OGI School of Science & Engineering at OHSU

& Catalog 01/02 Science Engineering OGI School of www.ogi.edu/catalog

OGI School of Science & Engineering 01/02 Catalog (503) 748-1285 fax www.ogi.edu URL (800) 685-2423 toll toll free [email protected] (503) 748-1027 (503) 748-1027 e-mail 20000 N.W. Walker Road Road 20000 • N.W. Walker Beaverton, OR • 97006-8921 phone & Catalog 01/02 Science Engineering OGI School of www.ogi.edu/catalog

www.ogi.edu/catalog

TABLE OF CONTENTS | OGI

WELCOME TO THE OGI SCHOOL OF SCIENCE & ENGINEERING HISTORICAL BACKGROUND AND RECENT MERGER ...... 4 ACADEMIC CALENDAR ...... 4 LETTER FROM THE DEAN ...... 5 SCHOOL MISSION...... 5 EQUAL OPPORTUNITY ...... 5 ABOUT THIS CATALOG ...... 5

OVERVIEW ACADEMIC DEPARTMENTS...... 6 DEGREE PROGRAMS ...... 6 CERTIFICATE PROGRAMS...... 6 STUDENTS NOT SEEKING DEGREES...... 6 COLLABORATIVE/JOINT PROGRAMS ...... 6 ACCREDITATION...... 6

ADMISSIONS PROCEDURES...... 6

TUITION/FINANCES ...... 7

ACADEMIC POLICIES ...... 7

SCHOOL CAMPUS GEOGRAPHIC SETTING ...... 9 LIBRARY...... 9 COMPUTER FACILITIES ...... 9 HOUSING ...... 9 STUDENT COUNCIL ...... 9

ACADEMIC DEPARTMENTS/PROGRAMS/RESEARCH/FACULTY BIOCHEMISTRY AND MOLECULAR BIOLOGY...... 11 COMPUTER SCIENCE AND ENGINEERING ...... 23 ELECTRICAL AND COMPUTER ENGINEERING...... 45 ENVIRONMENTAL SCIENCE AND ENGINEERING...... 67 MANAGEMENT IN SCIENCE AND TECHNOLOGY ...... 79

3 OGI | ACADEMIC CALENDAR

2001 | 2002 ACADEMIC CALENDAR WELCOME HISTORICAL BACKGROUND FALL QUARTER 2001 The OGI School of Science & Engineering’s August 6 Registration begins for fall quarter roots go back to the early 1960s when September 20 Last day to register without late fees Oregon Governor Mark Hatfield and an September 21 New student orientation (Dept of Grad.Ed closed 1-5 p.m.) advisory committee of industrial and educational leaders recommended creating September 24 Fall quarter instruction begins an independent institution for graduate November 12 Registration begins for winter quarter education and research in the Portland November 22-23 Thanksgiving holiday (no classes, OGI offices closed) metropolitan area. In 1963 they established December 3-7 Final exams the Oregon Graduate Center for Study and December 25 Christmas holiday (OGI offices closed) Research, which changed its name to Oregon Graduate Institute of Science and Technology in 1989. WINTER QUARTER 2002 November 12 Registration begins for winter quarter By the 1990s OGI had emerged as a mature January 1 New Year’s holiday (OGI offices closed) institution, and over the course of the decade it awarded more than 1,000 January 3 Last day to register without late fees graduate degrees, offered hundreds of January 7 Winter quarter instruction begins continuing education classes and January 21 Martin Luther King, Jr.’s Birthday workshops, and pursued more than $100 (no classes, OGI offices closed) million in largely federally funded research. February 11 Registration begins for spring quarter Then, in July 2001, laying the groundwork February 18 Presidents’ Day (no classes, OGI offices closed) for the next phase of the institution’s growth, OGI merged with Oregon Health March 18-22 Final exams & Science University, becoming OHSU’s fourth school alongside the Schools of SPRING QUARTER 2002 Dentistry, Medicine and Nursing. February 11 Registration begins for spring quarter The merger was particularly timely because March 28 Last day to register without late fees of the growing need for collaboration April 1 Spring quarter instruction begins between the health sciences, the May 6 Registration begins for summer quarter information sciences and the environmental May 27 Memorial Day holiday (no classes, OGI offices closed) sciences. The resulting benefits will include June 10-14 Final exams the design of new medical instrumentation, June 15 Commencement the development of bioinformatics databases, a better understanding of the relationship between the environment and SUMMER QUARTER 2002 human health, and the cross-fertilization May 6 Registration begins for summer quarter that takes place whenever interdisciplinary June 20 Last day to register without late fees investigations occur. The merger is also June 24 Summer quarter instruction begins helping OGI expand its programs in July 4 Independence Day holiday (no classes, OGI offices closed) computer science, computer engineering September 2 Labor Day holiday (OGI offices closed) and environmental science. September 3-6 Final exams

4 LETTER FROM THE DEAN | OGI

MISSION The mission of the OGI School of Science & Engineering is to provide outstanding graduate and professional education and conduct internationally acclaimed research in science and engineering to meet regional and national needs.

TO ACCOMPLISH THIS MISSION, THE SCHOOL: • provides students with the necessary knowledge, skills and breadth for A LETTER FROM THE DEAN leadership in a technological society; The OGI School of Science & Engineering at Oregon Health & Science • supports, through research, education and training, the people, industries and University is one of the most innovative, exciting and productive schools of organizations that drive the economic its size anywhere in the world. growth of the Pacific Northwest; Indeed the school’s modest size has long been one of its attractions. Students • attracts and develops high-quality faculty, students and staff. have close access, for instance, to top-notch faculty in both the classroom and the research lab, plus we pride ourselves on our flexibility in meeting students’ academic needs. And our recent merger with OHSU further raises EQUAL OPPORTUNITY our stature as one component of a highly regarded institution that shares The OGI School of Science & Engineering our dedication to education and research. at Oregon Health & Science University is committed to providing equal opportunity We have long been extremely successful in competing for limited research and access to all school facilities and funding. A wide variety of public- and private-sector funding organizations academic programs to everyone without believe in us so firmly, in fact, that they support nearly $20 million in regard to race, color, religion, gender, research annually at OGI. Students can thus be assured that OGI faculty are national origin, age, sexual orientation, providing instruction grounded on leading-edge research in their discipline. disability or veteran’s status. Such research-informed education has always been the cornerstone of our approach to graduate education in disciplines such as computer science, ABOUT THIS CATALOG environmental science, electrical engineering and molecular biology. And This catalog is as accurate as possible as of our merger with OHSU will bring added growth in those disciplines as well Oct. 1, 2001. Information contained in the as more interdisciplinary activities, including a major new initiative in catalog may be changed during the course biomedical engineering. of any academic year, including but not OGI’s close relationship with the high-tech industry is also very important. limited to changes in policies, fees, course Many of our part-time students, for instance, are full-time employees of offerings and requirements. This document should not be construed as forming the companies both large and small. As a result, these students acquire basis of a contract. pragmatic knowledge and skills that will enhance their careers, plus our full- time students establish valuable contacts within industry. And classroom interactions benefit from a healthy measure of real-world experience. Classroom and research interactions are further enhanced by the diverse backgrounds of our faculty and students, who represent a cross section of cultures and sub-disciplines. All of which taken together helps explain why our alumni find great success in a variety of career paths — whether their inclinations lead them toward academia, entrepreneurship or advancement with established companies. We pride ourselves on their achievements.

5 OGI | OGI SCHOOL OF SCIENCE & ENGINEERING

OVERVIEW Contact the Department of Graduate • Official transcripts from each college or Education for details. university attended. ACADEMIC DEPARTMENTS • Three letters of recommendation. The OGI School of Science & Engineering has The OGI School also participates in the five academic departments: Biochemistry and Oregon Master of Software Engineering • Official GRE scores. (OMSE) program, a joint program with Molecular Biology (BMB), Computer Science The GRE general test is required for M.S. Portland State University, Oregon State and Engineering (CSE), Electrical and applicants in Computational Finance (GMAT University and the University of Oregon. Computer Engineering (ECE), Environmental could be substituted); Computer Science and Students apply for this master’s degree Science and Engineering (ESE), and Engineering; Environmental Science and through one of the participating schools. Management in Science and Technology Engineering; Environmental Systems Please direct inquiries to (503) 725-2900 or (MST). Research and educational interaction Management, and the Oregon Master of [email protected]. among these departments is ensured in part Software Engineering. by research programs that utilize faculty ACCREDITATION members from multiple departments. This The GRE general test is required for PhD Oregon Health & Science University is encourages the exchange of ideas between applicants in Biochemistry and Molecular accredited by the Commission on Colleges of persons working in related research areas Biology (subject test is also required); the Northwest Association of Schools and and enables the fullest use of the wide range Computer Science and Engineering; Electrical Colleges, an institutional accrediting body of instrumentation available at the School. and Computer Engineering, and recognized by the Council for Higher Environmental Science and Engineering. DEGREE PROGRAMS Education Accreditation and the U.S. Applications may be submitted as early as Department of Education. The commission’s The OGI School of Science & Engineering one year before the proposed date of address is 11130 NE 33rd Place, Suite 120, offers Master of Science degrees and Ph.D. enrollment. degrees in Biochemistry and Molecular Bellevue, WA 98004. Biology, Computer Science and Engineering, Applications received by March 1 (Feb. 15 for Electrical Engineering, and Environmental ADMISSIONS PROCEDURES the Environmental Science and Engineering Science and Engineering. The school offers Department) will receive priority review for Printed application forms are available from Master of Science degrees in Management admission and financial support. the school’s Department of Graduate in Science and Technology and in Education. Completed applications, CERTIFICATE PROGRAMS Computational Finance. OGI also offers transcripts and other application materials a professional degree, the Oregon Master of The following items must be submitted: should be sent to: Software Engineering. • Completed OGI certificate program Department of Graduate Education application form. CERTIFICATE PROGRAMS OGI School of Science & Engineering • $20 nonrefundable application fee, which Three certificate programs are offered in 20000 NW Walker Road Beaverton, OR 97006-8921 is valid for one year and cannot be waived Applied Computing, Computational Finance, or deferred. Phone: (503) 748-1027 and Management in Science and Technology. Toll-free: (800) 685-2423 ADDITIONAL REQUIREMENTS FOR Fax: (503) 748-1285 STUDENTS NOT SEEKING DEGREES INTERNATIONAL STUDENTS E-mail: [email protected] Any qualified student may take courses at OGI To be considered for admission to OGI for a in a part-time capacity without enrolling in a You may also apply for admission on-line at full course of study, international students degree program. Students may take a full-time www.ogi.edu/forms/application.html must also provide documents to show that course load for only one quarter while waiting Students may become matriculated (enrolled they meet the requirements described below. for a decision regarding admission to a degree in a degree program) only after completing • Evidence of adequate financial resources to pay program. Up to 21 credits taken at OGI prior the requirements for a bachelor’s degree or for their OGI education and their cost of living. to matriculation (enrollment in a degree its equivalent, although students may be program) may be accepted toward degree • Written TOEFL scores are required of all M.S. provisionally admitted prior to that time. and Ph.D. applicants whose native language is requirements. Individual departments’ not English. Students who have earned a degree regulations may be more restrictive. DEGREE PROGRAMS in the United States are exempt from this The following items must be submitted: requirement. Minimum required TOEFL scores COLLABORATIVE/JOINT PROGRAMS vary by department: BMB 550; CSE 600; ECE Full-time students in the school’s Computer • Complete OGI School of Science & Engineering 575; ESE 600; MST 625. The minimum desired application form or Oregon Master of Software Science and Engineering (CSE) and Electrical TOEFL score for admission is 575, but a lower Engineering (OMSE) degree program application score may be offset by excellent GRE scores. and Computer Engineering (ECE) form, if applicable. departments may take certain courses at Please note: the minimum TOEFL scores above • $50 nonrefundable application fee, which Portland State University at no additional are for the paper-based test only. The computer- is valid for one year and cannot be waived based TOEFL uses a different score scale. For cost. Similar arrangements are being or deferred. more information on the computer-based score explored for other OGI departments. scale, please visit www.toefl.org. 6 OGI SCHOOL OF SCIENCE & ENGINEERING | OGI

TUITION AND FINANCES part-time M.S. students who are U.S. citizens M.S.: Three years of full-time study or four may apply for low-interest student loans. years of part-time study. TUITION For the 2001-2002 academic year, tuition for Fellowships, scholarships and assistantships Petitions for extensions must be approved by full-time matriculated students (defined as 9 are awarded by individual departments. the department and submitted to the Educational Policy Committee for approval. or more credit hours per quarter) is $4,905 Title IV Federal Student Loan programs are per quarter. Part-time tuition for regular OGI administered through the OHSU Financial Aid CONTINUOUS ENROLLMENT School of Science & Engineering courses is office. These loans are available to U.S. A Ph.D. or Master’s student who has begun $545 per credit hour or audit unit. Please citizens and eligible non-citizens. For work on the dissertation or thesis must note that there is no full-time tuition rate for application materials and additional infor- register and pay for at least one credit hour non-matriculated students, except when an mation, contact Cherie Honnell, Director of of research per quarter in order to maintain admission decision is pending. There are no Financial Aid & Registrar, at (503) 494-5117 matriculated status. If all requirements have student fees. or [email protected]. Applications for not been satisfied at the end of four • Tuition for Computational Finance core courses federal student loans (FAFSA) are available consecutive academic quarters of registering is $695 per credit hour or audit unit. Students from OGI’s Department of Graduate for only one credit per quarter, or if an matriculated in the Computational Finance Education, or www.ogi.edu/students/fin.html. degree pay only for credits required to fulfill alternate plan of completion has not been degree requirements. Credits taken during the approved by the department and the 12-month program beyond the 45 required to ACADEMIC POLICIES Educational Policy Committee, matriculated fulfill degree requirements will not incur charges status will be terminated. If the student The following is a summary of select OGI (up to a limit of 54 credits). Full-time quarterly wishes to return to his or her program at a tuition for students not matriculated in the School of Science & Engineering academic later date, it will be necessary to reapply for Computational Finance program who take one policies. A more comprehensive listing can be admission. Continuous enrollment is not Computational Finance course is $5,355; with found in the school’s Student Handbook at two Computational Finance courses it is $5,805. required of Master’s students not pursuing a www.ogi.edu/students/studenthandbook.pdf. Full-time Ph.D students do not incur additional thesis, nor of Master’s or Ph.D. students who cost for registering for Computational ON SITE (RESIDENCY) REQUIREMENTS have not yet begun working on the thesis or Finance courses. The school has a two-year Ph.D. residency dissertation. However, all matriculated • ESE students pay tuition on an annual basis. requirement. For full-time students, this students are required to register for classes That tuition may be paid in full at the beginning OR to indicate temporary inactive status by of the year or in quarterly installments. requirement is normally met by an on-site dissertation project. In exceptional filing a Temporary Inactive Status form with • Courses in the Oregon Master of Software circumstances (e.g., dissertation topics the Department of Graduate Education. Engineering program are $495 per credit hour. requiring access to special facilities only Full-time matriculated students may register for LEAVE OF ABSENCE OMSE courses when paying full-time tuition. available elsewhere), other arrangements In special circumstances, leaves of absence may be proposed to the Educational Policy from a graduate program may be allowed. A Committee (EPC). In such cases, a written Note: Payment or arrangement for deferred student considering a leave should first payment for all courses must be made before plan of the research, with a schedule and discuss the issue with his or her advisor or your place in a class is confirmed. The school description of the special circumstances and another faculty member. If the department offers students the option of deferring most of understandings between the student, thesis the payment through no-interest promissory supports the leave of absence, the student advisor and Student Program Committee notes. Students who are reimbursed for their then submits a petition to the school’s (SPC), must be included. Approval of this courses must make payment arrangements with Educational Policy Committee for approval. their employer, but those students still incur plan by the EPC is required before a student financial responsibility for courses. Courses is granted candidacy status for Ph.D. work STUDENT STATUS sponsored by the Oregon Center for Advanced under such an arrangement. For part-time Technological Education (OCATE), whether taken A matriculated student is one enrolled in a Ph.D. students, the first year of the residency for credit or audit, must be paid in full at the degree program. A non-matriculated student requirement can be satisfied by attendance in time of registration. is not working toward completing a degree. classes on the OGI campus. The second year Full-time matriculated students carry a FINANCIAL AID of residency, however, must be spent full-time minimum of nine credits per quarter. (Audit Entering full-time Ph.D. students can obtain on campus under the advisement of an OGI units do not count toward this minimum financial support though a combination of faculty member. except in special circumstances.) Academic tuition scholarships, OGI fellowships, named There is no residency requirement for M.S. or departments may require students to carry fellowships, graduate research assistantships certificate programs at OGI. more than nine credits per quarter as a and (for U.S. citizens only) low-interest condition of eligibility for a stipend and/or student loans. Part-time Ph.D. students may TIME LIMITS TO COMPLETE THE DEGREE tuition scholarship. Part-time matriculated be eligible for some of the above. Partial- Ph.D.: Six years of full-time study or eight students are admitted to a degree program, tuition scholarships may be awarded to years of part-time study. carry fewer than nine credits per quarter and entering full-time M.S. students, and full- and pay tuition at the appropriate per credit rate. 7 OGI | OGI SCHOOL OF SCIENCE & ENGINEERING

Non-matriculated students have not been GRADING/SATISFACTORY ACADEMIC PROGRESS extension will be granted, as long as the plan admitted into a degree program, typically All OGI courses are graded with a letter is specific, includes a date by which the grade carry fewer than nine credits per quarter, grade; an exception is that Ph.D. students will be assigned, and is submitted to the and pay tuition at the appropriate may receive P/NP for work in a seminar. Graduate Education manager in writing. hourly rate. In addition, faculty may assign P/NP or 400-LEVEL COURSES letter grades to research work, but grades AUDITING A COURSE for research cannot be counted in a Courses offered and designated by 400-series OGI courses are offered for graded graduate student’s GPA. numbers within academic departments at the credit hours or ungraded audit units. school are not considered to satisfy any Students may register to audit an OGI course The following scale is employed at the school: degree requirements. These courses do not on a space-available basis. Students taking a A = 4.0 B- = 2.67 C = 2.0 carry graduate credit at the school, but are course for credit have priority over students entered on the transcript. taking a course for audit. Audits are recorded A- = 3.67 B = 3.0 C- = 1.67 CONFIDENTIALITY OF STUDENT RECORDS on the student’s transcript at the discretion of B+ = 3.33 C+ = 2.33 F = 0.0 the instructor, based upon a reasonable With the passage of the Federal Family expectation of attendance and minimal The grading system is defined as: Educational Rights and Privacy Act (FERPA) participation. Audits are charged at the A = Excellent of 1974, OGI adopted rules to govern the standard tuition rate. Audit units do not count collection, use and disclosure of student B = Satisfactory toward a student’s full-time status. records with the goal of ensuring their Instructors have final discretion over allowing C = Below graduate standard privacy. Students have the right to inspect audits of their classes and defining the their educational records that are maintained F = Failure academic expectations of audits. by OGI; the right to a hearing to challenge the The following marks are also used: contents of those records when they allege CREDIT LOAD PER QUARTER the records contain misleading or inaccurate Twelve credits per quarter is considered a AU = Audit, no credit information; and the right to give their normal course load for full-time students, P = Satisfactory completion written consent prior to the release of their although nine or more is also considered full- records to any person, agency or organization time. Up to 18 credits/audits may be taken NP = No credit, unsatisfactory other than OGI officials and certain with the approval of the department. I = Incomplete authorized federal and state authorities. Registering for more than 18 credits requires Educational Policy Committee permission; 18 PI = Permanent Incomplete DIRECTORY INFORMATION credits plus up to 4 audit units does not W = Withdrawn (after the add/drop period) Certain public domain information, known as require EPC permission and does not incur Matriculated students must maintain a directory information, can be released by the additional cost. Students in the Electrical and cumulative GPA of 3.0 on all work taken at school unless a student files a written Computer Engineering Department are OGI. Failure to do so may result in probation request in the Graduate Education limited to 12 credits per quarter, but may or dismissal. Department. The school limits this take up to16 with their advisor’s and home information to the student’s name, home department’s written approval. INCOMPLETES address, e-mail address, dates of attendance, The school’s policy is that an Incomplete must degrees and awards received, number of TRANSFER CREDIT be completed by the end of the quarter credits earned and the fact of enrollment, OGI accepts transfer credit from accredited following that in which the Incomplete was including whether the student is enrolled full- institutions provided that such prior awarded. In cases where the Incomplete is or part-time. The school does not make this academic work has not been previously not completed, the instructor has the choice information available to vendors. applied toward another degree. A maximum of assigning a grade or converting the TRANSCRIPTS of 21 credits earned prior to matriculation at Incomplete into a Permanent Incomplete. The OGI may be applied. This may include up to grade may be an F if the course work was not Your transcript is a formal, written record of 12 credits transferred from another completed, but instructors have the option of your educational experience at the OGI institution (up to 18 from Portland State assigning another grade if they feel quality School of Science & Engineering. All courses University, University of Oregon and Oregon and quantity of work that was accomplished you take at the school are recorded on it, as State University) and/or up to 21 credits warrants it. If an extension of this one- are all grades and degrees you earn while at taken at OGI prior to matriculation. Contact quarter deadline is desired, the student may OGI. If you have transferred credits from each academic department for specific petition the Educational Policy Committee, another institution, they will be recorded on policies and procedures. Transfer credit showing the instructor’s support of the your transcript as well. By law, requests for grades, other than those from OGI, are extension (a separate letter or signature on transcripts must be in writing and submitted not calculated in the OGI grade-point the petition will suffice). Normally an by fax, mail or in person to the Department average (GPA). of Graduate Education. Official transcripts

8 OGI SCHOOL OF SCIENCE & ENGINEERING | OGI are on special paper and have the official biochemistry, molecular biology, and HOUSING school seal; unofficial transcripts are management as related to science and While OGI has no on-campus housing, it printed on regular paper without the seal. technology. In addition, the OHSU Library is located in the midst of a very large There is no charge for unofficial transcripts; holds more than 74,000 monographs and residential area. There are numerous official transcripts cost $4 per copy. Requests 1,200 journal subscriptions. These print apartment complexes, rental houses, bu are usually processed immediately, but we collections are available for use when visiting and light rail lines, and shopping areas ask that you allow three days. Your request the libraries. Materials unavailable at OGI near the school. The Office of Student must have your name, signature and social are obtained on interlibrary loan for faculty, Services in the Graduate Education security number (if applicable); indicate staff and students. An on-line catalog, Department maintains a list of local whether you will pick up the transcript(s) or acquisitions and circulation system is in apartment buildings for students to include the address(es) to which the place. Access to other college and university reference. In addition, the Student Council transcript(s) should be mailed; and include collections is provided by access to has a Web site for current, new and payment information, if relevant. You can databases, library catalogs and grants prospective OGI students who are looking send a check, submit a credit card number or circulation privileges to OGI students at 13 for housing information, roommates, pay cash. Sending cash through the mail is other area institutions, including Portland etc. This service is found at not recommended. State University and Reed College. cslu.cse.ogi.edu/council/st_forum.html.

OGI library workstations not only enable STUDENT COUNCIL THE CAMPUS students and faculty to search the catalog The Student Council serves as the liaison and the library’s databases but also provide GEOGRAPHIC SETTING between the student body and the faculty and entry to Web resources, telnetting and ftp The greater-Portland metropolitan area has a administration, and it strives to improve OGI options for faculty, staff and students. The population of about 1.5 million, nearly half students’ quality of life. Student OGI librarians will perform searches on the the population of Oregon. It provides diverse representatives make themselves available to systems and databases that are not directly cultural activities, including art, music, students in their department in order to available to students. Library orientation is entertainment and sports. Portland has an forward their comments, ideas and concerns part of the introduction to OGI for new extensive park system, including the largest to the Student Council and to promote their students, and classes on library research wilderness park within the limits of any city involvement in student body activities. methods are offered throughout the year. in the United States. The OGI School of Representatives also serve to disseminate all Science & Engineering is located 10 miles Most of OGI’s electronic library resources will pertinent information to the students in their west of downtown. We are the newest school be integrated with those of the other OHSU departments. As liaisons, members of the within Oregon Health & Science University schools and institutes by 2003. Student Council represent the student body (OHSU), joining the Schools of Medicine, and student interests on a wide variety of OGI COMPUTER FACILITIES Dentistry and Nursing, which are located on task forces and committees, including the the main campus on Marquam Hill The OGI School of Science and Engineering’s Faculty Senate, the Educational Policy overlooking downtown Portland. OGI is now computing environment gives members of the Committee and the Safety Committee. Each part of OHSU’s newly named West Campus, community access to a rich array of quarter the Student Council also sponsors which also includes the Neurological technologies and information resources. and coordinates at least one major social Sciences Institute, the Oregon Regional Many of these resources, including networks event, which is open to everyone at OGI. Primate Research Center, and the Vaccine and telecommunications, are the These events have included a coffeehouse and Gene Therapy Institute. OGI’s campus responsibility of OHSU’s central Information with live music performed by people from consists of modern, attractive buildings, Technology Group (ITG). In addition, many throughout the school, an annual providing spacious laboratories, offices and school departments and laboratories maintain international food and cultural fair, and an a research library. their own computing facilities. Most of OGI’s educational forum. There are also monthly computers connect to a school-wide local- and weekly events, including movie nights LIBRARY area network and to the Internet, providing and bagel breakfasts in the student lounge. The Samuel L. Diack Memorial Library’s convenient access to the World Wide Web. More information on the Student Council is collection includes more than 18,000 The local-area network is connected to the available on its Web site at monographic titles and 400 print journal Internet through two high-speed data paths. cslu.cse.ogi.edu/council/ or by e-mail at subscriptions. These support the teaching and In addition, it is also connected to Internet 2 [email protected]. research efforts at OGI by providing texts, (Internet2.edu) resources. The Internet 2 conference proceedings, reference materials, connection was made possible through an journals and research monographs in the alliance of local academic institutions. subject areas of computer science, electrical engineering, environmental sciences,

9 THE DEPARTMENT OF BIOCHEMISTRY AND DEGREE REQUIREMENTS Department of MOLECULAR BIOLOGY offers graduate M.S. PROGRAMS study leading to M.S. and Ph.D. Two options are offered for the M.S. in Biochemistry and degrees. Participation in research biochemistry and molecular biology. Molecular Biology begins immediately upon entering NON-THESIS OPTION our program.This early exposure to The non-thesis M.S. requires satisfactory www.bmb.ogi.edu research allows each student to completion of 44 credits, 28 of which are in graded courses and 16 of which are derived become familiar with the variety of from an experimental research project DEPARTMENT HEAD activities represented in the (BMB610); and a written report on the Ninian J. Blackburn (503) 748-1384 department and aids the student in research. Graded courses include 12 credits in BMB527-528-529, and 16 or more credits E-mail: [email protected] thesis research selection. in advanced courses (BMB532-542), student DEPARTMENT ADMINISTRATOR seminars (BMB594 or 596) and Special RESEARCH AREAS INCLUDE: Nancy Christie Topics (BMB580). The research for the non- • Metallobiochemistry (with an emphasis on the (503) 748-1070 structure and function of metal ions in proteins thesis degree is typically a specific E-mail: [email protected] and the mechanisms of metal trafficking in cells) contribution to a larger project, providing the student with extensive hands-on experience ADMINISTRATIVE COORDINATOR • Fungal and yeast biochemistry and molecular Terrie Hadfield biology (with an emphasis on gene regulation in biochemical and molecular biological (503) 748-1071 and enzyme characterization) techniques. The non-thesis M.S. degree can be completed in one year of full-time study. E-mail: [email protected] • Ion transport across biological membranes (with BMB GENERAL INQUIRIES an emphasis on molecular biology and THESIS OPTION reconstitution of cation or anion carriers) E-mail: [email protected] The thesis M.S. is a research degree that (503) 748-1070 The research experience at OGI is extensive. requires satisfactory completion of 44 Much of the research is interdisciplinary, credits, 20 of which are in graded courses covering basic and applied aspects. Students (12 credits in BMB 527-528-529 and eight or are involved in all aspects of the more credits in advanced courses), and a departmental research program and have written thesis based on independent research ready access to modern research (BMB700). The thesis M.S. degree can be instrumentation. As a result, our graduates completed in 18 months of full-time study. are well qualified for research careers in academia, government and industry. PH.D. PROGRAM The department offers a Ph.D. in ADMISSION REQUIREMENTS biochemistry and molecular biology. Ph.D. candidates are required to take the BMB Admission requirements are the same as the 527-528-529 biochemistry sequence and general requirements of the institution. In three of the following core courses: addition, Ph.D. applicants must submit BMB532 Bioenergetics and Membrane Transport, 4 credits general GRE scores and a GRE subject score for one of the following tests: (a) biology, (b) BMB533 Enzyme Structure, Function and Mechanisms, 4 credits chemistry or (c) biochemistry, cell and BMB534 Instrumental Methods in Biophysics I, 4 credits molecular biology. M.S. applicants are not BMB540 Advanced Molecular Biology, 4 credits required to submit GRE scores. Prospective BMB542 Molecular Cell Biology, 4 credits students should carefully examine the faculty Students must register for 12 credits per research interests and departmental quarter. These credits typically include research programs to determine whether student seminars (BMB594 or BMB596), their specific professional needs can be Department Seminar (BMB 591) and fulfilled at OGI. Communication with Research (BMB600 or BMB800). individual faculty members is encouraged prior to applying or enrolling. The qualifying examination for the Ph.D. is a comprehensive examination. The qualifying exam must be completed within two years of entering OGI. An oral defense of the Ph.D. dissertation is required. Cheng Wu is a doctoral student in Matt Sachs’s lab. BMB | BIOCHEMISTRY AND MOLECULAR BIOLOGY

COURSE DESCRIPTIONS BMB539 Chemical Group Theory BMB596 Molecular Biology/Biochemistry Properties of mathematical groups; symmetry proper- Student Seminar BMB527 Biochemistry I: Proteins and Enzymes ties of molecules; symmetry groups, representations Presentation and discussion of journal articles from Primary, secondary and tertiary structure of proteins; and character tables. Applications of group theory to the recent literature in molecular biology, genetics enzyme mechanisms; enzyme kinetics. 4 credits the study of structure and spectroscopy of organic and and biochemistry. 2 credits, repetitive BMB528 Biochemistry II: Introduction to inorganic molecules; Hückel molecular orbital theory; BMB600 Research Molecular Biology ligand field theory; electronic spectroscopy and vibra- Supervised research participation. DNA replication, RNA synthesis and protein synthe- tional spectroscopy. 4 credits Variable and repetitive credit sis; genetic code; gene regulation. 4 credits BMB540 Advanced Molecular Biology BMB610 Nonthesis Research BMB529 Biochemistry III: Metabolism An in-depth study of the molecular mechanisms gov- Supervised research as a component of the nonthe- and Bioenergetics erning the replication, recombination, transcription sis M.S. degree. Variable and repetitive credit Metabolism of carbohydrates, lipids and amino and translation of genetic material. Emphasis is acids; bioenergetics; photosynthesis; oxidative placed on experimental approaches that have led to BMB620 Professional Internship phosphorylation. 4 credits our understanding of these fundamental processes. These courses provide the student with an opportu- 4 credits nity to earn credit for relevant work experience in BMB532 Bioenergetics and Membrane Transport industry. Students gain valuable industrial experi- Critical evaluation of the chemiosmotic theory with BMB541 Molecular Genetics of Development ence that allows them to both apply the knowledge specific reference to oxidative phosphorylation, A focused study of selected topics examining the gained in the classroom and prepare for their future photophosphorylation and metabolite transport. regulation of gene expression during cellular differ- careers. Enrollment requires a faculty advisor Biochemical mechanisms of energy transduction entiation. Emphasis is placed on the molecular and is limited by the number of internship opportu- common to bacterial and mitochondrial respiration, nature of cell-cell interactions and the genetic con- nities available. Variable credit and bacterial and plant photosynthesis are reviewed. trol of complex cellular responses to developmental 4 credits and environmental stimuli. 4 credits BMB700 M.S. Thesis Research Research toward the thesis for the M.S. degree. BMB533 Enzyme Structure, Function and Mechanisms BMB542 Molecular Cell Biology Variable and repetitive credit Provides an in-depth analysis of the structural ori- The techniques of molecular biology have created an gins of protein interactions and catalysis that are the explosion in knowledge of cell structure and func- BMB800 Ph.D. Dissertation Research basis for biological function. The course develops the tion. This course examines the following topics: Research toward the dissertation for the Ph.D. degree. basic principles of structural biology through an cellular organization; cell signaling; cell differentia- Variable and repetitive credit overview of X-ray crystal structures and folding tion; cell evolution. Knowledge of the cell is obtained processes, acquainting students with computational through combining core readings and lectures with resources for protein structure analysis. The struc- student-led discussions of primary research papers. RESEARCH PROGRAMS tural foundation is expanded into a detailed 4 credits Translational Control in Fungal Amino Acid Biosynthesis investigation of enzyme active sites, including the BMB543 Current Topics in Proteomics A greater understanding of many human health application of kinetic approaches to understanding Proteomics is a new area of molecular biology that issues relies on increased knowledge of how cells enzymatic reaction mechanisms. 4 credits aims to identify and map the total protein comple- express genetic information. Gene expression can BMB534 Instrumental Methods in Biophysics I ment of a genome. It expands the scope of biological be controlled by regulating the synthesis and Theory and application of physical techniques to investigation from studying single proteins to sys- stability of functional RNA and protein. The goal of problems in biochemistry. Optical, fluorescence, cir- tematically studying all proteins. Proteomics has our research is to obtain a greater understanding cular dichroism, infrared and Raman spectroscopy broad applications in disease diagnosis, drug dis- of how these mechanisms work using the of chromophoric groups. Magnetic susceptibility and covery and agriculture. The key technologies used in Neurospora crassa arg-2 and Saccharomyces nuclear magnetic resonance of metalloproteins. proteomics are two-dimensional gel electrophore- cerevisiae CPA1 genes as models. These 4 credits sis, mass spectrometry (ESI-MS, MALDI-TOF), homologous genes encode the first enzyme in imaging and database software. This course will use arginine biosynthesis, and they are negatively BMB535 Instrumental Methods in Biophysics II lectures, student seminars and literature readings regulated at transcriptional and translational levels Investigation of physical techniques particularly to focus on electrophoresis, mass spectrometry and in response to the availability of arginine. An useful for studying metalloproteins. Electron para- applications. 3 credits evolutionarily conserved upstream open reading magnetic resonance, electron spin echo, magnetic frame (uORF) present in the 5’-leader regions of circular dichroism, and X-ray absorption spec- BMB544 Introduction to Bioinformatics these transcripts is responsible for translational troscopy. The course has significant “hands-on” Primary literature of computational biology and control. Synthesis of the uORF-encoded peptide exposure to instrumentation and computer simula- hands-on experience in data manipulation from causes ribosomes to stall when the level of arginine tion techniques. 4 credits local and remote databases. 3 credits is high, blocking access of ribosomes to the BMB537 Metals in Biochemistry BMB580 Special Topics in Biotechnology translation initiation site for the polypeptide encoding the arginine biosynthetic enzyme. Our Comprehensive study of the chemistry and biochem- Examination of current and past research papers in current work is focused on developing a molecular istry of metal ions in biological molecules and living a specific area of biotechnology that is of mutual understanding of how synthesis of this uORF- systems. Topics include metalloprotein structure, interest to the student and the faculty member. encoded peptide causes ribosomes to stall, since metal ion specificity, biological oxidation mecha- Requires a written review paper or seminar presen- this will provide important insights into the nisms, metal ion catalysis in enzymes, metal ion tation in one of the Student Seminar series. fundamental cellular process of protein synthesis. transport and gene regulation. 4 credits Variable and repetitive credit Sachs BMB538 Coordination Chemistry BMB591 Department Seminar: Biochemistry/ Translational Control of Human Proto-Oncogenes Structures and stabilities of transition metal coordi- Molecular Biology The transcripts specified by many genes involved in nation compounds with mono- and multi-dentate 1 credit, repetitive human cancers contain uORFs; these include the ligands; coordination compounds as models for bio- BMB594 Metallobiochemistry Student Seminar her-2 and bcl-2 proto-oncogenes. Using methods logical metal centers; strategies for synthesis of Presentations and discussions of selected topics similar to those developed for understanding the transition metal complexes. 4 credits from the recent literature and of ongoing research roles of the uORFs of N. crassa arg-2 and S. projects in the department. 2 credits, repetitive cerevisiae CPA1 gene expression, we are examining 12 BIOCHEMISTRY AND MOLECULAR BIOLOGY | BMB

the functions of these mammalian uORFs, to better adrenaline and amphetamine); enzymes protecting oxygen metabolites. The key question is: How do understand their role in controlling the expression against oxidative cellular damage caused by interactions between the protein, metal ion and of these critically important genes. Sachs reduced oxygen metabolites; and enzymes exogenous ligands tune the redox potential and catalyzing the biosynthesis of neuropeptide chemistry of these complexes? We are combining The Neurospora Genome hormones. A major goal is to understand the the powerful tools of molecular biology with We are part of a team that is sequencing and catalytic role of copper and the molecular advanced spectroscopic and computational annotating the genome of Neurospora crassa mechanism of oxygen binding and utilization by approaches to explore the structure and dynamics (see www.genome.wi.mit.edu/annotation/fungi/ these oxidase and oxygenase enzymes. Blackburn of Mn active sites. For MnSD, we find an neurospora/), and are gearing up to apply this unexpected temperature dependence for the information to large-scale community-wide efforts Spectroscopy of Copper Proteins structures of anion complexes, which change in functional genomics. This is the first genome of a Spectroscopic techniques are used to probe the coordination as the temperature is raised. This filamentous fungus that has been sequenced with structures of the copper sites in the native proteins thermal transition implies that the stability of the public funds; the annotation of this sequence is and their complexes with substrates and inhibitors. active site structure is determined by dynamical proving invaluable for understanding fungal genome Since the chemistry of the catalytic processes is features of the complex and that dynamical evolution; many fungi important for agriculture and generally centered on the Cu(I) forms of the excitation may play an important role in controlling medicine are closely related to N. crassa. We enzymes, we are concentrating on the challenging the energetics of ligand binding and redox. A wide recently began experiments aimed at cloning and task of developing spectroscopic probes of the Cu(I) range of projects relating to the chemistry and analyzing the telomeric regions of N. crassa and oxidation state, which is transparent to most biology of Mn are in progress. Whittaker the closely related pathogenic rice blast fungus common spectroscopic techniques. Our work thus Magnaporthe grisea because mounting evidence includes Fourier transform infrared, X-ray Electronic Spectroscopy of Biological Metal Complexes indicates that genes near telomeres evolve more absorption edge and EXAFS spectroscopies, and Electronic spectroscopy extends structural studies quickly and are frequently involved in pathogenic emphasizes the use of computer simulation of of biomolecules beyond the atomic resolution of interactions with hosts. Sachs spectra on our Alpha work station. Data for the X-ray crystallography to a level of structural detail latter two techniques are collected at national and that directly relates to chemistry. The techniques Mechanisms of Mammalian Chemical Communication and Vomeronasal Olfaction international synchrotron radiation facilities. used in these studies span five decades of the Proteins under investigation include dopamine-beta electromagnetic spectrum, from microwaves to Chemical communication plays a significant role in hydroxylase, cytochrome c oxidase, hemocyanin, the ultraviolet and beyond. At the lowest energy, life strategies for many mammals. Our research peptide amidating enzyme, Menkes and Wilson’s electron paramagnetic resonance (EPR) focuses on chemical identification of pheromones disease proteins, and copper chaperones. Blackburn spectroscopy gives information on the electronic functioning during reproductive events in the ground state, defining the molecular orbital that Asian elephant, Elephas maximus. A female- Radical Copper Oxidases contains the unpaired electron in a paramagnetic to-male preovulatory urinary sex pheromone, Radical copper oxidases are a new class of redox complex. At higher energy, UV-visible absorption (Z)-7-dodecen-1-yl acetate, has been identified and metalloenzymes (including the fungal enzymes spectroscopy excites orbital transitions between demonstrated to be robust in its synthetic form. galactose oxidase and glyoxal oxidase) containing a electronic states, giving information on This compound is also bioactive in many protein free radical directly coordinated to a characteristic metal-ligand interaction energies Lepidoptera, making it a good example of copper center. This free radical-coupled Cu that can be understood in terms of a ligand field or convergent evolution of structure and function. complex catalyzes the two-electron oxidation of molecular orbital analysis. Polarization Biochemical studies have established the presence simple alcohols and aldehydes and the reduction of spectroscopy (linear dichroism, circular dichroism of the pheromone in the serum, and future studies O to hydrogen peroxide, fueling extracellular 2 and magnetic circular dichroism) can give more will investigate its biosynthetic pathways. peroxidases involved in lignin degradation. In these detailed information on ground and excited state Considerable progress has been made on proteins, the free radical is localized on a tyrosine electronic wave functions using geometric features establishing the proteins functioning as pheromone residue covalently crosslinked to a cysteinyl side of light to probe the active site. These experimental transporters prior to signal transduction in the chain (a Tyr-Cys dimer). The catalytically active approaches can be complemented by spectroscopic neuroreceptive cells of the vomeronasal organ. enzyme is an intense green color, a result of modeling and computational biology methods to Radiolabeled analogs, competition experiments and unusual optical spectra arising from electronic provide a detailed description of a metalloprotein molecular biological studies have established transitions within the copper radical complex. Low complex and its interactions. Whittaker unusual roles for elephant albumin and olfactory energy transitions in the near IR result from binding protein. A second pheromonal system is interligand redox in this metal complex, ligand- Vibrational Spectroscopy of Metalloprotein Active Sites actively being investigated. The facial temporal to-ligand charge transfer (LLCT) processes that are Many spectroscopic methods are available for the gland, breath and urine exude unusual chemical closely related to the electron transfer coordinate investigation of structural and functional properties compounds during musth in Asian male elephants. for substrate oxidation. The active site metal of metal ions in enzymes and proteins. We use These signals have a role in mate choice by female complex is surprisingly flexible, twisting through a electronic, vibrational (especially resonance elephants, spatial distribution by male elephants pseudorotation distortion when exogenous ligands Raman) and EPR spectroscopy to characterize and other reactions by conspecifics. Utilizing bind, thereby modulating the basicity of a second metal-ion active sites. Our laboratory has a several state-of-the-art gas chromatographic/mass tyrosine ligand that serves as a general base in sensitive, state-of-the-art Raman instrument: a fast spectrometric techniques, we are identifying catalysis. Many of these aspects of electronic spectrograph with a liquid N2-cooled CCD detector. specific compounds that have a chemical structure and dynamics of the radical copper We also use a combined FT-IR/FT-Raman communication function, i.e., elicit behavioral oxidases are the focus of active research. Whittaker instrument for protein and model compound responses, and correlating the release of such studies. Our research focuses on the description of Manganese Metalloenzymes compounds with serum androgen levels. the molecular and electronic structures of heme Manganese is an essential element for life, forming Rasmussen (iron porphyrin), nonheme-iron and copper the active site for a large number of enzymes to gain an understanding of the role of the Chemistry of Copper-Containing Enzymes metalloenzymes catalyzing hydrolytic or redox metal ion in enzymatic catalysis. Of particular Increasing numbers of important enzymes are reactions, including the photosynthetic oxygen interest is the biochemistry of O . Metalloproteins known to contain copper at their active sites. Of evolving complex. We are interested in the Mn 2 are involved in O binding (hemoglobin or particular interest are enzymes involved in biogenic redox sites in Mn superoxide dismutase (MnSD, 2 hemocyanin) and in oxidative chemistry whereby amine biosynthesis and metabolism (including mononuclear Mn) and Mn catalase (MnC, dinuclear O is reduced and substrates are oxygenated or important neuroactive amines such as nor- Mn), enzymes that provide protection from toxic 2 oxidized. Trapped reaction intermediates and model 13 BMB | BIOCHEMISTRY AND MOLECULAR BIOLOGY

compounds help us unravel these complex denitrification — the process by which certain inhibition and binding of CPTI but not for catalysis.

processes and define reaction mechanisms. In all organisms convert nitrate to N2 or N2O. The We will determine the structural basis for the high projects, modern molecular biology techniques production of NO is the first opportunity for fixed malonyl-CoA sensitivity of M-CPTI by constructing provide site-directed mutants that permit nitrogen to be lost from the soil to the atmosphere, chimeras between M-CPTI and L-CPTI and by site- alterations in structures and reactivities. Loehr with implications ranging from fertilizer loss to directed mutagenesis. We will prepare milligram atmospheric pollution. Throughout biological NO quantities of the expressed highly purified human Heme Oxygenase chemistry, proteins with Fe- or Cu-containing heart M-CPTI and liver L-CPTI for structural Heme oxygenase is a fascinating system that uses active sites play a central role in generating and characterization studies. Finally, we plan to study the O -binding affinity of its heme substrate in the 2 releasing NO as well as in sensing and initiating the regulation of human heart M-CPTI gene cellular degradation of heme to open-chain chemistry in response to changes in NO levels. Our expression by hormonal, developmental and dietary biliverdin. These studies are carried out with Paul research is aimed at investigating the structures factors. Our goal is to elucidate the molecular R. Ortiz de Montellano’s group at U.C. San and mechanisms of these metalloproteins through mechanism of the regulation of fatty acid transport Francisco. The resting heme-heme oxygenase the use of a variety of spectroscopic, biochemical and oxidation in mammalian cells. Woldegiorgis enzyme substrate complex is much like myoglobin: and kinetic techniques. Andrew The heme is linked to the enzyme by an iron- The Mitochondrial ATP-sensitive K+ Channel (mitoKATP) Regulation of Long Chain Fatty Acid Transport and histidine bond, and the iron exists mainly in a six- MitoKATP resides in the inner membrane of coordinate, high-spin state with an additional water Oxidation in Mammalian Heart and Liver mitochondria, where it serves to regulate the ligand. The Fe-N(His) bond was identified from its The rate-limiting step in ß-oxidation is the volume of mitochondrial compartments and also to resonance Raman vibration at 216 cm-1 in the conversion of long-chain acyl-CoA to acylcarnitine, trigger cell signaling leading to cardioprotection a reaction catalyzed by the outer mitochondrial Fe(II)-heme complex. The absence of this and gene transcription. We showed that mitoKATP fingerprint frequency in the H25A mutant clearly membrane enzyme carnitine palmitoyltransferase I mediates the actions of potassium channel openers identified His25 as the axial ligand. Remarkably, (CPTI) and inhibited by malonyl-CoA. The and ischemic preconditioning to protect the heart when imidazole was added to the inactive H25A acylcarnitine is then translocated across the inner against ischemia-reperfusion injury. We are now preparation, activity was fully restored. Our mitochondrial membrane by the working to understand the mechanisms of this carnitine/acylcarnitine translocase and converted current efforts, in collaboration with Angela Wilks effect and the normal physiological role of mitoKATP at the University of Maryland, examine the back to acyl-CoA by CPTII. This reaction in intact in heart and brain. We introduced techniques for mitochondria is inhibited by malonyl-CoA, the first structure and activity of several bacterial heme purification and reconstitution of mitoKATP in lipid oxygenases. Loehr and Moënne-Loccoz intermediate in fatty acid synthesis, suggesting vesicles and use this preparation to study the coordinated regulation of fatty acid oxidation and transport kinetics of the channel. We have Oxygen Activation by Iron Proteins synthesis. Although CPTII has been examined in purified the mitoK subunits to homogeneity Several diiron enzymes react with molecular ATP detail, studies on CPTI have been hampered by an and will use these to obtain the molecular oxygen to form powerful oxidizing agents important inability to purify CPTI in an active form from structure of mitoKATP. Garlid in biology. Examples include (i) ribonucleotide CPTII. In particular, it has not been conclusively Mitochondrial Uncoupling Proteins reductase protein R2, which oxidizes its tyrosine demonstrated that CPTI is even catalytically active, 122 to its catalytically important neutral radical or whether sensitivity of CPTI to malonyl-CoA is an Our laboratory was the first to demonstrate form; (ii) methane monooxygenase, whose intrinsic property of the enzyme or is contained in reconstitutive activity of the new uncoupling hydroxylase component oxidizes hydrocarbons to a separate regulatory subunit that interacts with proteins, UCP2 and UCP3, and we have long been alcohols; (iii) plant desaturases, which oxidize fatty CPTI. To address these questions, the genes for active in the study of UCP1. Flux studies in acids to olefins, e.g., stearoyl to oleoyl; and (iv) human heart muscle M-CPTI and rat liver LCPTI proteoliposomes containing UCP have led to a new ferroxidase reactions, in which Fe2+ is oxidized to and CPTII were separately expressed in Pichia mechanism of UCP-mediated uncoupling in which Fe3+. A common feature of these enzymes appears pastoris, a yeast with no endogenous CPT activity. the fatty acid anion is transported by UCP and the to be the formation of an initial peroxo High levels of CPT activity were present in purified protonated fatty acid cycles spontaneously back intermediate from the reduced enzyme. However, in mitochondrial preparations from both CPTI- and across the bilayer to deliver protons. Garlid the respiratory protein, hemerythrin, binding of CPTII-expressing strains. Furthermore, CPTI Mitochondrial Bioenergetics dioxygen is accomplished by reduction to peroxide activity was highly sensitive to inhibition by Progress in understanding mitochondrial in a reaction that is readily reversible. In malonyl-CoA while CPTII was not. Thus, CPT bioenergetics has not kept pace with the enormous ribonucleotide reductase, peroxide is similarly catalytic activity and malonyl-CoA sensitivity are progress in structure-function of the enzymes of formed but decomposes irreversibly to a ferryl contained within a single CPTI-polypeptide in oxidative phosphorylation. This occurs at a time intermediate that is capable of carrying out mammalian mitochondrial membranes. My when understanding bioenergetics at the oxidative chemistry. This dichotomy of behavior is laboratory is the first to describe the kinetic physiological level is most needed, in view of the reminiscent of the respiratory vs. peroxidase characteristics for the yeast-expressed CPTIs, the increased recognition of the roles played by functions of different heme-containing proteins. We first such report for a CPTI enzyme in the absence mitochondria in cell physiology and are interested in determining common principles of CPTII. Both yeast-expressed M-CPTI and L-CPTI pathophysiology. A number of unresolved questions that influence the pathways of oxygen utilization. are inactivated by detergent solubilization. relating to the mechanism of energy conservation This problem is being approached by structural However, removal of the detergent in the presence in mitochondria are being addressed by theoretical elucidation of the iron sites in the proteins of phospholipids resulted in the recovery of and experimental approaches. Subjects being themselves and in model complexes, as well as by malonyl-CoA-sensitive CPTI activity, suggesting that investigated include the question of redox slip; studying mechanisms of their reactions with oxygen- CPTI requires a membranous environment. CPTI is volume activation of electron transport; and the containing substrates. Loehr and Moënne-Loccoz thus reversibly inactivated by detergents. We have role of the intermembrane space in regulating Interaction of Nitric Oxide with Metalloproteins isolated and sequenced the promoter region of the energy transfers between matrix and cytosol. Garlid Nitric oxide (NO) is of intense interest due to its gene for the human heart M-CPTI. We have mapped Anaerobiosis of Bacillus subtilis role in a diverse range of biological processes. The the malonyl-CoA and substrate binding sites in importance of NO in mammalian physiology is human heart M-CPTI and liver A gram-positive soil bacterium, B. subtilis, is indicated by the award of the 1998 Nobel Prize for L-CPTI by deletion, site-directed mutagenesis and highly amenable to genetic analysis and has been Medicine for the discovery of its role as a signaling chemical modification studies using residue- used as a model system to study fundamental molecule in the cardiovascular system. In bacteria, specific reagents. Our deletion and point mutation microbiological research. In addition, B. subtilis is NO is produced as an intermediate during analyses have demonstrated that glutamate-3 and medically and industrially important since it histidine-5 are necessary for malonyl-CoA produces a variety of antibiotics and extracellular 14 BIOCHEMISTRY AND MOLECULAR BIOLOGY | BMB enzymes. Although the organism has been widely flavohemoglobin is involved in detoxification of RESEARCH FACILITIES used, it has been mistakenly referred to as a strict nitric oxide. B. subtilis hmp was identified among aerobe until recently. Our studies, together with genes, expression of which is induced by oxygen The department is well equipped to carry on others, have shown that B. subtilis is able to grow limitation. The anaerobic induction of hmp requires a vigorous research program. Instruments and under anaerobic conditions by utilizing nitrate or the ResD-ResE signal transduction pairs and equipment available in the department include: nitrite as an alternative electron acceptor. In the nitrite. The expression is also induced by • Gas chromatograph/mass spectrometer absence of terminal electron acceptors, it exogenous nitric oxide through ResDE-dependent with computer data system undergoes fermentative growth. Our research aims and -independent mechanisms. The detailed include elucidation of the regulatory mechanisms regulatory mechanism of hmp expression and its • High-resolution mass spectrometer through which the cells adapt to oxygen limitation. functional role in anaerobiosis are under • Capillary column gas chromatographs with flame Molecular genetic and biochemical approaches are investigation. Nakano ionization detectors applied. Nakano Peptide Antibiotic Biosynthesis • Fourier transform infrared spectrometers Two Physiological Roles of Nitrate and Nitrite Reductases Our research is aimed at understanding the Nitrate and nitrite reductases have two roles in mechanism of antimicrobial peptide biosynthesis. • Fourier transform Raman metabolism of B. subtilis: assimilation of Peptide antibiotics are synthesized either by the spectrometer with CW Nd:YAG laser nitrate/nitrite and anaerobic respiration. Two non-ribosomal thiotemplate mechanism or are • X-band electron paramagnetic genetically and biochemically distinct nitrate bacteriocins that are gene-encoded and synthesized resonance spectrometer reductases are present to fulfill the dual roles; in on ribosomes. Both classes are used as bio-control contrast, a single nitrite reductase functions in agents in medicine, agriculture and the food • Ultraviolet/visible/near-infrared spectrophotometers both assimilation and respiration. The functional industry. Non-ribosomally synthesized peptides also • Scanning fluorescence spectrophotometers differences of the enzymes correspond to the include iron-scavenging siderophores which are difference in gene regulation. We have studied how required for virulence by some bacterial pathogens • Magnetic circular dichroism (MCD) spectrometer these nitrate and nitrite reductase genes are and toxins produced by a variety of bacterial and • Diode array UV/VIS spectrophotometer regulated in response to nitrogen and oxygen fungal species that infect plants. A knowledge of • Laser Raman spectrophotometer limitation by promoter analysis of these genes and how peptide and bacteriocin biosyntheses are identification of trans-acting factors. The carried out at the molecular level may provide • Raman spectrograph with CCD detector mechanisms of transcriptional activation of the information that can ultimately be used to design • Ar, Kr, He-Cd, He-Ne, and dye lasers nitrate/nitrite reductase genes are being ways to control the virulence of pathogenic investigated. Nakano microorganisms and to synthesize peptides with a • High-vacuum lines defined structure and bioactivity. The spore- ResD-ResE Two-Component Signal Transduction System • Phosphor imager forming bacterium Bacillus subtilis will produce an • Controlled atmosphere reaction chamber Bacteria often encounter sudden environmental abundance of peptide antibiotics and bacteriocins changes. Cells cope with such changes by an under conditions of nutritional stress and oxygen • Super speed centrifuges elaborate network of adaptive responses. The two- limitation. The genes encoding the enzymes that • Ultracentrifuges component signal transduction system senses and catalyze peptide biosynthesis have been cloned, then processes information derived from and we are engaged in genetic engineering of the • HPLCs environmental changes so that the cell can choose enzymes to understand the mechanism of • FPLCs the appropriate adaptive response. This simple antimicrobial peptide biosynthesis. Zuber signal transduction system is widespread in • Fraction collectors Prokaryotic Signal Transduction/Gene Regulation bacteria and also found in plants and lower • Liquid scintillation systems eukaryotes. ResE is a histidine kinase and ResD is Bacteria can respond in a variety of ways to a a response regulator of this large protein family. growth-restricting environment. Prolonged • Gel electrophoresis systems We have shown that ResD and ResE are exposure to a nutritionally poor environment • Laminar flow hoods for sterile culture indispensable for anaerobic respiration in results in the induction of antibiotic biosynthesis, • Growth chambers B. subtilis. A specific signal derived by oxygen functions required for cell motility and processes of limitation is recognized by the N-terminal input cellular differentiation that give rise to highly • Constant temperature rooms domain of the ResE kinase leading to resistant cell types. How cells respond to • Light and electron microscopes autophosphorylation of a conserved histidine nutritional stress is profoundly influenced by cell residue in the C-terminal transmitter domain. This density. Extracellular signal molecules accumulate • Ultrafiltration systems phosphoryl group is then transferred to aspartate in the local environment of densely populated cell • Autoclaves in the conserved N-terminal domain of ResD, cultures and trigger antibiotic production and • Photographic facilities altering the activity of its C-terminal domain as a developmental processes such as sporulation and transcriptional activator. The ResD-ResE signal genetic competence. The objective of our research • Probe type sonicators and extruder transduction system is activated by oxygen is to understand, in molecular terms, the limitation or by addition of nitric oxide generators. regulatory networks that cells utilize to choose the The objectives of our studies are to determine how most appropriate response to harsh conditions. In ResE senses oxygen limitation or nitric oxide and the spore-forming bacterium Bacillus subtilis, how anaerobically induced genes are activated by establishment of genetic competence is co- ResD. Nakano regulated with peptide antibiotic biosynthesis by a complex network of signal transduction pathways Flavohemoglobin (Hmp) that utilize protein components common to all Flavohemoglobin is a ubiquitous protein present in prokaryotic and most eukaryotic organisms. Zuber organisms ranging from Escherichia coli to Saccharomyces cerevisiae. The N-terminal part of Biochemistry of Lignin Degradation the protein has similarity to hemoglobin, and the Lignin is the most abundant renewable aromatic C-terminus is homologous to reductase with a polymer, constituting approximately 25 percent of flavin-binding domain. Recent studies showed that woody plant cell walls. Our multidisciplinary

15 BMB | BIOCHEMISTRY AND MOLECULAR BIOLOGY

research program aims to understand and exploit processes. We are attempting to characterize these the fungal degradation of this underutilized enzymes and their encoding genes to more fully resource. The metabolic pathways and enzymatic understand the mechanisms involved in the components of the lignin degradative system are degradation of these pollutants. Recently we examined using biochemical, enzymological and discovered a novel reductive dechlorination system molecular biological methods. Two novel in white-rot fungi that removes chlorines from extracellular heme peroxidases (lignin peroxidase chlorinated hydroquinones. This system is being and manganese peroxidase) involved in the examined by biochemical and molecular biological degradation of lignin were discovered in our methods. Gold laboratory. Lignin peroxidase oxidizes a variety of Oxidative Enzymes Involved in Fungal nonphenolic lignin model compounds and priority Cellulose Degradation pollutants. Manganese peroxidase oxidizes MnII to Cellulose constitutes 40 percent to 60 percent of MnIII, which in turn oxidizes phenolic and plant cell wall material; its biotechnological nonphenolic substrates. The structures, active conversion, initially to glucose and then to ethanol, sites, mechanisms, catalytic cycles and regulation can provide an alternative source of energy. This of these enzymes are being characterized in our application requires a complete understanding of laboratory and via collaborations using the various enzymes involved in fungal cellulose spectroscopy, stopped-flow kinetics, protein degradation. The cellulose-degrading cultures of chemistry, enzymology, X-ray crystallography and Phanerochaete chrysosporium produce a unique bio-organic and molecular genetic methods. hemoflavoenzyme, cellobiose dehydrogenase (CDH), Recently, we developed a homologous expression which oxidizes cellobiose to cellobionolactone. We system for these peroxidases. This system allows have purified CDH to homogeneity in high yields. structure/function studies by site-directed Cellulases bind to crystalline cellulose using a mutagenesis. Applications for lignin-degrading specific cellulose-binding domain. CDH appears to systems include the more efficient utilization of have a similar domain for cellulose binding. The biomass, nonpolluting forest products technologies amino acid sequence responsible for cellulose and toxic waste cleanup. We also are studying binding and the binding mechanism are under several intracellular enzymes such as quinone investigation. Our recent research suggests that a reductases, ring-cleaving dioxygenases and possible physiological role of CDH is to enhance reductive dehalogenases that are involved in lignin crystalline cellulose degradation by cellulases, the and pollutant degradation. Gold rate-limiting step in the bioconversion of cellulose Molecular Biology and Genetics of Phanerochaete to glucose. A detailed study of the structure, chrysosporium and Its Lignin-Degrading System function and mechanism of CDH using We are isolating and sequencing the genes spectroscopic, biochemical and molecular encoding components of the P. chrysosporium biological methods is in progress. Gold lignin-degrading system. These include genes encoding lignin and manganese peroxidases, a novel quinone reductase and several other genes. We are analyzing the coding and promoter regions of these genes and studying the regulation of their transcription. We have discovered that Mn peroxidase is regulated by Mn ion, the substrate for the enzyme, as well as by nutrient nitrogen, heat shock and oxidative stress. Using reporter genes and RT-PCR, we are elucidating the molecular mechanisms involved in Mn peroxidase gene regulation. Recently we developed a transcriptional reporter system based on the gene encoding green fluorescent protein from jellyfish. We also are undertaking molecular biology studies on the manganese peroxidase gene of Dichomitus squalens and on its heterologous expression in P. chrysosporium. Gold Biodegradation of Aromatic Pollutants The nonspecific and oxidative nature of the lignin degradation system of the fungus Phanerochaete chrysosporium enables this organism to degrade a variety of toxic aromatic pollutants, including polychlorinated phenols, polychlorinated dioxins, chlorophenoxyacetic acid and nitrotoluenes. We are examining the biochemical pathways, enzymes and regulatory mechanisms involved in the total degradation of these compounds. We have shown that the fungus utilizes extracellular peroxidases as well as intracellular quinone reductases, reductive dehalogenases and dioxygenases to carry out these

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NINIAN J. BLACKBURN COLIN ANDREW KEITH D. GARLID MICHAEL H. GOLD Professor and Department Head Research Assistant Professor Professor Institute Professor Ph.D., Inorganic Chemistry Ph.D., Chemistry, M.D., The Johns Hopkins Ph.D., Biochemistry University of Dundee, University of Newcastle University School State University of N.Y. Scotland, U.K., 1975 Upon Tyne, 1992 of Medicine, 1961 at Buffalo, 1970 [email protected] [email protected] Dr. technicae norwegiensis, [email protected] Physical Chemistry RESEARCH INTERESTS RESEARCH INTERESTS Norwegian Institute RESEARCH INTERESTS of Technology, 1987 Structure and function of oxidase Bioinorganic chemistry; structure, Biochemistry; molecular biology; [email protected] and oxygenase metalloenzymes; function and spectroscopy of genetics of fungi; fungal spectroscopy of metal sites in metalloenzymes; generation, degradation of lignin and proteins with emphasis on EPR, mobilization and sensing of nitric RESEARCH INTERESTS environmental pollutants; EXAFS, absorption edge, and FTIR oxide by metalloproteins; The structure-function of the structure and function of novel spectroscopies; coordination redox-active copper proteins. mitochondrial ATP-sensitive K+ peroxidases; structure expression chemistry and biochemistry of channel (mitoKATP) and its role in and regulation of fungal genes; copper. Biochemistry of metal REPRESENTATIVE PUBLICATIONS cardioprotection and cardiac biotechnology. trafficking in cells. C.R. Andrew, E.L. Green, D.M. Lawson physiology; the structure-function and R.R. Eady, “Resonance Raman of uncoupling proteins; REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS Studies of Cytochrome c Support the mitochondrial and cellular G.V.B. Reddy and M.H. Gold, Binding of NO and CO to Opposite Sides F.C. Rhames, N.N. Murthy, K.D. Karlin bioenergetics. “Purification and Characterization of the Heme: Implications for Ligand and N.J. Blackburn, “Isocyanide Binding of Glutathione Conjugate Reductase: Discrimination in Heme-Based Sensor.” to the Copper(I) Centers of the A Component of the Biochemistry 2001, 40, 4115-4122. REPRESENTATIVE PUBLICATIONS Catalytic Core of Peptidylglycine Tetrachlorohydroquinone Reductive R. Bajgar, S. Seetharaman, A.J. Monooxygenase (PHMcc).” J. Biol. D.M. Lawson, C.E.M. Stevenson, C.R. Dehalogenase System from Kowaltowski, K.D. Garlid and P. Paucek, Inorg. Chem. 2001, 6, 567-577. Andrew and R.R. Eady, “Unprecedented Phanerochaete chrysosporium.” Arch. “The ATP-Sensitive Potassium Channel Proximal Binding of Nitric Oxide to Heme: Biochem. Biophys. 2001, 391, 271-277. S. Jaron and N.J. Blackburn, of Brain Mitochondria.” J. Biol. Chem. Implications for Guanylate Cyclase.” “Characterization of a Half-Apo 2001, 276, 33369-33374. F.A.J. Rotsaert, B. Li, V. Renganathan EMBO J. 2000, 19, 5661-5671. Derivative of Peptidylglycine and M.H. Gold, “Site-directed A.J. Kowaltowski, S. Seetharaman, P. Monooxygenase. Insight into the J.P. Hannan, S.L. Davy, G.R. Moore, Mutagenesis of the Heme Axial Ligands Paucek and K.D. Garlid, “Bioenergetic Reactivity of Each Active Site Copper.” R.R. Eady and C.R. Andrew “Effect of in the Hemoflavoenzyme, Cellobiose Consequences of Opening the Biochemistry 2001, 40, 6867-6875. Nickel(II) Substitution on the Dehydrogenase.” Arch. Biochem. ATP-Sensitive K+ Channel of Heart Resonance Raman and NMR Spectra Biophys. 2001, 390, 206-214. N.J. Blackburn, F.C. Rhames, M. Mitochondria.” Am. J. Physiol. Heart of Alcaligenes xylosoxidans Azurin II: Ralle and S. Jaron, “Major Changes Circ. Physiol. 2001, 280, H649-H657. H.L. Youngs, M.D. Sollewijn Gelpke, Implications for Axial-Ligand Bonding in Copper Coordination Accompany D. Li, M. Sundaramoorthy and M.H. Interactions in Cupredoxin Active K.D. Garlid, M. Jaburek, P. Jezek II Reduction of Peptidylglycine Gold, “The Role of E39 in Mn Binding Sites.” Biol. Inorg. Chem. 1998, 3, and M. Varecha, “How Do Uncoupling Monooxygenase: Implications for and Oxidation by Manganese 282-291. Proteins Uncouple?” Biochim. Biophys. Electron Transfer and the Catalytic Peroxidase from Phanerochaete Acta 2000, 1459, 383-389. Mechanism.” J. Biol. Inorg. Chem. C.R. Andrew, J. Han, T. den Blauuwen, chrysosporium.” Biochemistry 2001, 2000, 5, 341-353. G. van Pouderoyen, E. Vijgenboom, G.J. Grover and K.D. Garlid, 40, 2243-2250. G.W. Canters and J. Sanders-Loehr, “ATP-Sensitive Potassium Channels: J.F. Eisses, J.P. Stasser, M. Ralle, D. Li, H.L. Youngs and M.H. Gold, “Cysteine Ligand Vibrations are A Review of Their Cardioprotective J.H. Kaplan and N.J. Blackburn, “Heterologous Expression of a Responsible for the Complex Resonance Pharmacology.” J. Mol. Cell. Cardiol. “Domains I and III of Human Copper Thermostable Manganese Peroxidase Raman Spectrum of Azurin.” Biol. 2000, 32, 677-695. Chaperone for Superoxide Dismutase from Dichomitus squalens in Inorg. Chem. 1997, 2, 98-107. Interact via a Cysteine-Bridged K.D. Garlid, P. Paucek, V. Yarov- Phanerochaete chrysosporium.” Arch. Dicopper(I) Cluster.” Biochemistry C.R. Andrew and J. Sanders-Loehr, Yarovoy, H.N. Murray, R.B. Darbenzio, Biochem. Biophys. 2001, 385, 348-356. 2000, 38, 7337-7342. “Copper-Sulfur Proteins: Using Raman A.J. D’Alonzo, N.J. Lodge, M.A. Smith B. Ma, M.B. Mayfield and M.H. Gold, Spectroscopy to Predict Coordination and G.J. Grover, “Cardioprotective N.J. Blackburn, M. Ralle, R. Hassett “The Green Fluorescent Protein Gene Geometry” [Review]. Acc. Chem. Res. Effect of Diazoxide and its Interaction and D.J. Kosman, “Spectroscopic Functions as a Reporter of Gene 1996, 29, 365-372. with Mitochondrial ATP-Sensitive K+ Analysis of the Trinuclear Cluster in the Expression in Phanerochaete Channels. Possible Mechanism of Fet3 Protein from Yeast, a Multinuclear chrysosporium.” Appl. Environ. Cardioprotection.” Circ. Res. 1997, 81, Copper Oxidase.” Biochemistry 2000, Microbiol. 2001, 67, 948-955. 1072-1082. 39, 2316-2324.

17 BMB | BIOCHEMISTRY AND MOLECULAR BIOLOGY | FACULTY

THOMAS M. LOEHR PIERRE MOËNNE-LOCCOZ MICHIKO NAKANO PETR PAUCEK Professor Assistant Professor Research Associate Professor Research Assistant Professor Ph.D., Inorganic Chemistry Ph.D., Biophysics Ph.D., Cell Biology Dr.Rer.Nat., Biophysics Cornell University, 1967 University of Pierre & Marie Curie, University of Tokyo, 1976 and Chemical Physics [email protected] Paris VI, 1989 [email protected] Palacky University (CZ), 1988 [email protected] Ph.D., Biological Science RESEARCH INTERESTS RESEARCH INTERESTS The Academy of Sciences of the Czech Republic, 1991 Metallobiochemistry; biological RESEARCH INTERESTS Anaerobiosis of Bacillus subtilis; [email protected] role of transition metals; Structure-function relationships oxygen-controlled gene regulation; molecular and electronic within proteins. Metallo- and two-component signal transduction structures of metalloenzyme active heme-proteins. Spectroscopic system; transcriptional activation; RESEARCH INTERESTS

sites; chemistry of O2 metabolism; studies of enzyme-active sites nitrate/nitrite reductases; Molecular biophysics of metal-oxo intermediates; and their cofactors. Reaction flavohemoglobin; anaerobic mitochondrial cation transporters resonance and FT Raman, intermediates within catalysts. electron transport; nitric and channels, with emphasis on FT-IR, and EPR spectroscopy. oxide signaling. the ATP-dependent K+ channel in REPRESENTATIVE PUBLICATIONS cardiac and brain mitochondria; REPRESENTATIVE PUBLICATIONS R.A. Ghiladi, K.R. Hatwell, K.D. Karlin, REPRESENTATIVE PUBLICATIONS receptor properties and their roles J. Hirst, S.K. Wilcox, J. Ai, P. Moënne- H.-w. Huang, P. Moënne-Loccoz, M.M. Nakano and Y. Zhu, “Involvement in cellular signaling, bioenergetics Loccoz, T.M. Loehr and D.B. Goodin, C. Krebs, B.H. Huynh, L.A. Marzilli, of the ResE Phosphatase Activity in and pharmacology. “Replacement of the Axial Histidine R.J. Cotter, S. Kaderli and A.D. Down-Regulation of ResD-Controlled Zuberbuhler, “Dioxygen Reactivity of Ligand with Imidazole in Cytochrome Genes in Bacillus subtilis During REPRESENTATIVE PUBLICATIONS c Peroxidase. 2. Effects on Heme Mononuclear Heme and Copper Aerobic Growth.” J. Bacteriol. 2001, Coordination and Function.” Components Yielding a High-Spin 183, 1938-1944. R. Bajgar, S. Seetharaman, A.J. Biochemistry 2001, 40, 1274-1283. Heme-Peroxo-Cu Complex.” Kowaltowski, K.D. Garlid and P. Paucek, J. Am. Chem. Soc. 2001, 123, M.M. Nakano, Y. Zhu, M. LaCelle, “Identification and Properties of a J. Baldwin, W.C. Voegtli, N. Khidekel, 6183-6184. X. Zhang and F.M. Hulett, “Interaction Novel Intracellular (Mitochondrial) P. Moënne-Loccoz, C. Krebs, B.A. Ley, of ResD with Regulatory Regions of ATP-Sensitive Potassium Channel in B.H. Huynh, T.M. Loehr, A. C. K. Auclair, P. Moënne-Loccoz and Anaerobically Induced Genes in Brain.” J. Biol. Chem. 2001, 276, Rosenzweig and J.M. Bollinger, Jr., P.R. Ortiz de Montellano, “Roles of the Bacillus subtilis.” Mol. Microbiol. 2000, 3369-33374. “Rational Reprogramming of the R2 Proximal Heme Thiolate Ligand in 37, 1198-1207. Subunit of Escherichia coli Cytochrome P450cam.” J. Am. Chem. G.J. Grover, A.J. D’Alonzo, K.D. M.M. Nakano, Y. Zhu, J. Liu, D.Y. Ribonucleotide Reductase into a Self- Soc. 2001, 123, 4877-4885. Garlid, N.J. Lodge, P.G. Sleph, R.B. Reyes, H. Yoshikawa and P. Zuber, Hydroxylating Monooxygenase.” J. Am. Darbenzio, T.A. Hess, M.A. Smith, P. P. Moënne-Loccoz, O.-M.H. Richter, “Mutations Conferring Amino Acid Chem. Soc. 2001, 123, 7017-7030. Paucek and K.S. Atwal, “Pharmacologic H.-w. Huang, I. Wasser, R.A. Ghiladi, Residue Substitutions in the Carboxy- Characterization of BMS-101-05, a E.L. Green, S. Taoka, R. Banerjee and K.D. Karlin and S. de Vries, “Nitric Terminal Domain of RNA Polymerase Mitochondrial KATP Opener with No T.M. Loehr, “Resonance Raman Oxide Reductase from Paracoccus alpha Can Suppress clpX and clpP with Peripheral Vasodilator or Cardiac Characterization of the Heme Cofactor denitrificans Contains an Oxo-Bridged Respect to Developmentally Regulated Action Potential Shortening Activity.” in Cystathionine Beta-Synthase. Heme/Non-Heme Diiron Center.” J. Am. Transcription in Bacillus subtilis.” J. Pharmacol. Exp. Ther. 2001, 297, Identification of the Fe-S(Cys) Vibration Chem. Soc. 2000, 122, 9344-9345. Mol. Microbiol. 2000, 37, 869-884. 1184-1192. in the Six-Coordinate Low-Spin Heme.” A. Wilks and P. Moënne-Loccoz, M.M. Nakano, G. Zheng and P. Zuber, Biochemistry 2001, 40, 459-463. A.J. Kowaltowski, S. Seetharaman, “Identification of the Proximal Ligand “Dual Control of sbo-alb Operon P. Paucek and K.D. Garlid, “Bioener- Y. Liu, L. Koenigs Lightning, H.-w. His-20 in Heme Oxygenase (HmuO) Expression by the Spo0 and ResDE getic Consequences of Opening the from Corynebacterium diphtheriae. Huang, P. Moënne-Loccoz, D.J. Systems of Signal Transduction Under ATP-Sensitive K+ Channel of Heart Schuller, T.L. Poulos, T.M. Loehr and Oxidative Cleavage of the Heme Anaerobic Conditions in Bacillus Mitochondria.” Am. J. Physiol. Heart P.R. Ortiz de Montellano, “Replacement Macrocycle Does Not Require the subtilis.” J. Bacteriol. 2000, 182, Circ. Physiol. 2001, 280, H649-H657. of the Distal Glycine 139 Transforms Proximal Histidine.” J. Biol. Chem. 3274-3277. Human Heme Oxygenase-1 into a 2000, 275, 11686-11692. M. Jaburek, V. Yarov-Yarovoy, C. Jourlin-Castelli, N. Mani, M.M. Peroxidase.” J. Biol. Chem. 2000, 275, P. Paucek, W. Li and K.D. Garlid P. Moënne-Loccoz, C. Krebs, Nakano and A.L. Sonenshein, “CcpC, 34501-34507. “State-Dependent Inhibition of the K. Herlihy, D.E. Edmondson, E.C. Theil, a Novel Regulator of the LysR Family Mitochondrial KATP Channel by L.S. Koo, R.A. Tschirret-Guth, W.E. B.H. Huynh and T.M. Loehr, “The Required for Glucose Repression of the Glyburide and 5-Hydroxydecanoate.” Straub, P. Moënne-Loccoz, T.M. Loehr Ferroxidase Reaction of Ferritin citB Gene in Bacillus subtilis.” J. Mol. J. Biol. Chem. 1998, 273, 13578. and P.R. Ortiz de Montellano, “The Reveals a Diferric mu-1,2 Bridging Biol. 1999, 295, 865-878. Active Site of the Thermophillic cyp119 Peroxide Intermediate in Common with K.D. Garlid, P. Paucek, V. Yarov- from Sulfolobus solfataricus.” J. Biol. Other O2 - Activating Non-Heme Diiron Yarovoy, H.N. Murray, R.B. Darbenzio, Chem. 2000, 275, 14112-14123. Proteins.” Biochemistry 1999, 38, A.J. D’Alonzo, N.J. Lodge, M.A. Smith 5290-5295. and G.J. Grover. “Cardioprotective Effect of Diazoxide and Its Interaction with Mitochondrial ATP-Sensitive K+ Channels: Possible Mechanism of Cardioprotection.” Circ. Res. 1997, 81, 1072.

18 FACULTY | BIOCHEMISTRY AND MOLECULAR BIOLOGY | BMB

MARTINA RALLE L.E.L. (BETS) RASMUSSEN MATTHEW S. SACHS JAMES W. WHITTAKER Research Scientist Research Professor Associate Professor Associate Professor Ph.D., Chemistry Ph.D., Neurochemistry Ph.D., Biology Ph.D., Biochemistry University of Bonn, Germany, 1993 Washington University Massachusetts Institute of University of Minnesota, 1983 [email protected] (St. Louis), 1964 Technology, 1986 [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Metallobiochemistry; structure- RESEARCH INTERESTS RESEARCH INTERESTS Electronic structures and function analysis of Mammalian chemocommunication: Mechanisms of translational and dynamics of metalloenzyme metalloenzymes. Spectroscopic the transport, olfactory and transcriptional control that active sites; spectroscopic and characterization of copper vomeronasal organ reception of regulate the expression of the computational approaches to transporters such as Wilson’s and (Z)-7-dodecenyl acetate, the sex Neurospora crassa arg-2 and biomolecular structure; Menkes disease protein, using pheromone of the Asian elephant; Saccharomyces cerevisiae metalloenzyme mechanisms; extended X-ray absorption fine the origin and synthesis of (Z)-7- CPA1 genes; translational enzyme engineering; biology structure spectroscopy (EXAFS). dodecenyl acetate; identification control of human proto-oncogenes; of metal ions. Cloning, overexpression and and function of pheromones and fungal genomes. characterization of proteins chemical signals of the elephant- REPRESENTATIVE PUBLICATIONS involved in copper transport in the unique temporal gland. REPRESENTATIVE PUBLICATIONS M.M. Whittaker and J.W. Whittaker, mammalian cell. D.D. Perkins, A. Radford and M.S. “Catalytic Reaction Profile for Alcohol REPRESENTATIVE PUBLICATIONS Sachs, The Neurospora Compendium: Oxidation by Galactose Oxidase.” Biochemistry 2001, 40, 7140-7148. REPRESENTATIVE PUBLICATIONS L.E.L. Rasmussen, “Source Chromosomal Loci. Academic Press, 2001. J.F. Eisses, J.P. Stasser, M. Ralle, J.H. and Cyclic Release Pattern of (Z)-7- R.A. Edwards, M.M. Whittaker, J.W. Kaplan and N.J. Blackburn, “Domains I Dodecenyl Acetate, the Preovulatory H.S. Kelkar, J. Griffiths, M.E. Case, Whittaker, E.N. Baker and G.B. and III of Human Copper Chaperone for Pheromone of the Female Asian S.F. Covert, D.A. Hall, C. Keith, Jameson, “Outer Sphere Mutations Superoxide Dismutase Interact via a Elephant.” Chem. Senses 2001, 26, J.S. Oliver, M.J. Orbach, M.S. Sachs, Perturb Metal Reactivity in Manganese Cysteine-Bridged Dicopper(I) Cluster.” 611-623. J.R. Wagner, M.J. Weise, Superoxide Dismutase.” Biochemistry 2001, 40, 15-27. Biochemistry 2000, 38, 7337-7342. L.E.L. Rasmussen and V. J.K. Wunderlich and J. Arnold, “The Neurospora Crassa Genome: Libraries N.J. Blackburn, M. Ralle, R. Hassett Krishnamurthy, “How Chemical Signals M.M. Whittaker and J.W. Whittaker, Sorted by Chromosome.” Genetics and D.J. Kosman, “Spectroscopic Integrate Asian Elephant Society: The “Expression of Recombinant Galactose 2001, 157, 979-990. Analysis of the Trinuclear Cluster in the Known and the Unknown.” Zoo Biol. Oxidase by Pichia pastoris.” Protein Fet3 Protein from Yeast, a Multinuclear 2000, 19, 405-423. P. Fang, Z. Wang and M.S. Sachs, Expr. Purif. 2000, 20, 105-111. Copper Oxidase.” Biochemistry 2000, L.E.L. Rasmussen, “Elephant “Evolutionarily Conserved Features of M.M. Whittaker and J.W. Whittaker, 39, 2316-2324. Olfaction.” ChemoSenses, 1999, 2, 4-5. the Arginine Attenuator Peptide Provide “Recombinant Superoxide Dismutase the Necessary Requirements for its M. Ralle, M.L. Verkhovskaya, from a Hyperthermophilic Archaeon, L.E.L. Rasmussen and T.E. Perrin, Function in Translational Regulation.” J.E. Morgan, M.I. Verkhovsky, M. Pyrobaculum aerophilium.” J. Biol. “Physiological Correlates of Musth: J. Biol. Chem. 2000, 275, 26710- Wikstrom and N.J. Blackburn, Inorg. Chem. 2000, 5, 402-408. Lipid Metabolites and Chemosignal 26719. “Coordination of CuB in Reduced and Composition.” Physiol. Behav. 1999, 67, M.M. Whittaker, V.V. Barynin, S.V. CO-liganded States of Cytochrome bo3 539-549. A.P. Geballe and M.S. Sachs, Antonyuk and J.W. Whittaker, “The from Escherichia coli. Is Chloride Ion a “Translational Control by Upstream Oxidized (3,3) State of Manganese L.E.L. Rasmussen, “Chemical Cofactor?” Biochemistry, 1999, 38, Open Reading Frames,” in Catalase. Comparison of Enzymes from Communication: An Integral Part of 7185-7194. Translational Control of Gene Thermus thermophilus and Functional Asian Elephant (Elephas Expression (N. Sonenberg, J.W. B. N.J. Blackburn, M. Ralle, E. Gomez, Lactobacillus plantarum.” maximus) Society.” Ecoscience 1998, Hershey and M.B. Mathews, eds.), M.G. Hill, A. Pastuszyn, D. Sanders and Biochemistry 1999, 38, 9126-9136. 5, 410-426. Cold Spring Harbor Laboratory Press, J.A. Fee, “Selenomethionine-substituted New York, 2000, pp. 595-614. Thermus thermophilus Cytochrome ba3: Characterization of the CuA Site by Se Z. Wang, A. Gaba and M.S. Sachs, and Cu K-EXAFS.” Biochemistry, 1999, “A Highly Conserved Mechanism of 38, 7075-7084. Regulated Ribosome Stalling Mediated by Fungal Arginine Attenuator Peptides M. Ralle, M.J. Cooper, S. Lutsenko That Appears Independent of the and N.J. Blackburn, “The Menkes Charging Status of Arginyl-tRNAs.” Disease Protein Binds Copper via Novel J. Biol. Chem. 1999, 274, 2-Coordinate Cu(I)-Cysteinates in the 37565-37574. N-Terminal Domain.” J. Am. Chem. Soc. 1998, 120, 13525-13526.

19 BMB | BIOCHEMISTRY AND MOLECULAR BIOLOGY | FACULTY

JOINT FACULTY HONG-WEI HUANG Ph.D., Pharmaceutical Science DAVID R. BOONE Kanazawa University, Japan Environmental Biology Portland State University MARTIN JABÜREK Ph.D., Molecular Biology JAMES M. GREGG and Biochemistry Keck Graduate Institute OGI School of Science of Applied Life Sciences & Engineering at OHSU GEBRETATEOS WOLDEGIORGIS PETER ZUBER BERNARD A. FOX SUBRAMANIAM SEETHARAN Associate Professor Professor Ph.D., Nutritional Biochemistry Ph.D., Microbiology Earle A. Chiles Research Institute M.D., Stanley Medical College University of Wisconsin- University of Virginia Providence Medical Center University of Madras Madison, 1976 [email protected] Madras, India [email protected] STEPHEN B. HALL MALAYALAM SRIDHAR RESEARCH INTERESTS Pulmonary and Critical Care Medicine Ph.D., Organic Chemistry RESEARCH INTERESTS Regulation of prokaryotic gene Oregon Health & Science University Indian Institute of Science Regulation of carnitine expression and development in Bangalore, India palmitoyltransferase I; regulation response to stress; signal JAMES F. PANKOW of long-chain fatty acid transport transduction; regulation and MEI M. WHITTAKER and oxidation in mammalian cells; mechanism of peptide antibiotic Environmental Science regulation of cell metabolism and biosynthesis; regulation of genetic and Engineering Ph.D., Biochemistry signaling by long-chain acyl CoA competence in Bacillus subtilis. OGI School of Science University of Minnesota esters; mitochondrial ion transport & Engineering at OHSU and bioenergetics. REPRESENTATIVE PUBLICATIONS GUOLU ZHENG PAUL G. TRATNYEK P. Zuber, “Specificity Through Ph.D., Food Microbiology REPRESENTATIVE PUBLICATIONS Flexibility.” Nat. Struct. Biol. 2000, Environmental Science University of Arkansas C. Nicot, F.G. Hegardt, G. Woldegiorgis, 7, 1079-1081. and Engineering D. Haro and P.F. Marrero, “Pig Liver J. Liu and P. Zuber, “The ClpX OGI School of Science Carnitine Palmitoyltransferase I, Protein of Bacillus subtilus Indirectly & Engineering at OHSU SENIOR STAFF with low Km for Carnitine and High Influences RNA Polymerase Sensitivity to Malonyl-CoA Inhibition, Holoenzyme Composition and Directly DEEPALI DATTA H is a Natural Chimera of Rat Liver and Stimulates Sigma -Dependent ADJUNCT FACULTY M.Sc., Zoology Muscle Enzymes.” Biochemistry 2001, Transcription In Vitro.” Mol. Microbiol. 40, 2260-2266. Delhi University, India 2000, 37, 885-897. G. DOYLE DAVES J. Dai, H. Zhu, J. Shi and G. G. Zheng, R. Hehn and P. Zuber, Consultant KAITLIN GRAMMER Woldegiorgis, “Identification by “Mutational Analysis of the Mutagenesis of Conserved Arginine sbo-alb Locus of Bacillus subtilis: B.S., Geology and Tryptophan Residues in Rat Liver Identification of Genes Required for KENT HERMSMEYER University of Alaska-Fairbanks Carnitine Palmitoyltransferase I Subtilosin Production and Immunity.” Oregon Regional Primate Important for Catalytic Activity.” J. Bacteriol. 2000, 182, 3266-3273. Research Center MARY MAYFIELD-GAMBILL J. Biol. Chem. 2000, 275, M.M. Nakano, Y. Zhu, J. Liu, D.Y. 22020-22024. B.S., Microbiology Reyes, H. Yoshikawa and P. Zuber, JAMES K. HURST Oregon State University J. Shi, H. Zhu, D.N. Arvidson and G. “Mutations Conferring Amino Acid Woldegiorgis, “The First 28 N-Terminal Residue Substitutions in the Carboxy- Washington State University Amino Acid Residues of Human Heart Terminal Domain of RNA Polymerase SHUNJI NAKANO Muscle Carnitine Palmitoyltransferase I Alpha Can Suppress clpX and clpP with GEORGE D. OLSEN B.S., Molecular Biology are Essential for Malonyl CoA Respect to Developmentally Regulated Oregon Health & Science University Nagoya University, Japan Sensitivity and High-Affinity Binding.” Transcription in Bacillus subtilis.” Biochemistry 2000, 39, 712-717. Mol. Microbiol. 2000, 37, 869-884. V. RENGANATHAN JARMILA PAUCKOVA G. Woldegiorgis, J. Shi, H. Zhu M.M. Nakano, G. Zheng and P. Zuber, and D.N. Arvidson, “Functional “Dual Control of sbo-alb Operon Consultant M.D., Palacky University Characterization of Mammalian Expression by the Spo0 and ResDE Czech Republic Mitochondrial Palmitoyltransferases I Systems of Signal Transduction Under CARL C. WAMSER and II Expressed in the Yeast Pichia Anaerobic Conditions in Bacillus Portland State University CRAIG SEMRAD pastoris.” J. Nutr. 2000, 130, 310S- subtilis.” J. Bacteriol. 2000, 182, 314S. 3274-3277. B.S., Physics Stanford University L. Abu-Elheiga, W.R. Brinkley, L. Zhong, S.S. Chirala, G. Woldegiorgis RESEARCH ASSOCIATES and S.J. Wakil, “The Subcellular MICHELLE TREBER ELENA CRUCERESCU Localization of Acetyl-CoA Carboxylase B.S., Biological Sciences 2.” Proc. Natl. Acad. Sci. USA 2000, Ph.D., Microbiology California Polytechnic 97, 1444-1449. and Parasitology State University University of Medicine and Pharmacy, Iassy, Romania.

20 THE DEPARTMENT OF COMPUTER SCIENCE preferably three, courses from the MS Core Department of AND ENGINEERING has an internationally (list follows). Students must earn an overall Grade Point Average of 3.0 and a B or better acclaimed research program.The in each MS Core class to be eligible to apply Computer Science breadth and depth of the research through Advanced Placement: and Engineering program is evidenced by the CSE500 Introduction to Software Engineering CSE511 Principles of Compiler Design research projects and research www.cse.ogi.edu centers listed below, and by the CSE513 Introduction to Operating Systems CSE514 Introduction to Database Systems educational program. CSE521 Introduction to Computer Architecture DEPARTMENT HEAD Jim Hook Four degrees are offered: Master of Science CSE532 Analysis and Design of Algorithms (503) 748-1169 in Computer Science and Engineering, Master CSE533 Automata and Formal Languages E-mail: [email protected] of Science in Computational Finance, Oregon If a student applies to the Computational Master of Software Engineering, and Doctor Finance program through advanced placement, DEPARTMENT ADMINISTRATOR of Philosophy in Computer Science and the 12 credits earned may be from CSE, ECE APC Dana Director or FIN courses. Engineering. In addition to these degrees, we (503) 748-1358 offer a Certificate in Computational Finance, E-mail: [email protected] Applied Computing, and Oregon Master of DEGREE REQUIREMENTS ACADEMIC COORDINATOR Software Engineering. A Student Program Committee (SPC) that Shirley Kapsch provides academic advising is assigned for (503) 748-1255 each matriculating student. The student’s SPC ADMISSION REQUIREMENTS E-mail: [email protected] also approves the application of courses Admission requirements are the same as the toward the degree requirements. DEPARTMENT SECRETARY general requirements of the institution. Barbara Mosher A maximum of 21 credits earned prior to General aptitude GRE scores are required, (503) 748-1151 matriculation at OGI may be applied toward except in cases of advanced placement E-mail: [email protected] admission for M.S. students (see below). A the master’s degree. This may include up to candidate must hold a bachelor’s degree in 12 credits transferred from other institutions CSE GENERAL INQUIRIES computer science, mathematics, engineering, (up to 18 from Portland State University, the (503) 748-1151 one of the biological or physical sciences, or University of Oregon or Oregon State E-mail: [email protected] one of the quantitative social sciences. University) and credits taken at OGI prior to Candidates with a degree in a field other than matriculation. computer science must have completed The program of study for each master’s courses in the following subject areas: student may be tailored to meet individual • An introduction to programming in needs by the SPC. Students are particularly a high-level language encouraged to include special-topic courses • Data structures* (CSE 58X) relevant to their interests. • Discrete mathematics* CSE MS PROFESSIONAL INTERNSHIP OPTION Participation is limited by available industrial • Logic design and computer organization internships. Students declaring this option must • Calculus or other college-level mathematics complete 45 credits of course work and up to an additional 3 credits of a professional internship. *APC515 Data Structures and Discrete (CSE620) Mathematics may be taken to meet the prerequisite. MASTER OF SCIENCE IN COMPUTER SCIENCE AND ENGINEERING All M.S. students must complete the M.S. core of ADVANCED PLACEMENT ADMISSIONS 21 credits. FOR MS STUDENTS M.S. CSE CORE Students who are currently studying at OGI The following courses are required of all M.S. and have earned 12 credits in computer CSE students: science classes are exempt from the GRE and CSE500 Introduction to Software Engineering 3 credits TOEFL requirements. Only two letters of CSE511 Principles of Compiler Design 3 credits recommendation are required; all other CSE513 Introduction to Operating Systems 3 credits admissions requirements remain the same. CSE514 Introduction to Database Systems 3 credits Doctoral student Francis Chang (left) and faculty The CSE courses must include at least two, CSE521 Introduction to Computer Architecture 3 credits member Wu-chang Feng are working on network support for streaming digital media. CSE | COMPUTER SCIENCE AND ENGINEERING

CSE532 Analysis and Design of Algorithms 3 credits 2. COMPUTATIONAL FINANCE CORE (18 credits): 1. M.S. CSE Core (listed above) CSE533 Automata and Formal Languages 3 credits Required: (Choose 6 of the following:) 2. DATA-INTENSIVE SYSTEMS CORE (12 credits)

M.S. THESIS OPTION FIN541 Principles of Modern Finance 3 credits Four of: Students choosing the thesis option must FIN544 Investment and Portfolio Management 3 credits CSE515 Distributed Computing Systems 3 credits submit and defend a master’s thesis and may FIN547 Global Markets and Foreign Exchange 3 credits CSE526 Modern Operating System Design 3 credits apply up to 12 credits of thesis research FIN551 Options and Futures 3 credits CSE541 Database Implementation 3 credits (CSE 700) toward the 45 credit requirement. FIN552 Options and Futures II 3 credits CSE542 Object Data Management 3 credits 1. M.S. CSE CORE (listed above) FIN558 Advanced Numerical Computing in Finance CSE58X Informational Retrieval and the Internet 3 credits 3 credits 2. CSE 700 M.S. THESIS (maximum 12 credits) FIN561 Risk Management 3 credits CSE58X Any special topics course in the database area 3. ELECTIVES (12 credits), as directed by the thesis advisor or SPC FIN573 Financial Time-Series Analysis 3 credits One course from the System Software Core Please note: Students may not receive credit for FIN576 Financial Markets and Trading 3 credits One course from the Software Engineering Core or the both CSE504 and OMSE533. FIN585 Topics in Computational Finance 3 credits Software Engineering for Industry Professionals Core 3. SUGGESTED ELECTIVES (6 credits) 3. SUGGESTED ELECTIVES (12 credits) M.S. NONTHESIS OPTIONS CSE509 Object-Oriented Programming 3 credits Any CSE class not already taken. Students choosing the nonthesis M.S. option CSE540 Neural Network Algorithms & Architecture Please note: Students may not receive credit for must complete 15 courses and a minimum of 3 credits both CSE504 and OMSE533. 45 credits; up to six credits of nonthesis CSE544 Introduction to Probability and HUMAN-COMPUTER INTERFACES AREA OF EMPHASIS research (CSE 610) may be included, with Statistical Inference 3 credits NONTHESIS M.S. CSE DEGREE the approval of the student’s SPC. Students CSE545 Advanced Neural and 1. M.S. CSE CORE (listed above) matriculated prior to Winter Quarter 2002 Adaptive Algorithms 3 credits 2. HUMAN-COMPUTER INTERFACES CORE (18 credits) are exempt from the 15 course requirement. CSE546 Data and Signal Compression 3 credits Required: Students pursuing the non-thesis option may CSE547 Statistical Pattern Recognition 3 credits choose one of the nine areas of emphasis CSE560 Artificial Intelligence 3 credits CSE548 Statistical Computing 3 credits defined below or consult their SPC to define CSE564 Human-Computer Interaction 3 credits CSE549 Applied Business Forecasting 3 credits a custom program. Choose four of: CSE555 Mathematical Methods for Engineering ADAPTIVE SYSTEMS AREA OF EMPHASIS & Finance 3 credits CSE547 Statistical Pattern Recognition 3 credits NONTHESIS M.S. CSE DEGREE CSE564 Human-Computer Interaction 3 credits CSE551 Structure of Spoken Language 3 credits 1. M.S. CSE CORE (listed above) CSE568 Empirical Research Methods 3 credits CSE552 Hidden Markov Models for Speech Recognition 2. ADAPTIVE SYSTEMS CORE (12 credits): CSE58X Special Topics 3 credits Required: ECE525 Analytical Techniques in Process CSE561 Dialogue 3 credits CSE547 Statistical Pattern Recognition 3 credits & Communication 4 credits CSE562 Natural Language Processing 3 credits CSE560 Artificial Intelligence 3 credits ECE555 Engineering Optimization 4 credits CSE563 Multi Agent Systems 3 credits (or) any CSE class not already taken Choose two of: CSE567 Developing User-Oriented Systems 3 credits Please note: Students may not receive credit for CSE568 Empirical Research Methods 3 credits CSE540 Neural Network Algorithms & Architecture 3 credits both CSE504 and OMSE533 CSE58X Any special topics course appropriate to this area CSE545 Advanced Neural and Adaptive Algorithms 3 credits COMPUTER SECURITY AREA OF EMPHASIS 3. SUGGESTED ELECTIVES (6 credits) CSE546 Data and Signal Compression 3 credits NONTHESIS M.S. CSE DEGREE CSE507 Logic Programming 3 credits CSE548 Statistical Computing 3 credits 1. M.S. CSE CORE (listed above) CSE515 Distributed Computing Systems 3 credits CSE550 Spoken Language Systems 3 credits 2. COMPUTER SECURITY CORE (15 credits) CSE540 Neural Network Algorithms & Architecture CSE562 Natural Language Processing 3 credits Required: 3 credits CSE564 Human-Computer Interaction 3 credits CSE503 Software Engineering Processes 3 credits CSE569 Scholarship Skills 3 credits CSE568 Empirical Research Methods 3 credits CSE524 TCP/IP Internetworking Protocols 3 credits (or) any CSE class not already taken. ECE554 Adaptive Signal Processing 4 credits CSE527 Principles and Practices of System Security Please note: Students may not receive credit for 3. SUGGESTED ELECTIVES (12 credits) 3 credits both CSE 04 and OMSE533. CSE563 Multi-Agent Systems 3 credits CSE58X Cryptography 3 credits SOFTWARE ENGINEERING AREA OF EMPHASIS CSE569 Scholarship Skills 3 credits CSE58X Security Assurance 3 credits NONTHESIS M.S. CSE DEGREE CSE58X appropriate special topics course (or) 3. SUGGESTED ELECTIVES (9 credits) 1. M.S. CSE CORE (listed above) any CSE class not already taken CSE515 Distributed Computing Systems 3 credits 2. SOFTWARE ENGINEERING CORE (15 credits) Please note: Students may not receive credit for (or) any CSE class not already taken. Required: both CSE504 and OMSE533. Please note: Students may not receive credit for CSE503 Software Engineering Processes 3 credits COMPUTATIONAL FINANCE AREA OF EMPHASIS both CSE504 and OMSE533 NONTHESIS M.S. CSE DEGREE CSE504 Object-Oriented Analysis and Design 3 credits DATA-INTENSIVE SYSTEMS AREA OF EMPHASIS CSE509 Object-Oriented Programming 3 credits 1. M.S. CSE Core (listed above) NONTHESIS M.S. CSE DEGREE 24 COMPUTER SCIENCE AND ENGINEERING | CSE

MST512 Project Management 3 credits ECE551 Introduction to Digital Signal Processing for each track are representative, not exhaustive. 4 credits Students with strong backgrounds or special Choose one of: interests may request approval to substitute other ECE552 Digital Signal Processing II 4 credits CSE564 Human-Computer Interaction 3 credits OGI courses in place of those listed below: ECE554 Adaptive Signal Processing 4 credits CSE567 Developing User-Oriented Systems 3 credits A. APPLIED COMPUTING 3. SUGGESTED ELECTIVES (8-12 credits) 3. SUGGESTED ELECTIVES (9 credits) APC500 Development with Visual Basic for Applications Courses in the Spoken Language Systems core, 3 credits Any CSE class not already taken or any CSE classes not already taken. Please note: Students may not receive credit for APC501 Accelerated Development with Visual Basic Please note: Students may not receive credit for 3 credits both CSE504 and OMSE533. both CSE 504 and OMSE 533. APC503 Web Development with Perl 5 3 credits SOFTWARE ENGINEERING FOR INDUSTRY PROFESSIONALS AREA SYSTEMS SOFTWARE AREA OF EMPHASIS APC505 Applications Programming in C++ 3 credits OF EMPHASIS NONTHESIS M.S. CSE DEGREE NONTHESIS M.S. CSE DEGREE 1. M.S. CSE CORE (listed above) APC506 Advanced Applications Programming in C++ 1. M.S. CSE CORE (listed above) 3 credits 2. SOFTWARE ENGINEERING FOR INDUSTRY PROFESSIONALS 2. SYSTEMS SOFTWARE CORE (12 credits) CORE (15 credits) APC508 Web Development with Java 2 3 credits Choose four of: Required: APC511 Computational Tools for Engineering and Finance CSE515 Distributed Computing Systems 3 credits 3 credits OMSE511 Managing Software Development 3 credits CSE524 TCP/IP Internetworking Protocols 3 credits APC515 Data Structures and Discrete Math 3 credits OMSE521 Using Metrics & Models 3 credits CSE526 Modern Operating System Design 3 credits B. COMPUTER SCIENCE OMSE531 Software Requirements Engineering 3 credits CSE527 Principles and Practices of System Security CSE500 Principles of Software Engineering 3 credits OMSE533 Software Design Techniques 3 credits 3 credits CSE503 Software Engineering Processes 3 credits Choose one of: CSE541 Database Implementation 3 credits CSE504 Object-Oriented Analysis and Design 3 credits CSE564 Human-Computer Interaction 3 credits CSE58X Internet Technology 3 credits CSE509 Object-Oriented Programming 3 credits CSE567 Developing User-Oriented Systems 3 credits CSE58X Multi-Media Networking 3 credits CSE514 Introduction to Database Systems 3 credits 3. SUGGESTED ELECTIVES (9 credits) CSE58X plus any special topics courses appropriate CSE532 Analysis and Design of Algorithms 3 credits Any CSE course not already taken. to this area C. APPLIED MATHEMATICS, STATISTICS, AND MACHINE LEARNING Please note: Students may not receive credit for 3. SUGGESTED ELECTIVES (12 credits) CSE540 Neural Network Algorithms and Architectures both CSE504 and OMSE533. Any course in the Systems Software area core 3 credits or any CSE class not already taken. SPOKEN LANGUAGE SYSTEMS AREA OF EMPHASIS CSE544 Introduction to Probability and NONTHESIS M.S. CSE DEGREE Please note: Students may not receive credit for Statistical Inference 3 credits both CSE 504 and OMSE 533. 1 M.S. CSE CORE (listed above) CSE545 Advanced Neural and Adaptive Algorithms 3 credits 2. SPOKEN LANGUAGE SYSTEMS CORE (12-16 credits) MASTER OF SCIENCE IN COMPUTATIONAL FINANCE CSE547 Statistical Pattern Recognition 3 credits Three of: The Master of Science in Computational CSE548 Modern Applied Statistics 3 credits CSE550 Spoken Language Systems 3 credits Finance is an interdisciplinary program CSE549 Applied Business Forecasting 3 credits CSE551 Structure of Spoken Language 3 credits offering students the flexibility to learn CSE555 Mathematical Methods for Science technical skills directly relevant to CSE552 Hidden Markov Models for Speech Recognition and Engineering 3 credits 3 credits quantitative or computational work in the CSE556 Simulation and Optimization 3 credits CSE561 Dialogue 3 credits financial securities industry. A professional D. ENGINEERING CSE562 Natural Language Processing 3 credits internship track is also available. (see below) ECE525 Analytical Techniques in Statistical ECE541 Speech Processing 3 credits 1. M.S. IN COMPUTATIONAL FINANCE CORE (24 credits) Signal Processing 4 credits ECE545 Speech Systems 4 credits Choose eight of: ECE544 Introduction to Signals, Systems and ECE58X Speech Synthesis 4 credits FIN541 Principles of Modern Finance 3 credits Information Processing 4 credits Choose one of the following or one more from the FIN544 Investment and Portfolio Management 3 credits ECE550 Linear Systems 4 credits above list: FIN547 Global Markets and Foreign Exchange 3 credits ECE551 Introduction to Digital Signal Processing 4 credits CSE540 Neural Network Algorithms & Architectures (S) FIN551 Options and Futures I 3 credits 3 credits ECE554 Adaptive Signal Processing 4 credits FIN552 Options and Futures II 3 credits CSE545 Advanced Neural & Adaptive Algorithms 3 credits ECE555 Engineering Optimization 3 credits FIN558 Advanced Numerical Computing in Finance CSE547 Statistical Pattern Recognititon 3 credits 3 credits E. MANAGEMENT SCIENCE CSE560 Artificial Intelligence 3 credits FIN561 Risk Management 3 credits MST501 Managerial & Financial Accounting 4 credits CSE564 Human Computer Interaction 3 credits FIN573 Financial Time Series Analysis 3 credits MST502 Financial Management 4 credits CSE568 Empirical Research Methods 3 credits FIN576 Financial Markets and Trading 3 credits MST512 Project Management 3 credits ECE540 Auditory & Visual Proc. by Human & Machine FIN585 Topics in Computational Finance MST520 Managing in Science and Technology 4 credits 4 credits 2. BREADTH REQUIREMENT (21 credits) MST540 International Management in Science ECE544 Intro to Signals, Systems and Info. Processing & Technology 3 credits 4 credits Breadth requirement courses must come from at least two of the following tracks. The course lists 25 CSE | COMPUTER SCIENCE AND ENGINEERING

F. FINANCE The courses on software development in context master’s program in computer science and provide instruction in the basic areas of software Finance core courses beyond the 8-course engineering at the beginning of their senior development: requirements, architecture, design, year. In two years of residence at OGI, core requirement. implementation, and testing. The course material in the student can simultaneously fulfill MASTER OF SCIENCE, COMPUTATIONAL each of these areas provides instruction in underlying principles, development methods and requirements for the bachelor’s degree at the FINANCE PROFESSIONAL INTERNSHIP PROGRAM tools, and analytic methods and tools with a focus undergraduate institution and the master’s Participation in this program option is limited on applying principles, techniques and tools. degree at OGI. by available industrial internships. For Course material focuses on applying techniques and skills from the foundation courses to realistic students declaring this option, the breadth examples of the products of each development PH.D. PROGRAM requirement courses must come from at least phase. Course emphasis is on understanding the one of the tracks previously listed, plus application and effect of the techniques covered in The Ph.D. program is strongly oriented FIN620 Professional Internship in Finance. the context of real software development. toward preparation for research. Each OMSE 531 Software Requirements Engineering 3 credits student has the opportunity to work closely OREGON MASTER OF SOFTWARE with a faculty research advisor throughout OMSE 532 Software Architecture and Domain Analysis ENGINEERING (OMSE) 3 credits his or her residency at OGI. A student must OGI School of Science and Engineering, OMSE 533 Software Design Techniques 3 credits satisfy the institutional requirements for the Ph.D. Portland State University, Oregon State OMSE 535 Software Implementation and Testing 3 credits University, and the University of Oregon PART 3: PROGRAM INTEGRATION AND STRATEGIC Candidacy is satisfied in three parts: jointly offer the Oregon Master of Software DEVELOPMENT SKILLS (9 Credits) Engineering (OMSE) degree to meet the FOUNDATION REQUIREMENTS: Students are required to Courses in this area focus on integrating the skills take six foundation courses. Particularly well- needs of software professionals. The taught in the OMSE program and on the ability to prepared students can waive some of these courses curriculum emphasizes the technical and think abstractly about the processes and products by passing an examination on the course material. leadership aspects of software engineering, of software engineering. Students must have completed Part 1 and Part 2 of the OMSE program AREA REQUIREMENTS: Students choose three courses teamwork and communication skills, and the before beginning Part 3. (Exception: A student may within one area and three courses out of that area, business aspects of developing industrial- begin taking courses in Part 3 in the same term as as outlined below. strength software. Admission requirements taking any remaining courses in the first two RESEARCH SKILLS ASSESSMENT: Students are required parts.) In OMSE 551, Strategic Software include a B.S. with pre-foundation courses in to take CSE 569 Scholarship Skills and to pass the Engineering students learn the skills necessary to programming, discrete mathematics, data research proficiency examination (RPE), which understand, model, and adapt their software structures, operating systems, and computer requires a written and oral presentation of a engineering processes to meet emerging needs. In research paper. The RPE normally takes place in architecture as well as two years of working OMSE 555/556, the Software Development the spring quarter of the second year of residence. experience. Courses may be taken on non- Practicum, students participate in the end-to-end admitted basis. For additional information, development of a significant software product and Ph.D. students must obtain a grade of ‘B’ or see www.omse.org. apply the personal competencies and development better on each required course. Required skills learned throughout the program in a Oregon Master of Software Engineering students development context that includes the essential courses should be completed by the end of will take the following courses: characteristics of real commercial software the second year. The doctoral dissertation development. OMSE500 Principles of Software Engineering 3 credits will document a significant, original research contribution and must be of publishable OMSE511 Managing Software Development 3 credits OMSE 551 Strategic Software Engineering 3 credits quality, both in content and presentation. OMSE512 Understanding the Software Business 3 credits OMSE 555 Software Development Practicum I 3 credits OMSE513 Professional Communication Skills for OMSE 556 Software Development Practicum II 3 credits The faculty strongly recommends that Software Engineers 3 credits PART 4: ELECTIVES (6 credits) students prepare a formal thesis proposal OMSE521 Using Metrics and Models to Support Any CSE or OMSE class not already taken. between 9 and 18 months before the Ph.D. QuantitativeDecision Making 3 credits defense. The proposal is not a candidate OMSE522 Modeling and Analysis of Software Systems OREGON GRADUATE ENGINEERING screening tool, but instead a means to ensure 3 credits INTERNSHIP PROGRAM an acceptable level of intellectual vigor and OMSE525 Software Quality Analysis 3 credits For information and availability regarding maturity. Starting in the second year, the OMSE531 Software Requirements Engineering 3 credits the OGI School’s Department of Computer faculty strongly recommends that students OMSE532 Software Architecture and Domain Analysis Science Internships, please contact deliver yearly research talks. The RPE, 3 credits the department. presentation at the student research OMSE533 Software Design Techniques 3 credits symposium, the thesis proposal, and talks at OMSE535 Software Implementation and Testing 3 credits COOPERATIVE COMPUTER SCIENCE PROGRAMS refereed conferences satisfy this OMSE551 Strategic Software Engineering 3 credits OGI has established undergraduate/graduate requirement. Practice talks for conference OMSE555 Software Development Practicum I 3 credits cooperative programs with Lewis & Clark papers should be open for commentary. OMSE556 Software Development Practicum II 3 credits College, Pacific University, Reed College, and The program of study for each Ph.D. student Any two CSE or OMSE classes not already taken. Willamette University. These programs allow is tailored to meet individual needs and 6 credits selected undergraduate students to enter the interests. Each student’s Student Program

26 COMPUTER SCIENCE AND ENGINEERING | CSE

Committee provides academic advisement CSE568 Empirical Research Methods 3 credits data objects and their representations to functions that act on data. Programs are formulated as com- and is in direct control of each student’s CSE58X Special Topics: Computer Graphics variable program of study. The SPC will work with positions of functions, rather than as sequences of ECE540 Auditory and Visual Processing by Human statements. This leads to a programming methodol- the student to set and review goals on a and Machine 4 credits ogy that is quite different from that learned in using twice-yearly basis. Students must write a Programming Languages and Software Engineering statement-oriented languages. This course intro- progress report for all SPC meetings except duces the student to functional notation, recursion, CSE500 Introduction to Software Engineering 3 credits the first one. higher-order functions, reasoning about functions, CSE502 Functional Programming 3 credits and polymorphic type systems. Functional program- FOUNDATION REQUIREMENTS (18 credits) CSE503 Software Engineering Processes 3 credits ming languages are known for their increased productivity and reliability, due in part to the higher Required: CSE504 Object-Oriented Analysis and Design 3 credits levels of abstraction provided by functional lan- CSE513 Introduction to Operating Systems 3 credits CSE507 Logic Programming 3 credits guages. Course is taught by lecture with small CSE521 Introduction to Computer Architecture 3 credits CSE509 Object-Oriented Programming 3 credits weekly programming assignments. Experience is CSE532 Analysis and Design of Algorithms 3 credits CSE511 Principles of Compiler Design 3 credits gained by programming in the functional language Haskell or one of its close derivatives. Recent CSE533 Automata and Formal Languages 3 credits CSE512 Compiling Functional Languages 3 credits advances in functional programming languages Choose one programming language course: CSE518 Software Design and Development 3 credits allow them to use updatable state in a safe manner and to cause effects on the real world. Students gain CSE502 Functional Programming 3 credits CSE530 Introduction to Mathematical Logic 3 credits experience by writing programs using these features CSE531 Foundations of Semantics 3 credits CSE507 Logic Programming 3 credits to program interactive window-based programs CSE509 Object-Oriented Programming 3 credits CSE567 Developing User-Oriented Systems 3 credits using an embedded “widget” library. 3 credits CSE531 Foundations of Semantics 3 credits Systems Software CSE503 Software Engineering Processes Choose one interactive and adaptive CSE509 Object-Oriented Programming 3 credits This course is concerned with examining and systems course: CSE510 Software Tools 3 credits improving the software development processes, including the technical, managerial, and cultural CSE514 Introduction to Database Systems 3 credits CSE540 Neural Network Algorithms and Architectures processes, used by organizations to develop and 3 credits CSE515 Distributed Computing Systems 3 credits maintain high quality software systems in a timely CSE560 Artificial Intelligence 3 credits CSE524 TCP/IP Internetworking Protocols 3 credits and economical manner. Various process models, CSE564 Human-Computer Interaction 3 credits CSE526 Modern Operating System Design 3 credits including the SEI Capability Maturity Models, the ISO SPICE model, the Team Software Process, and DISTRIBUTION REQUIREMENTS (18 credits) CSE527 Principles and Practices of System Security the Personal Software Process are studied and con- Three courses from one of the following six areas, 3 credits trasted. Tailoring of process models to fit local and three other courses not from that area not CSE541 Database Implementation 3 credits situations and various approaches to software already taken: CSE542 Object Data Management 3 credits process improvement are presented. Students select and complete term projects that address top- Adaptive Systems and Applications Theory ics in software process improvement. 3 credits CSE540 Neural Network Algorithms and Architectures CSE530 Introduction to Mathematical Logic 3 credits CSE504 Object-Oriented Analysis and Design 3 credits CSE531 Foundations of Semantics 3 credits This course presents an integrated set of techniques CSE545 Advanced Neural and Adaptive Algorithms CSE534 Computability and Intractability 3 credits for software analysis and design based on object- 3 credits CSE535 Categories in Computer Science 3 credits oriented concepts. The techniques focus on CSE546 Data and Signal Compression 3 credits producing the artifacts and work products, RESEARCH SKILLS REQUIREMENT (3 credits) CSE547 Statistical Pattern Recognition 3 credits expressed in UML, appropriate for the analysis and CSE569 Scholarship Skills 3 credits design phases of the software development lifecycle. CSE568 Empirical Research Methods 3 credits Research Proficiency Exam We adopt a use case model for requirements and a FIN573 Financial Time Series Analysis 3 credits responsibility-driven approach for the development ECE540 Auditory and Visual Processing by Human of object models. Design patterns and frameworks and Machine 4 credits COURSE DESCRIPTIONS are also emphasized. Note that CSE 509 Object- ECE553 Control Systems: Classical, Neural and Fuzzy CSE500 Introduction to Software Engineering Oriented Programming is intended as a follow-on 4 credits Software engineering is concerned with the ways in course for CSE 504. 3 credits which people conduct their work activities and ECE554 Adaptive Signal Processing 4 credits CSE507 Logic Programming apply technology to produce and maintain software Logic programming is an attempt to construct com- Human-Computer Interactive Systems products and software-intensive systems. Issues puter languages with completely declarative of concern include specification, design, implemen- CSE550 Spoken Language Systems 3 credits semantics: The programmer only states “what” tation, verification, validation, and evolution of CSE551 Structure of Spoken Language 3 credits should be done; the interpreter or compiler must software artifacts. Related topics include software decide “how.” This course examines existing logic CSE552 Hidden Markov Models for Speech Recognition metrics, project management, configuration programming languages, notably Prolog; provides 3 credits management, quality assurance, peer reviews, the foundations in logic and theorem proving for CSE560 Artificial Intelligence 3 credits risk management, and process improvement. such languages; and covers implementation of This course presents an integrated view of CSE561 Dialogue 3 credits logic programming languages. Other topics may these topics and related issues. It is an essential include an introduction to modal logic and intuition- CSE562 Natural Language Processing 3 credits course for anyone working in development, mainte- istic logic. 3 credits CSE563 Multi-Agent Systems 3 credits nance, management, or related areas in a software CSE564 Human-Computer Interaction 3 credits organization. 3 credits CSE509 Object-Oriented Programming This course provides a rigorous introduction to the CSE567 Developing User-Oriented Systems 3 credits CSE502 Functional Programming concepts behind object-oriented programming. It is In functional programming, we shift our focus from 27 CSE | COMPUTER SCIENCE AND ENGINEERING

for students who are already familiar with the con- encouraged to read the Linux source code for dis- commercial cluster interfaces and systems; and cept of object-orientation and with object-oriented cussions in class. 3 credits presence of clusters in data centers. Commercial analysis and design techniques. One way to learn and academic examples will be covered for each of CSE514 Introduction to Database Systems this background material is by taking CSE 504 the above topics, such as InfiniBandTM, Virtual Object-Oriented Analysis and Design. In CSE 509, A survey of database fundamentals emphasizing the Interface Architecture (VIA), ServerNet, Beowulf, students gain a thorough understanding of incre- use of database systems. Topics include database Memory Channel, etc. Prerequisite: CSE 521. mental programming, type-safety, polymorphism, design, data dependencies and normalization, sec- 3 credits encapsulation, and set-based abstraction, and apply ondary storage structures, query languages, query CSE524 TCP/IP Internetworking Protocols these concepts through a variety of programming processing, query optimization, transactions, recov- This course provides an overview of the structure projects. We study several programming languages, ery, and embedded SQL. This course focuses on and algorithms used in the TCP/IP networking pro- including Java and Smalltalk, so students are relational database systems and the SQL query lan- tocols that make up the foundation of the Internet. exposed to different realizations of these concepts guage. Students participate in a project to design, Protocols and technologies covered will include an and gain an appreciation for the programming lan- populate, and query a database. Prerequisites: introduction to the link layer, ARP, IP, ICMP, UDP, guage design space. We also look at published Data structures, discrete mathematics, and mathe- TCP, routing protocols, and application protocols object-oriented design patterns and see how they matical logic. 3 credits and systems like the DNS, NFS, SMTP, FTP, HTTP, can be implemented in different object-oriented pro- CSE515 Distributed Computing Systems and multicasting protocols and applications. To programming languages. Students are required to read This course concentrates on distributed computing vide architectural insight into protocol design issues appropriate research papers, complete several from a systems software perspective. Major topics and operating system implementation techniques, short programming assignments, complete a sub- include communications middleware (remote proce- typically in terms of the Berkeley UNIX socket pro- stantial programming project, and write some short dure call, remote method invocation and causal gramming model. To provide socket programming essays. Prerequisite: CSE 504 or equivalent. broadcast), operating system support, distributed experience with the client/server model. To provide 3 credits file systems, distributed transaction processing, experience reading Internet RFC’s and/or drafts. CSE511 Principles of Compiler Design load balancing, distributed programming languages Prerequisites: familiarity with the functions of a This course introduces the student to the basics of and systems, fault-tolerance and replication algo- modern multiuser operating system such as is cov- building a compiler using a multi-phase translation rithms, distributed timing issues, and distributed ered in CSE 513 or in PSU’s CS 533; familiarity with process. It covers lexical analysis, parsing, and algorithms. Prerequisites: CSE513 Introduction to C programming on modern UNIX computers. translation to abstract syntax using modern parser Operating Systems. (Also a basic understanding of 3 credits generator technology. It discusses binding of identi- computer communications problems and protocols.) CSE526 Modern Operating System Design fiers and symbol table organization, and a variety of 3 credits This course includes an in-depth study of modern intermediate representations that are suitable for CSE518 Software Design and Development back end analysis. It investigates back end transfor- operating system design. The course is based on a Contemporary, object-oriented software design, collection of recent research papers, and includes mations and optimizations for a number of using the Java programming language. An introduc- languages. Other topics include type checking, stat- an emphasis on evaluating the papers in addition to tion to the eXtreme Programming software understanding the systems they describe. Topics ic analysis, and basic runtime support. Compiling is development methodology, which is based upon the essentially a process of symbolically manipulating include micro-kernel operating systems, lightweight principle that change is inevitable and successful interprocess communication, extensible operating program representations represented by tree and software designs undergo continual evolution. graph-like data structures. Because of this, we will systems, file systems, mobile computing, worksta- Techniques that will be taught in the course include tion clusters, adaptive resource manage-ment, and use tools that facilitate symbolic manipulation and program refactoring, automated unit testing, pair definition of such structures as parser and lexical OS support for multimedia systems. Prerequisites: programming, participatory design and managing CSE 513 and CSE 521. 3 credits generators, and tools for generating code from pat- short product development cycles. These principles tern-based descriptions. Prerequisite: CSE 533. and techniques will be illustrated in a term-length CSE527 Principles and Practices of System Security 3 credits project that provides members of the class with In the Internet age, host system security is essential CSE512 Compiling Functional Languages design and implementation experience. 3 credits and difficult. This course will educate students in the principles and practices of securing host sys- A project-oriented course on the theory and design CSE521 Introduction to Computer Architecture of a compiler for a typed, functional programming tems. Students learn the principles of how to build This course provides a broad introduction to com- secure systems and how various real systems suc- language. Topics include understanding a formal puter architecture. The course covers a large ceed and fail in living up to these principles. We will definition of programming language semantics, com- amount of material in moderate depth, giving the study various security enhancing technologies, in piling pattern analysis, lifting abstractions, student a good understanding of the basic issues in each case relating the security enhancement to the continuation-passing style of implementation, computer system design. Specifically, the course principles of secure systems. Prerequisite: abstract machines, code generation and address covers instruction set design, pipelining, the memo- CSE 513. 3 credits assignment, register allocation and assignment on ry heirarchy, I/O systems, networking issues, and general-register machines, run-time storage admin- multiprocessors. Example systems include the Intel CSE530 Introduction to Mathematical Logic istration, data-flow analysis, and code improvement. x86, MIPS, and DEC Alpha processors. Provides a theoretical foundation for the logic of Prerequisite: CSE 511. 3 credits Prerequisites: Experience writing software, prefer- computation. Propositional and first-order predicate CSE513 Introduction to Operating Systems ably with some C or assembler programming. NOTE: calculi, soundness and completeness, incomplete- A study of the design and implementation of modern Computer architecture has become a quantitative ness and incomputability, the Church-Turing thesis, operating systems. The course concentrates on science, so there will be considerable algebraic term-rewriting systems, and application to program operating system kernel design, and includes the manipulation involved in the performance analysis verification. 3 credits component of the course. 3 credits following topics: concurrent processes, interprocess CSE531 Foundations of Semantics communication, synchronization, scheduling, CSE522 Advanced Computer Architecture Formal semantics aims to answer two important resource allocation, memory management, the con- This course covers new architectural trends in questions: 1) when are two programs equal? And cept of virtual memory and the required underlying designing high-performance clusters with examples. 2) when does a program faithfully implement a hardware support, secondary storage management, Topics to be covered include I/O & IPC interconnects mathematical specification? The course explores file systems, and security. We will use the Linux (routing, switch designs, virtual lanes, etc.); single denotational semantics, operational semantics, and operating system to ground the discussion of system image and scheduling; lightweight messaging program logic, studying how they are related and abstract concepts. Interested students will be and use-level networking; suitable I/O architectures; how they can answer the motivating questions. 28 COMPUTER SCIENCE AND ENGINEERING | CSE

Programming language concepts, such as impera- found widespread application in computer science. exploratory data analysis, sampling distribution theo- tive programming, functional programming, This course introduces the basic notions of ry, confidence intervals, hypothesis testing, linear call-by-name, call-by-value, and continuations, are category theory, including functors, natural trans- regression, goodness-of-fit, ANOVA, maximum likeli- contrasted and explained in terms of their semantic formations, products, sums, limits, colimits, hood estimation, Bayesian inference, cross-validation, foundations. Key concepts include full abstraction monads, and adjunctions. These concepts are illus- nonparametric tests, random walks, martingales, sto- and the use of least fixed point constructions to trated with examples from computer science and chastic processes and stochastic differential solve recursive equations. The course is designed mathematics, including the relationship between equations. The goal of the course is to provide a com- for students interested in the mathematical founda- cartesian closed categories and the lambda-calcu- prehensive review of essential concepts in probability tions of programming languages and programming lus. Familiarity with discrete mathematics is an and statistics. The primary analysis tools for this logics. Prerequisite: Discrete mathematics. 3 credits essential prerequisite. 3 credits course are S-PLUS and MATLAB. 3 credits CSE532 Analysis and Design of Algorithms CSE540 Neural Network Algorithms and Architectures CSE545 Advanced Neural and Adaptive Algorithms An introduction to the design and analysis of algo- This course introduces the fundamentals of connec- An advanced treatment of architectures and algorithms. The course covers design techniques, such tionist and neural network models. Paradigms for rithms for pattern recognition, regression, as dynamic programming and greedy methods, as both unsupervised and supervised learning are cov- timeseries prediction, and datamining. Typical top- well as fundamentals of analyzing algorithms for ered. Topics include introduction to neural ics include convergence, effects of noise, correctness and time and space bounds. Topics processing elements, Hebbian learning, LMS and optimization methods, probabilistic framework include advanced sorting and searching methods, back propagation algorithms, competitive learning, (including Bayesian estimation), generalization abil- graph algorithms and geometric algorithms. computational capability, and elements of statistical ity and regularization and pruning, Hebbian Other areas vary from year to year, and may include pattern recognition. Specific architectures covered learning, and clustering and density modeling. computational geometry, matrix manipulations, include Hopfield nets, single and multilayer Prerequisites: CSE 540 or instructor permission. string and pattern matching, set algorithms, Perceptrons, and Kohonen maps. Programming 3 credits polynomial computations, and the fast Fourier projects involve network simulations and applica- CSE546 Data and Signal Compression transform. Prerequisite: Data structures and dis- tion problems. Prerequisites: Some knowledge of The need for signal and data compression is ubiqui- crete mathematics. 3 credits linear algebra and calculus is required. tous in image, video, and speech processing, Programming experience is necessary. 3 credits CSE533 Automata and Formal Languages finance, and computational science. Where data Automata theory introduces fundamental models CSE541 Database Implementation stores become very large (e.g. video, finance, earth that are used over and over again in computer sci- This course provides hands-on experience imple- science), the need is not met by simple lossless file ence for programming languages, in compiler menting high-performance database management compression schemes, and we must turn to sophis- construction, and in algorithms. These models are a systems. The goal of the course is to implement ticated coding techniques.This course addresses valuable part of the repertoire of any computer sci- database software and to understand techniques both the theoretical basis and practical algorithms entist or engineer. This course introduces used to provide maximum performance and func- for data and signal compression. Topics include loss- progressively more powerful models of computation, tionality on modern architectures. Typical topics less entropy based coding including Huffman and starting with finite automata and moving through discussed include benchmarking, transaction pro- Lempel-Ziv, and lossy compression techniques counter, stack, and Turing machines. It also pres- cessing, file and index implementation, buffer including: scalar quantizers, transform coding ents the regular, context-free, recursive, and management, concurrency control, recovery, query (Karhunen-Loeve, DCT, and nonlinear transform recursively enumerable languages, and shows how optimization, and a variety of query processing algo- codes), predictive coding, vector quantization, adap- they correspond to the various models of computa- rithms. The data model to be implemented, and the tive codes, and wavelets. The relation between tion and to generation mechanisms such as regular computer architecture to be used, will change compression schemes and probabilistic data model- expressions and grammars. The emphasis is on between offerings. Prerequisite: CSE 514. This ing is emphasized in conjunction with each understanding the properties of these models, the course is offered at Portland State University as technique. Application to speech, image, and video relationships among them, and how modifications CS 545. 3 credits coding are discussed. Students will have the oppor- such as nondeterminism and resource bounds affect tunity to design compression schemes for such CSE542 Object Data Management them. The course includes application of these con- diverse applications as earth science data, finance, cepts to problems arising in other parts of computer A variety of products for managing object data have speech, or video depending on their specific inter- science. Prerequisite: Discrete mathematics. emerged in the marketplace. Object-oriented data- ests. Prerequisites: Undergraduate calculus, 3 credits base systems and persistent programming introductory probability and statistics, some pro- languages have been joined by object-relational gramming experience. 3 credits CSE534 Computability and Intractability databases and middleware component technologies, Computability and complexity theory identify class- such as Enterprise Java Beans. Other storage CSE547 Statistical Pattern Recognition es of languages based on characteristics of engines, such as LDAP and XML servers, have an Theory and practice of statistical pattern recogni- machines that recognize them. The course presents object flavor. This course begins with the concepts tion. Students will learn fundamental theory and elementary results from recursive function theory, in types, data models, and languages that underlie practices that are common to a broad range of pat- including recursive and recursively enumerable object data management. It then looks at example tern recognition applications and technologies, and sets, and degrees of undecidability. Using recursion prototype and commercial systems, and examines apply principles to real-world examples.The empha- theory as a model, it develops the classical results design dimensions such as data model, persistence, sis is on developing tools, both theoretical and of complexity theory, including time and space com- encapsulation, hierarchies, query languages, and practical, that provide grounding in pattern recogni- plexity classes, hierarchy theorems, and elementary transactions. It touches on application development tion problems and methods; rather than on results from parallel complexity. The course con- and data management issues and concludes with showcasing particular technologies. The course will cludes by studying classes of problems that are treatment of software architecture and implementa- benefit those whose work may use any of a variety of provably intractable, with a particular emphasis on tion techniques. Students will do a project using a recognition technologies in broad-ranging applica- NP-complete problems. Prerequisites: CSE 532 or commercial product. 3 credits tions such as speech and image processing, data CSE 533. 3 credits mining, finance. Topics include: random vectors, CSE544 Introduction to Probability and detection problems (binary decision problems), like- CSE535 Categories in Computer Science Statistical Inference lihood ratio tests, ROC curves, parametric and Category theory provides a powerful and concise This course provides a comprehensive introduction to non-parametric density estimation, classification notation for abstract properties of functions. probability, statistical inference and stochastic models, theoretical error bounds and practical error Originally developed for algebraic topology, it has processes. The topics include the elements of 29 CSE | COMPUTER SCIENCE AND ENGINEERING

estimation through cross-validation. Maximum likeli- Toolkit. The course materials are included in will be based on assignments and a group project, hood and Bayesian parameter estimation. Feature http://www.cse.ogi.edu/ CSLU/hltsurvey/hltsurvey.html. and these will involve programming in Matlab. The extraction for dimensionality reduction, and for clas- 3 credits assignments, project and examples in class will be sification. Prerequisites: The course is designed to be drawn from practical problems in engineering and CSE551 Structure of Spoken Language self-contained. Familiarity with undergraduate prob- finance. Prerequisites: Programming experience, ability and statistics is useful. 3 credits This course provides a foundation for subsequent linear algebra, calculus, CSE544 Introduction to learning and research in computer speech recogni- Probability and Statistical Inference (or equivalent). CSE548 Statistical Computing tion. We examine the structure of spoken English 3 credits This course provides an introduction to modern through selected readings in speech perception and applied statistics. The topics include distributions acoustic phonetics and examination of visual dis- CSE560 Artificial Intelligence and data summaries, density estimation, general- plays of speech. The goals are to understand the This course surveys the foundations and applica- ized linear models, modern nonlinear regression, acoustic cues for each major phonetic category, tions of symbolic approaches to artificial robust statistics, factor analysis, linear and nonlin- understand how these cues are affected by context, intelligence. The approach emphasizes the formal ear classifiers, Bayesian classifiers, cluster understand the perceptual strategies that listeners basis of automated reasoning and includes an intro- analysis, decision trees, ensemble learning meth- use to understand speech, and evaluate the assump- duction to programming in Prolog. Fundamentals ods, validation techniques and Bootstrap and Monte tion that speech can be described as anordered covered include search, knowledge representation, Carlo methods. The goal of the course is to provide sequence of phonetic segments. 3 credits automated inference, planning, nonmonotonic rea- a solid understanding of practical statistical infer- soning, and reasoning about belief. Applications CSE552 Hidden Markov Models for Speech Recognition ence methods and proficiency in using modern include expert systems, natural language processing statistical tools. The primary analysis tool for this Hidden Markov Model-based technology is used and agent architectures. 3 credits course is S-PLUS. Prerequisite: CSE544 widely in today’s speech recognition systems. This CSE561 Dialogue Introduction to Probability and Statistical Inference course is an introduction to speech recognition or equivalent. 3 credits using HMM technology. Topics include the theory of This course provides an in-depth treatment of the Hidden Markov Models (discrete, semi-continuous, major theories of dialogue, including finite-state, CSE549 Applied Business Forecasting and continuous) and their applications to speech plan-based, and joint action theories. Dialogue is This course is taught over the World Wide Web using recognition, along with the basic mathematics examined at a level general enough to encompass WebCT; enrollment limitations may apply. An applied (probability theory, statistics, stochastic process, conversations between humans, between human course in business forecasting, the course empha- information theory, and signal processing) that are and computer, and among computers, while at the sizes generating and implementing business necessary for speech recognition. The course is same time being precise enough to support imple- forecasts. Designed for those wishing to understand focused on understanding the theory behind these mentations. The course introduces basic speech act the basics of modern forecasting, the course empha- fundamental technologies, and applying the technol- theory, planning, and reasoning through a number of sizes modern statistical methods widely used to ogy to develop speech recognition systems. classic papers. Plan-based theories are examined in generate business forecasts. Specific applications to Prerequisite: Some knowledge of engineering math- detail, including their incorporation into spoken dia- business include forecasting sales, production, ematics (calculus and linear algebra) is required; logue systems, and their potential effects upon inventory, macroeconomic variables such as inter- C programming experience is necessary. 3 credits speech recognition components. Students will devel- est rates and exchange rates, and other applications op dialogue components and integrate them into CSE555 Mathematical Methods for Engineering related to business planning, both short- and long- working systems. Prerequisite: CSE 560. and Finance term. Topics include data considerations and model 3 credits selection, applied statistics, moving averages and This course explores the essential mathematical CSE562 Natural Language Processing exponential smoothing, regression analysis, time- methods required for quantitative analysis in engi- series decomposition, Box-Jenkins (ARIMA) models, neering and finance. The course examines a An introduction to artificial intelligence techniques bootstrapping, optimal forecast combination, and selection of topics from multivariate calculus, dif- for machine understanding of human language. The forecast implementation. The course is based upon ferential equations, stochastic calculus and course introduces key aspects of natural language, mathematical optimization. Advanced topics include along with the analyses, data structures and algo- the FORECASTXTM integrated econometric and statistical analysis language for Windows 95 and NT, partial differential equations, Ito calculus, martin- rithms developed for computers to understand it. which accompanies Wilson and Keating’s Business gales, stochastic control and constrained Computational approaches to phonology, morpholo- Forecasting, McGraw Hill-Irwin, 4th Edition. optimization. The focus is on explaining the key gy, syntax, semantics, and discourse are covered. Knowledge of basic statistics and regression analy- Mathematical results and, by means of examples Programming assignments are written in Prolog. sis is highly recommended, but not required. and assignments, showing how they may be applied Prerequisite: CSE 560 or equivalent. 3 credits in engineering and finance. Prerequisites: Knowledge 3 credits CSE563 Multi-Agent Systems of calculus, linear algebra and basic differential CSE550 Spoken Language Systems equations. 3 credits This course covers the emerging theory and practice In the not too distant future, spoken language sys- of multi-agent systems: semi-autonomous, semi- CSE556 Simulation and Optimization tems will revolutionize human-computer interaction intelligent distributed computing systems that can by enabling natural conversations between people This course introduces modern, advanced numerical be organized ad hoc to meet the immediate needs of and machines. In addition to telephony applications, methods for quantitative work in engineering, a user. The course covers a variety of individual and such as voice browsing of the web, these systems finance and operations research, focusing on Monte multi-agent architectures, including the Contract also will support face-to-face communication with Carlo Simulation and Optimization techniques. In Net protocol, distributed blackboard systems, and intelligent animated agents. These animated human- Monte-Carlo simulation we will cover pseudo-ran- mobile agents. Also discussed are principles for like agents will combine acoustic information with dom and quasi-random number generators, building networks of heterogeneous agents, ranging the speaker’s facial cues and gestures to understand generation of stochastic processes, variance reduc- from simple rule-based systems to databases and speech, and produce natural and expressive speech tion techniques, bootstrapping and other statistical humans. In order to collaborate to solve a user’s with accurate facial movements and expressions. techniques. In Optimization we will briefly review problem, agents need to communicate. We examine This course reviews the state of the art in human classical methods, and study in detail new tech- agent communication languages, including KQML language technology, and explains how key techniques such as genetic algorithms, differential and FIPA, as well as the underlying general speech nologies are combined to produce spoken language evolution, simulated annealing and ant colony opti- act theories. Students learn how to model these sys- systems. The course combines lectures by experts in mization. Students will be introduced to tems formally, and will develop and program the field with hands-on experience using and mathematical modeling, and learn the science and individual agents that can participate in a multi- building spoken language systems using the CSLU art of effectively applying these techniques. Grading agent system. 3 credits 30 COMPUTER SCIENCE AND ENGINEERING | CSE

CSE564 Human-Computer Interaction scientific documents (such as conference abstracts, FIN544 Investment and Portfolio Management This course emphasizes the experience of comput- journal papers, theses, and proposals), how to pre- This course provides students with an overall intro- ing, which centers on an understanding of real users pare and deliver short and long presentations, the duction to practical and theoretical aspects of and the specific tasks they need to accomplish when refereeing process, and how to prepare and respond investment analysis and portfolio management. computing. In the pursuit of optimal user support, to a review. This course is required for Ph.D. stu- Specifically, the course surveys various models of an interdisciplinary approach to system design and dents and strongly recommended for master’s asset valuation and their use in constructing effec- evaluation is stressed. The course reviews current students, especially those pursuing the thesis tive investment portfolios. Topics include investment research viewpoints and activities in the field of option. It also is useful for professionals who must vehicles and asset classes, market structure and human-computer interaction, surveys key research write or speak to a technical audience. 3 credits market efficiency, security valuation models, finan- challenges that exist, and discusses trends in next- cial statement analysis, setting investment goals CSE58X Special Topics generation system design. Students gain hands-on and policies, designing investment portfolios, equity Under this number, we offer courses of particular experience by critiquing existing interfaces, as well and fixed-income portfolio strategies, measuring relevance to the research interests of faculty or in as hearing reports from experts in industry on the investment performance, and managing investment state-of-the-art subjects of interest to the community. state of the field. An introduction to this topic is risk. To help students integrate the course knowl- essential for everyone working in the field of com- CSE600 Research edge into their actual investment practice, the puter science. 3 credits Supervised research activity. course includes team projects to analyze actual investment securities and design investment portfo- CSE567 Developing User-Oriented Systems Variable and repetitive credit. lios. Students have access to investment data and This course explores a range of issues and methods CSE610 Nonthesis Research analytics provided by Barra and Standard and needed to design and evaluate user-oriented soft- Supervised research for up to six credits as a com- Poor’s Micropal. 3 credits ware applications. Topics focus on field and ponent of the nonthesis master’s degree. Students ethnographically based design studies, participatory are required to produce concrete research deliver- FIN547 Global Markets and Foreign Exchange design methods, user laboratory studies, and usabil- ables, including a final report equivalent to a CSE This course surveys the modern paradigms in inter- ity testing. The purpose is to have access to a range technical report. national finance. Specifically, the course examines of methods that help uncover opportunities, break- the theory linking the world’s various foreign downs, and interactions that affect the design and CSE620 Professional Internship exchange, money, and securities markets, empha- use of developing systems. Students are challenged These courses provide the student with an opportu- sizing global investment and risk management. to evaluate the underlying perspectives of the nity to earn credit for relevant work experience in Topics include spot and forward FX markets, FX approaches and decide which approach or combina- industry. Students gain valuable industrial experi- options, interest rate parity, purchasing power par- tion of approaches works best for particular ence that allows them to both apply the knowledge ity, exchange rate theory, global investing, global FX problems. They apply the methods in field and class- gained in the classroom and prepare for their future risk management, and emerging markets and cur- room exercises and produce a real-world project or careers in computer science. A written report must rency crises. Course assignments make use of paper using course methods. The intended result is be submitted to the CSE faculty advisor at the end of MATLAB’s-Plus and Barra on campus. 3 credits to make students more effective not only at gathering the experience. FIN551 Options and Futures I relevant user-based information, but also at inte- Enrollment requires a faculty advisor and is limited This course introduces the trading, pricing and risk- grating it into the development process. 3 credits by the number of internship opportunities available. management applications of financial derivatives CSE568 Empirical Research Methods 1 to 3 credits per quarter including futures, swaps, and option contracts. This course introduces principles of experimental CSE700 M.S. Thesis Research Emphasis is given to pricing models including arbi- design and data analysis for empirical research. Research toward the thesis for the M.S. degree. trage pricing theory, risk-neutral valuation, and Topics include the goals and logic of experimental Variable and repetitive credit. Black-Scholes analysis. Topics covered include design, hypothesis formation and testing, probabili- futures and swap pricing, methods for pricing ty and sampling theory, descriptive statistics, CSE800 Ph.D. Dissertation Research American style options, hedging and speculation correlation and regression, basic parametric and Research toward the dissertation for the Ph.D. degree. using derivatives, Ito calculus, portfolio insurance, nonparametric tests of statistical significance (e.g., Variable and repetitive credit. option trading strategies, dynamic hedging strate- Binomial, t-test, chi-square, analysis of variance), gies, and numerical models. Course assignments FIN541 Principles of Modern Finance standard designs for single- and multi-factor exper- require use of MATLAB. 3 credits This course examines the theory and practice of iments, and strategies of scientific investigation modern corporate finance stressing the six central FIN552 Options and Futures II (e.g., Exploratory vs. Directed). The course is fun- concepts in finance: Net Present Value, Capital damental for anyone who plans to conduct A continuation of FIN551 Options and Futures I, this Asset Pricing Model, Efficient Capital Markets, independent research in the future or needs to crit- course examines derivative pricing models since Value Additivity (Capital Structure Theory), Option ically evaluate the research of others. Students Black-Scholes, models for the term structure of Theory and Agency Theory. participate in designing and analyzing data in order interest rates and relevant numerical methods. The course begins with a review of stochastic calculus to answer scientific questions and present the Topics include discounted cash flow analysis, capital and stochastic differential equations. Specific topics results of these activities both orally and in writing. budgeting, capital structure theory, mean-variance include arbitrage pricing, equivalent martingale 3 credits portfolio theory, arbitrage-pricing theory, Black- measures, risk neutrality, and optimal stopping Scholes option pricing, and real options theory. In CSE569 Scholarship Skills times as applied to American options. Equilibrium addition, students will learn the nuances of evaluat- Scientific results have little value if they are not and no-arbitrage term structure models are pre- ing an Ebusiness. The principal goal of the course is communicated clearly or are disconnected from sented, from Vasicek through Heath-Jarrow-Morton. to provide students with an intuitive foundation of prior work in a field. This course teaches students to In addition, emphasis is given to pricing fixed- modern finance upon which the student can apply research, write, present, and review effectively for income derivatives, credit derivatives, and exotics advanced computational techniques. This will be the computer sciences. It emphasizes learning by using numerical solution methods such as the accomplished through interaction between the text, doing, and students have frequent writing and pres- Crank-Nicholson, finite difference methods, and instructor, case studies, MATLAB assignments, and entation assignments. Students learn how to locate Monte Carlo search. Prerequisite: FIN551 Options student presentations/discussions. This course ful- and organize background materials, how to write and Futures I or permission from instructor. fills all or part of the prerequisite requirements for clearly about technical topics, organizing web con- 3 credits FIN576 Financial Markets and Trading. 3 credits tent, the structure and stylistic conventions of

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FIN558 Advanced Numerical Computing in Finance valuable industrial experience that both allows them opment. Assignments include writing programs and This course introduces the major numerical meth- to learn to apply their knowledge gained in the a project to develop a web application. ods needed for quantitative work in finance, focusing classroom and to better prepare for their future Prerequisites: knowledge of a programming lan- on derivatives pricing and fixed income applications. careers in finance. Enrollment requires the permis- guage and basic HTML. 3 credits Topics include binomial and trinomial methods, sion of the instructor and is limited by the number of APC505 — Applications Programming in C++ finite difference solution of partial differential equa- internship opportunities available. 1-3 credits This course provides an introduction to program- tions, Crank-Nicholson methods for various exotic ming in C++, which is used widely for developing options, treatment of discrete dividends, projected- APPLIED COMPUTING COURSES engineering and business applications. This course SOR method for American options, numerical meth- These courses may be applicable to the introduces students to C++ language constructs, ods for stochastic differential equations, random Master in Computational Finance or as a data structures and classes. The student will also be number generators, Monte-Carlo methods for shown how access class and template libraries, European and least-squared Monte-Carlomethods prerequisite for the Master in Computer including the standard template library (STL). The for American options. The course is lab oriented. Science and Engineering or the Oregon course is suitable for students in engineering, man- Prerequisite: FIN552 Options and Futures II or per- Master of Software Engineering. agement and finance who wish to gain an mission from instructor. 3 credits APC500 Development with Visual Basic for Applications understanding of the language. On completion, stu- FIN561 Risk Management This course introduces Visual Basic for Applications dents will be in a position to contribute to the design This course explores various aspects of manage- as a tool for rapid application development, cus- and development of systems using C++. ment of risk associated with operating a tomization and system integration in Windows Assignments include writing programs and a pro- multinational enterprise. Emphasis is on evaluating environments. The course focuses on combining VBA gramming project. Prerequisites are knowledge of a and hedging financial risks (fixed-income, equity, with Microsoft Office. Topics covered include the programming language. 3 credits commodity, and foreign exchange risk exposures), structure of the VBA programming language and APC506 Advanced Applications Programming in C++ with emphasis on value-at-risk (VAR) models. Topics built-in functions, enhancing recorded macros using This course explores advanced topics concerning include sources and measurement of risk and expo- VBA code, applying the MS Office object models and applications programming in C++. The course will sure, value at risk, hedging linear and nonlinear accessing relational databases using ActiveX Data focus on writing efficient, extensible and reusable derivatives risk, delta-normal VAR, historical simu- Objects (ADO). Students will gain expertise in programs, and introduce concepts in software engi- lation VAR, Monte Carlo approaches to VAR, and advanced analysis and data manipulation, develop- neering, program analysis and design, and data implementation and evaluation of risk management ing and customizing applications, and integrating modeling. Students will develop class libraries, and systems. Course assignments make use of MATLAB them with existing systems. Prerequisites: experi- learn how to apply design patterns. The course is and BARRA On Campus. 3 credits ence with MS Excel and Access, and knowledge of a suitable for students in science, engineering and FIN573 Financial Time-Series Analysis programming language. 3 credits finance who wish to further their understanding of This course reviews advanced time-series tech- APC501 Accelerated Development with Visual Basic the language. On completion, students will be in a niques and their application to the analysis and This course uses Visual Basic 6.0 and Visual Basic position to the design and develop systems using forecasting of financial time-series. Emphasis is for Applications as tools to introduce the concepts of C++. Assignments include writing programs and a given to multivariate and nonlinear methods applied rapid application development, systems integration programming project. Prerequisites: APC 505 or to high-frequency financial data. Topics covered and customization on Windows platforms. While equivalent knowledge of C++. 3 credits include ARIMA models, GARCH models, martingales studying Visual Basic, students will gain an under- APC508 Web Development with Java 2 and random walks, stochastic trends, co-integration standing of the architecture of Windows applications This course uses “Java 2” technology to introduce and error-corrections models. The primary analysis and create COM components, ActiveX controls and the essential concepts needed to develop web appli- tool for this course is S-PLUS. Prerequisite: CSE548 executable programs. Students will also learn how cations with client side scripting. Topics include the Modern Applied Statistics. 3 credits to apply basic analysis and design techniques, and structure and elements of Java, Java Foundation FIN576 Financial Markets and Trading how to make their user interfaces friendly and effi- Classes (JFC), Java applets and servlets, Java cient. Assignments involve practical work with these This course provides a survey of the structure and Beans and Remote Method Invocation (RMI). Other software tools, using applications from dynamics of financial markets, the behavior of finan- topics, such as JDBC and XML may be introduced, industry/business as case studies. This fast-paced cial price series, and trading techniques. Topics time permitting. On completion, students will under- course is intended for experienced programmers include market microstructure, market efficiency stand the conceptual architecture of web wishing to augment their skills with knowledge of and documented anomalies, noise traders and applications with client side automation and be in a Visual Basic. Prerequisites are programming experi- bounded rationality, properties of high frequency position to contribute to their design and develop- ence with C, C++ or Java. APC500 is not a data, nonlinear price behavior, speculative bubbles ment. Assignments include writing programs and a prerequisite for this course. 3 credits and crashes, market psychology, and technical trad- project to develop a web application. Prerequisites: ing systems. The course draws upon the academic APC503 Web Development with Perl 5 knowledge of a programming language. 3 credits literature and the practitioners’ lore. Students use This course uses “Perl 5” technology to introduce APC511 Computational Tools for Engineering and Finance MATLAB, S-PLUS, and extensive data resources to the essential concepts needed to develop web appli- This course provides an introduction to essential analyze price behavior and build and test simple cations with server side scripting. Topics include the programming skills needed for engineering and technical trading systems. Prerequisites: FIN541 structure and elements of the Perl 5 language (vari- finance. The course reviews key topics in linear Principles of Modern Finance and FIN573 Financial ables, control structures, file I/O, regular algebra, explores basic numerical methods, and Time-Series Analysis. 3 credits expressions, objects and built-in functions), impor- provides a comprehensive introduction to computing FIN620 Professional Internship in Finance tant Perl libraries, writing CGI scripts, building in Matlab. Mathematical topics include vector dynamic web pages and extracting data from data- This course provides the student with an opportuni- spaces, matrix computation, solution of linear sys- bases using basic SQL queries. Important issues, ty to earn credit for relevant work experience in tems, interpolation, regression, approximation, such as the security of web applications, will be finance and related industries. It enables students numerical precision, convergence and algorithm addressed and additional topics, such as XML, may to enhance their understanding of the practical real- complexity. Matlab topics include language features, be introduced, time permitting. On completion, stu- ities of modern finance, including such areas as handling vectors, matrices and cells, programming dents will understand the conceptual architecture of corporate treasury operations, investment analysis, in Matlab (functions and script files), 2D and 3D web applications with server side automation and be portfolio management, risk management, deriva- graphics, using key toolboxes, developing a graphi- in a position to contribute to their design and devel- tives pricing, forecasting and trading. Students gain cal user interface, and other advanced features. 32 COMPUTER SCIENCE AND ENGINEERING | CSE

Programming assignments focus on the practical OMSE513 Professional Communication Skills for architecture to requirements and its effects on use of Matlab. Prerequisites: knowledge of a pro- Software Engineers downstream design. Students will examine domain gramming language. 3 credits This course covers the skills necessary for appro- analysis and the architectural design process and priate professional conduct and effective products in context including the effect of decisions APC515 Data Structures and Discrete Math communication in a professional setting. It includes on function, quality, cost, and schedule. This course covers fundamental topics in data struc- technical writing, making effective presentations, Prerequisites: OMSE 500, OMSE 522. 3 credits tures and discrete mathematics. The topics are conducting effective meetings, conflict resolution, presented in an integrated manner that provides the OMSE533 Software Design Techniques team and decision-making skills, and professional discrete math foundations for data structures and This course covers the principles of software design ethics. Prerequisite: OMSE 500. 3 credits computing applications of discrete mathematics and a survey of design methods, techniques, and concepts. Topics covered include stacks, queues, OMSE521 Using Metrics and Models to Support tools. In-depth and hands-on study of at least one linked lists, trees, algorithms for searching and sort- Quantitative Decision Making method such as object-oriented design as applied to ing, finite state automata, and concepts of This course provides the knowledge and skills need- a realistic industrial problem. It examines the computability and decidability. Topics from discrete ed to apply quantitative tools based on metrics and effects ofdesign decisions on the functional and non- math include sets and various types of relations models of the software product and development functional properties of the software (e.g., Ease of (functions, graphs, trees, lattices), recursion and process to make decisions under uncertainty. Topics understanding, maintainability, reuse) and how soft- inductive proofs, boolean logic, relational algebra, covered will include measurement concepts, deci- ware engineering principles are applied to make predicate calculus, series and limits, and asymptot- sion-making under uncertainty, and model and appropriate trade-offs. Students also examine the ic behavior of searching and sorting algorithms. metric development for the software development design process and products in context including the Programming exercises are assigned throughout the enterprise. Prerequisite: OMSE 500. 3 credits effect of design decisions on function, quality, cost, course. Prerequisites: APC505 or equivalent knowl- and schedule. Prerequisites: OMSE 500, OMSE 522. edge of C or C++. 3 credits OMSE522 Modeling and Analysis of Software Systems CSE students may not receive credit for both CSE Abstract models are used to formalize specifications 504 and OMSE 533 because there is significant OREGON MASTER OF SOFTWARE ENGINEERING of software systems. Formalized reference specifi- overlap in content. 3 credits cations serve as a basis for the design of software COURSE OFFERINGS implementations and for validating critical proper- OMSE535 Software Implementation and Testing OMSE500 Principles of Software Engineering ties of software systems. This course provides the This course covers the principles of implementing This course serves as an introduction to software fundamental mathematical concepts needed to and verifying computer software. Implementation engineering. The course’s focus is on understanding understand abstract models of software and to rea- topics include coding style, packaging principles, the software engineering process and its attendant son about them as well as examples showing how reuse, testability, and maintainability. Verification problems as manifest in real development projects. they are applied. Prerequisite: OMSE 500. 3 credits topics include structural (white box) testing and The course compares and contrasts different models techniques for code verification. Also included will OMSE525 Software Quality Analysis be verification and integration of foreign code, test- of the software engineering process and approaches This course covers processes, methods, and tech- to process improvement. It includes the analysis of ing techniques and how to apply them, including niques for developing quality software, for assessing code-based and specification-based testing, hands- where and how things go wrong motivated by case software quality, and for maintaining the quality of studies. This course is intended as a leveling course on application of the testing process, including test software. Course material emphasizes the tradeoffs case generation, and test adequacy, test validation, for entering students who have not had prior between software cost, schedule time, and quality; instruction in software engineering and may be test execution, and automation. Prerequisites: the integration of quality into the software develop- OMSE 500, OMSE 522, OMSE 525. 3 credits waived for students with an equivalent senior-level ment process; formal review and inspection or master’s-level course or equivalent work experi- methods; principles of testing and test planning; OMSE551 Strategic Software Engineering ence. Prerequisite: Knowledge of programming. module design for testability; and maintaining qual- Where traditional software engineering focuses on Relevant work experience recommended but not ity while supporting existing software. Prerequisite: the development and maintenance of individual sys- required. 3 credits OMSE 500. 3 credits tems strategic software engineering addresses the OMSE 511 Managing Software Development development of multiple systems over time. Recent OMSE531 Software Requirements Engineering work has shown that significant gains in productivi- This course provides the knowledge and skills need- This course covers the principles, tools, and tech- ed to plan, organize, lead, and control software ty, cost, and schedule can result from systematic niques for requirements elicitation, specification, improvement of a company’s overall software devel- projects. Topics include planning and estimating, and analysis. The course focus is on understanding measuring and controlling, and achieving results in opment process and systematic reuse of life-cycle the role of requirements in system development and products over multiple developments. This course environments that include a great deal of ambiguity maintenance, goals of the requirements phase, and contradictory information. Quantitative meas- covers the principles, methods, and tools for such essential difficulties of specifying requirements for strategic software development including long-term ures and risk management will be emphasized real systems, and effective methods tools and tech- throughout the course. Students will prepare project process modeling and improvement, developing pro- niques. The course covers techniques for formally grams as instances of families of systems, and plans for real or hypothetical software projects, to modeling and specifying software requirements with include effort, cost, and schedule estimates and risk systematic approaches to code generation and the hands-on experience as well as the role of prototyp- reuse of non-code products including requirements management plans. Prerequisite: OMSE 500. ing in validating requirements. Prerequisites: OMSE 3 credits and design. Prerequisites: OMSE Foundation and 500, OMSE 522, and the Formal Inspections part Context courses. 3 credits OMSE512 Understanding the Software Business ofQuality Analysis. 3 credits OMSE555 Software Development Practicum I This course provides a familiarity with the business OMSE532 Software Architecture and Domain Analysis 3 credits and economic aspects of software companies and This course covers the principles and methods of the other high-technology companies that develop soft- architectural design of complex software systems. It OMSE556 Software Development Practicum II ware. Topics include fundamental macro-economic includes a survey of the major architectural styles, The development practicum provides an opportunity concepts, basic accounting and financial principles strengths and weaknesses of each style, and trade- for students to apply the knowledge and skills gained and methods, basic business law, and the functions offs among them; application of domain analysis to in other courses as they synthesize a solution to a and role of marketing in enterprises that develop identifying and capturing common architecture in significant, realistic, and practical problem. software products or products that include soft- software domains (e.g., Product lines); the impact of Students work in teams to analyze a problem, devel- ware. Prerequisite: OMSE 500. 3 credits platform dependence and independence on architec- op a software concept, plan a software development tural decisions; and the relation of software effort, define requirements, and implement a solu- 33 CSE | COMPUTER SCIENCE AND ENGINEERING

tion. Each offering of the practicum will include at Constructing Software from Specifications Machine Learning and Adaptive Systems least one hour of lecture per week. Students will Research in formal methods for software engineer- Machine learning, neural computation and work closely with OMSE program faculty and, where ing has been concerned primarily with software adaptive systems are studied from both theoretical possible, reviewers from industry to apply advanced specification. This research explores the next and practical standpoints. Research in theory, software engineering techniques to a disciplined step: given a declarative specification, to generate architectures, and algorithm design includes development of a realistic product and evaluate the practical and efficient software by the technologies learning algorithms (supervised, unsupervised, results. Software development artifacts created as of program transformation and specialization. and reinforcement), generalization theory part of the practicum will become part of the stu- (including model selection and pruning, invariant dent’s professional portfolio. Contents of the We have demonstrated a new software learning), deterministic and stochastic optimiza- portfolio include such products as the concept defi- development method in which software components tion, context-sensitive learning, signal processing, nition, cost estimate, project plan and schedule, are constructed from executable specifications by time series analysis, and control. Practical appli- formal requirements specification, test plan, soft- typed, staged functional programs and a cation domains include adaptive signal processing, ware quality assurance plan, software architecture, translation directed by an interface specification pattern recognition, speech recognition, image software design, implementation artifacts, test that determines data representations. Systematic processing, medical screening technology, control results, and metrics collected. The portfolio techniques for proving the semantic validity of rep- systems, macroeconomics, and finance. contents provide examples of the student’s profes- resentations for data types are explored. Kieburtz, Hermansky, Leen, Moody, Pavel, Song, Wan sional capabilities. 3 credits Hook, Sheard, Launchbury Multimodal Systems Digital Government Multimodal interfaces enable more natural and RESEARCH PROGRAMS DOT is collaborating with the US Forest Service, efficient interaction between humans and machines Bureau of Land Management, Fish and Wildlife by supporting multiple coordinated channels The specific research projects under way at any Service and other government agencies to build a through which input and output can pass. The given time depend upon current interests and obli- forest information portal for the Adaptive Center for Human-Computer Communication is gations of faculty, students, and research sponsors. Management Area (AMA) program. The AMAs engaged in empirical investigation of multimodal Agent-Based Systems develop and test innovative approaches to forest interaction. This informs our research and develop- management. We are developing an information This project will design a new agent ment of architectures for multimodal language model called Metadata++ to locate documents and communication language (AGENTTALK) and processing, work which draws on a range of fields document fragments along several dimensions and multiagent architecture. Unlike DARPA’s current such as cognitive science, natural language to search for documents based on ìsimilarity language (KQML), the language offers a true processing, multimedia, user interface design, search between locations. The Forest project also semantics, and provably correct dialogue protocols, speech recognition, gesture recognition, and visual includes participants from the MST and ESE based on joint intention theory. The Adaptive Agent parsing. The Quickset system developed at CHCC departments at OGI, from UNLV and from the pri- Architecture, a successor to our earlier Open supports multimodal pen/voice interaction with vate sector. Delcambre, Maier, Toccalino, Phillips, Agent Architecture, offers platform and application complex visual/spatial displays such as maps. Steckler, Tolle, Landis, Palmer interoperability, facilitated communication, proper Cohen, Oviatt concurrent operation, dynamic reconfigurability of Domain Specific Languages Natural Language Dialogue facilitators, and separation of data and control. A domain-specific language can provide a declara- The performance of speech recognition systems Quickset has been reimplemented to use this archi- tive programming interface for specialists in an improves significantly when the spoken language tecture, gaining a more robust capability for application domain who are not primarily software understanding system can predict the next utter- supporting human-human collaboration, multime- engineers. A well-designed domain-specific ance. Accordingly, we are performing perceptual dia, and dynamic adaptation to processing language improves productivity, reduces the inci- studies of dialogue and building models of human- environments. Cohen dence of programming errors and furnishes an human and human-computer dialogue in order to Autonomix: Component, Network, and System Autonomy easily understood medium for documentation of a develop computational models of conversation that software artifact. A barrier to the widespread Autonomix pragmatically seeks to provide can be used to track and predict spoken language. adoption of domain specific languages is the inher- autonomic defenses for commodity information This work is based on speech-act theory, multi- ent difficulty of language design and systems. Our contribution is in three complementa- agent architectures, and models of spontaneous implementation. We are developing semantics com- ry areas: Component Autonomy, to make existing speech. Cohen, Heeman, Oviatt binators to allow rapid implementation of individual components more robust to attack, declarative, domain-specific languages. We are also Net Data Management Network Autonomy, to allow existing components pursuing staged implementations as a means of We believe that data management systems of the to access CIDF capabilities via current Internet efficiently embedding a domain specific language future must stress data movement over data storage. standard protocols, and Systemic Autonomy, to into a broad-spectrum functional language frame- NIAGARA is an initial effort, conducted with the model, analyze and implement coordinated, adap- work. Sheard, Hook, Kieburtz, Launchbury University of Wisconsin, to move beyond disk- tive responses of multiple components. Component centric data management to net-centric systems. autonomy is developing a family of tools Functional Programming Languages Current work includes algebras and special opera- (StackGuard, PointGuard, FormatGuard, and Functional programming languages are based upon tors for XML, exploiting stream semantics for RaceGuard) that make applications vulnerability the idea that programs can be designed as mathe- efficient processing, and data-query hybrids for dis- tolerant by making broad classes of vulnerabilities matical functions with logical properties. tributed query evaluation. Maier, DeWitt, Naughton (buffer overflows, printf format string bugs, and Functional abstraction is a powerful and flexible temporary file races) unexploitable. Network and means of constructing concise programs. PacSoft Operating Systems Systemic Autonomy are providing a family of tools faculty have a continuing interest in techniques for Our operating systems-related research focuses to enable large-loop intrusion tolerant responses, analysis and efficient implementation of functional primarily on adaptive systems software and its where in a distributed network of machines can programming languages including ML and Haskell. application in distributed, mobile, and multimedia adaptively respond to intrusions. Component These techniques include staged programming, par- computing environments. Several large projects Autonomy work is being done at WireX tial evaluation, effects encapsulation with monads, are currently under way in the areas of quality of Communications, Inc., and Network and Systemic automatic program transformation, and advanced service control, adaptive resource management Autonomy work is being done at OGI. Cowan, type systems. Black, Hook, Jones, Kieburtz, and dynamic specialization for enhanced perform- Maier, Delcambre Launchbury, Sheard ance, survivability and evolvability of large software systems. Black, Steere, Walpole 34 COMPUTER SCIENCE AND ENGINEERING | CSE

Query Optimization Tracking Footprints through an Information Space: CHCC organizes an annual Distinguished Lecture Our work on query optimization and evaluation Leveraging the Document Selections of Experts Series on the Future of Human-Computer deals with both general frameworks and specific The goal of this project is to help expert problem Interaction. World-class researchers are invited to techniques for different data model and query solvers find needed information in a large, complex share current topics. language features. Columbia is a C++-based, top- information space. The focus is on one example of Dr. Philip Cohen and Dr. Sharon Oviatt are co- down framework for construction of cost-based expert problem solving; the physician seeking to directors of the center. Other center faculty include query optimizers. We are currently examining diagnose and treat a patient while using the med- Dr. Peter Heeman, and Dr. Misha Pavel. For more pruning techniques for searching, transforms for ical record. Sorting through a heterogeneous information, visit CHCC’s web pages at collection-valued attributes and nested queries, collection of electronic and other media materials www.cse.ogi.edu/CHCC/. and ìmultiplex query optimization for efficiently to find needed information, sometimes under time optimizing groups of queries. Columbia is a joint pressures, can be formidable. This project propos- PACIFIC SOFTWARE RESEARCH CENTER project with Portland State University. Maier, es to capture the trace of information used by Shapiro experts-to monitor the paths taken and collection Kelly Atkinson, Center Administrator resources used by physicians, in moving from 503-748-1336 Speech Recognition observation, to information gathering, to solution [email protected] The goal of Large Vocabulary Continuous Speech of a given health care problem. By capturing the Sheri Dhuyvetter, Center Administrator Recognition research is to enable normal human trace information artifacts associated with speech as an input device in next generation com- 503-748-1476 information seeking and selection, it is [email protected] puters alongside today’s keyboard and mouse input. hypothesized that greater insight can be gained This technology can be used for dictation and into behaviors of users and patterns of usage. The Pacific Software Research Center (PacSoft) is command control applications when used by itself. This knowledge can then be fed-back into the a team of faculty, students and professional It can also form part of a powerful information design and development of new information envi- research staff who study mathematically based processing system when used together with infor- ronments. The work is conducted by a cross- techniques for the specification, development and mation retrieval and natural language disciplinary team comprised of an MD focusing on validation of complex computer software. Our goals understanding systems. The research focuses information seeking behaviors of physicians, and a are to explore and test new techniques that can include accurate acoustic modeling, speaker adap- group of computer scientists focusing on extracting support the development of software products in tation, confidence measure and rejection, and and using regularly structured information. The which clients can have high confidence. modeling spontaneous speech. Yan, Heeman usefulness of the approaches will be tested in PacSoft’s approach to software specification and Spoken Language Systems domains other than health care, in particular the development is grounded in functional aircraft design industry through the active support Spoken language systems make it possible for programming, type theory, and formal semantics of of the Boeing Corp. Delcambre, Maier, and Dr. people to interact with computers using speech, programming languages. Our research methods Paul Gorman, Oregon Health & Science University the most natural mode of communication. A spoken extend from theoretical investigation through language system combines speech recognition, prototype software tool development to natural language understanding and human experimental validation. interface technology. It functions by recognizing the RESEARCH CENTERS Much of our work during the past decade has person’s words, interpreting the words in terms of CENTER FOR HUMAN-COMPUTER COMMUNICATION the context and goals of the task, and providing an focused on techniques for the design and Kimberly Tice, Center Administrator appropriate response to the user. We are involved implementation of domain-specific languages. (503) 748-7806 in the analysis and development of various compo- A domain-specific language is able to express the [email protected] nents of such systems, ranging from empirical abstractions and operations used in a particular studies of human dialogues through the construc- The Center for Human-Computer Communication is engineering domain, in terms familiar to domain tion of interactive systems to the development of dedicated to realizing a vision of transparent experts. One domain in which this work has abstract models of behavior. Cohen, Oviatt, information and service access. Research projects demonstrated considerable success is the design Heeman, van Santen are broadly interdisciplinary, and include of complex microarchitectures for high- performance microprocessors. Superimposed Information and Superimposed Applications collaborations with numerous universities, federal research laboratories, and the Data-Intensive We are interested in providing typical database The Hawk project has exploited abstraction and Systems Center at OGI. system capabilities in an environment where we equational specification techniques from functional do not own or manage the underlying, base Research activities focus on: programming languages to produce a new kind of information. We seek to develop a superimposed hardware specification language. A layer of information that can reference selected • Multimodal human-computer interaction that microarchitecture specification written in Hawk information from the base layer and can also add allows people to state their needs using speech, can be directly executed as a simulation, new information to highlight, interconnect, elabo- writing, and gestures, and that provides symbolically manipulated as a hardware algebra, or rate, or annotate the selected information. We have multimedia output. submitted to formal verification of its properties by model checking or by a theorem prover. defined an architecture for building superimposed • User-centered design of next-generation applications and have implemented our first tool: interface technology, including spoken language Among current PacSoft projects is Programatica, SLIMPad, a scratchpad application that allows and multimodal interfaces, and interfaces for an exploration of computer-supported techniques users to easily create “scraps” that reference mobile and multimedia technology. for developing property-certified programs selected items from the base layer and organize (ìprogramming as if properties matteredî). Project scraps into bundles. The tendency to use scraps • Intelligent agent technologies - software systems Timber is developing new means of programming and bundles to organize our thoughts is common that assist users in accomplishing tasks and can embedded applications that involve both time- practice, as confirmed by our observational reason about how and where to carry out the critical and critical-rate tasks. research team that is studying how clinicians seek users’ requests in a worldwide distributed and use information in a hospital intensive care information environment. Dr. Tim Sheard is the current Director of the unit. Observational team: Gorman, Ash,Lavelle; Center. Dr Richard Kieburtz is the founding • Collaboration technologies to support human- computer science team: Delcambre, Maier Director. Other faculty members of PacSoft are Dr. human communication, and collaborative James Hook, Dr. Mark Jones and Dr. John decision making among groups of people. 35 CSE | COMPUTER SCIENCE AND ENGINEERING

Launchbury of OHSU/OGI and Dr. Andrew Tolmach domain-specific languages, and quality of service of Portland State University. The Center employs management to enable them to operate effectively six postdoctoral researchers and has numerous in today’s rapidly evolving and widely visitors each year. heterogeneous distributed environments. We emphasize the real-world applicability of our Research by PacSoft scientists is supported by research results and we continue to build grants and contracts from the National Science distributed and scalable prototype systems for Foundation, DARPA, the National Security Agency, application areas such as multimedia computing Intel Corp. and Compaq. and communications, active networks, Internet- For additional information, visit the PacSoft web based information management, and survivable site, http://www.cse.ogi.edu/PacSoft/. distributed systems. We collaborate closely with industry sponsors such as Intel and IBM, and have THE SYSTEMS GROUP strong federal funding from DARPA and NSF. Dr. Database and Object Technology Laboratory Jonathan Walpole is the director of SySL. Jo Ann Binkerd, Center Administrator Additional SySL-affiliated faculty are Drs. Wu-chi 503-748-1112 Feng, Wu-chang Feng, Andrew Black and David [email protected] Steere of OGI, and Dr. Molly Shor of OSU. Systems Software Laboratory Cynthia Pfaltzgraff, Center Administrator FACILITIES 503-748-7109 OGI’s Department of Computer Science and [email protected] Engineering provides a state-of-the-art computing The Systems Group consists of two research environment designed to support the needs of laboratories — the Systems Software Laboratory research and education. The computing facilities and the Database and Object Technology staff has a wide range of skills that allows the Laboratory. computing environment at CSE to be flexible and responsive in meeting the changing needs of The Database and Object Technology Lab (DOT) the department. conducts theoretical and applied research related to database management and object-oriented Support for central services such as mail, dial-up systems. Query processing is a long-term focus, access, video conferencing, database access, and particularly query optimization frameworks as well file and printer sharing as well as access to as design, optimization and evaluation of object- Internet and Internet2 services are distributed oriented query languages. Another area of interest across a group of Sun computers and a Network is scientific data management, most recently in Appliance file server that comprise the core support of multi-disciplinary studies in forest support environment. canopy science. While Sun computers are highly visible at CSE, DOT research includes conceptual modeling, both Intel and Alpha based machines running including semantic and object-oriented database Windows or Linux are mainstays of our research models, models for object-oriented analysis and activities. The generous support of our industry and design, and models for superimposed information. government research partners allows CSE to Other topics include data dissemination, focusing maintain a high-quality computing infrastructure particularly on information utility and capable of supporting a high degree of superimposed information management. heterogeneity as required for high-quality research. Superimposed information enhances the utility In all, a facilities staff of nine supports almost and value of existing data sources by layering 400 computer systems, X terminals, and small amounts of information over them. We are peripheral devices spanning multiple networks examining superimposed information in connection using a variety of automated techniques, many with improving accessibility of medical records. developed internally, to cope with the high Finally, we are investigating architectures for degree of complexity inherent in such a adaptable software and middleware support heterogeneous environment. for application building, especially object- oriented approaches. Dr. Dave Maier of OGI is the director of DOT. Additional DOT-affiliated faculty members are Dr.Crispin Cowan, Dr. Lois Delcambre, and Dr. Dylan McNamee of OGI, and Dr. Leonard Shapiro of Portland State University. The Software Systems Lab (SySL) is a center for research spanning the areas of distributed and mobile computing, operating systems, networking, and wide-area-network based information management systems. SySL focuses on the development of adaptive systems that utilize techniques such as feedback-control, specialization,

36 FACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

JAMES HOOK DAVID BASTERFIELD ANDREW P. BLACK THOMAS BUNDT Associate Professor and Assistant Professor Professor Associate Professor Department Head Ph.D., Decision Theory D. Phil, University of Oxford, Ph.D., Economics Ph.D., Computer Science University of Manchester, 1984 (Balliol College) England Michigan State University, 1985 Cornell University, 1988 [email protected] [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Numerical computing, Programming languages; International monetary theory and Domain-specific languages, simulation, optimization, distributed systems; streaming empirical models of exchange rate formal methods, and genetic algorithms, information infrastructure for wide-area determination, time series analysis functional programming. systems, time series analysis networks; object-oriented and forecasting and pedagogical and computational finance. languages and systems; tools in finance. Professor Bundt REPRESENTATIVE PUBLICATIONS programming environments; and has also written instructional J. Hook, E. Meijer, & D. Leijen, REPRESENTATIVE PUBLICATIONS the ways in which all of these manuals (distance learning “Client-side web scripting in Haskell”, D. Basterfield, “Error bounds on areas interrelate. courses) in Managerial Economics, in proceedings of Practical Applications Tree methods for Calculating Business Forecasting and of Declarative Languages, Options Prices”, Paper Presented REPRESENTATIVE PUBLICATIONS Ebusiness Valuations. January 1999. at Computational Finance 2000, A. P. Black, J. Huang and J. Walpole, June 2000. J. Hook, E. Meijer, & D. Leijen, “Reifying Communication at the REPRESENTATIVE PUBLICATIONS “Haskell as an Automation Controller”, D. Basterfield, T. Bundt and Application Level”. Oregon Graduate T. Bundt, T.F. Cosimano & in “Advanced Functional Programming”, G.Murphy, “The Stable Paretian Institute, Department of Computer J.A. Halloran, “DIDMCA and Bank Swierstra, Henriques and Oliveira Hypothesis and the Asian Currency Science & Engineering, Beaverton, OR, Market Risk: Theory and Evidence,” (Eds.), Springer Verlgan, LNCS Crisis”, Paper Presented at Technical Report CSE-01-006, Journal of Banking and Finance, 16, Vol. 1608. Computational Finance 2000, May 2001. 1179-1193, 1992. T. Widen &J. Hook, “Software Design June 2000. C. Pu, A. Black, C. Cowan, J. Walpole, T. Bundt & J.H. Bergstrand, Automation: Language Design in the & C. Consel, “Microlanguages for “Currency Substitution and Monetary Context of Domain Engineering,” Sere Operating System Specialization,” Autonomy: The Foreign Demand for 98, June 1998. Proc. First ACM SIGPLAN Workshop U.S. Demand Deposits,” Journal of J. Bell, F. Bellegarde & J. Hook, on Domain-Specific Languages, Paris, International Money and Finance, “Type-driven Defunctionalization,” France, p. 49-57, January 1997. 9, 325-334, 1990. ICFP ‘97, June 1997. C. Pu, T. Autrey, A.P. Black, C. Consel, T. Bundt & R. Schweitzer, R. Kieburtz, F. Bellegarde, et al., C. Cowan, J. Inouye, L. Kethana, “Deregulation, Deposit Markets, and “Calculating Software Generators from J. Walpole & K. Zhang, “Optimistic Banks’ Costs of Funds,” The Financial Solution Specifications,” TAPSOFT ‘95, Incremental Specialization: Review, 24(3), 417-430, August 1989. Springer-Verlag, LNCS, May 1995. Streamlining in a Commercial Operating System,” Proceedings of the T. Bundt, J.S. Chiesa & B.P. Keating, F. Bellegarde & J. Hook, “Substitution: 15th ACM Symposium on Operating “Common Bond Type and Credit Union A Formal Methods Case Study using Systems Principles, December 1995. Behavior,” Review of Social Economy, Monads and Transformations,” Science 47(1), 27-42, Spring 1989. of Computer Programming, 22(2-3), A.P. Black & M.P. Immel, T. Bundt & A. Solocha, “Debt, 287, 1994. “Encapsulating Plurality,” Proceedings of European Conference on Object- Deficits and the Dollar,” Journal J. Bell, J. Hook, et al., “Software Oriented Programming, July 1993. of Policy Modeling, 10(4), 581-600, Design for Reliability and Reuse: A October 1988. Proof-of-Concept Demonstration,” R.K. Raj, E.D. Tempero, H.M. Levy, TRI-Ada ‘94 Proceedings, ACM Press, A.P. Black, N.C. Hutchinson & E. Jul, November 1994. “Emerald, A GeneralPurpose Programming Language,” Software F. Bellegarde & J. Hook, “Monads, Practice & Experience, 21(1), 91, Indexes, and Transformations,” January 1991. Proceedings of the Colloquium on Formal Approaches to Software A.P. Black & Y. Artsy, Digital Engineering (TAPSOFT ‘93), LNCS, Equipment Corp., “Implementing April 1993. Location Independent Invocation,” IEEE Trans. On Parallel and Distributed Systems, 1(1), 107, January 1990.

37 CSE | COMPUTER SCIENCE AND ENGINEERING | FACULTY

PHIL COHEN CRISPIN COWAN LOIS DELCAMBRE RICHARD E. (DICK) FAIRLEY Professor and Co-Director, Assistant Research Professor Professor Professor and Director Center for Human-Computer Ph.D., Computer Science Ph.D., Computer Science of Software Engineering Communication University of Western Ontario, University of Southwestern Ph.D., Computer Science Ph.D., Computer Science 1995 Louisiana, 1982 UCLA, 1971 University of Toronto, 1978 [email protected] [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS System security and survivability, Superimposed information, All aspects of software Multimodal interfaces, human- operating systems, distributed database system data models, engineering, including but not computer interaction, natural systems, computer architecture, scientific data management. limited to systems engineering of language processing, dialogue, optimism, programming languages. software-intensive systems, delegation technology, cooperating REPRESENTATIVE PUBLICATIONS software process modeling and agents, communicative action, REPRESENTATIVE PUBLICATIONS S. Bowers and L. Delcambre. process improvement, software applications to mobile computing, C. Cowan, S. Beattie, C. Wrigth, & A generic representation for exploiting requirements engineering, information management, network G. Kroah-Hartman, “RaceGuard: model-based information. To appear, software design, software quality management, manufacturing. Automatic Adaptive Detection and ETAI Journal, 2001. engineering, software metrics, Prevention of Buffer-Overflow Attacks,” L. Delcambre, D. Maier, S. Bowers, software project management, Tenth USENIX Security Conference REPRESENTATIVE PUBLICATIONS L. Deng, M. Weaver, P. Gorman, software cost and schedule 2001. J. Ash, M. Lavelle, and J. Lyman. Oviatt, Sharon & Cohen, Philip. estimation, software risk Bundles in captivity: An application “Multimodal Interfaces That C. Cowan, M. Barringer, S. Beattie, of superimposed information.“ management, and software Process What Comes Naturally”, G. Kroah-Hartman, M. Frantzen, & Proceedings of the IEEE International engineering policies, procedures, Communications of the ACM, Vol. 43, J. Lokier, “FormatGuard: Automatic Conference on Data Engineering, standards, and guidelines. No. 3, pp. 45-53, March 2000. Adaptive Detection and Prevention of Buffer-Overflow Attacks,” Tenth Heidelberg, Germany, April 2001. D. McGee, P. Cohen, & L. Wu, (2000) USENIX Security Conference 2001. S. Bowers and L. Delcambre. REPRESENTATIVE PUBLICATIONS “Something from nothing: Augmenting Representing and transforming model- Software Project Management, a paper-based work practice with D. McNamee, J. Walpole, C. Cowan, based information. In Proceedings of Encyclopedia of Computer Science, multimodal interaction,” in Proceedings C. Pu, C. Krasic, P. Wagle, C. Consel, the International Workshop on the Groves Dictionaries, 2001. of the Designing Augmented Reality G. Muller & R.Marlet, “Specialization Tools and Techniques for Systematic Semantic Web, in conjunction with Environments Conference, ACM Press, “Software Estimation Risk,” Optimization of Systems Software,” ECDL 2000, Lisbon, Portugal, pp. 71-80, Copenhagen, Denmark, Encyclopedia of Software Engineering, ACM Transactions on Computer September 2000. April 12-14, 2000. Volume 2, John Wiley and Sons, 2000. Systems, Volume 19, No. 2, May 2001. P. Gorman, J. Ash, M. Lavelle, S. Kumar, & P. Cohen, “Towards a J. Lyman, L. Delcambre, D. Maier, R. Fairley, “A Process-Oriented Fault-Tolerant Multi-Agent System C. Cowan, C. Pu, D. Maier, H. Hinton, S. Bowers and M. Weaver. Bundles in Approach to Software Product Architecture.” To appear in The J. Walpole, P. Bakke, S. Beattie, the wild: Tools for managing informa- Improvement,” PROFES’99 Conference Fourth International Conference on A. Grier, P. Wagle, & Q. Zhang, tion to solve problems and maintain Proceedings, Oulu, Finland, June 1999. Autonomous Agents (Agents 2000), “Stackguard: Automatic Adaptive situation awareness. Library Trends R. Fairley, “The Concept of Barcelona, Spain, June 3-7, 2000. Detection and Prevention of Buffer- Overflow Attacks,” Seventh USENIX 49(2), Fall 2000. Operations-The Bridge from L. Wu, S.L. Oviatt, & P. Cohen, Security Conference, 1998. D. Maier and L. Delcambre, Operational Requirements to Technical “Multimodal Integration — Specifications,” Annals of Software C. Cowan & H. Lutfiyya, “A Wait-Free ìSuperimposed information for the A Statistical View,” IEEE Transactions Engineering, Vol. 3, Baltzer Publishers, Algorithm for Optimistic Programming: Internetî, in Proc. of the ACM SIGMOD on Multimedia, Vol. 1, No. 4, Amsterdam, The Netherlands, HOPE Realized,” 16th International Workshop on The Web and Databases pp. 334-341, December 1999. September 1997. Conference on Distributed Computing (WebDB ‘99), pages 1-9, June 1999. P. Cohen, D. McGee, S.L. Oviatt, Systems (ICDCS’96), Hong Kong, 1996. L. Delcambre and D. Maier, R. Fairley, “Standard for Concept L. Wu, J. Clow, R. King, S. Julier, & “Models for superimposed information,” of Operations Documents,” IEEE L. Rosenblum, “Multimodal Interactions C. Cowan, T. Autrey, C. Krasic, in Advances in Conceptual Modeling Standard Vol. 1362, IEEE Computer for 2D and 3D Environments,” IEEE C. Pu, & J. Walpole, “Fast Concurrent (ER ‘99), Volume 1727, Lecture Notes Society, 1997. Computer Graphics and Applications, Dynamic Linking for an Adaptive in Computer Science, pages 264-280, R. Fairley, “Standard for Software pp.10-13, July/August 1999. Operating System,” in The International Conference on Configurable Distributed November 1999. Project Management Plans,” IEEE S. Kumar, P. Cohen, & H. Levesque, Systems (ICCDS’96), Annapolis, MD, L. Delcambre & E. Ecklund, “A Standard, Vol. 1058, IEEE Computer “The Adaptive Agent Architecture: 1996. Behaviorally Driven Approach to Society, 1997. Achieving Fault-Tolerance Using Object-Oriented Analysis and Design R. Fairley, “Risk-Based Cost Persistent Broker Teams.” To appear C. Pu, T. Autrey, A. Black, C. Consel, with Object-Oriented Data Modeling,” Estimation,” Proceedings of the 11th in The Fourth International Conference C. Cowan, J. Inouye, L. Kethana, J. in Object-Oriented Data Modeling, COCOMO Users Group, Los Angeles, on Multi-Agent Systems (ICMAS 2000), Walpole, & K. Zhang, “Optimistic M. Papazouglu, S. Spaccateria, & Z. CA, November 1996. Boston, MA, USA, (Acceptance rate Incremental Specialization: Tari (Eds), MIT Press, 1999. 20%), July 7-12, 2000. Streamlining a Commercial Operating R. Fairley, “Some Hard Questions System,” in Proceedings of the 15th for Software Engineering Educators,” ACM Symposium on Operating Systems keynote presentation, CSEE 95 Principles (SOSP’95), Copper Proceedings, ACM Conference on Mountain, Colorado, 1995. Software Engineering Education, New Orleans, March 1995. 38 FACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

WU-CHANG FENG WU-CHI FENG PETER A. HEEMAN MICHAEL JOHNSTON Assistant Professor Associate Professor Assistant Professor and (on leave 2001-02) Ph.D., Computer Science Ph.D., Computer Science Ph.D., Computer Science Assistant Research Professor University of Michigan, 1999 University of Michigan, 1996 University of Rochester, 1997 Ph.D., Linguistics, University of [email protected] [email protected] [email protected] California at Santa Cruz, 1994 [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Scalable Internet systems, Internet Networking, multimedia systems, Spontaneous speech recognition, congestion control and queue multimedia networking, video modeling disfluencies and Natural language processing, management, wireless networking, coding, middleware services, and intonation, dialogue management, human-computer interaction, programmable network massively scalable streaming collaboration, spoken dialogue multimodal interfaces, spoken infrastructure. infrastructures. systems, natural language dialogue systems, syntax, processing. semantics, and pragmatics of REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS human language, computational W. Feng, D. Kandlur, D. Saha, K. Shin, Guohong Cao, Wu-chi Feng, REPRESENTATIVE PUBLICATIONS models of phonology, morphology, “Blue: An Alternative Approach to Mukesh Singhal, Online VBR Video P. Heeman & J. Allen, “Improving and the lexicon, natural Active Queue Management,” NOSSDAV Traffic Smoothing, to appear Computer Robustness by Modeling Spontaneous language understanding and 2001, June 2001. Communications. Speech Events,” in J. Junqua and computational semantics. W. Feng, D. Kandlur, D. Saha, K. Shin, Wu-chi Feng, Ming Liu, Extending G. van Noord (Ds.), Robustness in lan- “Stochastic Fair Blue: A Queue Critical Bandwidth Allocation guage and speech technology, Kluwer REPRESENTATIVE PUBLICATIONS Academic Publishers, 2000. Management Algorithm for Enforcing Techniques for Stored Video Delivery M. Johnston, P. Cohen, D. Mcgee, Fairness,” INFOCOM 2001, April 2001. Across Best-Effort Networks, to K. Ward & P. Heeman, “Acknowledgments S.L. Oviatt, J.A. Pittman, I. Smith, appear International Journal of W. Feng, D. Kandlur, D. Saha, K. Shin, in Human-Computer Interaction,” in “Unification-based Multimodal Communication Systems. “A Self-Configuring RED Gateway,” Proceedings of the 1st Conference of Integration,” Proceedings of the 35th INFOCOM 1999, May 1999. Ali Saman Tosun, Wu-chi Feng, the North American Chapter of the Annual Meeting of the Association for Lightweight Security Mechanisms for Association for Computational Computational Linguistics, Madrid, W. Feng, D. Kandlur, D. Saha, K. Shin, Wireless Video Transmission, in Linguistics, Seattle, May 2000. Spain, 281-288, 1997. “Adaptive Packet Marking for Proceedings of the IEEE International Maintaining End-to-End Throughput in P. Heeman, “Modeling Speech Repairs P. Cohen, M. Johnston, D. Mcgee, Conference on Information Technology: a Differentiated Services Internet,” and Intonational Phrasing to Improve S.L. Oviatt, J.A. Pittman, I. Smith, L. Coding and Computing 2001, Las Vegas, IEEE/ACM Transactions on Networking, Speech Recognition,” in IEEE Workshop Chen, & J. Clow, “quickset: Multimodal Nevada, April 2001. v. 7, n. 5, October 2001. on Automatic Speech Recognition and interaction for distributed Ali Saman Tosun, Wu-ch Feng, On Understanding, Keystone, Colorado, applications,” Proceedings of the Fifth W. Feng, D. Kandlur, D. Saha, K. Shin, Improving Quality of Video for H.263 December 1999. ACM International Multimedia “Understanding and Improving TCP over Wireless CDMA Networks, in Conference, CM Press, New York, 1997. Performance over Networks with P. Heeman & J. Allen, “Speech Proceedings of the IEEE Wireless Minimum Rate Guarantees,” IEEE/ACM Repairs, Intonational Phrases and M. Johnston, “The Telic/Atelic Communications and Networking Transactions on Networking, Vol. 7, No. Discourse Markers: Modeling Distinction and the Individuation of Conference, Chicago, Illinois, 2, pp. 173-187, April 1999. Speakers’ Utterances in Spoken Quantificational Domains,” in Empirical September 2000. Dialog,” Computational Linguistics, Issues in Formal Syntax and Semantics: Amit Agarwal, Wu-chi Feng, Christine Vol. 25-4, 1999. Selected Papers from the Colloque de Wolfe, A Multi-Differential Video Coding P. Heeman, “POS Tags and Decision Syntaxe et de Sémantique de Paris Algorithm for Robust Video Trees for Language Modeling,” in (CSSP 95), Daniéle Godard and Francis Conferencing, in Proceedings of the Proceedings of the Joint SIGDAT Corblin (Eds.). Peter Lang, Bern, 269- SPIE Voice, Video, and Data Conference on Empirical Methods in 290, 1997. Communications Conference, Boston, Natural Language Processing and Very J. Pustejovsky, B. Boguraev, M. Massachusetts, November 2000. Large Corpora, College Park, Maryland, Verhagen, P. Buitelaar & M. Johnston, Ali Saman Tosun, Amit Agarwal, Wu- June 1999. “Semantic Indexing and Typed chi Feng, Providing Efficient Support P. Heeman, M. Johnston, J. Denney Hyperlinking,” in Proceedings of the for Lossless Video Transmission and & E. Kaiser, “Beyond Structured AAAI Spring Symposium on Natural Playback, in 10th International Dialogues: Factoring Out Grounding,” Language Processing for the World Workshop on Network and Operating in Proceedings of the Internatial Wide Web, American Association for Systems Support for Digital Audio and Conference on Spoken Language Artificial Intelligence, 1997. Video, Chapel Hill, North Carolina, Processing (ICSLP-98), Sydney, M. Johnston & F. Busa, “Qualia June 2000. Australia, December 1998. Structure and the Compositional P. Heeman & G. Damnati, “Deriving Interpretation of Compounds,” in Phrase-based Language Models,” IEEE Proceedings of ACL SIGLEX Workshop Workshop on Speech Recognition and 1996: Breadth and Depth of Semantic Understanding, Santa Barbara, Lexicons, Association for Computational California, December 1997. Linguistics, 1996.

39 CSE | COMPUTER SCIENCE AND ENGINEERING | 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 Functional programming, program Functional programming languages, Machine learning including: and implementation; programming transformation, domain-specific semantics-based program analysis, neural networks, local and paradigms; module and component languages, program verification, program transformation, and mixture models, stochastic systems; type theory; semantics; high-confidence software partial evaluation. learning, model complexity, and program transformation invariance; applications to signal and analysis. REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS compression, sensor fusion, and R. B. Kieburtz, Real-time Reactive J. Lewis, M. Shields, E. Maijer, anomaly detection, adaptation in REPRESENTATIVE PUBLICATIONS Programming for Embedded & J.Launchbury, “Implicit Parameters,” biological systems. Mark P. Jones , Type Classes with Controllers, (QAPL 2001) Implicit Parameters, ACM Principles of Functional Dependencies, in September 2001. Programming Languages, 2000. REPRESENTATIVE PUBLICATIONS Proceedings of the 9th European R. B. Kieburtz, A Logic for J. Matthews & J. Launchbury, “ R. Sharma, T.K. Leen, and M. Pavel, Symposium on Programming, ESOP Rewriting Strategies, (Strategies ë01) Elementary Microarchitecture Algebra,” “Bayesian Image Sensor Fusion Using 2000, Berlin, Germany, March 2000, June 2001. Computer Aided Verification, 1999. Local Generative Models,” Optical Springer-Verlag LNCS 1782. Engineering, 2001, in press. R. B. Kieburtz, Defining and J. Launchbury, J. Lewis, & B. Cook. “ M.P. Jones, “First-class Polymorphism Implementing Closed Domain-Specific On embedding a microarchitecture C. Archer and Todd K. Leen, “The with Type Inference,” in Proceedings of Languages, (SAIG 00), design language within Haskell,” Coding Optimal Transform,” in Data the Twenty Fourth Annual ACM September 2000. International Conference on Functional Compression Conference 2001, IEEE SIGPLAN-SIGACT Symposium on R. B. Kieburtz, Taming Effects with Programming. ACM, 1999. Computer Society Press, 2001. Principles of Programming Languages, Monadic Typing, Richard Kieburtz, in Paris, France, Jan. 15-17, 1997. J. Launchbury & A. Sabry, C. Archer and T.K. Leen, “From Proc.3rd International Conf. on “Axiomatization and Type Safety Mixtures of Mixtures to Adaptive M.P. Jones, “Using Parameterized Functional Programming, ACM Press, of Monadic State,” Proc. ACM Transform Coding,” in T. Leen, Signatures to Express Modular April 1998. International Conference on Functional T. Dietterich, and V. Tresp (eds.), Structure,” in Proceedings of R. B. Kieburtz, Reactive Functional Programming, 1997. Advances in Neural Information the Twenty Third Annual ACM Programming, in PROCOMET’98, Processing Systems 13, The MIT SIGPLAN-SIGACT Symposium on J. Launchbury & R. Paterson, pp. 263-284, Chapman and Hall, Press, 2001. Principles of Programming Languages, “Parametricity and Unboxing with June 1998. St. Petersburg Beach, Florida, Unpointed Types,” Proc. European R. Sharma, T.K. Leen & M. Pavel, Jan. 21-24, 1996. R.B. Kieburtz, L. McKinney, J. Bell, Symposium on Programming, “Probabilistic Image Sensor Fusion,” J. Hook, A. Kotov, J. Lewis, D. Oliva, Linkoping, 1996. in Advances in Neural Information M.P. Jones, “Simplifying and T. Sheard, I. Smith & L.Walton, “A Processing Systems 11, Kearn, Solla, Improving Qualified Types,” in J. Launchbury & S.P. Jones, “State Software Engineering Experiment in Cohn (Eds.), The MIT Press, 1999. proceedings of FPCA ‘95: Conference in Haskell,” J. Of Lisp and Symbolic Software Component Generation,” in on Functional Programming Languages Computation, December 1995. W. Wei, T. Leen & E. Barnard, Proceedings of the 18th International “A Fast Histogram-Based Post-proces- and Computer Architecture, La Jolla, J. Launchbury & S.P. Jones, “Lazy Conference on Software Engineering, sor that Improves Posterior Probability CA, June 1995. Functional State Threads,” in Proc. SIG- Berlin, March 1996. Estimates,” Neural Computation, M.P. Jones, “A system of constructor PLAN Programming Languages Design R.B. Kieburtz, F. Bellegarde, J. Bell, Vol. 11, No. 5, 1999. classes: overloading and implicit and Implementation, Orlando, FL, 1994. J. Hook, J. Lewis, D. Oliva, T. Sheard, T.K. Leen, B. Schottky, & D. Saad, higher-order A. Gill, J. Launchbury & S.P. Jones, L. Walton & T. Zhou,” Calculating “Optimal Asymptotic Learning Rates: “A Short Cut to Deforestation,” in polymorphism,” Journal of Functional Software Generators from Solution Macroscopic Versus Microscopic Proc. SIGPLAN/SIGARCH Functional Programming, 5, 1, Cambridge Specifications,” TAPSOFT ‘95, Springer- Dynamics,” Physical Review, E-59, Programming and Computer Architecture, University Press, January 1995. Verlag, series LNCS, 915, 546, 1995. 985-991, 1999. Copenhagen, Denmark, 1993. S. Liang, P. Hudak, & M.P. Jones, R.B. Kieburtz, “Programming with T.K. Leen, “Exact and Perturbation J. Launchbury, “A Natural Semantics “Monad Transformers and Modular Algebras,” Advanced Functional Solutions for the Ensemble Dynamics,” for Lazy Evaluation,” in Proc. SIGPLAN Interpreters,” in Conference Record of Programming, E. Meijer & J.Jeuring in Online Learning in Neural Networks, Principles of Programming Languages, POPL’95: 22nd ACM SIGPLAN-SIGACT (Eds.), Springer-Verlag, Series LNCS, The Newton Institute Series, D. Saad Charleston, SC, 1993. Symposium on Principles of Vol. 925, 1995. (Ed.), Cambridge University Press, Programming Languages, San R.B. Kieburtz, “Results of the SDRR J. Hughes & J. Launchbury, Cambridge, 1998. Francisco, CA, January 1995. “Projections for Polymorphic First- Validation Experiment,” Pacific T.K. Leen, B. Schottky & D. Saad, Order Strictness Analysis,” in M.P. Jones, Qualified Types: Theory Software Research Center Software “Two Approaches to Optimal Mathematical Structures in Computer and Practice, Cambridge University Design for Reliability and Reuse: Annealing,” in Advances in Neural Science, 2, 301, C.U.P., 1992. Press, November 1994. Phase I Final Scientific and Technical Information Processing Systems 10, Report, Vol. VI, CDRL No. 0002.11, J. Hughes & J. Launchbury, The MIT Press, 1998. February 1995. “Relational Reversal of Abstract Interpretation,” in Journal of Logic and Computation, 2(4), 465, O.U.P., 1992. 40 FACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

DAVID MAIER JOHN E. MOODY SHARON L. OVIATT CALTON PU Professor Professor Professor Professor Ph.D., Electrical Engineering Ph.D., Theoretical Physics Co-Director for Center for Ph.D., Computer Science and Computer Science Princeton University, 1984 Human-Computer Communication University of Washington, 1986 Princeton University, 1978 [email protected] Ph.D., Experimental Psychology [email protected] [email protected] University of Toronto, 1979 RESEARCH INTERESTS [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Computational finance, Transaction processing, Database systems (including time series analysis, RESEARCH INTERESTS distributed databases, scientific object-oriented database analysis of financial markets, Multimodal and spoken language databases, parallel and distributed management systems, query forecasting, and statistical systems, modality effects in operating systems. processing, scientific information learning theory and algorithms. communication (speech, writing, management, superimposed Applications of machine keyboard, etc.), communication REPRESENTATIVE PUBLICATIONS information and net data learning to problems models, telecommunications L. Liu & C. Pu, “An Adaptive Object- management), object-oriented and in finance, economics and and technology-mediated Oriented Approach to Integration and logic programming languages, the sciences. communication, mobile and Access of Heterogeneous Information algorithms, survivability of interactive systems, human- Sources,” International Journal on Distributed and Parallel Databases, information systems, and health REPRESENTATIVE PUBLICATIONS computer interaction, 5(2), April 1997. information technology. Learning to Trade via Direct empirically based design and K.L. Wu, P.S. Yu & C. Pu, “Divergence Reinforcement, John Moody and evaluation of human-computer Control for Epsilon-Serializability,” REPRESENTATIVE PUBLICATIONS Matthew Saffell, IEEE Transactions interfaces, cognitive science, on Neural Networks, Vol. 12, No. 4, IEEE Transactions on Knowledge J. Shanmugasundaram, K. Tufte, and research methodology. July 2001. and Data Engineering, 9(2), D. DeWitt, J. Naughton, D. Maier. March/April 1997. Architecting a Network Query Engine Term Structure of Interactions of REPRESENTATIVE PUBLICATIONS J. Biggs, C. Pu, A. Groeninger & for Producing Partial Results. In The Foreign Exchange Rates, John Moody S. L. Oviatt, ìMultimodal Input and P.E. Bourne, “pdbtool: An Interactive World Wide Web and Databases (Third and Howard Yang, in Computational Output, Handbook of Human-Computer Browser and Geometry Checker for International Workshop WebDB 2000), Finance 1999, edited by Y. S. Abu- Interaction, (ed. By J. Jacko & A. Protein Structures,” Journal of Applied Lecture Notes in Computer Science, Mostafa, B. LeBaron, A. W. Lo, and Sears), Lawrence Erlbaum Assoc: Crystallography, 29(4), 1996. Vol. 1997, Springer-Verlag, 2001. A. S. Weigend, Cambridge, MA: Mahwah, New Jersey, invited book MIT Press, 2000. L. Liu, C. Pu, R. Barga & T. Zhou, L. Delcambre, D. Maier, S. Bowers, chapter to appear in 2002. “Differential Evaluation of Continual L. Deng, M. Weaver, P. Gorman, J. Ash, Predicting Blood Glucose Metabolism S. L. Oviatt, P. R. Cohen, L. Wu, J. Queries,” Proceedings of the 16th M. Lavelle, and J. Lyman. Bundles in in Diabetics -- A Machine Learning Vergo, L. Duncan, B. Suhm, J. Bers, T. International Conference on Distributed captivity: An application of Solution, Volker Tresp and John Moody, Holzman, T. Winograd, J. Landay, J. Computing Systems, Hong Kong, superimposed information. Proceedings IEEE Transactions on BioMedical Larson, & D. Ferro. ìDesigning the user May 1996. of the IEEE International Conference Engineering, 1999. interface for multimodal speech and on Data Engineering, Heidelberg, K. Ramamrithan & C. Pu, “A Formal Performance Functions and gesture applications: State-of-the-art Germany, April 2001. Characterization of Epsilon Reinforcement Learning for Trading systems and research directions. Serializability,” IEEE Transactions on Gorman, J. Ash, M. Lavelle, J. Lyman, Systems and Portfolios, John Moody, Human Computer Interaction, 15(4), Knowledge and Data Engineering, 7(6), L. Delcambre, D. Maier, S. Bowers and Lizhong Wu, Yuansong Liao and 263-322, 2000. (to be reprinted in J. December 1995. M. Weaver. ìBundles in the wild: Tools Matthew Saffell, Journal of Forecasting, Carroll (Ed.) Human-Computer for managing information to solve vol. 17, pp. 441-470, 1998. Interaction in the New Millennium, C. Pu, T. Autrey, A.P. Black, C. Consel, problems and maintain situation aware- High Frequency Foreign Exchange Addison-Wesley Press: Boston, 2001). C. Cowan, J. Inouye, L. Kethana, ness. Library Trends 49(2), Fall 2000. J. Walpole & K. Zhang, “Optimistic Rates: Price Behavior Analysis and S. L. Oviatt, ìMultimodal System Incremental Specialization: L. Fegaras and D. Maier. Optimizing `True Price' Models, John Moody and Processing in Mobile Environments, Streamlining a Commercial Operating object queries using an effective calcu- Lizhong Wu, Chapter 2 of Nonlinear Proceedings of the Thirteenth Annual System,” Proceedings of the Fifteenth lus. ACM Transactions on Database Modelling of High Frequency Financial ACM Symposium on User Interface Symposium on Operating Systems Systems 25(4), December 2000. Data, Christian Dunis and Bin Zhou, Software Technology (UIST’2000), 21- editors, Wiley Financial Publishing, Principles, December 1995. Q. Wang, D. Maier and L. Shapiro. The 30, ACM: New York, N.Y., 2000. London, 1998. R. Barga & C. Pu, “A Practical and hybrid technique for reference materi- S. L. Oviatt, ì Multimodal Signal Modular Implementation Technique of alization in object query processing. Stochastic Manhattan Learning: Time- Processing in Naturalistic Noisy Extended Transaction Models,” Proceedings of the 4th International evolution Operator for the Ensemble Environments. In B. Yuan, T. Huang & Proceedings of the 21st International Conference on Database Engineering Dynamics, Todd Leen and John Moody, X. Tang (Eds.), Proceedings of the Conference on Very Large Data Bases, and Applications (IDEAS2000), Tokyo, Physical Review E, 1997. International Conference on Spoken Zurich, Switzerland, September 1995. Japan, September 2000. Smoothing Regularizers for Projective Language Processing (ICSLP’2000), Vol. Basis Function Networks, John Moody 2, (pp. 696-699). Beijing, China: K. Ramamrithan & C. Pu, “A Formal and Thorsteinn Rognvaldsson, in Chinese Friendship Publishers. Characterization of Epsilon Serializability,” IEEE Transactions on Advances in Neural Information S. L. Oviatt, ìTaming Recognition Knowledge and Data Engineering, 7(3), Processing Systems 9, M.C. Mozer, Errors with a Multimodal Architecture, June 1995. M.I. Jordan and T. Petsche, eds, MIT Communications of the ACM, 43 (9), Press, Cambridge, 1997. 45-51, September 2000 (special issue on “Conversational Interfaces”). 41 CSE | COMPUTER SCIENCE AND ENGINEERING | FACULTY

TIM SHEARD DAVID C. STEERE JONATHAN WALPOLE Associate Professor, Director Assistant Professor Professor Pacific Software Research Center Ph.D., Computer Science Ph.D., Computer Science Ph.D., Computer and Carnegie Mellon University, 1997 University of Lancaster, 1987 Information Science [email protected] [email protected] University of Massachusetts at Amherst, 1985 RESEARCH INTERESTS RESEARCH INTERESTS [email protected] Operating systems, mobile Adaptive systems software and its computing, distributed application in distributed, mobile, RESEARCH INTERESTS information systems. and multimedia computing Functional programming, software environments and environmental specification, program generation, REPRESENTATIVE PUBLICATIONS observation and forecasting meta-programming and staging. D.C. Steere, A. Goel, J. Gruenberg, D. systems. Quality of service McNamee, C. Pu, & J. Walpole, “A specification, adaptive resource REPRESENTATIVE PUBLICATIONS Feedback-driven Proportion Allocator management and dynamic for Real-Rate Scheduling,” Operating T. Sheard. “Accomplishments specialization for enhanced Systems Design and Implementation, and Research Challenges in Meta- February 1999. performance, survivability and Programming.” Invited talk, Second evolvability of large software J. Walpole, C. Krasic, L. Liu, D. Maier, International Workshop on Semantics, systems. Applications, and Implementation of C. Pu, D. McNamee, & D.C. Steere, Program Generation (SAIG 2001). “Quality of Service Semantics for LNCS 2196. Florence, Italy, Multimedia Database Systems,” to REPRESENTATIVE PUBLICATIONS September 2001. appear in Proceedings Data Semantics K. Li, C. Krasic, J. Walpole, 8: Semantic Issues in Multimedia M. Shor, C.Pu, The Minimal Buffering T. Sheard. “Generic Unification via Systems IFIP TC-2 Working Conference, Requirements of Congestion Controlled Two-Level Types and Parameterized Rotorua, New Zealand, January 1999. Interactive Multimedia Applications, in Modules.” Sixth ACM SIGPLAN Proceedings of the 8th International International Conference on Functional D. McNamee, D. Revel, D.C. Steere, & Workshop on Interactive Distributed Programming (ICFP’01). ACM Press. J. Walpole, “Adaptive Prefetching for Multimedia Systems, iDMS 2001, Florence, Italy, September 3-5, 2001. Device Independent File I/O,” in Proceedings of Multimedia Computing Lancaster, UK, September 2001. Also T. Sheard, Z. Benaissa, & E. Pasalic. and Networking 1998 (MMCN98), published in Springer Verlag’s Lecture “DSL Implementation Using Staging and January 1998. Notes in Computer Science Series. Monads,” Usenix, Second Conference on Black, J. Huang, J. Walpole, Reifying Domain Specific Languages. Austin, D.C. Steere, “Exploiting the Non- Communication at the Application Texas. October 3-5, 1999. Determinism and Asynchrony of Set Iterators to Reduce Aggregate File I/O Level, in Proceedings of the W. Taha, Z. Benaissa, & T. Sheard. Latency,” in Proceedings of the 16th International Workshop on Multimedia “Multi-Stage Programming: acmsymposium on Operating Systems Middleware, Ottawa, Canada, October Axiomatization and Type Safety,” Principles, October 1997. 2001. Also available as OGI Technical 25th International Colloquium on Report CSE-01-006, June 2001. Automata, Languages and D.C. Steere & J. Wing, “Specifying C. Krasic, J. Walpole, Priority- Programming, July 1998. Weak Sets,” in Proceedings of the 15th International Conference on Distributed Progress Streaming for Quality- M. Shields, T. Sheard, & S. Peyton Computing Systems, 414-421, Adaptive Multimedia, in Proceedings Jones, “Dynamic Typing as Staged Type Vancouver, BC, June 1995. of the ACM Multimedia Doctoral Inference,” ACM-SIGPLAN-SIGACT Symposium, Ottawa, Canada, Symposium on Principles of Program- M. Satyanarayanan, H.H. Mashburn, October 2001. ming Languages (POPL ‘98), San Diego, P. Kumar, D.C. Steere & J.J. Kistler, R. Koster, A. Black, J. Huang, CA, January 1998. “Lightweight Recoverable Virtual Memory,” ACM Transactions on J. Walpole, C. Pu, Thread Transparency T. Sheard, “A Type-Directed, On-Line, Computer Systems, 12(1), 33-57, in Information Flow Middleware, Partial Evaluator for a Polymorphic February 1994. Corrigendum: ACM Middleware 2001-IFIP/AcM Language,” ACM-SIGPLAN Conference Transactions on Computer Systems, International Conference on Distributed on Partial Evaluation and Semantics- 12(2), 165-172, May 1994. Systems Platforms, Heidelberg, Based Program Manipulation, Germany, November 2001. Also Amsterdam, June 1997. M. R. Ebling, L.B. Mummert & D.C. available as OGI Technical Report Steere, “Overcoming the Network W. Taha & T. Sheard, “Multi-Stage CSE-01-004. Bottleneck in Mobile Computing,” in Programming with Explicit Proceedings of the First Workshop on J. Huang, A. Black, J. Walpole, Annotations,” ACM-SIGPLAN Mobile Computing Systems and C. Pu, ìInfopipes ñ An Abstraction for Conference on Partial Evaluation and Applications, 34-36, Santa Cruz, CA, Information Flow, in proceedings of the Semantics-Based Program December 1994. ECOOP Workshop on the Next 700 Manipulation, Amsterdam, June 1997. Distributed Object Systems, Budapest, Hungary, June 2001.

42 FACULTY | COMPUTER SCIENCE AND ENGINEERING | CSE

JOINT FACULTY PART-TIME FACULTY ADJUNCT FACULTY MR. SANJEEV QAZI Intel Corporation DR. ANTONIO BAPTISTA DR. FRANCOISE BELLEGARDE DR. LOUGIE ANDERSON MR. DAN SAWYER Environmental Science University of Franche Gemstone Systems Inc. and Engineering Comte, France MR. BRUCE SCHAFER OGI School of Science MR. JON BATCHELLER Oregon College of Engineering and Engineering Synopsys, Inc. DR. CHARLES CONSEL and Computer Science University of Bordeaux DR. FRANCOISE BELLEGARDE MR. ROBERT BAUER MR. RANDAL SCHWARTZ University of Franche Rational Software Corp. DR. DAVID G. NOVICK Stonehenge Consulting Comte, France University of Texas, El Paso DR. C. MIC BOWMAN DR. RICHARD SPROAT DR. DAN HAMMERSTROM Intel Corporation AT&T Labs, New Jersey Electrical and DR. TED BRUNNER Computer Engineering MS. ELISABETH SULLIVAN OGI School of Science Tektronix Inc. TruSec Solutions and Engineering DR. SHANWEI CEN DR. ANDREW TOLMACH DR. HYNEK HERMANSKY Tektronix Inc. Portland State University Electrical and DR. CHRISTOPHER DUBAY Computer Engineering MR. PERRY WAGLE OGI School of Science Oregon Health & Computer Science and Engineering Science University and Engineering OGI School of Science DR. JODY HOUSE DR. EARL ECKLUND & Engineering Electrical and Objective Technology Group Computer Engineering DR. MAZIN YOUSIF OGI School of Science MS. ANNIE GROENINGER Intel Corporation and Engineering Performance Logic, Inc.

DR. MISHA PAVEL MR. ROY HALL Electrical and Crisis in Perspective Computer Engineering OGI School of Science DR. DAVID HANSEN and Engineering George Fox University

DR. LEONARD SHAPIRO DR. SEBASTIEN HILY Department of Computer Science Intel Corporation Portland State University DR. HOLLY JIMISON DR. XUBO SONG Oregon Health & Electrical and Science University Computer Engineering OGI School of Science DR. JAMES LARSON and Engineering Intel Corporation

DR. ANDREW TOLMACH MR. SCOTT LYMAN Department of Computer Science Merix Corporation Portland State University DR. ERIC MEIJER DR. JAN P. H. VAN SANTEN Microsoft Electrical and Computer Engineering MR. MARK MORRISSEY OGI School of Science Portland State University and Engineering DR. GIL NEIGER DR. ERIC WAN Intel Corporation Electrical and Computer Engineering DR. HARRY PORTER OGI School of Science Consultant and Engineering

DR. YONGHONG YAN Electrical and Computer Engineering OGI School of Science and Engineering 43 The primary mission of the Cypress, Maxim and Triquint. There is one center in this area, the Center for Biologically Department DEPARTMENT OF ELECTRICAL AND Inspired Information Engineering (CBIIE). COMPUTER ENGINEERING is to provide of Electrical The Biomedical Engineering (BME) program quality graduate education, research concentrates on Biomedical Optics, Tissue and Computer and technology transfer in the areas Engineering, and Medical Informatics. of Intelligent Signal Processing, Biomedical Optics develops optical Engineering technologies for imaging and characterizing Semiconductor Materials and tissues and laser-tissue interactions for www.ece.ogi.edu Devices, Computer and Systems machining tissues and surgical techniques. Engineering, and Biomedical Faculty are emphasizing tissue engineering with research at the affiliated Oregon DEPARTMENT HEAD Engineering. Medical Laser Center (OMLC). Several Dan Hammerstrom We currently have a very successful and people are also faculty at Oregon Health & (503) 748-4037 well-focused program in Intelligent Signal Science University (OHSU) with a laboratory E-mail: [email protected] at OGI where students conduct research that Processing, which includes speech DEPARTMENT ADMINISTRATOR interfaces with medical clinicians and recognition and synthesis, image processing, Don Johansen investigators. adaptive filtering and control, and (503) 748-1315 anthropomorphic signal processing. The The department offers a wide variety of E-mail: [email protected] department has two centers in this area, the formal courses in core areas as well as in ACADEMIC COORDINATOR Center for Information Technology (CIT) and specific research areas. The curriculum for Barbara Olsen the Center for Spoken Language each student is determined in part by his or (503) 748-1418 Understanding (CSLU). Close interaction with her academic background and interest, and is E-mail: [email protected] the high-tech industry is a critical element of set after discussion with a faculty advisor. the activities reflected in numerous ADMINISTRATIVE COORDINATOR The major fields of research activity in the collaborative projects funded by industrial Joan Sims department are: organizations including Intel, Qualcomm, and (503) 748-1144 many others. • Advanced Lithography E-mail: [email protected]

The Semiconductor Materials and Devices • Atmospheric Optics GENERAL INQUIRIES program has many new people and is in the • Biomedical Engineering (503) 748-1130 middle of a rebuilding process. We have an E-mail: [email protected] excellent group, and investment includes a • Biosensors 5-year, $1 million Intel grant. We are creating • Digital Signal Processing a number of new laboratories. Although some • Display Technology including Thin Film semiconductor processing will be done, most Transistors and Phosphors of the effort and laboratory space will be • Electro-Optic Systems devoted to education and to semiconductor materials and device characterization, • Human Information Processing including high-speed devices. These, plus our • Image and Video Processing existing electron microscopy facility, are of • Man-Machine Interfaces value to local industry. • MEMS Computer and Systems Engineering is focused primarily on research into hardware • Neural Networks and systems for implementing intelligent • Optical Remote Sensing signal processing and robotic control. This • Pattern Recognition process also includes the VLSI design of specialized devices for computation and • Processing for Ultra Shallow Device Technology intelligent sensing. Computational • Semiconductor Electronic Devices neuroscience plays an important part of this • Semiconductor Materials and Processing work. A new laboratory with 8 stations for DSP and FPGA programming is available, • Speech Recognition, Enhancement, and Synthesis with help from Intel and Altera, to support Jinshan Huo is a Ph.D. student and Intel education and research in this area. This • Systems Dynamics intern whose interests involve copper area has several adjunct faculty from • Technology Transfer interconnects for microelectronic device companies such as Intel, RadiSys, IDT, and materials characterization. ECE | ELECTRICAL AND COMPUTER ENGINEERING

• Transient Thermal Processing electrical engineering programs are broad and a minimum of 8 credits of research • VLSI/FPGA Design and diverse, students with undergraduate (ECE610). The research project is more degrees in applied mathematics as well as limited in scope than a thesis and may • VLSI Architecture for Intelligent Computing other branches of engineering are encouraged include experimental work, a critical Students may become involved in relatively to apply. literature review, or a specific contribution to fundamental investigations (such as a larger project. Completion of the non-thesis OGI offers the Ph.D. in Electrical atmospheric effects on laser beams, and project requires the submission of a written Engineering. Students must have a Master of semiconductor materials characterization and report to satisfy the research grade Science degree acceptable to the ECE processing) or in advanced engineering requirements. The student is encouraged to Department to be considered for the Ph.D. applications (such as video display work with a faculty advisor in formulating an program. The M.S. degree may be from OGI technology or signal/image processing). In all appropriate project. or another institution of higher education. cases, the emphasis is on scientific and THESIS OPTION engineering investigations having well-defined goals and real utility in an atmosphere DEGREE REQUIREMENTS The M.S. thesis option requires successful completion of a minimum of 32 credits of resembling that of a working research and MASTER OF SCIENCE (M.S.) PROGRAM development laboratory. The academic graded course work and a minimum of 16 The M.S. program in Electrical Engineering is program, while rigorous, is innovative and credits of graded research (ECE700). The designed to enable professionals or recent individually planned to meet each student’s thesis is an original independent work graduates to adapt quickly to the changing needs. The limited number of students in resulting in publication. The student will work needs of their fields. ECE’s M.S. program residence assures close attention to each with a faculty member to select courses and offers three degree options for full-time and student and progress at a rate determined by design an appropriate thesis research part-time students. The M.S. degree requires the student’s ability and effort. program. A thesis committee is assigned to successful completion of 48 credits and may guide and advise the research program. DEPARTMENT SEMINARS be obtained with a non-thesis option, a non- Completion of the M.S. thesis requires the The department and other local educational thesis project option, or a thesis option. All submission of the written thesis and a and corporate organizations host invited talks courses, non-thesis research, and thesis successful oral defense. Thesis research and seminars on topics of interest in the field research must be taken for graded credit to credits earned towards an M.S. degree must of electrical engineering. M.S. students are be counted towards the ECE M.S. degree. be graded. required to obtain at least three credits of Courses taken outside of the ECE Department SUMMER PROJECTS seminar to graduate. Seminar schedules are must also be taken for graded credit; Pass/No posted each quarter. Additionally, the ECE Pass is not acceptable. A minimum grade Although not required, students should Department in conjunction with Portland point average of 3.0 must be maintained seriously consider taking at least one project State University’s Department of Electrical throughout the degree program. Students’ course for the M.S. degree. Because most and Computer Engineering sponsor the course of study should be reviewed and faculty use the summer to do research, it is Portland Area Semiconductor Seminar Series approved by a faculty advisor. Students are an ideal time to do a project. In addition, (PASSS). These seminars offer an opportunity limited to 12 credits per quarter unless a there are often summer internships available to meet leading local and nationally waiver is obtained from their advisor. at local companies, which also qualify. The department is not required to provide recognized EE professionals and learn about NON-THESIS OPTION the latest technical advancements in the projects for students, but usually there are The non-thesis option requires completion of high-technology industry. many opportunities. Projects can involve real a minimum of 48 credits of graded course implementation and often are done in a team work. While students are strongly encouraged setting, which make them an ideal ADMISSIONS REQUIREMENTS to focus on courses in ECE, students may preparation for a career in engineering. Admission requirements are the same as the take up to 24 credits of course work in other Projects are done as Special Topics courses, general requirements of the institution. The OGI academic departments provided the ECE 580, and they are graded. The specifics GRE is not required for the part-time courses fall within the curriculum standards of a project are the responsibility of the program or the twelve-month M.S. program. set by the ECE Department. For students sponsoring faculty member. Industrial adjunct It is recommended for M.S. students who may seeking an M.S. degree in Electrical faculty may also advise projects. want to apply for the Ph.D. at a later date. Engineering, a minimum of 24 credits must TRANSFER CREDITS The GRE is required for all applicants to the be taken from the OGI’s ECE department Ph.D. program. The TOEFL is required of all curriculum. All courses, regardless of OGI Up to 12 credits from accredited institutions international student applicants for both the department, must be taken for graded credit. may be transferred to OGI. Students may M.S. and Ph.D. programs. petition for transfer of up to 18 credits from NON-THESIS PROJECT OPTION the following institutions: Portland State Prerequisite: B.S. or M.S. in physics, applied The non-thesis project option requires University, Oregon State University, and physics, engineering physics, electrical completion of a minimum of 48 graded University of Oregon. Students petitioning for engineering, or equivalent. Since modern credits, comprising 40 credits of course work acceptance of transfer credits should provide 46 ELECTRICAL AND COMPUTER ENGINEERING | ECE

(1) written request, (2) detailed course ECE CURRICULUM FOCUS AREAS ECE500 Introduction to Electronics and Instrumentation descriptions from institution catalogs and/or Students can elect to focus exclusively within ECE525 Analytical Techniques in Statistical Signal website, and (3) original transcript verifying one area of specialization or may combine Processing & Communications credit hours and grades earned. two or more of these focus areas into a ECE529* Optical Fibers Upon approval from the department head, broader course of study. ECE532* Biomedical Optics I: Tissue Optics ECE533* Biomedical Optics II: Laser Tissue Interactions students may apply to their ECE degree a • Biomedical Engineering maximum of 21 credits from other OGI ECE534* Biomedical Optics III: Engineering Design • Communications & Networking departments towards their ECE degree. ECE551 Introduction to Digital Signal Processing Acceptance of all transfer credits will be • Computer Engineering & Design ECE552 Digital Signal Processing II subject to review and approval by the ECE • Materials, Semiconductors & Devices ECE554 Adaptive Signal Processing department’s Curriculum Committee. Transfer • Signal Processing, Speech & Imaging ECE540 Auditory and Visual Processing by Human credits will not replace the degree/credit and Machine requirement of 24 credits from OGI’s ECE Students should refer to the ECE Department’s ECE541 Speech Processing department curriculum. Cross-listed courses 12-month Curriculum Plan for the scheduled ECE542 Introduction to Image Processing may not be used as part of these 24 credits. offering of courses in the 2001/2002 ECE580-PGO Physical and Geometric Optics academic year. PH.D. PROGRAM ECE580-CLT Computational Approaches to Light Transport in Biological Tissues OGI offers a PhD degree program in BIOMEDICAL ENGINEERING ECE580-CLI Computational Approaches to Laser Electrical Engineering. Admission to the PhD Biomedical engineering is a rapidly developing Interaction with Biological Tissues program generally requires a prior M.S. in broad field of study comprising basic biology and ECE580 Optical Non-Destructive Evaluation medicine, bioinformatics, biomedical signal Electrical Engineering, Computer Engineering -ONDE or related field, whether from OGI or from processing, imaging, biomaterials, information technology and many other areas. Within the Other OGI School Courses another institution. Upon entry into the biomedical engineering program the ECE CSE514 Introduction to Database Systems program a Student Program Committee (SPC) Department, in conjunction with other departments CSE540 Neural Network Algorithms and Architectures of three faculty members is formed. The in the OGI School of Science and Engineering as student discusses feasible research areas and well as departments at the OHSU Schools of CSE544 Probability and Statistical Inference eventual research directions with the Medicine, Dentistry, and Nursing, offers students a CSE547 Statistical Pattern Recognition variety of opportunities to acquire breadth and committee and together they chart an CSE548 Statistical Computing depth of knowledge and expertise in this field. The individualized course of study to prepare the research efforts are expanding to cover an CSE564 Human-Computer Interaction student for the Qualifying Exam. increasing number of areas, including biomedical BMB534 Instrumental Methods in Biophysics I & II sensors and instrumentation, biomechanics BMB540 Advanced Molecular Biology The Qualifying Exam may be written or oral (including laser-tissue interaction and tissue BMB541 Molecular Genetics of Development or both, at the discretion of the SPC, and may engineering), intelligent biomedical signal additionally involve a formal research processing and analysis, computational ESE500 Numerical Methods proposal. It is normally taken within 12 neuroscience, biomedical image analysis, data- ESE506 Environmental Systems Analysis mining, and technology in healthcare delivery. months of enrolling in the program, and is ESE550 Environmental Microbiology Current research topics also include intelligent scheduled at any time during the year. The rehabilitation and assistive technologies for future ESE570 Principles of Toxicology and Risk Assessment amount of course work to be completed before healthcare delivery in smart homes (home health) Oregon Health & Science University School of Medicine Courses taking the Qualifying Exam is dependent on using wearable sensors and networked devices, CON621 Molecular and Cell Biology I: Topics the individual’s level of preparation at entry. exploiting intelligent data fusion and incorporating in Biochemistry the latest results in functional genomics. At minimum, 3 graded courses from OGI’s CON622 Molecular and Cell Biology II: Molecular Genetics ECE department must be successfully Because of the diversity of the field, each student is CON627 Systems Neurophysiology completed before taking the exam. encouraged to devise a program tailored to his or her specific career objectives. The available BMB610 Medical Biochemistry After the Qualifying Exam is passed, student courses include introductory courses in biology and BCH611/612 Biochemistry and Committee then work closely together to medicine, biomedical sensors and instrumentation, BCH511 Advanced Biochemistry laser-tissue interactions, biomaterials, develop a research plan specifically for the BMB618 Biochemical Properties of Proteins and biomechanics, neuroscience, molecular Protein Engineering dissertation. Ph.D. students are required to engineering, audio and video processing by humans make annual reports to the SPC on the status and machines, biomedical signal processing, BMB620 Biochemical & Biophyiscal Properties of their research, and may be called upon to biological pattern recognition and datamining, of Membranes deliver timely research presentations as the bioinformatics, and medical informatics. To be CBA610 Gross Anatomy prepared for the challenge, students are expected work progresses. The dissertation itself must AN611 Gross Anatomy to take, in addition to specific biomedical constitute a significant research contribution engineering courses, a number of basic engineering CBA611 Histology and must be of publishable quality. The Ph.D. courses in statistical signal analysis and AN613 General Histology degree is granted following the presentation recognition, digital signal processing, image CBA607 Seminar: Cancer Biology of an acceptable dissertation and successful processing, pattern recognition, databases, and information retrieval. PHC610 Pharmacology oral defense. PHY610 Human Physiology 47 ECE | ELECTRICAL AND COMPUTER ENGINEERING

PHY611 Physiology - Nervous and Cardiovascular Systems ECE551 Introduction to Digital Signal Processing ECE521* Microwave Engineering Concepts PHY612 Physiology Respiratory, Renal, and ECE557* Computer-Aided Analysis of Circuits ECE535* Thin Film Deposition and Applications in Alimentary Systems (alternating years-FY03) Semiconductor Fabrication PHY615 Physiological Instrumentation and Techniques ECE558 High Speed Interconnect Design ECE558 High Speed Interconnect Design PHY607 Seminar: Biophysical Physiology ECE559 Design with Programmable Logic ECE560 Microelectronic Device Fabrication I PHY617 Advanced Cardiovascular Physiology ECE571 Analog Integrated Circuit Design ECE561 Microelectronic Device Fabrication II MED791 Electrocardiology ECE572 Digital Integrated Circuit Design ECE562 Microelectronic Device Fabrication III NEU792 Experimental Neurology ECE573 Introduction to Computer Logic Design ECE563 Plasma Processing of Semiconductors I PTH610 General Pathology ECE574 CMOS Digital VLSI Design I ECE565 Analytical Scanning Electron Microscopy * May be offered in alternating years, ECE575 CMOS Digital VLSI Design II ECE566 Focused Ion Beam Technology beginning FY03 ECE580 Introduction to Computer Organization ECE567 Transmission Electron Microscopy -COD and Design ECE568 Failure and Reliability in Microelectronics COMMUNICATIONS AND NETWORKING ECE580-AIC Analog CMOS IC Design ECE569 Electronic Materials and Device Characterization Job opportunities in communications and computer ECE580-ACD Special Topics in Analog IC Design4 credits networking are exploding. This field is enjoying a ECE571 Analog Integrated Circuit Design renaissance due to the rapid progress of optical Other OGI School courses ECE572 Digital Integrated Circuit Design fiber technology and digital signal processing CSE521 Introduction to Computer Architecture 3 credits ECE580-FSM Fundamentals of Sensors & MEMS Fabrication techniques, and the need to move larger and larger CSE522 Advanced Computer Architecture 3 credits ECE580-ISM Introduction to Sensor Microfabrication amounts of information on a global basis. Portland State University (Lab Only) ECE525 Analytical Techniques in Statistical Signal PSU ECE510 Design for Test ECE580-MPEModern Photolithographic Engineering Processing & Communications PSU ECE672 Advanced Logic Synthesis ECE580Simulation & Modeling of VLSI Interconnect ECE526 Analog and Binary Digital -SMVI Communications Systems Oregon State University ECE580-SSE Semiconductor Sensors ECE540 Auditory and Visual Processing by Human OSU ECE619 Low Power IC Design ECE580-TP Technology of Photoresists and Machine OSU ECE527 VLSI System Design ECE541 Speech Processing * May be offered in alternating years, ECE580-CP Copper Plating ECE542 Introduction to Image Processing beginning FY03 ECE580 Microelectromechanical Systems (MEMS) -MEM ECE543 Introduction to Digital Video Processing MATERIALS, SEMICONDUCTORS & DEVICES ECE580-RFD Reliability and Failure of Device Packaging ECE544 Introduction to Signals, Systems and ECE offers a broad spectrum of courses in Information Processing semiconductor synthesis, processing, device ECE580-CCM Capstone Course: MEMS & Microsensors Project ECE550 Linear Systems physics, and integrated circuits. Courses are ECE580-MTFMechanics and Thin Films designed to prepare the student for growth areas in ECE551 Introduction to Digital Signal Processing * May be offered in alternating years, semiconductor-based technology. Specific groups of beginning FY03 ECE552 Digital Signal Processing II courses are designed to provide a strong, cohesive, ECE554 Adaptive Signal Processing and marketable body of knowledge in device SIGNAL PROCESSING, SPEECH & IMAGING processing, device physics and design, and ECE557* Computer-Aided Analysis of Circuits With rapid advances in technology, we are integrated circuit design. Course selections can be (alternating years, FY03) experiencing a paradigm shift toward information- tailored to create unique specializations that will intensive systems for sophisticated multimedia ECE580-DDC Design of Digital Communication Circuits prepare students for careers in this important telecommunication and human-machine ECE580-CN Introduction to Computer Networks technology field. interaction. This master-level program represents a ECE580-DCS Digital Fiber-Optic Communication Systems ECE507 Introduction to Electromagnetics for unique combination of traditional engineering signal processing with human information ECE580-IE Internet Engineering Modern Applications processing that prepares students for the ECE580-IVC Information Visualization and ECE508 Electromagnetics for Modern Applications II information-intensive society of the coming century. Computer Graphics ECE509 Electromagnetics for Modern Applications III Multimodal communication is an emerging ECE580 Wireless Communications Systems ECE510* Introduction to Quantum Mechanics for engineering area that comprises multiple -WCSI Electrical and Computer Engineers disciplines extending from human factors and algorithm development to network protocols and ECE580-MC Multimedia Communications ECE511* Advanced Quantum Mechanics for Electrical designing electronic devices. Existing and future and Computer Engineers ECE580-SSY Speech Synthesis multimedia applications combine audio and video * May be offered in alternating years, ECE512 Operation of Semiconductor Devices: (and other possible modalities) to extend the beginning FY03 Diodesand Bipolar Transistors capabilities of a human operator. Students benefit ECE513 Operation of Semiconductor Devices: from exposure to real problems through COMPUTER ENGINEERING AND DESIGN MOS Transistors partnerships with industry and government. Computer engineering is a hybrid program utilizing ECE514 MOSFET Modeling for VLSI Circuit Design ECE525 Analytical Techniques in Statistical Signal electrical engineering and computer science ECE515 Introduction to Semiconductors Processing & Communications courses. It involves the engineering aspects of ECE516 Fundamental Semiconductor Device Structures ECE540 Auditory and Visual Processing by Human hardware, including logic design, integrated circuit and Machine design, and computer architecture. ECE517 Advanced Semiconductor Devices: Structures & Materials ECE541 Speech Processing ECE500 Introduction to Electronics and Instrumentation ECE520* Transmission Line Theory ECE542 Introduction to Image Processing 48 ELECTRICAL AND COMPUTER ENGINEERING | ECE

ECE543 Introduction to Digital Video Processing conductor device operation, IC design, optics, trans- some linear algebra, or consent of instructor. mission lines, and antenna design. Covered are 4 credits ECE544 Introduction to Signals, Systems and waves in conductors and skin effect.Retarded poten- ECE 512 Operation of Semiconductor Devices: Diodes Information Processing tials for time-varying fields. Electromagnetics of and Bipolar Transistors. ECE545 Speech Systems lumped-element circuit theory. Plane wave propaga- Short review of semiconductor basics; metal-semi- ECE551 Introduction to Digital Signal Processing tion, reflection, and refraction. Polarization states and Stokes parameters. Analytical methods for conductor contacts and Schottky diodes; pn junction ECE552 Digital Signal Processing II boundary-value problems and numerical solution by diodes: Depletion approximation, capacitance/volt- ECE553* Control Systems: Classical, Neural and Fuzzy boundary-element method. Introductory (TEM) field age behavior and current/voltage characteristics, role of minority carrier diffusion and storage, ideal ECE554 Adaptive Signal Processing theory of transmission lines, and its relation to circuit model. Prerequisite: ECE507 and some linear and nonideal behavior, Shockley-Hall-Read recombi- ECE555 Engineering Optimization algebra or consent of instructor. 4 credits nation. Fundamentals of bipolar transistors: Ideal ECE580-SSY Speech Synthesis Shockley model, current gain, low- and high-level ECE509 Electromagnetics for Modern Applications III injection effects, transit-time concepts. Ebers-Moll ECE580-SSL Structure of Spoken Language This course covers advanced transmission line and and Gummel-Poon models. Device parameter Other OGI School courses waveguide field theory for high speed interconnects, extraction for SPICE models. 4 credits CSE540 Neural Network Algorithms and Architectures microwave and optical waveguides; resonant cavi- ECE 513 Operation of Semiconductor Devices: 3 credits ties for frequency control and lasers; and radiation MOS Transistors. CSE546 Data and Signal Compression 3 credits basics for communications and optics. Topics include TE and TM transmission-line and wave- Fundamentals: Contact potentials and semiconduc- CSE547 Statistical Pattern Recognition 3 credits guide modes. Field theory of multiple-conductor tor surfaces, analysis of the MOS capacitor, the role CSE550 Spoken Language Systems 3 credits transmission lines: Modes, coupling, crosstalk, and of oxide charge. MOSFET modeling, one-dimensional approaches based on depletion and charge sheet CSE551 Structure of Spoken Language 3 credits termination. Dielectric waveguides. Resonant cavi- ties. Radiation from antennas and apertures. approximations: Threshold voltage and body effect, CSE552 Hidden Markov Models 3 credits Additional topics as time permits, chosen from: sub-threshold behavior based on concepts of weak, * May be offered in alternating years, electromagnetic properties of materials; variational moderate, and strong inversion; ion implanted chan- beginning FY03 formulation of field problems and finite element nels; short and narrow channel effects, such as numerical solution; analytical and numerical calcu- channel length modulation, velocity saturation, effec- lation of charged-particle motion in electromagnetic tive threshold variations, series resistance effects, COURSE DESCRIPTIONS fields; suggestions of students. Prerequisite: breakdown and punch-through; device parameter extraction for SPICE models, device scaling.4 credits ECE500 Introduction to Electronics and Instrumentation ECE508 and some linear algebra or consent of Review of fundamental electronics components and instructor. 4 credits ECE 514 MOSFET modeling for VLSI circuit design design: passive components, transistor circuits, op ECE510 Introduction to Quantum Mechanics for A comprehensive study of compact models used in amps, RC circuits, frequency domain, and time Electrical and Computer Engineers circuit simulators for VLSI design. Topics covered domain response. Feedback theory, op amp limita- Courses ECE510-511 present basic quantum theory include modeling of small geometry effects, high tions, precision op amp circuits. Noise, interference, for understanding practical applications such as speed and frequency (non-quasistatic) models, grounding, and shielding. Phase-locked loops, lock- solid state devices, lasers and other optoelectronic quantum effects, substrate and gate current models in amplifiers. Practical advice on component devices, properties of electronic materials, band- for reliability simulation and device scaling issues. selection and circuit design. Equipment and circuit gap engineering, quantum effects due to shrinking IC In-depth study of parameter extraction, optimization demonstrations in class. Homework includes Pspice feature sizes, quantum-dot and quantum-well and device characterization techniques required for circuit simulation problems. 4 credits devices, and quantum computing. The first course developing compact models. Development of statistical, mismatch and noise models for analog circuit ECE507 Introduction to Electromagnetics for introduces basic concepts and results essential to design. Review of state of the art models used in Modern Applications understanding solid-state band structure, devices industry. Implementation algorithms for MOSFET This series (ECE507-509) cover essentials of elec- based on tunnelling, and quantum-well devices. models in circuit simulators. 4 credits tromagnetic theory for modern practitioners in such Topics include a review of classical mechanics. The areas of engineering and applied science as semi- Schroedinger equation, postulates of Quantum ECE515 Introduction to Semiconductors conductor devices; IC design; optics, lasers, and Mechanics, and basic Hilbert-Dirac formalism. The The fundamental properties and concepts needed to optoelectronics; wireless and optical communica- free particle. One-dimensional quantum-well bound understand semiconductors are introduced in this tions; electronic displays; electron and ion beam states and tunneling through potential barriers. course. We begin with semiconductor crystals, their technology; vacuum electronic devices; and various Bloch functions in periodic potentials and the origin structure and bonding, and thermal properties. We biomedical applications. The course is practically of solid-state band structure. Prerequisite: Calculus then examine electron interactions in semiconduc- oriented, and presents both analytical and numeri- through ordinary and partial differential equations, tor crystals. The physics behind the energy bandgap cal methods. The first course introduces basic or consent of instructor. 4 credits in semiconductors are examined, and used to ulti- experimental laws and theoretical concepts. ECE511 Advanced Quantum Mechanics for Electrical and mately derive the energy band structure, effective Laplace and Poisson equations for static electric Computer Engineers mass, and equilibrium carrier statistics. Next, we and magnetic potentials. Basic properties of elec- This course covers two- and three-dimensional use these statistics to define carrier transport in tromagnetic materials. Maxwell equations for static applications, and introduces new physical phenom- semiconducting materials. Finally, we study and and time-varying fields. Wave equations and ena, mathematical formulations, and tools essential understand the dielectric and optical response of Poynting theorem. Finite-difference numerical solu- for understanding materials science, lasers, solid semiconductors.. This course is recommended if you tion of boundary-value problems. Prerequisite: state devices, quantum optics, and quantum com- have never taken a semiconductor device course (or Some undergraduate electromagnetism, calculus puting. Covered are two- and three-dimensional if you need a refresher). The materials covered will through ordinary and partial differential equations, quantum wells. The simple harmonic oscillator and provide you with background for other semiconduc- some vector calculus, or consent of instructor. algebraic methods. Angular momentum and spin. tor device, processing, and characterization courses 4 credits Matrix formulation of Quantum Mechanics. Atomic offered at OGI. Although not required, you will achieve a more advanced understanding of the con- ECE508 Electromagnetics for Modern Applications II structure. Approximation methods, including per- cepts discussed in this class if you have taken This course introduces additional mathematical turbation theory. Interaction of matter and quantum mechanics. 4 credits tools and covers topics basic to circuit design, semi- electromagnetic waves. Prerequisite: ECE510 plus 49 ECE | ELECTRICAL AND COMPUTER ENGINEERING

ECE516 Fundamental Semiconductor Device Structures encoding, pulse code modulation, quantizing, quanti- techniques. Applications in medicine and biology are Semiconductor bulk, junction and surface proper- zation and noise error in PCM, bandpass random discussed. Prerequisites: ECE 532 or permission of ties. We develop the fundamentals of semiconductor processes, quadrature representation, Wiener-Hopf instructor. 4 credits structures; bulk defects; mechanisms affecting elec- filter, amplitude modulation systems (AM, DSB, Course offered every other year; next session, tron/hole transport at low and high electric fields; SSB, VSB), angle modulated systems (PM, FM) pre- Winter 02/03 junction formation/stability (p-n, metal-semiconductor, emphasis/de-emphasis. MATLAB and the MATLAB ECE534 Biomedical Optics III: Engineering Design and metal-insulator); and relationships between Statistics Tool Box are used in this course. 4 credits The students work as a team in preparing five busi- semiconductor properties and device performance. ECE527 M-ary Communication Systems, ness plans throughout the quarter. Each business The underlying concepts of minority carrier and Information Theory, and Coding plan is devoted to a potential medical device or pro- majority carrier devices are expounded and clarified. Often times in communication systems, the band- tocol using optical technologies. The team is divided 4 credits width available for the system is fixed. This into a CEO, scientific officer, marketing manager, ECE517 Advanced Semiconductor Devices: constrains the communication rate to a maximum of regulatory affairs manager, and manufacturing man- Structures and Materials twice the bandwidth if a binary digital system is ager. The roles are rotated amongst the students for The complex interplay between materials proper- used. However, in many modern systems such as each business plan. Feasibility studies are conduct- ties, fabrication technologies, and device wireless communications and computer communi- ed in a laboratory exercise designed by the students. performance will be examined in the context of elu- cations, communication rates in excess of twice the The team formally presents a business plan every cidating such current technology developments as bandwidth are needed. This problem has been two weeks. Prerequisites: ECE 532 and ECE 533, or silicon on insulator (SOI), high-K dielectrics, SiGe solved by using M-ary communication systems permission of instructor. 4 credits heterojunctions, heterojunction bipolar transistors where the digital system has M distinct states Course offered every other year; next session, (HBT), pseudomorphic high electron mobility tran- rather than just two. Using M-ary communication in Spring 02/03 sistors (PHEMT), Vertical Cavity Surface Emitting conjunction with long sequences for communication ECE535 Thin Film Deposition and Applications in Lasers (VCSEL), quantum dots, single electron tran- efficiency and coding for error correction allows for Semiconductor Fabrication sistors, and organic semiconductors. 4 credits modern communication systems that meet the requirements of such systems. This course covers Covers thin film deposition topics, such as thermal ECE520 Transmission-Line Theory topics that relate to modern communication sys- evaporation, plasma deposition, chemical vapor Maxwell’s equations; Field analysis of transmission- tems, including Optimum threshold detection, deposition (CVD and MOCVD), molecular beam epi- lines; Circuit analysis of transmission-lines geometrical representation of signals, optimum M- taxy (MBE), atomic layer epitaxy (ALE), (telegrapher’s equations, equivalent circuit models); ary Communication (MASK, MPSK, MFSK) systems, electrochemical deposition, and electroless deposi- Microstrip; Stripline; Signal integrity (transient Gram-Schmidt orthogonalization procedure, meas- tion. Thin film deposition forms the basis for response, impedance mismatch, reflections, bounce ure of information, source encoding, channel manufacture of modern integrated circuits; a knowl- diagrams); Skin effect; Dispersion; Discontinuities capacity, error-correcting codes (linear block, edge of methods available for thin film deposition is (bends, vias); Multi-conductor transmission-lines in cyclic, burst-error detecting and correcting, inter- essential for IC process engineers. Course is multi-layered dielectric systems ([L] and [C] matri- laced, convolutional), Viterbi’s Algorithm. MATLAB designed to cover the theory and applications of ces). Numerical analysis of multi-conductor and the MATLAB Statistics Tool Box are used in this main deposition techniques in use or being consid- transmission-line networks (method of moments course. 4 credits ered for future IC fabrication processes. 4 credits technique); Crosstalk. 4 credits ECE529 Fiber Optics ECE536 Surface Science for Semiconductor Technology ECE521 Microwave Engineering Concepts An introductory course in fiber optics aimed at sci- The study of gas-solid surface science with empha- Traveling waves and transmission-line concepts; entists and engineers from widely varying sis on understanding semiconductor systems and Time harmonic transmission-line equations; Smith backgrounds. Topics include light propagation in the mechanisms of epitaxial growth of semiconduc- chart (construction and applications); Impedance dielectric media, attenuation in optical fibers, step- tor films by molecular beam epitaxy (MBE), matching networks; Impedance transformation; and index-graded fibers, photon generation and metal-organic molecular beam epitaxy (MOMBE), Matrix representation of multi-port transmission- detection devices used in fiber optics, and integra- atomic layer epitaxy (ALE), etc. The study of ther- line networks ([S], [Z], [Y], and chain matrices); [S] tion of fiber optics with the photon devices.4 credits mal desorption, surface diffusion. Surface electronic parameters properties; Matrix conversions ([Z] to properties such as work function. Physical absorp- [S] and vice-versa); Numerical analysis of transmis- ECE532 Biomedical Optics I: Tissue Optics tion, the growth of multilayer films and the sion-line discontinuities at microwave engineering Light propagation in tissue: This course treats light application of this phenomena to the study of the frequencies (Finite Difference Time Domain, FDTD transport in scattering and absorbing media such as BET equation as a tool for the determination of sur- technique). 4 credits biological tissue. Light transport is modeled using a face area. 4 credits variety of theories and computational techniques, ECE537 Characterization of Thin Films for ECE525 Analytical Techniques in Statistical Signal including Monte Carlo simulations and approximate Semiconductor Technology Processing and Communications solutions of the radiative transport equation. Development of the mathematical techniques need- Steady-state and time-dependent problems are An introduction to the techniques of surface analy- ed to analyze systems involving random variables treated. Spectroscopy and fluorescence measure- sis, such as Auger analysis, X-ray photoelectron and/or stochastic processes with particular applica- ments are introduced. Optical imaging techniques spectroscopy, energy dispersive X-ray analysis, X- tion to communications and instrumentation. Topics Are presented. Students learn the basics required ray wavelength dispersive spectroscopy, secondary include Bayes Theorem (discrete and continuous for design of optical devices for therapy and diag- ion mass spectroscopy, Rutherford Back scattering forms), Tchebycheff inequality, Chernoff Bound, nostics. 4 credits Spectroscopy, together with their interpretations. Central Limit Theorem, stationary processes and Course offered every other year; next session, Particular emphasis on semiconductor technology linear systems, mean square estimation, Poisson Fall 02/03 applications. 4 credits process, Gaussian process, Markoff process, and ECE540 Auditory and Visual Processing by Human series representations. MATLAB and the MATLAB ECE533 Biomedical Optics II: Laser-Tissue Interactions and Machine Statistics Tool Box are used in this course. 4 credits Physics of laser-tissue interactions: The course treats the immediate physical processes that Interaction between humans and machines could be ECE526 Analog and Binary Digital accompany the absorption of light by biological tis- greatly enhanced by machines that could communi- Communications Systems sues, including photochemical reactions, heating cate using human sensory signals such as speech Mathematical descriptions of signals and noise, and tissue coagulation, vaporization, creation of and gestures. Knowledge of human information pro- bandwidth requirements, sampling theorem, inter- plasmas, and production of stress waves in tissue. cessing including audition, vision, and their symbol interference, digital multiplexing, line Such processes are modeled using finite-difference combination is, therefore, critical in the design of 50 ELECTRICAL AND COMPUTER ENGINEERING | ECE effective human-machine interfaces. The course systems to a deeper level and introduce a host of design of asymptotic observers, state-feedback com- introduces selected phenomena in auditory and useful properties which the time perspective alone pensation schemes. Linear Quadratic Regulator and visual perception, and motor control. Students learn does not reveal. Basic applications taken from the Kalman Filter are also introduced. The Linear how to interpret empirical data, how to incorporate areas of information processing, communication and Algebra material required for this study — matrices these data in models, and how to apply these mod- control will serve to fill out the mathematically as linear operators , solutions of sets of linear equa- els to engineering problems. The anthropomorphic derived results. tions, eigenvalues and eigenvectors, eigenstructure (human-like) signal processing approach is illustrat- factorizations and spectral decompositions — will ed on engineering models of perceptual phenomena. A greater portion of the syllabus in ECE 544 is allot- be presented and developed concurrently, as need- 4 credits ted to continuous time signals/systems than to ed. The relevant Differential Equations material will discrete time signals/systems, for reason that the also be concurrently reviewed. 4 credits ECE541 Speech Processing latter are taken up in detail in other information Speech is one of the most important means of com- processing courses, particularly ECE 551. A goal of ECE 551 Introduction to Digital Signal Processing munication. This course teaches theory of human the presentation in ECE 544 is to impart the essen- The representation and processing of signals and speech production, properties of speech signal and tial unity of all the Transforms and the almost systems in the discrete or digital domain is the pre- techniques for its processing in speech coding, and perfect correspondence of approach in continuous- ferred mode in todayís computer and information automatic speech and speaker recognition. time and discrete-time contexts. You then become a driven technologies. DSP provides the core building Emphasis is on active research in auditory modeling well equipped practitioner who knows the way block from cell phones to modems, HDTV to video that exploits special properties of speech to improve around the entire territory. This course is a useful conferencing, or from speech recognition to MP3 performance of speech technology in practical prerequisite or co-requisite to ECE 551 and all audio.This classes covers the fundamental concepts applications. Prerequisites: ECE 540, ECE 551, or other courses in the information processing area. and mathematics including representation and consent of instructor. 4 credits 4 credits analysis of discrete time signals and systems, Z- Transforms, Discrete-Time Fourier Transform ECE542 Introduction to Image Processing ECE545 Speech Systems (DTFT), and the Discrete Fourier Transform (DFT), Course covers basic image processing principles Speech is one of the most natural means for com- sampling and windowing techniques pertaining to and techniques with a brief introduction to machine munication and carries information from many discrete time processing of continuous signals, vision. Students acquire theoretical and working sources. The explosive growth of communications analysis and design of recursive (IIR) and nonrecur- knowledge of image processing approaches includ- and computer technologies puts new demands on sive (FIR) digital filters, signal flow graph ing image representation, transform methods, image techniques for machine extraction of information realizations of finite word-length implemented dis- filtering, multi-resolution representation, edge content of speech signals, for its storage or trans- crete time linear systems, and applications of the detection, texture characterization, and motion mission, and for reconstruction of the speech signal Fast Fourier Transform (FFT) to convolution, spec- analysis. Course demonstrates application of these from its parametric representation. Course covers tral analysis, and audio processing. 4 credits methods to image enhancement, image restoration, techniques for processing of speech signal used for and image compression, with emphasis on image speech coding and synthesis, enhancement of ECE552 Digital Signal Processing II quality metrics based on human visual perception. degraded speech, speech recognition, speaker This follow-up course to ECE 551 examines several Selected areas in machine vision include image seg- recognition, and language identification. 4 credits widely used advanced signal processing. Topics mentation, elementary techniques in pattern include computational complexity considerations in ECE547 Signals for Multimedia Engineering recognition, and object representation. Application DSP algorithm development; multirate signal proof these techniques is illustrated in numerous exam- The course discusses concept of signal as a carrier cessing; filterbanks and wavelets, and their ples. Prerequisite: ECE 551. 4 credits of information, basic principles of signal analysis in application in audio and image processing (e.g. engineering, and fundamentals of human auditory MPEG standards). Topic coverage is weighted ECE543 Introduction to Digital Video Processing and visual perception. It is intended for those who toward the interests of the students enrolled. Course provides introduction to digital video pro- have a good undergraduate-level of basic knowledge 4 credits cessing for multimedia systems. The course first in mathematics and physics but who need an intro- introduces video capture, image formation, analog duction to or refreshing of fundamental concepts of ECE553 Control Systems: Classical, Neural, and Fuzzy and digital video signal and standards, and spatio- signals, systems, and human information process- Applications of modern control systems range from temporal sampling. Subsequent topics include ing, necessary for further mastering specialized advanced fighter aircraft to processes control in motion estimation, segmentation and tracking,video multi-media topics in speech and image processing, integrated circuit manufacturing, to fuzzy washing filtering, and video standards conversion. Students classification, and transmission. 4 credits machines. The aim of this class is to integrate dif- are familiarized with video compression techniques ferent trends in control theory. Background and ECE550 Linear Systems and standards (JPEG, MPEG2, H.261, H.263), and perspective are provided through the study of basic This course introduces the State Variable represen- model-based video quality estimation. Students gain classical techniques in feedback control (root locus, tation of linear dynamical systems and studies a working knowledge of these video techniques bode, etc.), as well as state-space approaches (lin- large body of State Space techniques to reveal both through class projects. Familiarity with digital sig- ear quadratic regulators, Kalman estimators, and inner structure and external behavior of the systems nal processing and transform methods is desirable. introduction to optimal control). The course covers modeled in this way. A general framework for treat- 4 credits recent movements at the forefront of control tech- ing time-varying linear systems is developed and nology. Neural network control is presented with ECE544 Introduction to Signals, Systems and utilized. Major emphasis is placed, however, on the emphasis on nonlinear dynamics, back-propagation- Information Processing time-invariant systems, whose structure and through-time, model reference control, and This course provides the essential mathematical dynamics are investigable and knowable to the very reinforcement learning. The course also covers tools and analytical techniques needed for the utmost detail. Both continuous-time and discrete- fuzzy logic and fuzzy systems as a simple heuristic- analysis of continuous-time and discrete-time sys- time linear systems are explicitly studied. The based, yet often effective, alter-native for many tems. Basic signal and system characteristics — course provides a strong body of foundational mate- control problems. Prerequisite: ECE 551, ECE 554, linearity, time-invariance, convolution and correla- rial, which is utilized either explicitly or implicitly in or equivalent. 4 credits tion — are first examined from the time domain virtually all applications-specific areas pertaining to perspective. We then proceed to study a family system analysis/design and signal/information pro- ECE 554 Adaptive Signal Processing of Transforms - Fourier Series, Fourier Integral cessing. The major topics covered are: canonical The field of adaptive filters and systems constitutes Transform, Laplace Transform, Discrete Time Fourier realizations, equivalent systems, canonical transfor- an important part of statistical signal processing. An Transform (DTFT), Discrete Fourier Transform (DFT) mations, canonical decompositions, solution of state adaptive system alters or adjusts its defining and z-Transform — which take the study of these equations, stability, controllability and observability, parameters in such a way that it improves perform- 51 ECE | ELECTRICAL AND COMPUTER ENGINEERING

ance through contact with the environment. ECE557 Computer-Aided Analysis of Circuits nects (e.g., Cu), multilevel metallization, and low k Adaptive filters are currently applied in such Course covers the algorithms and techniques for for- dielectrics. This followed by discussion of deposition diverse fields as communications, control, radar, mulation and solution of circuit equations for and properties of different dielectric films. Finally, seismology, and biomedical electronics. This course large-scale VLSI circuits. Topics include Equation processing issues of epitaxial growth and properties will cover the theory and applications of adaptive formulation, linear AC and DC networks, linear tran- of SOI devices are covered. Class assignments linear systems. Topics include Wiener filters, least sient networks, and stability analysis. Solution of include computer simulation of device fabrication. squares, steepest descent, LMS, RLS, Newton’s nonlinear DC and transient problems. Frequency 4 credits method, FIR and IIR adaptive structures, and domain (AWE) techniques for VLSI interconnections, ECE562 Microelectronic Device Fabrication III Kalman filters. Applications covered include noise Sensitivity analysis, harmonic balance, circuit opti- This class starts with electron beam, x-ray, and pho- canceling, signal enhancement, adaptive control, mization, and statistical design.The implementation tolithography, including discussion of resist adaptive beam-forming, system identification, and of device models in circuit simulators and conver- technology (e.g., chemically amplified resists). This adaptive equalization. The theory also lays the foun- gence issues is covered. Assignments stress followed by fundamentals and applications of plas- dation for study in nonlinear signal processing with computer-aided implementation techniques and use mas for etching and deposition (e.g., high density neural networks and will be introduced in the later of simulators such as PSPICE. 4 credits half of the class. This course should be of interest to plasmas), including plasma damage. Other topics electrical and computer engineers specializing in ECE558 High Speed Interconnect Design considered are process integration that includes signal processing and the information sciences. This Electrical analysis, design, and validation of inter- several devices such as BiCMOS and memories. course should also be taken as background for addi- connect for digital buses operating at speeds greater Finally yield and reliability statistics as related to tional classes offered in artificial neural networks, than 1 GHz. Key topics include: transmission line microelectronic device fabrication is discussed. connectionist models, and machine learning. analysis and tools, digital signals and timing analy- Class assignments include computer simulation of 4 credits sis, measurement equipment and techniques, lossy device fabrication and testing. 4 credits and coupled transmission lines, advanced signaling ECE563 Plasma Processing of Semiconductors I ECE555 Engineering Optimization techniques, design tools and methodology. A design Fundamental plasma properties. Plasma produc- Issues of Optimization appear in virtually every area project is used to give students practical insight into tion, properties, and characterization. DC and of Engineering and Applied Research. Most practi- high speed bus design problems. 4 credits tioners tend merely to rely on “canned” routines RF plasmas. Sputtering as a deposition process for when optimization needs to be performed. But suc- ECE559 Design with Programmable Logic the growth of thin films. Multicomponent films. cessful Optimization entails both a lot of science and Programmable logic, such as FPGA and PLD Plasma etching. 4 credits devices, has become a major component of digital a lot of art — deep mathematical derivations and ECE564 Plasma Processing of Semiconductors II design. This course will discuss design tools and formal convergence proofs on the one hand, conven- This course, a continuation of ECE 563, covers spe- techniques for creating logic designs using program- tional engineering “folklore and experiential “rules cific applications of plasmas for processing mable logic. A design is first created in Verilog, a of thumb on the other. Through this course you will semiconductor materials. Topics include etching and high-level Register Transfer Level (RTL) language, be able to choose intelligently among the very wide deposition and the dependence of these processes and simulated. Synthesis to a programmable logic range of available optimization strategies, customize on plasma parameters. Materials based on both sil- device is then performed. In addition, common prob- given algorithms; to your own specific applications, icon and III-V technology are examined. 4 credits and even write your own routines entirely from lems of poor routing and placement are discussed scratch when this approach is needed or preferred. while presenting the student with a comprehensive ECE565 Analytical Scanning Electron Microscopy After reviewing some necessary mathematical fun- understanding of the operation of synthesis tools. This course introduces the operation and theory of damentals from Linear Algebra and Multivariable The course has a strong project orientation. SEM and covers sources, lenses, accelerating volt- Calculus, including Lagrange Multipliers and Kuhn- Students will take several designs from concept age, detectors, image formation, beam-specimen Tucker conditions, the following topics will be to RTL verification and synthesis, then to program- interactions, beam-produced signals, the combined covered. Unconstrained and Constrained nonlinear mable device implementation. A commercial set effects of signal-to-noise ratio and spot size in deter- Multivariable Optimization, via direct-search and of software tools will be used. PREREQUISITES: mining resolution, and stereo imaging SEM. The gradient-based methods, including: Pattern Search, ECE573 Intro to Computer Logic Design or consent process of specimen preparation, metallo-graphic Simplex Search, Conjugate Gradient, Variable of instructor. 4 credits. grinding and focused ion beam-produced transverse Metric, Feasible Directions, Cutting Plane, Gradient ECE560 Microelectronic Device Fabrication I cross sections, planar sections, coating techniques for nonconductors, sampling of powders, and isola- Projection and Penalty Function methods. This course is the first in a full year, three term tion of contaminants are some of the topics covered. Algorithms for specially structured problems, such sequence that treats both the science and practice Students are encouraged to work on materials they as: Linear Programming, Quadratic Programming, of modern microelectronic fabrication. The princi- provide. The course covers the operation of energy Integer Programming, Geometric Programming. ples of crystal growth and wafer preparation, ion dispersive X-ray detectors, qualitative analysis, Methods which utilize random heuristics, including: implantation, doping and diffusion, and oxidation quantitative analysis, elemental mapping, spectrum Genetic Algorithm, Dynamic Evolution and are all covered. Emphasis is placed on understand- artifacts, and contaminant and compound identifica- Simulated Annealing. Time permitting, an introduc- ing the basic chemistry, physics, and material tion. The lecture portion of this course can be tion to Dynamic Programming and the Optimal science of wafer processing. This includes crystal presented on site at companies in a 6 week period. Control problem will also be included. 4 credits structure and defects, heterogeneous chemical Corresponding lab sessions are done at OGI. A proj- reactions, the thermodynamics and kinetics of diffu- ECE556 Principles of Electronic Packaging ect requiring operation of the SEM at the studentsí sion, etc. In addition, the practical implementation This course introduces the principles and tradeoffs convenience during the remainder of the quarter of these processes is also discussed. This includes involved in the design of electronic packaging for and a written report is the basis for a grade. realistic process flows, physical metrology, device integrated circuits. Topics include packaging archi- 4 credits tecture, electrical design concepts in electronic structure and electrical behavior, trade-offs, etc. packaging design, thermal management, mechanic The course is intended to serve a wide community ECE566 Focused Ion Beam Technology design, electrical contacts, reliability and testing, including both working process engineers and This course covers operation and theory of a FIB material selection and fabrication, plated through- matriculating graduate students. 4 credits workstation, including ion sources, accelerating hole technology, etching by wet processes, joining ECE561 Microelectronic Device Fabrication II voltage, electrostatic lenses, beam-material interactions, resolution, beam intensity distribution, beam materials, stress issues, diffusion problems, chemi- In the second class of this series emphasis is on produced signals, detectors, metal and oxide depo- cal and physical methods of analysis, and trends in metallization and dielectrics. Metallization issues sition, and enhanced etch. FIB-produced site- electronic packaging. 4 credits examined include silicides, barrier layers, intercon- 52 ELECTRICAL AND COMPUTER ENGINEERING | ECE specific SEM transverse cross sections, the location lecture portion of this course can be presented on gate design/transistor sizing; pass transistors and and sectioning of micron and sub-micron scale site at companies in a 6 week period. Corresponding complimentary pass transistor logic; dynamic domi- structures on the surface and buried in multilayered lab sessions are done at OGI. A project requiring no and precharge/discharge circuits; memory stacks or bulk materials, cross sections in metals, operation of the SEM at the students convenience element design (RAM/ROM/flip-flops) and subsystem semiconductors, ceramics, and composites are cov- during the remainder of the quarter and a written design (adders, multipliers, etc.). An understanding ered. The location and sectioning of micron and report is the basis for a grade. 4 credits of basic digital design concepts is assumed. Lab submicron surface and buried structures to create exercises use industry standard design tools. ECE569 Electronic Materials and Device Characterization electron transparent foils with little or no damage in Laboratories include circuit validation and charac- metals, semiconductors, ceramics, and composites, This class is designed for engineers and scientists terization. Prerequisite: ECE 573. 4 credits and artifacts of specimen preparation are present- who wish to understand the basic principals behind ECE575 CMOS Digital VLSI Design II ed.† Ion beam lithography and microfabrication of the electrical and optical techniques used to char- structures on the micron and sub-micron scales are acterize semiconductor materials and devices. Concentration on advanced digital VLSI circuit also covered.† This course uses a combination of These techniques are crucial in determining the design techniques. Architecture and micro-architec- lectures and hands-on practice to cover these top- causes of failure in semiconductor devices. Among ture of VLSI components, clocking schemes, ics. The lecture portion of this course can be the parameters to be covered include contact resist- input/output circuits, and special functional blocks presented on site at companies in a 6 week period. ance, carrier mobility and lifetime, defects, oxide such as random access memories, read only memo- Corresponding lab sessions are done at OGI. A proj- and interface trapped charges, as well as series ries and programmable logic arrays. The course ect requiring operation of the FIB at the students resistance, channel length /width, threshold voltage covers design tradeoffs, especially considering cost, convenience during the remainder of the quarter and hot carriers in MOSFETs. This class will include power and performance. The course devotes a con- and a written report is the basis for a grade. some lab time. 4 credits siderable amount of time to layout, parasitics and performance verification. Introduction to design and 4 credits ECE570 Gallium Arsenide MESFET Integrated verification tools with hands-on experience. Circuit Design ECE567 Transmission Electron Microscopy Prerequisites: ECE 574, familiarity with MOS tran- Technology overview, device structures, SPICE mod- Electron microscopy is a continually evolving disci- sistor operation; computer architecture and els, limitations, regions of MESFET operation. pline, which, has developed a wide range of organization; logic design. 4 credits Transconductance, output resistance, biasing. techniques to solve specific problems. This course is Single-stage, high-gain, and feedback amplifiers, ECE577 Principles for Technology Development and designed to help the student develop a broad appre- current sources, compensation. Buffered FET logic, Introduction to Manufacturing ciation and knowledge of the important techniques enhancement/depletion technology,data conversion, for the analysis of crystalline and amorphous mate- A project-oriented course on management proce- comparators, digital-to-analog converters. 4 credits rials. Modern transmission electron microscopes dures and key underlying concepts for effective manufacturing technology planning and develop- can give the investigator detailed information of ECE571 Analog Integrated Circuit Design ment; an introduction to commercial production in a crystal structure, crystal defects and quantitative Design techniques for analog integrated circuits. competitive environment. While emphasis is on local chemistries on a nanometer scale. This infor- Silicon bipolar and JFET analog integrated circuit semiconductor technology, most principles and mation is often critical to the understanding of design. Technology overview, device structures, methodology are generally applicable to both hard- material properties. Principles, methods and appli- Ebers-Moll equations, hybrid-pi model. Single-stage ware and software technology management. Issues cation of transmission electron microscopy to amplifiers, current sources, active loads, output of technology strategic planning, process definition crystalline materials. The construction and design of stages. Operational amplifiers, frequency response, and characterization, decision making, technology electron microscopes, electron diffraction, recipro- feedback, stability. Design project. 4 credits cal lattice and Ewald Sphere construction will be transfer, product definition, yield and reliability covered. Kinematic and dynamic theories of image ECE572 Digital Integrated Circuit Design improvement, and concurrent engineering are formation will be introduced. Combining lectures Design techniques for digital integrated circuits. explored to identify effective management with hands-on laboratory practice, students will be Silicon bipolar and MOS digital integrated circuit approaches to shorten time-to-volume production, instructed in the use of sample preparation equip- design. Technology overview, device structures, reduce risk, and minimize engineering effort. ment and an analytical transmission electron modeling. Standard logic families. NMOS and CMOS 4 credits microscope. Students will be expected to carry out logic design. Regenerative circuits and memory. ECE578 Embedded and Real Time Operating Systems basic experiments on selected materials which illus- Design project. 4 credits A study of concepts, techniques, and standards in trate fundamental concepts covered in the lecture. ECE573 Introduction to Computer Logic Design embedded operating systems including real time The lecture portion of this course can be presented This course constitutes a basic introduction to the embedded operating systems. Topics include kernel on site at companies in a 6 week period. design and implementation of computer logic. Basic design, device driver and interface techniques, Corresponding lab sessions are done at OGI. A proj- principles of discrete logic will be presented, includ- scheduling, robustness and industry standards such ect requiring operation of the SEM at the students ing boolean algebra, finite-state machine theory, as Windows-CE and Tornado (VxWorks). This is a convenience during the remainder of the quarter minimization, and optimization. Students will apply hands-on lab course where students will experience and a written report is the basis for a grade. logic design theory to actual PLD (Programmable real-world real time embedded systems using com- 4 credits Logic Devices) and FPGA (Field Programmable Gate mercial software tools. Prerequisites: CSE 521 ECE568 Failure and Reliability in Microelectronics Array) devices. In addition, students will learn the Introduction to Computer Architecture or a demon- strable understanding of computer architecture. The failure and reliability of microelectronics basics of the hardware design languages, Verilog 4 credits depends on the stability of thin films and the purity and VHDL. This course or its equivalent is a prereq- of the bulk semiconductors. Contamination, film uisite to all other ECE Electronics Design ECE579 Embedded Computer Systems thickness, diffusion and phase changes all drive Automation courses. 4 credits A study of concepts, techniques, and standards in mechanisms of failure. Characterization of a failed ECE574 CMOS Digital VLSI Design I embedded systems from design through deployment device depends on analysis of thin film structure, An introduction to CMOS digital IC design. Course to retirement. Topics include programmable logic, crystalline structures, contaminant identification covers basic MOS transistor theory; operation of interfacing, power supply, packaging, robustness, and microchemistry. This requires a variety of basic CMOS inverter; noise margins; switch level certification, and maintenance. This is a hands-on microanalytical techniques involving the SEM, TEM, modeling of MOS devices; capacitive characteristics lab course based on a student project, where stu- and FIB. This course covers the potential defects, of MOS devices; introduction to device fabrication, dents will experience real-world embedded systems failure mechanisms and the methodology used to design rules and layout issues; power consumption; using commercial software and hardware tools. analyze them. Case studies also are discussed. The Prerequisites: CSE581 Introduction to Computer 53 ECE | ELECTRICAL AND COMPUTER ENGINEERING

Architecture, ECE 578 Embedded and Real Time ECE580-TP Technology of Photoresists Many information-processing applications involve Operating Systems, or permission from instructor. huge amounts of real world data that have to be 4 credits ECE580-WCS Wireless Communication Systems processed and analyzed for making decisions. The ECE580-UOS Understanding Operation of complexity of the analysis is often beyond current ECE580-XXX Special Topics Semiconductor Devices science and engineering’s techniques and Under this number, we offer courses of particular methodologies. Yet, natural evolution has evolved relevance to the research interests of faculty or in ECE591 Independent Study very sophisticated information processing systems, state-of-the-art subjects of interest to the communi- Student works with professor on selected topic(s). and the information analysis performed by the ty. Individual course descriptions are listed as Requires pre-approval of professor, ECE Depart- human brain, or even by the brain of simple follows. Special Topic courses are subject to change ment, as well as formal agreement between student animals, is far superior to what current state-of- and are offered intermittently. For Special Topics and professor outlining objectives and expectations the-art human-developed techniques can achieve. offered during the current term, please view of independent study topic. May only be taken once www.ogi.edu/schedule. during a student’s graduate program at OGI for a A new research area is now coalescing which is devoted to consolidating and refining existing ECE580-ACD Selected Topics in Analog IC Design maximum of 3 credits. solutions, and finding better solutions to these ECE580-ACS Advanced Control Systems: Nonlinear, ECE600 Prequalifying Ph.D. Research transformation problems. The term Intelligent Neural & Fuzzy Supervised research participation. Pre-qualifying Signal Processing (ISP) is being used to describe ECE580-AFA Applied Functional Analysis Ph.D. research prior to passing ECE department algorithms and techniques that involve the qualifying examination. creation, efficient representation, and effective ECE580-AIC Analog CMOS Integrated Circuit Design Variable and repetitive credit. utilization of complex models of semantic and ECE580-CLI Computational Approaches to Laser Interaction ECE610 M.S. Nonthesis Project Research syntactic relationships. Even the most primitive with Biological Tissues biological systems perform complex ISP. In Supervised research for up to eight credits as a ECE580-CLT Computational Approaches to Light Transport addition, biological computing is robust in the component of the nonthesis M.S. degree. Students in Biological Tissues presence of faulty and failing hardware, and is are required to produce cogent research deliver- fundamentally asynchronous. Biological computing ECE580-CMP Chemical Mechanical Planarization able(s) including, but not limited to, a final report is energy efficient, consists of networks of equivalent to an EE project paper. This research ECE580-CN Introduction to Computer Networks sparsely connected and sparsely activated nodes, classification requires the approval of the depart- ECE580-COD Introduction to Computer Organization and requires only moderate levels of ment head and the student’s SPC. and Design computational precision. Variable and repetititive credit ECE580-CP The New Millenium in Copper Plating: ECE620 Professional Internship We believe that the merging of neuroscience and Faster Chips with Slower Plating semiconductor engineering is creating what Andy This course provides the student with an opportuni- ECE580-DDC Design of digital Communication Circuits Grove, ex-CEO of Intel, refers to as a strategic ty to earn credit for relevant work experience in inflection point. Therefore, the mission of the ECE580-FLC Fabrication Lab Class industry. Students gain valuable industrial experi- Center for Biologically Inspired Information ECE580-FSM Fundamentals of Sensors and MEMS Fabrication ence that allows them to both apply the knowledge Engineering is to harvest biology for solutions to gained in the classroom and prepare for their future ECE580-GAP Introduction to Genetic Algorithms real-world information engineering and Intelligent careers.U.S. citizens, permanent residents, students and Programming Signal Processing problems, and leverage the on F-1 visas enrolled in Curricular Practical incredible functional density of GSI (Giga-Scale ECE580- IB Introduction to Biomaterials (formerlyMSE589) Training take ECE620 and must obtain additional Integrated) Silicon. The Center was established in ECE580-IE Internet Engineering permission from OGI personnel department. 2001 and currently consists of two professors - Enrollment requires a faculty advisor and is limited ECE580-ISM Introduction to Sensor Microfabrication Dan Hammerstrom and Marwan Jabri - and their by the number of internship opportunities available. ECE580-IVC Information Visualization and Computer Graphics staff and graduate students. The Center currently Variable and repetitive credit. ECE580-LCD Introduction to Liquid Crystal Displays receives funding from NASA, NSF, SRC, ONR ECE700 M.S. Thesis and Intel. ECE580-MBD Introduction to Modeling of Business Dynamics Research toward the thesis for the M.S. degree. Current projects focus on: ECE580-MC Multimedia Communications Variable and repetitive credit. ECE580-MEM Microelectromechanical Systems ECE800 Ph.D. Dissertation • Computational models of sensorimotor control; ECE580-MPE Modern Photolithographic Engineering Research toward the dissertation for the Ph.D. • High-level visual feature extraction using ECE580-MTF Mechanics and Thin Films degree. Variable and repetitive credit. unsupervised learning techniques; ECE580-ONE Optical Non-destructive Evaluation • Top-down/bottom up sensory fusion and ECE580-PEM Phase Equilibria in Microelectronics RESEARCH CENTERS sensorimotor control; (offered Fall 2001) CENTER FOR BIOLOGICALLY INSPIRED INFORMATION • Simulation of large-scale networks on ECE580-PGO Physical and Geometric Optics, PC clusters; ENGINEERING (CBIIE) ECE580-QM Quantitative Microscopy Science and engineering have achieved great • Mapping computational neurobiology to ECE580-RFD Reliability and Failure of Electronic Devices, advances in automating and creating information FPGAs and eventually custom silicon; and Packages, and Assemblies processing and analysis tools. Microelectronics, • Understanding the issues involved in scaling ECE580-SJM Soldering and Joining in Microelectronics programming, signal processing and information neural models to very large configurations. ECE580-SLD Statistical Learning and Data Mining theory underpin these achievements. Modern microprocessors and those that will be produced ECE580-SMVI Simulation & Modeling of VLSI Interconnect CENTER FOR INFORMATION TECHNOLOGY (CIT) over the next decade will provide huge ECE580-SSE Semiconductor Sensors computational power, enabling new information Digital signal processing has made a significant impact on human lives since its introduction ECE580-SSL Structure of Spoken Language processing applications. In fact, it will soon be possible to place one billion transistors on a single several decades ago. The broad field of information ECE580-SSY Speech Synthesis piece of silicon. technologies has become a vital driving force in the

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United States economy, both regionally and Within CSLU there are five collaborating with concurrent theoretical work, are contributing nationally. Industries are in the process of shifting research groups: significantly to fundamental understanding of the emphasis from instrumentation and manufacturing effects of atmospheric turbulence on laser beam, to multimedia and communications services. Wide • Neural Speech Enhancement Lab speckle propagation and its application to optical arrays of technologies, ranging from digital • Anthropic Signal Processing Group remote sensing. Holmes telephones to the ability to accurately predict the Biomedical Optics behavior of complex systems, rely on elegant • Speech Recognition Group The program in Biomedical Optics prepares the mathematical concepts and on the power of digital • Speech Synthesis Research Group student to use lasers and light to measure, image, computers. Even the most advanced techniques, modify and machine materials, with emphasis on however, fail to carry out many tasks that are • Natural Dialog Group biological materials but with broad application to a effortlessly performed by humans. These groups focus on specific problem areas such variety of materials. The program offers a series of The mission of the Center for Information as: robust methods for enhancing speech in noisy courses and labs on tissue optics, laser-tissue Technology (CIT) is to support the development and environments; large vocabulary recognition of interactions, and engineering design, with elective deployment of signal-processing systems that continuous speech, as in broadcast news; unit courses in optics, spectroscopy, optical fibers, bio- would emulate and surpass human information selection and voice conversion for more realistic mechanics, imaging and image analysis, optical processing capabilities. CIT activities focus on the speech synthesis; robust parsing and interpretation measurement techniques, and computational meth- “human-like,” or anthropic, processing side of of spoken and multimodal input; modeling of ods for simulating light transport through and information systems. The anthropic signal disfluencies in spontaneous speech; and effective interaction with biological materials. Students have processing is the synthesis of robust signal- methods for dialog management. CSLU research the opportunity to work in the hospital-based processing techniques that exceed the performance projects incorporate and evaluate these research research laboratories at the Oregon Medical Laser of standard classical signal-processing methods by advances. For example, one project involves the Center at Providence St. Vincent Medical Center appealing to human-like processing strategies and development of an animated conversational agent and the Biomedical Optics Laboratory on the OHSU capabilities. This unique combination of for learning and language training with profoundly Medical Center campus. Jacques, Kirkpatrick, engineering and human information processing deaf children. The center is also highly active in the Prahl, Song strategies is strengthened by recent incorporation development and distribution of a wide variety of Electronic Materials of OGI into Oregon Health & Sciences University language resources, including corpora of An active research program in the area of that allows for close collaboration between transcribed telephone and cellular speech data for electronic materials growth and characterization is engineering and humanistic sciences. over 20 languages. focused on demands of the ever shrinking The center’s efforts focus on several target- Professor Jan van Santen is the director of OGI’s microelectronic devices. The main materials engineering systems, including robust feature Center for Spoken Language Understanding. The growth technique investigated is atomic layer depo- extraction for speech recognition systems, speech center is co-directed by Professors Peter Heeman, sition which allows growth of highly conformal thin quality enhancement in cellular communications, John-Paul Hosom, Yonghong Yan, and Eric Wan. films, one atomic layer at a time. Materials investi- automatic target detection and identification, Other center faculty includes Professors Todd Leen, gated using this approach include thin gate and a forward visibility system for aviation. Hynek Hermansky, and Xubo Song. The center dielectrics, including nanolaminates and metallic These projects are supported by basic research receives support from government agencies films which include copper seed layers and barrier on several key-supporting technologies, i including NSF, DARPA, and ONR, as well as metals. Another area of research involves ncluding neural networks, prediction, image industrial sources. For additional information, electrodeposition of copper films for microelectron- and speech representation, information fusion visit the CSLU web site: www.cslu.ogi.edu. ic device interconnect applications. The focus of and the incorporation of prior knowledge in this investigation is to determine the correlation adaptive systems. between the bath chemistry to the physical proper- RESEARCH PROGRAMS ties of the films and their electromigration Within the OGI School, CIT provides a natural lifetimes. Solanki, Freeouf, McCarthy complement to other centers, including the Center Advanced Lithography for Spoken Language Understanding and its Center Lithography is the key technology pacing the evolu- Flat Panel Displays for Human-Computer Communication. CIT tion of microelectronics. Research is ongoing in The video screen is becoming an indispensable link compliments CSLU by developing advanced signal developing a viable patterning technology for use between information processing electronics processing techniques used in speech processing. in large scale manufacturing of semiconductor systems and human beings. Although the cathode In a similar way, CIT is developing solutions to a devices. By using either semiconductor technology ray tube (CRT) remains the dominant display tech- variety of signal-processing problems in natural or new cathode materials, it should be possible to nology, its size, weight, and power requirements communication using images, sound and gestures. generate arrays with significantly enhanced speed become unsuitable for many applications. As a CIT is an important component in the ECE and improved pattern fidelity. Berglund, Freeouf, replacement for CRTs, several flat panel display department’s focus on intelligent signal processing. McCarthy technologies are being explored due to their com- Atmospheric Optics pactness, light weight and low power consumption. CENTER FOR SPOKEN LANGUAGE UNDERSTANDING The use of laser systems to transmit signals A flat panel display research group has been estab- The research program of the Center for Spoken through the atmosphere for purposes of communi- lished to develop research capabilities and to work Language Understanding (CSLU) encompasses a cation, radar, recognition, and designation is closely with the emerging display companies to broad range of technologies critical to advances in severely limited by scattering due to turbulence assist them in overcoming technological hurdles. At the development of interactive conversational and particulates such as water droplets or dust. present, research is directed towards electrolumi- systems. Such research is inherently Turbulence, which causes shimmer on a hot day nescent, field emission, and liquid crystal displays. multidisciplinary, and the center brings together a and makes stars seem to twinkle, results in the Berglund, Solanki, Rananavare, McCarthy team with expertise in signal processing, speech random steering, spreading and breaking-up (scin- Image Processing and Analysis recognition, speech synthesis, dialogue modeling, tillation) of a laser beam. Particulate scattering The main research interests of our group are natural language processing, multimodal systems, that severely attenuates the received signal also twofold. One thrust is image processing and image linguistics and human-computer interaction. causes depolarization and multiple path effects recognition. One of the techniques we are investi- such as pulse stretching and scrambling of the sig- gating is incorporating contextual information into nal. Experimental studies, which in conjunction recognition. Context incorporation is a mechanism 55 ECE | ELECTRICAL AND COMPUTER ENGINEERING

that ensures accurate perception and appropriate Speech and Speaker Recognition in Adverse RESEARCH FACILITIES interpretation of ambiguities. Ambiguities arise Communication Environments The department has a complete eitherbecause information is missing or because Biological signals such as speech carry large information is partially or completely obscured by amounts of information from different information complement of electronic measuring, noise. Probabilistic or statistical models can be sources. Typical engineering applications such as recording, amplifying, signal generating, developed for context incorporation, and it has automatic speech recognition, speaker verification, data processing, and servicing gear been demonstrated that utilizing contextual infor- or low bit-rate coding of speech may require infor- with associated power supplies and mation is crucial for improving recognition mation from only one particular source, and all component stocks. Additional facilities accuracy. Another research thrust is on machine other information introduces undesirable and learning and data mining. We are interested in a harmful variability into the signal. Humans appear and equipment include: fundamental understanding of learning, and in the to be able to partially separate the various infor- • Access to FT-IR, fluorescence, diode array UV/VIS, development of learning systems that achieve state mation sources in the speech signal. This ability scanning UV/VI Snear IR spectrophotometers of the art performance. Song spurred interest in modeling human-like processing • NT/PC Computer Lab of speech by modern discrete signal processing Modification of Semiconductor Materials • Solaris Servers with X-terminal access techniques. The anthropomorphic signal processing Research is under way on the processing and char- techniques could, in principle, yield improved per- • DTV Lab acterization of semiconductor materials as affected formance of man/machine I/O technologies in real • Intel Semiconductor Educational Lab by localized transient heating, plasma passivation, practical environments. Our research project on • Embedded Computer Lab and thermal annealing. The recrystallization of speech analysis, carried on jointly with the • High-end PCs & workstations polysilicon is studied using various laser sources International Computer Science Institute, Berkeley, and rapid thermal annealing. Solanki, Freeouf, • Far-infrared Fourier spectrometer Calif., focuses on human-like processing of speech McCarthy • Parallel field-vibrating sample magnetometer in realistic telecommunications environments to • Mossbauer spectrometer Neural Networks and Adaptive Systems ensure reliable recognition of speech in adverse • Field electron and ion microscopes Neural computation and adaptive systems are stud- conditions such as the current mobile cellular ied from both theoretical and practical standpoints. telephone. Hermansky • Ultra-high vacuum systems • Thin-film evaporation equipment Current research in theory, architecture, and algo- Speech Synthesis rithm design includes deterministic and stochastic • Electron energy analyzers for Auger and field Speech is the most natural and efficient means by network dynamics, learning algorithms electron spectroscopy which individuals may access most information, (supervised, unsupervised, and reinforcement), and the need for speech-based interfaces is grow- • Micromachining capabilities generalization theory (including model selection ing as computing gradually moves off of the • Scanning electron microscope and transmission and pruning, invariant learning), context-sensitive desktop and into mobile devices. Since most on-line electron microscope learning, signal processing, time series analysis, information is represented as ASCII text, the auto- • High-resolution electron and ion microprobes and control. Practical application domains include matic conversion of text to speech provides a adaptive signal processing, pattern recognition, • Work function analysis instrumentation critical component in voice-based systems. Text-to- speech recognition, image processing, control sys- • Quadrupole mass spectrometers for surface speech synthesis (TTS) has the further advantage tems, macroeconomics, and finance. Leen, Moody, desorption studies of providing textual information to people who are Pavel, Song, Wan • Arc zone refinement system for single crystal visually impaired or functionally illiterate. The cur- specimen preparation Optical Remote Sensing rent trend in TTS research is to develop algorithms • Wire bonder Analytical and experimental studies are being that rely on automatic training of models from made on the use of the interaction of electromag- labeled data, rather than hand-tuned rules as used • Die attach system netic radiation and turbulence to measure winds historically. This strategy leads to systems that can • X-ray diffraction generator and cameras and turbulence. Recent efforts include analytical, be “trained” rapidly to speak in a new language or • Facility for electronic transport and luminescence numerical and experimental work on a CO2, speaking style. Our work has been focused on sig- measurements as a function of temperature optical heterodyne system for remote measurement nal processing models of the human voice and their • Visible, ultraviolet, and infrared gas, solid state, of atmospheric cross winds and strength of use in data-driven speech synthesis algorithms. and dye lasers turbulence. Holmes This is an interdisciplinary field that draws • MOCVD crystal growth reactors elements from linguistics, computer science, • 1.25 meter visible and IR spectrometer Organizational Evolution machine learning, human perception, and digital In recent years an increased understanding of signal processing. van Santen, Hosom • High-performance optical microscope evolutionary processes has emerged from work in • Depth profiling ellipsometer molecular biology, computer science and complex VLSI Architecture for Intelligent Computing • Photolithography and semiconductor metallization Some of the most fundamental problems in systems analysis. This new understanding poten- • Sputter etching tially can be harnessed by managers to create computing involve teaching computers to act in • Device interconnect and packaging human organizations which evolve rapidly in a more intelligent manner. Key to this is the desired directions. Our objective is to develop a efficient representation of knowledge or contextual • C-V, I-V measurement facilities conceptual toolkit for “evolutionary management”. information. In this project a variety of highly • Pulsed uv-laser processing system In our research, we draw analogies between parallel algorithms are studied, including • Electrical characterization (Hall) policies and genes, between mutations and policy neuromorphic structures, with the intent of • Sputtering machine innovations, and between recombination and implementing knowledge representation and • Atomic layer epitaxy learning. We present a theoretical framework manipulation in silicon. Hammerstrom • Liquid crystal display lab with pretilt rubbing, and drawing on a computer simulation environment MEMS and Micro-sensors single-cell electro-optic characterization facilities combining system dynamics modeling with genetic Microelectromechanical systems (MEMS) and • Scanning Auger Microprobe algorithms. Currently, we use this framework to micro-sensors are rapidly becoming ubiquitous in explore the evolutionary implications of • Spectroscopic Ellipsometers technological society. Research applications range management hierarchy and team learning. House from micro-cilia, micro-turbines, and chips that

56 ELECTRICAL AND COMPUTER ENGINEERING | ECE walk to MEMS & micro-sensors that have been tronics companies were taken here at OGI. commercialized in diverse applications such as Focused ion beams are used to locate micron and airbag accelerometers and ‘electronic noses’ used sub-micron structures and produce cross-sections to detect gases and chemicals. While VLSI fabrica- of these structures for examination in scanning tion techniques are exploited to produce MEMS and transmission electron microscopes. The deep and micro-sensor devices economically, these sub-micron development efforts now in progress devices can be fabricated by an even greater require the nano- and atomic scale characteriza- range of processes and with a far wider variety of tion feedback on fabrication processes provided by materials. The MEM/micro-sensor microfabrica- these FIB produced cross-sections for the develop- tion laboratory in ECE is building glucose sensors, ment efforts to be successful. The FIB is also used pressure sensors, and even micro-peristaltic to modify existing microelectronic devices by pumps with a multidisciplinary exposure to adding or removing components by the removal or mechanics, electronics, physics and fluid dynam- addition of conductors and insulators. This permits ics. Research and courses on MEMS and designers to test a change in a device quickly and micro-sensors are focused on developing inexpensively before making a costly change to a understanding of a large toolbox of processes and fabrication line or a mask. More generally the FIB materials to design and fabricate these devices. provides the ability to micro-machine and micro- Scholl, House, McCarthy form on the micron and sub-micron scale in three dimensions. This has applications in the MEMS, Microanalysis sensor and biotechnology fields as a micron and The characterization, failure studies and in-situ sub-micron prototype fabrication tool. The FIB is testing of materials and structures used in micro- also a lithography tool that does not require electronics, opto-electronics, micro electro- resists. A region is made chemically more active mechanical systems(MEMS), sensors and biotech- by careful control of the area of beam scan, beam nology require a range of techniques that allow the energy and dwell to produce a volume of material measurement of properties on an ever decreasing that reacts when subjected to wet or dry etches. scale. Probing materials on the sub-micron and There is active research at OGI-ECE on the devel- nanometer scales was first necessary in the fabri- opment of sub-micron cantilevers as high cation of sub-micron transistors to provide frequency electromechanical switches using ion feedback on the thin film fabrication processes. lithography. McCarthy These same thin film processes are now being employed by the budding biotechnology, MEMS and sensor industries. The probing is accomplished by scanned atomic force microscope tips, light, electron and ion beams. The signals produced by the probes are used to create high resolution images of surfaces and internal structures, measure compositions, thickness, roughness and identify crystal structures. The geometries, crystal structures, elements present and compositions revealed can then be correlated with electrical, mechanical, thermal and optical properties or more generally the performance of a microelctronic device, MEMS or sensor. The development of microanalysis techniques and application to research and development projects at OGI-ECE has a long history and continues to be a major portion of efforts here. Optical, atomic force, scanning electron, scanning Auger electron and transmission electron microscopes are used to characterize materials following tests, changes in processes or failures in service. The recent addition of a heating straining stage to the SEM and a heating stage with electrical feed-through’s to the TEM will permit the complete evolution of microstructures during thermal processing or mechanical failures to be recorded digitally giving a more complete and accurate picture of mechanisms of change in materials on the micron and nanometer scales. McCarthy, House, Freeouf Focused Ion Beam Technology The use of focused ion beam workstations(FIB) in the microelectronics industry as development and production tools is widespread. The first research and development steps in producing practical FIB workstations in collaboration with local microelec-

57 ECE | ELECTRICAL AND COMPUTER ENGINEERING | FACULTY

DAN HAMMERSTROM ANTHONY E. BELL C. NEIL BERGLUND JOHN L. FREEOUF Doug Strain Professor Associate Professor Professor Professor and Department Head Ph.D., Physical Chemistry Ph.D., Electrical Engineering Ph.D., Physics, Ph.D., Electrical Engineering University of London, 1962 Stanford University, 1964 University of Chicago, 1973 1977, University of Illinois [email protected] [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS Development of liquid metal field Management of technology, and The large and growing Neuromorphic computing. ion sources; field ionization, advanced lithography for semiconductor industry has clearly Application of FPGAs to image surface physics, and chemistry; semiconductor fabrication. established that to control processing, digital video, field emission microscopy and something you must be able to intelligent and neuromorphic energy distribution measurements. REPRESENTATIVE PUBLICATIONS measure it. A major thrust of my computing. VLSI design. Highly Selected area processing for J. Ye, M. Takac, C.N. Berglund, research efforts is to determine parallel computer architecture microcircuit fabrication using G. Owen & R.F.W. Pease, “An Exact how to measure the specific and microarchitecture. focused electron beams. Direct- Algorithm for the Self-Calibration of parameters required to best Technology transfer. write electron-beam lithography Precision X-Y Stages,” Conference on understand and improve our Electron, Ion & Photon Beam for both mask making and IC Technology and Nanofabrication, semiconductor materials and REPRESENTATIVE PUBLICATIONS fabrication using multiple photo- May 1996. devices. Typically, these D. Hammerstrom, “Computational emitted electron beams. Plasma measurements will involve M.T. Takac, J. Ye, M.R. Raugh, R.F.W. Neurobiology Meets Semiconductor processing for thin film deposition Pease, C.N. Berglund & G. Owen, incident photons; the output may Engineering,” Invited Paper MultiValued and etching. “Self-Calibration in Two Dimensions: be either photons or some Logic 2000, May 2000. The Experiment,” 1996 SPIE electrical response. S. Rehfuss & D. Hammerstrom, REPRESENTATIVE PUBLICATIONS International Symposium on Microlithography, March 1996. “Comparing SFMD and SPMD A.E. Bell & D.F. Barofsky, “Field REPRESENTATIVE PUBLICATIONS Computation for On-Chip Emission and Field Ionization,” in W. Wang, J. Ye, A.B. Owen, C.N. Seung-Gu Lim, Thomas N. Jackson, Multiprocessing of Intermediate Level Encyclopedia of Applied Physics, Berglund & R.F.W. Pease, “Adaptive W.C. Mitchel, R. Bertke and J.L. Image Understanding Algorithms,” 6, 379, 1993. Metrology: An Economical Strategy for Freeouf, Optical Characterization of Proceedings of the conference for Judging the Acceptability of a Mask 4H-SiC by Far Ultraviolet Spectroscopic Computer Architectures for Machine A.E. Bell, K. Jousten & L.W. Swanson, Pattern,” J. Vac. Sci. Technol., B13(6), Ellipsometry, Applied Physics Letters, Perception 1997, Boston, MA, “High Field Ion Sources,” Rev. Sci. Intr., November/December 1995. vol. 79, No. 2, 2001. October 1997. 61(1) Part II, 363, 1990. J. Ye, C.N. Berglund & R.F.W. Pease, Todd Holden, P. Ram, Fred H. Pollak, D. Hammerstrom & D. Lulich, “Image S. Rao, A.E. Bell, G.A. Schwind & “Field Distortion Characterization Using J. L. Freeouf, B. X. Yang and M. C. Processing Using One-Dimensional L.W. Swanson, “Angular Distribution Linewidth or Pitch Measurement,” Tomargo, Spectral Ellipsometry Processor Arrays,” The Proceedings of of Ions from a AuSi Liquid Metal J. Vac. Sci. Technol. B13(6), Investigation of Zn Cd Se Lattice the IEEE, 84(7), 27-43, July 1996. Source,” J. Vac. Sci. Technol., A8(3), November/December 1995. 2258, 1990. Matched to InP, Physical Review B56, S. Rehfuss & D. Hammerstrom, J. Ye, C.N. Berglund, J. Robinson & 4037, 1997. “Model Matching and Single Function S. Rao, A.E. Bell, G.A. Schwind & R.F.W. Pease, “A Review of Mask Errors M. Leibovitch, P. Ram, L. Malikova, Multiple Data Computation (SFMD),” L.W. Swanson, “A Combination on a Variety of Pattern Generators,” Fred H. Pollak, J. L. Freeouf, L. Kronik, NIPS Proceedings, November 1995. Electron/Ion Field Emission Source,” IEEE Transactions on Semiconductor J. Vac. Sci. Technol., B7, 1793, 1989. B. Mishon, Yoram Shapira, A. R. D. Hammerstrom, “Digital VLSI for Manufacturing, 8(3), 319-325, Clawson, and C. M. Hanson, Reflection Neural Networks,” Handbook of Brain L.W. Swanson & A.E. Bell, “Liquid August 1995. Anisotropy Spectroscopy, Surface Theory and Neural Networks, M. Arbib Metal Ion Sources,” I.G. Brown (Ed.), J. Ingino, G. Owen, C.N. Berglund, Photovoltage Spectroscopy, and (Ed.), Bradford Books/MIT Press, 1995. The Physics and Technology of Ion R. Browning & R.F.W. Pease, Contactless Electroreflectance Sources, John Wiley & Co., 313, 1989. D. Hammerstrom, “A Digital VLSI “Workpiece Charging in Electron Beam Investigation of the InP/In0.53Ga0.47As Architecture for Real World Lithography,” J. Vac. Sci. Technol., (001) Heterojunction System, J. Vac. Applications,” An Introduction to B12(3), 1367-1371, May/June 1994. Sci. Technol. B14, 3089, 1996. Neural and Electronic Networks, J. L. Freeouf, N. Braslau, and M. S.F. Zornetzer, J.L. Davis, C. Lau Wittmer, Lifetime Measurements on & T.McKenna (Eds.), Academic Silicon on Insulator Wafers, Appl. Phys. Press, 1995. Lett. 63, 198, 1993. M. Wittmer and J. L. Freeouf, Ideal Schottky Diodes on Passivated Silicon, Phys. Rev. Lett. 69, 2701, 1992. J. L. Freeouf, D. A. Buchanan, S. L. Wright, T. N. Jackson, and B. Robinson, Accumulation Capacitance for GaAs SiO2 Interfaces With Si Interlayers, Appl. Phys. Lett. 57, 1919, 1990.

58 FACULTY | ELECTRICAL AND COMPUTER ENGINEERING | ECE

KENTON GREGORY HYNEK HERMANSKY J. FRED HOLMES JODY HOUSE Associate Professor Professor Professor Emeritus Assistant Professor M.D. School of Medicine Dr. Eng., Electrical Engineering Ph.D., Electrical Engineering Sc.D., Electrical University of Southern California, University of Tokyo, 1983 University of Washington, 1968 Engineering 1998. 1980 [email protected] [email protected] Massachusetts Institute of Technology RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS [email protected] Application of laser energy for the Communication between human Speckle propagation through treatment of altherosclerotic and machine; human perception turbulence, optical remote RESEARCH INTERESTS vascular disease, laser and its computer simulation; sensing of wind and turbulence, Electronic and photonic device thrombolysis in acute myocardial speech production and perception; electro-optic systems, design for microsensor infarction and stroke, vascular automatic recognition of speech, instrumentation signal processing, applications with a current smooth muscle response to light, speech coding, synthesis and and biomedical optics. concentration on materials. Elastin biomaterials for tissue enhancement; identification Applications in genetic algorithms replacement and repair, and dye- and extraction of linguistic REPRESENTATIVE PUBLICATIONS and programs as applied to targeted laser-tissue fusion. information in realistic J. Fred Holmes, Steven L. Jacques, electronic materials and devices communication environments. and John M. Hunt, “Adapting as well as human organizations. REPRESENTATIVE PUBLICATIONS atmospheric lidar techniques to imag- System dynamics modeling of ing biological tissue”, SPIE, Bios 2000 M.J. Girsky, K.W. Gregory, A. Shearin REPRESENTATIVE PUBLICATIONS human organizations for public Conference, San Jose, California, & S.A. Prahl, “Photoacoustic Drug H. Hermansky, “Should Recognizers January 22 - 28, 2000. policy development. The role early Delivery to Arterial Thrombus: A New Have Ears?” Speech Communication, engineering education processes M. Becker, J.F. Holmes, & L. Meekisho, Method for Local Drug Delivery,” Publishers, Holland, June 1998. have in retention and attraction of American Heart Association, 69th “Interdisciplinary Curriculum Annual Scientific Session, New Orleans, H. Hermansky, “Modulation Spectrum Development in Electronics Packaging female engineering students. LA, November 1996. in Speech Processing, in Signal Using Course Segmentation,” ASEE Analysis and Prediction,” Prochazka, 1998 Frontiers in Education REPRESENTATIVE PUBLICATIONS K.W. Gregory, “Laser Thrombolysis Uhlir, Rayner, Kingsbury, Eds., 1998. Conference, Tempe, Arizona, in Acute Myocardial Infarction,” Hines, J. and House, The Source of November 4-7, 1998. Current Review of Interventional H. Hermansky & N Malayath, Poor Policy: Controlling Learning Drift Cardiology (D. Holmes Jr. & P. “Speaker Verification using Speaker- J.F. Homes & B. J. Rask, “Range and Premature Consensus in Human Serruys), 3rd Edition, August 1996. Specific Mappings,” Proceedings Resolved, 3-D Optical Remote Sensing Organization. System Dynamics Review, of Speaker Recognition and its of Atmospheric Winds Using a CW 17(1); p. 3-32, 2001. E.N. LaJoie, A.D. Barofsky, K.W. Commercial and Forensic Application, Lidar,” Advances in Atmospheric Gregory & S.A. Prahl, “Welding Artifical Hines, J.H. and J.L. House. France, 1998. Remote Sensing with Lidar, A. Biomaterial with a Pulsed Diode Laser Management fads & poor policies: A Amsmann, R. Neuber, P. Rairoux, and and Indocyanine Green,” SPIE, Laser C. Avendano & H. Hermansky, “On year of organization evolution research. U. Wandinger (eds.), Springer-Verlag, Tissue Interaction VI (S.L. Jacques, the Properties of Temporal Processing In 2001 NSF Design and Manufacuring Berlin, 1997. Ed.), San Jose, CA, 1995. for Speech in Adverse Environments,” Research Conference. Tampa, FL, 2001 Proceedings of 1997 Workshop on J. F. Holmes & C. Zhou, “Path H. Shangguan, L.W. Casperson, House, J.A. Kain and J. Hines. Application of Signal Processing to Resolved, Optical Remote Sensing of A. Shearin, K.W. Gregory & S.A. Prahl, Evolutionary Algorithm: Metaphor for Audio and Acoustics, Mohonk Mountain the Strength of Turbulence Using a “Photoacoustic Drug Delivery: The Learning. In Genetic and Evolutionary House, New Paltz, New York, Pseudo Random Code Modulated CW Effect of Laser Parameters on Spatial Computation Conference. Las Vegas, October 1997. Lidar and Coherent Optical Distribution of Delivered Drug,” SPIE, NV: Morgan Kaufmann, 2000. Processing,” 9th Conference on Laser Tissue Interaction VI (S.L. S. Tibrewala & H. Hermansky, “Multi- Coherent Laser Radar, Linkoping, Jacques, Ed.), San Jose, CA, 1995. band and Adaptation Approaches to Robust Speech Recognition,” to appear Sweden, June, 1997. K.W. Gregory & J.M. Grunkemeier, in Proceedings of EUROSPEECH ‘97, J.F. Holmes & B.J. Rask, “The Effect “Arterial Reconstruction using an Rhodos, Greece, September 1997. of Aerosol Speckle Phase Decorrelation Elastin-based Biopolymer with Dye on the Allowable Signal Averaging Time Targeted Diode Laser Fusion,” S. van Vuuren & H. Hermansky, for Coherent Optical Receivers,” SPIE American Society for Laser Medicine “Data-driven Design of RASTA-like Annual Meeting, August 1996. and Surgery, 15th Annual Meeting, Filters,” Proceedings of EUROSPEECH San Diego, CA, April 1995. 97, Rhodos, Greece, September 1997. J.F. Holmes & B.J. Rask, “Range H. Hermansky, C. Avendano, S. van Resolved, 3-D, Optical Remote Vuuren, & S. Tibrewala, “Recent Sensing of Atmospheric Winds Using a Advances in Addressing Sources of CW Lidar,” 18th International Laser Non-Linguistic Information,” Radar Conference, Berlin, Germany, Proceedings of ESCA-NATO Tutorial July 1996. and Research Workshop on Robust J.F. Holmes & B.J. Rask, “Optimum, Speech Recognition for Unknown Optical Local Oscillator Levels for Communication Channels, 103-106, Coherent Detection Using Photodiodes,” Pont-a-Mousson, France, April 1997. Appl. Opt., 34, February 1995.

59 ECE | ELECTRICAL AND COMPUTER ENGINEERING | FACULTY

ROBERT S. JAFFE MARWAN JABRI M. Schenkel and M.A. Jabri,† “Low STEVEN L. JACQUES Instructor Gordon and Bettie Moore resolution degraded document recogni- Professor tion using neural networks and hidden Ph.D., in Electrical and Professor of Microelectronics Markov models,” Pattern Recognition Ph.D., Biophysics Computer Engineering Ph.D., Electrical Engineering Letters, V19 N3-4 pp. 365-371, 1998. and Medical Physics Portland State University in 1988 University of Sydney 1988 University of California, M. Partridge and M.A. Jabri, [email protected] [email protected] “Template Decision Trees,” Journal of Berkeley, 1984 Applied Intelligence, 1997. [email protected] RESEARCH INTERESTS RESEARCH INTERESTS M.A. Jabri and E. Tinker, “Classifier Robert S. Jaffe is a full-time Artificial intelligence, computer architectures for Single Chamber RESEARCH INTERESTS Arrhythmia Recognition,” Journal of instructor in ECE. He teaches in architecture. The understanding Biomedical optics and laser-tissue Applied Intelligence, Kluwer Academic the areas of signals and systems, of the principles by which Press, 6:3, pp. 215-224, July 1996. interactions. Development of applied mathematics and humans and/or other organisms diagnostic and therapeutic devices M.A. Jabri, R. Coggins and B. Flower, mathematical systems theory. His perceive the environment, “Adaptive Analog Neural Systems,” for medicine and biology using area of specialization is linear process sensory signals, reason, Chapman and Hall, UK, 1996. optical technologies. systems and robust control. He make decisions and learn. The M.A. Jabri, “Neural Networks for received a Ph.D. in Electrical and design and engineering of ECG Signal Interpretation,” Handbook REPRESENTATIVE PUBLICATIONS Computer Engineering from humanoids that exhibit faculties of Neural Computation, Institute of S. L. Jacques, J. R. Roman, K. Lee, Portland State University in 1988. similar to humans. Physics Publishing and Oxford “Imaging superficial tissues with polar- During an earlier career phase he University Press, G2.5, 1996. ized light,” Lasers Surg. Med. was a Professor of Philosophy and REPRESENTATIVE PUBLICATIONS 26:119-129, 2000. a researcher in the philosophy of O. Coenen, M. Arnold, T. Sejnowski L. V. Wang, S. L. Jacques, “Source of education. and M. Jabri, Bayesian analysis of error in calculation of optical diffuse parallel fiber coding in the Cerebellum, reflectance from turbid media using dif- ICONIPí2000, pp 1301-1306, fusion theory,” Comput Methods Korea, 2000. Programs Biomed. 61(3):163-170, 2000. M.A. Jabri and R. Coggins, “Micro Power Adaptive Circuits for S. L. Jacques, “Modeling photon Implantable Devices,” Low Power – transport in transabdominal fetal Low Voltage Circuits and System, oximetry,” J Biomed. Optics, in press, E. Sanchez-Sinencio & Andreas 2000. Andreou Editors, IEEE Press, USA, S. L. Jacques, “Light distributions pp. 500-518, 1999. from point, line, and plane sources for Raymond J. W. Wang and Marwan photochemical reactions and fluores- Jabri, “A Computational Model of cence in turbid biological tissues,” the Auditory Pathway to the Superior Photochem. Photobiol. 67:23-32, 1998. Colliculus,” in Brain-like computation S. L. Jacques, S. J. Kirkpatrick, and Intelligent Information Systems, “Acoustically modulated speckle imag- Shun-ichi Amari and Nikola Kasabov ing of biological tissues,” Optics (Eds.), Springer Verlag, pp. 81-104, Letters, 23:879-881, 1998. 1998. S. L. Jacques, “Path integral descrip- R. Coggins, R. Wang and M.A. Jabri, tion of light transport in tissue,” Ann N “A micropower adaptive linear trans- Y Acad Sci. 9;838:1-13, 1998. form vector quantiser,” to appear in Analog integrated circuits and signal processing, Kluwer, February 1999. R. Coggins, M.A. Jabri, A Low Complexity Intracardiac Electrogram Compression Algorithm, IEEE Transactions on Biomedical Engineering, Vol. 46, No. 1, pp. 82-91, January 1999. X.Q. Li and M.A. Jabri, “Machine learning based VLSI Cells Shape Function Estimation,” IEEE Transactions on CAD for Integrated Circuits and Systems, Vol 17, No. 7, pp. 613-623, 1998.

60 FACULTY | ELECTRICAL AND COMPUTER ENGINEERING | ECE

JOHN-PAUL HOSOM SEAN J. KIRKPATRICK Kirkpatrick, S.J. and Jacques, S.L., JACK McCARTHY Acoustically modulated speckle imaging Assistant Professor Associate Professor of soft tissue, ASME BED vol. 43, 1999 Assistant Professor Ph.D., Computer Science Ph.D., Biomechanics Advances in Bioengineering, Wayne, Ph.D., Materials Science and Engineering University of Miami, 1992 J.S. (Ed.), American Society of and Engineering 2000, Oregon Graduate [email protected] Mechanical Engineers, N.Y., 1999. Oregon Graduate Institute of Institute of Science and Technology Kirkpatrick, S. J. Transform method Science and Technology, 1996 [email protected] RESEARCH INTERESTS for laser speckle strain rate measure- [email protected] ments in biological tissues and Development and application of biomaterials. In “Light Scattering RESEARCH INTERESTS coherent light techniques to Technologies in Biomedicine and RESEARCH INTERESTS Automatic speech recognition address issues in biomaterials Materials Science”, SPIE Press, Mechanisms of change in (ASR). Time alignment of science and tissue mechanics. Bellingham, WA, 1998. metallization and insulator thin phonemes. Acoustic-phonetic Laser speckle techniques are of Kirkpatrick, S.J. and Cipolla, M.J. films used in microelectronic analysis of speech. particular interest. Recent High resolution imaged laser speckle applications, in-situ testing of Assistive technology. investigations have focused on the strain gauge for vascular applications. these films in transmission and J. Biomed. Optics (accepted), 1998. evaluation of the micromechanical scanning electron microscopes to REPRESENTATIVE PUBLICATIONS behavior of vascular, Jacques, S.L. and Kirkpatrick, develop better processing S.J. Acoustically modulated speckle Hosom, J.P., “Automatic Speech dermatological, and skeletal techniques and more reliable thin imaging of biological tissue. Opt. Recognition,” in H. Bidgoli, S. B. Eom, tissues using novel laser speckle Letters 23:879-881, 1998. films. The development of focused A. Prestage (Eds.), Encyclopedia of strain measurement methods. ion beam processes for the Information Systems. San Francisco: We envision that these Kirkpatrick, S.J. and Brooks, fabrication of structures on the Academic Press, 2001. B.W. Micromechanical behavior of investigations will lead not only cortical bone as inferred from laser micron and sub-micron scales to Hosom, J.P. and Cole, R.A., “Burst to an expansion of our basic speckle data. J. Biomed. Mater. Res. produce sensors and electro- Detection Based on Measurements of science understanding of tissue 3:373-379, 1998. mechanical devices for testing the Intensity Discrimination,” Proceedings of ICSLP 2000, Beijing, vol. IV, pp. 564- mechanics and laser-tissue physical properties of sub-micron 567, October 2000. interaction, but will also result thin films. Thin film transmissive Cosi, P. and Hosom, J. P., “High in optical instrumentation to photocatodes for use in multi- Performance General Purpose Phonetic assist in the diagnosis and beam electron lithography and Recognition for Italian,” Proceedings of treatment of disease. Other surface reactions at the emission ICSLP 2000, Beijing, vol. II, pp. 527- interests include experimental site. Materials characterization 530, October 2000. investigations into the techniques using analytical Hosom, J.P., Cole, R.A, and Cosi, P., micromechanics of synthetic electron microscopy and focused “Improvements in Neural-Network biomaterials used to replace ion beam technology. Training and Search Techniques for or augment damaged or Continuous Digit Recognition,” pathological tissue. REPRESENTATIVE PUBLICATIONS Australian Journal of Intelligent Information Processing Systems (AJI- F. Radulescu, J.M.McCarthy, “The IPS), vol. 5, no. 4, pp. 277-284, REPRESENTATIVE PUBLICATIONS Effect of Stress in the PdGe Mediated Summer 1999, (invited paper). Kirkpatrick, S.J. and Duncan, Solid Phase Epitaxial Growth of Ge on GaAs,” MRS Symposium Proceedings, Cole, R.A., Serridge, B., Hosom, J.P., D.D., Processing techniques for laser speckle data derived from Substrate Engineering for Epitaxy, Cronk, A., and Kaiser, E., “A Platform 587, 1999. for Multilingual Research in Spoken biological tissues, J. Biomed. Optics Dialogue Systems,” Proceedings of the (in press), 2001. F. Radulescu, J.M.McCarthy, E.Stach Workshop on Multi-Lingual Kirkpatrick, S.J. and Duncan, “In-Situ Annealing Transmission Interoperability in Speech Technology D.D. Acousto-optic elastography, Electron Microscopy of Pd/Ge/Pd/GaAs (MIST), Leusden, The Netherlands, Proceedings SPIE 4257, 2001. Interfacial Reactions,” MRS Symposium September 1999. Proceedings, Advances in Materials Patrickeyev, I., Kirkpatrick, S.J., and Problem Solving with the Electron Hosom, J. P. and Yamaguchi. M., Duncan, D.D., Tracking speckle motion Microscope, 589, 1999. “Proposal and Evaluation of a Method with directional wavelets, Proceedings for Accurate Analysis of Glottal Source SPIE 4257, 2001. J.McCarthy, Z. Pei, M.Becker, Parameters,” The Institute of D.Atteridge “FIB Micromachined Kirkpatrick, S.J. and Cipolla, Electronics, Information and Submicron Thickness Cantilevers for M.J., High resolution images laser Communication Engineers (IEICE) the Study of Thin Film Properties,” speckle strain gauge for vascular Transactions on Information and Thin Solid Films 358 (2000) p146-151. applications, J. Biomed Optics, 5(1): Systems, vol. E77-D, no. 10, pp. 1130- Accepted 8/31/99. 62-71, 2000. 1141, October 1994.

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S. Gosavi, J.M.McCarthy, C.N. MISHA PAVEL H. Hermansky & M. Pavel, SCOTT A. PRAHL Berglund, W.A.Mackie, L.A.Southall Professor “Psychophysics of Speech Engineering Assistant Professor “Practical Gold Thin Film Systems,” invited paper, Proceedings Ph.D., Experimental Psychology Ph.D., Biomedical Engineering Photocathodes for Advanced Electron of the 13th International Congress on Beam Lithography,” BACUS Symposium New York University, 1980 Phonetic Science, Stockholm, Sweden, University of Texas at Austin, 1988 on Photomask Technology, SPIE [email protected] August 1995. [email protected] Vol.3873, September 1999. P. Suppes, M. Pavel & J. Falmagne, Z. ei, J.McCarthy, C.N.Berglund, RESEARCH INTERESTS “C. Representations and Models in RESEARCH INTERESTS T.H.P.Chang, M.Mankos, K.Y.LEE Psychology,” Annu. Rev. Psycho., Analysis and modeling of complex Diagnostic and therapeutic and M.L.Yu, “Thin Film Gated 45, 517, 1994. Photocathode for e-Beam Lithography,” behaviors of biological systems, applications of light in medicine: M. Pavel, “Predictive Control of J.VAC.Sci.Technol.B 17(6), including visual and auditory laser thrombolysis, non-invasive Eye Movement,” in E. Kowler (Eds.), p2814, 1999. processing, pattern recognition, Eye Movement and Their Role in optical diagnostics, hemostasis J.M. McCarthy, SEM and TEM information fusion and decision Visual and Cognitive Processes, and tissue repair. Characterization of Materials making. Development of 71-114, Amsterdam, Elsvier, 1990. Using a Focused Ion Beam Milling engineering systems mimicking REPRESENTATIVE PUBLICATIONS Workstation, IMS Conference these abilities to support Wadia Y, Xie H, Kajitani M, and Prahl Proceedings in Materials multimodal communication SA, Liver repair and hemorrhage con- Characterization.Accepted 1997. between humans and machines trol using laser soldering of liquid (speech and video), machine albumin in a porcine model, in SPIE Proceedings of Lasers in Surgery, vol. vision, visually guided vehicular 3907, 74-81, 2000. control, and virtual reality. Viator JA, Jacques SL, and Prahl SA, Applications of these Depth profiling of absorbing soft mate- techniques to the development rials using photoacoustic methods, of future biomedical and IEEE Journal of Selected Topics in healthcare systems. Quantum Electronics 5:989-996, 1999. Viator JA and Prahl SA, Laser REPRESENTATIVE PUBLICATIONS thrombolysis using long pulse frequen- J. Palmer, P. Verghese, and M. Pavel, cy-doubled Nd:YAG lasers, Lasers in The psychophysics of visual search, Surgery and Medicine 25:379-388, Vision Research, 40, 1227-1268, 2000. 1999. Arai, T., Pavel, M., Hermansky, H., Prahl SA, Denison T, and La Joie EN, and Avendano, C. Syllable intelligibility Laser repair of liver, in Malek RS, ed., for temporally filtered LPC cepstral SPIE Proceedings of Lasers in Surgery: trajectories, The Journal of the Advanced Characterization, Acoustical Society of America, 105, Therapeutics and Systems XI, 2783-2791, 1999. vol. 4244, 2001. Sharma, R.K., Leen, T.K., and Pavel, Paltaulf G, Viator JA, Prahl SA, M. Probabilistic image sensor fusion. In and Jacques SL, Iterative reconstruc- M.S. Kearns, S.A. Solla, and D.A. Cohn tion method for three-dimensional (Eds.), Advances in Neural Information optoacoustic imaging, Journal Processing Systems 11. Cambridge, of Acoustic Society of America MA: MIT Press, 1999. (submitted). M. Pavel and H. Hermansky: Janis AD, Nyara AN, Prahl SA, “Information Fusion by Human and Gregory KW, and Buckley LA, A Machine,” in Proccedings of the First reconstituted in vitro clot model for European Conference on Signal evaluating laser thrombolysis, Lasers Analysis and Prediction, pp. 350-353, in Surgery and Medicine, (submitted). Prague, Czech Republic, June 1997. Moffitt TP and Prahl SA, Dual-sized M. Pavel & H.A. Cunningham, fiber reflectometry for measuring local “Eye Movements and the Complexity optical properties, IEEE Journal of of Visual Processing,” in M.S. Landy, Selected Topics in Quantum L.T. Maloney and M. Pavel (Eds.), Electronics, (submitted). Exploratory Vision: The Active Eye, 101-120 New York, NY, Springer-Verlag, 1996.

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SHANKAR RANANAVARE MILTON R. SCHOLL M. Scholl & P. Clayton, “Surface RAJ SOLANKI Associate Research Professor Associate Professor Texture and Abrasive Wear Resistance Professor of Some High Velocity Air Plasma Ph.D., Physical Chemistry Ph.D., Materials Science Sprayed Coatings,” Proceedings of the Ph.D., Physics University of Missouri, and Engineering 1991 National Thermal Spray Colorado State University, 1982 St. Louis, 1983 OGI School of Science Conference, Pittsburgh, PA, May 1991. [email protected] [email protected] and Engineering, 1987 [email protected] RESEARCH INTERESTS RESEARCH INTERESTS Atomic Layer Deposition, copper Nanotechnology: Nanoparticles RESEARCH INTERESTS electrodeposition and and Photoresists, Dynamics of Micro-mechanical systems and electromigration, multilevel complex systems, Ferroelectric, their design and use, particularly metallization, high k gate Antiferroelectric and Amphitropic the mechanics, the materials, and dielectrics, inorganic and organic Liquid Crystals, Flat Panel interaction of contacting surfaces, electroluminescent devices, Displays, Phase Transitions and i.e. tribology of microsystems. polysilicon thin film transistors. Critical Phenomena. Tribological systems ranging from chemical mechanical polishing, to REPRESENTATIVE PUBLICATIONS REPRESENTATIVE PUBLICATIONS fiber-plate interactions in chip H. Zhang and R. Solanki, Atomic Layer Ciro Di Meglio, S. B. Rananavare, refining and woodcutting, to Deposition of High Dielectric Constant S. Sorenson, D. H. Thompson, “ wheel-rail interactions. Nanolaminates, J. Electrochem. Soc. Bolaamphiphilic Phosphocholines: Tribological performance of 63, 148, 2001. Structure and Phase Behavior in materials including abrasive and (Invited paper) B. Pathangey and Aqueous Media,” Langmuir, 16, 128, R. Solanki, Atomic layer deposition for 2000. erosive wear, sliding behavior, rolling / sliding conditions and the nanoscale thin film coatings, Vacuum V.G.K.M. Pisipati & S.B. Rananavare, Tech. and Coatings, 1 , 32, 2000. interactions of the phenomena “X-Ray Diffraction Studies of 10O.14 with the working environment, R. Solanki and B. Pathangey, Atomic and 10O.8,” Mol. Cryst. Liq. Layer Deposition of Copper Seed focusing on surface response to Cryst.,238,, 207-214, 1994. Layers, Electrochem and Solid-State J.H. Freed, A. Naveem & S.B. external stimuli and mitigation Letters, 3 , 479, 2000. techniques to reduce or eliminate Rananavare, “ESR and Liquid Crystals: H. Zhang, R. Solanki, B. Roberds, Statistical Mechanics and Generalized surface damage. G. Bai, and I. Banerjee, High Smoluchowski Equations,” Chapter 4, Permittivity Thin Film Nanolaminates, 71-84, “ESR and Molecular Motions in REPRESENTATIVE PUBLICATIONS J. Appl. Phys. 87, 1921, 2000. Liquid Crystals,” “Thermodynamics of M. Scholl, “Abrasive wear of titanium Liquid Crystals and the Relation to A.T. Voutsas, M.A. Marmorstein, nitride coatings,” Wear, Vol. 203-204, Molecular Dynamics: ESR Studies,” and R. Solanki, The Effect of Laser 57- 64, 1997. “ESR Studies of Molecular Dynamics at Annealing Ambient on the Performance Phase Transitions in Liquid Crystals,” M. Scholl, “Unique Thermal Spray of Excimer Laser Annealed Thin Film “ESR and Slow Motions in Liquid Coatings by High Energy Plasma Transistors,î J. Electrochemical Soc. Crystals,” Chapters 12-15, 271-402, Spraying,” Proceedings of the 146 , 3500, 1999. The Molecular Dynamics of Liquid International Conference on Advances R. Engelmann, J. Ferguson, and Crystals, (G. R. Luckhurst and in Welding Technology: Joining of High R.Solanki, “Quantum Well Activated C. A. Veracini eds.), NATO ASI Series, Performance Materials, Columbus, Phosphors-A New Concept for Kluwer Academic Publishers, Ohio, Nov. 6-8, 1996. Electroluminescent Displays,” Appl. Netherlands, 1994. D. Christensen, Y. Jia, M. Scholl, Phys. Lett. 70, 411, 1997. S.B. Rananavare, V.G.K.M. Pisipati & P. Clayton, & S. Abubakr, “Surface J. Fogarty, W. Kong, and R. E.W. Wong, “The ACC Multicritical Point Deterioration of Refiner Plates for Solanki,”Monte Carlo Simulation of in Ferroelectric Liquid Crystals,” Phys. Thermo-Mechanical Pulping,” High Field Electron Transport in ZnS,” Rev. Lett, 72, 3558, 1994. Proceedings of the 1994 Pulping Solid-State Electronics, 38, 653, 1995. Conference, Nov. 6-10, 1994, San S.B. Rananavare, V.G.K.M. Pisipati Diego, California, pub. by TAPPI Press, W. Kong and R. Solanki, “The Effect & E.W. Wong, “A Lifshitz Point in Atlanta, 1994, pp. 193-203. of Ultraviolet Radiation on a ZnS:Tb Ferroelectric Liquid Crystals,” Liquid Thin Film Electroluminescent Device,” Crystal Materials, Devices and M. Scholl, “Plasma Spraying with Wire J. of Appl. Phys.75, 3311, 1994. Applications III, (R. Shashidhar, ed.), Feedstock,” Proceedings of the 1994 2175, 108-119, SPIE-94, San Jose, CA, National Thermal Spray Conference, T. Dosluoglu and R. Solanki, “Self- Feb. 8-10, 1994. Boston, MA, June 1994. Consistent Calculations of Carrier Distribution and Energy Bands in V. G. K. M. Pisipati and S. B. M. Scholl, C. Steinkamp & W.E. Wood, InGaAs/InP PIN Diodes,” Solid State Rananavare, “Interdigitated Smectic A “Acoustic Emission Monitoring of Comm., 85, 243, 1993. and B Mesophases in Higher Plasma Sprayed Tubes,” EWI Research Homologues of 50.m Series,” Liquid Report, 1994. Crystals, 13,757-764, 1993.

63 ECE | ELECTRICAL AND COMPUTER ENGINEERING | FACULTY

XUBO SONG JAN P.H. VAN SANTEN ERIC A. WAN YONGHONG YAN Assistant Professor Professor and Center Director Associate Professor Associate Professor Ph.D., Ph.D., Electrical Engineering of CSLU Ph.D., Electrical Engineering Computer Science California Institute Ph.D., Mathematical Psychology Stanford University, 1994 & Engineering, 1995 of Technology, 1998 University of Michigan, 1979 [email protected] [email protected] [email protected] [email protected] RESEARCH INTERESTS RESEARCH INTERESTS RESEARCH INTERESTS: RESEARCH INTERESTS Learning algorithms and Human computer interface Digital Image/Video Processing; Speech timing, intonation, signal architectures for neural design, spoken language system, Sensor Fusion; Computer Vision; processing, statistical analysis of networks and adaptive signal large vocabulary speech Pattern Recognition; Machine text and speech corpora, and text- processing; applications to recognition, computer vision, Learning; Information Theory and to-speech (TTS) system evaluation. time-series prediction, speech real time embedded system, Coding; Biomedical Engineering. enhancement, adaptive control, speech signal processing. REPRESENTATIVE PUBLICATIONS and telecommunications. REPRESENTATIVE PUBLICATIONS Gu W., Shih C., and van Santen J. REPRESENTATIVE PUBLICATIONS Xubo Song, Yaser Abu-Mostafa, Joseph “An Efficient Speaker Adaptation REPRESENTATIVE PUBLICATIONS X. Wu & Y. Yan. Linear regression Sill, Harvey Kasdan, “Image Recognition Method for TTS Duration Model”. E. A. Wan and R. van der Merwe, under maximum a posteriori criterion in Context: Application to Microscopic Proceedings of EUROSPEECH 99, The Unscented Kalman Filter. In with markov random field prior. In Urinalysis,” in Advances in Neural Budapest, Hungary, 1999. Kalman Filtering and Neural Networks, proceedings IEEE ICASSP2000, Information Processing Systems, chap. Chapter 7, Wiley Publishing, Eds. June 2000. S.A. Solla, T.K. Leen and K.-R.Muller, van Santen J., and Sproat R., “High- S. Haykin, 2001. Editors, MIT Press, pp. 963-969, 2000. accuracy automatic segmentation”. C. Liu and Y. Yan. Speaker change Proceedings of EUROSPEECH 99, E. Wan & A. Nelson, “Networks for detection using minimum message Xubo Song, Yaser Abu-Mostafa, Budapest, Hungary, 1999. Speech Enhancement,” in Handbook length criterion. In proceedings 6th Joseph Sill, Harvey Kasdan, of Neural Networks for Speech International Conference on Spoken “Incorporating Contextual Information Sproat R., van Santen J., “Automatic Processing, Edited by Shigeru Katagiri, Language Processing, vol 3. pp 514- into White Blood Cell Image Ambiguity Detection.” Proceedings of Artech House, Boston, USA, 1999. 515, October 2000. Recognition,” in Advances in Neural ICSLP 98. Sydney, Australia, 1998. Information Processing Systems, M.I. van Santen J. “Evaluation.” In E. Wan & F. Beaufays, “Diagrammatic C. Zheng, Y. Yan. Efficiently Using Jordan, M.J. Kearns and S.A. Solla, Multilingual Text-to-Speech Synthesis: Methods for Deriving and Relating Speaker Adaptation Data. In proceed- Editors, MIT Press, pp. 950-956, 1998. The Bell Labs Approach Kluwer, Temporal Neural Networks Algorithms, ings ICSLP, 2000. In Adaptive Processing of Sequences Yaser Abu-Mostafa, Xubo Song, Dordrecht, 1998. Y. Yan. Speech Recognition using cor- and Data Structures,” Lecture Notes “Bin Model for Neural Networks,” van Santen J., Sproat R.W., Olive J., relation generated neural network in Artificial Intelligence, M. Gori & in Proceedings of the International and Hirschberg J. (Eds.). Progress in target. IEEE Trans. on Speech and C.L. Giles (eds.), Springer Verlag, Conference on Neural Information speech synthesis. Springer Verlag, Audio Processing, May 1999. 1998. Processing, S. Amari, L. Xu, L. Chan, New York, 1996. E. Barnard,Y. Yan. Toward new I. King and K. Leung, Editors, Springer, E. Wan and A. Nelson, “Neural language adaptation for language pp. 169-173, 1996. Dual Extended Kalman Filtering: identification. Speech Communication, Applications in Speech Enhancement Xubo Song, “Contextual Pattern 21(4):245-254, May 1997. and Monaural Blind Signal Separation,” Recognition with Applications to IEEE Workshop on Neural Networks Y. Yan, E. Barnard, R.A. Cole. Biomedical Image Identification,” and Signal Processing, 1997. Development of an Approach to PhD Thesis, California Institute of Automatic Language Identification Technology, 1999. E. Wan, “Adjoint LMS: An Alternative based on Phone Recognition. In to Filtered-X LMS and Multiple Error Yaser Abu-Mostafa, Xubo Song, Computer, Speech Language, Volume LMS,” ICASSP96, 3, 1842-1845, 1996. Alexander Nicholson, Malik Magdon- 10(1), pp. 37-54, January 1996. Ismail, “The Bin Model,” under revision E. Wan, “Time Series Prediction Using for IEEE Transactions on Information a Neural Network with Embedded Theory, 2001. Tapped Delay-Lines,” in Predicting the Future and Understanding the Past, A. Xubo Song, “Pattern Recognition in Weigend and N. Gershenfeld (eds.), SFI Context,” to be submitted to IEEE Studies in the Science of Complexity, Transactions on Pattern Analysis and Proc., 17, Addison-Wesley, 1993. Machine Intelligence, 2001. E. Wan, “Discrete Time Neural Xubo Song, “Contextual Biomedical Networks,” Journal of Applied Image Recognition,” to be submitted Intelligence, 3(1), 91-105, 1993. to IEEE Transactions on Biomedical Engineering, 2001. E. Wan, “Neural Network Classification: A Bayesian Malik Magdon-Ismail, Xubo Song, Interpretation,” IEEE Transactions “Effective Choice of Weight Decay on Neural Networks, 1(4), 303-305, Parameters,” to be submitted to Neural December 1990. Computation, 2001.

64 FACULTY | ELECTRICAL AND COMPUTER ENGINEERING | ECE

JOINT FACULTY ADJUNCT FACULTY ROY KRAVITZ APPOINTMENTS Radisys Corporation JOHN C. ABELE ROB DAASCH Lewis and Clark College WILLIAM A. MACKIE Electrical Engineering Linfield College Portland State University SHARIAR S. AHMED Intel Corp. V. DAKSHINA MURTY JACK FERRACANE University of Portland School of Dentistry CHEDLEY AOURIRI Oregon Health & Intel Corp. HAMID RABIEE Science University Intel Corp. AHMED RAHHAL-ARABI ANDREW FRASER Intel Corp. KARTIK RAOL Portland State University Intel Corp. SHEKHAR BORKAR TODD LEAN Intel Corp. EDWARD F. RITZ, JR. Computer Science and Engineering Consultant OGI School of Science STEVE BRAINERD & Engineering Integrated Device Technology, Inc. LAWRENCE RUBY University of California, Berkeley SHIH-LIEN LU ROB CONTOLINI Computer Science Novellus LYNWOOD W. SWANSON Oregon State University FEI Co. ALAN COPPOLA JOHN E. MOODY Cypress Semiconductor, Inc. STEWART S. TAYLOR Computer Science and Engineering Maxim OGI School of Science DOUGLAS C. DRAPER & Engineering Portland Community College THOMAS THOMAS Intel Corp. NELSON MORGAN STEPHEN R. EARLY Electrican Engineering & Consultant TRAN THONG Computer Sciences Microsystems Engineering, Inc. University of California YOUSSEF A. EL-MANSY MINGDE YAN Intel Corp. JAMES A. VAN VECHTEN Transient Thermal Processing Chemistry REINHART ENGLEMANN Portland State University Consultant

DAVID EVANS Sharp Microelectronics Technology Inc.

WAYNE K. FORD Intel Corp.

MARK FRANK Conexant

R. THOMAS HAWKINS II Consultant

HOWARD HECK Intel Corp.

DAE MANN KIM Pohang Institute of Science & Tech., Korea

RICHARD Y. KOYAMA TriQuint Semiconductor Inc.

65 THE DEPARTMENT OF ENVIRONMENTAL part-time degree programs are invited from Department of SCIENCE AND ENGINEERING is one of the persons with bachelor’s degrees in the physical or biological sciences, mathematics, oldest stand-alone environmental and or engineering. Previous course work in Environmental Science engineering programs in the country. chemistry, biology, and mathematics (through Founded more than 25 years ago, we at least one year of calculus) is expected. and Engineering are known for our research and Requirements for admission to the www.ese.ogi.edu graduate education programs that Department of Environmental Science and Engineering are the same as the OGI School balance practical applications with of Science and Engineering’s admission DEPARTMENT HEAD fundamental investigations of the requirements, except for the minimum António M. Baptista (503) 748-1147 physical, chemical, and biological TOEFL score. The department requires TOEFL scores of all applicants whose native E-mail: [email protected] processes underlying environmental language is not English. The minimum DEPARTMENT ADMINISTRATOR phenomena.The curriculum is highly acceptable TOEFL score is 600 for the Therese Young interdisciplinary and is built on a written test or 250 for the computer-based (503) 748-1247 test. Students who earned undergraduate E-mail: [email protected] solid foundation of fundamental degrees in the United States are not required science and engineering. to submit TOEFL scores. GRE general ESE GENERAL INQUIRIES aptitude scores are required for admission to E-mail: [email protected] The department offers graduate study leading all of the department’s M.S. and Ph.D. to the degrees of Doctor of Philosophy (Ph.D.) programs. A GRE subject examination score and Master of Science (M.S.). M.S. programs is not required. are offered with both thesis and non-thesis options. All programs may be pursued on a Completed Ph.D. applications should be full-time or part-time basis. Ph.D. students received by February 15 for matriculation and M.S. thesis students participate in a in the fall of the same year. M.S. applications program that includes both formal course are accepted year-round, although most work and research. The research experience new M.S. students apply by July for is intensive and consists of laboratory, matriculation in the fall. Prospective computational, theoretical and/or field applicants for the Ph.D. program should studies. Thesis students are involved in all examine the faculty research programs at aspects of departmental research and have http://www.ese.ogi.edu/people.html to ready access to modern analytical determine whether their professional goals instrumentation and computers. can be fulfilled in the department. Communication with individual faculty The Ph.D. program can be completed in 4 to members prior to applying is encouraged. 5 years, and the M.S. thesis option takes approximately 2 years to complete. Thesis students can concentrate their studies in the DEGREE REQUIREMENTS following areas: DISTRIBUTION REQUIREMENTS

• Environmental Science and Engineering (ESE) To achieve the necessary breadth in training, (traditional program) students in all programs take courses that cover a • Environmental Information Technology (EIT) range of scientific disciplines and environmental media. Five courses must be taken that satisfy the The non-thesis M.S. program can be following distribution requirements. No course can completed in 12 months. Students in the non- satisfy more than one requirement. thesis M.S. program can concentrate their At least one course must be taken from three of the studies in the following areas: following four discipline groups: • Environmental Science and Engineering (ESE) Applied Mathematics ESE500; ESE504; ESE506; ESE508 (traditional program) Chemistry ESE510; ESE511; ESE514; ESE516 • Ecosystem Management and Restoration (EMR) Fluid Dynamics ESE520; ESE530; ESE537; ESE539 • Environmental Information Technology (EIT) (beginning Fall 2002) Biology ESE550; ESE554 And, at least one course must be taken from each of the following environmental media groups: Global positioning system (GPS) technology is ADMISSION REQUIREMENTS an important component of field-investigation Surface Waters ESE520; ESE530; ESE537; ESE539 Applications for admission to full-time and acitivities in the department’s curriculum. Ground Water ESE540; ESE541; ESE542; ESE543 ESE | ENVIRONMENTAL SCIENCE AND ENGINEERING

All full-time students are required to take EIT program receive their degree in ECOSYSTEM MANAGEMENT Environmental Science Seminar (ESE599) Environmental Science and Engineering with AND RESTORATION (EMR) during the Fall, Winter, and Spring quarters. a concentration in EIT. The Ecosystem Management and Restoration However, this course does not count toward Students pursuing the M.S. thesis option (EMR) program is a 12-month, non-thesis degree credit requirements. must complete at least 45 credits. These M.S. track offered within the Department of For all ESE educational programs, up to 8 credits include the distribution requirements Environmental Science and Engineering. The credits may be granted for courses taken in outlined above, additional courses selected objective of the EMR program is to integrate other OHSU departments. Up to 12 quarter with the approval of the SPC, and research rigorous environmental principles, field and credits may be transferable from other credits. Master’s thesis research (ESE 700) laboratory applications, modeling, project accredited institutions for graduate courses is usually no more than 9 credits. management, and policy/regulation into a comparable in content and level to courses Comprehensive examinations are not cohesive curriculum. The program emphasis offered in the department. The Student required of M.S. thesis students. However, a is on timely issues, including nonpoint Program Committee (SPC) decides on written M.S. dissertation with an oral defense source pollution, water quality, and the appropriateness of internship and is required. ecological and human risk assessments. transfer credits. For more information, please see M.S. NON-THESIS OPTIONS http://www.ese.ogi.edu/EMR/. Requirements Transfer credits do not reduce the annual Students may pursue the M.S. non-thesis for the EMR program are the same as for the tuition, but may allow for greater flexibility options in Environmental Science and non-thesis M.S. option described above, in scheduling. Engineering (ESE), Ecosystem Management except that students must include ESE570 PH.D. IN ENVIRONMENTAL SCIENCE and Restoration (EMR) or, beginning Fall and ESE589 in their elective course work. 2002, Environmental Information Technology AND ENGINEERING (EIT). The EMR and EIT programs are tracks ENVIRONMENTAL INFORMATION Students may complete the Ph.D. program within the ESE Department. Students who TECHNOLOGY (EIT) in Environmental Science and Engineering complete the EMR or EIT programs receive The Environmental Information Technology (ESE) or Environmental Information their degree in Environmental Science and (EIT) program is the newest program offered Technology (EIT). The EIT program is a track Engineering with a concentration in EMR within the Department of Environmental within the ESE Department. Students who or EIT. Science and Engineering. The Ph.D. option in complete the EIT program receive their EIT began Fall 2001, and the M.S. thesis and For the non-thesis M.S. degree, 5 distribution degree in Environmental Science and non-thesis options in EIT will begin Fall courses must be taken as outlined above. Engineering with a concentration in EIT. 2002. The EIT program combines the Students must complete additional courses expertise and coursework found in ESE and Ph.D. students must complete 5 distribution for a total of at least 45 credit hours. Up in the Computer Science and Engineering courses as outlined above. Students must to 8 credits may be granted for approved (CSE) and Electrical and Computer also complete additional courses for a total participation in non-thesis research or Engineering (ECE) Departments at the OGI of at least 52 credit hours of course work, approved work as an intern with a local School of Science and Engineering. The goal selected with the approval of their SPC. company or government agency. No of the EIT program is to combine a deep comprehensive examinations are required Ph.D. candidates must also pass a two-part understanding of environmental processes for the non-thesis M.S. options. comprehensive exam. The first part is a with mastery of sensing, modeling, and written examination covering four subject information technology. Requirements for the areas selected by the department. The DEGREE PROGRAMS EIT program are the same as the thesis and second part is the preparation and oral non-thesis options described above, except ENVIRONMENTAL SCIENCE AND ENGINEERING (ESE) defense of a proposal that defines the that students in the EIT program complete (TRADITIONAL PROGRAM) student’s Ph.D. dissertation research. A approximately 20% of their coursework in the written Ph.D. dissertation with an oral The department offers Ph.D., M.S. thesis, and CSE and ECE Departments. The EIT defense is also required. M.S. non-thesis options in Environmental curriculum includes fundamental courses, Science and Engineering (ESE). The ESE M.S. IN ENVIRONMENTAL SCIENCE science courses, technology courses, elective program is known for its research and courses, and capstone integrative courses. AND ENGINEERING education programs that balance practical Elective courses may include classes offered M.S. THESIS OPTIONS applications with fundamental investigations through OHSU’s Medical Informatics Students may pursue M.S. thesis options of the physical, chemical, and biological program. For more information on the EIT in Environmental Science and Engineering processes underlying environmental program and its curriculum, please see (ESE) or, beginning Fall 2002, Environmental phenomena. The curriculum is highly http://www.ese.ogi.edu/EIT/. Information Technology (EIT). The EIT interdisciplinary and is built on a solid program is a track within the ESE foundation of fundamental science and A NOTE ABOUT TUITION Department. Students who complete the engineering. For more information, please Tuition for the full-time non-thesis M.S. see http://www.ese.ogi.edu/curriculum.html. program is $19,620 for the 2001-2002

68 ENVIRONMENTAL SCIENCE AND ENGINEERING | ESE academic year, which is typically spread ESE514 Distribution and Fate of Organic Pollutants ESE523 Introduction to Remote Sensing of equally over the first four quarters. Upon Discussion of the physico-chemical processes that the Environment admission to the department, a $100 deposit control the behavior and fate of organic chemicals in This course will explore the acquisition, analysis the environment. Introduction considers all environ- and visualization of remotely sensed data. The is required with the return of a student’s mental compartments, water, soil, and air, and physics behind the collection of remotely sensed acceptance to reserve a place in the partitioning between those phases. Recommended data will be introduced as will both airborne-plat- department. This deposit will be applied prerequisite: ESE 510. 4 credits form and satellite-platform sensors. Data from the Light Detection and Ranging (LIDAR) sensor as it toward tuition and is non-refundable. ESE516 Chemical Degradation and Remediation pertains to Airborne Topographic Mapping will be A thorough introduction to the transformation reac- used. Single band, multi-spectral and hyper-spectral tions that contribute to the fate of organic data sets will be used to discuss such concepts as COURSE OFFERINGS substances in the environment. The course covers ESE500 Introduction to Discrete Methods image statistics, radiometric and geometric correc- pathways, mechanisms and kinetics of hydrolysis, tions, spatial filtering and special transformations This course is an introduction to discrete methods oxidation, reduction, elimination, conjugation, etc. like the Normalized Difference Vegetation Index. for environmental fluid dynamics. Lectures cover Treatment is balanced to reflect the importance of Supervised and Unsupervised classification the theory and application of the numerical solution these processes in all types of environmental waters schemes will be discussed as will change detection. of boundary-value and mixed initial-boundary value ranging from engineered systems to groundwater, The course pedagogy is designed to address the problems. Emphasis is on finite differences, finite surface water, rain, and fog. Recommended prepa- needs of the advanced level Environmental Science elements and finite volumes. Prerequisites: Calculus. ration: ESE 510 and ESE 514. 4 credits and Engineering graduate student. While there is no new for 2002/2003 4 credits ESE519 Air Pollution: Origins, Chemistry, and Control prerequisite for this course, many topics from ESE504 Uncertainty Analysis This course will focus on tropospheric air pollution ESE522, Introduction to Spatial Science are incor- A survey of basic probability concepts followed by with particular emphasis on the urban and regional porated into this course. It is therefore introductions to several statistical advanced tech- scales. It will discuss the following items: basic recommended that students unfamiliar with classifi- niques that play an important role in environmental structure of the atmosphere and relevant meteoro- cation methods and the fundamental concepts of data analysis. Topics may include distribution func- logical considerations; sources of tropospheric air Geographic Information Systems complete ESE522 tions, propagation of error, hypothesis testing, pollutants; atmospheric photochemistry; the ozone, or equivalent. 4 credits analysis of variance, experimental design, sampling oxide of nitrogen, and hydrocarbon chemical cycles; ESE530 Transport Processes theory, regression analysis, time-series analysis, chemistry of toxic organic compounds in the atmos- An introductory course in the physics of transport and spatial statistics techniques. The course pro- phere; gas and aqueous phase chemistry of sulfur processes in the natural environment. The course vides a balance of theory and application using dioxide; size distributions, lifetimes, origins and for- examines heat, mass, and momentum transport via environmental data sets. mation mechanisms of aerosols; and control of conservation principles and the Reynolds Transport not offered 2001/2002 4 credits atmospheric emissions. 3 credits Theorem, but strongly emphasizes the environmen- ESE506 Environmental Systems Analysis ESE520 Introduction to Environmental Observation and tal applications of these processes. Example studies Introduction to techniques of systems analysis Forecasting Systems include atmospheric and oceanic circulation, flow applied to environmental quality management. This course introduces environmental observation and dispersion in rivers, and heat budgets for lakes Emphasis is placed on development and application and forecasting systems and their application and reservoirs. 4 credits of mathematical models with computer simulation towards the enhanced understanding and manage- ESE532 Modeling Coastal Circulation and Transport I and optimization. Analysis is efficient computational ment of natural resources. Emphasis is on estuaries This course introduces the students to the process algorithms and search techniques. Linear and sepa- and coasts. Students are exposed to a novel, cross- of modeling coastal circulation and transport. Topics rable programming applied to evaluate management disciplinary culture for understanding and include governing equations, review of state-of-the- alternatives. Applications to air, water, solid, and interacting with environmental systems. This cul- art models, in-depth description of selected models, hazardous waste management. Prerequisites: ture relies heavily on “real-time” generation of and solution of benchmark problems. Prerequisites: Computer programming and calculus. modeling and observational data, which are inte- ESE500 or ESE508, and ESE530. not offered 2001/2002 4 credits grated and distributed through information new for 2001/2002 4 credits ESE508 Computational Fluid Dynamics networks designed to bring the right environmental information at the right time to the right user. ESE533 Modeling Coastal Circulation and Transport II This course describes advanced topics in computa- Prerequisite: Instructor permission. 4 credits This course provides an advanced treatment of tional fluid dynamics, including specialized discrete coastal circulation and transport modeling. Students methods (e.g., for advection-dominated problems), ESE522 Introduction to Spatial Sciences are introduced to the detailed modeling of complex formal analysis of stability and accuracy, and select- Students will learn theoretical and practical appli- estuarine, plume, and continental shelf processes, ed simulations of complex environmental and cations of geospatial sciences within the context of through a combination of lectures and labs focused biological systems. Prerequisites: Advanced calcu- Environmental Sciences and Engineering. Theory of on specific sites and processes. Prerequisites: lus and ESE 500. satellite-based Geographic Positioning Systems ESE532. new for 2003/2004 4 credits (GPS) will be studied while performing practical, new for 2002/2003 4 credits ESE510 Aquatic Chemistry hands-on laboratory experiments using the latest in GPS equipment. Classroom discussions will then ESE534 Modeling Coastal Flow and Transport General acid/base concepts (mono- and polyprotic focus on relating location on the Earth’s surface to a Description of state-of-the-art modeling principles systems); activity corrections; numerical calcula- common mapping grid. Non-projected and projected and techniques for simulation of flow and of conser- tions; titration concepts as applied to natural maps, ellipsoids and spheroids, and geoids will be vative and nonconservative transport in coasts and systems; buffer intensity; dissolved CO2 chemistry; discussed. Spatial relationships, or analysis, of con- estuaries. Students have the opportunity to model pH, acidity, and alkalinity in open CO2 systems; tinuous and categorical data will be addressed an actual coastal system through a hands-on term minerals and their role in controlling natural water through the application of standard statistics and project that includes a realistic sequence of chemistry; solubility characteristics of oxide and probability. ARCVIEW, a popular Geographic modeling steps: data analysis, grid generation, hydroxides; redox chemistry in natural systems; Information System (GIS) software tool will flow modeling, modeling of conservative transport, pe-pH diagram. 4 credits be stressed. 4 credits and modeling of nonconservative transport. Prerequisites: ESE 500, ESE 532. not offered 2001/2002 4 credits 69 ESE | ENVIRONMENTAL SCIENCE AND ENGINEERING

ESE537 Methods in Oceanography micro-biological factors, and medium properties statutory and regulatory interpretation, application This course covers the fundamentals of processing that determine the pathways and kinetics of bio- to specific facilities, and negotiation of Clean Air Act estuarine and coastal oceanographic data, including degradation. Recommended preparation: ESE 550. issues with EPA and the states time series (e.g., surface elevation, currents, and 4 credits not offered 2001/2002 2 credits winds) and data obtained from vessels (e.g., profile offered in combination with ESE 550 in 2001/2002 ESE589 Special Topics: Advanced Topics in Field and bathymetric data). ESE560 Environmental Soil Science Sampling and Analysis not offered 2001/2002 2 credits Soil physics, chemistry, and microbiology; soil An intensive capstone course that integrates field ESE539 Methods in Estuarine Oceanography: development, soil description and mapping, soils processes with theory from previous lecture materi- Field Observation and land use, agricultural and urban forestry; soil- al. Approximately 1 week is spent at site locations This course covers the fundamentals of estuarine plant relationships for environmental restoration; where students critically examine current tech- and coastal oceanographic data collection using ves- soil process modeling. Prerequisites: ESE 510 and niques for collecting surface water, groundwater, sels and remotely moored equipment. Topics include ESE 550. and soil samples to characterize chemical, biologi- vessel logistics and sampling, navigation systems, not offered 2001/2002 4 credits cal, and physical properties. Laboratory methods interfacing of instruments with personal computers, for analyzing organic and inorganic chemicals are ESE562 Ecosystem Ecology types of moorings and their deployment and recov- included. Students work in teams on projects to col- Principles of ecology and of ecosystem process, ery, and telemetry. lect and evaluate data, write reports, and make description, and measurement, with emphasis not offered 2001/2002 2 credits recommendations for future management of the on ecosystem health assessment. Simulation sites. Anticipate overnight travel. Variable credit ESE540 Subsurface Hydrology modeling of ecosystem processes; transport Hydrologic cycle infiltration theory; principles of and transformation. ESE598 Organization of Environmental Science and unsaturated and saturated flow in the subsurface; not offered 2001/2002 4 credits Engineering Seminar well hydraulics; analytical models of drawdown, This course is for the Ph.D. student responsible for ESE570 Principles of Toxicology and Risk Assessment capture zones and velocity plots; porous media managing the weekly Environmental Science and This course applies toxicological principles to both characterization methods and tools. 4 credits Engineering Seminar series (ESE599). Students human and ecological risk assessments. The princi- enroll for this course with their advisor’s approval. ESE541 Groundwater Modeling ples and methodologies for risk assessments are 1 credit Applied groundwater modeling using finite differ- presented within a regulatory context. Topics ence and finite element methods. Introduction to include hazard identification, exposure assessment, ESE599 Environmental Science Seminar

numerical methods for solving the partial differen- LD50, dose-response relationships, deterministic Weekly seminars by invited guests on all aspects of tial equations for saturated and unsaturated and probabilistic risk assessments, responses of environmental science, and by ESE faculty and stu- subsurface flow. Model execution and calibration. various receptors to different contaminants, and dents on their research. Visitors are welcome. Prerequisite: ESE 540. environmental management decisions. 3 credits Schedules are available on the World Wide Web at not offered 2001/2002 4 credits http://www.ese.ogi.edu/seminars/, or by request at ESE58X Special Topics [email protected]. 1 credit ESE542 Contaminant Hydrology Typically involves a scholarly and critical review of Processes controlling subsurface contaminant an advanced scientific topic by one or more students ESE600 Research movement in porous and fractured media, including together with one or more faculty members. Research toward the dissertation for the Ph.D. groundwater flow, dispersion, diffusion, sorption, Requirements of the student typically include a writ- degree before completing the comprehensive exam- and degradation. Parameter estimation, math- ten review paper and/or a seminar to be given as inations. Variable and repetitive credit ematical and laboratory modeling of aquifers is part of ESE 599. Selection of this course for credit ESE610 Non-Thesis Research also covered. 4 credits and the topic to be investigated must be approved by the Student’s Program Committee. Supervised research as a component of the non-the- ESE543 Modeling in Contaminant Hydrogeology Variable and repetitive credit sis M.S. degree. The plan of research and final This course is designed to be taken concurrently deliverables must be approved by the research advi- with ESE 542. It emphasizes the hands-on use of ESE580 Ecosystem Management and Restoration sor and the Student Program Committee. common mathematical models for groundwater flow This course will provide an overview of ecosystem Deliverables include a written report and/or semi- and transport (e.g., MODFLOW, RANDOMWALK, management and restoration at the local and region- nar given as part of ESE 599. A maximum of 8 SUMATRA) to examine real groundwater contamina- al scale. It will follow the hydrologic cycle from credits from ESE 610 and ESE 620 can be applied tion problems. Prerequisite: ESE 542. upland watersheds through streams, rivers and to a degree. Variable and repetitive credit not offered 2001/2002 4 credits estuaries to the ocean and will track important sys- ESE620 Professional Internship tem parameters such as water flow and This course provides the student with an opportuni- ESE550 Environmental Microbiology temperature. 4 credits Introduction to environmental microbiology, with ty to earn credit for relevant work experience in emphasis on the role of microbes in the environment ESE586 Environmental Law and Regulation industry. Students gain valuable experience that and in remediation processes. Microbes and their A survey of environmental law and regulation con- allows them to both apply the knowledge gained in interaction and activities in soil and aquatic envi- cepts essential to practicing scientists and the classroom and prepare for their future careers. ronments will be discussed, as well as elemental engineers. Topics covered include the theory and Enrollment requires a faculty advisor and is limited cycling as influenced by microbes. Microbially- practice of environmental regulation, environmental by the number of internship opportunities available. mediated transformation of organic pollutants, litigation, and legislation including Superfund International students need to submit appropriate transformation kinetics, and remediation technolo- (CERCLA), the Clean Water Act, the Resource paperwork for the Immigration and Naturalization gies will be considered. 4 credits Conservation and Recovery Act (RCRA), the Clean Service. A maximum of 8 credits from ESE 610 and offered in combination with ESE554 in 2001/2002 Air Act, and the Toxic Substances Control Act (TSCA). 3 credits ESE 620 can be applied to a degree. ESE554 Biodegradation and Bioremediation Variable and repetitive credit A process-oriented survey of microbially mediated ESE587 Clean Air Act Laws and Regulations ESE700 M.S. Thesis Research transformations of organic pollutants. A thorough introduction to the Clean Air Act in its Research toward the M.S. thesis degree. Transformations occurring in the natural environ- federal and state permutations, as well as the Variable and repetitive credit ment as well as in remediation technologies are detailed regulations guiding the Act’s implementa- considered. Emphasis is on the pollutant properties, tion. The course focuses on the practical aspects of

70 ENVIRONMENTAL SCIENCE AND ENGINEERING | ESE

ESE800 Ph.D. Dissertation Research OGI/LEAP facility is used to study the movement of On-going work in this area includes modeling of Research toward the dissertation for the Ph.D. gasoline components in the vapor, aqueous, and MTBE infiltration to the groundwater, laboratory degree after completing the comprehensive exami- pure-product phases. This work will help establish studies of MTBE biodegradation, and field studies nations. Variable and repetitive credit which of a variety of leak-detection technologies is of several contaminated sites for MTBE and its best suited to detect leaks under a range of envi- possible breakdown products. For more informa- ronmental conditions. Johnson tion on this work, see http://cgr.ese.ogi.edu/mtbe/. RESEARCH PROGRAMS Pankow, Tratnyek, Johnson Remediation of Halocarbon-Contaminated Groundwater Contaminant Diffusion in Clay There is enormous demand for improved ways to Hydrocarbon Biodegradation in Soil Clay liners are often used in waste disposal clean up aquifers that have been contaminated Petroleum hydrocarbon contamination is prevalent facilities to prevent the advective transport of with halogenated hydrocarbon solvents like carbon in soils and groundwater. Efforts to clean up this contaminants into the surrounding groundwater. tetrachloride and TCE. Recent field-scale tests extensive petroleum contamination have prompted Even when advective transport is small, however, have shown that technologies based on dechlorina- research into in-situ bioremediation. Depending contaminant transport through liners may be sig- tion with granular iron may have substantial on site characteristics, in-situ hydrocarbon nificant as the result of molecular diffusion. This value. The goal of our research in this area is to biodegradation is a cost effective and environmen- phenomenon has been studied in the laboratory provide a sound scientific basis for designing and tally sound remediation alternative or partner to and at actual waste disposal facilities to evaluate operating such technologies by determining the pump-and-treat and vacuum extraction technolo- its roles in mass transport and groundwater con- mechanisms of dechlorination by iron and the gies. We have studied the processes by which the tamination. Johnson geochemical and microbiological processes that biodegradation rates of organic compounds can be Processes Controlling the Subsurface Transport affect the performance of this technique in the optimized. Toccalino field. For more information on this work, see of Dense Chlorinated Solvents Human-Health Assessment of Water Quality http://cgr.ese.ogi.edu/iron. Tratnyek The uncontrolled release of chlorinated solvents is A national effort is underway with the U.S. a common cause of serious groundwater contami- Reduction Reactions of Organic Pollutants in Geological Survey’s National Water-Quality nation in many parts of the world. It is in this Anaerobic Environments Assessment (NAWQA) program, in collaboration context that it is important to understand the Some organic pollutants undergo rapid reduction in with the U.S. Environmental Protection Agency physical and chemical principles that govern the anaerobic sediments, soils, and groundwaters. (USEPA) and State agencies to conduct a pilot movement of these dense nonaqueous phase liquids Despite the potential importance of this process, effort to develop, test, and refine concepts to more (DNAPLs). Experiments under way at OGI and in little is known about the natural reducing agents effectively communicate water-quality information conjunction with the University of Waterloo are that are responsible for these reactions. In this in a human-health context. The study includes examining the behavior and remediation of chlori- project, assays are being developed that will iden- determining how to effectively communicate the nated solvents in the saturated and unsaturated tify and quantify environmental reducing agents in data from this study in a human-health context to zones. Johnson situ. These assays will be used in kinetic studies of Congress, the media, the public, etc. Toccalino important pollutant reduction reactions. Tratnyek Simulation of Subsurface Processes Using Very Large Distribution of Organic Compounds Between the Gas Scale Experimental Aquifers Oxidation Reactions of Organic Pollutants and Urban Aerosol Particulate Phases Many important chemical, physical, and biological Some organic pollutants undergo rapid oxidation in The behavior of organic compounds in the atmos- processes are difficult to study in the laboratory natural waters, when catalyzed by sunlight, and in phere depends in large part on the extent to which because of problems of scaling. Many of these technological systems, when chemical oxidants are they partition from the gas phase to aerosol partic- processes are also difficult to characterize in the added to effect remediation. These reactions are ulate matter. Processes that are affected by this field, because of the complex and uncontrolled usually mediated by “activated oxygen species” partitioning process include precipitation scaveng- nature of environmental systems. For these such as hydroxyl radical. We are studying the ing of gases and particles as well as dry deposition reasons, OGI has established the Large kinetics, mechanisms, and products of these reac- of gases and particles. Fundamental gas/solid sorp- Experimental Aquifer Program (OGI/LEAP). At tions with a wide variety of contaminants. The aim tion theory is being used to investigate important present, the facility consists of five large aquifers of this work is help assess the suitability of various aspects of atmospheric gas/particle partitioning. used to examine the movements of organic solvents advanced oxidation technologies (AOTs) for remedi- The study involves the investigation of basic parti- and petroleum compounds in the unsaturated and ation of groundwater, as well as to better tioning behavior of a wide range of representative saturated porous media. Future LEAP aquifers will understand the fate of contaminants in natural atmospheric compounds (including alkanes and examine inorganic geochemistry and the interac- waters that are exposed to sunlight. Tratnyek polycyclic aromatic hydrocarbons) on a variety of tions between chemical, biological, and physical representative model particulate substrates, Correlation Analysis of Contaminant Reactivity processes in contaminated aquifers. Johnson and including elemental carbon, organic carbon, silica, other faculty Quantitative Structure-Activity Relationships and clay. Pankow (QSARs) are of enormous importance in environ- Gas-Phase Transport in Unsaturated Porous Media mental chemistry and toxicology because of their Thermodynamics of Inorganic Solid Solutions Gas-phase transport is important in controlling predictive power, but they also reveal a great deal The manner in which inorganic solid solutions many subsurface processes including respiration, about reaction mechanisms and the nature of sub- behave is one of the last major research frontiers pesticide behavior, and contaminant volatilization stituent effects. We are involved in the in ambient temperature aqueous geochemistry. and movement. Laboratory experiments have been development of QSARs for a wide range of redox Coprecipitation of metal ions is well known in conducted to determine diffusion rates of a variety reactions involving organic contaminants. This nature, e.g., Sr2+ can form a solid solution in calci- of organic compounds in porous media and the work involves the use of computational chemistry um carbonate (CaCO3(s)). Unfortunately, little is kinetics of adsorption and desorption for a variety methods as well as advanced statistical techniques known about the thermodynamics of such solid of soil types and a range of water contents. in exploratory data analysis. Tratnyek solutions. That is, little is known about how the Johnson activity coefficients of metal ions vary as a function Fate and Effects of Fuel Oxygenates Multi-Phase Monitoring of Gasoline Movement Using of composition in solid solutions of various types. The recent realization that oxygenated fuel The values of the activity coefficients are of inter- a Very Large Physical Model (OGI/LEAP) additives such as MTBE are becoming widely dis- Leaks from underground storage tanks (UST) rep- est because they control the extent to which the tributed groundwater contaminants has created a constituents in the solid solutions will be soluble in resent a major ongoing source of groundwater sudden and pressing demand for data on the contamination. The rapid detection of leaks is, water, e.g., the extent to which a toxic metal ion processes that control their environmental fate. 2+ therefore, a major goal of UST legislation. The like Cd that is present in calcium carbonate will 71 ESE | ENVIRONMENTAL SCIENCE AND ENGINEERING

be soluble in water. In this work, activity results obtained are essential ingredients in deter- during the last century. This research program is coefficient values for a variety of environmentally mining the sources and fates of atmospheric trace designed to determine the role of rice agriculture important divalent metal ions are being sought as gases and in estimating the effects of human activi- in the global methane cycle. Field experiments are a function of composition in calcium carbonate. ties on the future warming of the earth or depletion being conducted in China, Indonesia and the U.S. Pankow of the ozone layer. Rasmussen Laboratory experiments and theoretical research are being done at the Global Change Research Global Distributions and Mass Balances of Halocarbons, Studies of Atmospheric Methane Center (Portland State University) in a comprehen- Nitrous Oxide, and Other Trace Gases Considerable evidence has been accumulated sive research program. This work includes Gases such as CCl F (F-11), CCl F (F-12) CHClF showing that methane (CH ) is increasing in the 3 2 2 2 4 modeling the production, oxidation and transport of (F-22), CF (F-14), C Cl F (F-113), CH CCl , atmosphere, most likely as an indirect result of 4 2 3 2 3 3 methane in the rice paddy ecosystem and measur- CH Cl and N O are being added to the atmosphere growing human population. In the future, such an 3 2 ing the controlling parameters. Rasmussen by various industrial processes and the use of increase of CH4 can lead to a global warming by high-technology products by the public. Such chlo- enhancing the earth’s natural greenhouse effect Land-Margin Ecosystem Research in the Columbia rine-containing compounds are believed to threaten and create more ozone and carbon monoxide in the River Estuary the earth’s natural ozone layer high in the atmos- atmosphere. However, it might also prevent some The Columbia River Estuary Land-Margin phere (stratosphere). This research will of the destruction of the stratospheric ozone layer Ecosystem Research (LMER) Program funded by systematically obtain a long-time series of concen- by the man-made fluorocarbons 11 and 12. In this the National Science Foundation focuses on the tration measurements by a flask sampling system. project, experimental and theoretical research is estuarine turbidity maximum, which is the heart of The results are then interpreted with global mass focused on statistical trend analyses for the global the estuarine ecosystem. Long-term funding allows

balance models and sophisticated statistical tech- increase of CH4, its seasonal variation, sources and analysis of seasonal and interannual variability in niques to quantify the sources and lifetimes of sinks, models of its effect on the CO, O3, and OH estuarine processes and evaluation of the impacts these gases in the environment. Such data are now cycles and its role in the future of the environment. of flow regulation on the system. The extensive obtained from sites all over the world extending Rasmussen data sets collected by this program provide a basis from the Arctic Circle to the South Pole. for studies of estuarine circulation, hydraulic con- Development of Experimental Methods for Trace| Rasmussen trol processes at the estuary mouth, nonstationary Gas Measurements tidal processes, suspended sediment transport, Studies of Past Atmospheres At present, some 50 atmospheric gases can be turbulence and mixing, and biological processes. Atmospheric gases such as N O, CO , CO, CH Cl, measured at the Trace Gas Laboratory. Still, new 2 2 3 Jay, Baptista, and external collaborators carbonyl sulfide (OCS), and CH4 are primarily pro- methods are needed to improve the accuracy and duced by natural processes, but over the past precision of measurements and to satisfy the strin- Internal Circulation in Tidal Channels and Straits century human activities have been adding growing gent demands of ultra-clean background air This project, funded by the Office of Naval amounts to their natural abundance. This process sampling. New methods are also being developed Research, seeks to use wavelet data analysis tech- can upset the cycles of these gases and lead to for automated real-time analysis of many trace niques and novel modeling strategies to improve possibly adverse environmental effects such as the gases. Research programs include development of our conceptual understanding of estuarine circula-

warming of the earth’s surface (N2O, CO2, CH4). gas chromatographic and mass spectrometric tion and scalar transport. Continuous wavelet When both natural and anthropogenic processes methods for the analysis of trace gases. At present, transforms allow resolution of time variation in contribute to the current atmospheric abundance GC/MS systems in the laboratory are being used to tidal processes in each frequency band. Dr. Jay’s of a trace gas, it is of interest to determine the routinely measure C2-C12 nonmethane hydrocar- group is using this technique to understand estuar- amount which existed before human activities had bons at tens of parts per trillion levels. Techniques ine internal circulation and shelf internal tides in any effect. Perhaps the only realistic method to for collecting and storing air and water samples buoyant plumes. Modeling efforts use symbolic determine the composition of the ancient also are being developed. Rasmussen mathematics software to provide a balance atmosphere is to analyze the air in bubbles buried between the intuitive understanding and compact deep in polar ice. The depth of the ice indicates the Biogenic Sources of Atmospheric Gases nature of analytical solutions and the superior flexibility and accuracy of full-numerical solutions. Jay age of the air in the bubbles. By going far enough Living organisms produce and consume a variety of back in time, the relationship between past atmos- gases and may therefore form an integral part of CORMIX Graphic User Interface and GIS pheric composition and climate might be found. the global cycle of a trace gas. Selected plants and Database Integration The novel and simple method of studying the old animals, living in the sea or on land, are being This project develops computer information atmosphere of the earth is beset by many problems studied to determine their role in the cycles of CH , that complicate the relationship between the gases 4 systems for the CORMIX mixing zone water quality N2O, CH3CI, CH3I, isoprene and other hydrocarbons. model. A fully interactive Windows-based applica- in the bubbles and the composition of the old Rasmussen atmosphere. Theoretical and experimental tion is proposed, designed to give CORMIX research for resolving these problems as well as The Global Cycle of Carbon Monoxide (CO) additional functionality, flexibility, and power using the measurement of trace gases are the major Based on 15 years of global sampling and the object-oriented rule-base technology for forms- goals of this project. Rasmussen application of modern trend analysis techniques, based interactive data entry, flow classification, our data have shown that CO increased in the simulation logic description, and GIS database inte- Ocean-Air Exchange of Gases atmosphere until around 1987 and has since gration. Doneker Some atmospheric gases are greatly influenced by declined. These changes in CO have major implica- D-CORMIX Decision Support System the earth’s oceans. For instance, a large amount of tions for atmospheric chemistry and the role of This project involves development, validation, and the atmospheric methyl chloride (CH Cl) and 3 biomass burning in causing global increases of scientific review of the D-CORMIX decision support methyl iodide (CH I) are produced in the oceans, 3 trace gases. Present research includes modeling of possibly by biogenic processes. It has also been system. D-CORMIX is a physically-based simulation the global budgets, seasonal cycles, and potential shown recently that carbonyl sulfide (OCS) is pro- model linked to a knowledge-based classification environmental effects. Rasmussen duced in the oceans and subsequently emitted to system for predicting of water quality and sediment the atmosphere. On the other hand, man-made Methane Emissions from Rice Fields deposition impacts resulting from dredging operations. The purpose of the project is to assist water gases such as CCl F (F-11) can dissolve in the Methane concentrations have nearly tripled com- 3 quality managers in performing waste load alloca- oceans and thus be removed from the atmosphere. pared to the natural atmosphere of 300 years ago tions for continuous dredge discharges. The This research project is devoted to determining the (based on ice core analyses). The increase of rice methodologies developed in this project are also solubility of such gases in water and to modeling agriculture to sustain an increasing population may necessary for long term pollutant fate and trans- the flux of gases into or out of the oceans. The be a major contributor to the increase of methane 72 ENVIRONMENTAL SCIENCE AND ENGINEERING | ESE port studies by providing information on initial preparatory phase, we designed, constructed and water remediation methods. boundary conditions. This project also develops instrumented a meso-scale biogechemical rotating The Center operates the Large Experimental validation studies and documentation for USEPA annular flume (RALF). We are beginning the Aquifer Program (LEAP) which contains the experi- Science Advisory Board (SAB) review of process-based research phase on the project, in mental cells outlined below. The LEAP facility D-CORMIX. Doneker which we will focus on elements important for both provides staff with the capability to conduct both water quality and ecosystem dynamics, namely the CORMIX Documentation Development, Workshop bench-scale experiments and pilot-scale cycling of Fe, Mn, and other divalent metals at Instruction, and Technical Support demonstrations. Current projects include transport sediment-water interfaces (SWI). We are especially through fractured clay, air sparging of source OGI has a 3-year cooperative agreement to main- interested in quantifying the effect of episodic sedi- petroleum zones containing MTBE, and a pilot tain, update and distribute the CORMIX user ment disruptions on the speciation and phase scale demonstration of zeolite as an in-situ perme- manual, conduct technical training workshops on (dissolved, particulate, and colloidal) of these met- able barrier material. mixing zone models, and to provide technical assis- als. We are also interested in the effect of shear tance to CORMIX model users. The CORMIX water upon particle desegregation, differential settling, Students involved in LEAP research graduate with quality model has approximately 1000 users world- sorption, precipitation, and dissolution. We will a rare combination of experience in full-scale wide, feedback from them through technical place the chemical reactions in a controlled, yet remediation engineering and a process-level under- support and training workshops directly supports realistic, shear-driven physical environment by standing of contaminant hydrology and chemistry. current model development activities. Doneker conducting primary experiments in the controlled environment of RALF. For more information on Additional information about CGR may be CORIE: A PILOT ESTUARINE NOWCAST-FORECAST this work, see http:www.ccalmr.ogi.edu/ralf/. obtained from: SYSTEM (http://www.ccalmr.ogi.edu/CORIE) Baptista, Tratnyek, external collaborators DR. RICHARD JOHNSON Since 1996, we have been developing CORIE, phone: (503) 748-1193 e-mail: [email protected] an observation and forecasting system for the OCEAN SURVIVAL OF SALMONIDS CGR Web site: cgr.ese.ogi.edu. Columbia River estuary. The motivation is two fold. We are initiating an integrated observational/ mod- First, the Columbia River and its near-shore plume eling study of the physical variability of the CGR FACULTY are a dominant oceanographic feature of the Columbia River plume and estuary, to provide Richard Johnson, Associate Professor northeastern Pacific Ocean and the focus of con- oceanographic context for research on the role of Paul Tratnyek, Associate Professor troversial ecosystem management issues. CORIE the coastal ocean on the life cycle of salmon. James F. Pankow, Professor represents a novel, promising, and much needed Baptista, Jay, external collaborators Patricia L. Toccalino, Assistant Professor infrastructure for physical and ecological research in this system. Second, we envision that multi- CASCADIA SUBDUCTION ZONE TSUNAMIS LEAP EQUIPMENT purpose nowcast-forecast systems will become Large tsunamis are believed to be locally generat- • Five tanks: one 10 m x 10 m x 3 m, two 10 m x 10 m x 5 m, central to the management of coasts and estuaries ed in the Cascadia Subduction Zone (CSZ) every one 10 m x 2.5 m x 0.5 m, and one 8 m x 2.5 m x 0.5 m worldwide. The Columbia River estuary is a chal- 200 to 600 years, based on geological records. The • In situ instrumentation, including: automated lenging natural laboratory to test concepts and last large tsunami dates back about 300 years, temperature, pressure, and water level monitoring; multilevel samplers; down hole video camera; and tools, and CORIE is a pilot system developed to raising concerns about the protection of coastal automated vapor and product sensing equipment anchor our observation and forecasting research. communities in Oregon, Washington, California, and British Columbia. The coastal impact of poten- • Remediation equipment, including soil vapor extraction CORIE has three main components. The first com- and air sparging capabilities ponent is a real-time data acquisition system, tial CSZ tsunamis is being investigated through numerical modeling. The need to use geological evi- • Automated on-site analytical equipment, including including an array of 12 permanent stations, a capillary GC-MS instrumentation variable number of temporary stations, and one dence on paleotsunamis as the sole, loose mobile station. We currently monitor, in various reference for model validation makes this an CENTER FOR COASTAL AND LAND combinations at each station: temperature, conduc- unusually interesting and challenging problem. The MARGIN RESEARCH (CCALMR) Oregon Department of Geology and Mineral tivity, water pressure, water velocities, acoustic The Center for Coastal and Land-Margin Research backscatter, wind speed and direction, air temper- Industry (DOGAMI) has incorporated our joint research results into the development of tsunami (CCALMR) is an interdisciplinary research center ature, and atmospheric pressure. “Real-time” is affiliated with the Department of Environmental defined by latencies of typically a few seconds, and inundation maps for the Oregon and Washington coasts. Baptista, external collaborators Science and Engineering. CCALMR conducts is achieved through a telemetry network based on research, graduate education and advanced tech- spread-spectrum radio technology. The second nology development that directly address the need component of CORIE is a suite of circulation and RESEARCH CENTERS for better scientific understanding of coasts, land transport models currently extending from the margins and estuaries. Improved knowledge of Bonneville dam to the coastal vicinity of the CR CENTER FOR GROUNDWATER RESEARCH these complex systems is necessary to preserve estuary, and including parts of the Willamette and The principal mission of the Center for and enhance their environmental integrity, main- Cowlitz rivers. Hindcast model runs are being used Groundwater Research (CGR) is to conduct state- tain the economic viability of communities to benchmark systematically all models, individual- of-the-art research in areas relating to the dependent on them and protect human populations ly and in their contrasting features. The third transport and fate of contaminants in the subsur- from natural and man-made hazards. component of CORIE is a data management and face. This is accomplished through a combination distribution system, with real-time and archival Real-world natural resource management issues of research grants and contracts, support from access through the web to script-generated graphi- motivate CCALMR research and education activi- Center corporate sponsors, and through collabora- cal displays and actual data. Baptista ties. Insights drawn from the experience of science tion with other universities, industries, and and engineering professionals in the public and government agencies. COUPLED PHYSICAL AND BIOGEOCHEMICAL private sectors influence the identification of PROCESSES AT SEDIMENT-WATER INTERFACES The Center coordinates a range of projects relating emerging research challenges, the design of The overall goal of this project is to advance our to the transport and fate of contaminants in soils research projects, the development of supporting quantitative understanding of the fate and bioavail- and groundwater. The scope of the Center includes, tools and applications and the transfer of knowledge ability of chemical elements in estuaries by among other things, the development of: 1) new and technology. sampling and site characterization techniques; 2) coupling meso-scale experimentation with diagnos- Additional information about CCALMR may be new analytical techniques; and 3) improved ground- tic numerical modeling and field observations. In a obtained from: 73 ESE | ENVIRONMENTAL SCIENCE AND ENGINEERING

DR. ANTÓNIO M. BAPTISTA • DLK-100 Potentiostat (AIS) RESEARCH FACILITIES phone (503) 748-1147 e-mail [email protected] • Solid State Au/Hg amalgam microelectrodes The department is well equipped to carry on a CCALMR Web site: www.ccalmr.ogi.edu/ • Bipotentiostat equipped with rotating disk electrode (Pine) vigorous research program Instruments and equip- CCALMR FEATURED PROJECTS ment available, in addition to those listed for the centers, include: • Cascadia Subduction Zone tsunamis • CORIE: a pilot estuarine nowcast-forecast system GENERAL AND ANALYTICAL EQUIPMENT • CORMIX: mixing zone decision support system • Carbon/nitrogen/sulfur analyzer • Coupled physical and biogeochemical processes at • Several high-performance liquid chromatographs with UV-absorbance, fluorescence, refraction index, sediment-water interfaces and conductivity detectors. • Internal circulation in tidal channels and straits • Ion chromatograph • Land-margin ecosystem research in the Columbia • Graphite furnace atomic absorption River estuary spectrophotometer • Access to FT-IR, fluorescence, diode array UV/VIS, • Ocean survival of salmonids scanning UV/VI Snear IR spectrophotometers • Reduction reactions of organic pollutants in • Access to scanning electron microscopes anaerobic environments • Access to a complete Raman spectroscopy facility • Trace element distributions • Purge and trap concentrator and thermal desorption apparatus • Watershed analysis • Rain and air sampling equipment CCALMR FACILITY • Groundwater and soil sampling equipment • Groundwater monitoring equipment, including The Center is well equipped to conduct water table, ambient, and ground temperature state-of-the-art scientific research. The following is measurement, and pressure transducers all a list of facilities and instruments available in addi- integrated into a data logging system tion to those available through the Department of • Equipment for supercritical fluid extraction and Environmental Science and Engineering. supercritical fluid chromatography • Several rapid flow injection analysis systems OCEANOGRAPHIC EQUIPMENT • Sediment samplers • 300, 600 and 1200 kHz Acoustic doppler current • Two-dimensional polyacrylamide| gel densitometer profilers (RD) • Aerosol samplers • Trace reduction-gas analyzer • 500 and 1500 kHz Acoustic doppler profilers (Sontek) • Liquid nitrogen freezer • Conductivity and temperature pairs (Seabird) • Conductivity, temperature and pressure sensors (Coastal COMPUTER EQUIPMENT Leasing and Ocean Sensors) • Computer lab with numerous Pentium and Pentium Pro PCs running Windows NT • Echosounder and digitizer (Ross) • SPARC workstations • Optical backscatter sensors (Downing Associates) • Network access via X-terminals and • Wind gauges (Coastal Leasing) personal computers • Numerous IBM compatible and Apple Macintosh • High-density thermistor chains (CCALMR) computers with HP LaserJet printers, digitizing • Differential GPS (Trimble) tablets, plotters and a film image recorder

• Spread spectrum radio data modems (FreeWave) SUPPORT FACILITIES • Fully equipped machine shop REAL-TIME DATA ACQUISITION NETWORK (CORIE) • Toxic chemicals handling laboratory The pilot nowcast-forecast system CORIE includes • Electronics support personnel a real-time data acquisition network with twelve • Greenhouse facility and growth chambers multi-sensor oceanographic stations in the Columbia River estuary. Field operations are conducted from the Marine Environmental Research and Training Station (MERTS). MERTS is a facility developed in partnership with and operated by the Clatsop Community College (CCC). CCC operates two training and research vessels: the 50-foot M/V Forerunner and the 21-foot R/V Tansy Point.

BIOGEOCHEMICAL ROTATING ANNULAR FLUME (RALF) RALF, a 2-meter biogeochemical rotating annular flume, supports research on coupled physical and biogeochemical processes at sediment-water interfaces. Instrumentation providing real-time or pseudo real-time data include: • 3-dimensional Acoustic Doppler Velocimeter (Sontek) • DO (Orion) and pH/ISE (Orion)

74 FACULTY | ENVIRONMENTAL SCIENCE AND ENGINEERING | ESE

ANTÓNIO M. BAPTISTA ROBERT L. DONEKER, P.E. DAVID A. JAY RICHARD L. JOHNSON Professor and Department Head Assistant Professor Associate Professor Associate Professor and Director, Director, Center for Coastal and Ph.D., Environmental Engineering Ph.D., Physical Oceanography Center for Groundwater Research Land-Margin Research Cornell University, 1989 University of Washington, 1987 Ph.D., Environmental Science [email protected] [email protected] Oregon Graduate Center, 1985 Ph.D., Civil Engineering [email protected] Massachusetts Institute of Technology, 1987 RESEARCH INTERESTS RESEARCH INTERESTS [email protected] Development of decision support River basin, estuarine, and RESEARCH INTERESTS systems for environmental continental shelf processes, Physical and chemical behavior RESEARCH INTERESTS simulation modeling, engineering turbulent mixing, tides and tidal of organic contaminants in the design optimization, and natural analysis. A unifying theme is the air, soil, and water; analytical Integrated understanding and resource management. Current influence of hydrodynamic organic chemistry; groundwater prediction of hydrodynamic research areas focus on processes on ecosystems. transport, fate, and modeling of and environmental processes development of technology transfer contaminants in porous and in estuaries and coasts. systems with emphasis on water REPRESENTATIVE PUBLICATIONS fractured porous media. Development of associated quality modeling and control of Cudaback, Cynthia N. and D. A. Jay, concepts and technologies: point and nonpoint source 2001, “Tidal asymmetry in an estuarine REPRESENTATIVE PUBLICATIONS environmental observation and pollutant transport. pycnocline, 2”, Transport J. Geophys. Thomson, N.R. and R.L. Johnson. forecasting systems, numerical Res. 106: 2639-2652. “Air Distribution During In Situ Air methods and models, physically- REPRESENTATIVE PUBLICATIONS Cudaback, C. N., and D. A. Jay, 2000, Sparging: An Overview of Mathematical based ecological indicators. Modeling”, J. Hazardous Materials Doneker, R. L. And G. H. Jirka, 1999. “Tidal asymmetry in an estuarine pycnocline: Depth and thickness”, J. 72(2-3), 265-282 (2000). REPRESENTATIVE PUBLICATIONS Discussion of “Mixing In Inclined Dense Jets” by P.W. Roberts, A. Ferrier, and Geophys. Res. 105: 26,237-26,252. Johnson, R.L., J.F. Pankow D. Bender, Baptista, A.M, “Environmental G. Daviero, Journal of Hydraulic Jay, D. A., W. R. Geyer and C. Price and J. Zogorski. “To What Observation and Forecasting Systems,” Engineering, ASCE, vol. 125 No.3 D. R. Montgomery, 2000, “An ecological Extent Will Past MTBE Releases Encyclopedia of Physical Science and pp.317-318. perspective on estuarine classification: Contaminate Community Water Supply Technology, 3rd Edition, Volume 5, Wells?” Environ. Science and Technol. Ford D.A., A.P. Kruzic, and R.L. Estuarine Science, A Synthetic Academic Press, in press. 34, 2A-7A, (2000). Doneker, “Using GLEAMS to Evaluate Approach to Research and Practice”, J. E. Hobbie (ed.), Island Press, Myers, E.P. and A.M. Baptista, the Agricultural Waste Application Slater, L., A.M. Binley, W. Daily and pp. 149-175. “Inversion for Tides in the Eastern Rule-Based Decision Support System R.L. Johnson. “Cross-hole electrical North Pacific Ocean”, Advances in (AWARDS) Computer Program”, Water Flinchem, E. P. and D. A. Jay, 2000, imaging of a controlled saline tracer Water Resources, Vol. 24(5), Science and Technology, Vol. 28, No-35, “An introduction to wavelet transform injection.” J. Applied Geophysics, |pp. 505-519, 2001. pp.625-634, 1993. tidal analysis methods”, Coast. Estuar. 44, 85-102 (2000). Shelf Sci. 51: 177-200. Myers E.P. and A.M. Baptista, Doneker, R.L., and G.H. Jirka “Expert Johnson, P. C.; M. W. Kemblowski, “Analysis of Factors Influencing Systems for Mixing Zone Analysis and Jay, D. A. and Flinchem, E. P., 1997, R. L. Johnson. “Assessing the signifi- Simulations of the 1993 Hokkaido Design Aqueous Pollutant Discharges,” “Interaction of fluctuating river flow cance of subsurface contaminant vapor Nansei-Oki and 1964 Alaska Tsunamis,” Journal of Water Resources Planning with a barotropic tide: A test of wavelet migration to enclosed spaces: site-spe- Natural Hazards, 23(1):1-28, 2001. and Management, ASCE, Vol. 117, tidal analysis methods”, J. Geophys. cific alternatives to generic estimates.” No. 6, November/December 1991. Res. 102: 5705-5720. J. Soil Contam. 8(3), 389-421 (1999). Oliveira A., A.B. Fortunato, and A.M. Baptista “Mass Balance in Eulerian- Jirka, G.H. and R.L. Doneker B.M. Hickey, L.J. Pietrafesa, D.A. Jay Daily, W., A. Ramirez and R.L. Lagrangian Transport Simulations in “Hydrodynamic Classification of &W.C. Boicourt, 1996, “The Columbia Johnson. “Electrical Impedance Estuaries,” ASCE Journal of Hydraulic Submerged Single Port Discharges”, River Plume Study:subtidal variability Tomography of a Perchloroethylene Engineering, 126(8):605-614, 2000. Journal of Hydraulics Division, ASCE, in the velocity and salinity field,” Release”, J. Explor. Eng. Geology, Vol. 117, No. 9, September 1991. J. Geophysical Research, 103(10), 2, 189-201 (1998). Yang Z., A.M. Baptista, and J. 229-368. Darland, “Numerical Modeling of Flow Jirka G.H., R.L. Doneker, and T.O. Johnson, P.C., R.L. Johnson, Characteristics in a Rotating Annular Barnwell, “CORMIX: A Comprehensive D.A. Jay & J.D. Musiak, 1996, C. Neaville, E.E. Hansen, S.M. Stearns, Flume,” Dynamics of Atmospheres and Expert System for Mixing Zone Analysis “Internal Tidal Asymmetry in Channel and I.J. Dortch. “An Assessment of Oceans, 31:271-294, 2000. of Aqueous Pollutant Discharges,” Flows: Origins and Consequences”, Conventional In situ Air Sparging Water Science and Technology, 24, C. Pattiaratchi (Ed.), “Mixing Processes Tests.” Ground Water, 35(5), Baptista, A.M., M. Wilkin, P. Pearson, No. 6, 267-274, 1991. in Estuaries and Coastal Seas, an 765-774, (1997). P. Turner, C. McCandlish, and P. American Geophysical Union,” Coastal Barrett, “Coastal And Estuarine Doneker R.L., and G.H. Jirka, and Estuarine Sciences, 53, 219-258. Forecast Systems: A Multi-Purpose “Schematization in Regulatory Mixing Infrastructure for the Columbia River,” Zone Analysis”, Journal of Water D.A. Jay & J.D. Musiak, 1994, Earth System Monitor, 9(3), National Resources Planning and Management, “Particle trapping in estuarine turbidity Oceanic and Atmospheric ASCE, Vol 128, No. 1, Jan./Feb. 2002. maxima,” J. of Geophysical Research, Administration, Washington, D.C, 1999. Doneker, R.L., and G.H. Jirka, 99(20), 446-461. Oliveira A. and A.M. Baptista, “On the “CORMIX-GI Systms for Mixing Zone Role of Tracking on Eulerian- Analysis of Brine Wastewater Lagrangian Solutions of the Transport Disposal,” Desalination, 139, 2001. Equation,” Advances in Water Resources, 21(7), 539-554, 1998. 75 ESE | ENVIRONMENTAL SCIENCE AND ENGINEERING | FACULTY

JAMES F. PANKOW REINHOLD A. RASMUSSEN PATRICIA L. TOCCALINO PAUL G. TRATNYEK Professor Professor Assistant Professor and Associate Professor Ph.D., Environmental Ph.D., Botany Plant Physiology Director of Education Ph.D., Chemistry Engineering Science Washington University, Ph.D., Environmental Science Colorado School of Mines, 1987 California Institute of St. Louis, 1964 and Engineering [email protected] Technology, 1978 [email protected] Oregon Graduate Institute of [email protected] Science and Technology, 1992 RESEARCH INTERESTS [email protected] RESEARCH INTERESTS Mechanistic and kinetic aspects of RESEARCH INTERESTS Atmospheric chemistry of trace the fate of organic pollutants in Physical and analytical chemistry gases; biogenic and anthropogenic RESEARCH INTERESTS the environment; degradation of organic compounds and metals emissions of trace gases and their Human and ecological risk reactions involving pesticides, in natural waters and in the roles in stratospheric ozone assessments, water-quality phenols, munitions, dyestuffs and atmosphere; the formation and destruction and tropospheric assessments, optimization of chlorinated hydrocarbon solvents; chemistry of atmospheric aerosols; ozone formation; measurements hydrocarbon biodegradation in chemical and microbiological the chemistry of nicotine in of trace gases at parts per trillion soil and subsurface systems, processes in sediments, soils and tobacco smoke. to parts per quadrillion levels; contaminant fate and transport groundwaters as well as sources and sinks of isoprene in various environmental media. photochemical processes in REPRESENTATIVE PUBLICATIONS and other hydrocarbons. surface waters; natural and Pankow, J.F., J.H. Seinfeld, REPRESENTATIVE PUBLICATIONS engineered remediation systems. W.E. Asher, G.B. Erdakos, “Modeling REPRESENTATIVE PUBLICATIONS AND TECHNICAL REPORTS the Formation of Secondary Organic C. Geron, R.A. Rasmussen, R.R. Arnts, Toccalino, P. L., L. Nowell, and REPRESENTATIVE PUBLICATIONS Aerosols. 1. Theory and A. Guenther, “A review and synthesis of R. Phillips. 2001. “Recommendations Tratnyek, P. G.; Scherer, M. M.; Measurements for the (-Pinene-, monoterpene speciation from forests in for the development of health-based Deng, B.; Hu, S. (2001) “Effects of (-Pinene-, Sabinene-, (3-Carene, the United States,” Atmos. Environ, screening levels.” Report to U.S. natural organic matter, anthropogenic and Cyclohexene-Ozone Systems,” 34(11), 1761-1781 (2000). Geological Survey, U.S. Environmental surfactants, and model quinones on Env. Sci. Technol., 35, 1164-1172 Protection Agency, and N.J. Department the reduction of contaminants by zero- (2001). See also Errata, Env. Sci. J. Zhang, K.R. Smith, R. Uma, Y. Ma, of Environmental Protection. valent iron.” Wat. Res., in press. Technol., 35, 3272 (2001). V.V.N. Kishore, K. Lata, M.A.K. Khalil, R.A. Rasmussen, S.T. Thorneloe, Toccalino, P. L. and R. Binder. Scherer, M. M.; Johnson, K.; Westall, Seinfeld, J.H., W.E. Asher, “Carbon monoxide from cookstoves in 2000. “Methodologies for presenting J. C.; Tratnyek, P. G. (2001) “Mass G.B. Erdakos, J. F. Pankow, “Modeling developing countries: 2. Exposure contaminant concentration data from transport effects on the kinetics of the Formation of Secondary Organic potentials,” Chemosphere: Global the Glassboro, New Jersey study area nitrobenzene reduction by iron metal.” Aerosols. 2. The Predicted Effects of Change Sci., 1(1-3), 367-375 (1999). in a human-health risk context.” Environ. Sci. Technol., 35(13), Relative Humidity on Aerosol Formation Report to U.S. Geological Survey, J. Zhang, K.R. Smith, R. Uma, Y. Ma, 2804-2811. in the (-Pinene-, (-Pinene-, Sabinene-, U.S. Environmental Protection Agency, V.V.N. Kishore, K. Lata, M.A.K. Khalil, (3-Carene, and Cyclohexene-Ozone and N.J. Department of Environmental Tratnyek, P. G.; Reilkoff, T. E.; Lemon, R.A. Rasmussen, S.T. Thorneloe, Systems,” Env. Sci. Technol., 35, Protection. A.; Scherer, M. M.; Balko, B. A.; Feik, 1806-1817 (2001). “Carbon monoxide from cookstoves L. M.; Henegar, B. (2001) “Visualizing in developing countries: 1. Emission Toccalino, P. L., K. M. Auer, redox chemistry: Probing environmental Johnson, R.L., J. Pankow, D. Bender, factors,” Chemosphere: Global Change D. A. Mervyn, and B. Stirling. 1997. oxidation-reduction reactions with indi- C. Price, J. Zogorski, “MTBE, To What Sci., 1(1-3), 353-366 (1999). Phase II Remedial Investigation/Risk cator dyes.” The Chemical Educator, Extent will Past Releases Contaminate Assessment Report for Westside Light E. Grosjean, R.A. Rasmussen, 6(3), 172-179. Community Water Supply Wells?” Rail Transit (LRT) Construction Spoils D. Grosjean, “Toxic air contaminants in Environmental Science & Technology, at the Port of Portland’s Portland Nam, S.; Tratnyek, P. G. (2000) Porto Alegre, Brazil,” Environ. Sci. 210A-217A (2000). International Center, Portland, OR. “Reduction of azo dyes with zero-valent Technol., 33(12) 1970-1978 (1999) iron.” Wat. Res., 34(6), 1837-1845. J.F. Pankow, B.T. Mader, Toccalino, P. L. 1997. Evaluation of R.A. Rasmussen, M.A.K. Khalil & L.M. Isabelle, W. Luo, A. Pavlick, the Contained Burn of Two M88 NIKE Tratnyek, P. G.; Macalady, D. L. F. Moraes, “Permafrost Methane C. Liang, “Conversion of Nicotine in Rocket Motors for Environmental Safety (2000) “Oxidation-reduction reactions Content: 1. Experimental Data from Tobacco Smoke to its Volatile and & Health Implications, Nevada Test Site in the aquatic environment.” In: Sites in Northern Alaska,” Available Free-Base Form through X-Tunnel Facility (U25X), Las Vegas, NV. Handbook of Property Estimation the Action of Gaseous Ammonia,” Chemosphere, 26:591 (1993). Methods for Chemicals: Environmental Toccalino, P. L., R. L. Johnson, and Environmental Science and Technology, M.A.K. Khalil, R.A. Rasmussen, and Health Sciences; Mackay, D.; D. R. Boone. 1993. “Nitrogen limita- 31, 2428-2433 (1997). J.R. French & J. Holt, “The Influence Boethling, R. S., Eds.; Lewis: Boca tion and nitrogen fixation during alkane of Termites on Atmospheric Trace Raton, FL; pp. 383-415. C. Liang & J.F. Pankow, “Gas/Particle biodegradation in a sandy soil.” Appl. Gases: CH4, CO2, CHCl3, N2O, CO, Partitioning of Organic Compounds Environ. Microbiol. 59:2977-2983. Church, C. D.; Pankow, J. F.; to Environmental Tobacco Smoke: H2 and Light Hydrocarbons,” Tratnyek, P. G. (1999) “Hydrolysis of Partition Coefficient Measurements by J. Geophys. Res., 95:3619 (1990). Toccalino, P. L., K. M. Harmon, tert-butyl formate: Kinetics, products, and J. Harmon. 1988. “Hydrogen Desorption,” Environ. Sci. Technol. D.A. Hegg, L.F. Radke, P.V. Hobbs, and implications for the environmental bonding. Part 26. Thermodynamics 30(9), 2800-2805 (1996). R.A. Rasmussen & P.J. Riggan, impact of MTBE.” Environ. Toxicol. of dissociation and infrared “Emissions of some trace gases from Chem., 18(12), 2789-2796. J.F. Pankow, “An Absorption Model spectra-crystal structure correlations biomass fires,” J. Geophys. Res., of Gas/Particle Partitioning in the for betaine monohydrate and trimethy- 95:5669 (1990). Atmosphere,” Atmos. Environ., 28, lamine oxide dihydrate.” J. Mol. Struct. 189 (1994). 189:373-382. 76 FACULTY | ENVIRONMENTAL SCIENCE AND ENGINEERING | ESE

JOINT APPOINTMENTS RESEARCH SCIENTISTS SENIOR STAFF

DR. J. FRED HOLMES ARUN CHAWLA BOB DALLUGE Electrical and Computer Research Scientist Research Associate Engineering Ph.D., Civil Engineering, B.S., Psychology, OGI School of Science University of Delaware Washington State University and Engineering WENTAI LUO ANNA FARRENKOPF DR. JAMES HUNTZICKER Research Scientist Research Associate Center for Ph.D., Environmental Science Ph.D., Marine Studies, Professional Development and Engineering, University of Delaware at Lewes OGI School of Science Oregon Graduate Institute and Engineering LORNE M. ISABELLE TODD SANDERS Senior Research Associate Research Scientist ADJUNCT FACULTY M.S., Chemistry, Ph.D., Physical Oceanography, San Francisco State University University of Delaware DR. MARY ABRAMS COLE MC CANDLISH DEQ Laboratory Division DOUG WILSON Oregon Department of Scientific Programmer Research Scientist Environmental Quality M.S., Atmospheric Sciences, Ph.D., Physical Oceanography, Oregon State University Memorial University of DR. DAVID BOONE Newfoundland ROSEMARIE MIEHR Department of Research Associate Environmental Biology, YINGLONG (JOSEPH) ZHANG Portland State University Ph.D., Chemistry, Research Scientist Technical University, Ph.D., Applied Mathematics DR. NORMAN EDER Munich, Germany and Fluid Mechanics, Conkling Fiskum & University of Wollongong, JIM MOHAN McCormick, Inc. Australia Systems Manager M.S., Management in DR. WILLIAM FISH MICHAEL ZULAUF Department of Environmental Science and Technology, Research Scientist Oregon Graduate Institute Sciences and Resources, Ph.D., Meteorology, Portland State University University of Utah INGA O’BRIEN DR. BRUCE HOPE Research Associate Environmental Toxicologist, M.A., Health Communication Oregon Department of & Development, Environmental Quality Ohio University

DR. ASLAM KHALIL PHILIP ORTON Department of Physics Research Associate Portland State University B.S., Physical Oceanography, University of Michigan KENNETH ROSENBAUM, J.D. ROBYN PHILLIPS Environmental Law Institute (Visiting Scholar), Research Associate Washington, D.C. M.S., Environmental Management/Toxicology, DR. JOHN C. WESTALL Duke University Department of Chemistry, CHARLES SEATON Oregon State University Research Assistant M.S. Environmental Science & Engineering Oregon Graduate Institute

BOB WATKINS Research Technician B.S., Chemical Engineering, Washington State University

MICHAEL WILKIN Research Associate B.S., Oceanography and Geology, University of Southampton, U.K. 77 THE DEPARTMENT OF MANAGEMENT for their own career development in Department of IN SCIENCE AND TECHNOLOGY specific areas. provides the rigorous Management in Science CERTIFICATE OPTIONS educational preparation The MST department offers certificates and Technology necessary for highly effective in Management Studies and Technology, managerial- and professional- Building the General Manager, and www.ogi.edu/MST/ level work in industries, Industrial Design. organizations and departments MANAGEMENT STUDIES DEPARTMENT HEAD that have a strong technical, MST offers a six-course certificate in Fred Phillips (503) 748-1353 engineering, manufacturing Management Studies. The following five courses, plus an additional MST elective E-mail: [email protected] or scientific orientation. course chosen in consultation with a faculty DEPARTMENT ADMINISTRATOR Our courses, certificate and master’s degree advisor, are required: Victoria Tyler programs focus on managing people and MST501/501D Managerial and Financial Accounting (503) 748-1335 processes and building effective and for Science and Technology 4 credits E-mail: [email protected] competitive organizations in the specific MST503/503D Marketing in Science and Technology 4 credits PROGRAM ASSISTANTS contexts of technology and science. Managing MST510/510D Principles and Trends in Staci Sutton change and competing in the global Technology Management 3 credits (503) 748-7804 marketplace are prominent themes in the MST512/512D Project Management 3 credits E-mail: [email protected] MST program. MST520/520D Managing in Science and Technology 4 credits Maryann Burningham Elective to be chosen after consultation (503) 748-1794 LEARN ON-LINE, ANYTIME, ANYWHERE with faculty advisor 3-4 credits MST delivers challenging and engaging E-mail: [email protected] versions of its courses over the Internet. BUILDING THE GENERAL MANAGER (BGM) GENERAL INQUIRIES This is an excellent option for students A CERTIFICATE PROGRAM FOR SENIOR MANAGERS (503) 748-1418 facing time pressures or working in IN TECHNOLOGY-INTENSIVE COMPANIES E-mail: [email protected] locations where travel to the OGI campus is The program focuses on building general not feasible. The course delivery system is management skills needed to successfully based on interactive multimedia lectures manage the established but still-growing and lessons, faculty-managed chat, and on- high-tech business, and can be completed in line discussions, all in a seamless browser- a series of long weekends over the course of centric environment. Students can take one year. individual courses, enroll in the Certificate in Management in Science and Technology The ideal BGM participant does not need an program, or apply for the full Master of additional degree for career advancement, Science degree (currently only the Managing can spare the time only for a concentrated the Technology Company degree option is program, and wishes to leverage the learning offered on-line). Courses offered on-line will experience to build a network of peers in have a “D” designation following the course other technology companies. number. For further information dial toll The three key areas of the BGM Certificate free in the U.S. 1-877-GO TO OGI (1-877- are: Business Management Foundations, 468-6644) or visit the MST on-line learning which selectively draws on MST courses; and Web site: http://elearning.cenquest.com/ Executive Assessment and Coaching, which is incorporated into the program with pre- and INDIVIDUAL COURSES IN MST post-assessment and jointly undertaken with Each MST course has been designed as a incumbent companies; and Building Executive valuable professional development Leadership Skills, which serves as the core of experience for working professionals. the program. Project Management, Quality Management, Building Effective Organizations in Science BUILDING EXECUTIVE LEADERSHIP SKILLS CORE and Technology, for example, may be taken (6 CREDITS) as stand-alone courses. We encourage non- MST541/541D Seminar in Leadership Development 3 credits matriculated students to join our courses MST522/522D Building Effective Organizations 3 credits MST student Dave Kennedy presents a business plan for his Capstone Project. MST | MANAGEMENT IN SCIENCE AND TECHNOLOGY

In addition, four workshops, chosen in • GMAT or GRE scores are not required, except MST540/540D International Management in Science consultation with the firms employing each under certain circumstances and Technology 3 credits BGM participant, help build executive skills. Part-time students may apply for admission MST541/541D Seminar in Leadership Development 3 credits Workshops conclude with a team project-a to the M.S. program during any quarter. Full- ELECTIVES: Any course in the above list not high-impact business project for the time students must begin in the fall quarter. already taken and/or any of the following company. Nationally recognized instructors (6-7 credits): join the OGI faculty to teach these executive DEGREE REQUIREMENTS ECE555 Engineering Optimization 4 credits workshops. Titles include: Leading the ECE577 Principles for Technology Development Strategy Process; Mindset and Skills for MST offers a non-thesis M.S. in Management and Introduction to Manufacturing 3 credits Managing Globally; Managing Development in Science and Technology. Students elect one ESE504 Uncertainty Analysis 4 credits Projects for Profits, Growth and Renewal; and of three areas of concentration within the ESE586 Environmental Law and Regulation 3 credits Managing for Innovation and Leading Change. degree program: Managing the Technology CSE503 Software Process Processes 3 credits Company, Computational Finance or INDUSTRIAL DESIGN CSE549 Applied Business Forecasting 3 credits Managing in the Software Industries. CSE568 Empirical Research Methods 3 credits This certificate program introduces Students must complete a minimum of 53 participants to the full range of activities credits with an average of ‘B’ or better; up to FIN541 Principles of Modern Finance 3 credits involved in the design of products for industry four courses or twelve credits taken in the FIN544 Investment and Portfolio Management 3 credits and the marketplace. The role of the ID department prior to matriculation may be FIN547 Global Markets &Foreign Exchange 3 credits process within the organization is addressed, used toward the degree requirements. FIN551 Options and Futures I 3 credits as are the key elements of an effective design FIN552 Options and Futures II 3 credits MST CORE SEQUENCE project from conceptualization to product FIN558 Advanced Numerical Computing All M.S. students must take the MST core manufacturing, product launch and in Finance 3 credits sequence, consisting of the following courses or marketing program. their equivalent (38 credits). The courses listed FIN561 Risk Management 3 credits Topics taught include new product below are offered both on-campus and on-line. FIN573 Financial Time-Series Analysis 3 credits Either is acceptable for the M.S. in Management in FIN576 Financial Markets and Trading 3 credits development and design management Science and Technology degree. If you intend to strategy, application of CAD in product take ONLY on-line courses, please see the Distance MST504 Marketing: Going to Market 3 credits development (including CAD/CAE/CAM Degree Requirements after this section. MST515 Supply Chain Management 3 credits integration), and an overview of future MST501/501D Managerial and Financial Accounting MST517 Global Logistics and development in technology for ID and for Science & Technology 4 credits Financial Management 3 credits manufacturing. During the previous year, MST502/502D Financial Management 4 credits MST521/ Human Resource Management in 521D Science and Technology 3 credits certificate requirements included 40 contact- MST503/503D Marketing: Planning for Market 4 credits MST523 New Products Development 4 credits hours in Industrial Design, 40 contact-hours MST510/510D Principles and Trends in in Modeling Computer Aided Development, 20 Technology Management 3 credits MST524 Digital Economy: Strategy for Success 4 credits contact-hours in management seminars, plus MST512/512D Project Management 4 credits MST531 Software Commercialization 3 credits a number of site visits. MST513/513D Manufacturing Practices MST542 Seminar in Social Issues in Management 3 credits and Management 3 credits MST543 Commercialization Practicum 3 credits ADMISSION REQUIREMENTS MST520/520D Managing in Science and Technology 4 credits MST544/ MST530/530D Strategic Management and Planning 4 credits MST544D Strategic Alliances 3 credits Admission requirements are the same as the MST550/550D Capstone Project: Business Plan 4 credits MST58X Special Topics (special electives offered general requirements for the institution. In on a one-time only basis) addition, the MST department requires: MST590/590D Effective Business Writing for Management OR 1 credit Students may petition the MST department for • A bachelor, master or doctoral degree from an elective credit for other OGI School academic MST591/590D Professional Writing for accredited institution courses relevant to the theory or practice of Non-native Speakers 1 credit management. • A recommended cumulative undergraduate grade point average of 3.0 AREA OF EMPHASIS COMPUTATIONAL FINANCE SEQUENCE All emphasis areas require the completion of the MST Core Sequence plus the following three • A minimum of two years of full-time work 34-credit M.S. core sequence. Specific courses courses are required (9 credits): experience-preferably at the professional, required for each emphasis area are as follows: supervisory or managerial level-in a technical, FIN541 Principles of Modern Finance 3 credits scientific, business, or related area MANAGING THE TECHNOLOGY COMPANY SEQUENCE FIN551 Options and Futures 1 3 credits • Three letters of recommendation, one of which Core Sequence plus three of the following FIN561 Risk Management 3 credits should come from an employer or supervisor MST Core Sequence plus three of the following five courses are required (9 credits): Electives: three of the following courses are • Recommended TOEFFL score of 625 if English required (9 credits) is not the applicant’s first language. Scores are MST511/511D Quality Management 3 credits not required for students who earned an under- MST514/514D Issues in R&D Management 3 credits FIN544 Investment and Portfolio Management 3 credits graduate degree in the United States, or who have MST522/522D Building Effective Organizations in FIN547 Global Markets and Foreign Exchange 3 credits worked for a business for at least two years and Science and Technology 3 credits FIN552 Options and Futures II 3 credits where the primary business language is English 80 MANAGEMENT IN SCIENCE AND TECHNOLOGY | MST

FIN558 Advanced Numerical Computing MST512D Project Management 4 credits techniques of practical application. Prerequisite: MST 501. 4 credits in Finance 3 credits MST513D Manufacturing Practices FIN573 Financial Time-Series Analysis 3 credits and Management 3 credits MST 503, MST 503D Marketing in Science FIN574 Financial Markets and Trading 3 credits MST520D Managing in Science and Technology 4 credits and Technology The course introduces the graduate student to the Students should note that tuition for the CSE MST530D Strategic Management and Planning 4 credits full range of issues and activities involved in the Computational Finance courses listed above MST550D Capstone Project: Business Plan 4 credits marketing of technology-based products. The role of (FINxxx) is higher than for other OGI courses. MST590D Effective Business Writing marketing within the organization is addressed, as MANAGING IN THE SOFTWARE INDUSTRIES SEQUENCE (4 workshops at .25 credits each) OR 1 credit are the key elements of an effective marketing program. The course is organized to cover the full MST Core Sequence plus the following two courses MST 591D Professional Writing for Non-native product introduction process, from market identifi- are required (6 credits): Speakers (with dept. approval; cation to product conception and definition, to 4 workshops at .25 credits each) 1 credit MST531 Software Commercialization 3 credits market research, to competitive analysis, and ultimately, to product launch. Topics include pricing, CSE500 Introduction to Software Engineering 3 credits AREA OF EMPHASIS — sales and distribution alternatives, and marketing Electives: Four of the following courses are DISTANCE DEGREE communications. To the extent possible, assign- required (12-13 credits): ments utilize or draw from students’ work CSE503 Software Process Practicum 4 credits MST currently offers only the Managing the experiences in technology, engineering, manufactur- Technology Company emphasis to students ing, and science. 4 credits CSE504 Object-Oriented Analysis and Design 3 credits who take only online classes. CSE514 Introduction to Database Systems 3 credits MST 504, Marketing: Going to Market MANAGING THE TECHNOLOGY COMPANY DISTANCE SEQUENCE The overall goal of this course is to teach students CSE518 Software Design and Development 3 credits to write a marketing plan that develops a product CSE560 Artificial Intelligence 3 credits MST Distance Core Sequence plus three of the or service’s business model and persuasively makes following four courses are required (9 credits) CSE564+ Human-Computer Interaction 3 credits the business case. This goal is achieved by using two strategies: by helping students understand and CSE567+ Developing User-Oriented Systems 3 credits MST511D Quality Management 3 credits apply the critical concepts and principles driving MST514D Issues in R&D Management 3 credits MST504 Marketing: Going to Market 3 credits the implementation of a high technology-oriented MST511/511D Quality Management 3 credits MST522D Building Effective Organizations in marketing plan; and by helping students acquire Science and Technology 3 credits and develop the language, methodologies, models, MST522/ Building Effective Organizations in processes, standards, tools, and skills for analyzing 522D Science and Technology 3 credits MST540D International Management in Science and Technology 3 credits and dealing with the high technology opportunities MST540/ International Management in Science and challenges facing marketing at the dawn of this Electives: any course in the above list not already 540D and Technology 3 credits new century. 3 credits taken and/or any of the following (9 credits) MST541 Seminar in Leadership Development 3 credits MST 510, MST 510D Principles and Trends MST521D Human Resource Management in +Credit will be given for no more than one of the in Technology Management Science and Technology 3 credits indicated courses. This course is about how companies choose, MST544D Strategic Alliances 3 credits Students may petition the MST department head acquire, and develop the technologies that they use for elective credits for other OGI academic courses MST58XD Special Topics Variable credits to develop, manufacture, deliver and support their relevant to the theory or practice of management. Students may petition the MST department head products. We look at these practices both from the for elective credits for other OGI School academic vendor and buyer points of view, and also consider YOU CAN COMPLETE YOUR ENTIRE DEGREE ON LINE! courses relevant to the theory or practice of internal technology development for internal use. management. Other topics addressed include profitably managing technology cycles; standards; technology forecast- MST DISTANCE DEGREE REQUIREMENTS ing; and the technology startup company. Related topics such as competitive analysis, managing The department of Management in Science COURSE DESCRIPTIONS researchers, and maintaining an innovative organi- and Technology recommends that students MST 501, MST 501D Managerial and Financial zational atmosphere are dealt with in MST 503 and take at least two on-campus courses. A Accounting for Science and Technology MST 514. The format includes lectures, discussions, proctored comprehensive exam may be The course focuses on understanding and evaluating guest speakers, and team and homework projects. financial reports and information for use in making 3 credits required at or near the completion of the MST decisions, particularly as they pertain to managing in Distance degree requirements. Students must science, technology, engineering, and manufacturing. MST 511, MST 511D Quality Management complete a minimum of 52 credits with an 4 credits The course covers total quality management (TQM) average of B or better. MST 502, MST 502D Financial Management from the managerial vantage point-that is, both the MST DISTANCE CORE SEQUENCE for Science and Technology behavioral and operations management aspects, The course combines a survey of the relevant excluding sophisticated statistical analysis, of TQM All M.S. student must take the MST core sequence, aspects of micro- and macroeconomics with in- are addressed. Classroom discussion, based on the consisting of the following courses or their depth study of key concepts in financial participants’ experiences and the assigned read- equivalent (34 credits): management of a firm, financial structure and finan- ings from the text and cases, is the primary source MST501D Managerial and Financial Accounting cial analysis of the firm, working capital of learning for many students. Lectures are used for Science and Technology 4 credits management and short- and long-term financing. but generally as a basis for a facilitated discussion led by the instructor. The limitations of TQM also MST502D Financial Management 4 credits Particular attention is paid to valuation of investment alternatives through study of risk and rates of are discussed, given the inherent risks of excessive MST503D Marketing in Science and Technology 4 credits return, bond and stock valuation, and capital budg- optimism associated with any social trend or per- MST510D Principles and Trends in eting. The course is designed to achieve balance ceived panacea. 3 credits Technology Management 3 credits between understanding theoretical foundations and 81 MST | MANAGEMENT IN SCIENCE AND TECHNOLOGY

MST 512, MST 512D Project Management sells it in Europe. Wage-rate differentials, expand- includes a limited overview of employment law, with The course focuses on the managerial aspects of ing foreign markets, and improved transportation a particular focus on recent cases and changes in project selection and management. Topics addressed are breaking down barriers of time and space employment legislation. 3 credits include planning, design, scheduling, implementa- between countries forcing the logistics function to MST 522, MST 522D Building Effective Organizations tion, control, evaluation, and termination. 4 credits take a global dimension. Global logistics is the in Science and Technology response to the increasing integration of interna- This course focuses on designing effective organiza- MST 513, MST 513D Manufacturing Practices tional markets as firms try to remain competitive. and Management tions and managing change in organizations in which Topics covered include practices and trends in the The emphasis of the course is the operations and engineering, manufacturing, and/or scientific tech- overall design, analysis, organization, and control of logistics function in firms that source, produce, dis- nologies are critical. Tools for assessing the need for manufacturing operations, as well as relationships tribute and market in multiple nations. The reorganization and implementing structural changes with vendors, suppliers, and customers. 3 credits management of logistics in such firms differs from are emphasized. The course pays special attention its domestic counterpart along several key dimen- to organizing for lateral coordination and integra- MST 514, MST 514D Issues in R & D Management sions. First, there is the need to be able to identify tion, as this is a required capability in technology- Participants examine issues in managing R&D and and analyze factors that differ across nations, which intensive organizations. Students are invited to con- technological innovation in an environment of influence the effectiveness of this function. These sider the relationship between organizational theory increasing time- and competence-based competi- include worker productivity, process adaptability, and practice. A range of theoretical perspectives is tion, a competition that is simultaneously global governmental concerns, transportation availability, reviewed, and students are encouraged to compile and local in both markets and technology, where culture and soon. In addition, because of the dis- their own approach by combining those presented. competitors draw on an existing technology base tances involved, transportation and distribution are Extensive use is made of cases and actual examples that supports incremental innovation through radi- of greater significance. Finally, these geographically drawn from the readings and from course partici- cal innovation, and where quality is a given. dispersed set of facilities and markets must be inte- pants’ experiences. Taking MST 520 first is Particular attention is given to R&D management grated and manage to enhance the strategy of the recommended. 3 credits issues in integrating technology into business strat- business unit. Therefore, some of the sessions of the MST 523 New Product Development egy and operations, managing internal development course will focus on cross-national decisions and Successful product development has been key to and external sourcing of technology, seeking com- others will focus on managing across nations. survival in today’s competitive markets. This course petitive advantage through collaborative advantage, 3 credits and building new technical competence as a part of was designed to address professionals who are in every project. Key trends, new conceptual frame- MST 520, MST 520D Managing in Science product development organizations or support such works, management tools and techniques, and best and Technology organizations. It has been seen that technology inte- practices in R&D management are examined This course focuses on developing participants’ abil- gration and creating innovative environments have through presentation, interactive class discussions, ity to understand and influence human behavior. been critical to developing profitable products in selected readings, case studies, and a number Four theory-based frames are elaborated and used today’s technology oriented companies. The course of invited speakers from both small and large for understanding human behavior. Using the struc- will review cases and published articles addressing companies. 3 credits tural frame, we examine work design and redesign key issues in new product development. Topics such for individuals and groups, and consider the impact as Disruptive Technologies, Technology Integration, MST 515 Supply Chain Management of restructuring. Using the human resource frame, Concurrent Engineering, and Managing Technological This is a course in Supply Chain Management, a we examine interpersonal and group dynamics, Innovation will be covered. 4 credits term which denotes a total system approach to the communication and creativity. Using the political MST 524 Digital Economy: Strategy for Success management of all of those activities involved in frame, we consider power, conflict, and differences physically moving raw materials, inventory, and fin- in the workplace. Using the symbolic frame, we The purpose of this course is to equip the student ished goods inventory from point of origin to point of examine the impact of individual leadership and cor- with a practical and conceptual understanding of consumption. Supply Chain Management (SCM) is a porate culture on organizational outcomes. what it takes to develop and maintain a competitive system approach to managing the entire flow of advantage in the new economy. We will look at it from information, materials, products, and financial The course also examines the influence processes several perspectives. We will start by investigating funds to and from suppliers and end-customers. and network of relationships required for managing the fundamental changes that the Internet and other 3 credits research scientists, engineers, and other profes- technologies introduce in the economy and how this sionals, as individuals and in teams, in a fast- completely changes the rules of the competitive MST 516 SCM – Advanced Modeling changing environment. Self-assessment, network- game. We will then look at how entire industries and This course will introduce the use of mathematical ing, and developmental relationships are explored activities are being transformed and why. programming in supply chain modeling. The empha- as means of developing influence and having impact sis will be mainly on large-scale optimization of within a technologically driven organization. In the second part of the course we will look at real-world supply chain distribution networks. The 4 credits strategy from several angles. The first one will major skills taught are problem definition, model address the question of what a company should formulation, and solution analysis. We will teach MST 521, MST 521D Human Resource Management consider to develop its competitive advantage and the use of commercial software, which include the in Science and Technology its competitive strategy. The second angle will MAPLE algebraic modeling system for planning This course focuses on the development, implemen- address the Internet marketing side or how to go to problems, What’s BEST for decision-making, and tation, and evaluation of human resource market and rise to the top. The third angle is GSCM for large mixed-integer programming net- management (HRM) systems, and the relationship addressing the question of how successful compa- work design. 3 credits between an organization’s HRM practices and the nies organize and what they do to operate at the organization’s effectiveness and competitive suc- “speed of change.” Students will use the learning MST 517 Global Logistics and Financial Management cess. Specifically, the course addresses the choices they acquire to develop a business concept to be The global environment that characterizes the busi- an organization must make in three HRM policy presented at the last session. The course will be ness world of today has pointed out the importance areas: organization of work and employee influence; supported by a Web site, where course materials of developing strategies that go beyond the geo- personnel flows and development; and measurement and resources will be made available. We will also graphical boundaries of one country. Nowadays, it is and rewards. We consider the perspectives of both carry discussions off-line. Several executives from not uncommon to see a company that develops a the line manager and the HRM specialist in examin- local companies have been invited to share their new product in the US manufactures it in Asia and ing these three policy areas. The course also experience in the dot-com world. 4 credits

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MST 530, MST 530D Strategic Management Each team adopts a real technology held by Batelle- and Planning Pacific Northwest Laboratories, OHSU, OGI, This course focuses on the analysis of the competi- Oregon Medical Laser Center, or others. Students tive environment and on the decision-making will make one or more field trips to these institu- process leading to the formulation and implementations. The technologies may be in the areas of tion of strategy. Other topics include using time, environmental, health, genetics, multimedia, com- knowledge, and technologies as competitive advan- puters or other fields. tages, managing strategic change, and developing Each team’s final paper - which may include market strategic plans. Prerequisites: MST 502, MST 503, research, a design for a manufacturable product, MST 520. 4 credits profiles of desired management teams, licensing MST 531 Software Commercialization plans, tech-marketing feasibility, and/or preliminary This course examines the structure of the software startup business plan, will be submitted to the insti- industry, and problems of marketing privately devel- tution that originated the technology. MST students oped software and commercializing software from may choose to use their 581 project as a prelimi- the government and nonprofit sector. Because the nary exercise for the capstone project. 3 credits business models for hardware and software compa- MST 544, MST 544D Strategic Alliances nies are quite different, the course focuses on the This course explores a model of implementing special problems of marketing, entrepreneurship, strategic alliances, business partnering and joint globalization, and alliances experienced by software ventures originally outlined by Robert Lynch, senior firms. Relationships between marketing strategy partner of The Warren Company, in his book and development strategy also are examined. Business Alliances Guide (John Wiley and Sons, 3 credits 1993). The book is a compilation of best practices in MST 540, MST 540D International Management strategic alliance formation and implementation dis- in Science and Technology tilled from approximately 40 different high Topics in this course include trends in the conduct of performance international and domestic strategic international business, the international business alliances. It offers a well-articulated framework, environment, the operation of multinational enter- which is applicable across a broad range of alliance prises, international technology transfer, and the types. The objective of this course is to provide each special considerations associated with managing on student with an opportunity to learn practical, effec- the international level. 3 credits tive methods for forming, implementing and executing high-performance strategic alliances. MST 541 Leadership and Negotiation 3 credits This course focuses on the negotiation and interpersonal communication skills required to exercise MST 550 Capstone Project: Business Plan effective leadership. Topics include creating clarity In the program’s capstone course, students com- about one’s own values and mission, exercising plete major integrative projects as members of influence through both formal and informal authori- teams. Prerequisites: MST 530 and approval of ty channels, and being a catalyst for change. instructor. 4 credits 3 credits MST 58X, MST 58XD – Special Topics MST 542 Seminar in Social Issues in Management Under this number, courses of particular relevance This course focuses on ethical dilemmas, social and interest to students and faculty are offered. issues and responsibilities, and government regula- Variable credits. tions and influences. First, the course examines MST590, MST 590D Effective Business Writing different frameworks for individual decision making for Management in an organizational setting. Next, the impact of This course will review several aspects of conven- organizational policies and practices, and the words tional punctuation and grammar that address the and actions of managers, on the behavior of individ- needs of the participants. In addition, attention is uals within those organizations is examined. Finally, given to stylistics for clear, concise communication the course focuses on the relationship between necessary in business writing. Class size is limited organizations and the societies in which they oper- to ten students. 1 credit ate. We consider the perspectives of key stakeholders, including government regulators, MST 591, MST 591D Professional Writing for community representatives, customers, employees, Non-native Speakers managers, and stockholders, and examine different An intensive review of English grammar and sen- views on corporate social responsibility. 3 credits tence structure with a focus on formal English for MST 543 Commercialization Practicum professional purposes. Some attention to the academic essay as well as business writing. Class size Students will have the opportunity to work in teams is limited to ten students. No prerequisite. 1 credit with real technologies. Student teams will produce assessments and plans for bringing new technolo- Note: descriptions for Computational Finance courses, gies to market using Vijay Jolly’s Mind to Market designated FINxxx, are found in the catalog under the Technology Commercialization and other frame- Department of Computer Science and Engineering works such as a Total Life Cycle Planning approach. Course Description section. Wherever possible, industry advisors will mentor students in their area of expertise within the design, management and product manufacturing process.

83 MST | MANAGEMENT IN SCIENCE AND TECHNOLOGY | FACULTY

F. Phillips, “Conditional Information FRED YOUNG PHILLIPS Characterization of Brand Shifting in a C. NEIL BERGLUND MARIANNE KOCH Professor and Department Head Hierarchical Market Structure,” Professor/Joint Appointment Visiting Associate Professor Ph.D., Management Journal of the Operational Research with Department of Electrical Ph.D., Human Resource Science/Business Administration Society, 45(8), 901, 1994. and Computer Engineering Management and The University of Texas F. Phillips, R.K. Srivastava and Ph.D., Electrical Engineering Industrial Relations at Austin, 1978 R.S. Springer, “Project Valuation and Stanford University, 1964 Columbia University, 1989 [email protected] Scheduling with Recourse,” Proceedings [email protected] [email protected] of PICMET 91, the Portland International Conference on RESEARCH INTERESTS Management of Engineering and RESEARCH INTERESTS RESEARCH INTERESTS Technology. IEEE Engineering Market research, marketing Management Society, 1991. Management of technology, and The human side of technology innovation and high-technology advanced lithography for transfer; work/family policies and products, managing the new F. Phillips and B. Golany, “A Heuristic semiconductor fabrication. practices; coaching faculty in the for Estimating Densities from Data in product development process, Histogram Form,” Decision Sciences, development and teaching of incubation and commercialization 24(4), 862-881, 1990. REPRESENTATIVE PUBLICATIONS e-learnings courses. of new technologies, strategic and J. Ye, M. Takac, C.N. Berglund, innovative use of computers G. Owen & R.F.W. Pease, “An Exact REPRESENTATIVE PUBLICATIONS: Algorithm for the Self- Calibration of M. Koch & D Moshavi, “The Adoption REPRESENTATIVE PUBLICATIONS Precision X-Y Stages,” Conference on of Family-Friendly Policies in Family- Electron, Ion & Photon Beam F. Phillips, “Market-Oriented Owned Firms: Paragon or Paradox, Technology & Nanofabrication Proceedings of the 2001 Southern Technology Management: Innovating (May 1996). for Profit in Entrepreneurial Times.” Management Association Annual Springer-Verlag, Heidelberg, 2001. M.T. Takac, J. Ye, M.R. Raugh, R.F.W. Meeting, New Orleans, LA, 2001. Pease, C.N. Berglund & G. Owen, F. Phillips and M. Burningham, M. Koch, L. Long, & A. Meyer, “Self-Calibration in Two Dimensions: “Adoption of Innovations in Hospitals: “WTO vs. WTA? Exploring the World The Experiment,” 1996 SPIE Trade Organization’s Impact on Exploring the Validity of a Multi-Stage International Symposium on Model,” forthcoming, International Technopolis.” Presented at 4th Microlithography (March 1996). International Conference On Technology Journal of Technology Management; Policy & Innovation, Curitiba, Brazil, W. Wang, J. Ye, A.B. Owen, C.N. alsoin Academy of Management Best August, 2000. Berglund & R.F.W. Pease, “Adaptive Papers Proceedings, August, 1996. Metrology: An Economical Strategy for M. Koch & G. Hundley, “The Effects of F. Phillips and S. Tuladhar, “Measures Judging the Acceptability of a Mask of Organizational Flexibility.” Unionism on Recruitment and Selection Pattern,” J. Vac. Sci. Technol., B13(6) Practices,”Industrial Relations, Vol.36, Technological Forecasting & Social (November/December 1995). Change 64/1, May, 2000. No.3, pp.349-370, 1997. J. Ye, C.N. Berglund & R.F.W. Pease, F. Phillips, L. Ochs, and M. Schrock, M. Koch & R. McGrath, “Improving “Field Distortion Characterization Using Labor Productivity: Human Resource “The Product is Dead; Long Live the Linewidth or Pitch Measurement,” Product-Service.” Research Technology Management Policies Do Matter,” 1996, J. Vac. Sci. Technol. B13(6) Strategic Management Journal, Vol.17, Management, vol. 42, no. 4, (November/December 1995). July-August, 51-56, 1999. pp.335-354, 1996. Awarded an Anbar J. Ye, C.N. Berglund, J. Robinson & Electronic Intelligence Citation of F. Phillips, A. Donoho, W. Keep, R.F.W. Pease, “A Review of Mask Errors Excellence Award for 1997. W. Mayberry, J.M. McCann, K. Shapiro on a Variety of Pattern Generators,” M. Koch. “Hiring Practices and and D. Smith, “Electronically IEEE Transactions on Semiconductor Connecting Retailers and Customers: Labor Productivity”, 1995. Garland Manufacturing, 8(3), pp. 319-325 Publishing, Inc., New York, N.Y., 1995. Summary of an Expert Roundtable,” (August 1995). Journal of Shopping Center Research, 4(2), 63-94, 1997. J. Ingino, G. Owen, C.N. Berglund, R. Browning & R.F.W. Pease, F. Phillips and N. Kim, “Implications “Workpiece Charging in Electron of Chaos Research for New Product Beam Lithography,” J. Vac. Sci. Forecasting.” Technological Forecasting Technol., B12(3), pp. 1367-1371 and Social Change, Vol. 54, No. 1, (May/June 1994). 1996. P. Brockett, A. Charnes, W.W. Cooper, D.B. Learner and F. Phillips, “Marketing Research Unification by Information Theoretic Methods,” European Journal of Operations Research, 84, pp. 310-329,1995. S. Thore, G. Kozmetsky and F. Phillips, “DEA of Financial Statements Data: The U.S. Computer Industry,” Journal of Productivity Analysis, 5(3), 229, 1994. 84 FACULTY | MANAGEMENT IN SCIENCE AND TECHNOLOGY | MST

JACK RAITON ADRIAN ROBERTS NICOLE STECKLER ALVIN H. TONG Senior Fellow Senior Advisor Associate Professor Professor of Management MBA, Finance & Statistics Ph.D., Metallurgy Ph.D., Organizational Behavior Ph.D., Electrical Engineering University of Washington, 1967 University of Manchester, England Harvard University, 1990 University of Minnesota, 1967 [email protected] [email protected] [email protected] Adrian Roberts is a consultant on Jack Raiton has been VP and CFO technology management, RESEARCH INTERESTS RESEARCH INTERESTS at Planar Systems for the last four specializing in R&D management years, and also served as VP and and technology commercialization. Tools for diagnosing and Alvin Tong teaches Project CFO at Smith’s Home Furnishings. Acting as advisor to Battelle improving leadership Management and the His prior experience includes Memorial Institute and other effectiveness, roles in CapstoneProject (Business Plan) working at Tektronix for about 22 clients on technology projects and implementing (and resisting) course, and has been with MST years, the last 12 as the Corporate new business creation, Adrian was organizational change, since 1996. Alvin served as a Controller and serving as Plant recently appointed Interim interpersonal communication mentor for the 1999 student team, Controller for Fairchild Camera Director of Battelle-Pacific and influence in organizations, ArtCentral that won first place in and Instruments. Jack earned his Northwest National Laboratories. and lateral coordination the New Venture Championship BS in Mathematics from Oregon This past year, he has contributed in organizations. 2000, a national/international State University in 1966 and his to the Center for Entrepreneurial business plan competition held in REPRESENTATIVE PUBLICATIONS MBA in Finance and Statistics Growth and has taught the MST Beaverton, Oregon. Alvin has from the University of Washington course on Technology N.A. Steckler & N. Fondas, thirty years of working experience “Building Team Leader Effectiveness: in the computer and related in 1967. He attended Harvard Management, as well as working A Diagnostic Tool,” Organizational University’s three-month Advanced with Brookhaven, Oak Ridge and industry, which includes serving as Dynamics, Vol. 23, 20-35, chief operating officer of Acer, Management Program, and passed Pacific Northwest National Winter/Spring 1995. the CPA exam in 1979. Laboratories on programs for the Inc., a Taiwan-based manufacturer J. White, S. Jacobson, R. Jacques, of personal computers. While with US Department of Energy. N. Fondas & N.A. Steckler, “You Acer, he also served as President AREAS OF EXPERTISE Just Don’t Understand: Gendered of their venture capital arm. Prior Performance Measurement, AREAS OF EXPERTISE Interaction and the Process of ‘Doing’ Organizational Scholarship,” to Acer, he worked for fourteen Capital Structure, Stock Options Technology management, Journal of Management Inquiry, years at IBM. In addition, he also and Incentive Plans, Forensic commercialization of technologies, 4(4), p. 370-379, December 1995. had a significant role as the first Accounting R&D management, strategic N.A. Steckler & A. Donnellon, deputy director-general of the planning. “Review of Peter K. Manning’s Hsin-chu Science-Based Industrial ‘Organizational Communication’,” Park (SBIP) in Taiwan. Alvin Academy of Management Review, has conducted numerous Vol. 18, 374-377, 1993. management-training seminars N.A. Steckler & R. Rosenthal, “Sex and is frequently invited to speak Differences in Nonverbal and Verbal and lecture on the subject of Communication with Bosses, Peers, and Subordinates,” Journal of Applied Globalization and Hi-Tech Science- Psychology, Vol. 70, 157-163, 1985. Based Industrial Parks. N.C. Ware, N.A. Steckler & J. Leserman, “Undergraduate women: REPRESENTATIVE PUBLICATIONS Who chooses a science major?” P. Schumann, D. Prestwood, A. Tong, Journal of Higher Education, & J. Vanston, “Innovate!”, McGraw-Hill, Vol. 56, 73-84, 1985. Inc., 1994.

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ADJUNCT FACULTY PAUL NEWMAN Cooper Mountain Research, Inc. KEN ANTHONY Rapid Innovations LYLE OCHS Technology & Innovation JEAN CLAUDE BALLAND Management Inc. JCB Associates RICHARD PRINS TUGRUL DAIM Group 3 Intel Corporation JESSE REEDER DEAN DERRAH Leadership Dynamics Infocus Systems YONG-IN SHIN RICHARD DORF Intel Corporation University of California at Davis JAY SHUTTER DAVID DRAKE Momentum Research Group Catalyst Communications, Inc. LESLIE SMID WILLIAM DRESSELHOUS IBM Dresselhaus Design Group THOI TRUONG RICHARD FOURNIER Emery Worldwide Oregon Health & Science University HARVEY UTECH Oregon Health & RICHARD GOLDGAR Science University Covasoft JOHN WALLNER STEPHEN GOMES Tektronix, Inc. Oregon Health & Science Unversity EUGENE Y. WEISSMAN Weissman Associates JULIAN GRESSER LogosNet

JILL B. KELLY Oregon Health & Science University

KEITH LARSON Intel Corporation

RITA LAXTON-BENZAN IMMEDIAD’s ChildRom Productions

KATHY MANGEL-DAVIS Professionally Speaking

MICHAEL MCLEAN AC Transit

DEIRDRE MENDEZ University of Texas at Austin

MIGUEL MENDEZ Oregon Health & Science University

86 OHSU is an equal opportunity, affirmative action institution. OHSU includes four schools, two hospitals, numerous primary care and specialty clinics, multiple research institutes, and several public service and outreach units.

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