Alumni can be found here

Felice Lightstone.  Group Leader.  Computational biochemistry.  Electronic structure methods, atomistic modeling, and molecular dynamics simulations to predict and understand the interaction of small molecules and their interactions with proteins.  Design and development of small molecule therapeutics, elucidating enzymatic mechanisms, and design of biomimetics.

Christa Manning.  Group Administrator. 

Drew Bennett.  Biophysics.  Molecular dynamics simulations of lipid membrane systems.  Using free energy calculations and multiscale methods to characterize lipid bilayers at the molecular level.  Current research areas are investigating drug-membrane interactions, ion channels, and protonation states of amphiphiles.

Brian Bennion.  Medicinal chemistry.  Small molecule-protein interactions for discovery of cancer therapeutics and chemical warfare countermeasures.

Paola Bisignano.  Biophysics.  Conformational dynamics of membrane proteins, structure-based drug design, and protein conformational changes upon small-molecule┬ábinding.  I seek to understand how molecular-level details, such as disease mutations, influence the function of a protein, its ability to undergo conformational change, and its binding of endogenous substrates or drugs.

Robert Blake.  Numerical analysis.  Electrophysiological and elctromechanical cardiac simulations, as well as high-throughput in-silico drug screening, cardiac device testing and validation, and image-based simulations of individual-patient etiologies.

Tim Carpenter.  Molecular Biophysics.  Modeling and biomolecular simulation of integral membrane proteins, heterogeneous membrane lipid dynamics, and protein-lipid interactions.  Recent focus on critical neuroreceptors and how they interact with small molecules. 

Konstantia Georgouli.  Chemometrics, biosimulation.  Development and implementation of a general purpose, high-performance, multi-scale, parallel simulation framework optimized to execute a variety of modeling algorithms in biological simulation.

Helgi Ingolfsson.  Biophysics.  Lipid organization of cellular membranes and their perturbation by small molecules. Functional regulation of membrane proteins by the lipid environment -- including how drugs/amphiphiles can change bilayer properties and thus indirectly alter protein function. Exploring these questions using a combination of experimental and computational methods, including atomistic, coarse-grained, and multi-scale molecular dynamics simulations.

Dan Kirshner.  Physics, programming.  Computational data generation and analysis – currently of drug-protein interactions – for the “ATOM consortium”, which seeks to accelerate drug development through “active learning” approaches to machine learning, where the most potentially-informative “missing data” can be identified and then generated with computational and/or experimental methods, and then used to estimate a refined machine learning model.

Ed Lau.  Chemistry.  Computational chemistry, molecular dynamics simulations and quantum mechanical calculations of biological molecules, computational docking.

Ali Navid.  Computational Systems Biology.  Systems biology of microbial communities, multi-cellular organisms, and host-pathogen interactions. Use of dynamic and steady state models to examine the workings of deadly pathogens such as Trypanosoma brucei and Yersinia pestis. Also, systems pharmacology: development and use of physiology-based pharmacokinetic and pharmacodynamic models to predict the transient outcome of drug metabolism and therapeutic or toxic events.

Delin Sun.  Theoretical Chemistry, Chemical Engineering.  Developing new simulation models and algorithms to understand and solve problems associated with small drug-like molecules and biomaterials interacting with biomolecules.

Yue Yang.  Computational chemistry.  Cytochrome P450 (CYP) catalysis.  Molecular dynamics computer simulations to explore the binding process, the chemical reactions involved, and the release of product.  Classes of CYPs exhibit different substrate selectivities and product regioselectivities even though the classes share a nearly identical heme complex.  Understanding the CYP catalysis mechanism can help predict unwanted drug adverse effects in the early stage of drug discovery.

Sergio Wong.  Biophysics.  Development of computational methods for bio-molecular simulation, modeling of protein-ligand interactions, and discovery of small-molecule therapeutics. 

Xiaohua Zhang.  Computational chemistry.  Novel applications of theoretical/computational chemistry methods and software to implement these methods, including (i) drug discovery and high-throughput drug screening C++ toolkit development; (ii) fragment- and structure-based drug design; (iii) high performance computing applied to computational chemistry; and (iv) algorithm derivation and program engineering for molecular simulation.

Fangqiang Zhu.  Theoretical and computational biophysics.  Applications (such as simulations) as well as method development for improving the quantitative understanding of biomolecular systems.


Alumni

Mikel Landajuela, Engineering Directorate, LLNL

Michele Corzett, retired

Geoffrey Feld – Study Director, Metabolon, Inc., North Carolina

Sebnem Essiz Gokhan – Assistant Professor, Kadir Has University, Istanbul, Turkey

Marc Griesemer – Las Positas College, Livermore, CA

Lucas Koziol – Member of the Technical Staff, ExxonMobil Research and Engineering, Annandale, New Jersey

Heather Kulik – Assistant Professor, Massachusetts Institute of Technology, Boston, Massachusetts

Catherine Lacayo –  Cairn Biosciences, San Francisco, California

Richard Law – Vice President of Business Development, Evotec, United Kingdom

Jerome Nilmeier – Data Scientist, IBM Spark Technology Center, San Francisco, California

Tom O'Hara – Engineering Manager, Boutique Air, San Francisco, California