NIH Center Member Profiles

Emad Tajkhorshid directs the leads the NIH Center for Macromolecular Modeling and Bioinformatcis and the Computational Structural Biology and Molecular Biophysics Group at the Beckman Institute. He is Hastings Endowed Chair in the Biochemistry Department, as well as holds additional appointments across multiple colleges that include Chemistry, Bioengineering, Pharmacology, Biophysics and Quantitative Biology, Computational Science and Engineering, and the Carle-Illinois College of Medicine at the University of Illinois. He joined the faculty of the Departments of Biochemistry (LAS) and Pharmacology (UI COM) in 2007 and was fast tracked to associate professor with tenure in 2010 and then again to the rank of professor in 2013. His tenure dossier was selected as one of the two top UIUC tenure cases on campus. In 2015, Professor Tajkhorshid was named a University of Illinois Scholar, after being nominated by both UIUC and UIC campuses. In 2016, he was awarded the Faculty Excellence Award from the School of Molecular and Cellular Biology at UIUC. Later that year he was named Endowed Chair in Biochemistry. His research focuses on developing and applying advanced computational techniques to characterization of biological phenomena, particularly membranes and membrane proteins, with the aim of achieving the most detailed microscopic view of structural and dynamical bases underlying biological function. Major areas of his extensive research portfolio, which have enjoyed continuous support from multiple federal funding agencies (NIH, NSF, DOE, DOD) over many years, include mechanistic studies of membrane transport proteins, principles of energy transduction and coupling in bioenergetic proteins, and lipid modulation of protein function, e.g., in signaling proteins associated with the cellular membrane. Dr. Tajkhorshid has authored over 200 research articles (H-index 60) with over 20,000 citations in such high-profile journals as Nature, Science, Cell, eLife, and PNAS. He has delivered nearly 150 invited lectures at international meetings, universities, and research institutes. He has served on the Editorial Boards of multiple major journals, including Biophysical Journal, Journal of Biological Chemistry, and PLoS Computational Biology, and Biochemical and Biophysical Research Communication.

Emad Tajkhorshid
Klaus Schulten was Swanlund Professor of Physics and was affiliated with the Department of Chemistry as well as with the Center for Biophysics and Computational Biology. He received his Ph.D. from Harvard University in 1974. He founded and led the Theoretical and Computational Biophysics Group as well as the NIH Center for Macromolecular Modeling and Bioinformatics, both at the Beckman Institute, for nearly 25 years. He was also co-director of an NSF-funded Physics Frontier Center, the Center for the Physics of Living Cells. He was a leader in the field of biophysics, conducting seminal work in the area of molecular dynamics simulations, illuminating biological processes and structures in ways that weren't possible before. His research focused on the structure and function of supramolecular systems in the living cell, and on the development of non-equilibrium statistical mechanical descriptions and efficient computing tools for structural biology. Honors and awards received by Schulten include: Distinguished Service Award, Biophysical Society (2013); IEEE Computer Society Sidney Fernbach Award (2012); Fellow of the Biophysical Society (2012); 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
Aleksei Aksimentiev has a background in soft matter physics and now deploys computational methods to investigate physical phenomena at the interface of solid-state nanodevices and biological macromolecules. The focus of his current research program includes systems comprising silicon-based synthetic membranes and biomolecules - DNA, proteins, and lipids - assembled into novel silicon circuits that can act as sensors, tweezers, and scaffolds for assembly of biosynthetic complexes. His theoretical work on DNA translocation through nanopores is recognized as the first computational study of that kind. He is an expert in modeling membrane proteins and molecular motors. Within the NIH Center for Macromolecular Modeling and Bioinformatics (UIUC), he directs development of the software solutions for computer modeling in biotechnology, which are used by many researchers worldwide.

Aleksei Aksimentiev
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
Rafael Bernardi is an Assistant Professor of Biophysics at the Department of Physics at Auburn University, and an external faculty member of the Theoretical and Computational Biophysics Group. Before joining Auburn's faculty, Dr. Bernardi was a Postdoc (2012-2017), and then a Research Scientist (2017-2020), at the TCBG at the Beckman Institute at the University of Illinois. Dr. Bernardi concluded his PhD in Biophysics, in 2010, at the Carlos Chagas Filho Institute of Biophysics at Federal University of Rio de Janeiro (Brazil), advised by Prof. Pedro G. Pascutti. With a major in Physics (2005) and a Master degree also in Physics (2007), Rafael did an internship in 2008, during his PhD studies, at the University of Pennsylvania, in the Center for Molecular Modeling, working with Prof. Michael L. Klein and Prof. Werner Treptow. During his PhD, Rafael worked mainly with molecular dynamics studies of anesthetics and their effect in both biological membranes and the TREK-1 potassium channel. This work awarded him the Best Thesis Award in Biophysics and Biotechnology in 2010 by the Secretariat of Strategic Affair of the Brazilian Presidency. He is also a collaborator in several studies simulating biological membranes, and was responsible for the first QM/MM dynamics of lipid membranes in which some lipids were studied in the DFT level. For the last couple of years, Rafael has been working with molecular modeling of cellulose, cellulases and cellulosomes, first at INMETRO (Brazil), in a group that aims to develop a new second-generation biofuel, and more recently, at TCBG.

Rafael C. Bernardi
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
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
Christopher Maffeo is a post doctoral researcher working with Aleksei Aksimentiev to develop and apply atomistic and coarse-grained simulation techniques to study biomolecular and biotechnological systems. His work has focused on DNA-DNA and DNA-protein interactions, highlighting the importance of the physical properties of DNA in determining its behavior. Christopher recently developed a coarse-grained model of single-stranded DNA interacting with single-stranded DNA binding protein that was capable of quantitatively matching experiment. Now he is actively working to develop features in the Center's software, ARBD, that allow such models to be simulated at scale with high efficiency using GPU accelerators.

Christopher Maffeo
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
Mariano Spivak did a Master and PhD in Computational Chemistry from the Univeristat Rovira i Virgili in Spain. His research focused on transition metal chemistry using a diverse set of Quantum Chemistry methods, including ab-initio molecular dynamics. He was interested in the benefits of hybrid QM/MM methods for studying complex systems. He joined the TCBG group as a post-doctoral researcher in 2018, and he has been working in the implementaation of new features for NAMD QM/MM. In addition, he is working on VMD plugins for QM applications. This software developments are motivated by the study of proton transport in confined water through carbon nanotubes.

Mariano Spivak