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: 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

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

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

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

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

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

Juan R. Perilla started his undergraduate studies as a physics major at the Universidad Nacional de Colombia. Marveled by the complexity of living systems, he decided to devote his graduate studies at Johns Hopkins University to biophysics. During his PhD, Juan developed different methods that have been successfully applied to sample conformational transitions for systems of different sizes and complexities. Juan also developed methods for the analysis of long simulations of large macromolecules by using nonlinear analysis and information theory. While at Hopkins, Juan saw the opportunity to work in both clinical and basic research that could have a direct impact on human health, that is why in collaboration with structural biologist he studied the dynamical properties of the epidermal growth factor receptor (EGFr), a well known oncogene associated with different types of cancer. At the Johns Hopkins Hospital, Juan worked shoulder to shoulder with physicians and scientists at the Epilepsy Center in the neurology department. In the center, Juan developed new procedures and methods for the reconstruction of medical images, and the analysis of EEGs allowing the accurate localization of epileptic seizure foci by the use of subdural electrodes in human patients. Juan joined TCBG in 2011 in order to continue his studies on living systems. Juan is trying to understand the uncoating mechanism of the HIV-1 capsid, a step that is crucial to the replication cycle of the virus. He is also studying the conformational pathways that lead to the insertion of proteins into membranes. Juan is working on bringing his methods into NAMD and VMD.

Juan Perilla

Rafael C. 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

Zhe Wu received his Bachelor degree from the University of Science and Technology of China, and obtained his Ph.D from the University of Wisconsin – Madison in 2012 (co-advised by Arun Yethiraj and Qiang Cui). Interested in understanding various biophysical phenomena with theoretical approaches, he focused on both computational model development and biomolecular simulations. Specifically, he is the developer of the BMW-MARTINI coarse-grained force field, and he contributes in understanding the origin of entropy driven hydrophobic interactions in water, the ion Hofmeister effects in water dynamics, and the microscopic mechanisms in peptide-induced membrane remodeling process. As a continuation of his endeavor, he joins the TCB group in 2012 as a postdoctoral fellow in the Center for the Physics of Living Cells, and his study will mainly focus on extending understandings in the membrane fusion processes.

Zhe Wu

Christopher Mayne received his Ph.D. in Chemistry from the University of Illinois (2011) in the laboratory of Prof. John A. Katzenellenbogen. Chris's thesis research focused on the computer-aided design and chemical synthesis of ligands targeting the estrogen (ER) and progesterone (PR) receptors for use as anti-cancer, anti-inflammatory, and tumor-imaging agents. In 2011, Chris joined the Tajkhorshid laboratory at the Beckman Institute as a postdoctoral research associate, where he utilizes molecular dynamics (MD) simulations to study the effects of sequence mutations on agonist and antagonist conformations of ER-ligand complexes, and develops the Forcefield Toolkit (ffTK)--a VMD plugin that aids users in parameterizing small molecules for use in MD simulations. Most recently, Chris has joined the TCBG software development team where he will continue to develop VMD plugins that facilitate the application MD technologies towards drug discovery.

Christopher Mayne

Abhi Singharoy received a Bachelor's Degree from Saint Xavier's College, University of Calcutta in 2005. He completed his Master's degree from the Indian Institute of Technology Bombay in 2007 before moving to Indiana University Bloomington for a PhD in Chemistry under the auspices of Prof. Peter J. Ortoleva. The underlying theme of his research is to delineate ways in which laws of physics and chemistry operate across a diverse range of scales in space and time to yield biologically relevant structure and function. Specifically, his work focuses on the develoment of multiscale methods that extend all-atom simulations of macromolecular systems to biologically relevant timescales. This technique is applied to the computer-aided design of vaccines against the Human Papilloma Virus. In 2013, he joined the TCB group as a Beckman postdoctoral fellow. His immediate endeavor involves developing a Molecular Dynamics Flexible Fitting software that interprets poorly resolved structures from X-ray crystallography experiments.

Abhi Singharoy

Till Rudack received a diploma degree in physics (2007) and a doctoral degree (2013) from the Ruhr University Bochum, Germany. During his diploma thesis under the supervision of PD Dr. Jürgen Schlitter he developed new force field parameters for GTP. Fascinated by the possibilities of interdisciplinary research to investigate biological mechanisms he decided to accomplish his doctoral thesis at the Department of Biophysics of the Ruhr University Bochum under supervision of Prof. Dr. Klaus Gerwert. There he worked at the interface between theory and experiment, developing methods to combine results from biomolecular simulations with results from time-resolved FTIR spectroscopic measurements. By these methods he was able to investigate the small GTPase Ras from the atomic to the molecular level by various simulation techniques. Ras is involved in about 20% of all known cancer cases. By the calculation of theoretical IR spectra with the help of QM/MM simulations he gained experimentally validated dynamic structural computer models of different states of Ras during the signaling cascade of cell growth. The atomic resolution far beyond the resolution of X-ray structure analysis made it possible to decode the essential parts of the catalysis mechanism of GTP hydrolysis by Ras. Till joined the TCBG in 2014 in order to investigate the mechanism of large molecular machines. Here, he has the opportunity to look at all scales from the atomic to the molecular level with different theoretical methods in collaboration with experimentalists. This is essential for a deep understanding of the vital processes in the cell.

Till Rudack

João Ribeiro received his diploma degree in Bioinformatics in 2009 from the Faculty of Biotechnology, Portuguese Catholic University, and his Ph.D. in Sustainable Chemistry in 2014 from Faculty of Science, Faculty of Pharmacy and Institute of Biomedical Sciences Abel Salazar of University of Porto in association with the Nova Lisboa University, advised by Prof. Maria J. Ramos. During his Bioinformatics degree, he had the opportunity to combine Biology and Biochemistry with software development to produce user-friendly Bioinformatics tools. The pursuit for the integration of Biochemistry with software development followed João to his Ph.D studies, where he developed third-party tools (plugins) for the widely used molecular visualization program VMD, developed by Klaus Schulten's Theoretical and Computational Biophysics Group. These plugins aimed to assist non-expert users of computational Chemistry software at different stages of the computer-aided drug design process, such as molecular docking, protein mutagenesis and molecular dynamics simulation analysis. João joined the TCB group in 2014 to employ molecular dynamics simulation to study the cellulose degradation process for biofuel production while keeping the software development always present in his work. He is currently the main developer of the newest VMD plugin to assist MD novice users in the preparation, execution and analysis of MD simulations, QwikMD. This plugin smooths the initial learning curve imposed by the MD programs and allows more advanced users to speed-up tedious structure preparation procedures.

Joao Ribeiro

Following her undergraduate training in Chemistry, Jodi completed her doctoral work in Computational Chemistry in the laboratory of Robert J. Woods, where the widely used GLYCAM force field for carbohydrates is developed. In the Woods group, Jodi gained extensive exposure to force field parameterization and a rare specialization in the modeling and molecular dynamics simulation of carbohydrates, glycoproteins, and protein-carbohydrate complexes. During her postdoctoral phase in the laboratory of Klaus Schulten, Jodi has broadened her expertise to include large-scale MD simulations of biomedically-relevant proteins and multimeric protein complexes, focusing on the dynamical properties of molecular machines. Jodi's current research projects include study of the effects of small-molecule drugs on the dynamic structure of the Hepatitis B virus capsid and the mechanism and mechanical properties of the cytoplasmic dynein motor domain. While part of the Schulten group, Jodi is also taking the opportunity to work closely with the developers of NAMD and VMD to expand support for carbohydrate force fields and visualization schemes in these widely used software packages.

Jodi Hadden

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

Mike Hallock received his undergraduate degree in Computer Science from the University of Illinois in 2004, and since graduating has worked in the Computer Center of the School of Chemical Sciences as a Research Programmer and supports high-performance computing resources for the departments of Chemistry and Chemical and Biomolecular Engineering. After taking an interest in the research going on in the department, he went in to a graduate program and completed a Masters in Bioinformatics at the University of Illinois in 2014. Mike took an interest in GPU computing and began working with the Luthey-Schulten group on Lattice Microbes, working on further accelerating RDME simulations by combining the computing power of multiple GPUs. He now leads development of Lattice Microbes, helping researchers to build and simulate whole-cell models of growing complexity. Mike is also a co-author of pyLM, the Python problem-solving environment for building cellular models and analyzing simulations.

Mike Hallock

Tyler Earnest, a postdoctoral researcher through the National Center for Supercomputing Applications, received his Bachelor's Degrees in Chemistry and Physics from the South Dakota School of Mines and Technology in 2008, and obtained a Ph.D in Physics at the University of Illinois at Urbana-Champaign working under Zan Luthey-Schulten in 2016. His research focuses on the development and application of software to study whole organisms at the single cell level using stochastic, spatially resolved computer simulations. Earnest is a lead developer of Lattice Microbes: a GPU accelerated simulation code which includes highly efficient methods to sample trajectories from the solution to both the chemical master equation, as well as the reaction-diffusion master equation. His primary research interest is building detailed kinetic models of cellular processes which approach the genome scale.

Tyler Earnest

Marian Breuer earned his B.Sc. in Chemistry from Jacobs University Bremen, Germany (2010) and his Ph.D. in Physics from University College London, UK, in the group of Prof. Jochen Blumberger (2015). During his Ph.D., he used classical molecular dynamics in combination with density functional theory to study the thermodynamics and kinetics of electron transfer (ET) through multi-heme proteins, discovering how electronic interactions can offset unfavorable thermodynamics of ET. He joined the lab of Prof. Luthey-Schulten in 2015 as a postdoctoral fellow in the Center for the Physics of Living Cells, moving to the modeling of whole-cell behavior. His current work is focused on modeling the genome-scale metabolic network in a minimal cell.

Marian Breuer