stanford university PPHYSICSHYSICS Newsletter DEPARTMENT FEBRUARY 2007

February, 2007

ment of Physics and SLAC. Prof. tions relevant to interpreting observa- Letter from the Chair Wechsler was a Hubble Fellow and tional data, especially large surveys Enrico Fermi Fellow at the Kavli Insti- and multi-wavelength studies of galaxy Dear Physics alumni and friends, tute for Cosmological Physics at the properties. Her work with the Sloan University of Chicago. Her research Digital Sky Survey and as a member of interests are primarily in the areas of the Dark Energy Survey collaboration reetings and Happy New Year! theoretical cosmology and galaxy for- has provided essential theoretical input This past year marked the comple- mation. Risa’s work has involved mak- to the survey planning. We are very G tion of our new Physics and Astro- ing detailed predictions for the evolu- continued on page 8 physics building next door to Varian tion of structure in R

Physics. We invite those of you who cold dark matter E T L E have not seen our new building, or the models, studying the F D A new Physics Main Office adjacent to assembly history L G it, to stop by campus for a visit. The and clustering of E V E Physics and Astrophysics building hous- T dark matter halos S : es both Kavli and HEPL activities, as O

and galaxies, galaxy T O well as the teaching laboratories. We formation modeling, H P are very pleased with the new construc- and the use of galax- tion, which will allow for much needed ies and clusters as expansion and increased productivity probes of cosmology for the future. and fundamental physics. A primary This past fall, we were happy to welcome focus of her work new faculty member Risa Wechsler as a has been to make joint Assistant Professor in the Depart- theoretical predic- New faculty appointee, Risa Wechsler

Professor David Griffiths Visits Stanford Professor John W. Harris: avid Griffiths of Reed College gave a lecture for the Society of Physics Students this past Decem- the 2007 Robert Hofstadter ber. Thirty undergraduate physics majors and a D smattering of graduate students and faculty Memorial Lecturer attended, eager to meet the author of their favorite textbooks. Professor Griffiths discussed the charge e are pleased to announce that distribution on two-dimensional and one-dimension- the annual Robert Hofstadter al conductors, and results for force laws other than Memorial Lectures will be giv- the inverse-square law. Emboldened by the genial David Griffiths W en this year by John W. Harris, speaker, students asked questions on a variety of top- Professor of Physics and Group Leader ics: How does one become a good teacher? What makes some physicists of the Relativistic Heavy Ion Group at famous? And how will the future discoveries in physics compare to those Yale University. Professor Harris is a of the past? Many students took the opportunity to have their textbooks Fellow of the American Physical Society, autographed by the award-winning educator. David Griffiths will return to was voted one of the top 40 Distin- Stanford this spring to work on the second edition of his particle physics continued on page 2 textbook and co-teach Physics 121 (Intermediate Electricity & Magnetism). stanford university PHYSICS NEWSLETTER

Hofstadter Lecture – from page 1 Committee of the Institute of guished Alumni of Stony Brook Uni- Nuclear Theory at the University of versity, and is the recipient of the Washington. Alexander von Humboldt Senior Research Award. Prof. Harris has The Hofstadter lectures are sched- been both a collaborator and uled for Monday, April 30, 2007 spokesperson for the STAR exper- (an evening public lecture at 8:00 iment at Brookhaven National Lab- PM) and Tuesday, May 1 (an after- oratory and a National Coordina- noon colloquium at 4:15 PM). tor of ALICE-USA, at the CERN Both lectures will be held at Stan- Large Hadron Collider. He has also ford University, and we hope that served on the National Advisory you will plan to attend. h John W. Harris

EVENING PUBLIC LECTURE AFTERNOON COLLOQUIUM 8:00 pm – Monday, April 30, 2007 4:15 pm – Tuesday, May 1, 2007 Hewlett Building, Room 200 Hewlett Building, Room 201

“What is that Black Hole “Evidence for a Quark-Gluon Plasma Doing in My Quark Soup?” in the Laboratory”

It’s hot – at an absolute temperature of 1012 K – one hun- Ultra-relativistic collisions of heavy nuclei are being investigated for dred thousand (105) times hotter than the center of the the first time at the Relativistic Heavy Ion Collider (RHIC) at Brook- sun. It’s runny – runnier than anything known to man – haven National Laboratory and will soon be investigated at the even superfluids. What is it made from – its ingredients? Large Hadron Collider at CERN. These collisions heat nuclear mat- Tiny quarks and gluons. Where did it come from? It’s ter to energy densities previously reached only within the first few nothing ever made by man, it existed ten millionths microseconds after the Big Bang. Temperatures of 2 x 1012 K are (10-5) of a second after the beginning of the Universe or reached, melting the vacuum into a plasma of quarks and gluons. about thirteen billion years ago. Can we figure out how The goal of physicists in this field is to re-create and uniquely iden- to make it – is there a recipe? Yes, we have and we are tify properties the primordial quark-gluon plasma in order to under- cooking it up right now. It’s a Quark Soup. stand Quantum Chromodynamics at high energy densities. After six years of operation, RHIC and its experiments have established the I will address these and other questions about the recent presence of such extreme energy densities, temperatures and pres- creation of a primordial quark soup in the laboratory. Why sures. The system that is created behaves somewhat unexpect- would we even want to cook it up? What does this soup edly as a strongly-interacting, low viscosity liquid of quarks and taste like? It seems to have a unique flavor – has any- gluons and is opaque to energetic quark and gluon probes. I will one ever really sampled a soup of quarks and gluons? present an overview of the results establishing the creation and Perhaps there is a secret ingredient? And by the way – behavior of a hot (T = 2 x 1012 K) quark-gluon liquid at RHIC and its what is that tiny Black Hole doing in my Quark Soup? quenching of energetic probes. The quark-gluon liquid has behav- ior and properties similar to those of strongly-interacting classical fluids that are studied in atomic physics. Remarkably, a theoretical approach to black holes involving strings in five dimensions can describe the unique properties observed in this quark-gluon liquid.

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RNA – the “Dark Matter” of the Genome by Jan Lipfert and Sebastian Doniach

he “central dogma” of molecu- lar biology was formulated in the 1950s, soon after the dis- T covery of DNA structure by Watson and Crick. It states that the information flow in the cell is from DNA (which stores the genetic infor- mation) to RNA (which acts as a “messenger”) to proteins (which car- ry out the bulk of cellular func- tions). DNA is copied to RNA in a process called transcription. The base sequence of RNA is then trans- lated (using the genetic code as a “dictionary”) into the amino acid sequence of proteins. In this picture, still largely present in textbooks, Physics graduate student Jan Lipfert with the SAXS measurement set-up at RNA is the -somewhat boring- beamline 12 of the Advanced Photon Source. “middle man” between DNA and proteins. whom were awarded Nobel Prizes in While traditionally in the realm of 2006. Roger D. Kornberg received biochemistry and molecular biology, This picture started to change in the the Nobel Prize in chemistry for his RNA science offers interesting ques- early 1980s, when Tom Cech, Sidney contributions to the understanding tions to physicists. The RNA back- Altman and others discovered that of the intricate machinery that car- bone is highly negatively charged and certain RNA molecules, much like ries out transcription and Andrew in order to fold into a distinct 3- proteins, can fold into distinct 3- Z. Fire (shared with Craig C. Mello dimensional shape, RNA must over- dimensional shapes and catalyze of the University of Massachusetts) come an enormous Coulombic repul- chemical reactions, a discovery for was awarded the Nobel Prize in sion. Overcoming this free energy bar- which they shared the Nobel Prize Medicine for their discovery of rier is facilitated by the presence of in Chemistry in 1989. Even more “RNA interference,” one of the positively charge counter ions, such as recently, it has become increasingly mechanisms by which RNA can Mg2+. The resulting problem of com- clear that RNA molecules control regulate genes. puting the arrangement and interac- transcription and translation tion energies of negatively charged through a variety of mechanisms RNA surrounded by a cloud of and play a key role in regulating the Unfolded mobile ions is a classical analogy to metabolic state of the cell. Only 2% the quantum mechanical problem of of the human genome codes for pro- computing the electron density around teins, but as much as 50% is tran- Glycine Bound Buffer only + 10 mM Glycine charged nuclei. The energy scale of scribed to RNA, a sizable fraction the classical problem is set by kT, as of which is presumably involved in 2+ Partially Folded opposed to h-bar in the quantum gene regulation and other cellular + 10 mM Mg mechanical case. functions in ways that we are only Low resolution 3-D reconstructions from small-angle beginning to understand. It is in that X-ray scattering measurements of a glycine binding We are currently working on expand- sense that RNA can be called the riboswitch. Unfolded conformation in the absence of ing the traditional Poisson-Boltzmann “dark matter” of the genome. A divalent counterions, partially folded conformation in mean-field approach to the problem number of researchers at Stanford the presence of Mg2+ counterions and fully folded are involved in RNA science, two of conformation in the presence of Mg2+ and glycine. continued on page 7 3 stanford university PHYSICS NEWSLETTER Mysterious Neutrinos By Stanley Wojcicki

eutrinos are believed to be among the 12 fundamental number of neutrinos you have available for your study is constituents in our universe, but they are probably the small, even with a multi-kiloton detector. We observe N least understood because their interaction with matter roughly 1-2 accelerator produced neutrino interactions per is so weak, and thus they are hard to study. day in the Soudan detector. To give those few interactions, about 10 billion neutrinos have to pass through the detec- A little over a decade ago we began an experiment called tor each day. the Main Injector Neutrino Oscillation Search (MINOS) with a goal to investigate in detail early hints of anom- But all the barriers and challenges notwithstanding, alous neutrino behavior from the atmospheric neutrino MINOS and the associated infrastructure are now work- experiment in Japan, Kamiokande (and supporting evi- ing, probably better than our most optimistic expectations. dence from the U.S. from the Soudan II experiment), using The first results on atmospheric neutrinos were published a well controlled accelerator produced beam of neutrinos. over a year ago. This past November the results from our The neutrinos were to be produced by the 120 GeV Fermi- first data obtained with the accelerator beam were pub- lab Main Injector proton accelerator and detected some lished in Phys. Rev. Letters. Our results confirm the earlier 735 km away in a former iron mine in Soudan, MN. indication that muon neutrinos do indeed “disappear” as they travel through space and that this disappearance is To make the experiment a reality, we had to build a highly consistent with oscillations into tau neutrinos. We also sophisticated proton and neutrino beam line at Fermilab, obtained the most accurate to date measurement of mass excavate a new cavern (more than half the size of a foot- squared difference between two neutrino mass states. The ball field) in the Soudan mine (700 m underground) and value for mass squared difference between two neutrino build 2 large detectors, one at Fermilab and another in the states is about 2.7 x 10-3 eV2. The absolute mass scale is Soudan cavern, the latter with a mass of about 5400 tons. still known only very poorly, but this indicates that the And to make this happen, we had to create a new collabo- neutrino masses are in range between one ten millionth ration (currently about (10-7) and one millionth 150 scientists from 32 (10-6) of the mass of the institutions in 6 countries electron, the lightest — the United States, Unit- known particle so far. ed Kingdom, France, Greece, Brazil, and Russia) The experiment will con- and last, but far from tinue to take data for the least, obtain endorsements, next 3-5 years and we approvals and, very hope to increase the sta- importantly, funding from tistics by at least an order the relevant funding agen- of magnitude. We hope to cies. So it is not surprising significantly improve the that it took a decade to get accuracy of neutrino it all accomplished and parameters, investigate obtain first results. whether there is any con- tribution from neutrino The fact that neutrinos decay, search for sterile hardly interact allows us neutrinos, and search for to send them 735 km as yet unseen oscillation through the earth without mode numu->nue which having to build a tunnel of is known to be small but that length. But it also cre- may hold the clues to the ates a drawback — the Detector in Soudan continued on page 6

4 stanford university PHYSICS NEWSLETTER Black Holes made with Silicon By Tom Abel

upermassive black holes existed most recent calculation not only even when the universe was less captures the formation of early S than one billion years old, and galaxies, but also follows how parts Black Holes form in a Simulation they power some of the most lumi- of the galaxies collapse to scales nous objects in the universe — smaller than a single star. Their tech- quasars. But how do they form? Do nique is called adaptive mesh refine- small black holes, left behind by the ment, which behaves like a telescope earliest stars, feed continuously from that never loses resolution no matter the surrounding gases to grow in how far one zooms in on a region of mass some 100 million fold? That is interest. They demonstrated this one theory — another possibility is ability by capturing even regions one that they form on rare occasions. hundred trillion times smaller than When an unusually large amount of the entire volume they considered! material is compressed in the center Wise and Turk carried out their sim- of a galaxy, it may collapse very rap- ulation on KIPAC’s Silicon Graphics idly. In fact, this can happen so fast supercomputer using some 20,000 that it does not have time to break processor hours. This series of pictures show the inner 60 light- up into smaller lumps and form years of the first galaxy and are centered on the stars. Instead, the gaseous cloud A small fraction of the entire cloud densest structure, which might form a supermas- attempts to make a star many thou- collapses very rapidly to high densi- sive black hole that contains thousands of solar sands of times the mass of our sun. ties. At different scales, multiple masses. The first snapshot only samples The huge inward gravitational pull nested disk- and bar-like structures 1/5000th of the simulation scope, which calcu- of this enormous mass cannot be form as their angular momentum lates the large scale dynamics of galaxy forma- countered by even the thermal pres- becomes important. What was un- tion. Between slides, the field of view decreases sure from nuclear fusion in the cen- expected and unseen in any previous by a factor of two in length. Different shades of ter of the cloud, and as a result, the investigations is that these disks and gray highlight the volumes which have similar mass collapses. In this complicated bars all point in uncorrelated direc- densities. This visualization technique allows us process, it could be that the cloud tions. In hindsight, this seems an to peer into a structure that contains densities flattens into a disk and then breaks obvious outcome for an initially ranging over 25 orders of magnitude, of which up into smaller pieces, or stars. turbulent cloud collapsing under its only 4 are visible on these scales. Their explosions could push the rest own gravity. It makes a big differ- of the gas out of the system, leaving ence whether there is one isolated just some regular stars and a few disk or multiply-nested ones, as the small black holes orbiting each other. friction of one disk with its sur- It has been difficult to study any of rounding disk can preferentially these processes theoretically. One slow fast-moving material and force early universe. This increase in capa- needs to follow regions thousands of it to collapse more rapidly than it bility makes many other physical light years across from where the would without that drag. details more important. Turk and gas contracts to scales much smaller Wise are working hard to follow the than a star. This calculation demonstrated that formation of stars, feedback from the new algorithms make it compu- their radiation, and the ensuing Physics graduate students John Wise tationally feasible to start with real- supernovae explosions. Nature may and Matthew Turk made enormous istic initial conditions and follow all hold more surprises than computa- progress in developing the numer- relevant physics in order to study tional cosmological models can cap- ical tools to study many of these whether black holes can form from ture today, but the virtual universes processes in stunning detail. Their collapsing gas clouds in the very are more realistic than ever. h

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Apker Award Finalist 2006

e are pleased to report that INNA VISHIK, one of our W outstanding Physics under- graduates (now a graduate stu- dent in Applied Physics) was selected as a finalist for the cov- eted Apker Award. The Apker Award recognizes outstanding achievements in physics by under- graduate students and provides en- Former Physics Dept. members gathered recently to recall their 1966 collaboration with couragement to Professor Arthur Schawlow. Left to right: Fred-a Jurian Keever, Stan Stokowski (KLA-Tencor), young students Bill Yen (Univ. of Georgia), Rick Greene (Univ. of Maryland), Bob White (Stanford - MSE) and with great poten- Darrell Sell (Cisco). tial for future scientific accom- plishments. Two Inna Vishik – ented former Stanford undergraduate awards are pre- Neutrinos from page 4 who passed away a little over a year sented each year, one to a student ago — and more recently with Rob from a Ph.D. granting institution matter antimatter asymmetry in our Plunkett from Fermilab. Other mem- and one to a non-Ph.D. granting universe. bers of the Stanford group are sen- institution. Inna was chosen as an ior research associate George Irwin, Apker finalist for her outstanding The Stanford group has played an postdocs Hyejoo Kang and Simona undergraduate achievements in important role in the experiment Murgia and graduate student research (her work was also rec- from the very beginning. I served as Tingjun Yang. Former postdocs ognized by a Firestone Award last the spokesperson for the experiment Carlos Arroyo, Larry Wai and Sergei for the first 8 years and then subse- Avvakumov made crucial contribu- year). Congratulations, Inna! h quently as a co-spokesperson, first tions in the earlier stages of the with Doug Michael — a highly tal- experiment. h

ÖÖÖÖ 2006 Student Awards ÖÖÖÖ number of student awards were outstanding physics student in the nial Teaching Awards. announced at our Physics/Applied field of astronomy. The Paul Kirk- The Firestone Award for excel- A Physics Commencement ceremo- patrick Award, given to outstand- lence in Undergraduate Research ny last June. ARIEL SOMMER received ing physics teaching assistants, was presented to INNA VISHIK, who the David Levine Award, presented to was given to EREZ BERG and ERAN was also a finalist for the presti- the outstanding Junior physics major. MUKAMEL. ASIMINA ARVANIKTAKI, gious Apker Award (see article this JENNIFER MEYER received the Jeffrey AMIN MUSAFA and NAVIN Sivanan- page). Congratulations to all of our Willick Memorial Award, given to the dam were all recipients of Centen- outstanding Physics students! h

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ÖÖÖÖ Physics Alumni Reception ÖÖÖÖ

hanks very much to those of you who attended our Physics alumni reunion T reception on October 13, 2006, as part of the Reunion Homecoming Week- end. The Physics department reception was attended by approximately 35 physics alumni, in addition to a number of Physics faculty, staff and current students. Depart- ment Chair Stan Wojcicki, along with Pro- fessors Patricia Burchat, Sarah Church, Giorgio Gratta, Peter Michelson and Bob Wagoner, were happy to chat with some of their former students and colleagues.

The celebratory event provided another opportunity for alumni, faculty, and staff to get together, and we were pleased to pres- ent our new Physics and Astrophysics build- ing to the attendees. It was wonderful to catch up with former students and some of their young families. Please look for an- nouncements of future alumni events on our Professor Peter Michelson (left) chats with physics alumni and friends at our October website, and plan to attend! h 2006 reception.

– Stanford Synchrotron Radiation the cell’s environment. Our measure- RNA from page 3 Laboratory to study the structure of ments provide a first glimpse into RNA in solution. Our small-angle the molecular details of how this (which is analogous to Hartree-Fock X-ray scattering measurements riboswitch achieves its function. theory in quantum mechanics) to allowed us to explore the conforma- For more information see [1]. h account for the finite ion size and tional “landscape” of a “riboswitch,” ion-ion correlations. an RNA molecule that changes [1] Jan Lipfert, Rhiju Das, Vincent B. Chu, shape in response to binding a Madhuri Kudaravalli, Nathan Boyd, Daniel In a collaboration with Dan Her- small-molecule ligand. In the cell, Herschlag, and Sebastian Doniach, “Struc- schlag in the medical school, we are this conformational change controls tural Transitions and Thermodynamics of a using synchrotron radiation at the the expression of a genes, “switch- Glycine-Dependent Riboswitch from Vibrio Advanced Photon Source and at the ing” them on or off in response to cholerae,” J. Mol. Biol., 65:1393-1406 (2007)

We are pleased to report that the Physics Department received a generous gift from one of our former students in honor of Karl van Bibber, a former Stanford Physics Department colleague in experimental nuclear physics, now working at Lawrence Livermore National Laboratory. The Karl A. van Bibber Post- doctoral Fund in Physics will support postdoctoral scholars in the Department of Physics over the next five years. Postdoctoral scholars Peter Fierlinger, who works with Prof. Giorgio Gratta, and Judy Lau, who will be working with Prof. Sarah Church, were selected as the first recipients of this fellowship.

7 – country’s oldest honorary learned on page 6). A new class of 28 stu- Letter from page 1 societies. Shoucheng Zhang was elect- dents entered our Ph.D. program in ed a fellow of the American Physical 2006. The incoming graduate stu- pleased to have this talented young Society for his pioneering contribu- dents include three women and ten cosmologist join our faculty. tions to the development and foreign students. We are very pleased exploitation of the effective field the- to welcome these bright new students A search has been underway for one ories of highly correlated electronic to our department. or two new junior experimental systems. David Goldhaber-Gordon astrophysics faculty covering two received the Award for Initiatives in We hope you will enjoy reading areas; one in gamma ray astronomy Research from the National Academy about some of the research going on and the other cosmology, with an of Sciences, an award which recog- in our department, and that you will emphasis on developing new or nizes innovative young scientists, and consider attending the upcoming advanced instrumentation. Please encourages research likely to lead Robert Hofstadter Memorial lectures consult our website (http://www. toward new capabilities for human this spring (see article for details). stanford.edu/dept/physics/jobs.html) benefit. for updates on this and other faculty Thanks to those of you who were searches. I am also pleased to report that Sarah able to attend our Physics alumni Church was promoted to Associate reception last October — it is always Sadly, the physics community lost Professor with tenure this past year, a pleasure to meet with Physics alum- two distinguished colleagues and and that Todd Hoeksema, a Senior ni, and I encourage you to stop by exceptional friends this past year. Research Scientist in Professor Phil the department for a visit whenever Walter Meyerhof and Melvin Scherrer’s Solar Physics group, you are in the area. On behalf of the Schwartz, both of whom served on received the NASA Distinguished department, I thank you for your the Physics faculty for many years, Public Service Medal. This award continued interest and support. each made important contributions resulted in Todd’s significant work to the physics community. Walter on NASA’s heliospheric physics pro- Best wishes, Meyerhof was Chair of the Physics grams at both NASA and Stanford. Department from 1970 to 1977, and also served as department Our Physics students have also been Ombudsperson. In addition to his recognized for their exceptional work Stanley Wojcicki excellence in research and teaching, with a number of awards (see article Chair and Professor of Physics Meyerhof encouraged minority and women students to study physics. Melvin Schwartz shared the Nobel A C

Prize in Physics in 1988 “for the , K R

neutrino beam method and the A NON-PROFIT ORG. P demonstration of the doublet struc- O L

U.S. POSTAGE N ture of the leptons through the dis- E

PAID M ,

covery of the muon neutrino.” They O PALO ALTO, CA I D will both be deeply missed, but the PERMIT NO. 28 U T S

legacy of their outstanding work will S C I H

continue for years to come. P A

DEPARTMENT OF PHYSICS R G S

A number of our Physics faculty Stanford University K R received prestigious awards in 2006. Stanford, CA 94305-4060 O W C

Associate Chair Patricia Burchat A M

received a Gabilan Professorship, — N A

given to support an outstanding E L C female faculty in the sciences. Prof. c M

Burchat was chosen in recognition of A N N

her noteworthy research in experi- A O J

mental particle physics and her influ- : N G ence in understanding the differences I S E in the way matter and antimatter D evolve over time. Savas Dimopoulos and Steve Shenker were both elected as fellows of the American Academy of Arts and Sciences, one of the 8