property of the enzyme or is contained in with peptide antibiotic biosynthesis by a complex António M. Baptista, Professor and Director a separate regulatory subunit that interacts with network of signal transduction pathways that Arun Chawla, Associate Research Scientist CPTI. To address these questions, the genes for utilize protein components common to all human heart muscle M-CPTI and rat liver LCPTI prokaryotic and most eukaryotic organisms. Zuber Wu-Chi Feng, Associate Professor and CPTII were separately expressed in Pichia (Computer Science and Engineering) pastoris, a yeast with no endogenous CPT activity. Wu-Chang Feng, Assistant Professor High levels of CPT activity were present in purified Role of Chaperones/Proteases in the Control of (Computer Science and Engineering) mitochondrial preparations from both CPTI- and Gene Expression Juliana Freire, Assistant Professor CPTII-expressing strains. Furthermore, CPTI There is growing evidence that protein (Computer Science and Engineering) activity was highly sensitive to inhibition by complexes that function in protein folding, Todd Leen, Professor malonyl-CoA while CPTII was not. Thus, CPT remodeling and degradation interact directly (Computer Science and Engineering) catalytic activity and malonyl-CoA sensitivity are with the molecular machinery that initiates gene David Maier, Professor contained within a single CPTI-polypeptide in expression. In mammalian, fungal and bacterial (Computer Science and Engineering) mammalian mitochondrial membranes. Our cells, components of ATP-dependent protease Claudio Silva, Associate Professor laboratory is the first to describe the kinetic complexes have been implicated in the control of (Computer Science and Engineering) characteristics for the yeast-expressed CPTIs, the RNA polymerase activity through direct protein- Jon Walpole, Professor (Computer Science and Engineering) first such report for a CPTI enzyme in the absence protein interaction. In the spore-forming Yinglong (Joseph) Zhang, Associate Research Scientist of CPTII. Both yeast-expressed M-CPTI and L-CPTI bacterium, Bacillus subtilis, developmentally are inactivated by detergent solubilization. regulated transcription during the early stages of Mike Zulauf, Assistant Research Scientist However, removal of the detergent in the presence sporulation, genetic competence development of phospholipids resulted in the recovery of and antibiotic biosynthesis is profoundly affected CCALMR RESEARCH FACILITIES malonyl-CoA-sensitive CPTI activity, suggesting by members of the heat shock protein family that CCALMR is well equipped to conduct state-of-the- that CPTI requires a membranous environment. normally function as chaperones and multi- art scientific research. The following is a list of CPTI is thus reversibly inactivated by detergents. component proteases. Evidence from our studies facilities and instruments available in addition to We have isolated and sequenced the promoter indicates that these proteins operate closely with those available through EBS. region of the gene for the human heart M-CPTI. RNA polymerase during the process of regulated We have mapped the malonyl-CoA and substrate transcription initiation. Our work is aimed at binding sites in human heart M-CPTI and liver determining the nature of these interactions and REAL-TIME DATA ACQUISITION NETWORK L-CPTI by deletion, site-directed mutagenesis and their effects on the systems controlling bacterial The coastal observatory CORIE includes a real- chemical modification studies using residuespecific developmental processes. Zuber time data acquisition network with close to 20 reagents. Our deletion and point mutation analyses multisensor oceanographic stations in the have demonstrated that glutamate-3 and histidine- Columbia River estuary and plume. Field 5 are necessary for malonyl-CoA inhibition and RESEARCH CENTERS operations are conducted from the Marine binding of CPTI but not for catalysis. We will Environmental Research and Training Station determine the structural basis for the high (MERTS). MERTS is a facility developed in malonyl-CoA sensitivity of M-CPTI by constructing CENTER FOR COASTAL AND LAND-MARGIN partnership with and operated by the Clatsop chimeras between M-CPTI and L-CPTI and by site- RESEARCH (CCALMR) Community College (CCC). CCC operates a training directed mutagenesis. We will prepare milligram www.ccalmr.ogi.edu and research vessel, the 50-foot M/V Forerunner. quantities of the expressed highly purified human The Center for Coastal and Land-Margin CCALMR operates a 21-foot research vessel, the heart M-CPTI and liver L-CPTI for structural Research (CCALMR) is an interdisciplinary R/V CORIE. characterization studies. Finally, we plan to study research center affiliated with the Department of the regulation of human heart M-CPTI gene Environmental and Biomolecular Systems. OCEANOGRAPHIC EQUIPMENT expression by hormonal, developmental and dietary CCALMR conducts research, graduate education factors. Our goal is to elucidate the molecular and advanced technology development that • 600-kHz Acoustic Doppler current mechanism of the regulation of fatty acid transport directly address the need for better scientific profilers (RD) and oxidation in mammalian cells. Woldegiorgis understanding of coasts, land margins and • 500 and 1500 kHz Acoustic Doppler estuaries. Improved knowledge of these complex profilers (Sontek) systems is necessary to preserve and enhance Prokaryotic Signal Transduction/Gene Regulation • Conductivity and temperature pairs (Seabird) their environmental integrity, maintain the • Conductivity, temperature and pressure sensors Bacteria can respond in variety of ways to a economic viability of communities dependent on (Coastal Leasing and Ocean Sensors) growth-restricting environment. Prolonged them and protect human populations from • Optical backscatter sensors exposure to a nutritionally poor environment natural and manmade hazards. Real-world (Downing Associates) results in the induction of antibiotic biosynthesis, natural resource management issues motivate functions required for cell motility and processes of CCALMR research and education activities. •Wind gauges (Coastal Leasing) cellular differentiation that give rise to highly Insights drawn from the experience of science • High-density thermistor chains (CCALMR) resistant cell types. How cells respond to and engineering professionals in the public and •Differential GPS (Trimble) nutritional stress is profoundly influenced by cell private sectors influence the identification of • Spread spectrum radio data modems density. Extracellular signal molecules accumulate emerging research challenges, the design of (FreeWave) in the local environment of densely populated cell research projects, the development of supporting cultures and trigger antibiotic production and tools and applications and the transfer of developmental processes such as sporulation and knowledge and technology. Additional information COMPUTATIONAL ENGINES AND ON-LINE STORAGE genetic competence. The objective of our research about CCALMR may be obtained from: • 16 parallel Intel dual CPU compute nodes (2.4 is to understand, in molecular terms, the GHz, 4 Gb) regulatory networks that cells utilize to choose the ANTÓNIO M. BAPTISTA, PH.D. •6 single CPU Alpha compute nodes most appropriate response to harsh conditions. In Phone: 503 748-1147 • 10 TB primary storage the spore-forming bacterium, Bacillus subtilis, E-mail: [email protected] 53 EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS

CENTER FOR GROUNDWATER RESEARCH RESEARCH FACILITIES www.cgr.ese.ogi.edu. The EBS department is well equipped to carry on The principal mission of the Center for a vigorous research program. Instruments and Groundwater Research (CGR) is to conduct state- equipment available in the department include: of-the-art research in areas relating to the transport and fate of contaminants in the • Gas chromatograph/mass spectrometer subsurface. This is accomplished through a with computer data system combination of research grants and contracts and • High-resolution mass spectrometer collaboration with other universities, industries • UV/Visible spectrometer and government agencies. • Capillary column gas chromatographs with The Center coordinates a range of projects relating flame ionization detectors to the transport and fate of contaminants in soils • Fourier transfor-infrared spectrometers and groundwater. The scope of the Center includes, • Fourier transfor-Raman spectrometer among other things, the development of: 1) new with CW Nd:YAG laser sampling and site characterization techniques; 2) new analytical techniques; 3) improved • X-band electron paramagnetic groundwater remediation methods and 4) physical resonance spectrometer and numerical models of groundwater- and • Ultraviolet/visible/near-infrared watershed-scale processes. spectrophotometers • Scanning fluorescence spectrophotometers The Center operates the Large Experimental Aquifer Program (LEAP), which contains the • Magnetic circular dichroism experimental facilities outlined below. The LEAP (MCD) spectrometer facility provides staff with the capability to conduct • Diode array UV/Visible spectrophotometer both bench-scale experiments and essentially full- • Laser Raman spectrophotometer scale pilot demonstrations. Students involved in • Raman spectrograph with CCD detector LEAP receive a rare combination of experiences, • Ar, Kr, HeCd, HeNe and dye lasers including full-scale remediation engineering and • High-vacuum lines process-level understanding of contaminant hydrology and chemistry. • Phosphor imager • Controlled atmosphere reaction chamber For additional information about CGR, contact: • Super speed centrifuges RICHARD JOHNSON, PH.D. • Ultracentrifuges Phone: 503 748-1193 • HPLCs E-mail: [email protected] • FPLCs • Fraction collectors • Liquid scintillation systems CENTER FACULTY •Gel electrophoresis systems Richard Johnson, Associate Professor and Director James F. Pankow, Professor • Laminar flow hoods for sterile culture Patricia L. Toccalino, Assistant Professor • Growth chambers Paul Tratnyek, Associate Professor • Constant temperature rooms • Light and electron microscopes LEAP EQUIPMENT • Ultrafiltration systems •Five tanks: one 10 m x 10 m x 3 m; two 10 m x • Autoclaves 10 m x 5 m; one 10 m x 2.5 m x 0.5 m; and one • Photographic facilities 8 m x 2.5 m x 0.5 m • Probe-type sonicators and extruder • In-situ instrumentation, including automated See additional research equipment listings in the temperature, pressure and water-level Research Centers section. monitoring; multilevel samplers; down-hole video camera; and automated vapor and product-sensing equipment • Remediation equipment, including soil vapor extraction and air sparging capabilities • Automated on-site analytical equipment, including capillary GC-MS

54 F ACULTY | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | EBS FACULTY

ANTÓNIO M. BAPTISTA NINIAN J. BLACKBURN WILLIAM H. GLAZE DAVI D A. JAY Professor and Department Head Professor Professor Associate Professor Director, Center for Coastal Ph.D., Inorganic Chemistry Ph.D., Physical Chemistry Ph.D., Physical Oceanography and Land-Margin Research University of Dundee, University of Wisconsin, University of Washington, 1987 Ph.D., Civil Engineering Scotland, U.K., 1975 Madison, 1961 [email protected] Massachusetts Institute [email protected] [email protected] of Technology, 1987 RESEARCH INTERESTS [email protected] RESEARCH INTERESTS RESEARCH INTERESTS River basin, estuarine and Structure and function of oxidase Integration of ecological sciences continental shelf processes, RESEARCH INTERESTS and oxygenase metalloenzymes; with human health sciences turbulent mixing, tides and tidal Integrated understanding and spectroscopy of metal sites in including the integration of analysis. A unifying theme is the prediction of hydrodynamic proteins with emphasis on EPR, functional genomics. Sustainable influence of hydrodynamic and environmental processes EXAFS, absorption edge and FT-IR technologies applied to urban processes on ecosystems. in estuaries and coasts. spectroscopies; coordination design and to the energy and Development of associated chemistry and biochemistry of transportation sectors. REPRESENTATIVE PUBLICATIONS concepts and technologies: copper. Biochemistry of metal Kukulka T., and D. A. Jay, “Impacts of coastal observatories, trafficking in cells. REPRESENTATIVE PUBLICATIONS Columbia River Discharge on Salmonid W.H. Glaze, D.S. Maddox and P. Bose, Habitat I. A Nonstationary Fluvial Tide environmental information Model,” J. Geophys. Res., in press. technology, numerical methods REPRESENTATIVE PUBLICATIONS “Degradation of RDX by Various Advanced Oxidation Processes: and modeling systems, error F.C. Rhames, N.N. Murthy, K.D. Karlin Kay, D. J. and D. A. Jay, “Interfacial I. Reaction Rates,” Water Research, Mixing in a Highly Stratified Estuary. and uncertainty analysis, and N.J. Blackburn, “Isocyanide Binding to the Copper(I) Centers of the 997-1004, 1998. 1. Characteristics of Mixing,” and physically based Catalytic Core of Peptidylglycine P. Bose, W.H. Glaze and D.S. Maddox, J. Geophys. Res., in press. ecological indicators. Monooxygenase (PHMcc),” J. Biol. “Degredation of RDX by Various Kay, D. J. and D. A. Jay, “Interfacial Inorg. Chem., 6, 567-577, 2001. Advanced Oxidation Processes: II. Mixing in a Highly Stratified Estuary. REPRESENTATIVE PUBLICATIONS S. Jaron and N.J. Blackburn, Organic By-Products,” Water Research, 2. A Method of Constrained Difference Archer C., A.M. Baptista and T. Leen, “Characterization of a Half-Apo 1005-1018, 1998. Approach for the Determination of the “Fault Detection for Salinity Sensors Derivative of Peptidylglycine David R. Pesiri, David K. Morita, Momentum and Mass Balances and in the Columbia Estuary,” Water Monooxygenase. Insight into the William Tumas and William Glaze, the Energy of Mixing,” J. Geophys. Resources Research, to appear in Reactivity of Each Active Site Copper,” “Selective Epoxidation in Dense-Phase Res., in press. 39 (3), 2003. Biochemistry, 40, 6867-6875, 2001. Carbon Dioxide,” Chem. Commun. Fain, A.M.V., D. A. Jay, D. J. Wilson, A.M. Baptista, “Environmental N.J. Blackburn, F. C. Rhames, (Cambridge), Issue 9, 1015-1016, P. M. Orton and A. M. Baptista, Observation and Forecasting Systems,” M. Ralle and S. Jaron, “Major Changes 1998. “Seasonal, Monthly and Tidal Patterns in Encyclopedia of Physical Science in Copper Coordination Accompany John L. Ferry and William H. Glaze, of Particulate Matter Dynamics in the and Technology, 3rd Edition, Vol. 5, Reduction of Peptidylglycine “Photocatalytic Reduction of Nitro Columbia River Estuary,” Estuaries 24, Academic Press, 2002. Monooxygenase: Implications for Organics over Illuminated Titanium 770-786, 2001. E.P. Myers and A.M. Baptista, Electron Transfer and the Catalytic Dioxide: Electron Transfer Between D.A. Jay, W. R. Geyer and “Inversion for Tides in the Eastern Mechanism,” J. Biol. Inorg. Chem., Excited-State TiO2 and D. R. Montgomery, in An Ecological North Pacific Ocean,” Advances in 5, 341-353, 2000. Nitroaromatics,” J. Phys. Chem. B Perspective on Estuarine Classification: Water Resources, 24 (5), 505-519, J.F. Eisses, J.P. Stasser, M. Ralle, 102(12), 2239-2244, 1998. Estuarine Science, A Synthetic 2001. J.H. Kaplan and N.J. Blackburn, John L. Ferry and William H. Glaze, Approach to Research and Practice, “Domains I and III of Human Copper “Photocatalytic Reduction of Nitro J. E. Hobbie, ed., Island Press, E.P. Myers and A.M. Baptista, pp. 149-175, 2000. “Analysis of Factors Influencing Chaperone for Superoxide Dismutase Organics over Illuminated Titanium Simulations of the 1993 Hokkaido Interact via a Cysteine-Bridged Dioxide: Role of the TiO2 Surface,” E.P. Flinchem and D. A. Jay, “An Nansei-Oki and 1964 Alaska Tsunamis,” Dicopper(I) Cluster,” Biochemistry, Langmuir, 14(13), 3551-3555, 1998. Introduction to Wavelet Transform 38, 7337-7342, 2000. Natural Hazards, 23 (1), 1-28, 2001. H.S. Weinberg and W.H. Glaze, Tidal Analysis Methods,” Coast. Estuar. Shelf Sci., 51, 177-200, 2000. D.C. Steere, A.M. Baptista, D. N.J. Blackburn, M. Ralle, R. Hassett “A Unified Approach to the Analysis of McNamee, C. Pu and J. Walpole, and D.J. Kosman, “Spectroscopic Polar Organic By-Products of Oxidation D.A. Jay and E.P. Flinchem, “Research Challenges in Environmental Analysis of the Trinuclear Cluster in the in Aqueous Matrices,” Water Research, “Interaction of Fluctuating River Flow Observation and Forecasting Systems,” Fet3 Protein from Yeast, a Multinuclear 1555-1572, 1997. with a Barotropic Tide: A Test of in Proceedings of the 6th Annual Copper Oxidase,” Biochemistry, 39, Wavelet Tidal Analysis Methods,” International Conference on Mobile 2316-2324, 2000. J. Geophys. Res., 102, 5705-5720, Computing and Networking (Mobicom 1997. 2000), Boston, 292-299, 2000. B.M. Hickey, L.J. Pietrafesa, D.A. Jay A. Oliveira, A.B. Fortunato and and W.C. Boicourt, “The Columbia River A.M. Baptista “Mass Balance in Plume Study: Subtidal Variability in the Eulerian-Lagrangian Transport Velocity and Salinity Field,” J. Geophys. Simulations in Estuaries,” ASCE Res., 103(10), 229-368, 1996. Journal of Hydraulic Engineering, 126 (8), 605-614, 2000. 55 EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | F ACULTY

RICHARD L. JOHNSON PIERRE MOËNNE-LOCCOZ MICHIKO M. NAKANO JAMES F. PANKOW Associate Professor, Assistant Professor Research Associate Professor Professor Director, Center for Ph.D., Biophysics Ph.D., Cell Biology Ph.D., Environmental Groundwater Research University of Pierre & Marie Curie, University of Tokyo, 1976 Engineering Science Ph.D., Environmental Science Paris VI, 1989 [email protected] California Institute of Technology, Oregon Graduate Center, 1985 [email protected] 1978 [email protected] RESEARCH INTERESTS [email protected] RESEARCH INTERESTS Anaerobiosis of Bacillus subtilis; RESEARCH INTERESTS Structure-function relationships oxygen-controlled gene regulation; RESEARCH INTERESTS Physical and chemical behavior of within proteins. Metallo- and two-component signal transduction Physical and analytical chemistry organic contaminants in the air, heme-proteins. Spectroscopic system; transcriptional activation; of organic compounds and metals soil and water; environmental studies of enzyme-active sites and nitrate/nitrite reductases; in natural waters and in the analytical organic chemistry; their cofactors. Reaction flavohemoglobin; anaerobic atmosphere; the formation and transport and fate of contaminants intermediates within catalysis. electron transport; nitric oxide chemistry of atmospheric aerosols; at the watershed scale; modeling signaling. the chemistry of nicotine in of contaminant transport. REPRESENTATIVE PUBLICATIONS tobacco smoke. R.A. Ghiladi, K.R. Hatwell, K.D. Karlin, REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS H.-w. Huang, P. Moënne-Loccoz, C. S. Nakano, M. M. Nakano, Y. Zhang, REPRESENTATIVE PUBLICATIONS Amerson, I.L. and R.L. Johnson,” Krebs, B.H. Huynh, L.A. Marzilli, R.J. M. Leelakriangsak and P. Zuber, J.F. Pankow, J.H. Seinfeld, W.E. Asher A Natural Gradient Tracer Test to Cotter, S. Kaderli and A.D. Zuberbuhler, “A Regulatory Protein that Interferes and G.B. Erdakos, “Modeling the Evaluate Natural Attenuation of MTBE “Dioxygen Reactivity of Mononuclear with Activator-Stimulated Transcription Formation of Secondary Organic Under Anaerobic Conditions,” Heme and Copper Components Yielding in Bacteria,” Proc. Natl. Acad. Sci. USA, Aerosols. 1. Theory and Measurements Groundwater Monitoring and a High-Spin Heme-Peroxo-Cu Complex,” 100, 4233-4238, 2003. for the (-Pinene-, (-Pinene-, Sabinene-, J. Am. Chem. Soc., 123, 6183-6184, Remediation, 23(1), 54-61, 2003. M.M. Nakano and P. Zuber, (3-Carene, and Cyclohexene-Ozone 2001. Systems,” Environ. Sci. Technol., 35, R.L. Johnson, P.C. Johnson, “Anaerobiosis,” in Bacillus subtilis and 1164-1172, 2001. See also Errata, T.L. Johnson and A. Leeson, “Helium K. Auclair, P. Moënne-Loccoz and P.R. Its Closest Relatives, A.L. Sonenshein, Environ. Sci. Technol., 35, 3272, 2001. Tracer Tests for Assessing Contaminant Ortiz de Montellano, “Roles of the J.A. Hoch and R. Losick, eds., American Vapor Recovery and Air Distribution Proximal Heme Thiolate Ligand in Society for Microbiology, Washington, J.H. Seinfeld, W.E. Asher, G.B. During In-Situ Air Sparging,” Cytochrome P450cam,” J. Am. Chem. D.C., pp. 393-404, 2002. Erdakos and J. F. Pankow, “Modeling Soc., 123, 4877-4885, 2001. Bioremediation Journal, 5(4), 321-336, M.M. Nakano, “Induction of ResDE- the Formation of Secondary Organic 2001. P. Moënne-Loccoz, O.-M.H. Richter, dependent Gene Expression in Bacillus Aerosols. 2. The Predicted Effects of Relative Humidity on Aerosol Formation R.L. Johnson, P.C. Johnson, H.-w. Huang, I. Wasser, R.A. Ghiladi, subtilis in Response to Nitric Oxide in the (-Pinene-, (-Pinene-, Sabinene-, T.L. Johnson, Neil R. Thomson and K.D. Karlin and S. de Vries, “Nitric and Nitrosative Stress,” J. Bacteriol., (3-Carene, and Cyclohexene- Ozone A. Leeson, “Diagnosis of In-Situ Air Oxide Reductase from Paracoccus 184, 1783-1787, 2002. Systems,” Environ. Sci. Technol., 35, Sparging Performance Using Transient denitrificans Contains an Oxo-Bridged M.M. Nakano and Y. Zhu, “Involvement 1806-1817, 2001. Groundwater Pressure Changes During Heme/Non-Heme Diiron Center,” J. Am. Chem. Soc., 122, 9344-9345, 2000. of the ResE Phosphatase Activity in Startup and Shutdown,” Bioremediation Down-Regulation of ResD-Controlled R.L. Johnson, J. Pankow, D. Bender, Journal, 5(4), 299-320, 2001. A. Wilks and P. Moënne-Loccoz, Genes in Bacillus subtilis During C. Price and J. Zogorski, “MTBE, To What Extent Will Past Releases R.L. Johnson, P.C. Johnson, “Identification of the Proximal Ligand Aerobic Growth,” J. Bacteriol., 183, Contaminate Community Water Supply I.L. Amerson, T.L. Johnson, C.L. Bruce, His-20 in Heme Oxygenase (HmuO) 1938-1944, 2001. Wells?” Environ. Sci. Technol., A. Leeson and C.M. Vogel, “Diagnostic from Corynebacterium diphtheriae. Oxidative Cleavage of the Heme M.M. Nakano, Y. Zhu, M. LaCelle, 210A-217A, 2000. Tools for Integrated In-Situ Air Sparging X. Zhang and F.M. Hulett, “Interaction Pilot Tests,” Bioremediation Journal, Macrocycle Does Not Require the J.F. Pankow, B.T. Mader, Proximal Histidine,” J. Biol. Chem., of ResD with Regulatory Regions of 5(4), 283-298, 2001. Anaerobically Induced Genes in L.M. Isabelle, W. Luo, A. Pavlick and 275, 11686-11692, 2000. C. Liang, “Conversion of Nicotine in N.R. Thomson and R.L. Johnson, Bacillus subtilis,” Mol. Microbiol., Tobacco Smoke to Its Volatile and “Air Distribution During In-Situ Air P. Moënne-Loccoz, C. Krebs, K. 37, 1198-1207, 2000. Available Free-Base Form through the Sparging: An Overview of Mathematical Herlihy, D.E. Edmondson, E.C. Theil, Action of Gaseous Ammonia,” Environ. Modeling,” J. Hazardous Materials 72 B.H. Huynh and T.M. Loehr, “The Sci. Technol., 31, 2428-2433, 1997. (2-3), 265-282, 2000. Ferroxidase Reaction of Ferritin Reveals a Diferric mu-1,2 Bridging C. Liang and J.F. Pankow, R.L. Johnson, J.F. Pankow, D. Bender, Peroxide Intermediate in Common with “Gas/ Particle Partitioning of Organic C. Price and J. Zogorski, “To What Other O2-Activating Non-Heme Diiron Compounds to Environmental Tobacco Extent Will Past MTBE Releases Proteins,” Biochemistry, 38, 5290- Smoke: Partition Coefficient Contaminate Community Water Supply 5295, 1999. Measurements by Desorption,” Environ. Wells?” Environ. Science and Technol., Sci. Technol., 30 (9), 2800-2805, 1996. 34, 2A-7A, 2000. J.F. Pankow, “An Absorption Model L. Slater, A.M. Binley, W. Daily and of Gas/Particle Partitioning in the R.L. Johnson, “Cross-hole Electrical Atmosphere,” Atmos. Environ., 28, Imaging of a Controlled Saline Tracer 189, 1994. Injection,” J. Applied Geophysics, 44, 85-102, 2000. 56 F ACULTY | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | EBS

FACULTY

L. E. L. (BETS) RASMUSSEN REINHOLD A. RASMUSSEN MATTHEW S. SACHS PATRICIA L. TOCCALINO Research Professor Professor Associate Professor Assistant Professor Ph.D., Neurochemistry Ph.D., Botany/Plant Physiology Ph.D., Biology Ph.D., Environmental Science Washington University Washington University, Massachusetts Institute and Engineering (St. Louis), 1964 (St. Louis), 1964 of Technology, 1986 Oregon Graduate Institute, 1992 [email protected] [email protected] [email protected] [email protected]

RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Mammalian chemocommunication: Atmospheric chemistry of trace Mechanisms of translational and Human and ecological risk the transport, olfactory and gases; biogenic and anthropogenic transcriptional control that assessments, water-quality vomeronasal organ reception of emissions of trace gases and their regulate the expression of the assessments, contaminant fate (Z)-7-dodecenyl acetate, the sex roles in stratospheric ozone Neurospora crassa arg-2 and and transport in various pheromone of the Asian elephant; destruction and tropospheric Saccharomyces cerevisiae CPA1 environmental media. the origin and synthesis of (Z)-7- ozone formation; measurements of genes; fungal genomes. dodecenyl acetate; identification trace gases at parts per trillion to REPRESENTATFIVE PUBLICATIONS and function of pheromones and parts per quadrillion levels; REPRESENTATIVE PUBLICATIONS AND TECHNICAL REPORTS chemical signals of the sources and sinks of isoprene and Sachs, M. S., and Geballe, A. P., P.L. Toccalino, J. Zogorski, L. Nowell, elephantunique temporal gland. other hydrocarbons. “Biochemistry. Sense and Sensitivity - J. Donohue, C. Eiden, S. Krietzman and Controlling the Ribosome,” Science G. Post, “Health-based Screening Level REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS 297, 1820-1821, 2002. Methodology for State-level Analyses,” technical report to U.S. Geological Sachs, M. S., Wang, Z., Gaba, L.E.L. Rasmussen, H.S. Riddle and C. Geron, R.A. Rasmussen, R.R. Arnts Survey, U.S. Environmental Protection A., Fang, P., Belk, J., Ganesan, V. Krishnamurthy, “Mellifluous Matures and A. Guenther, “A Review and Agency and New Jersey Department of R., Amrani, N., and Jacobson, A., to Malodorous in Musth,” Nature, 415, Synthesis of Monoterpene Speciation Environmental Protection, 2002. 975-976, 2002. from Forests in the United States,” “Toeprint Analysis of the Positioning Atmos. Environ, 34 (11), 1761-1781, of Translational Apparatus Components R. Johnson, D. Grady and P. Toccalino, L.E.L. Rasmussen and G. Wittemyer, 2000. at Initiation and Termination Codons “Impact of Remediation on Long-term “Chemosignaling of Musth by Individual of Fungal mRNAs,” Methods 26, Leaching Due to Recharge in a Wild African Elephants (Loxodonta J. Zhang, K.R. Smith, R. Uma, Y. Ma, 105-114, 2002. Contaminated Fractured Till,” technical africana): Implications for Conservation V.V.N. Kishore, K. Lata, M.A.K. Khalil, report to the American Petroleum Fang, P., Wu, C., and Sachs, M. S., and Management,” Proc. Royal Soc. R.A. Rasmussen and S.T. Thorneloe, Institute, 2001. London, 269, 853-860, 2002. “Carbon Monoxide from Cookstoves in “Neurospora crassa Supersuppressor Developing Countries: 2. Exposure Mutants are Amber Codon-specific,” P.L. Toccalino and R. Binder, L.E.L. Rasmussen, J. Lazar, Potentials,” Chemosphere: Global Fungal. Genet. Biol., 36, 167-175, “Methodologies for Presenting D.R. Greenwood and G.D. Prestwich, Change Sci., 1 (1-3), 367-375, 1999. 2002. Contaminant Concentration Data from “Albumin - An Ideal Pheromone the Glassboro, New Jersey, Study Area Gaba, A., Wang, Z., Krishnamoorthy, Carrier,” Chem. Senses, 26, 1102, J. Zhang, K.R. Smith, R. Uma, Y. Ma, in a Human-Health Risk Context,” T., Hinnebusch, A. G., and Sachs, 2001. V.V.N. Kishore, K. Lata, M.A.K. Khalil, technical report to U.S. Geological R.A. Rasmussen and S.T. Thorneloe, M. S. “Physical Evidence for Distinct L.E.L. Rasmussen, “Source and Cyclic Survey, U.S. Environmental Protection “Carbon Monoxide from Cookstoves in Mechanisms of Translational Control Release Pattern of (Z)-7-Dodecenyl Agency and New Jersey Department of Developing Countries: 1. Emission by Upstream Open Reading Frames,” Acetate, the Preovulatory Pheromone Environmental Protection, 2000. factors,” Chemosphere: Chemosphere: EMBO J. 20, 6453-6463, 2001. of the Female Asian Elephant,” Chem. P.L. Toccalino, K. M. Auer, Global Change Sci., 1 (1-3), 353-366, D.D. Perkins, A. Radford and M.S. Senses, 26, 611-623, 2001. D. A. Mervyn and B. Stirling, “Phase II 1999. Sachs, The Neurospora Compendium: Remedial Investigation/Risk Assessment L.E.L. Rasmussen. “Elephant Chromosomal Loci. Academic Press, E. Grosjean, R.A. Rasmussen and Report for Westside Light Rail Transit; Olfaction,” ChemoSenses, 2, 4-5, 1999. San Diego, 2001. D. Grosjean, “Toxic Air Contaminants Construction Spoils at the Port of L.E.L. Rasmussen and T.E. Perrin. in Porto Alegre, Brazil,” Environ. Sci. H.S. Kelkar, J. Griffiths, M.E. Case, Portland’s Portland International “Physiological Correlates of Musth: Technol., 33 (12), 1970-1978, 1999. S.F. Covert, D.A. Hall, C. Keith, J.S. Center,” Portland, Oregon, 1997. Lipid Metabolites and Chemosignal Oliver, M.J. Orbach, M.S. Sachs, J.R. R.A. Rasmussen, M.A.K. Khalil and P.L. Toccalino, “Evaluation of the Composition,” Physiol. Behav., 67, Wagner, M.J. Weise, J.K. Wunderlich F. Moraes, “Permafrost Methane Contained Burn of Two M88 NIKE 539-549, 1999. and J. Arnold, “The Neurospora Crassa Content: 1. Experimental Data from Rocket Motors for Environmental Safety Genome: Libraries Sorted by L.E.L. Rasmussen. “Chemical Sites in Northern Alaska,” & Health Implications,” Nevada Test Chromosome,” Genetics, 157, Communication: An Integral Part of Chemosphere, 26, 591, 1993. Site X-Tunnel Facility (U25X), Las Functional Asian Elephant (Elephas 979-990, 2001. M.A.K. Khalil, R.A. Rasmussen, Vegas, 1997. maximus) Society, Ecoscience, 5, J.R. French and J. Holt, “The Influence 410-426, 1998. P.L. Toccalino, R. L. Johnson and of Termites on Atmospheric Trace D. R. Boone, “Nitrogen Limitation and Gases: CH4, CO2, CHCl3, N2O, CO, H2 Nitrogen Fixation During Alkane and Light Hydrocarbons,” J. Geophys. Biodegradation in a Sandy Soil,” Appl. Res., 95, 3619, 1990. Environ. Microbiol., 59, 2977-2983, D.A. Hegg, L.F. Radke, P.V. Hobbs, 1993. R.A. Rasmussen and P.J. Riggan, “Emissions of Some Trace Gases from Biomass Fires,” J. Geophys. Res., 95, 5669, 1990. 57 EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | F ACULTY

PAUL G. TRATNYEK KAREN WATANABE JAMES W. WHITTAKER GEBRETATEOS WOLDEGIORGIS Associate Professor Research Assistant Professor Associate Professor Associate Professor Ph.D., Chemistry Ph.D., Mechanical Engineering Ph.D., Biochemistry Ph.D., Nutritional Biochemistry Colorado School of Mines, 1987 University of California, University of Minnesota, 1983 University of Wisconsin, [email protected] Berkeley 1993 [email protected] Madison, 1976 [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Mechanistic and kinetic aspects of RESEARCH INTERESTS Electronic structures and RESEARCH INTERESTS the fate of organic pollutants in Bioaccumulation in aquatic dynamics of metalloenzyme active Structure-function studies with the environment; degradation environments, mathematical sites; spectroscopic and mitochondrial carnitine reactions involving pesticides, modeling of living systems computational approaches to palmitoyltransferases I and II phenols, munitions, dyestuffs and and health and ecological biomolecular structure; (CPTI and CPTII); regulation of chlorinated hydrocarbon solvents; risk assessment. metalloenzyme mechanisms; CPTI gene expression, fatty acid chemical and microbiological enzyme engineering; biology of transport, and oxidation in processes in sediments, soils and REPRESENTATIVE PUBLICATIONS metal ions. mammalian cells; role of CPTI in groundwaters as well as Watanabe, K.H., Desimone, F.W., diabetes, obesity, and heart photochemical processes in Thiyagarajah, A., Hartley, W.R. and REPRESENTATIVE PUBLICATIONS disease; investigation of the surface waters; natural and Hindrichs, A.E. (2003). Fish tissue M.M. Whittaker and J.W. Whittaker, molecular basis of human CPT quality in the lower Mississippi River engineered remediation systems. “Characterization of Recombinant deficiency diseases using animal and health risks from fish consumption. Barley Oxalate Oxidase Expressed by The Science of the Total Environment Pichia pastoris,” J. Biol. Inorg. Chem., models; regulation of cell REPRESENTATIVE PUBLICATIONS 302(1-3): 109-126. 7, 136-145, 2002. metabolism and signaling by long- Tratnyek, P. G., E. J. Weber and Watanabe, K.H. (2002). Fundamentals chain acyl-CoA esters; R. P. Schwarzenbach, “Quantitative V.V. Barynin, M.M. Whittaker, S.V. of physiologically-based toxicokinetic mitochondrial ion transport and Structure-Activity Relationships Antonyuk, V.S. Lamzin, P.M. Harrison, models. In: Endocrine Disrupters and bioenergetics. (QSARs) for Chemical Reductions of P.J. Artymiuk and J.W. Whittaker, Carcinogenic Risk Assessment. Organic Contaminants,” Environ. “Crystal Structure of Manganese L. Chyczewski, J. Niklinski and Toxicol. Chem. 22(8), in press. Catalase from Lactobacillus REPRESENTATIVE PUBLICATIONS E. Pluygers, Eds. Amsterdam, plantarum,” Structure, 9, 725-738, M. Treber, J. Dai, and G. Woldegiorgis, Netherlands, IOS Press: 271-280. Canonica, S., and P. G. Tratnyek, 2001. “Identification by Mutagenesis of “Quantitative Structure-Activity Watanabe, K.H. and Chen, C. (2001). Conserved Arginine and Glutamate Relationships (QSARs) for Oxidation M.M. Whittaker and J.W. Whittaker, The role of physiologically based Residues in the C-Terminal Domain of Reactions of Organic Chemicals in “Catalytic Reaction Profile for Alcohol toxicokinetic models in biologically Rat Liver Carnitine Palmitoyltransferase Water,” Environ. Toxicol. Chem. 22(8), Oxidation by Galactose Oxidase,” based risk assessment. Folia I That Are Important for Catalytic in press. Biochemistry, 40, 7140-7148, 2001. Histochemica et Cytobiologica Activity and Malonyl CoA Sensitivity,” J. Nurmi, J. T., and P. G. Tratnyek, 39(Suppl. 2): 50-51. R.A. Edwards, M.M. Whittaker, J.W. Biol. Chem., 278, 11145-11149, 2003. “Electrochemical Properties of Natural Whittaker, E.N. Baker and G.B. Watanabe, K.H. and Travis, C.C. H. Zhu, J. Shi, M. Treber, J. Dai, J., Organic Matter (NOM), Fractions of Jameson, “Outer Sphere Mutations (1997). Mathematical modeling of skin D.N. Arvidson and G. Woldegiorgis, NOM, and Model Biogeochemical Perturb Metal Reactivity in Manganese papilloma data in SENCAR mice. “Substitution of Glutamate-3, Valine-19, Electron Shuttles,” Environ. Sci. Superoxide Dismutase,” Biochemistry, Toxicology and Applied Pharmacology Leucine-23, and Serine-24 with Alanine Technol. 36(4), 617-624, 2002. 40, 15-27, 2001. 147: 419-430. in the N-Terminal Region of Human Gaspar, D. J., A. S. Lea, M. H. M.M. Whittaker and J.W. Whittaker, Muscle Carnitine Palmitoyltransferase I Watanabe, K.H. and Bois, F.Y. (1996). Engelhard, D. R. Baer, R. Miehr and P. “Expression of Recombinant Galactose Abolishes Malonyl CoA Inhibition and Interspecies extrapolation of G. Tratnyek, “Evidence for Localization Oxidase by Pichia pastoris,” Protein Binding,” Arch. Biochem. Biophys., physiological pharmacokinetic of Reaction upon Reduction of CCl4 by Expr. Purif., 20, 105-111, 2000. 413, 67-74, 2003. parameter distributions. Risk Analysis Granular Iron,” Langmuir 18(20), 16(6): 741-754. M.M. Whittaker and J.W. Whittaker, J. Dai, H. Zhu and G. Woldegiorgis, 7688-7693, 2002. “Recombinant Superoxide Dismutase “Leucine-764 Near the C-Terminal End Watanabe, K.H. and Bois, F.Y., Daisey, Agrawal, A., W. J. Ferguson, B. O. from a Hyperthermophilic Archaeon, of Carnitine Palmitoyltransferase I Is J.M., Auslander, D.M. and Spear, R.C. Gardner, J. A. Christ, J. Z. Bandstra Pyrobaculum aerophilium,” J. Biol. Important for Activity,” Biochem. (1994). Benzene toxicokinetics in and P. G. Tratnyek, “Effects of Inorg. Chem., 5, 402-408, 2000. Biophys. Res. Comm., 301, 758-763, humans — Bone marrow exposure to Carbonate Species on the Kinetics of 2003. metabolites. Occupational and 1,1,1-trichloroethane by Zero-valent Environmental Medicine 51(6): G. Zheng, J. Dai and G. Woldegiorgis, Iron,” Environ. Sci. Technol. 36(20), 414-420 and Lawrence Berkeley “Identification by Mutagenesis of a 4326-4333, 2002. Laboratory Report LBL-34432/UC-607. Conserved Glutamage (Glu487) Residue Tratnyek, P. G., M. M. Scherer, B. Important for Catalytic Activity in Rat Watanabe, K.H., Bois, F.Y. and Zeise, Deng and S. Hu, “Effects of Natural Liver Carnitine Palmitoyltransferase L. (1992). Interspecies extrapolation: Organic Matter, Anthropogenic II,” J. Biol. Chem., 277, 42219-42223, A reexamination of acute toxicity data. Surfactants, and Model Quinones on 2002. Risk Analysis 12: 301-310. the Reduction of Contaminants by Zero- valent Iron,” Water Research, 35(18), 4435-4443, 2001.

58 F ACULTY | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | EBS PROFESSOR EMERITUS RESEARCH SCIENTISTS WILLAM ASHER Ph.D., Environmental Science and Engineering Oregon Graduate Center ARUN CHAWLA Ph.D., Civil Engineering University of Delaware PETER ZUBER THOMAS M. LOEHR JOANN SANDERS-LOEHR WENTAI LUO Professor Professor Emeritus Professor Emeritus Ph.D., Environmental Science Ph.D., Microbiology Ph.D., Inorganic Chemistry Ph.D., Biochemistry and Engineering University of Virginia Cornell University, 1967 Cornell University, 1969 Oregon Graduate Institute [email protected] [email protected] of Science & Technology RESEARCH INTERESTS TODD SANDERS RESEARCH INTERESTS RESEARCH INTERESTS Investigation of the role of metal Ph.D., Physical Oceanography Regulation of prokaryotic gene Metallobiochemistry; biological ions in proteins by resonance University of Delaware expression and development in role of transition metals; Raman spectroscopy; oxygen response to stress; signal molecular and electronic activation and metabolism; active- YINGLONG (JOSEPH) ZHANG transduction; regulation and structures of metalloenzyme active site structures and redox reactions Ph.D., Applied Mathematics mechanism of peptide antibiotic sites; chemistry of O2 metabolism; of iron proteins, copper proteins and Fluid Mechanics biosynthesis; regulation of genetic metal-oxo intermediates; and quinone-containing proteins. University of Wollongong, Australia competence in Bacillus subtilis. resonance and FT-Raman, FT-IR and EPR spectroscopy. REPRESENTATIVE PUBLICATIONS MICHAEL ZULAUF REPRESENTATIVE PUBLICATIONS F.J. Rotsaert, J.D. Pikus, B.G. Fox, Ph.D., Meteorology Kawulka, K., T. Sprules, R. T. McKay, REPRESENTATIVE PUBLICATIONS J.L. Markley and J. Sanders-Loehr, University of Utah P. Mercier, C. M. Diaper, P. Zuber and S. Taoka, E.L. Green, T.M. Loehr and “N-Isotope Effects on the Raman J. C. Vederas, “Structure of Subtilosin R. Banerjee, “Mercuric Chloride- Spectra of Fe(2)S(2) Ferredoxin and A, An Antimicrobial Peptide from Induced Spin or Ligation State Changes Rieske Ferredoxin: Evidence for Bacillus subtilis with Unusual Post- in Ferric or Ferrous Human Structural Rigidity of Metal Sites,” translational Modifications Linking Cystathionine beta-Synthase Inhibit J. Biol. Inorg. Chem. 8, 318-326, 2003. Cysteine Sulfurs to ∂-carbons of Enzyme Activity,” J. Inorg. Biochem., E.L. Green, N. Nakamura, Phenylalanine and Threonine,” J. Am. 87, 253-259, 2001. D.M. Dooley, J.P. Klinman and Chem. Soc. 125, 4726-4727, 2003. L.K. Lightning, H. Huang, P. Moënne- J. Sanders-Loehr, “Rates of Oxygen Nakano, M. M., S. Nakano and P. Loccoz, T.M. Loehr, D.J. Schuller, T.L. and Hydrogen Exchange as Indicators Zuber, “Spx (YjbD), a Negative Effector Poulos and P.R. Ortiz de Montellano, of TPQ Cofactor Orientation in Amine of Competence in Bacillus subtilis, “Disruption of an Active Site Hydrogen Oxidases,” Biochemistry, 241, Enhances ClpC-MecA-ComK Bond Converts Human Heme 687-696, 2002. Interaction,” Mol. Microbiol. 44, 1341- Oxygenase-1 into a Peroxidase,” J. Biol. I.M.C. van Amsterdam, M. Ubbink, 1350, 2002. Chem., 276, 10612-10619, 2001. M. van den Bosch, F. Rotsaert, Nakano, S., G. Zheng, M. M. Nakano J. Hirst, S.K. Wilcox, J. Ai, P. Moënne- J. Sanders-Loehr and G.W. Canters, and P. Zuber, “Multiple Pathways of Spx Loccoz, T.M. Loehr and D.B. Goodin, “A New Type-2 Copper Cysteinate (YjbD) Proteolysis in Bacillus subtilis,” “Replacement of the Axial Histidine Azurin. Involvement of an Engineered J. Bacteriol. 184, 3664-3670, 2002. Ligand with Imidazole in Cytochrome c Exposed Cysteine in Copper Binding Zuber P., “Control of Gene Expression Peroxidase. 2. Effects on Heme through Internal Rearrangement,” in Gram-positive Bacteria: Extensions Coordination and Function,” J. Biol. Chem., 277, 44121-44130, of and Departures from Enteric Biochemistry, 40, 1274-1283, 2001. 2002. Paradigms,” Front. Biosci. 2002 Aug J. Baldwin, W.C. Voegtli, N. Khidekel, C.S. Farmer, D.M. Kurtz, Jr., 1;7:D1857-66, 2002. P. Moënne-Loccoz, C. Krebs, B.A. Ley, Z.J. Liu, B.C. Wang, J. Rose, J. Ai Nakano, S., M. M. Nakano, Y. Zhang, B.H. Huynh, T.M. Loehr, A. C. and J. Sanders-Loehr, “The Crystal M. Leelakriangsak and P. Zuber, “A Rosenzweig and J.M. Bollinger, Jr., Structures of Phascolopsis gouldii Wild Regulatory Protein that Interferes with “Rational Reprogramming of the R2 Type and L98Y Methemerythrins: Activator-stimulated Transcription in Subunit of Escherichia coli Structural and Functional Alterations Bacteria,” Proc. Natl. Acad. Sci. (Mar Ribonucleotide Reductase into a Self- of the O2 Binding Pocket,” J. Biol. 17, e-pub ahead of print), 2003. Hydroxylating Monooxygenase,” J. Am. Inorg. Chem., 6, 418-429, 2001. Chem. Soc., 123, 7017-7030, 2001. Nakano, M. M., F. Hajarizadeh, Y. Zhu M.L. Alvarez, J. Ai, W. Zumft, and P. Zuber, “Loss-of-Function E.L. Green, S. Taoka, R. Banerjee J. Sanders-Loehr and D.M. Dooley, Mutations in yjbD Result in clpX- and and T.M. Loehr, “Resonance Raman “Characterization of the Copper-Sulfur clpP-independent Competence Characterization of the Heme Cofactor Chromophores in Nitrous Oxide Development of Bacillus subtilis,” Mol. in Cystathionine beta-Synthase. Reductase by Resonance Raman Microbiol., 42, 383-394, 2001. Identification of the Fe-S(Cys) Vibration Spectroscopy: Evidence for Sulfur in the Six-Coordinate Low-Spin Heme,” Coordination in the Catalytic Cluster,” Biochemistry, 40, 459-463, 2001. J. Am. Chem. Soc., 123, 576-587, 2001.

59 EBS | ENVIRONMENTAL AND BIOMOLECULAR SYSTEMS | F ACULTY

JOINT FACULTY RESEARCH ASSOCIATES REASEARCH STAFF ROBERT (BRAD) THOMS M.S. Environmental Science DAVID R. BOONE LUISA ANDRUZZI DEEPALI DATTA and Engineering Environmental Biology Ph.D., Polymer Chemistry M.Sc., Zoology OGI School of Science Portland State University University of Pisa, Italy Delhi University, India & Engineering JAMES M. CREGG TOM CHISHOLM KAITLIN GRAMMER MICHELLE TREBER Keck Graduate Institute Ph.D., Marine Science B.S., Geology B.S., Biological Sciences of Applied Life Sciences College of William and Mary University of Alaska-Fairbanks California Polytechnic BERNARD A. FOX HONG YAN LIU JON GRAVES State University Earle A. Chiles Research Institute Ph.D., Immunology M.S. Oceanography and PAUL J. TURNER Providence Medical Center Norman Bethune University Marine Resource Management B.S. Mathematics of Medical Sciences Oregon State University STEPHEN B. HALL Boise State University China Pulmonary and Critical LORNE M. ISABELLE ETHAN VAN MATRE Care Medicine ROSEMARIE MIEHR M.S., Chemistry Software Engineering Oregon Health & Ph.D., Chemistry San Francisco State University Kennedy Western University Science University Technical University, GUANGZHI LIU Munich, Germany BOB WATKINS JAMES J. HUNTZICKER M.S., Computer Science B.S., Chemical Engineering Center for Professional JAIMIE POWELL and Engineering Washington State University Development Ph.D., Entomology Oregon Health & OGI School of Science University of Wisconsin Science University MICHAEL WILKIN & Engineering MARTINA RALLE MARY MAYFIELD-GAMBILL B.Sc. (Hons), RICHARD L. STOUFFER Ph.D., Chemistry B.S., Microbiology Oceanography and Geology Oregon National Primate University of Bonn, Germany Oregon State University University of Southampton, Research Center and NICK D. RUBIE STEFAN MINASIAN U.K. Department of Physiology and Pharmacology Ph.D., Chemistry B.A., Chemistry Oregon Health & University of New Mexico Reed College Science University MEI M. WHITTAKER COLE MCCANDLISH Ph.D., Biochemistry M.S., Atmospheric Sciences ADJUNCT FACULTY University of Minnesota Oregon State University BRUCE HOPE JIM MOHAN Environmental Toxicologist M.S., Management in Oregon Department of Science and Technology Environmental Quality Oregon Graduate Institute JAMES K. HURST JULIA NORMAN Department of Chemistry M.S., Environmental Science Washington State University and Engineering Oregon Health & ASLAM KHALIL Science University Department of Physics Portland State University SHUNJI NAKANO B.S., Molecular Biology GEORGE D. OLSEN Nagoya University, Japan Oregon Health & Science University PHILLIP B. PEARSON M.S. Environmental Science JEFFREY RING and Engineering Port of Portland Oregon Graduate Institute KENNETH ROSENBAUM ROBYN PHILLIPS Environmental Law Institute M.S., Environmental Washington, D.C. Management/Toxicology Duke University STEWART ROUNDS U.S. Geological Survey CHARLES SEATON M.S. Environmental Science BRUCE STIRLING and Engineering Oregon Department of Oregon Graduate Institute Environmental Quality of Science & Engineering JOHN C. WESTALL Department of Chemistry Oregon State University 60 THE DEPARTMENT OF MANAGEMENT IN commitments at work and home. Students Department of SCIENCE AND TECHNOLOGY focuses on may begin taking classes in any quarter, and may take individual courses for professional educating leaders and managers development prior to enrolling in the degree Management in Science in a technology-intensive world. program. Our online presence makes our All MS in Management courses degree program available to students and Technology around the world, as well as to those have a strong technology focus, students from our region for whom online meeting the educational needs of courses are more convenient. www.ogi.edu/MST/ students working in high- Collaborative. Management in Science and INTERIM DEPARTMENT HEAD technology industries and/or Technology equips students with the Jack Raiton functional expertise and the people skills 503 748-3075 technology-intensive professions. to manage cross-boundary partnerships E-mail: [email protected] Our curriculum also emphasizes effectively. The curriculum and faculty DEPARTMENT ADMINISTRATOR leadership and the communication emphasize the development of leadership Shelly Charles and communications skills that are critical and teamwork skills needed to 503 748-1335 to collaboration between people from E-mail: [email protected] work effectively with people. different functions, companies, and countries. Team projects, group exercises and oral ADMINISTRATIVE ASSISTANT presentations are emphasized throughout Staci Sutton WHAT SETS MANAGEMENT IN SCIENCE 503 748-7804 AND TECHNOLOGY APART? the curriculum. In addition, small class sizes make interactions and discussions E-mail: [email protected] The M.S. in Management is: between faculty and students an enriching PROGRAM ADMINISTRATOR learning experience. Technology-focused. Our graduate Maryann Burningham management program is designed with a Entrepreneurial. The M.S. in Management 503 748-1794 very specific intent: to prepare students to program emphasizes entrepreneurship E-mail: [email protected] effectively lead and manage in a technology- through the integrative Capstone experience, GENERAL INQUIRIES intensive organization. Compared to a culminating in the Jim Hurd New Venture 503 748-7804 traditional MBA, the learning from the M.S. Competition. Students form management E-mail: [email protected] in Management is much more relevant to teams and develop business plans requesting the student’s professional situation. Go to investment from a panel of distinguished http://www.ogi.edu/MST/degreechart.html venture capitalists who evaluate their oral for a more detailed comparison of the M.S. and written presentations. in Managment with traditional M.B.A. and M.S. in Engineering Management degrees. INDIVIDUAL COURSES FOR Relevant. Management in Science and CAREER DEVELOPMENT Technology courses are taught by faculty with outstanding professional and academic Each Management in Science and Technology credentials. Faculty have developed their course has been designed as a valuable expertise through years of professional professional development experience for work in the private sector as well as in working professionals. Project Management distinguished research careers. Each class (MST 512), Managing Organizational is designed to deliver cutting-edge knowledge Relationships (MST 520) and Leadership about best practices. Managers and and Communication Skills (MST 541), for executives from the region’s high-technology example, may be taken as stand-alone companies visit classes to share their courses. We encourage non- matriculated experience with the students. Students and students to join our courses for their own managers alike tell us that the “M.S. in career development in specific areas. Management classes offer knowledge you can apply Monday morning.” ONLINE COURSES, REMOTE Flexible. We designed the program for CLASSROOM SITES AND ALLIANCES working people, making it possible for M.S. in Management student David Kennedy Management in Science and Technology students to attend intensive weekend or presents his team’s business plan in the delivers challenging and engaging versions weeknight classes and continue to fulfill their Jim Hurd New Venture Competition as part of its courses over the Internet. of the Capstone course. MST | MANAGEMENT IN SCIENCE & TECHNOLOGY

U.S. News & World Report chose MST-Online Individual courses are open to interested MST 562 Health Care Program ...... 4 credits as one of the “Best of the Online Grad persons without the need to matriculate into Management MST 563 The Regulation and Legislation . . 4 credits Programs” in 2001. This is an excellent the degree or certificate programs. Enroll- of Health Care Delivery option for students facing time pressures or ment is available to any qualified student. ELECTIVES: Two of the following courses are required working in locations where travel to campus (4-8 credits) is not feasible. The course delivery system is MANAGEMENT IN SCIENCE AND TECHNOLOGY CERTIFICATE MST 564 Business Planning and Strategy . . 4 credits based on interactive Web pages, multimedia in the Health Care Industry lectures and lessons, and online discussions, The Management in Science and Technology MST 565 Human Resources ...... 4 credits in Health Care all in a seamless browser-centric department offers a six-course certificate environment. Students can take individual MST 566 Health Care Information ...... 4 credits in Management in Science and Technology. Systems Management courses, enroll in the Certificate in The following five courses, plus an MST 567 Health Care Technology – . . . . . 4 credits Management in Science and Technology additional management elective course New Medical Advances program or apply for the full Master of chosen in consultation with a faculty advisor, MST 568 New Trends in Health ...... 2-4 credits Care Delivery Science degree. Courses offered online will are required: MST 507HC Seminar for Health ...... 2 credits have a “D” designation as the section number Care Management following the course number. For further MST 510 (D) Principles and Trends in ...... 3 credits Technology Management The following courses from MST and other OHSU information, visit the Management in MST 512 (D) Project Management ...... 4 credits departments may also be used as electives, as may Science and Techonology Web site at MST 520 (D) Managing Organizational ...... 4 credits other Oregon University System courses, by petition of www.ogi.edu/MST/. Links from this Web site Relationships the department. will lead a student directly to our online MST 571 (D) Managerial and Financial . . . . . 4 credits DEPARTMENT OF MANAGEMENT Accounting for Science IN SCIENCE & TECHNOLOGY: educational administration partner, Cenquest. and Technology MST 512 (D) Project Management ...... 4 credits The M.S. in Management program also offers MST 573 (D) Technology Marketing: ...... 4 credits Planning for Market MST 520 (D) Managing Organizational ...... 4 credits on-site courses at our remote classroom Elective to be chosen after consultation . . . . . 3-4 credits Relationships location at the Wilsonville Training Center, with faculty advisor MST 522 (D) Change Leadership for ...... 3 credits 29353 Town Center Loop East, Wilsonville, Building Effective Organizations OR 97070. Currently, one or two MST HEALTH CARE MANAGEMENT CERTIFICATE MST 541 Leadership and ...... 3 credits Communication Skills courses per term are offered at the The Management in Science and Technology MST 542 Business Ethics and ...... 3 credits Wilsonville Training Center. Please refer to Corporate Social Responsibility department’s graduate-level certificate in the department’s Web site at www.ogi.edu/MST/ Health Care Management is designed for DEPARTMENT OF MEDICAL INFORMATICS for updated course schedule information. working professionals in administration, & OUTCOMES RESEARCH: The Management in Science and Technology reimbursement or management roles in MINF 510 Introduction to Medical Informatics health care organizations. The program MINF 517 Organizational Behavior and department has established an alliance with Management in Informatics the Engineering Technology Management provides an overview of the financial, policy, MINF 518 Project Management in Informatics graduate program at Portland State University. organizational and operational environment SCHOOL OF NURSING: Students from either degree program may of health care-related enterprises. Students cross-register and receive full course credit gain focused skills for designing and NURS 531 Ethical Decisions in Health Care Management Marketing transferable to his or her matriculated degree managing organizations engaged in the program. ETM students will need to receive delivery of health care. faculty advisor approval first. NON-CREDIT CERTIFICATE PROGRAMS The Management in Science and Technology department blends the unique management ESSENTIALS OF GENERAL MANAGEMENT FOR EMERGING FOR-CREDIT CERTIFICATE PROGRAMS and planning expertise within the M.S. in HIGH TECHNOLOGY LEADERS: A Partnership between Management faculty with those of recognized OGI, PSU and AeA ADMISSION REQUIREMENTS FOR MANAGEMENT IN SCIENCE AND professionals in the health care community The Essentials of General Management TECHNOLOGY CERTIFICATE PROGRAMS at OHSU and elsewhere. program is an excellent foundation for those bound for senior management. It brings The Management For-Credit Certificate The program consists of six courses, together the region’s rising stars of high- Programs require the following for admission: including four core (required) courses, and two elective choices, for a total of at least technology, offering a high-quality, local, •A completed application with $25 20 credits, as listed below. affordable foundation for entry into senior- nonrefundable application fee level management. HEALTH CARE MANAGEMENT CERTIFICATE CORE • At least two years of relevant (16 credits) This unique executive development workshop professional experience MST 560 The Organization, Financing, . . . 4 credits series is ideal for functional managers and • For non-native speakers of English, and History of Health Care high-potential employees who are on their a score of 625 or better on the Delivery in the United States way up. It lays the groundwork for the next MST 561 Managerial and Financial ...... 4 credits TOEFL examination Accounting for Health Care Professionals level of leadership training, making future 62 MANAGEMENT IN SCIENCE & TECHNOLOGY | MST investments in more extensive management MANAGEMENT IN SCIENCE AND TECHNOLOGY be taken together with one’s Capstone team. programs even more valuable and CORE SEQUENCE MST 530, Strategic Management and meaningful. In addition, the program provides Planning, and MST 550, Capstone Project: All M.S. students must take the core an excellent environment for networking. Business Plan, both should be taken as close sequence, consisting of the following to the end of a student’s studies as possible. The format includes intensive one-day courses or their equivalent (35 credits). workshops taught by senior executives and The courses listed below are offered both AREAS OF EMPHASIS academics who are highly respected in the on-campus and online. Either is acceptable technology industry, an interactive online for the M.S. in Management degree. If you Both emphasis areas require the completion forum, immediate application and feedback intend to take only online courses, please of the 35-credit M.S. core sequence. Specific and a graduate ceremony. For more see the Online Degree Requirements after courses required for each emphasis area are information, contact Jack Raiton at this section. as follows. [email protected] or 503 748-3075. MST 510 (D) Principles and Trends in ...... 3 credits MANAGING THE TECHNOLOGY COMPANY SEQUENCE Technology Management MST 512 (D) Project Management ...... 4 credits Core Sequence plus three of the following six courses are required (9–10 credits): M.S. DEGREE PROGRAM MST 513 (D) Operations Management ...... 3 credits and Practices MST 511 (D) Quality Management ...... 3 credits ADMISSION REQUIREMENTS FOR THE MST 520 (D) Managing Organizational ...... 4 credits MST 514 (D) Issues in R&D Management . . . 3 credits M.S. DEGREE PROGRAM Relationships MST 522 (D) Change Leadership for ...... 3 credits Building Effective Organizations In addition to the general admission MST 530 (D) Strategic Management ...... 4 credits and Planning MST 540 (D) International Management in . . . 3 credits requirements for the institution, the MST 550 (D) Capstone Project: ...... 4 credits Science and Technology Management in Science and Technology Business Plan MST 541 Leadership and ...... 3 credits department requires: MST 571 (D) Managerial and Financial ...... 4 credits Communication Skills Accounting for Science MST 574 Going to Market: Delivering . . . . 4 credits •A minimum of two years of full-time and Technology Value to Customers and work experience-preferably at the MST 572 (D) Financial Management for . . . . . 4 credits Shareholders professional, supervisory or managerial Science and Technology ELECTIVES: Two or three elective courses, including any level-in a technical, scientific, business MST 573 (D) Technology Marketing: ...... 4 credits course in the above list not already taken and/or any of Planning for Market the following (8–10 credits): or related area MST 590 (D) Effective Business Writing ...... 1 credit EBS 547 Uncertainty Analysis ...... 4 credits for Management • Recommended TOEFL score of 625 – OR – EBS 583 Environmental Law ...... 3 credits and Regulation (paper-based test) if English is not the MST 591 (D) Effective Business Writing for . . . 1 credit applicant’s first language. Scores are not Non-native Speakers CSE 517 Software Engineering ...... 3 credits Processes required for students who earned an Based on experience, certain courses are CSE 568 Empirical Research Methods . . . 3 credits undergraduate degree in the United States, more beneficial when taken earlier or later MST 506 Special Topics ...... variable credits or who have worked for at least two years (special electives offered on a one-time in a student’s program of study. for a business where the primary business only basis) language is English. For more information It is strongly recommended that students MST 509 Commercialization Practicum . . . 3 credits on the computer-based score scale, please take MST 512, Project Management; MST 515 Supply Chain Management . . . . 3 credits visit www.toefl.org. MST 520, Managing Organizational MST 516 Global Logistics and Financial . . 3 credits Management Relationships; and MST 590, Effective GMAT or GRE scores are not required. MST 517 Supply Chain Management . . . . 3 credits Business Writing for Management or Advanced Modeling Part-time students may apply for admission MST 591, Effective Business Writing for MST 521 (D) Human Resource Management . . 3 credits to the M.S. in Management program during Non-native Speakers, as early as possible in Science and Technology any quarter. Full-time students are strongly in their studies. MST 523 New Product Development . . . . . 4 credits recommended encouraged to apply in the MST 524 eBusiness: Strategy and ...... 4 credits For the best possible Capstone experience, Roadmap winter or summer quarter and begin in the students form teams at least six months in MST 531 Software Commercialization . . . . 3 credits spring or fall quarter. advance of the quarter in which they plan to MST 542 Business Ethics and Corporate . . 3 credits Social Responsibility DEGREE REQUIREMENTS take MST 550 Capstone Project: Business MST 544 (D) Strategic Alliances ...... 3 credits Plan. Past Capstone students strongly recom- MST 549D Applied Business Forecasting . . 4 credits OGI offers a non-thesis M.S. in Management mend taking MST 573, Technology Marketing: MST 577 Principles for Process ...... 4 credits in Science and Technology. Students elect Planning for Market, late in their studies and Development and Introduction one of two areas of emphasis within the forming a Capstone team prior to completing to Manufacturing degree program: Managing the Technology MST 573 assignments. Elective MST 574, Students may petition the department for elective credit Company or Managing in the Software for other OGI academic courses relevant to the theory or Going to Market: Delivering Value to practice of management. Industries. Students must complete a Customers and Shareholders, is also highly minimum of 52 credits with an average recommended as a follow-on to MST 573, to GPA of 3.0 or better.

63 MST | MANAGEMENT IN SCIENCE & TECHNOLOGY

MANAGING IN THE SOFTWARE INDUSTRIES SEQUENCE MST 530D Strategic Management ...... 4 credits and Planning Core Sequence plus the following two courses are required (6 credits): MST 550D Capstone Project: ...... 4 credits Business Plan CSE 516 Introduction to Software . . 3 credits MST 571D Managerial and Financial ...... 4 credits Engineering Accounting for Science MST 531 Software Commercialization . . 3 credits and Technology Electives: Four of the following elective courses are MST 572D Financial Management for . . . . . 4 credits required (12–13 credits): Science and Technology CSE 514 Introduction to Database . . 3 credits MST 573D Technology Marketing: ...... 4 credits Systems Planning for Market MST 590D Effective Business Writing ...... 1 credit CSE 517 Software Engineering ...... 3 credits for Management Processes – OR – CSE 518 Software Design ...... 3 credits MST 591D Effective Business Writing ...... 1 credit and Development for Non-native Speakers CSE 519 Object-Oriented Analysis . . 3 credits and Design ONLINE MANAGING THE TECHNOLOGY CSE 560 Artificial Intelligence . . . . . 3 credits COMPANY SEQUENCE CSE 564 Introduction to Human . . . . 3 credits OGI currently offers the Managing the Technology Company Computer Interaction emphasis to students who take only online classes. The CSE 567 Developing User-Oriented . . 3 credits Online Core Sequence plus three of the following four Systems courses are required (9 credits): MST 511 (D) Quality Management . . . . . 3 credits MST 511D Quality Management ...... 3 credits MST 514 (D) Issues in R&D ...... 3 credits MST 514D Issues in R&D Management . . . 3 credits Management MST 522D Change Leadership for ...... 3 credits MST 522 (D) Change Leadership ...... 3 credits Building Effective Organizations for Building Effective Organizations MST 540D International Management in . . . 3 credits Science and Technology MST 540 (D) International Management . . 3 credits in Science and Technology Electives: Three elective courses, including any course in MST 541 Leadership and ...... 3 credits the above list not already taken and/or any of the following Communication Skills (9–10 credits): MST 574 Going to Market: ...... 4 credits MST 521D Human Resource ...... 3 credits Delivering Value to Customers Management in Science and Shareholders and Technology Students may petition the department head for elective MST 544D Strategic Alliances ...... 3 credits credits for other OGI academic courses relevant to the MST 549D Applied Business ...... 4 credits theory or practice of management. Forecasting Students may petition the department head for elective ONLINE DEGREE REQUIREMENTS credits for other OGI academic courses relevant to the theory or practice of management. The Department of Management in Science and Technology recommends that students take at least two on-campus courses. A proctored comprehensive exam may be required at or near the completion of the M.S. in Management Online degree requirements. Students must complete a minimum of 52 credits with an average GPA of 3.0 or better.

ONLINE MANAGEMENT IN SCIENCE AND TECHNOLOGY CORE SEQUENCE All online M.S. students must take the Management core sequence, consisting of the following courses or their equivalent (35 credits): MST 510D Principles and Trends ...... 3 credits in Technology Management MST 512D Project Management ...... 4 credits MST 513D Operations Management ...... 3 credits and Practices MST 520D Managing Organizational ...... 4 credits Relationships

64 F ACULTY | MANAGEMENT IN SCIENCE & TECHNOLOGY | MST FACULTY

JACK RAITON MARIANNE KOCH FRED YOUNG PHILLIPS NICOLE A. STECKLER Senior Fellow and Interim Visiting Associate Professor Professor Associate Professor Department Head Ph.D., Human Resource Ph.D. Management Ph.D., Organizational Behavior MBA, Finance and Statistics Management and Science/Business Administration Harvard University, 1990 University of Washington, 1967 Industrial Relations University of Texas at Austin, 1978 [email protected] [email protected] Columbia University, 1989 [email protected] [email protected] RESEARCH INTERESTS Having previously served as chief RESEARCH INTERESTS Information-sharing across financial officer of Planar Systems RESEARCH INTERESTS Market research, marketing organizational boundaries; leading and as corporate controller of The human side of technology innovation and high-technology organizational change; Tektronix, Jack brings a wealth of products, managing the new interpersonal communication and high-level management experience transfer; work/family policies and practices; coaching faculty in the product development process, influence in organizations; and in local industry to the MST incubation and commercialization tools for diagnosing and improving department. He is active in the development and teaching of e- learning courses. of new technologies, strategic and leadership effectiveness. leadership of the American innovative use of computers. Electronics Association and REPRESENTATIVE PUBLICATIONS: REPRESENTATIVE PUBLICATIONS Financial Executives International, REPRESENTATIVE PUBLICATIONS D.B. Drake, M.J. Koch, and N.A. M. Koch and D Moshavi, “The and serves on the Advisory Boards Steckler, “Scientist, Politician, and Adoption of Family-Friendly Policies F. Phillips, The Conscious Manager: Bureaucrat Subcultures as Barriers to of Compli, Inc, StoriedLearnings, in Family-Owned Firms: Paragon Zen for Decision Makers, General Information-Sharing in Government and two high tech start-ups. Jack or Paradox,” Proceedings of the Informatics, 2003. Agencies,” Proceedings of the 2003 earned his BS in Mathematics 2001 Southern Management L. Delcambre, T. Tolle, D. Maier, National Conference on Digital from Oregon State University in Association Annual Meeting, New F. Phillips, P. Toccalino, N. Steckler, Government Research, May 18-21, Orleans, LA, 2001. 1966 and his MBA in Finance and M. Koch, L. Shapiro, E. Landis, 2003, Boston, MA. Statistics from the University of M. Koch and G. Hundley, “The Effects B. Banga, S. Bowers, J. Brewster, N.A. Steckler and N. Fondas, of Unionism on Recruitment and A. Gutema, W. Howe, S. Murthy, Washington in 1967. He attended “Building Team Leader Effectiveness: Selection Practices,” Industrial J. Norman, R. Tummala, M. Weaver, Harvard University’s Advanced A Diagnostic Tool,” Organizational Relations, 36(3), 349–370, 1997. and K. Zillman. 2003. “Harvesting Management Program, and passed Information to Sustain our Forests.” Dynamics, 23, 20–35, Winter/Spring the CPA exam in 1979. M. Koch and R. McGrath, “Improving Communications of the ACM. 46(1): 1995. Labor Productivity: Human Resource 38-39. J. White, S. Jacobson, R. Jacques, Management Policies Do Matter,” 1996, AREAS OF EXPERTISE N. Fondas and N.A. Steckler, “You Strategic Management Journal, 17, F. Phillips, Market-Oriented Just Don’t Understand: Gendered Performance measurement, 335–354, 1996. (Awarded an Anbar Technology Management: Innovating Interaction and the Process of ‘Doing’ Electronic Intelligence Citation of for Profit in Entrepreneurial Times, capital structure, stock options Organizational Scholarship,” Journal of Excellence Award for 1997). Springer-Verlag, Heidelberg, 2001. and incentive plans, forensic Management Inquiry, 4(4), 370–379, accounting M. Koch, L. Long, and A. Meyer, F. Phillips and S. Tuladhar, “Measures December 1995. “Adoption of Innovations in Hospitals: of Organizational Flexibility,” N.A. Steckler and A. Donnellon, Exploring the Validity of a Multi-Stage Technological Forecasting & Social “Review of Peter K. Manning’s Model,” forthcoming, International Change 64/1, May 2000. ‘Organizational Communication’,” Journal of Technology Management; F. Phillips, L. Ochs and M. Schrock, Academy of Management Review, 18, also in Academy of Management Best “The Product is Dead; Long Live the 374–377, 1993. Papers Proceedings, August 1996. Product-Service,” Research Technology N.A. Steckler and R. Rosenthal, “Sex M. Koch. “Hiring Practices and Labor Management, 42(4), 51–56, July- Differences in Nonverbal and Verbal Productivity,” Garland Publishing, New August 1999. Communication with Bosses, Peers, and York, 1995. S. Thore, G. Kozmetsky and F. Phillips, Subordinates,” Journal of Applied “DEA of Financial Statements Data: Psychology, 70, 157–163, 1985. The U.S. Computer Industry,” Journal of Productivity Analysis, 5(3), 229, 1994. N.C. Ware, N.A. Steckler and J. Leserman, “Undergraduate Women: F. Phillips, “Conditional Information Who Chooses a Science Major?” Characterization of Brand Shifting in a Journal of Higher Education, 56, Hierarchical Market Structure,” 73–84, 1985. Journal of the Operational Research Society, 45(8), 901, 1994.

65 MST | MANAGEMENT IN SCIENCE & TECHNOLOGY | F ACULTY

ADJUNCT FACULTY KATHY LONG HOLLAND LongSherpa/Eco-D KEN ANTHONY MICHAEL MCLEAN Industrial Design AC Transit Construction (IDC) DEIRDRE MENDEZ JEAN-CLAUDE BALLAND Foreign Business JCB Associates Management Consultants GREG CHARLES RAJ MERCHANT ALVIN H. TONG Independent Consultant Strategy@work Professor MARK CHEN PAUL NEWMAN Ph.D., Electrical Engineering Softech Innovation LLC Cooper Mountain Research, Inc. University of Minnesota, 1967 [email protected] LINDA CRAFTS LYLE OCHS Cumulus Resources LLC Technology & Innovation Alvin Tong has 30 years of working Management, Inc. experience in the computer and TUGRUL DAIM related industries, which includes Intel Corporation JEFF OLTMANN serving as chief operating officer Synergy Professional Services of Acer, Inc., a Taiwan-based JERRY DAVIES manufacturer of personal EPIC Aviation, LLC JESSE REEDER Leadership Dynamics computers. While with Acer, he KATHY MANGEL DAVIS also served as President of Acer ADRIAN ROBERTS Venture, their venture capital arm. Professionally Speaking Independent Consultant Previously, he worked for 14 years DEAN DERRAH at IBM in New York as engineering RV Kuhns & Associates JAY SHUTTER and marketing manager. He also Momentum Research Group had a significant role as the first DAVID DRAKE Deputy Director-General of the Catalyst Communications, Inc. WILLIAM SEIDMAN Hsin-chu Science-Based Industrial Cerebyte, Inc. Park (SBIP) in Taiwan. Alvin has WILLIAM DRESSELHAUS conducted numerous management- Dresselhaus Design Group LESLIE SMID training seminars and is Waggener Edstrom TOM FLORA frequently invited to speak and THOI TRUONG lecture on the subject of OHSU – CFO, School of Medicine CNF Inc. globalization and high-tech RICHARD FOURNIER Science-Based Industrial Parks. Kaiser Foundation HARVEY UTECH Healthplans Northwest Independent Consultant REPRESENTATIVE PUBLICATIONS P. Schumann, D. Prestwood, A. Tong RICHARD GOLDGAR JOHN WALLNER and J. Vanston, Innovate!, McGraw-Hill, Texas Education Agency Tektronix, Inc. New York, 1994. STEPHEN GOMES ARTHUR WARD CEO2Inc. IBM JULIAN GRESSER LogosNet FRANK HALL EntreDigm Consulting ROBERT HARMON Portland State University JILL B. KELLY JK Editing RITA LAXTON IMMEDIAD’s ChildRom Productions DON LEWIS Lewis and Lewis Consulting

66 CROSS-INSTITUTIONAL PROGRAMS AND COURSES | OGI

CROSS-INSTITUTIONAL PROGRAMS OF STUDY IN SPOKEN APPLIED COMPUTING COURSES LANGUAGE UNDERSTANDING Applied computing (APC) courses provide PROGRAMS The research program of the Center the skills needed to accomplish AND COURSES for Spoken Language Understanding encompasses specific goals and provide prerequisite a broad range of speech technologies. knowledge for more advanced courses. Most courses at the OGI School of Such research is inherently Students should check with their advisors to determine whether these Science & Engineering are multidisciplinary, and the center brings together a team with expertise in signal courses should be taken and check applicable to a specific program processing, speech recognition, speech with their departments to determine of study. However, the following synthesis, dialog modeling, natural whether applied computing credit hours can be used to satisfy degree programs and subjects are not language processing, multimodal systems, linguistics and human- requirements in their programs identified with any one computer interaction. of study. department or program. These This program focuses on specific programs and courses are problem areas such as: multimodal, APPLIED MATHEMATICS COURSES relevant for students in various interactive reading tutors for children Applied math (MATH) courses provide with reading or hearing problems; departments and academic prerequisite knowledge for more robust methods for enhancing speech advanced courses. Students should programs, and are accessible in noisy environments; large check with their advisors to determine from more than one department. vocabulary recognition of continuous which, if any, of these courses are speech, as in broadcast news; unit needed for their programs of study selection and voice conversion for and check with their departments more realistic speech synthesis; to determine whether applied robust parsing and interpretation mathematics credit hours can be of spoken and multimodal input; used to satisfy degree requirements modeling of disfluencies in spontaneous in their programs of study. speech; and effective methods for dialog management. GENERAL EDUCATION COURSES The Center for Spoken Language Understanding participates in the General education (GEN) courses are master’s and Ph.D. programs of study provided as a service to the academic in the Departments of Biomedical community. They are intended to Engineering and Computer Science improve the general academic skills and Engineering. Students who are of participants. Credit hours earned interested in earning a master’s or from general education courses do Ph.D. degree in biomedical engineering, not usually apply toward degree computer science and engineering, requirements. Students should or electrical engineering, with check with their advisors concerning specialization in spoken language the desirability of taking general understanding, should consult the education courses. catalog information for those departments and consult an advisor in the Center for Spoken Language Understanding, the Department of Biomedical Engineering or the Department of Computer Science and Engineering.

OGI faculty advisors work closely with studentts to take advantage of the school’s cross-disciplinary educational opportunities. Here, MST professor Nicole Steckler counsels a prospective student. 671 concepts. Topics include stacks, queues, linked lists, are to provide the students with an overview of the COURSE DESCRIPTIONS trees, algorithms for searching and sorting, finite diverse opportunities for research and application, state automata, and concepts of computability and to foster development of critical analysis and think- Effective Fall quarter 2003, decidability. Topics from discrete math include sets ing, and to stimulate creative problem solving and and various types of relations (functions, graphs, research planning. Both faculty and students will the OGI School has renumbered trees, lattices), recursion and inductive proofs, present topics and lead discussions. Students will be many of its courses to better Boolean logic, relational algebra, predicate calculus, required to write a short paper that introduces a series and limits, and asymptotic behavior of topic and proposes an original project. align course numbers with the searching and sorting algorithms. Programming 1 credit, repetitive exercises are assigned throughout the course. Oregon Health & Science Prerequisites: APC 514 or equivalent knowledge of C BME 507b/607b Current Topics in Tissue Engineering University standard numbering or C++. 3 credits This course is a seminar course with both critical evaluations of papers in tissue engineering litera- scheme. To assist in relating the ture and guest speakers presenting their recent new course numbers to courses research. Specific topics will change with students’ BIOMEDICAL ENGINEERING interests and developments in the field. offered in the past, a course Prerequisites: Molecular and Cellular Biology for BME 501 M.S. Non-Thesis Research Biomedical Engineering. 1 credit, repetitive number crosswalk is available Supervised project research for Master’s students online at www.ogi.edu/schedule/ who are not pursuing a thesis. BME 507c/607c Readings in Neurology Variable and repetitive credit and Neuroscience crosswalk.shtml. This course is intended to develop skills in critical BME 502/602 Independent Study analysis of the basic and clinical neuroscience liter- Independent study allows a student to work one-on- 5xx Graduate courses offered primarily in ature through readings, presentations, and one with a faculty member on selected topic(s) of support of master’s programs. May be discussions. Topics will vary with the individual interest. Registering for independent study requires used towards a doctoral program as interests of the students and faculty and develop- pre-approval from the faculty member and the stu- ments in the field. 1 credit, repetitive appropriate. dent’s academic department. 6xx Graduate courses offered primarily in Variable and repetitive credit BME 511/611 Biochemistry for Biomedical Engineering The course will introduce the basics of biochemistry, support of doctoral programs. May be BME 503 M.S. Thesis Research emphasizing the chemical structure and physio- used towards a master’s program as Supervised original research towards a thesis for chemical behavior of biochemicals such as sugars appropriate. the Master’s degree. Variable and repetitive credit proteins, nucleic acids, water, various polymers and Master’s and certificate students should BME 504/604 Professional Internship other common components of cells and tissues. An overview of the basic metabolic pathways of cells register for the 5xx class and doctoral Professional internship credits provide students an and the integrated chemistry of different organs in students should register for the 6xx class opportunity to earn credit for relevant work experi- the whole body will be presented. A biochemical per- ence in industry. Students gain valuable industrial when available. spective on processing of biomaterials will be experience that allows them to both apply the presented, drawing examples from tissue engineer- knowledge gained in the classroom and prepare for ing and cooking. The goal is to give an introduction careers following graduation. Students on F-1 or J- APPLIED COMPUTING to biochemistry that enables the biomedical engi- 1 visas must obtain prior written approval for neer to better communicate with medical APC 514/614 Applications Programming in C++ internships from OGI’s Office of International researchers and clinicians, while also offering a (Formerly APC 505a and APC 505b) Students and Scholars before enrolling. Enrollment unique engineering perspective on the biochemical This course provides an introduction to program- requires a faculty advisor and is limited by the num- nature of biomaterials. 3 credits ming in C++, which is widely used for developing ber of internship opportunities available. engineering and business applications. This course Variable and repetitive credit BME 513/613 Biomedical Signal Processing I introduces students to the C++ language, and covers BME 505/605 Readings in Biomedical Engineering This series covers the analysis of biomedical signals. fundamental concepts such as classes, composition The first course introduces the basic tools for con- This course is designed to teach critical evaluation of and inheritance, polymorphism, virtual functions, tinuous- and discrete-time signal analysis and information in the field of Biomedical Engineering. overloading and overriding, abstract classes, pure modeling: Laplace and continuous-time Fourier Students will read articles and papers on timely top- virtual functions, streams, exceptions, operator transform, z-transform and discrete time Fourier ics related to the student’s area of interest. Students overloading and templates. The course is suitable transform, Fourier series, discrete Fourier trans- will be required to present a summary of the read- for students in engineering, science and finance who form, continuous time filter design, FIR and IIR filter ings to the class. 1 credit, repetitive wish to gain an understanding of the language. On design, wavelet transform. Applications areas cov- completion, students will be in a position to con- BME 506/606 Special Topics ered are ECG, IEGM, blood pressure measurement, tribute to the design and development of systems cardiac impedance measurement, and heart rate Special topics courses are offered in areas of par- using the main features in C++. Assignments include variability. Tool: MATLAB with Simulink. ticular relevance to the research interests of faculty writing programs and a programming project. Prerequisites: undergraduate signal and system or in response to industry needs. Special Topic Prerequisites: Knowledge of a programming language. course covering Laplace and Fourier transform. courses are subject to change and are offered 3 credits 3 credits intermittently. Variable and repetitive credit APC 515/615 Data Structures and Discrete Mathematics BME 507a/607a Biomedical Engineering Seminar BME 514/614 Biomedical Instrumentation — This course covers fundamental topics in data struc- Signals and Sensors This seminar course will feature presentations and tures and discrete mathematics. The topics are This course covers the concept and application of discussions on topics in biomedical engineering that presented in an integrated manner that provides the instrumentation techniques to biomedical subjects. exemplify the wide range of applications of biomed- discrete math foundations for data structures and Areas studied will include biopotentials, sensors, computing applications of discrete mathematics ical engineering to science and medicine. The goals 69 OGI | COURSE DESCRIPTIONS

stimulators, amplifiers, filters, displays, safety, and Green’s function and finite difference techniques will essary to perform advanced research in Tissue instrument design. This course includes a laborato- model thermal and water diffusion, surface evapo- Engineering. Techniques include the latest in imag- ry and a design project. Prerequisites: Calculus ration, and explosive vaporization. Arrhenius rate ing, stem cell isolation, growth factor treatments through differential equations. 3 credits process calculations will model thermal damage, and mechanical stimulation of engineered tissues. thermoelastic expansion and velocity potential mod- Prerequisites: BME 511/611 Molecular and Cellular BME 522/622 Biomedical Optics I: Tissue Optics els will simulate pressure wave generation and Biology for Biomedical Engineering, BME 541/641 Light propagation in tissue: This course treats propagation, spallation/cavitation models will model Biomaterials I, and BME 542/642 Biomaterials II. light transport in scattering and absorbing media initiation and growth of laser-induced material 3 credits such as biological tissue. Light transport is modeled defects leading to fragmentation. These methods using a variety of theories and computational tech- provide a tool kit for handling a wide variety of laser BME 544/644 Advanced Biomaterials niques, including Monte Carlo simulations and effects in biological tissues. 3 credits This course is a seminar-style course in which stu- approximate solutions of the radiative transport dents critically evaluate key papers in the equation. Steady- state and time-dependent prob- BME 527/627 Computational Approaches to Light biomaterials literature. Specifics topics will change lems are treated. Spectroscopy and fluorescence Transport in Biological Tissues with developments in the field as well as with the measurements are introduced. Optical imaging Understanding the movement of light through com- students’ interests. Students may take this course techniques are presented. Students learn the basics plex biological tissues or other complex media is the more than once. Prerequisites: BME 541/641 required for design of optical devices for therapy first step in design of optical devices or clinical pro- Biomaterials I and BME 542/642 Biomaterials II. and diagnostics. 3 credits tocols in medical applications of lasers and light. 3 credits This course will use various computational methods BME 523/623 Biomedical Optics II: to simulate such light propagation: (1) wave theory BME 545/645 Biocompatibility: Laser-Tissue Interactions to discuss the early loss of coherence and polariza- Host-Implant Interactions Physics of laser-tissue interactions: The course tion as light initially enters tissue; (2) small angle This course provides the student with a firm under- treats the immediate physical processes that scattering to discuss the transition of ballistic pho- standing of how the body reacts to implanted accompany the absorption of light by biological tons into scattering photons; (3) Monte Carlo biomaterials at the cell, tissue, organ, and systemic tissues, including photochemical reactions, heating simulations to discuss a variety of issues in energy levels. In addition, specific characteristics that hin- and tissue coagulation, vaporization, creation of propagation, including irregular boundary condi- der or improve the biocompatibility of materials will plasmas, and production of stress waves in tissue. tions; (4) diffusion theory to predict light fields be addressed. Prerequisites: BME 511/611 Such processes are modeled using finite-difference distant from sources; (5) perturbation theory to Molecular and Cellular Biology for Biomedical techniques. Applications in medicine and biology approximate optical heterogeneities with absorption Engineering and BME 542/642 Biomaterials II. are discussed. Prerequisite: BME 522/622 and scattering properties that vary from the back- 3 credits Biomedical Optics I, or permission of instructor. ground medium properties. These methods provide a 3 credits tool kit for handling a wide variety of optical prob- BME 561/661 Neuronal Control Systems lems encountered in design of optical systems This course explores various neuronal control sys- BME 524/624 Biomedical Optics III: Engineering Design involving tissues. 3 credits tems from an engineering perspective. Topics The students work as a team in preparing five include: control system theory; neuronal plasticity business plans throughout the quarter. Each busi- BME 528/628 Physical and Geometrical Optics and state dependence; sympathetic nervous system ness plan is devoted to a potential medical device or First-order Gaussian optics and thin-lens system control of cardiovascular functions, temperature, protocol using optical technologies. The team is layout. Photometric theory applied to optical sys- and respiration; and vestibulooculomotor control. divided into a CEO, scientific officer, marketing tems. Topics include: the eye, magnifiers, 3 credits manager, regulatory affairs manager, and manufac- microscopes, matrix optics, Seidel aberrations, turing manager. The roles are rotated amongst the scalar diffraction theory; Fresnel and Fraunhofer BME 562/662 Motor Control students for each business plan. Feasibility studies diffraction, and interferometry. 3 credits This course is intended to introduce the student to are conducted in a laboratory exercise designed by simple and complex mechanical, electronic, and dig- the students. The team formally presents a business BME 541/641 Biomaterials I ital control systems using human and animal plan every two weeks. Prerequisite: BME 523/623 The first of a two part series aimed at a graduate skeletomuscular systems and robotics as model sys- Biomedical Optics II, or permission of instructor. level introduction to the composition, properties, tems. The course will consist of three parts: first, 3 credits manufacture, design and application of synthetic the physiology and neural control of the neuromus- and naturally derived materials for the replacement cular system; second, control problems faced in BME 525/625 Optical Nondestructive Evaluation or augmentation of human tissue. Biomaterials I is designing robots with complex mechanical systems This course is aimed at introducing the field of opti- focused on a rigorous treatment of elastic and vis- and the relation to problems faced by the mam- cal NDE to engineering students. The course focuses coelastic theory, the mechanics of natural hard and malian motor control system; third, background and primarily on coherent light techniques such as inter- soft biological tissues, and numerical methods for design of clinical devices and procedures for motor ferometry, holography, and laser speckle methods. materials evaluation. 3 credits disorders, including stroke, spinal cord injury, bal- Moiré, photo-elastic, and structured light methods ance disorders, and neuroprostheses. 3 credits are also discussed. Specific applications to biomed- BME 542/642 Biomaterials II ical engineering, semiconductor, and electronic This is the second course in a two-class sequence on BME 563/663 Mathematic and Computational Modeling materials will be presented. 3 credits biomaterials. Biomaterials II covers an in-depth of Neuronal Systems analysis of specific materials used for implantatio This course introduces mathematical and computa- BME 526/626 Computational Approaches to Laser within the human body. Topics that will be covered tional techniques for modeling the dynamics of Interactions with Biological Tissues include biocompatibility, tissue engineering for hard biological systems. Topics will include analytical, Lasers and light from alternative conventional and soft tissues, applications of metals, ceramics numerical, and agent-based simulations using ordi- sources interact with biological tissues or other and polymers, and finite-element methods for bio- nary and partial differential equations, stochastic complex media through photochemical, photother- materials evaluation. Prerequisite: BME 541/641 dynamics, and discrete methods. Applications will mal and photomechanical mechanisms. This course Biomaterials I. 3 credits be drawn from topics including neural dynamics at will employ computational methods to simulate the cellular and circuit level, circulation, respira- interaction of lasers with tissues. Compartmental BME 543/643 Advanced Tissue Engineering Techniques tion, and immune system response, molecular modeling will model photochemical interactions. This course is designed to teach the techniques nec- evolution, enzyme kinetics, and development.

70 COURSE DESCRIPTIONS | OGI

Discussion will include techniques for validating els to engineering problems. The anthropomorphic BME 603 Ph.D. Dissertation Research models and for incorporating experimental data, and (human-like) signal processing approach is illustrat- Research toward the dissertation for the Ph.D. the roles of simulation and theory in the effort to ed on engineering models of perceptual phenomena. degree occurring after passing the qualifying exam. understand biological systems. 3 credits 3 credits Variable and repetitive credit

BME 564/664 Methods in Neuromedicine BME 571/671 Speech Systems This course includes topics on methods related to Speech is one of the most natural means for com- the diagnosis, treatment and intraoperative assess- munication and carries information from many COMPUTER SCIENCE & ENGINEERING ment of the nervous system in humans. Topics sources. The explosive growth of communications include: electrical stimulation (neuronal excitability, and computer technologies puts new demands on CSE 501 M.S. Non-thesis Research diagnostic testing of nerves and brain structures, techniques for machine extraction of information (Formerly CSE 610) surgical monitoring, neuronal rehabilitation, and content of speech signals, for its storage or trans- Supervised research for up to 6 credits as a compo- functional electrical stimulation); safety (coupling to mission, and for reconstruction of the speech signal nent of the non-thesis master’s degree. Students are biological tissues, excitotoxicity, neuronal vulnera- from its parametric representation. The course cov- required to produce concrete research deliverables, bilities, and special considerations with disease ers techniques for processing of speech signal used including a final report equivalent to a CSE techni- states); drug targeting; blood brain barrier; and for speech coding and synthesis, enhancement of cal report. Each 3 credits of CSE 501 may count as basic neuro-imaging. 3 credits degraded speech, speech recognition, speaker one class to fulfill the M.S. non-thesis graduation recognition, and language identification. 3 credits requirements. Variable and repetitive credit BME 565/665 Introduction to Computational Neurophysiology BME 572/672 Speech Synthesis CSE 502/602 Independent Study Overview of basic cellular neurophysiology, includ- This course will introduce students to the problem of Independent study allows a student to work one-on- ing action and membrane potentials, channels and synthesizing speech from text input. Speech synthe- one with a faculty member on selected topic(s) of channel blockers, gates, and ion pumps. Biophysical sis is a challenging area that draws on expertise interest. Registering for independent study requires models of the neuron including Hodgkin-Huxley and from a diverse set of scientific fields, including sig- pre-approval from the faculty member and the stu- Cable models. Models of synaptic function and plas- nal processing, linguistics, psychology, statistics, dent’s academic department. ticity. Central pattern generators and simple and artificial intelligence. Fundamental advances in Variable and repetitive credit invertebrate circuits. Organization of receptive each of these areas will be needed to achieve truly CSE 503 M.S. Thesis Research fields and topographic neural maps. Models of “human-like” synthesis quality and advances in (Formerly CSE 700) neural development, ocular dominance, and orienta- other realms of speech technology (like speech Research toward the thesis for the M.S. degree. tion columns. 3 credits recognition, speech coding, speech enhancement). Variable and repetitive credit In this course, we will consider current approaches BME 566/666 Biomedical Signal Processing II to sub-problems such as text analysis, pronuncia- CSE 504/604 Professional Internship The course covers advanced techniques of digital tion, linguistic analysis of prosody, and generation (Formerly CSE 620) signal processing for solving biomedical signal prob- of the speech waveform. Lectures, demonstra- These courses provide an opportunity to earn credit lems. Time and frequency domain filtering tions, and readings of relevant literature in the area for relevant work experience in industry. Students tech-niques, adaptive and optimal systems, detec- will be supplemented by student lab exercises using gain valuable industrial experience that allows them tion of biomedical waveforms, spectral estimation the Festival text-to-speech system and other hands- to both apply the knowledge gained in the classroom and system modeling are covered. Applications to on tools. 3 credits and prepare for careers in computer science. A problems in ECG and EEG are featured. written report must be submitted to the CSE faculty Prerequisites: BME 513/613 Biomedical Signal BME 581/681 Fourier Analysis advisor at the end of the experience. Enrollment Processing and I and EE 582/682 Introduction to Fourier analysis is used in nearly every field of engi- requires a faculty advisor and is limited by the num- Digital Signal Processing. 3 credits neering, including biomedical engineering. It ber of internship opportunities available. provides a unifying mathematical approach to the 1 to 3 credits per quarter BME 567/667 Visual Sensory Systems study of networks, electrical and mechanical sys- In this course, the anatomy, physiology and function tems, linear systems, image and signal processing, CSE 506/606 Special Topics of visual systems are examined with emphasis on as well as many other systems. This course will pro- (Formerly CSE 58X) the dynamic processing of visual inputs and on tech- vide a solid introduction to application of Fourier Under this number, we offer courses of particular nological approaches to functional analysis and on theory in biomedical engineering. Topics include: relevance to the research interests of faculty or in methods for diagnosis of eye diseases. Topics to be convolution and correlation; Fourier theorems; state-of-the-art subjects of interest to the communi- covered include optics, anatomy of the eye, retinal Numerical transforms; Sampling and series; ty. Some recent offerings include: physiology, signal processing, plasticity, perception, Discrete Fourier transform and the FFT; Related Advanced Functional Programming functional assessment with complex visual stimuli transforms. Prerequisites: one year of calculus. Building Secure Systems and evoked potentials, and new developments in 3 credits Formal Verification of Software visual prosthetic systems. 3 credits BME 599/699 Reciprocity Course High Assurance Software Engineering Information Integration BME 568/668 Auditory and Visual Processing by OGI students admitted to a degree program have the Information Retrieval on the Internet Human and Machine opportunity to take classes at other Oregon Internet Technology Interaction between humans and machines could be University System schools under the Joint Campus Networking Practicum greatly enhanced by machines that could communi- Agreement or Reciprocity Agreement. Contact the Principles of Database Systems cate using human sensory signals such as speech Department of Graduate Education for details. 3D Graphics and gestures. Knowledge of human information pro- Courses taken under these agreements are listed as Real-time Rendering Using Modern Graphic cessing including audition, vision, and their 599/699. Variable and repetitive credit combination is, therefore, critical in the design of Architecture effective human-machine interfaces. The course BME 601 Prequalifying Ph.D. Research Scientific Visualization introduces selected phenomena in auditory and Supervised Ph.D. research prior to passing the Security Protocols visual perception, and motor control. Students learn department’s qualifying exam. Web Data Management how to interpret empirical data, how to incorporate Variable and repetitive credit these data in models, and how to apply these mod- 71 OGI | COURSE DESCRIPTIONS

CSE 511/611 Principles of Compiler Design file systems, distributed transaction processing, We adopt a use case model for requirements and a This course introduces the basics of building a com- load balancing, distributed programming languages responsibility-driven approach for the development piler using a multiphase translation process. It and systems, fault-tolerance and replication algo- of object models. Design patterns and frameworks covers lexical analysis, parsing and translation to rithms, distributed timing issues and distributed are also emphasized. Note that CSE 529/629 Object- abstract syntax using modern parser generator algorithms. Prerequisites: CSE 513, Introduction Oriented Programming is intended as a follow-on technology. It discusses binding of identifiers and to Operating Systems as well as a basic under- course for CSE 519/619. 3 credits symbol table organization, and a variety of interme- standing of computer communications problems diate representations that are suitable for back-end and protocols. 3 credits CSE 520/620 Software Architecture analysis. It investigates back-end transformations The architecture of a software system specifies the and optimizations for a number of languages. Other CSE 516/616 Introduction to Software Engineering components, visible properties of the components, topics include type checking, static analysis and (Formerly CSE 500) and the structural and behavioral relationship basic run time support. Compiling is essentially a Software engineering is concerned with the ways in among the components of a software program or process of symbolically manipulating program rep- which people conduct their work activities and apply system. There are many different architectural resentations represented by tree and graph-like technology to produce and maintain software prod- styles, including pipes and filters, layers, client- data structures. Because of this, we will use tools ucts and software-intensive systems. Issues of server, OO frameworks, embedded-systems, that facilitate symbolic manipulation and definition concern include specification, design, implementa- plug-and-play, remote procedure call, and data-driv- of such structures as parser and lexical generators, tion, verification, validation and evolution of en architectures. Different styles satisfy different and tools for generating code from pattern-based software artifacts. Related topics include software constraints and influence the system’s performance, descriptions. Prerequisite: CSE 533. 3 credits metrics, project management, configuration man- reliability, safety, security, and other quality-of- agement, quality assurance, peer reviews, risk service attributes. Systematic architectural design CSE 512/612 Compiling Functional Languages management and process improvement. This course facilitates software reuse and the development of A project-oriented course on the theory and design presents an integrated view of these topics and product families. In this course, we will study archi- of a compiler for a typed, functional programming related issues. It is an essential course for anyone tectures and architectural styles from both the language. Topics include understanding a formal working in development, maintenance, management structural and behavioral viewpoints. In addition, definition of programming language semantics, com- or related areas in a software organization. we will examine design methods and tools for devel- piling pattern analysis, lifting abstractions, 3 credits oping software architectures. Students will learn continuation-passing style of implementation, the strengths and weaknesses of various architec- abstract machines, code generation and address CSE 517/617 Software Engineering Processes tures and will understand the circumstances under assignment, register allocation and assignment on (Formerly CSE 503) which various architectural styles might be used. general-register machines, run-time storage admin- This course is concerned with examining and The course will include lectures plus reading and istration, data-flow analysis and code improvement. improving the software development processes, discussion of papers from the literature of software Prerequisite: CSE 511. 3 credits including the technical, managerial and cultural architecture. Each student will conduct an in-depth processes, used by organizations to develop and investigation of an architecture or architectural CSE 513/613 Introduction to Operating Systems maintain high-quality software systems in a timely style and prepare a term paper based on the inves- A study of the design and implementation of modern and economical manner. Various process models, tigation. Prerequisites: Prior knowledge of UML is operating systems. The course concentrates on including the SEI Capability Maturity Models, the desirable but not required. 3 credits operating system kernel design and includes the fol- ISO SPICE model, the Team Software Process, and lowing topics: concurrent processes, interprocess the Personal Software Process are studied and con- CSE 521/621 Introduction to Computer Architecture communication, synchronization, scheduling, trasted. Tailoring of process models to fit local This course provides a broad introduction to com- resource allocation, memory management, the con- situations and various approaches to software puter architecture. It covers a large amount of cept of virtual memory and the required underlying process improvement are presented. Students material in moderate depth, providing a good under- hardware support, secondary storage management, select and complete term projects that address top- standing of the basic issues in computer system file systems and security. We will use the Linux ics in software process improvement. 3 credits design. Specifically, the course covers instruction operating system to ground the discussion of set design, pipelining, the memory hierarchy, I/O abstract concepts. Interested students will be CSE 518/618 Software Design and Development systems, networking issues and multiprocessors. encouraged to read the Linux source code for dis- Contemporary, object-oriented software design, Example systems include the Intel x86, MIPS and cussions in class. 3 credits using the Java programming language. An introduc- DEC Alpha processors. Prerequisites: Experience tion to the eXtreme Programming software writing software, preferably with some C or assem- CSE 514/614 Introduction to Database Systems development methodology, which is based upon the bler programming. NOTE: Computer architecture A survey of database fundamentals emphasizing the principle that change is inevitable and successful has become a quantitative science, so there will be use of database systems. Topics include database software designs undergo continual evolution. considerable algebraic manipulation involved in the design, data dependencies and normalization, sec- Techniques to be covered include program refactor- performance analysis component of the course. ondary storage structures, SQL, relational algebra, ing, automated unit testing, pair programming, 3 credits query processing, query optimization, transactions, participatory design and managing short product recovery and embedded SQL. This course focuses on development cycles. These principles and tech- CSE 522/622 Advanced Computer Architecture relational database systems and the SQL query lan- niques will be illustrated in a term-length project This course is a follow-up to CSE 521/621. It covers guage. Students participate in a project to design, that provides design and implementation experience. advanced computer architecture topics such as SMP populate and query a database. Prerequisites: 3 credits (Shared Memory Multiprocessors) and NUMA (Non- Data structures, discrete mathematics and mathe- Uniform Memory Access) Architectures. It also matical logic. 3 credits CSE 519/619 Object-Oriented Analysis and Design looks at new trends in designing high-performance (Formerly CSE 504) clusters with examples. Specific topics to be cov- CSE 515/615 Distributed Computing Systems This course presents an integrated set of techniques ered include: fundamentals of parallel architectures This course concentrates on distributed computing for software analysis and design based on object- (communication paradigms, programming models, from a systems software perspective. Major topics oriented concepts. The techniques focus on etc.), snoopy-based multiprocessors (cache include communications middleware (remote proce- producing the artifacts and work products, coherency, bus designs, multilevel caches, etc.), dure call, remote method invocation and causal expressed in UML, appropriate for the analysis and directory-based multiprocessors (NUMA and hybrid broadcast), operating system support, distributed design phases of the software development lifecycle. architectures), interconnection networks (routing,

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switch designs, virtual lanes, etc.). Examples of security enhancement to the principles of secure solve recursive equations. The course is designed commercial and prototype architectures such as systems. Prerequisite: CSE 513. 3 credits for students interested in the mathematical founda- IBM NUMAQ, InfiniBandTM and ServerNet. tions of programming languages and programming Prerequisite: CSE 521/621. 3 credits CSE 528/628 Cryptography logics. Prerequisite: Discrete mathematics. This course covers the major modern cryptographic 3 credits CSE 524/624 TCP/IP Internetworking Protocols techniques — the core technology for the area of This course provides an overview of the structure information security. We start with an overview of CSE 532/632 Analysis and Design of Algorithms and algorithms used in the TCP/IP networking pro- classical cryptography and information theory. Then An introduction to the design and analysis of algo- tocols that make up the foundation of the Internet. we examine in-depth the most widely used cryp- rithms. The course covers design techniques, such Protocols and technologies covered will include an tosystems: symmetric systems such as DES (Data as dynamic programming and greedy methods, as introduction to the link layer, ARP, IP, ICMP, UDP, Encryption Standard) and AES (Rijndael, the new well as fundamentals of analyzing algorithms for TCP, routing protocols and application protocols and standard), and public-key systems, notably RSA. correctness and time and space bounds. Topics systems like the DNS, NFS, SMTP, FTP, HTTP and Discrete log systems and standard digital signature include advanced sorting and searching methods, multicasting protocols and applications. Provides schemes are also covered, including elliptic curve graph algorithms and geometric algorithms. Other architectural insight into protocol design issues and cryptography. The course should be accessible to any- areas vary from year to year and may include com- operating system implementation techniques, typi- one who is willing to encounter some number theory. putational geometry, matrix manipulations, string cally in terms of the Berkeley UNIX socket 3 credits. and pattern matching, set algorithms, polynomial programming model. Provides socket programming computations and the fast Fourier transform. Pre- experience with the client/server model. Provides CSE 529/629 Object-Oriented Programming requisites: Data structures and discrete mathematics. experience reading Internet RFC’s and/or drafts. (Formerly CSE 509) 3 credits Prerequisites: Familiarity with the functions of a This course provides a rigorous introduction to the modern multiuser operating system such as is cov- concepts behind object-oriented programming. It is CSE 533/633 Automata and Formal Languages ered in CSE 513/613 or PSU’s CS 533; familiarity for students who are already familiar with the con- Automata theory introduces fundamental models with C programming on modern UNIX computers. cept of object-orientation and with object-oriented that are used over and over again in computer sci- 3 credits analysis and design techniques. One way to learn ence for programming languages, in compiler this background material is by taking CSE 519/619, construction and in algorithms. These models are a CSE 525/625 Advanced Networking Object-Oriented Analysis and Design. In CSE 509, valuable part of the repertoire of any computer sci- This course is a seminar-style course targeted at students gain a thorough understanding of incre- entist or engineer. This course introduces learning about advanced Internet technology and mental programming, type-safety, polymorphism, progressively more powerful models of computation, Internet research. In particular, we will choose from encapsulation and set-based abstraction, and apply starting with finite automata and moving through a range of contemporary papers and topics dealing these concepts through a variety of programming counter, stack and Turing machines. It also presents with gigabit switching and routing, web switching, projects. We study several programming languages, the regular, context-free, recursive and recursively firewalls, traffic engineering, MPLS, lambda switch- including Java and Smalltalk, so students are enumerable languages and shows how they corre- ing, issues in wide-area networking, internet exposed to different realizations of these concepts spond to the various models of computation and to routing, packet classification, fast IP routing and gain an appreciation for the programming lan- generation mechanisms such as regular expressions lookups, content-addressable networks, peer-to-peer guage design space. We also look at published and grammars. The emphasis is on understanding networking, wireless networking, Internet mapping object-oriented design patterns and see how they the properties of these models, the relationships and measurement, content distribution networks, can be implemented in different object-oriented pro- among them and how modifications such as nonde- overlay networks, sensor networks, ad hoc networks, gramming languages. Students are required to read terminism and resource bounds affect them. The power-aware networking, intrusion detection sys- appropriate research papers, complete several course includes application of these concepts to tems, distributed denial of service attacks and short programming assignments, complete a sub- problems arising in other parts of computer science. prevention, web and application server technology, stantial programming project and write some short Prerequisite: Discrete mathematics. 3 credits browser technology, and web cashing. Prerequisites: essays. Prerequisite: CSE 519/619 or equivalent. CSE524 TCP/IP Internetworking Protocols. 3 credits 3 credits CSE 534/634 Computability and Intractability Computability and complexity theory identify class- CSE 526/626 Advanced Topics in Operating Systems CSE 530/630 Introduction to Mathematical Logic es of languages based on characteristics of This course includes an in-depth study of modern Provides a theoretical foundation for the logic of machines that recognize them. The course presents operating system design. The course is based on computation. Propositional and first-order predi- elementary results from recursive function theory, reading recent research papers, and includes an cate calculi, soundness and completeness, including recursive and recursively enumerable emphasis on evaluating the papers in addition to incompleteness and incomputability, the Church- sets, and degrees of undecidability. Using recursion understanding the systems they describe. Topics Turing thesis, term-rewriting systems and appli- theory as a model, it develops the classical results vary from year to year but typically include micro- cation to program verification. 3 credits of complexity theory, including time and space com- kernel operating systems, lightweight inter-process plexity classes, hierarchy theorems and elementary communication, extensible operating systems, file CSE 531/631 Foundations of Semantics results from parallel complexity. The course con- systems, mobile computing, ubiquitous computing, Formal semantics aims to answer two important cludes by studying classes of problems that are workstation clusters, adaptive resource manage- questions: 1) when are two programs equal and 2) provably intractable, with a particular emphasis on ment, and OS support for multimedia applications. when does a program faithfully implement a mathe- NP-complete problems. Prerequisite: CSE 532 or Prerequisites: CSE 513 and CSE 521. 3 credits matical specification? The course explores CSE 533. 3 credits denotational semantics, operational semantics and CSE 527/627 Principles and Practices of System Security program logic, studying how they are related and CSE 535/635 Categories in Computer Science In the Internet age, host system security is essential how they can answer the motivating questions. Category theory provides a powerful and concise and difficult. This course explains the principles and Programming language concepts, such as impera- notation for abstract properties of functions. practices of securing host systems. Students learn tive programming, functional programming, Originally developed for algebraic topology, it has the principles of how to build secure systems and call-by-name, call-by-value and continuations, are found widespread application in computer science. how various real systems succeed and fail in living contrasted and explained in terms of their semantic This course introduces the basic notions of category up to these principles. We will study various securi- foundations. Key concepts include full abstraction theory, including functors, natural transformations, ty- enhancing technologies, in each case relating the and the use of least fixed-point constructions to products, sums, limits, colimits, monads and

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adjunctions. These concepts are illustrated with CSE 514; UNIX and C programming experience is tern recognition applications and technologies, and examples from computer science and mathematics, strongly recommended. 3 credits apply principles to real-world examples. The including the relationship between Cartesian closed emphasis is on developing theoretical and practical categories and the lambda-calculus. Familiarity with CSE 542/642 Object Data Management tools that provide grounding in pattern recognition discrete mathematics is an essential prerequisite. A variety of products for managing object data problems and methods, rather than on showcasing 3 credits have emerged in the marketplace. Object-oriented particular technologies. The course will benefit database systems and persistent programming lan- those whose work may use any of a variety of recog- CSE 536/636 Functional Programming guages have been joined by object-relational nition technologies in broad-ranging applications (Formerly CSE 502) databases and middleware component technologies, such as speech and image processing, data mining, In functional programming, we shift our focus from such as Enterprise Java Beans. Other storage finance. Topics include: random vectors, detection data objects and their representations to functions engines, such as LDAP and XML servers, have an problems (binary decision problems), likelihood that act on data. Programs are formulated as com- object flavor. This course begins with the concepts ratio tests, ROC curves, parametric and non-para- positions of functions, rather than as sequences of in types, data models and languages that underlie metric density estimation, classification models, statements. This leads to a programming methodol- object data management. It then looks at example theoretical error bounds and practical error estima- ogy that is quite different from that learned in using prototype and commercial systems, and examines tion through cross-validation. Maximum likelihood statement-oriented languages. This course intro- design dimensions such as data model, persistence, and Bayesian parameter estimation, model-based duces the student to functional notation, recursion, encapsulation, hierarchies, query languages and clustering, feature extraction for dimensionality higher-order functions, reasoning about functions transactions. It touches on application development reduction and for classification. 3 credits and polymorphic-type systems. Functional program- and data management issues and concludes with ming languages are known for their increased treatment of software architecture, implementation CSE 550/650 Spoken Language Systems productivity and reliability, due in part to the higher and benchmarking techniques. Students will do a Spoken language systems will revolutionize how levels of abstraction provided by functional lan- project using a commercial product. Prerequisite: people interact with machines, replacing the key- guages. Course is taught by lecture with small CSE 514 or other introductory database course. board and mouse with natural conversations. These weekly programming assignments. Experience is 3 credits systems will act like helpful human assistants and gained by programming in the functional language teachers for information access, commercial transac- Haskell or one of its close derivatives. Recent CSE 545/645 Advanced Neural and Adaptive Algorithms tions, and learning. You’ll review the state of the art advances in functional programming languages An advanced treatment of architectures and algo- in building spoken language systems. You will gain allow them to use updatable state in a safe manner rithms for pattern recognition, regression, hands-on experience using toolkits for building such and to cause effects on the real world. Students gain timeseries prediction and data mining. Typical top- systems, as well as learn the technologies needed for experience by writing programs using these features ics include convergence, effects of noise, next-generation systems, such as robust parsing, to program interactive window-based programs optimization methods, probabilistic framework semantic processing, dialogue management, and using an embedded “widget” library. 3 credits (including Bayesian estimation), generalization abil- agent architectures. Class projects will be done using ity and regularization and pruning, Hebbian learning the CSLU toolkit, Tcl/Tk, and VoiceXML. 3 credits CSE 540/640 Neural Network Algorithms and clustering and density modeling. Prerequisite: and Architectures CSE 540 or instructor permission. 3 credits CSE 551/651 Structure of Spoken Language This course introduces the fundamentals of connec- Speech is considered a key component in the future tionist and neural network models. Paradigms for CSE 546/646 Data and Signal Compression of human-computer communication. However, the supervised, unsupervised and reinforcement learn- The need for signal and data compression is ubiqui- success of speech recognition and text-to-speech ing are covered. Topics include LMS and tous in image, video and speech processing, finance synthesis systems depends on development of the backpropagation algorithms, network optimization and computational science. Where data stores technology as well as further research advances. techniques, theoretical and practical tools to become very large (e.g. video, finance, earth sci- Research and development of spoken-language tech- address generalization and complexity control, prin- ence), the need is not met by simple lossless file nology is facilitated by an understanding of the cipal components and independent component compression schemes, and we must turn to sophis- acoustic and symbolic structure of language, as well analysis, mixture models and clustering. The course ticated coding techniques. This course addresses as the capabilities and limitations of current sys- aims to develop the student’s statistical understand- both the theoretical basis and practical algorithms tems. This course will present some of what is ing of the use of neural network techniques. for data and signal compression. Topics include loss- known about speech in terms of phonetics, acoustic- Applications to classification, time series predic- less entropy-based coding, including Huffman and phonetic patterns, and models of speech perception tion, regression and data clustering are treated Lempel-Ziv, and lossy compression techniques and production. The goals are for the student to using real world data. 3 credits including scalar quantizers, transform coding understand how speech is structured, understand (Karhunen-Loeve, DCT and nonlinear transform and identify acoustic cues (especially in different CSE 541/641 Database Implementation codes), predictive coding, vector quantization, phonetic contexts), and understand how this infor- This course explores the internals of relational adaptive codes and wavelets. The relation between mation may be relevant to automatic speech database management systems. This course will compression schemes and probabilistic data recognition or generation systems. 3 credits give students a strong grounding in the design modeling is emphasized in conjunction with each tradeoffs and implementation issues that are technique. Application to speech, image and video CSE 552/652 Hidden Markov Models for addressed by large database systems. The course coding are discussed. Students will have the Speech Recognition will also help DBA’s understand how the tuning opportunity to design compression schemes for (Formerly ECE 580-HMM) parameters of commercial databases can affect such diverse applications as earth science data, Hidden Markov Model-based technology is used performance, and will help database application finance, speech or video, depending on their inter- widely in today’s speech recognition systems. This programmers to create applications better tuned to ests. Prerequisites: Undergraduate calculus, course is an introduction to speech recognition take advantage of the database internals. Typical introductory probability and statistics, some pro- using HMM technology. Topics include the theory of topics discussed include file and index implementa- gramming experience. 3 credits Hidden Markov Models (discrete, semi-continuous, tion, buffer management, query processing, and continuous) and their applications to speech cost-based query optimization, concurrency con- CSE 547/647 Statistical Pattern Recognition recognition, along with the basic mathematics trol, transaction processing, and logging and Theory and practice of statistical pattern recogni- (probability theory, statistics, stochastic process, recovery implementations. The class includes tion. Students will learn fundamental theory and information theory, and signal processing) that are hands-on programming assignments. Prerequisite: practices that are common to a broad range of pat- necessary for speech recognition. The course is

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focused on understanding the theory behind these covered include search, knowledge representation, hands-on experience by critiquing existing inter- fundamental technologies, and applying the technol- automated inference, planning, nonmonotonic rea- faces, as well as hearing reports from experts in ogy to develop speech recognition systems. soning and reasoning about belief. Applications industry on the state of the field. An introduction to Prerequisite: Some knowledge of engineering math- include expert systems, natural language processing this topic is essential for everyone working in the ematics (calculus and linear algebra) is required; C and agent architectures. 3 credits field of computer science. 3 credits programming experience is necessary. 3 credits CSE 561/661 Dialogue CSE 565/665 Advanced Topics in Human- CSE 558/658 Evolutionary Computation This course provides an in-depth treatment of the Computer Interaction The field of evolutionary computation encompasses major theories of dialogue, including finite-state, This course reviews advanced topics and current machine learning methods inspired by biological plan-based and joint action theories. Dialogue is research in the field of human-computer interaction, evolution, as well as the computational modeling of examined at a level general enough to encompass surveys key research challenges that exist, and dis- evolutionary processes in nature. The techniques of conversations between humans, between human cusses emerging trends in next-generation system evolutionary computation include genetic algo- and computer, and among computers, while at the design. Topics include advanced research and rithms, genetic programming, evolvable hardware, same time being precise enough to support imple- design methods, new recognition-based and multi- evolutionary robotics, and related methods. These mentations. The course introduces basic speech act modal interfaces, conversational interfaces and methods have been used to solve problems in engi- theory, planning and reasoning through a number of animated character design, mobile interfaces, ubiq- neering design and optimization, robot control, classic papers. Plan-based theories are examined in uitous and tangible interfaces, adaptive interfaces, bioinformatics and drug design, financial prediction, detail, including their incorporation into spoken dia- advanced user modeling and design for universal and image processing, to name a few applications. logue systems and their potential effects upon access, and other key issues. Topics are covered They are beginning to be widely used in the scientif- speech recognition components. Students will devel- from a broad multidisciplinary perspective, with an ic and commercial worlds. This course is a hands-on op dialogue components and integrate them into emphasis on real-world users and usage contexts. In introduction to these techniques and the theory working systems. Prerequisite: CSE 560. 3 credits addition to weekly classroom lectures, guest lec- behind them. Students will learn the basics of evo- tures, and discussion, this class includes a hands-on lutionary computation by implementing various CSE 562/662 Natural Language Processing practicum component in which students participate methods themselves and applying them to simple An introduction to artificial intelligence techniques in state-of-the-art research and interface design to versions of real-world problems (when possible, for machine understanding of human language. The complete a team project. Pre-requisites: CSE564 or related to the students’ own research or applica- course introduces key aspects of natural language, instructor’s consent. 3 credits tions interests). More advanced topics will include along with the analyses, data structures and algo- coevolutionary learning, agent-based and artificial rithms developed for computers to understand it. CSE 567/667 Developing User-Oriented Systems life simulations, and the theoretical foundations of Computational approaches to phonology, morpholo- This course explores a range of issues and methods evolutionary computation. Prerequisites: gy, syntax, semantics and discourse are covered. needed to design and evaluate user-oriented soft- Programming experience in any high-level language. Programming assignments are written in Prolog. ware applications. Topics focus on field and 3 credits. Prerequisite: CSE 560 or equivalent. 3 credits ethnographically based design studies, participatory design methods, user laboratory studies and usabil- CSE 559/659 Machine Learning CSE 563/663 Multi-Agent Systems ity testing. The purpose is to have access to a range This course provides a broad introduction to tech- This course covers the emerging theory and practice of methods that help uncover opportunities, break- niques for building computer systems that improve of multiagent systems: semi-autonomous, semi- downs and interactions that affect the design and through experience. It provides both conceptual intelligent distributed computing systems that can use of developing systems. Students are challenged grounding and practical experience with several be organized ad hoc to meet the immediate needs of to evaluate the underlying perspectives of the learning systems. The course provides grounding for a user. The course covers a variety of individual and approaches and decide which approach or combina- advanced study in statistical learning methods, and multiagent architectures, including the Contract Net tion of approaches works best for particular for work with adaptive technologies used in speech protocol, distributed blackboard systems and mobile problems. They apply the methods in field and class- and image processing, robotic planning and control, agents. Also discussed are principles for building room exercises and produce a real-world project or diagnostic systems, complex system modeling, and networks of heterogeneous agents, ranging from paper using course methods. The intended result is iterative optimization. Topics include: learning para- simple rule-based systems to databases and to make students more effective not only at gathering digms and concept learning, decision trees, artificial humans. In order to collaborate to solve a user’s relevant user-based information, but also at inte- neural networks, statistical sampling and empirical problem, agents need to communicate. We examine grating it into the development process. 3 credits error estimation, Bayesian learning (including an agent communication languages, including KQML introduction to belief networks), clustering, princi- and FIPA, as well as the underlying general speech CSE 568/668 Empirical Research Methods pal and independent component analysis, act theories. Students learn how to model these sys- This course introduces principles of experimental generalization theory, memory-based (instance) tems formally and will develop and program design and data analysis for empirical research. techniques, evolutionary computation, and rein- individual agents that can participate in a multia- Topics include the goals and logic of experimental forcement learning. Students will gain practical gent system. 3 credits design, hypothesis formation and testing, probabili- experience implementing and evaluating systems ty and sampling theory, descriptive statistics, applied to pattern recognition, prediction, and opti- CSE 564/664 Introduction to Human- correlation and regression, basic parametric and mization problems. Prerequisites: Some experience Computer Interaction nonparametric tests of statistical significance (e.g., with multi-variate calculus and linear algebra, at This course emphasizes the experience of comput- Binomial, t-test, chi-square, analysis of variance), least one high-level programming language, and an ing, which centers on an understanding of real users standard designs for single- and multi-factor exper- elementary undergraduate course in probability and and the specific tasks they need to accomplish when iments, and strategies of scientific investigation statistics. 3 credits. computing. In the pursuit of optimal user support, a (e.g., Exploratory vs. Directed). The course is fun- multidisciplinary approach to system design and damental for anyone who plans to conduct CSE 560/660 Artificial Intelligence evaluation is stressed. The course reviews basic independent research or needs to evaluate critical- This course surveys the foundations and applica- research methods, terminology, viewpoints, and ly the research of others. Students participate in tions of symbolic approaches to artificial activities in the broad field of human-computer designing and analyzing data to answer scientific intelligence. The approach emphasizes the formal interaction. It includes coverage of research on questions and present the results of these activities basis of automated reasoning and includes an intro- human computer interaction, as well as practical both orally and in writing. 3 credits duction to programming in Prolog. Fundamentals issues in system interface design. Students gain

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CSE 569/669 Scholarship Skills EBS 503 M.S. Thesis Research EBS 512/612 Biochemistry I: Proteins and Enzymes Scientific results have little value if they are not (Formerly BMB 700 and ESE 700) (Formerly BMB 527) communicated clearly or are disconnected from Research toward the M.S. thesis degree. Primary, secondary and tertiary structure of pro- prior work in a field. This course teaches students Variable and repetitive credit teins; enzyme mechanisms; enzyme kinetics. to research, write, present and review effectively 4 credits for the computer sciences. It emphasizes learning EBS 504/604 Professional Internship by doing, and students have frequent writing and (Formerly BMB 620 and ESE 620) EBS 513/613 Biochemistry II: presentation assignments. Students learn how to Professional internship credits provide students an Introduction to Molecular Biology locate and organize background materials, how to opportunity to earn credit for relevant work experi- (Formerly BMB 528) write clearly about technical topics, how to organ- ence in industry. Students gain valuable industrial DNA replication, RNA synthesis and protein synthe- ize Web content, the structure and stylistic experience that allows them to both apply the sis; genetic code; gene regulation. 4 credits conventions of scientific documents (such as con- knowledge gained in the classroom and prepare for ference abstracts, journal papers, theses and careers following graduation. Students on F-1 or J- EBS 514/614 Biochemistry III: proposals), how to prepare and deliver short and 1 visas must obtain prior written approval for Metabolism and Bioenergetics long presentations, the refereeing process, and how internships from OGI’s Office of International (Formerly BMB 529) to prepare and respond to a review. This course is Students and Scholars before enrolling. Enrollment Metabolism of carbohydrates, lipids and amino required for Ph.D. students and strongly recom- requires a faculty advisor and is limited by the num- acids; bioenergetics; photosynthesis; oxidative mended for master’s students, especially those ber of internship opportunities available. phosphorylation. 4 credits pursuing the thesis option. It also is useful for Variable and repetitive credit professionals who must write or speak to a techni- EBS 518/618 Metals in Biochemistry cal audience. 3 credits EBS 506/606 Special Topics (Formerly BMB 537) (Formerly BMB 58X and ESE 58X) Comprehensive study of the chemistry and biochem- CSE 599/699 Reciprocity Course Special topics courses are offered in areas of par- istry of metal ions in biological molecules and living (Formerly CSE 595) ticular relevance to the research interests of faculty systems. Topics include metalloprotein structure, OGI students admitted to a degree program have the or in response to industry needs. Special Topic metal ion specificity, biological oxidation mecha- opportunity to take classes at other Oregon courses are subject to change and are offered inter- nisms, metal ion catalysis in enzymes, metal ion University System schools under the Joint Campus mittently. Variable and repetitive credit transport and gene regulation. 4 credits Agreement or Reciprocity Agreement. Contact the Department of Graduate Education for details. EBS 507A/607A EBS Department Seminar EBS 520/620 Coordination Chemistry Courses taken under these agreements are listed as (Formerly BMB 591 and ESE 599) (Formerly BMB 538) 599/699. Variable and repetitive credit Weekly seminars by invited guests. Public visitors Structures and stabilities of transition metal coordi- are welcome. Schedules are available on the World nation compounds with mono- and multi-dentate CSE 601 Research Wide Web at www.ebs.ogi.edu/seminars/, or by ligands; coordination compounds as models for bio- (Formerly CSE 600) request at [email protected]. 1 credit, repetitive logical metal centers; strategies for synthesis of Ph.D. supervised research activity. transition metal complexes. 4 credits Variable and repetitive credit EBS 507B/607B Student Seminar: Metallobiochemistry (Formerly BMB 594) EBS 523/623 Chemical Group Theory CSE 603 Ph.D. Dissertation Research Presentations and discussions of selected topics (Formerly BMB 539) (Formerly CSE 800) from the recent literature and of ongoing research Properties of mathematical groups; symmetry prop- Research toward the dissertation for the Ph.D. degree. projects in the department. 2 credits, repetitive erties of molecules; symmetry groups,represen- Variable and repetitive credit tations, and character tables. Applications of group EBS 507C/607C Student Seminar: theory to the study of structure and spectroscopy of Molecular Biology/Biochemistry organic and inorganic molecules; Hückel molecular (Formerly BMB 596) orbital theory; ligand field theory; electronic spec- ENVIRONMENTAL AND Presentation and discussion of journal articles from troscopy and vibrational spectroscopy. 4 credits BIOMOLECULAR SYSTEMS the recent literature in molecular biology, genetics and biochemistry. 2 credits, repetitive EBS 525/625 Bioenergetics and Membrane Transport EBS 501 M.S. Non-Thesis Research (Formerly BMB 532) (Formerly BMB 610 and ESE 610) EBS 510/610 Aquatic Chemistry Critical evaluation of the chemiosmotic theory with Supervised research as a component of the M.S. (Formerly ESE 510) specific reference to oxidative phosphorylation, non-thesis degree. The plan of research and final General acid/base concepts (mono- and polyprotic photophosphorylation and metabolite transport. deliverables must be approved by the research advi- systems); pH; making activity corrections; numeri- Biochemical mechanisms of energy transduction sor and the SPC. Deliverables include a written cal calculations; titration concepts as applied to common to bacterial and mitochondrial respiration, report and/or seminar given as part of EBS 507A. A natural systems; buffer intensity; dissolved CO2 and bacterial and plant photosynthesis are reviewed. maximum of 8 credits from EBS 501 may be applied chemistry; acidity and alkalinity in open CO2 sys- 4 credits to a degree. Variable and repetitive credit tems; minerals and their role in controlling natural water chemistry; solubility characteristics of oxide EBS 528/628 Enzyme Structure, Function EBS 502/602 Independent Study and hydroxides; introduction to redox chemistry in and Mechanisms Typically involves a scholarly and critical review of natural systems; pe-pH diagrams. 4 credits (Formerly BMB 533) an advanced scientific topic by one or more students Provides an in-depth analysis of the structural ori- together with one or more faculty members. EBS 511/611 Advanced Aquatic Chemistry gins of protein interactions and catalysis that are the Requirements of the student typically include a writ- (Formerly ESE 511) basis for biological function. The course develops the ten review paper and/or a seminar to be given as Role of complexing ligands in solution chemistry; basic principles of structural biology through an part of EBS 507A/607A - EBS 507B/607B - EBS redox chemistry in natural systems; pe-pH diagram overview of X-ray crystal structures and folding 507C/607C. Selection of this course for credit and construction and use; solid/solution interfacial con- processes, acquainting the students with computa- the topic to be investigated must be approved by siderations; the electrical double layer; and selected tional resources for protein structure analysis. The the SPC. Variable and repetitive credit advanced topics. Prerequisite: EBS 510/610. structural foundation is expanded into a detailed 4 credits 76 COURSE DESCRIPTIONS | OGI

investigation of enzyme active sites, including the EBS 547/547 Uncertainty Analysis map projections will be discussed. Spatial rela- application of kinetic approaches to understanding (Formerly ESE 504) tionships, or analysis, of continuous and categor- enzymatic reaction mechanisms. 4 credits A survey of basic probability concepts followed by ical data will be addressed through the application introductions to several statistical advanced tech- of standard statistics and probability. ARCVIEW, a EBS 530/630 Introduction to Bioinformatics niques that play an important role in environmental popular Geographic Information System (GIS) soft- (Formerly BMB 544) data analysis. Topics may include distribution func- ware tool, will be stressed. 4 credits Primary literature of computational biology and tions, propagation of error, hypothesis testing, hands-on experience in data manipulation from analysis of variance, experimental design, sampling EBS 562/662 Introduction to Remote Sensing of local and remote databases. 3 credits theory, regression analysis, time-series analysis and the Environment spatial statistics techniques. The course provides a (Formerly ESE 523) EBS 535/635 Distribution and Fate of Organic Pollutants balance of theory and application using environmen- This course will explore the acquisition, analysis (Formerly ESE 514) tal data sets. 4 credits and visualization of remotely sensed data. The Discussion of the physico-chemical processes that physics behind the collection of remotely sensed control the partitioning of organic chemicals in the EBS 550/650 Environmental Systems Analysis data will be introduced as will both airborne-plat- environment. This introductory course considers all (Formerly ESE 506) form and satellite-platform sensors. Fundamentals environmental compartments, water, soil and air, Introduction to techniques of systems analysis of aerial photogrammetry, single-band, and multi- and partitioning between those phases. Recom- applied to environmental quality management. spectral and thermal infrared data will be mended prerequisite: EBS 510/610. 4 credits Emphasis is on development and application of addressed. Concepts of image statistics, radiometric mathematical models with computer simulation and and geometric corrections, spatial filtering and spe- EBS 537/637 Chemical Degradation and Remediation optimization. Analysis includes efficient computa- cial transformations like the Normalized Difference (Formerly ESE 516) tional algorithms and search techniques. Linear and Vegetation Index are explored. Supervised and A thorough introduction to the transformation reac- separable programming applied to evaluate man- Unsupervised classification schemes will be dis- tions that contribute to the fate of organic agement alternatives. Applications to air, water, cussed as will change detection. The course substances in the environment. The course covers solid and hazardous waste management. pedagogy is designed to address the needs of the pathways, mechanisms and kinetics of hydrolysis, Prerequisites: Computer programming and calculus. advanced Environmental Science and Engineering oxidation, reduction, elimination, conjugation, etc. 4 credits graduate student. While there is no prerequisite, the Treatment is balanced to reflect the importance of course incorporates many topics from EBS 561/661, these processes in all types of environmental waters EBS 555/655 Computational Fluid Dynamics “Introduction to Spatial Science.” It is therefore rec- ranging from engineered systems to groundwater, (Formerly ESE 508) ommended that students who are unfamiliar with surface water, rain and fog. Recommended prepara- This course describes advanced topics in computa- classification methods and the fundamental con- tion: EBS 511/611 and 535/635. 4 credits tional fluid dynamics, including specialized discrete cepts of Geographic Information Systems complete methods (e.g., for advection-dominated problems), EBS 561/661 or equivalent. 4 credits EBS 538/638 Air Pollution: formal analysis of stability and accuracy, and select- Origins, Chemistry and Control ed simulations of complex environmental and EBS 570/670 Groundwater and Watershed Hydrology (Formerly ESE 519) biological systems. Prerequisites: Advanced calcu- (Formerly ESE 540) This course will focus on tropospheric air pollution lus and EBS 545/645. 4 credits Hydrologic cycle, principles of unsaturated and sat- with particular emphasis on the urban and regional urated flow in the subsurface; characterization of scales. It will discuss the following items: basic EBS 560/660 Introduction to Environmental groundwater/surface interactions, water balance, structure of the atmosphere and relevant meteoro- Observation and Forecasting Systems modeling of watershed-scale processes. 4 credits logical considerations; sources of tropospheric air (Formerly ESE 520) pollutants; atmospheric photochemistry; the ozone, This course introduces environmental observation EBS 571/671 Groundwater Modeling oxide of nitrogen and hydrocarbon chemical cycles; and forecasting systems and their application (Formerly ESE 541) chemistry of toxic organic compounds in the atmos- toward the enhanced understanding and manage- Applied groundwater modeling using the finite dif- phere; gas and aqueous phase chemistry of sulfur ment of natural resources. Emphasis is on estuaries ference method. Introduction to numerical methods dioxide; size distributions, lifetimes, origins and for- and coasts. Students are exposed to a novel, cross- for solving the partial differential equations for sat- mation mechanisms of aerosols; measurement and disciplinary culture for understanding and urated and unsaturated subsurface flow. Model control of atmospheric pollutants. 3 credits interacting with environmental systems. This cul- execution and calibration. Prerequisite: EBS ture relies heavily on “real-time” generation of 570/670. 4 credits EBS 540/640 Instrumental Methods in Biophysics I modeling and observational data, which are inte- (Formerly BMB 534) grated and distributed through information EBS 572/672 Contaminant Hydrology Theory and application of physical techniques to networks designed to bring the right environmental (Formerly ESE 542) problems in biochemistry. Optical, fluorescence, cir- information at the right time to the right user. Processes controlling subsurface contaminant cular dichroism, infrared and Raman spectroscopy Prerequisite: Instructor permission. 4 credits movement in porous and fractured media, including of chromophoric groups. Magnetic susceptibility and groundwater flow, dispersion, diffusion, sorption, nuclear magnetic resonance of metalloproteins. EBS 561/661 Introduction to Spatial Sciences and degradation. Parameter estimation, mathe- 4 credits (Formerly ESE 522) matical and laboratory modeling of aquifers is Students will learn theoretical and practical appli- also covered. 4 credits EBS 541/641 Instrumental Methods in Biophysics II cations of geo-spatial sciences within the context (Formerly BMB 535) of Environmental Sciences and Engineering. EBS 573/673 Modeling in Contaminant Hydrogeology Investigation of physical techniques particularly Geographic Positioning Systems (GPS) will be (Formerly ESE 543) useful for studying metalloproteins. Electron para- studied while performing practical, hands-on labo- This course is designed to be taken concurrently magnetic resonance, electron spin echo, magnetic ratory experiments using the latest in GPS with EBS 572/672. It emphasizes the hands-on use circular dichroism and X-ray absorption spec- equipment. Classroom discussions will focus on of common mathematical models for groundwater troscopy. The course has significant “hands-on” relating location on the Earth’s surface to a com- flow and transport (e.g., MODFLOW/MODPATH/ exposure to both instrumentation and computer mon graticule. Horizontal and vertical datum, MT3D/RT3D) to examine real groundwater contami- simulation techniques. 4 credits theoretical spheroids and ellipsoids, geoids and nation problems. Prerequisite: EBS 572/672. 4 credits

77 OGI | COURSE DESCRIPTIONS

EBS 574/674 Introduction to Environmental practice of environmental regulation, environmental include hazard identification, exposure assessment, Forecasting Systems litigation, and legislation including Superfund dose-response relationships, deterministic and (Formerly ESE 538) (CERCLA), the Clean Water Act, the Resource probabilistic risk assessments, responses of various This course addresses the composition and novel Conservation and Recovery Act (RCRA), the Clean receptors to different contaminants, and environ- uses of observation and forecasting systems Air Act, and the Toxic Substances Control mental management decisions. 3 credits towards the enhanced understanding and manage- Act (TSCA). 3 credits ment of natural resources. Students are exposed to EBS 597/697 Ecosystem Ecology a novel, cross-disciplinary culture for understanding EBS 585/685 Advanced Molecular Biology (Formerly ESE 562) and interacting with environmental systems. This (Formerly BMB 540) Principles of ecology and of ecosystem process, culture relies heavily on “real-time” generation of An in-depth study of the molecular mechanisms gov- description, and measurement, with emphasis on modeling and observational data, which are inte- erning the replication, recombination, transcription, ecosystem health assessment. Simulation modeling of grated and distributed through information and translation of genetic material. Emphasis is ecosystem processes; transport and transformation. networks designed to bring the right environmental placed on experimental approaches that have led to 4 credits information at the right time to the right user. our understanding of these fundamental processes. Prerequisite: Instructor permission. 4 credits 4 credits EBS 598/698 Current Topics in Proteomics (Formerly BMB 543) EBS 575/675 Transport Processes EBS 586/686 Molecular Genetics of Development Proteomics is a new area of molecular biology which (Formerly ESE 530) (Formerly BMB 541) aims to identify and map the total protein comple- An introductory course in the physics of transport A focused study of selected topics examining the ment of a genome. It expands the scope of biological processes in the natural environment. The course regulation of gene expression during cellular differ- investigation from studying single proteins to sys- examines heat, mass and momentum transport via entiation. Emphasis is placed on the molecular tematically studying all proteins. Proteomics has conservation principles and the Reynolds Transport nature of cell-cell interactions and the genetic con- broad applications in disease diagnosis, drug dis- Theorem, but strongly emphasizes the environmen- trol of complex cellular responses to developmental covery, and agriculture. The key technologies used tal applications of these processes. Example studies and environmental stimuli. 4 credits in proteomics are 2-dimensional gel electrophore- include atmospheric and oceanic circulation, flow sis, mass spectrometry (ESI-MS, MALDI-TOF), and dispersion in rivers, and heat budgets for lakes EBS 587/687 Molecular Cell Biology imaging, and database. This course will focus on and reservoirs. 4 credits (Formerly BMB 542) electrophoresis, mass spectrometry, and applica- The techniques of molecular biology have created an tions, using lectures, student seminars, and EBS 578/678 Methods in Estuarine Oceanography: explosion in knowledge of cell structure and func- literature readings. 3 credits Field Observation tion. This course examines the following topics: (Formerly ESE 539) cellular organization; cell signaling; cell differentia- EBS 599/699 Reciprocity Course This course covers the fundamentals of estuarine tion; cell evolution. Knowledge of the cell is obtained OGI students admitted to a degree program have the and coastal oceanographic data collection using ves- through combining core readings and lectures with opportunity to take classes at other Oregon sels and remotely moored equipment. Topics include student-led discussions of primary research papers. University System schools under the Joint Campus vessel logistics and sampling, navigation systems, 4 credits Agreement or Reciprocity Agreement. Contact the interfacing of instruments with personal computers, Department of Graduate Education for details. types of moorings and their deployment and recov- EBS 590/690 Environmental Microbiology Courses taken under these agreements are listed as ery, and telemetry. 4 credits (Formerly ESE 550) 599/699. Variable and repetitive credit Introduction to environmental microbiology, with EBS 580/680 Physics of Pacific Northwest emphasis on the role of microbes in the environ- EBS 601 Ph.D. Prequalifying Research Coastal Ecosystems ment and in remediation processes. Microbes and (Formerly BMB 600 and ESE 600) Thie course considers the impacts of climate, their interaction and activities in soil and aquatic Research toward the dissertation for the Ph.D. degree hydrology, and coastal, estuarine and fluvial circula- environments will be discussed, as well as elemen- before completing the comprehensive examinations. tion on Pacific Northwest coastal ecosystems. tal cycling as influenced by microbes. Microbially Variable and repetitive credit Special attention will be given to human impacts on mediated transformation of organic pollutants, ecosystem through alteration of their physical con- transformation kinetics and remediation technolo- EBS 603 Ph.D. Dissertation Research text. Examples will include downstream effects of gies will be considered. In 2003-2004, may be (Formerly BMB 800 and ESE 800) water withdrawal, the interaction of climate change offered in combination with EBS 593/563. Research toward the dissertation for the and climate cycles with salmonids and the coastal 4 credits Ph.D. degree after completing the comprehensive upwelling ecosystem, and the interaction of examinations. Variable and repetitive credit microbes, particles, consumers and estuarine circu- EBS 593/693 Biodegradation and Bioremediation lation in estuarine turbidity maxima. Prerequisites: (Formerly ESE 554) EBS 575/675 Transport Processes. 4 credits A process-oriented survey of microbially medi- ELECTRICAL ENGINEERING COURSES ated transformations of organic pollutants. EBS 581/681 Ecosystem Management and Restoration Transformations occurring in the natural environ- EE 501 M.S. Nonthesis Project Research This course will provide an overview of ecosystem ment as well as in remediation technologies are (Formerly ECE 610) management and restoration at the local and considered. Emphasis is on the pollutant properties, Supervised project research for master’s students regional scale. It will follow the hydrologic cycle microbiological factors, and medium properties that who are not pursuing a thesis. A student’s academic from upland watersheds through streams, determine the pathways and kinetics of biodegradation. department may have additional requirements or rivers and estuaries to the ocean and will track Recommended preparation: EBS 590/690. 4 credits restrictions. Please contact your academic depart- important system parameters such as water flow ment for further details. and temperature. 4 credits EBS 596/696 Principles of Toxicology and Variable and repetitive credit Risk Assessment EBS 583/683 Environmental Law and Regulation (Formerly ESE 570) EE 502/602 Independent Study (Formerly ESE 586) This course applies toxicological principles to both (Formerly ECE 591) A survey of environmental law and regulation con- human and ecological risk assessments. The princi- Independent study allows a student to work one-on- cepts essential to practicing scientists and ples and methodologies for risk assessments are one with a faculty member on selected topic(s) of engineers. Topics covered include the theory and presented within a regulatory context. Topics interest. Registering for independent study requires 78 COURSE DESCRIPTIONS | OGI

pre-approval from the faculty member and the site-specific SEM transverse cross sections, the failure mechanisms and the methodology used to student’s academic department. Each department location and sectioning of micron and sub-micron analyze them. Case studies also are discussed. The may have additional requirements or restrictions. scale structures on the surface and buried in multi- lecture portion of this course can be presented on Please contact your academic department for layered stacks or bulk materials, cross sections in site at companies within a six-week period. further details. Variable and repetitive credit metals, semiconductors, ceramics, and composites Corresponding lab sessions are done at OGI. A proj- are covered. The location and sectioning of micron ect requiring operation of the SEM at the student’s EE 503 M.S. Thesis Research and submicron surface and buried structures to cre- convenience during the remainder of the quarter (Formerly ECE 700) ate electron transparent foils with little or no and a written report are the basis for a grade. Research toward the thesis for the M.S. degree. damage in metals, semiconductors, ceramics, and 3 credits Variable and repetitive credit. composites, and artifacts of specimen preparation are presented. Ion beam lithography and microfab- EE 525/625 Introduction to Electromagnetics for EE 504/604 Professional Internship rication of structures on the micron and sub-micron Modern Applications (Formerly ECE 620) scales are also covered. This course uses a combi- (Formerly ECE 507) Professional internship credits provide students an nation of lectures and hands-on practice to cover This series (EE 525/625-527/627) cover essentials opportunity to earn credit for relevant work experi- these topics. The lecture portion of this course can of electromagnetic theory for modern practitioners ence in industry. Students gain valuable industrial be presented on site at companies within a six-week in such areas of engineering and applied science as experience that allows them to both apply the period. Corresponding lab sessions are done at OGI. semiconductor devices; IC design; optics, lasers, knowledge gained in the classroom and prepare for A project requiring operation of the FIB at the stu- and optoelectronics; wireless and optical communi- careers following graduation. Students on F-1 or J- dent’s convenience during the remainder of the cations; electronic displays; electron and ion beam 1 visas must obtain prior written approval for quarter and a written report is the basis for a grade. technology; vacuum electronic devices; and various internships from OGI’s Office of International 3 credits biomedical applications. The course is practically Students and Scholars before enrolling. Enrollment oriented, and presents both analytical and numeri- requires a faculty advisor and is limited by the num- EE 513/613 Transmission Electron Microscopy cal methods. The first course introduces basic ber of internship opportunities available. (Formerly ECE 567) experimental laws and theoretical concepts. Variable and repetitive credit Electron microscopy is a continually evolving disci- Laplace and Poisson equations for static electric pline that has developed a wide range of techniques and magnetic potentials. Basic properties of elec- EE 506/606 Special Topics to solve specific problems. This course is designed tromagnetic materials. Maxwell equations for static (Formerly ECE 580-XXX) to help the student develop a broad appreciation and and time-varying fields. Wave equations and Special topics courses are offered in areas of knowledge of the important techniques for the Poynting theorem. Finite-difference numerical solu- particular relevance to the research interests of analysis of crystalline and amorphous materials. tion of boundary-value problems. Prerequisite: faculty or in response to industry needs. Special Modern transmission electron microscopes can give Some undergraduate electromagnetism, calculus Topic courses are subject to change and are the investigator detailed information of crystal through ordinary and partial differential equations, offered intermittently. Variable and repetitive credit structure, crystal defects and quantitative local some vector calculus, or consent of instructor. chemistries on a nanometer scale. This information 4 credits EE 511/611 Analytical Scanning Electron Microscopy is often critical to the understanding of material (Formerly ECE 565) properties. Principles, methods and application of EE 526/626 Electromagnetics for Modern Applications II This course introduces the operation and theory of transmission electron microscopy to crystalline (Formerly ECE 508) SEM and covers sources, lenses, accelerating volt- materials are covered as well as the construction This course introduces additional mathematical age, detectors, image formation, beam-specimen and design of electron microscopes, electron dif- tools and covers topics basic to circuit design, semi- interactions, beam-produced signals, the combined fraction, reciprocal lattice and Ewald Sphere conductor device operation, IC design, optics, effects of signal-to-noise ratio and spot size in deter- construction. Kinematic and dynamic theories of transmission lines, and antenna design. Waves in mining resolution, and stereo imaging SEM. The image formation will be introduced. Combining lec- conductors and skin effect are included. Retarded process of specimen preparation, metallo-graphic tures with hands-on laboratory practice, students potentials for time-varying fields. Electromagnetics grinding and focused ion beam-produced transverse will be instructed in the use of sample preparation of lumped-element circuit theory. Plane wave prop- cross sections, planar sections, coating techniques equipment and an analytical transmission electron agation, reflection, and refraction. Polarization for nonconductors, sampling of powders, and isola- microscope. Students will be expected to carry out states and Stokes parameters. Analytical methods tion of contaminants are some of the topics covered. basic experiments on selected materials that illus- for boundary-value problems and numerical solution Students are encouraged to work on materials they trate fundamental concepts covered of the lecture. by boundary-element method. Introductory (TEM) provide. The course covers the operation of energy The lecture portion of this course can be presented field theory of transmission lines and its relation to dispersive X-ray detectors, qualitative analysis, on site at companies within a six-week period. circuit model. Prerequisite: EE 525/625 and some quantitative analysis, elemental mapping, spectrum Corresponding lab sessions are done at OGI. A proj- linear algebra or consent of instructor. 4 credits artifacts, and contaminant and compound identifica- ect requiring operation of the SEM at the student’s tion. The lecture portion of this course can be convenience during the remainder of the quarter and EE 527/627 Electromagnetics for Modern Applications III presented on site at companies in a 6-week period. a written report are the basis for a grade. 3 credits (Formerly ECE 509) Corresponding lab sessions are done at OGI. A proj- This course covers advanced transmission line and ect requiring operation of the SEM at the students’ EE 514/614 Failure and Reliability in Microelectronics wave guide field theory for high speed intercon- convenience during the remainder of the quarter and (Formerly ECE 568) nects, microwave and optical wave guides; resonant a written report is the basis for a grade. 3 credits The failure and reliability of microelectronics cavities for frequency control and lasers; and radia- depends on the stability of thin films and the purity tion basics for communications and optics. Topics EE 512/612 Focused Ion Beam Technology of the bulk semiconductors. Contamination, film include TE and TM transmission line and wave-guide (Formerly ECE 566) thickness, diffusion and phase changes all drive modes. Field theory of multiple-conductor transmis- This course covers operation and theory of a FIB mechanisms of failure. Characterization of a failed sion lines: Modes, coupling, crosstalk, and workstation, including ion sources, accelerating device depends on analysis of thin film structure, termination. Dielectric wave guides. Resonant cavi- voltage, electrostatic lenses, beam-material interac- crystalline structures, contaminant identification ties. Radiation from antennas and apertures. tions, resolution, beam intensity distribution, beam and microchemistry. This requires a variety of Additional topics as time permits, chosen from: produced signals, detectors, metal and oxide depo- microanalytical techniques involving the SEM, TEM electromagnetic properties of materials; variational sition, and enhanced etch. FIB-produced and FIB. This course covers the potential defects, formulation of field problems and finite element

79 OGI | COURSE DESCRIPTIONS

numerical solution; analytical and numerical calcu- materials, band-gap engineering, quantum effects EE 534/634 Advanced MOSFET Analysis II: lation of charged-particle motion in electromagnetic due to shrinking IC feature sizes, quantum-dot and Dynamic Models. fields; suggestions of students. Prerequisite: quantum-well devices, and quantum computing. The (Formerly ECE 513) ECE526/626 and some linear algebra or consent first course introduces basic concepts and results Based on EE 533/633 the dynamic large-signal and of instructor. 4 credits essential to understanding solid-state band struc- small-signal models of MOSFET operation are ture, devices based on tunnelling, and quantum-well developed for digital and analogue applications EE 528/628 Introduction to Electronic Materials devices. Topics include a review of classical respectively: Large-signal modeling is analyzed in (Formerly ECE 515) mechanics. The Schroedinger equation, postulates detail for quasi-static operation (neglecting transit- The fundamental properties and concepts needed to of Quantum Mechanics, and basic Hilbert-Dirac for- time effects) in terms of the charges flowing in and understand electronic materials are introduced in malism. The free particle. One-dimensional out of all four MOSFET terminals covering the vari- this course. We begin with crystals, their structure quantum-well bound states and tunneling through ous charge conditions in the semiconductor and bonding, and thermal properties. We then exam- potential barriers. Bloch functions in periodic (accumulation to inversion); non-quasi-static model- ine electron interactions in metal and potentials and the origin of solid-state band struc- ing is introduced to include transit-time effects in semiconductor crystals. The physics behind the ture. Prerequisite: Calculus through ordinary and high-speed applications and is illustrated for a energy bandgap in semiconductors are examined, partial differential equations, or consent of instructor. channel in strong inversion. Small-signal modeling and used to ultimately derive the energy band struc- 4 credits for the description of equivalent circuit elements ture, effective mass, and equilibrium carrier starts with a simplified quasi-static analysis at low statistics. Next, we use these statistics to define EE 532/632 Advanced Quantum Mechanics for Electrical and medium frequencies at all channel conditions carrier transport in semiconducting materials. and Computer Engineers (weak to strong inversion). Then this model is Finally, we study and understand dielectrics and (Formerly ECE 511) extended to high frequencies in a complete quasi- insulators, magnetic properties, superconductivity, This course covers two- and three-dimensional static mode that includes transcapacitors at highest and the optical response of semiconductors. This applications, and introduces new physical phenom- frequencies near gain cut-off. Non-quasi-static mod- course is recommended if you have never taken a ena, mathematical formulations, and tools essential eling is discussed and applied to channels in strong semiconductor device course (or if you need a for understanding materials science, lasers, solid inversion. Finally, noise models are developed to refresher). The materials covered will provide you state devices, quantum optics, and quantum com- supplement the derived equivalent circuits with the with background for other semiconductor device, puting. Covered are two- and three-dimensional proper noise source elements. Prerequisite: processing, and characterization courses offered quantum wells. The simple harmonic oscillator and EE 533/633. 4 credits at OGI. Although quantum mechanics is not algebraic methods. Angular momentum and spin. required, taking the course will help achieve a more Matrix formulation of Quantum Mechanics. Atomic EE 535/635 MOSFET Modeling for VLSI Circuit Design advanced understanding of the concepts discussed structure. Approximation methods, including per- (Formerly ECE 514) in this class. 4 credits turbation theory. Interaction of matter and A comprehensive study of state of the art compact electromagnetic waves. Prerequisite: EE 531/631 models used in circuit simulators for VLSI design EE 529/629 Fundamentals of Semiconductor plus some linear algebra, or consent of instructor. and their underlying physics. Topics covered include Device Structures 4 credits high speed and high frequency (non quasi-static) (Formerly ECE 516) models, quantum effects, high field and hydrody- Semiconductor bulk, junction and surface proper- EE 533/633 Advanced MOSFET Analysis I: DC Models namic effects. Substrate current and gate current ties. We develop the fundamentals of semiconductor (Formerly ECE 512) modeling with applications for reliability modeling structures; bulk defects; mechanisms affecting elec- “No IC designer’s education is complete without in circuit simulators and circuit design impact. tron/hole transport at low and high electric fields; detailed exposure to MOS transistor operation and Discussion of device scaling issues, fundamental junction formation/stability (p-n, metal-semiconduc- modeling” (J.Tsividis). This is the first part of a limits to mos device and circuit performance. A tor, and metal-insulator); and relationships between three-course sequence addressing this important review of novel device architectures for future mos semiconductor properties and device performance. need. Starting with contact potentials and proper- devices, in particular SOI devices, double gate The underlying concepts of minority carrier and ties of semiconductor surfaces, we analyze, (within devices, their physics and operation in terms of ana- majority carrier devices are expounded and clarified. the charge sheet and depletion approximations), the lytic models. Study of parameter extraction, 4 credits charges and potentials in MOS capacitors from optimization and device characterization techniques accumulation to flat band to inversion (including the required for developing compact models. Develop- EE 530/630 Advanced Semiconductor Devices: role of oxide charge). With these results we discuss ment of statistical and mismatch models for the Structures and Materials various MOSFET dc current models based on the mosfet. Radio frequency models for the mosfet and S (Formerly ECE 517) gradual channel approach: Symmetric (body-refer- parameter characterization. Review and comparison The complex interplay between materials proper- enced) models and the concept of extrapolated of existing mosfet models such as BSIM4, EFLKV, ties, fabrication technologies, and device pinch-off potential, source-referenced models and PCIM. Implementation of mos models in circuit sim- performance is examined in the context of elucidat- the concept of extrapolated threshold voltage ulators. Project work will include evaluating various ing such current technology developments as silicon (including body effect); more compact models for models in SPICE, and their impact on circuits, as on insulator (SOI), high-K dielectrics, SiGe hetero- strong inversion and for sub-threshold behavior well as understanding device operation using a 2D junctions, heterojunction bipolar transistors (HBT), (weak inversion); interpolation models for moderate device simulator (MINIMOS) and a coupled 1D pseudomorphic high electron mobility transistors inversion. The compact models are then modified in Schrodinger-Poisson Solver (SPIN). 4 credits (PHEMT), Vertical Cavity Surface Emitting Lasers a semi-empirical way to describe the effects of ion- (VCSEL), quantum dots, single electron transistors, implanted channels (including buried channels), as EE 536/636 Operation of Semiconductor Devices and organic semiconductors. 4 credits well as those due to small channel dimensions (Formerly ECE 580-OSD) (channel length modulation, effective modification of This class is aimed at professionals and full time EE 531/631 Introduction to Quantum Mechanics for threshold voltage in short and narrow channels, students who wish to gain physical insight into oper- Electrical and Computer Engineers velocity saturation, series resistance effects, thin ation of semiconductor devices. Emphasis will be on (Formerly ECE 510) oxide/shallow deletion effects). Breakdown and conceptual understanding of the underlying princi- Courses EE 531/631-532/632 present basic quan- punch-through are discussed qualitatively. ples. The course content will include a review of tum theory for understanding practical applications Prerequisites: basic electrostatics, semiconductors junctions and MOS structures, followed by examina- such as solid state devices, lasers and other opto- and circuits. 4 credits tion of basic IC devices, including memory and electronic devices, properties of electronic

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power devices. Students seeking in-depth coverage realistic process flows, physical metrology, device the electrical and optical techniques used to char- of BJTs and MOSFETs are recommended to take the structure and electrical behavior, trade-offs, etc. The acterize semiconductor materials and devices. EE 533/633-535/635 series. 4 credits course is intended to serve both working process These techniques are crucial in determining the engineers and matriculating graduate students. causes of failure in semiconductor devices. Among EE 537/637 Thin Film Deposition and Applications in 4 credits the parameters covered are contact resistance, car- Semiconductor Fabrication rier mobility and lifetime, defects, oxide and (Formerly ECE 535) EE 541/641 Microelectronic Device Fabrication II interface trapped charges, as well as series resist- Covers thin film deposition topics, such as thermal (Formerly ECE 561) ance, channel length /width, threshold voltage and evaporation, plasma deposition, chemical vapor The second class of this series emphasizes metal- hot carriers in MOSFETs. This class includes some deposition (CVD and MOCVD), molecular beam epi- lization and dielectrics. Metallization issues include lab time. 4 credits taxy (MBE), atomic layer epitaxy (ALE), silicides, barrier layers, interconnects (e.g., Cu), electrochemical deposition, and electroless deposi- multilevel metallization, and low k dielectrics. This EE 546/646 Design of Digital Communication Circuits tion. Thin film deposition forms the basis for followed by discussion of deposition and properties (Formerly ECE 580-DDC) manufacture of modern integrated circuits; knowl- of different dielectric films. Finally, processing Digital communications concepts including trans- edge of methods available for thin film deposition is issues of epitaxial growth and properties of SOI mission, media, encoding, and synchronization. essential for IC process engineers. Course is devices are covered. Class assignments include Review of BJT and CMOS circuit design and analy- designed to cover the theory and applications of computer simulation of device fabrication. sis. Amplifiers, filters, amplitude control, main deposition techniques in use or being consid- 4 credits equalization. Phase locked loops, clock and data ered for future IC fabrication processes. 4 credits recovery. Transmitter and receiver design. EE 542/642 Microelectronic Device Fabrication III Networks. Project: complete design of a serial opti- EE 538/638 Surface Science for (Formerly ECE 562) cal link. 4 credits Semiconductor Technology This class starts with electron beam, x-ray, and pho- (Formerly ECE 536) tolithography, including discussion of resist EE 547/647 Statistical Process Control and DOE The study of gas-solid surface science with empha- technology (e.g., chemically amplified resists). This (Formerly ECE 580-DOE) sis on understanding semiconductor systems and followed by fundamentals and applications of plas- Over the past 30 years design of experiments (DOE) the mechanisms of epitaxial growth of semiconduc- mas for etching and deposition (e.g., high-density has proven to be an extremely value tool allowing tor films by molecular beam epitaxy (MBE), plasmas), including plasma damage. Other topics USA manufacturing to re-gain its lead as the highest metal-organic molecular beam epitaxy (MOMBE), considered are process integration, which includes quality producer in the world. Course is geared for atomic layer epitaxy (ALE), etc. The study of ther- several devices such as BiCMOS and memories. engineers in any industry/discipline seeking a prac- mal desorption, surface diffusion. Surface electronic Finally yield and reliability statistics as related to tical understanding of design of experiments. Class properties such as work function. Physical absorp- microelectronic device fabrication are discussed. will cover a review of basic statistical techniques, T- tion, the growth of multilayer films and the Class assignments include computer simulation of test, F-Test, full factorial design, Yates Algorithm, application of these phenomena to the study of the device fabrication and testing. 4 credits ANOVA, Hadamard designs, fractional factorial BET equation as a tool for the determination of sur- designs, block designs, Latin squares, regression face area. 4 credits EE 543/643 Plasma Processing of Semiconductors I analysis and response surface methodology. (Formerly ECE 563) Emphasis will be on practical applications of tech- EE 539/639 Computer-Aided Analysis of Circuits Fundamental plasma properties. Plasma produc- niques to real world problems and how to avoid (Formerly ECE 557) tion, properties, and characterization. DC and RF some of the typical errors made in designing, exe- This course covers the algorithms and techniques plasmas. Sputtering. Sputtering as a deposition cuting and analyzing an experiment. Actual for formulation and solution of circuit equations for process for the growth of thin films. Multicomponent industrial examples will be used throughout the large-scale VLSI circuits. Topics include equation films. Plasma etching. 4 credits class to allow the student to see the value of these formulation, linear AC and DC networks, linear tran- techniques. Class project will involve the student sient networks, and stability analysis. Solution of EE 544/644 Chemical Mechanical Planarization actually running a DOE on a topic of interest. nonlinear DC and transient problems. Frequency (Formerly ECE 580-CMP) 4 credits domain (AWE) techniques for VLSI interconnections, Chemical Mechanical Planarization (CMP) is rapid- Sensitivity analysis, harmonic balance, circuit opti- ly growing in use within the microelectronics EE 548/648 Fundamentals of Sensors and mization, and statistical design. The implementation industry to planarize wafers as one of the process- MEMS Fabrication of device models in circuit simulators and conver- ing steps. While simple in concept - chemical and (Formerly ECE 580-FSM) gence issues is covered. Assignments stress mechanical material removal processes, the CMP is The market for Micro-Sensors and MEMS devices is computer-aided implementation techniques and use a complex tribological system. Mechanical abrasion expanding at an ever-increasing rate. Ranging from of simulators such as PSPICE. 4 credits and polishing mechanisms interact and co-exist with simple environmental sensors to electronic noses to chemical layer removal processes. This course will micro-actuators, the applications are diverse. While EE 540/640 Microelectronic Device Fabrication I present some of the historical background to CMP conventional integrated circuit processing can be (Formerly ECE 560) from its inception to the current state of knowledge, modified and utilized for Micro-sensors and MEMS This course is the first in a full-year, three-term the underlying concepts behind the tribological fabrication, these devices can also be constructed sequence that treats both the science and practice of processes of abrasion, grinding, and polishing mech- using a wide variety of non-CMOS techniques and in modern microelectronic fabrication. The principles anisms and the principles behind the chemical many cases using non-CMOS materials. This course of crystal growth and wafer preparation, ion implan- phenomena. Building on these fundamental con- will explore micro-fabrication for Micro-Sensors tation, doping and diffusion, and oxidation are all cepts, this course will examine oxide CMP, tungsten and MEMS from the variety of photolithography covered. Emphasis is placed on understanding the CMP, and the role of CMP on the planarization of processes (conventional, LIGA, soft lithography, basic chemistry, physics, and material science of copper and other materials. 4 credits micro-contact printing), additive processes (CVD, wafer processing. This includes crystal structure and PVD coatings, electroplating), and subtractive defects, heterogeneous chemical reactions, the ther- EE 545/645 Electronic Materials and processes (chemical etching, DRIE and RIE) which modynamics and kinetics of diffusion, etc. In Device Characterization have been used to construct devices ranging from addition, the practical implementation of these (Formerly ECE 569) accelerometers to chemical sensors to actuators processes is also discussed. This includes This class is designed for engineers and scientists and microfluidic pumps. 4 credits who wish to understand the basic principals behind

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EE 549/649 Introduction to Nanomaterials et engines. This course covers the types, design, wide range of applications. In this course, we inves- (Formerly ECE 580-IN) processing, and analysis of MEMS devices. tigate the physics of sensing, the characteristics of As the transistor gate length approaches 50 4 credits different categories of sensors, and materials and nanometers, its electrical properties are subjected fabrication fundamentals in a case-based format. to novel quantum effects, necessitating a paradigm EE 553/653 Modern Photolithographic Engineering This course is intended for both electrical engineer- shift in design and fabrication of related semicon- (Formerly ECE 580-MPE) ing students and scientists whose work is expected ductor devices. This introductory course focuses on An in-depth course designed for students and indus- to require interaction with sensor technologies. applications of nanomaterials in a range of disci- try engineers seeking a better understanding of the Students will be asked to research and write a sen- plines spanning from semiconductors and displays photolithographic process as used to fabricate inte- sor case study or to research and demonstrate to to biochips. The topics covered will include synthe- grated circuits. All material presented is supported the class a specific sensor technology. Although not sis, fabrication and optoelectronic characterization. with examples from actual processes used by indus- required, it is recommended students take EE Selected device applications will emphasize (1) try leaders. 4 credits 550/650, Introduction to Sensor Microfabrication transistors based on silicon quantum dots and car- and EE 552/652, Micro-electro-mechanical Systems bon nano-tubes, (2) displays, and (3) DNA/Protein EE 554/654 Reliability and Failure of Electronic in conjunction with this course. 4 credits biochips. This cross-disciplinary course is for elec- Devices, Packages, and Assemblies trical engineering as well as biologists wishing to (Formerly ECE 580-RFD) EE 557/657 Technology of Photoresists learn the complementary technologies and assess- An overview of electronic devices, packages and (Formerly ECE 580-TP) ing the impact of nanostructured materials on their their reliability. Defects, contaminants, and yield; Modern semiconductor fabrication relies heavily on respective disciplines. 4 credits the mathematics of failure and reliability; mass the use of photoresists to fabricate integrated cir- transport-induced failure; electronic charge- cuits. This course will introduce basic chemical and EE 550/650 Introduction to Sensor Microfabrication induced damage; environmental damage to photo-physical properties of resists, with a discus- (Formerly ECE 580-ISM) electronic products; packaging materials, process sion of resists that are currently in use. Various Tired of simulating and modeling everything that you and stresses; degradation of contacts and package resist-processing steps involved in lithography, such have ever learned about semiconductor devices? interconnections; degradation and failure of electro- as surface-preparation, coating, optical/radiation This course brings you into the lab to give you the optical materials and devices; characterization and exposure, developing, etching and resist stripping opportunity to build microsensors. We will cover failure analysis of materials and devices; future will be presented. We will conclude with a discus- fundamental processing methods and introduce directions and reliability issues. 4 credits sion of materials used in emerging soft lithographic some background information on sensor operation. techniques that allow nanometers resolution. The rest of the course will be spent learning how to EE 555/655 Simulation & Modeling of VLSI Interconnect 4 credits grow oxides, dope semiconductors, carry out a full (Formerly ECE 580-SMV) photolithography process, evaporate metal, and Review of Maxwell’s equations and mathematical EE 560/660 Introduction to Electronics perform chemical processes that result in a fully methods relevant for computational electromagnet- and Instrumentation operational sensor. By the end of the course, you ics for VLSI. Boundary element / method of (Formerly ECE 500) will have fabricated and tested your devices. This moments, finite difference (2D/3D), finite element Review of fundamental electronics components and course is recommended if you have an interest in and stochastic methods for computation of capaci- design: passive components, transistor circuits, op the MEMS and Semiconductor Sensors courses. Lab tance and resistance. Fast capacitance simulation amps, RC circuits, frequency domain, and time fee of $100 is required. 4 credits using multipole and random walk methods. domain response. Feedback theory, op amp limita- Inductance simulation using partial equivalent ele- tions, precision op amp circuits. Noise, interference, EE 551/651 Introduction to Liquid Crystal Displays ment models (PEEC). Introduction to finite grounding, and shielding. Phase-locked loops, lock- (Formerly ECE 580-LCD) difference time domain (FDTD) and full-wave solu- in amplifiers. Practical advice on component Introduction to nematics, cholesterics, smectics, tion techniques. Large-scale extraction of selection and circuit design. Equipment and circuit and polymer-dispersed liquid crystals. Course capacitance, resistance and inductance from layout: demonstrations in class. Homework includes Pspice emphasizes methods used to probe electro-optic algorithms and models. Construction of equivalent circuit simulation problems. 4 credits properties of liquid crystals related to display device circuits and network reduction techniques. applications. Course delineates anisotropic interac- Wireability issues in VLSI circuits. Rents rule and EE 561/661 Analog Integrated Circuit Design tion of liquid crystals with applied electromagnetic stochastic wiring distribution models. Circuit design (Formerly ECE 571) fields. Consequences of liquid crystal-electric field issues related to interconnect: a discussion based Design techniques for analog integrated circuits. responses in relation to various addressing schemes on analytical models and metrics for noise and Silicon bipolar and JFET analog integrated circuit (passive vs. active) used in twisted nematics, super- delay. Inductance effects in high speed digital cir- design. Technology overview, device structures, twisted nematics, and ferroelectric liquid crystal cuits. Interconnect issues related to clock Ebers-Moll equations, hybrid-pi model. Single-stage displays, are discussed. LIQUID, a general-purpose distribution and power grid networks. Brief review amplifiers, current sources, active loads, output LCD simulation software, is used to simulate active of circuit simulation algorithms relevant to inter- stages. Operational amplifiers, bandgap references, matrix liquid crystal displays properties, switching connect such as AWE and scattering parameter frequency response, feedback, stability. Design project. speeds and viewing angles of LCD’s. Includes lab. based methods. Simulation of frequency dependent 4 credits 4 credits elements using convolution techniques. Review of lossy transmission line algorithms in SPICE . EE 562/662 Digital Integrated Circuit Design EE 552/652 Micro-electro-mechanical Systems Thermal and reliability issues and models relevant (Formerly ECE 572) (Formerly ECE 580-MEM) to VLSI interconnect. The course will include proj- Design techniques for digital integrated circuits. Combining the miniaturization and processing tech- ects where students will implement algorithms and Silicon bipolar and MOS digital integrated circuit niques of semiconductor technology with also use existing simulators and extractors to obtain design. Technology overview, device structures, mechanical structures, MEMS offer new opportuni- hands on experience. 4 credits modeling. Standard logic families. NMOS and CMOS ties for ‘devices’ and solutions. Graduating from logic design. Regenerative circuits and memory. initial development as electro-mechanical locks, EE 556/656 Semiconductor Sensors Design project. 4 credits MEMS devices are now ubiquitous in mirror assem- (Formerly ECE 580-SSE) blies for digital projectors, and optical handlers. The emergence of MEMS and the continual size EE 563/663 Analog CMOS Integrated Circuit Design Other applications include micro-manipulators, reduction of the transistor have enabled engineers (Formerly ECE 580-AC) fluid handling units, micro-turbines, and even rock- to design micro- and nano-sensor technologies for a Design techniques for CMOS analog integrated cir-

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cuits. Technology overview and models. Single-stage will be the Altera NIOS Development board and the EE 576/676 Algorithms for VLSI Design & Test amplifiers, current sources, biasing, active loads, NIOS soft core processor. Prerequisites: EE (Formerly ECE 580-VDT) class AB output stages. Low-voltage design, 570/670 or consent of instructor. 4 credits Computer-aided Design (CAD) of integrated circuits bandgap references, operational amplifiers, fre- require complex algorithms and software tools to quency response, compensation. Design project. EE572/672 Advanced Digital Design — enable designers develop designs that meet a host of 4 credits Timing Analysis and Test specifications such as area, performance, testabili- (Formerly ECE 580-TNT) ty and power to state a few. In this course we review EE 564/664 High Speed Interconnect Design This course focuses on timing and design-for-test the underlying algorithms and methods used in (Formerly ECE 558) topics in FPGA and ASIC design and implementa- design of integrated circuits and provide insight into Analysis, design, and measurement of digital inter- tion. The course uses industrial EDA tools. Topics the challenges faced today. This course may be of chip interconnects operating at multi-gigabits per covered include synchronization and crossing clock interest to graduate students in the area of digital second. Topics include: transmission line analysis, domains, metastability and synchronization failure, circuit design where the students are introduced to timing analysis, measurement equipment and tech- timing-driven logic synthesis, static timing analysis, underlying algorithms and principles of design tools niques, lossy and coupled transmission lines, skew and jitter analysis, clock distribution, phase- used in design of integrated circuits. This under- frequency domain analysis, differential signaling, and delay-locked loops, scan testing and automated standing will enable the designer to make equalization, modulation techniques, and design test pattern generation. Prerequisite: EE 571/671 appropriate educated choices required during the methodology. A design/research project is used to or consent of instructor. 4 credits design process. The next type of students interested give students practical insight into high-speed dif- in this course will be students of computer science ferential signaling challenges. 4 credits EE 573/673 Computer Organization and Design who are interested in seeing applications of algo- (Formerly ECE 580-COD) rithms and optimization techniques to the integrated EE 565/665 Introduction to Wireless Integrated Basic computer organization. Computer compo- circuit design process. 4 credits Circuit Design nents: memory systems, including caches, computer (Formerly ECE 580-ACD) arithmetic, number representation, floating point EE 580/680 Linear Systems Analog integrated circuit design for wireless com- arithmetic processors, controllers, input/output, (Formerly ECE 550) munications. Transistor models, biasing, distortion, buses, DMA. Data formats, addressing modes, This course introduces the State Variable represen- matching networks, noise modeling, low noise ampli- instruction sets, and microcode. Study of the design tation of linear dynamical systems and studies a fiers, mixers, power amplifiers. Design project. of a small computer from the logic level on up. This large body of State Space techniques to reveal both 4 credits course fills the gap between the EE computer engi- inner structure and external behavior of the systems neering design courses and CSE 521/621 Intro- modeled in this way. The course develops and uses EE 570/670 Advanced Logic Design duction to Computer Architecture. Prerequisites: a general framework for treating time-varying linear (Formerly ECE 573) EE 570/670 recommended. 4 credits systems. Major emphasis is placed, however, on the This course constitutes a basic introduction to the time-invariant systems, whose structure and design and implementation of computer logic. Basic EE 574/674 CMOS Digital VLSI Design I dynamics are investigable and knowable to the very principles of discrete logic will be presented, includ- (Formerly ECE 574) utmost detail. Both continuous-time and discrete- ing boolean algebra, finite-state machine design, An introduction to CMOS digital IC design covers time linear systems are explicitly studied. The logic minimization and optimization using both basic MOS transistor theory; operation of basic course provides a strong body of foundational mate- hand-compiled (Karnaugh maps) and CAD tool CMOS inverter; noise margins; switch level model- rial, which is utilized either explicitly or implicitly in based techniques. Students will apply logic design ing of MOS devices; capacitive characteristics of virtually all applications-specific areas pertaining to techniques to PLD (Programmable Logic Devices) MOS devices; introduction to device fabrication, system analysis/design and signal/information pro- and FPGA (Field Programmable Gate Array) design rules and layout issues; power consumption; cessing. The major topics covered are: canonical devices. In addition, students will learn the basics of gate design/transistor sizing; pass transistors and realizations, equivalent systems, canonical transfor- the hardware design language Verilog. The last part complimentary pass transistor logic; dynamic domi- mations, canonical decompositions, solution of state of the course will include a Verilog design project no and precharge/discharge circuits; memory equations, stability, controllability and observability, using the ModelSim simulation/compilation tool. element design (RAM/ROM/flip-flops) and subsys- design of asymptotic observers, state-feedback com- This course or its equivalent is a prerequisite to all tem design (adders, multipliers, etc.). An pensation schemes. Linear Quadratic Regulator and other EE Electronics Design courses. 4 credits understanding of basic digital design concepts is Kalman Filter are also introduced. 3 credits assumed. Lab exercises use industry-standard EE 571/671 System On a Chip (SOC) Design with design tools. Laboratories include circuit validation EE 581/681 Introduction to Signals, Systems and Programmable Logic and characterization. Prerequisite: EE 570/670. Information Processing (Formerly ECE 559) 4 credits (Formerly ECE 544) Programmable logic, such as FPGA and CPLD This course provides the essential mathematical devices, has become a major component of today’s EE 575/675 CMOS Digital VLSI Design II tools and analytical techniques for the analysis of digital designs. This course builds on skill gained in (Formerly ECE 575) continuous-time and discrete-time systems. Basic EE 570 to teach students how to implement complex Concentration on advanced digital VLSI circuit signal and system characteristics — linearity, time- digital designs with programmable logic. A design is design techniques. Architecture and micro-architec- invariance, convolution and correlation — are first first created in Verilog, a high-level Register ture of VLSI components, clocking schemes, examined from the time domain perspective. We Transfer Level (RTL) language, and simulated. input/output circuits, and special functional blocks then proceed to study a family of transforms - Synthesis to a targeted programmable logic device such as random access memories, read only memo- Fourier Series, Fourier Integral Transform, Laplace is then performed. Common synthesis problems are ries and programmable logic arrays. The course Transform, Discrete Time Fourier Transform (DTFT), discussed while presenting the student with a com- covers design tradeoffs, especially considering cost, Discrete Fourier Transform (DFT) and z-Transform prehensive understanding of the operation of the power and performance. The course devotes a con- — which take the study of these systems to a deep- tools. Systems on a Chip (SOC) design will also be siderable amount of time to layout, parasitics and er level and introduce useful properties which the covered. The course has a project orientation - stu- performance verification. Introduction to design and time perspective alone does not reveal. Basic appli- dents will take their designs from concept to RTL verification tools with hands-on experience. cations in information processing, communication verification and synthesis, then to programmable Prerequisites: EE 574/674, familiarity with MOS and control fill out the mathematically derived device implementation. The Mentor Graphics FPGA transistor operation; computer architecture and results. A greater portion of the syllabus in EE Advantage tools will be used. The hardware platform organization; logic design. 4 credits 581/681 is allotted to continuous time signals/sys-

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tems than to discrete time signals/systems, because image formation, analog and digital video signals Multi-path fading and its effects on performance and the latter are taken up in detail in other information and standards, and spatio-temporal sampling. diversity signaling. Synchronization architectures. processing courses, particularly EE 582/682. A goal Subsequent topics include motion estimation, seg- Spread spectrum. Channel equalization. Pre-requi- of the presentation in EE 581/681 is to impart the mentation and tracking, video filtering and video site: EE591/691 or equivalent or permission. essential unity of all the transforms and the almost standards conversion. Students are familiarized 3 credits perfect correspondence of approach in continuous- with video compression techniques and standards time and discrete-time contexts. The student (JPEG, MPEG2, H.261, H.263), and model-based EE 593/693 Analytical Techniques in Statistical Signal becomes a well-equipped practitioner who knows the video quality estimation. Students will gain working Processing and Communications way around the entire territory. This course is a use- knowledge of these video techniques through class (Formerly ECE 525) ful prerequisite or co-requisite to EE 582/682 and projects. Familiarity with digital signal processing Development of the mathematical techniques need- all other courses in the information processing area. and transform methods is desirable. Prerequisite: ed to analyze systems involving random variables 3 credits EE 584/684. 3 credits and/or stochastic processes with particular applica- tion to communications and instrumentation. Topics EE 582/682 Introduction to Digital Signal Processing EE 586/686 Adaptive and Statistical Signal Processing include Bayes Theorem (discrete and continuous (Formerly ECE 551) (Formerly ECE 554) forms), Tchebycheff inequality, Chernoff Bound, The representation and processing of signals and The field of adaptive filters and systems constitutes Central Limit Theorem, stationary processes and systems in the discrete or digital domain is the pre- an important part of statistical signal processing. linear systems, mean square estimation, Poisson ferred mode in today’s computer and information An adaptive system alters or adjusts its defining process, Gaussian process, Markoff process, and driven technologies. DSP provides the core building parameters in such a way that it improves per- series representations. MATLAB and the MATLAB block from cell phones to modems, HDTV to video formance through contact with the environment. Statistics Tool Box are used in this course. 3 credits conferencing, or from speech recognition to MP3 Adaptive filters are currently applied in such audio. This classes covers the fundamental concepts diverse fields as communications, control, radar, EE 599/699 Reciprocity Course and mathematics including representation and seismology, and biomedical electronics. This course (Formerly ECE 595) analysis of discrete time signals and systems, Z- will cover the theory and applications of adaptive OGI students admitted to a degree program have the Transforms, Discrete-Time Fourier Transform linear systems. Topics include Wiener filters, least opportunity to take classes at other Oregon (DTFT), and the Discrete Fourier Transform (DFT), squares, steepest descent, LMS, RLS, Newton’s University System schools under the Joint Campus sampling and windowing techniques pertaining to method, FIR and IIR adaptive structures, and Agreement or Reciprocity Agreement. Contact the discrete time processing of continuous signals, Kalman filters. Applications covered include noise Department of Graduate Education for details. analysis and design of recursive (IIR) and non- canceling, signal enhancement, adaptive control, Courses taken under these agreements are listed recursive (FIR) digital filters, and applications of the adaptive beam-forming, system identification, and as 599/699. Variable and repetitive credit Fast Fourier Transform (FFT) to convolution, spec- adaptive equalization. The theory also lays the tral analysis, and audio processing. Prerequisite: EE foundation for study in nonlinear signal processing EE 601 Prequalifying Ph.D. Research 581/681 or equivalent. 3 credits with neural networks and will be introduced in the (Formerly ECE 600) later half of the class. This course should be of Supervised research participation. Pre-qualifying EE 583/683 Digital Signal Processing II interest to electrical and computer engineers spe- Ph.D. research prior to passing qualifying (Formerly ECE 552) cializing in signal processing and the information examination. Variable and repetitive credit This follow-up course to EE 582/682 examines sev- sciences. This course should also be taken as back- eral widely used advanced signal processing ground for additional classes offered in artificial EE 603 Ph.D. Dissertation methods. Topics include computational complexity neural networks, connectionist models, and (Formerly ECE 800) considerations in DSP algorithm development; multi- machine learning. Prerequisites: EE 582/6821 plus Research toward the dissertation for the Ph.D. degree. rate signal processing; filterbanks and wavelets, and an undergraduate level course in probability Variable and repetitive credit their application in audio and image processing (e.g. and statistics. 3 credits MPEG standards). Topic coverage is weighted toward the interests of the students enrolled. 3 credits EE 590/690 Digital Communication I (Formerly ECE 526) APPLIED MATHMATICS EE 584/684 Introduction to Image Processing Communications system models for various modula- MATH 510/610 Multivariate Calculus and (Formerly ECE 542) tion and demodulation band limited base-band Differential Equations This course covers basic image processing princi- systems. Optimum detection, source encoding/ (Formerly CSE 555a) ples and techniques with a brief introduction to decoding. Waveform communications and signal This course reviews essential mathematical meth- machine vision. Students acquire theoretical and space representation. Pre-requisite: undergraduate ods required for the analysis of continuous time working knowledge of image processing approaches course in digital or analog communications. processes in science and engineering, focusing on including image representation, transform methods, 3 credits image filtering, multi resolution representation, multivariate differential and integral calculus and edge detection, texture characterization, and motion EE 591/691 Digital Communication II the solution of ordinary differential equations. analysis. This course demonstrates application of (Formerly ECE 527) Calculus topics include: continuity and convergence, these methods to image enhancement, image Channel noise and capacity. Typical random and fad- Taylor’s theorem, gradients and directional deriva- restoration, and image compression, with emphasis ing channels, optimum filters and signal design. tives, chain rules, and implicit functions. In the on image quality metrics based on human visual Probability of error in noisy band limited channels second half of the course, the fundamentals of ordi- perception. Selected areas in machine vision for different modulations. Optimal design of BFSK, nary differential equations are examined. include image segmentation, elementary techniques BPSK, QPSK, m-QAM, CPM modulators and demodu- Differential equations topics include: exact, numeri- in pattern recognition, and object representation. lators via MAP and ML techniques. Phase lock loops cal and power series solution methods, systems of Numerous examples show how to apply these tech- and Costas detectors. Energy-bandwidth tradeoffs in coupled ODEs, qualitative analysis of autonomous niques. Prerequisite: EE 582/682. 3 credits digital modulation. Pre-requisite: EE 590/690 or per- and nonautonomous linear and non-linear systems, mission, and statistics with probability. 3 credits linearization of non-linear systems, and Lyapunov EE 585/685 Introduction to Digital Video Processing stability analysis. An introduction will also be pro- (Formerly ECE 543) EE 592/692 Digital Communication Systems vided to the topics of bifurcations and chaos. This course introduces digital video processing for (Formerly ECE 529) 3 credits multimedia systems. It begins with video capture, Convolutional and RS coding, Viterbi decoding. 84 COURSE DESCRIPTIONS | OGI

MATH 511/611 Introduction to Discrete on application of the concepts. Topics include MST 506 — Special Topics Numerical Methods Poisson and Gaussian processes, Markov chains, (Formerly MST 58X) (Formerly ESE 500) spectral analysis, and Monte Carlo simulation. The Special topics courses are offered in areas of par- This course provides an introduction to discrete primary analysis tool for this course is Matlab. ticular relevance to the research interests of faculty numerical methods. Lectures cover the theory and 3 credits or in response to industry needs. Special Topic application of methods for the numerical solution of courses are subject to change and are offered initial-value, boundary-value and mixed initial- MATH 523/623 Combinatorics and Graph Theory intermittently. boundary-value problems by finite differences, Discrete mathematical models based on combina- weighted residuals, numerical integration and finite torics and graph theory have a wealth of MST 507HC Seminar for Healthcare Management elements. Prerequisite: Calculus. 3 credits applications, to computer science, communications, A Healthcare Management student participation transportation, genetics, experimental design, seminar and a topical paper or product. 2 credits MATH 513/613 Linear Algebra scheduling, and so on. This course is an introduction This course covers the fundamentals of linear alge- to the tools of combinatorics from an applied point MST 509 Commercialization Practicum bra. Major topics include: vector spaces and of view. Topics covered include counting techniques, (Formerly MST 543) subspaces, linear transformations and linear opera- generating functions and recurrence relations, mod- Student teams produce assessments and plans for tors, orthogonal bases and orthogonal projections, eling using graphs, digraphs and weighted graphs, bringing new technologies to market. The teams and the properties of eigenvalues and eigenvectors. graph properties and algorithms. 3 credits evaluate the commercial potential of real technolo- Particular emphasis will be given to: similarity gies, including those under development at OHSU. transformations to canonical forms such as the MATH 525/625 Partial Differential Equations Wherever possible, industry advisors will mentor Jordan form, canonical operator representations This course addresses the most common of the students in their area of expertise within the design, such as the Spectral Factorization and the Singular Partial Differential Equations used in science and management and product manufacturing process. Value Decomposition, and the interpretation of all engineering, namely second order linear equations. Each team’s final paper, which may include market matrix results as an application of general operator Topics covered are complex variable theory, a research, a design for a manufacturable product, theory to the particular class of finite-dimensional review of Linear Algebra (including vector spaces, profiles of desired management teams, licensing linear operators. Properties of determinants, matrices, and eigenvectors), Fourier Series, Fourier plans, tech-marketing feasibility and/or preliminary Moore-Penrose pseudoinverse, and solutions to sys- and Laplace Transforms, and Elliptic, Parabolic and startup business plan, will be submitted to the insti- tems of linear equations will also be studied in detail. Hyperbolic equations. The use of Separation of tution that originated the technology. M.S. in 3 credits Variables in solving these types of equations will be Management students may be able to extend a focus as will Boundary Conditions of the first, sec- work from this practicum into their MST 550 MATH 517/617 Probability and Statistics ond and third kinds. Sturm-Liouville theory for Capstone project. 3 credits (Formerly CSE 544a and CSE 544b) expansion and solutions in the Cartesian and Polar This course provides an introduction to probability, coordinate systems will also be discussed. 3 credits MST 510 Principles and Trends in statistical inference and statistical analysis. The Technology Management aims of the course are to provide scientists and MATH 527/627 Applied Functional Analysis This course is about how companies choose, engineers with a comprehensive introduction to (Formerly ECE 580-AFA) acquire, and develop the technologies that they use essential concepts in probability and statistics, and This course aims to make the guiding ideas of Real to develop, manufacture, deliver and support their for students to gain proficiency in applying these Analysis, Complex Analysis and formal Functional products. We look at these practices both from the concepts to data analysis. Topics include explorato- Analysis accessible to students, researchers and vendor and buyer points of view, and also consider ry data analysis, sampling distribution theory, practitioners in applied engineering areas. Basic internal technology development for internal use. confidence intervals, hypothesis testing, maximum algebraic, geometric and measure structures are Other topics addressed include profitably managing likelihood estimation, linear regression, goodness- defined, including: Group, Ring, Field, Vector Space, technology cycles, standards, technology forecast- of-fit, ANOVA, and parametric and non-parametric Inner Product Space, Topological Space, Metric ing, and the technology startup company. Related tests. The primary analysis tool for this course Space, Measure Space, Probability Space, Normed topics such as competitive analysis, managing is Excel. 3 credits Linear Space, Banach Space, Hilbert Space. We researchers, and maintaining an innovative organi- study the distinctive properties of mappings zational atmosphere are dealt with in MST 573 and MATH 519/619 Engineering Optimization between mathematical objects of these sorts, rang- MST 514. The format includes lectures, discussions, (Formerly CSE 5556 and CSE 556b and ECE 555) ing from the simplest set correspondences, through guest speakers, and team and homework projects. This course introduces advanced numerical opti- the basic real and complex functions, up to the high- 3 credits mization methods for quantitative work in science ly structured class of Hilbert Space operators, with and engineering. The course will cover important particular emphasis on generalized Fourier MST 511 Quality Management traditional methods for constrained and uncon- Analysis. Knowledge of this material greatly The course covers total quality management (TQM) strained multivariate optimization, including line enhances one’s ability to read sophisticated techni- from the managerial vantage point, that is, behav- search methods and gradient-based techniques, as cal material and to conduct one’s own advanced ioral and operational management aspects, well as linear, quadratic and dynamic programming. work in any highly mathematical area. 3 credits excluding sophisticated statistical analysis, of TQM. In addition, more heuristic techniques such as Classroom discussion, based on the participants’ genetic algorithms, differential evolution and simu- experiences and assigned readings from the text- lated annealing will also be presented. The primary MANAGEMENT IN SCIENCE book and cases, is the primary source of learning. programming tool for this course is Matlab. Some Lectures are used, but generally as a basis for a knowledge of linear algebra and multivariate calcu- AND TECHNOLOGY facilitated discussion led by the instructor. The lim- lus is required, as is a basic grasp of probability itations of TQM also are discussed, given the and statistics. 3 credits MST 502 Independent Study inherent risks of excessive optimism associated with Independent study allows a student to work one-on- any social trend or perceived panacea. 3 credits MATH 521/621 Random Processes and Simulation one with a faculty member on selected topic(s) of This course provides an introduction to random interest. Registering for independent study requires MST 512 Project Management processes and their application in science and engi- pre-approval from the faculty member and the stu- This is an introductory course that addresses the neering. The approach is non-theoretical, where key dent’s academic department. field of project management from a management results are explained heuristically and the focus is Variable and repetitive credit perspective rather than an engineering or mathe-

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matical perspective. Accordingly, we will adopt the strategy of the business unit. Therefore, some ses- theory and practice. A range of theoretical perspec- life cycle of a project and structure this course in sions will focus on cross-national decisions and tives is reviewed, and students are encouraged to three segments: Project Initiation, Project others on managing across nations. 3 credits compile their own approach by combining those pre- Implementation, and Project Conclusion. Class will sented. Extensive use is made of cases and actual be conducted in the setting of a seminar/workshop MST 517 Supply Chain Management: examples drawn from the readings and from course environment with guest speakers on real life Advanced Modeling participants’ experiences. Taking MST 520 first project experiences. 1 of the 4 credits is dedicated This course will introduce optimization in supply is recommended. 3 credits to Effective Presentation Skills. 4 credits chain modeling. The emphasis will be mainly on large-scale real-world supply chain distribution net- MST 523 New Product Development MST 513 Operations Management and Practices work design. The major skills taught are problem Technology integration and creating innovative envi- This course will introduce the study of business definition, model formulation, and solution analysis. ronments have been critical to developing profitable process management in the operation of a firm. We There will be use of commercial software such as products in today’s technology oriented companies. will utilize a systems view with an emphasis on the SAILS and GSCM for large mixed-integer program- The course will review cases and published articles understanding of current process performance as ming. Students will also be introduced to GAMS for addressing key issues in new product development. well as learning practices to enable higher levels of hands-on mathematical modeling. Other topics of Topics such as disruptive technologies, technology performance. The course will engage students from the course will be focused on how to manage finan- integration, concurrent engineering, and managing the perspective of a typical vice president of opera- cial uncertainty under market chaos using real technological innovation will be covered. Students tions, in order to ensure a comprehensive view of options methodology with Crystal Ball Monte Carlo- will form teams and develop a plan for a new operations from strategic through daily control. based software. 3 credits product. The plan will include risk assessments 3 credits in areas such as manufacturing, design, test, etc. MST 520 Managing Organizational Relationships The team will make several presentations through- MST 514 Issues in R & D Management This course develops participants’ ability to under- out the course. 4 credits Participants examine issues in managing R&D and stand and influence human behavior within technological innovation in an environment of technology-intensive organizations. By studying and MST 524 eBusiness: Strategy and Roadmap increasing time- and competence-based competi- applying four theory-based frames (structural, Successful companies are pursuing focused e-busi- tion, a competition that is simultaneously global and human resource, political, and symbolic), students ness strategies that build new kinds of enterprises. local in both markets and technology, where learn to identify and fill gaps in their current These enterprises are (re)designed to attract, competitors draw on an existing technology base understanding of challenging organizational situa- serve and retain customers, manage suppliers, that supports incremental innovation through radi- tions. The course also analyzes the influence inform and empower employees better than ever cal innovation, and where quality is a given. processes and network of relationships required for before. The course will provide students with a Particular attention is given to R&D management managing research scientists, engineers, and practical understanding of what it takes to develop issues in integrating technology into business strat- other professionals, both as individuals and in the “digital enterprise”. The first part will address egy and operations, managing internal development teams, in a fast-changing environment. Self- the issue of developing a robust business model and external sourcing of technology, seeking assessment, networking, and developmental that capitalizes on the new opportunities. The sec- competitive advantage through collaborative relationships are explored as means of devel- ond part will cover the e-business architecture and advantage, and building new technical competence oping influence and impact. 4 credits applications (like customer relationship manage- as a part of every project. Key trends, new concep- ment, supply chain management, selling chain tual frameworks, management tools and techniques, MST 521 Human Resource Management in Science management), and how to develop and implement and best practices in R&D management are exam- and Technology the e-business strategy. Cases and articles will be ined through presentation, interactive class This course focuses on the development, implemen- utilized to illustrate the successful strategies and discussions, selected readings, case studies, and a tation, and evaluation of human resource techniques used by leading companies. Taking number of invited speakers from both small and management (HRM) systems, and the relationship MST573 and MST530 previously is highly recom- large companies. 3 credits between an organization’s HRM practices and the mended. 4 credits organization’s effectiveness and competitive suc- MST 515 Supply Chain Management cess. Specifically, the course addresses the choices MST 530 Strategic Management and Planning Supply Chain Management (SCM) denotes a total an organization must make in three HRM policy This course focuses on the analysis of fast-changing system approach to the management of all of those areas: organization of work and employee influence; (“hyper-velocity”) competitive environments and on activities involved in physically moving raw materi- personnel flows and development; and measurement the decision-making process leading to the formula- als, inventory and finished goods inventory from and rewards. We consider the perspectives of both tion and implementation of strategy. The class point of origin to point of consumption. SCM is a sys- the line manager and the HRM specialist in examin- explores using time, knowledge, and technology as tem approach to managing the entire flow of ing these three policy areas. The course also competitive advantages, managing strategic change, information, materials, products and funds to and includes a limited overview of employment law, with and developing strategic plans for a future that from suppliers and end-customers. 3 credits a particular focus on recent cases and changes in cannot be known with certainty. Several different employment legislation. 3 credits models for strategy formulation such as game theo- MST 516 Global Logistics and Financial Management ry, portfolio analysis, the “Five-Forces”, and The course emphasizes operations and logistics in MST 522 Change Leadership for Building “Competing on the Edge” will be examined. As the firms that source, produce, distribute and market in Effective Organizations ultimate test of strategy in the business world is multiple nations. The management of logistics in This course focuses on designing effective organiza- running a company, class teams will play a such firms differs from its domestic counterpart tions and managing change in organizations in which computer simulation of operating a multi-product along several key dimensions. First, the company engineering, manufacturing, and/or scientific tech- business in a dynamic, competitive environment. must be able to identify and analyze factors that dif- nologies are critical. Tools for assessing the need for Prerequisites: MST 572, MST 573, MST 520 or fer across nations and that influence the reorganization and implementing structural changes instructor permission. 4 credits effectiveness of the logistics function. In addition, are emphasized. The course pays special attention because of the distances involved, transportation to organizing for lateral coordination and integra- MST 531 Software Commercialization and distribution are of greater significance. Finally, tion, as this is a required capability in technology- This course investigates the rapidly changing soft- these geographically dispersed facilities and mar- intensive organizations. Students are invitedto ware industry, and how to work in and run a kets must be integrated and managed to enhance the consider the relationship between organizational commercial software company. The course provides

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real-world perspective on the current issues implementing and executing high-performance program, this course will have more detailed empha- involved in creating and commercializing software. strategic alliances. 3 credits sis on business planning, program design, scheduling, Because the business models for hardware and soft- and resource management (e.g. human resources, ware companies are quite different, the course MST 549 Applied Business Forecasting capital equipment, software infrastructure). focuses on the special problems of marketing, entre- This web-based course emphasizes generating and 4 credits preneurship, globalization, and alliances implementing business forecasts. It is designed for experienced by software firms. Special attention is students who want to know how forecasts are actu- MST 563 The Regulation and Legislation of Health given to the creation of value, standardization, and ally developed and utilized, emphasizing modern Care Delivery competitive strategy for high-volume software mar- statistical methods that are widely used to generate The course reviews how governmental and non-gov- kets. The course includes lectures, discussions, business forecasts. Specific applications to business ernmental organizations influence health care speakers, assignments and class presentations. include forecasting sales, production, inventory, delivery. Special emphasis is placed on current reg- 3 credits macroeconomic factors such as interest rates and ulatory and legislative initiatives. 4 credits exchange rates, and other aspects of both short- and MST 540 International Management in Science long-term business planning. Topics include a statis- MST 564 Business Planning and Strategy in the Health and Technology tical review, data considerations, model selection, Care Industry Topics in this course include trends in the conduct of moving averages and exponential smoothing, The strategic management and planning of health international business, the international business regression analysis, time-series decomposition, care functional units, clinics and hospitals in today’s environment, the operation of multinational enter- Box-Jenkins (ARIMA) models, optimal forecast com- fast-changing technology intensive environments is prises, international technology transfer, and the bination, and forecast implementation. Anybody extremely challenging. It will be shown that the special considerations associated with managing on seeking to enhance his or her understanding of busi- planning and management of strategy at all levels, the international level. 3 credits ness forecasting from an applied perspective would not just the senior executives, is essential to the benefit from taking this course. Knowledge of basic organization. This class will focus on analyzing, MST 541 Leadership and Communication Skills statistics and regression analysis is highly recom- planning, decision-making, formulation of strategy This course helps students develop interpersonal mended, but not required. 4 credits and implementation in a world where “growing” communication and negotiation skills for effective today’s organization into an essentially unknowable leadership. The focus is on personal skill building MST 550 Capstone Project: Business Plan future is essential for long-term success. The through effectively influencing in-class working The course objective is to provide students with an approach uses a combination of lectures, materials groups. We explore nine leadership styles to discov- opportunity to demonstrate, through an integrative drawn from a text, and illustrative case studies, er where and when each is most effective. Students project, knowledge gained from other course work combined with first-hand information provided by discover and assess their negotiations skills based taken in the MST program. Business plans are use- invited speakers drawn from strategic decision mak- on five standard negotiation styles. Effective inter- ful in a variety of ways, including a bid for equity or ers in the health care industry. 4 credits personal communication is the core competency debt financing by startup companies, and requests from which we build the skills of personal influence, for additional financing by existing companies. The MST 565 Human Resources in Health Care coaching, conflict resolution, personal awareness, common theme in these situations is the undertak- This course focuses on the management of people in and leadership. Personal reflection and learning are ing to convince others to commit resources to bring healthcare organizations. This course is designed to required for maximum skill development. 3 credits new or additional products or services to market in provide the knowledge and tools for healthcare man- a profitable manner. Business plans are also useful agers to manage people in all aspects of their work: MST 542 Business Ethics and Corporate planning documents, aiding managers in their recruiting, hiring, motivating, and managing per- Social Responsibility efforts to develop viable strategies and communi- formance, conflict and change. In addition, aspects This course focuses on ethical dilemmas, social cate them to other stakeholders in the enterprise. In of the external environment that affect how people issues and responsibilities, and government regula- this Capstone course students will plan, research, are managed in the workplace, including employ- tions and influences. First, the course examines prepare and present a business plan in teams of 3 to ment laws and regulations and labor unions will be different frameworks for individual decision making 5 members. Presentation of the plan will be in both examined. The general objective of this course is to in an organizational setting. Next, the impact of written and oral form. Prerequisites: MST 571, MST provide the healthcare manager with current think- organizational policies and practices, and the words 572, MST 573, MST 512, MST 520, MST 530 and ing, theory, and best practices for the management and actions of managers on the behavior of individ- instructor approval. 4 credits of people in healthcare organizations in order that uals within those organizations is examined. Finally, s/he can be a better manager of people. 4 credits the course focuses on the relationship between MST 560 The Organization, Financing, and History of organizations and the societies in which they oper- Health Care Delivery in the United States MST 566 Health Care Information Systems Management ate. We consider the perspectives of key (Formerly MST 583) This course is aimed at health professionals, both stakeholders, including government regulators, This course provides a historical context for the cur- administrators and health care providers, who more community representatives, customers, employees, rent system: the current economic drivers, political and more find themselves needing to understand managers, and stockholders, and examine different pressures, ethical issues, and the roles of insurance how to manage the high technology systems, tools views on corporate social responsibility. 3 credits and pharmaceutical companies. 4 credits and products that have become such an integral part of the health delivery spectrum. Today’s health MST 544 Strategic Alliances MST 561 Managerial and Financial Accounting for practitioner has to use technology to find medical This course explores a model of implementing Health Care Professionals information and use accounting systems, personnel strategic alliances, business partnering and joint (Formerly MST 581) systems, health insurance company systems, inven- ventures. The course examines best practices in This is a practical course that addresses the financ- tory systems, patient billing systems, purchasing strategic alliance formation and implementation dis- ing of health care, budgeting, and metrics assessing systems, as well as input and retrieve data. This tilled from approximately 40 different the value-added use of funds. It also includes an course is focused on the business of health care and high-performance international and domestic understanding of the health care revenue cycle and how to understand, use and manage technology and strategic alliances. It offers a well-articulated common tools for managing service/product lines. systems in a medical environment. Its overall goal is framework, which is applicable across a broad 4 credits to give students a conceptual framework for under- range of alliance types. The objective of this course standing how to use technology to reduce costs and is to provide each student with an opportunity to MST 562 Health Care Program Management improve productivity, efficiency and effectiveness in learn practical, effective methods for forming, Focusing on managing and developing a health care their current and future work situations. 4 credits

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MST 567 Health Care Technology — MST 574 Going to Market: Delivering Value to MST 591 Effective Business Writing for New Medical Advances Customers and Shareholders Non-native Speakers Highlighting the role of technology and its influence (Formerly MST 504) Tailored to meet the individual writing needs of man- on treatment and health care delivery in the US, this The course will provide an understanding of the agement professionals, this course reviews and course includes the role of medical technology sup- tools, mechanics and management of operational practices the English grammar, punctuation, and pliers in shaping delivery as well as decision-making marketing implementation processes in high-tech- stylistics that challenge the advanced-level and strategy for acquisition of new technology. nology environments. Integrating lectures, class non-native and bilingual speaker of English. Using 4 credits discussions, case studies, videos and individual a highly interactive format, this course addresses papers and team projects, the course emphasizes both electronic and traditional managerial writing MST 568 New Trends in Health Care Delivery developing the detailed implementation plan to tasks with the goal of clearer, more concise business This course will be continuously updated to respond bring products or services to market. The goal is to communication. 1 credit to timely topics in health care (e.g. Compliance, show how to turn strategy into practice by imple- Patients Rights, Patient Safety, health care and menting the marketing plan begun in MST 573, MST 599 Reciprocity Course he Internet, B to B Internet transactions, etc.). It developing the specifics of a product or service’s (Formerly MST 595) will be taught by a specialist in the appropriate field business model and persuasively outlining the OGI students admitted to a degree program have the and will focus on practical knowledge needed blueprint of the business case. The course drills opportunity to take classes at other Oregon by managers. 2-4 credits down into the operational specifics of pricing, University System schools under the Joint Campus promotion, sales, advertising and customer relation- Agreement or Reciprocity Agreement. See the MST 571 Managerial and Financial Accounting for ship management, e-business and web marketing, Department of Graduate Education for details. Science and Technology supply chain and distribution logistics, channel Courses taken under these agreements are listed (Formerly MST 501) alliance building and implementation standards, as 599/699. Variable and repetitive credit The course focuses on understanding and evaluating metrics and controls. The course complements and financial reports and information for use in making completes the marketing knowledge and expertise decisions, particularly as they pertain to managing in gained through MST 573, which is a prerequisite. science, technology, engineering, and manufacturing. 4 credits 4 credits MST 577 Principles for Process Technology OREGON MASTER OF MST 572 Financial Management for Science Development & Introduction to Manufacturing and Technology This is a project-oriented course on the manage- SOFTWARE ENGINEERING (Formerly MST 502) ment procedures and key underlying concepts for OMSE 511 Managing Software Development The course combines a survey of the relevant effective manufacturing technology planning, devel- This course provides the knowledge and skills need- aspects of micro- and macroeconomics with an in- opment, and introduction into volume production in ed to plan, organize, lead and control software depth study of key concepts in the financial a competitive environment. While emphasis will be projects. Topics include planning and estimating, management of a firm. Key topics include the finan- on semiconductor technology and manufacturing, measuring and controlling, and achieving results in cial structure and financial analysis of the firm, most principles and methodology are generally environments that include a great deal of ambiguity working capital management and short- and long- applicable to both hardware and software technolo- and contradictory information. Quantitative meas- term financing. Particular attention is paid to gy management. Issues of technology strategic ures and risk management will be emphasized. valuation of investment alternatives through study planning, process definition and characterization, Students will prepare project plans for real or hypo- of risk and rates of return, bond and stock valuation, decision-making, technology transfer, product defi- thetical software projects; to include effort, cost and and capital budgeting. The course is designed to nition, yield improvement, and concurrent schedule estimates and risk management plans. achieve a balance between understanding theoreti- engineering principles will be explored to identify Prerequisite: OMSE 500. 3 credits cal foundations and techniques of practical effective management approaches for shortening application. Prerequisite: MST 571. 4 credits time to volume production, minimizing risks, and OMSE 521 Using Metrics and Models to Support minimizing engineering effort. As part of the course Quantitative Decision Making MST 573 Technology Marketing: Planning for Market students will form teams assigned either to develop (Formerly MST 503) This course provides the knowledge and skills need- a corporate procedure for the introduction of new ed to apply quantitative tools based on metrics and The course is designed to provide an advanced products and manufacturing processes, each for a understanding of the marketing process for technol- models of the software product and development specific company situation, applying the concepts process to make decisions under uncertainty. ogy-based products and organizations, from learned, or to carry out a case study of a specific opportunity identification to product introduction Topics covered will include measurement concepts, company’s procedures. There are no prerequisites decision- making under uncertainty, and model and and market development. The course is articulated for the course, although some technical background around three core areas: 1) how to create value for metric development for the software development and/or experience in industry are desirable. enterprise. Prerequisite: OMSE 500. 3 credits the customers, 2) how customers and value change 4 credits along the technology adoption lifecycle, and 3) how OMSE 531 Software Requirements Engineering to develop competitive advantage. Particular MST 590 Effective Business Writing for Management This course covers the principles, tools and tech- emphasis is placed on the front end of the market- Tailored to meet the individual writing needs of niques for requirements elicitation, specification ing process: understanding what customers value management professionals, this course reviews and and analysis. The focus is on understanding the role and then developing strategies and offerings that practices standard conventions in grammar and of requirements in system development and mainte- capitalize on that knowledge. A wide range of topics punctuation, and innovative stylistics using a highly nance, goals of the requirements phase, essential is explored: how to identify value opportunities, how interactive format. The course addresses both elec- difficulties of specifying requirements for real sys- disruptive innovation becomes accepted by the mar- tronic (email) and traditional (letter, summary, tems, and effective methods, tools and techniques. ket place, how values change along with time, how report) managerial writing tasks with the goal of The course covers techniques for formally modeling to segment and select markets, how to understand clearer, more concise business communication. For and specifying software requirements with hands-on and outmaneuver competitors, how to develop a native speakers of English and bilinguals with a experience as well as the role of prototyping in val- marketing strategy that creates strong competitive native-level of written English. 1 credit idating requirements. Prerequisite: OMSE 500. advantage, and, last but not least, how to price 3 credits products and go to market. 4 credits

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OMSE 533 Software Design Techniques This course covers the principles of software design and a survey of design methods, techniques and tools. In-depth and hands-on study of at least one method such as object-oriented design as applied to a realistic industrial problem. It examines the effects of design decisions on the functional and nonfunctional properties of the software (e.g., ease of understanding, maintainability, reuse) and how software engineering principles are applied to make appropriate trade-offs. Students also examine the design process and products in context, including the effect of design decisions on function, quality, cost and schedule. Prerequisite: OMSE 500. CSE students may not receive credit for both CSE 519/619 and OMSE 533 because there is significant overlap in content. 3 credits

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