TCB Group Member Profiles

Klaus Schulten received his Ph.D. from Harvard University in 1974. He is Swanlund Professor of Physics and directs the Theoretical and Computational Biophysics Group as well as the Center for Macromolecular Modeling and Bioinformatics funded by NCRR/NIH, both at the Beckman Institute . He is also co-director of an NSF-funded Physics Frontier Center, the Center for the Physics of Living Cells. His professional interests are theoretical physics and theoretical biology. His current research focuses on assembly and function of supramolecular systems in the living cell, on membrane processes, on cellular mechanics as well as on the development of non-equilibrium statistical mechanical descriptions and efficient computing tools for structural biology. Honors and awards received by Schulten include: Award in Computational Biology 2008; Humboldt Award of the German Humboldt Foundation (2004); Nernst Prize of the Physical Chemistry Society of Germany (1981).

Klaus Schulten
Professor Laxmikant Kale has been working on various aspects of parallel computing, with a focus on enhancing performance and productivity via adaptive runtime systems, and with the belief that only interdisciplinary research involving multiple CSE and other applications can bring back well-honed abstractions into Computer Science that will have a long-term impact on the state-of-art. His collaborations include the widely used Gordon-Bell award winning (SC'2002) biomolecular simulation program NAMD, and other collaborations on computational cosmology, quantum chemistry, rocket simulation, space-time meshes, and other unstructured mesh applications. He takes pride in his group's success in distributing and supporting software embodying his research ideas, including Charm++, Adaptive MPI and the ParFUM framework. L. V. Kale received the B.Tech degree in Electronics Engineering from Benares Hindu University, Varanasi, India in 1977, and a M.E. degree in Computer Science from Indian Institute of Science in Bangalore, India, in 1979. He received a Ph.D. in computer science in from State University of New York, Stony Brook, in 1985. He worked as a scientist at the Tata Institute of Fundamental Research from 1979 to 1981. He joined the faculty of the University of Illinois at Urbana-Champaign as an Assistant Professor in 1985, where he is currently employed as a Professor.

L. V. Kale
Currently William and Janet Lycan Professor of Chemistry at the University of Illinois at Urbana-Champaign (UIUC), Zaida (Zan) Luthey-Schulten received a B.S. in Chemistry from the University of Southern California in 1969, a M.S. in Chemistry from Harvard University in 1972, and a Ph.D. in Applied Mathematics from Harvard University in 1975. From 1975 to 1980 she was a Research Fellow at the Max-Planck Institute for Biophysical Chemistry in Goettingen, and from 1980 to 1985 a Research Fellow in the Department of Theoretical Physics at the Technical University of Munich. Her research interests, pursued via the Luthey-Schulten Group at the UIUC School of Chemical Sciences, include the evolution of translation, origins of life, physical bioinformatics, predication of protein structure and function with QR profiles, docking with steered molecular dynamics, VMD/Multiple alignment evolutionary analysis tools, and protein folding with a particular interest in hybrid molecular dynamics.
Zaida Luthey-Schulten
Emad Tajkhorshid earned his Ph.D. in 2001 from the University of Heidelburgh, before coming to a postdoctoral position at the Theoretical and Computational Biophysics Group. Now an Assistant Professor of Biochemistry and Biophysics at the University of Illinois at Urbana-Champaign, Dr. Tajkhorshid also leads the Computational Structural Biology and Molecular Biophysics Group at the Beckman Institute. His research focuses on structure function relationships in membrane proteins and understanding the mechanism of their function using simulation and computational methodologies. Examples of his research include the mechanism of permeation of water, ions, and other substrates through membrane channels; simulation of photoactivation in rhodopsin and other visual receptors; and, quantum mechanical calculations of the chromophore in bacteriorhodopsin.
Emad Tajkhorshid
Trained as a physicist, Jim Phillips has always gravitated towards the computational side of the field. During undergraduate summer internships he learned to program supercomputers and wrote software to visualize global earthquake and tomography data. In 1994, Phillips joined the TCB group as a graduate student, attracted by the opportunity to apply physical theory and high-performance computing to the problems of biology. Supported by Hertz and DOE fellowships, Phillips joined the NAMD team and learned the physical theory, numerical methods, parallel programming techniques, and biological applications of molecular dynamics simulation. The group's many experimental collaborations provided a stream of increasingly large simulations that drove the development of NAMD into a flexible, production-quality code. This work earned Phillips not only a Ph.D., but also a 2002 Gordon Bell Award for the parallel scalability of NAMD. Phillips remains with the group as a Senior Research Programmer, guiding NAMD development for the next generation of supercomputers, including the National Science Foundation's petascale machine to be installed at the University of Illinois.

Jim Phillips
John Stone has always liked a challenge. As a graduate student at the University of Missouri-Rolla, Stone developed ray tracing software on a wide variety of parallel computers. Early on, he collaborated with a fellow graduate student researching hypersonic air flow through jet engines by incorporating his graphics software into a computational fluid dynamics simulation code. For the first time, this allowed his colleague to perform in-place visualizations on the same parallel computer running the simulations, generating images of ongoing simulations in seconds rather than days. A decade later, Stone is still helping scientists uncover nature's mysteries. As Senior Research Programmer for TCB's Visual Molecular Dynamics (VMD) program, Stone develops state-of-the-art software that helps scientists visualize the structure and dynamics of large biomolecular complexes. Stone's parallel rendering system, Tachyon, is now used to render high quality images and movies within VMD, and is now part of the SPEC MPI2007 benchmark suite.
John Stone
Senior Research Programmer Kirby Vandivort started his career as a Nuclear Engineer and learned quickly that he found scientific computing very compelling. After receiving his Master's Degree in Computer Science from the University of Missouri-Rolla, Vandivort became a Teaching Fellow and taught several classes to undergraduate engineering majors. While teaching these classes, he developed computer programs such as a web-based gradebook program that both professors and students could use to record and track scores in classes. This program has been used by thousands of students over the past decade, and the knowledge that Vandivort learned proved invaluable for his work here in the TCB group. While teaching and writing programs, Vandivort learned about a job opportunity with the TCB group working on the cutting-edge collaborative project: BioCoRE. In 1999, Kirby joined the nascent BioCoRE team as a team leader. Since his arrival, BioCoRE has transformed from being a mere idea to a complete, web-accessible application that biomedical researchers can use to communicate, run supercomputing jobs, share molecular views, files, and simulation results. In 2007, Kirby started working on developing and implementing additions to VMD to enable Structural Systems Biology. This consists of features and extensions to VMD that are particularly applicable to large systems, and multi-modal systems.

Kirby Vandivort
Barry Isralewitz comes to software development as a simulation scientist who appreciates the power of a good tool. When he was a biochemistry undergraduate at Cornell University with an interest in programming, he worked on bioinformatics software for automating design and construction of multiple generations of recombinant DNA clones. Isralewitz set to switching fields to biophysics when he encountered computer simulations used to explore protein dynamics, a path which eventually led to graduate work in the TCB group studying large-scale protein motions with molecular dynamics (MD) simulations. In his doctoral work Isralewitz performed some of the earliest Steered Molecular Dynamics simulations, developing simulation protocols and additions to the TCB group's parallel-MD software NAMD needed for his studies, including titin extension and ATP synthase stalk rotation. Along the way to receiving his Ph. D. in 2007, Isralewitz also released software tools for VMD, the TCB group's molecular visualization software. Isralewitz's current software focus is Timeline, an analysis and graphing VMD plug-in for identifying events that take place during large MD simulations. Timeline displays temporally-changing attributes of a molecular structure as a 2-D box-plot linked to 3D structure display, with attribute values for each residue of a modeled system, or for other sets of system elements, plotted against time. Starting from an overview of all events for the entire structure, a user can zoom in to display the details of a few key residues over a brief time span. Once identified, notable events can be further explored with additional analysis methods and — particularly useful during coarse, initial examination of extermely large trajectories — by loading additional structure/trajectory detail around events and involved structures.
Barry Isralewitz
David Hardy has always had a fascination with computing and the logic required to solve problems through programming. Although he is also a trained pianist who began his undergraduate studies in music, his interest in mathematics eventually drew him back to the field of computation. Hardy earned his Ph.D. in computer science in 2006 under the guidance of Prof. Robert Skeel, a former principal investigator of the TCB group. Continuing work as a postdoc, Hardy's software development efforts include authorship of NAMD-Lite, a framework for developing molecular modeling software that was used to complete his Ph.D, and he has also made programming contributions to the TCB group's NAMD and VMD software. His research efforts include the development of faster methods for molecular dynamics and, more recently, the development of algorithms for the GPU acceleration of molecular modeling applications.

David Hardy
A keen interest in Chemistry drew Abhinav Bhatele towards working on a quantum chemistry application called OpenAtom at the Parallel Programming Laboratory. His experience with OpenAtom was useful when he started rewriting the load balancers used in NAMD to suit new classes of supercomputers with thousands of processors. Currently, Abhinav works on scaling performance analysis of NAMD to very large number of processors. He also helps scientists tune NAMD for specific molecular systems and specific machines they are trying to run their simulations on. Abhinav is working on his doctoral research with Prof. Laxmikant V. Kale at the Parallel Programming Laboratory at the University of Illinois at Urbana-Champaign. His thesis involves study of interconnects of large supercomputers to enhance the performance of scientific software. He received a B. Tech. degree in Computer Science and Engineering from the Indian Institute of Technology, Kanpur in 2005 and a M. S. degree in Computer Science from the University of Illinois at Urbana-Champaign in 2007.
Abhinav Bhatele
Chris Harrison works on various aspects of quantum biology relevant to cellular function and disease that represent promising targets for future bioengineering efforts. As a graduate student he studied biomolecules that repair DNA damage in cells through quantum events such as energy, electron and proton transfer. After completing his Ph.D., Harrison joined the TCB group to couple his experience in quantum calculations with large-scale simulation methods of biomolecular complexes to work on a variety of topics in bioenergetics and molecular design such as photosynthesis and molecular machines. His software development efforts are focused on developing methods to more easily and accurately study these topics, and include multi-scale or hybrid methods such as QM/MM, methods for accurate free energy calculations, and improved conformational and accelerated sampling methods in NAMD. Harrison is also involved in petascale simulation efforts with NAMD.

Chris Harrison
Xueqing Zou has always been fascinated by understanding our world better. After receiving her B.Sc. in Computer Science, she chose to study physics in graduate school of Peking University. During her graduate studies, she was interested in employing computational methods to solve physics problems. She developed a set of molecular dynamics (MD) simulation programs to study the mechanical properties of nanomaterials, in particular, irradiation-induced damage. She also used MD simulations to study DNA translocation through synthetic nanopores. In 2007, she came to the TCB group as a visiting student. After finishing her Ph.D. studies, she joined the TCB group again to continue research on computational biophysics. She currently works on DNA methylation-related epigenetics, including the impact of methylation on structure and dynamics of DNA and how proteins recognize methylation sites on DNA. She is also interested in understanding the function of protein sensors that transform extracellular signals into intracellular signals.

Xueqing Zou
Ryan McGreevy started his undergraduate studies as a biochemistry major to learn more about the fundamental workings of life. Soon his hobby of tinkering with computers led him to take computer science classes, eventually adding it as a second major. During this time he worked several years in an analytical chemistry laboratory studying the environmental effects of methylmercury. Not sure if he was cut out for a life in a wet lab, Ryan was excited to learn from a bioinformatics course that computers were playing an increasingly important role in science. After graduating in 2009, he spent some time writing software for military flight simulators. He then came to the TCB group as a research programmer in 2010, to work on simulations of a different sort. Here he was able to utilize the knowledge of both his fields of study, applying computational methods to scientific inquiry. He currently works on the group's molecular dynamics flexible fitting (MDFF) method. MDFF takes high resolution X-ray crystallography structures of molecules and coaxes them into the lower resolution yet more natural conformations captured by Cryo-EM. Much of his work so far has involved implementing new restraints for use with MDFF. Molecules in an MDFF simulation experience deforming forces from the additional potential and require restraining forces to hold together certain structural elements. Ryan is also working on his master's degree in bioinformatics from the University of Illinois at Chicago.
Ryan McGreevy

footer