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New Faculty in the Eberly College of Science

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Science Journal, Spring 2007

Michael John Axtell, assistant professor of biology

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Michael John Axtell is interested in the discovery and analysis of small molecules of RNA in plants. He uses a variety of techniques from plant biology, genetics, molecular biology, and computational biology to generate and test new hypotheses about their functions.

The production of small molecules of RNA—21 to 24 bases in length—is common in almost all complex cells. In plants, these microRNAs (miRNAs) frequently are found to be master regulators of plant development. Many of the miRNA-target interactions initially identified in the flowering plant Arabidopsis thaliana are conserved deeply among all land plants. Axtell seeks to test the functions of miRNAs directly in flowering plants such as Arabidopsis, and is interested in the functions of interactions between deeply conserved miRNAs and their molecular targets in the moss Physcomitrella patens.

Axtell is a member of the American Society of Plant Biologists and the American Association for the Advancement of Science . His research accomplishments have been recognized with the Dean’s Award in Natural Sciences and Mathematics from Ithaca College in 1998, and with a Past Presidents Award from the Phi Kappa Phi honorary society at Ithaca College in 1998. He received a Helen Hay Whitney Postdoctoral Fellowship in 2004, a National Science Foundation Graduate Research Fellowship in 1998, a Berkeley Fellowship in 1998, and a Barry M. Goldwater Fellowship in 1997.

Axtell has published several scientific papers about his research and has presented invited talks at scientific conferences and workshops in the United States and Taiwan. Prior to joining Penn State in August 2006, he was a postdoctoral fellow in the Whitehead Institute for Biomedical Research at the Massachusetts Institute of Technology.

Axtell earned a bachelor’s degree in biology at Ithaca College in 1998. He earned a doctoral degree in plant biology at the University of California at Berkeley in 2003.

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Tyce DeYoung, assistant professor of physics

Tyce DeYoung (portrait)

Tyce DeYoung conducts research in particle astrophysics. He presently is working on the IceCube neutrino observatory, under construction at the South Pole. IceCube uses photodetectors sunk into the Antarctic ice cap to detect Cherenkov radiation produced when high-energy elementary particles called neutrinos interact with atomic nuclei in the ice. Detection of these neutrinos will allow researchers to probe very energetic objects in the universe, studying their neutrino emission just as other astronomers study the photons they emit.

One major focus of the IceCube experiment is the detection of tau neutrinos, which are produced through quantum-mechanical oscillations as the neutrinos travel to Antarctica from distant sources both in our own galaxy and farther away in space, and which are nearly free of background contamination. DeYoung and his colleagues also are working on efforts to detect muon neutrinos from sources in the southern sky. They also are working to detect electron neutrinos produced in the decay of short-lived subatomic particles called charm mesons when cosmic rays bombard our atmosphere. These efforts use the existing Antarctic Muon And Neutrino Detector Array (AMANDA) telescope prototype, which will allow the scientists to improve IceCube’s sensitivity to lower-energy neutrinos. DeYoung heads the AMANDA-IceCube integration efforts and works on event-reconstruction software.

DeYoung also is interested in very-high-energy gamma-ray astronomy. He is working with colleagues at Los Alamos National Laboratory, the University of Maryland, and other institutions on the design of the proposed High-Altitude Water Cherenkov (HAWC) Observatory. This instrument would monitor the northern sky for sources of high-energy photons, such as gamma-ray bursts and active galactic nuclei. HAWC would complement instruments such as IceCube, the Swift Gamma-Ray Burst Explorer, and the Gamma-Ray Large-Area Space Telescope (GLAST) to give a more complete picture of the nature of these very energetic astrophysical objects.

DeYoung is a member of the American Physical Society and the Phi Beta Kappa honor society. He held a University of Wisconsin Prize Fellowship and a William F. Vilas Fellowship at the University of Wisconsin from 1996 to 1998, and received the H. George Apostle Prize in Physics from Grinnell College in 1996. He has published several papers about his research in scientific journals. He also has presented talks at scientific conferences and workshops across the United States and in Canada, China, France, Switzerland, the United Kingdom, and Vietnam.

Prior to joining the faculty at Penn State in 2006, DeYoung was a research associate in the Penn State Department of Physics from 2005 to 2006. He was at the University of Maryland as an assistant research scientist from 2004 to 2005 and as a postdoctoral researcher from 2003 to 2004. He was a postdoctoral researcher at the University of California’s Santa Cruz Institute for Particle Physics from 2001 to 2003. He was a research assistant at University of Wisconsin at Madison from 1997 to 2001, at the University of New Mexico in 1996, and at Grinnell College from 1994 to 1996.
DeYoung earned a bachelor’s degree with honors in Physics at Grinnell College in 1996 and a doctoral degree in Physics, with a concentration in astrophysics, at the University of Wisconsin at Madison in 2001.

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Dmitry Dolgopyat, professor of mathematics

Dmitry Dolgopyat (portrait)

Dmitry Dolgopyat studies how complex systems change over time. The behavior of complex systems can be seen either as regular, such as the motion of planets, or chaotic, such as the motion of a hurricane. Dolgopyat says most complex systems can be viewed as a composite of regular and chaotic systems. By analyzing changes within this composite structure, Dolgopyat’s mathematical models interpret data based on the effects of a small change in the initial conditions. The object of Dolgopyat’s research is to define techniques for choosing analytical methods to analyze these systems by determining which parameters are most important for defining the motion of individual systems.

Dolgopyat was assistant professor at Penn State from 1999 to 2003. He was an associate professor of mathematics at the University of Maryland from 2003 to 2006, then returned to Penn State in August 2006 as professor of mathematics. He has held visiting positions at several institutions including the Institute for Advanced Study; the Pierre and Marie Curie University in France; the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland; the Newton Institute in Cambridge, United Kingdom; the Hebrew University in Israel; Manchester University in the United Kingdom; and many others.

Dolgopyat’s accomplishments were recognized with selection as a Sloan Research Fellow in 2000. He received a Miller Fellowship from the University of California at Berkeley in 1997, a Charlotte Elizabeth Procter Fellowship from the Graduate School at Princeton University in 1996, and a Petrovsky Fellowship from Moscow State University in 1992 and 1993. In 2006, he was invited to speak at the International Congress of Mathematicians in Madrid, Spain. He co-organized a Maryland–Penn State Dynamics Meeting in 2005 and again in 2006. He also co-organized a conference on “Chaos and Disorder in Mathematics and Physics” in Bressanone, Italy, in 2005. He has published several scientific papers about his research and is on the editorial boards of the Journal of Modern Dynamics and Nonlinearity.

Dolgopyat earned a bachelor’s degree with highest honors at the Moscow State University in Russia in 1994 and a doctoral degree in mathematics at Princeton University in 1997. He was a research fellow at the University of California at Berkeley from 1997 to 1999.

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Alexay Kozhevnikov, assistant professor of physics

Alexay Kozhevnikov (portrait)

Alexay Kozhevnikov studies the neural mechanisms of singing and vocal learning in birds. Like humans, birds are vocal learners—the young bird first listens to its tutor’s song and then learns to imitate it. “The song of an adult bird has a robust behavioral pattern and the anatomy of the brain circuits involved is well-documented, allowing researchers to use songbirds as a model system for studying neural-sequence generation and learning of vocalization,” Kozhevnikov says.

Studying vocal learning in songbirds can answer fundamental neuroscience questions about the mechanisms of sensorimotor learning. The song-learning process in songbirds shows intriguing similarities to speech development in humans and can provide valuable insights into how human speech is synthesized by brain circuitry.

Kozhevnikov uses a motorized miniature microdrive to record neural activity in a bird’s brain while the bird is singing. “This cutting-edge technique allows the activity of identified neurons in a functioning neural circuit to be recorded and provides the most direct probe of the activity of brain circuitry and its relation to behavior,” Kozhevnikov says. “The recordings reveal a novel sparse neural code, suggesting that individual neurons may explicitly code for time in the motor sequence with sub-millisecond precision.” In the future, Kozhevnikov plans to perform neural recordings in birds during singing under various conditions—such as while manipulating auditory feedback and pharmacologically inactivating brain areas to elucidate their role in singing—with the goal of understanding how neurons in a bird’s brain are organized and how they function to enable the bird to produce a song.

Prior to joining Penn State in July 2006, Kozhevnikov was a postdoctoral fellow in the McGovern Institute and Department of Brain and Cognitive Science at the Massachusetts Institute of Technology from 2003 to 2006. He was a postdoctoral researcher in the Department of Biological Computation and Theoretical Physics at Lucent Technologies’ Bell Laboratories from 2001 to 2003. Kozhevnikov has published several papers in scientific journals and has co-written a chapter for a book titled Neural Mechanisms of Sequence Generation in the Songbird, published by the New York Academy of Sciences in 2004.

Kozhevnikov earned a bachelor’s degree with honors in biophysics at Moscow State University in Russia in 1995. He earned master’s and doctoral degrees in physics at Yale University in 1996 and 2001, respectively. He also studied neurobiology at the Marine Biological Laboratory in Woods Hole, Massachusetts in 2002.

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Irina Mocioiu, assistant professor of physics

Irina Mocioiu (portrait)

Irina Mocioiu studies phenomena at the interface between particle physics and astrophysics. She has collaborated with working groups in the Fermi National Accelerator Laboratory and Brookhaven National Laboratory to optimize the next generation of neutrino experiments that aim to extend the evidence for neutrino-particle oscillations, developing a better framework for understanding the experimental data and their implications for theoretical models.

Mocioiu and her colleagues expect very-high-energy neutrinos from astrophysical sources to be observed soon by detectors such as the Antarctic Muon And Neutrino Detector Array (AMANDA), the IceCube Neutrino Observatory, the Antarctic Impulse Transient Array (ANITA), and the Pierre Auger Cosmic-Ray Observatory. These detectors and their observations could have profound implications for both high-energy physics and astrophysics. “Neutrinos are unique probes,” says Mocioiu, “because they can escape from extreme environments and travel longer distances than photons or protons without being absorbed or deflected.” She has been working on a detailed exploration of possible high-energy-neutrino signals and their interpretation, emphasizing new ways of measuring some of the neutrino properties and studying how to distinguish the particle-physics effects from the astrophysical effects.

Mocioiu also has worked on other topics in particle physics, exploring new approaches for constraining theoretical models by using data from experiments outside high-energy physics.

Mocioiu’s research accomplishments have been recognized with a Peter B. Kahn Fellowship at the State University of New York and a Gertrude Scharff Goldhaber Prize from Brookhaven National Laboratory in 2001. She has published several scientific papers about her research, and has presented invited talks at scientific conferences and workshops in the United States, Canada, France, and Italy.

Prior to joining Penn State in the Fall of 2005, Mocioiu was a postdoctoral researcher at the Argonne National Laboratory and the Enrico Fermi Institute at the University of Chicago from 2004 to 2005. She was a postdoctoral research associate in physics and a member of the theoretical astrophysics program at the University of Arizona from 2002 to 2004. She was a research assistant at the C.N. Yang Institute for Theoretical Physics at the State University of New York in Stony Brook from 1998 to 2002.

Mocioiu began her physics education studying at the University of Bucharest in Romania from 1992 to 1994 and was an exchange student at the University of Quebec in Montreal, Canada, in 1994 and 1995. She earned a master’s degree in physics at the University of Quebec in 1997, and a doctoral degree in physics at the State University of New York at Stony Brook in 2002.

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Mary Poss, professor of biology

Mary Poss (portrait)

Mary Poss studies the molecular genetics of viruses. Her research focuses on understanding such questions as what features promote or constrain viral infection in new host species, why infection with a specific virus causes disease in some species but not in others, and how co-infection with several different viruses or other pathogens affects the dynamics of each virus.

Poss works with colleagues at Colorado State University to study cross-species infections using feline immunodeficiency virus (FIV)—similar to the human-immunodeficiency virus (HIV)—as a model system. Domestic cats develop an immunodeficiency syndrome when infected with FIV, but wild cats—such as cougars and African lions— often are infected with strains of FIV without developing disease symptoms. By studying domestic cats infected with FIV from cougars, Poss seeks to understand how the hosts respond to new cross-species viral infection. The researchers were able to demonstrate that a newly described RNA-editing enzyme acts on the foreign viral genome, rendering many genes defective. The viruses that survive have changes in their replicating enzyme, known as reverse transcriptase (RT), and an increased mutation and recombination rate. Poss says, “We are investigating the effect of these substitutions in RT to see if they are responsible for more errors during virus replication. An increased rate of replication errors in the viruses would result in greater genetic diversity, increasing the likelihood that a virus better suited for the changing host environment would emerge.” She points out that, despite the beating the cougar virus takes in the new domestic cat host, it manages to persist for over eight months.

In another study, Poss employed methods of virus genetics to identify recent changes in host demography—in this case, looking at feline-lentivirus infections in cougar populations in the western United States. Examination of host genetics had shown no evidence of distinct cougar populations in the northwestern United States; however, studies of genetic sequences in FIV viruses in cougars demonstrated that distinct populations do exist in the region. These studies allowed the researchers to determine how long each population had been present, and to measure the extent of mixing between the different populations of cougars in the region. They also were able to identify the original habitats of cougars that were re-colonizing new areas. “This technique may be a useful tool for ecologists and population biologists to study interactions of animals that are the source of some human pathogens,” says Poss.

Poss’s research accomplishments have been recognized with a National Research Service Award in 1988, a Clinical Investigator Award from the National Institutes of Health in 1994, a Center for Aids Research (CFAR) New Investigator Award from the University of Washington in 1995, and numerous investigator-initiated grants from both public and private institutions. She is a member of the American Association for the Advancement of Science (AAAS) , the American Society for Microbiology , the American Society of Virology , and the Wildlife Disease Association.

Poss has published scientific papers on topics ranging from biochemistry to conservation biology. She served as a grant reviewer for the Montana Academy of Science, the National Fish and Wildlife Foundation, the AAAS-First Award, the National Institutes of Health, and the National Science Foundation. She also has been a reviewer for several professional journals, including Science, Conservation Biology, and the Journal of Virology.

Prior to joining Penn State in July 2006, Poss was an assistant professor and associate professor in the Division of Biological Sciences and Wildlife Biology at the University of Montana from 1998 to 2006. She has been a clinical assistant professor at Tufts University School of Veterinary Medicine since 1999. She was a senior fellow at the University of Washington from 1994 to 1998 and was a postdoctoral fellow and senior staff scientist at ICOS Corporation in Washington from 1990 to 1993. She completed a residency in anatomical pathology at Colorado State University in Fort Collins, Colorado, from 1985 to 1987, and was an intern with the Navajo Nation in Tsaile, Arizona, and the U.S. Sheep Experimental Station in Dubois, Idaho, in 1984. She also worked as a veterinarian in Rushford, New York, in 1984.

Poss earned a bachelor’s degree in zoology at Duke University in 1975 and a master’s degree in biochemistry from the University of New Hampshire in 1979. She earned a doctoral degree in veterinary medicine from Ohio State University in 1984, and a doctoral degree in experimental pathology from Colorado State University in 1990.

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Radu Silviu Roiban, assistant professor of physics

 

Radu Roiban (portrait)

Radu Silviu Roiban studies string theory and quantum field theory. “Quantum-field theory is used to successfully describe the interactions of point-like elementary particles at accessible energies in the absence of gravity,” says Roiban. “String theory is a more general framework that incorporates the successes of quantum field theory and also holds promise to unify all known interactions among elementary particles in a quantum-mechanically consistent way.” Research in this area may lead to better understanding of phenomena ranging from particle physics to quantum gravity.

Roiban’s research interests cover many aspects of string theory. Roiban says, “Over time, important advances in our understanding of both string theories and field theories came from established and conjectured relationships between them.” He says his recent efforts are directed toward “the duality between gauge theory and string theory, the implications of integrability on the two sides of this duality, and the development of improved techniques for perturbative calculations in quantum field theories and finiteness properties of supergravity theories.” His past research includes tachyon condensation, matrix models, the topology of strings and their relation to gauge theories, and renormalization of noncommutative field theories.

Roiban has published several scientific papers about his research. He has been a referee for the scientific journals Nuclear Physics B, Physical Review D, Journal of High Energy Physics, Physical Review Letters, Advances in Theoretical and Mathematical Physics, and Mathematical Reviews. He recently received a Alfred P. Sloan Research Fellowship in recognition of his work.

Prior to joining Penn State in September 2005, Roiban was a member of the research staff at Princeton University from 2004 to 2005. He was a postdoctoral researcher at the University of California at Santa Barbara from 2001 to 2004. From 1997 to 2001, he was a graduate assistant and teaching assistant at the C.N. Yang Institute for Theoretical Physics at the State University of New York at Stony Brook, where he earned a doctoral degree in physics in 2001. He studied physics at the University of Bucharest in Romania, and earned a master’s degree in physics at the University of Quebec in Canada in 1997.

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Jorge Sofo, assistant professor of physics

Jorge Sofo (portrait)

Jorge Sofo studies the physics of materials that have important applications, such as thermoelectrics and fuel cells; and of materials that exhibit fascinating physical phenomena, such as the recently measured supersolid. He uses powerful computers to predict the structure of new compounds. One important recent development in his lab is the theoretical discovery of a new two-dimensional crystalline hydrocarbon—a fully saturated version of graphene called “graphane.” Using electronic-structure techniques, Sofo’s lab has demonstrated that this compound is stable enough that it should be possible to synthesize it in the lab. Several experimental groups have contacted him about attempting to produce this new compound.

Sofo’s group also studies proton conduction in confined aqueous systems. Using the Cray-X1E Supercomputer at the National Center for Computational Science at the Oak Ridge National Laboratory, he applies the basic principles of molecular dynamics to computer simulations of systems of acidic water confined by a variety of different materials ranging from polymers to oxide surfaces. His results have demonstrated that, in order to improve proton conductivity in fuel-cell membranes, the relevant factor to consider is the hydrogen-bond density produced by the proper alignment of water molecules. This research has many potential applications, including fuel-cell development and environmental remediation.

Sofo is the director of the Materials Simulation Center at Penn State, which provides students and faculty with access to computational resources and software for materials simulation. He has published several scientific papers about his research and has given presentations and invited talks at academic institutions and professional conferences worldwide. He was a member of the organizing committee for the International Conference on Applied Density Functional Theory in Austria in 2001. He has been a reviewer for the National Science Foundation, and for scientific journals including Physical Review Letters ; Physical Review B; the Journal of Chemical Physics; the Journal of Physics and Chemistry of Solids ; the solid-state physics journal Physica Status Solidi; and for Calphad—Computer Coupling of Phase Diagrams and Thermochemistry, the international research journal for calculation of phase diagrams. He is a member of the American Physical Society, the American Chemical Society, the International Thermoelectrics Society, and the Materials Research Society.

Sofo joined the faculty at Penn State in 2001 as the first director of the Materials Simulation Center, a facility of the Materials Research Institute. He was named associate professor of physics in 2002 and associate professor of materials science and engineering in 2003. Prior to joining Penn State, he was an assistant professor at the Instituto Balseiro of the National University of Cuyo in Argentina from 1996 to 2001. He was a part-time research associate professor at the University of Tennessee from 1997 to 2001. He was a research fellow with the National Research Council for Science and Technology of Argentina (CONICET) from 1995 to 2002. He was a research associate at Oak Ridge National Laboratory from 1993 to 1995 and at the University of Tennessee from 1992 to 1993. He was a guest professor at the Institute of Theoretical Physics at Karl-Franzens University in Austria in 2000 and 2001. He also was a consultant for Allied Signal Corporation from 1997 to 1999 and for Marlow Industries from 1994 to 1995. He earned a master’s degree and a doctoral degree at the Instituto Balseiro of the National University of Cuyo in Argentina in 1988 and 1991, respectively.

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Yu Zhang, assistant professor of statistics

Yu Zhang (portrait)

Yu Zhang uses computational methods to study genomic sequence analysis, gene evolution, and population-based genetic studies. In particular, he focuses on developing statistical models and computational algorithms using Markov-chain Monte Carlo (MCMC) sampling and Bayesian inference techniques.

Zhang’s recent research has focused on identifying genes that are responsible for complex diseases in humans, using genome-wide single-nucleotide-polymorphism (SNP) data from unrelated individuals. He has been developing models for identifying genetic factors associated with diseases and the possible interactions between them. 

Zhang also has been developing methods to delineate both fine-scale genetic-variation patterns and large-scale genomic aberrations using experimental data. During his doctoral study, he developed efficient algorithms to align large numbers of closely related DNA sequences, known as multiple-sequence alignment. His algorithms are particularly useful in resequencing studies. The goal of his research is to develop computational methods for studying evolution, identifying functional elements in DNA, and inferring mechanisms of gene regulation in biology.

Zhang is a member of the American Association for the Advancement of Science, the American Mathematical Society, the American Society of Human Genetics, and the International Society for Computational Biology. He has published several scientific papers about his research, and has been a reviewer for the Journal of Computational Biology, the Journal of Computational and Graphical Statistics, Genome Research, the Journal of the Royal Statistical Society Series B, and Algorithmica

Prior to joining Penn State in the Fall Semester of 2006, Zhang was a postdoctoral fellow at Harvard University . He held an internship at Celera Genomics in 2003 and at BioDiscovery Inc. in 2001. He also was a research assistant at Peking University in 1999 and 2000. He earned a doctoral degree in applied mathematics at the University of Southern California in 2004 and a bachelor’s degree in physics at Peking University in China in 2000.

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