Apr 2011 (from left): Sarah Rosen, Ben Madej, Ross Walker, Romelia Salomon, Robin Betz,
Jason Swails, Andreas Goetz, Matthew Clark

Prof. Walker serves as an Assistant Research Professor at the San Diego Supercomputer Center at the University of California, San Diego (UCSD), as an Adjunct Assistant Professor of Chemistry and Biochemistry at UCSD, an NVIDIA Fellow and as biosciences lead of the Scientific Applications Computing group at the San Diego Supercomputing Center. He is a principal developer of the AMBER Molecular Dynamics code and has extensive experience in developing and teaching classical and QM/MM molecular dynamics techniques. Prof. Walker holds a Ph.D. and Diploma of Imperial College in Computational Chemistry, a Masters in Science degree in Chemistry from the UK's Imperial College of Science, Technology and Medicine as well as an Associateship of the Royal College of Science. Prior to joining UCSD Prof. Walker worked as an applications scientist and postdoctoral research scholar at The Scripps Research Institute in La Jolla, CA.

Andreas Goetz

Dr. Goetz is an Assistant Project Scientist whose research covers a wide range of topics from advanced QM/MM molecular dynamics (MD) techniques to GPU accelerated MD in the AMBER software package for materials science and biomolecular simulations. This includes improvements to the semi-empirical and DFTB methods of AMBER as well as more elaborate electronic structure methods using the Amsterdam Density Functional (ADF) and other software packages. He collaborates with the National Renewable Energy Laboratory (NREL) and with the group of Prof. Francesco Paesani (Dept of Chemistry, UCSD) within the framework of a recently awarded Triton Research Opportunities (TRO) grant.
 

Dr. Salomon is a postdoctoral research associate working on advanced molecular dynamics simulations including reaction path sampling methods, more efficient scaling algorithms for parallel MD simulation and their application to enzymes of biological and pharmaceutical interest. She also works on GPU accelerated Molecular Dynamics in the AMBER software package for materials science and biomolecular simulations, incorporating new MD techniques within both the parallel CPU and GPU versions of the AMBER PMEMD as well as the SANDER packages.

Dr. Pierce is a postdoctoral research associate working on the development of computational methods to efficiently explore the complex landscape of biomolecules and the application of new computational tools to biological and biochemical problems.

Benjamin Madej

Ben is currently a chemistry and biochemistry Ph.D. student at the University of California San Diego. Ben received his Bachelor of Science in biomedical engineering from Washington University in St. Louis, Missouri. He is working on new methods for developing force fields used in molecular dynamics software, specifically the AMBER MD package.

Robin Betz

Robin is currently an undergraduate student at the University of California San Diego. She is working in the group as part of SDSC's Computational Research Experience for Undergraduates (CREU) program. Robin is developing software for the automated fitting of force field parameters for classical Molecular Dynamics Simulations.

Matthew Clark

Matthew is a undergraduate student from Caltech working in the lab as a XSEDE scholar in the student engagement program. He first worked in the lab the summer of 2010 under the Life Sciences Summer Institute Program. He is now working in the lab to extend and benchmark the interface between the AMBER package and multiple Quantum packages including TeraChem, Gaussian, Gamess and the Amsterdam Density Functional program to support ab initio based QM/MM MD simulations.

Mike Wu

Mike is a high school student from Torrey Pines High School working in SDSC as a visiting student, He also participated last summer (2011) in the SDSC Research Experiences for High School Students program . Mike is extensively working on testing the latest version of the GPU accelerated AMBER code.

Manita Singh

Manita is a visiting student from Canyon Crest Academy High School working in the lab for the summer of 2012 under the SDSC Research Experiences for High School Students program. She is a a prospective Bioengineering and Computer Science major at MIT. Her current research involves applying complex analysis tools to MD data to understand the activation pathway of an enzyme.

Roger Ouyang

Roger is a high school student from Westview High School working in the lab for the summer of 2012 under the SDSC Research Experiences for High School Students program. He is working part time in the lab to develop interface between the AMBER package and multiple Quantum packages including NWChem and Q-Chem programs to support ab initio based QM/MM MD simulations.

Raj Kesavan

Raj is a high school student from Westview High School working in the lab for the summer of 2012 under the SDSC Research Experiences for High School Students program. He is working part time in the lab to develop interface between the AMBER package and multiple Quantum packages including NWChem and Q-Chem programs to support ab initio based QM/MM MD simulations.

Age Skjevik

Age was a visiting graduate student from the University of Bergen, Norway. He worked on developing advanced classical force fields for membranes and still maintains an active collaboration with the group.

Thorsten Woelfle

Thorsten was a visiting graduate student from the University of Erlangen, Germany. He worked on developing a Windows port of the AMBER software as well as optimization of the AMBER code. Thorsten also worked on advanced Quantum Mechanical techniques for simulation of condensed phase biological systems.

Paul was a visiting undergraduate student from the University of Hope College, MI. He worked on developing parallel analysis techniques for Molecular Dynamics simulations including a parallel implementation of the AMBER Ptraj software.

Mark Williamson

Dr. Williamson was a postdoctoral research associate working on developing high performance molecular dynamics engines tailored for HPC resources. He is also the author of the CHAMBER software package which provides support for CHARMM force fields within the AMBER MD engines.

Dr. Xu was a postdoctoral research associate at SDSC and the Department of Chemistry, UCSD. He worked on studying the mechanism of action of the binding module of the cellulase enzyme CBH-I in support of bioethanol research as well as development of GPU accelerated versions of the AMBER software. He is now an Assistant Professor at Boise State, Idaho.

Parastou Sadatmousavi

Parastou is a visiting undergraduate student from the Department of Bioengineering at UCSD. She is working on understanding the mechanism of action of the binding module of the Cellulase enzyme CBH-I.

Prithvi Undavalli

Prithvi was a high school student from Canyon Crest academy working in the lab for the summer of 2010 under the Life Sciences Summer Institute Program. He worked jointly with Matthew Clark to develop an interface between the AMBER and the Amsterdam Density Functional programs to support DFT based QM/MM MD simulations.