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Walker Lab Members

 

 


Mar 2013 (from left):
Back: Andreas Goetz, Aditi Munshi, Ross Walker, Keshav Tadimete
Middle: Romelia Salomon, Jian Yin, Robin Betz, Sarah Witzke
Front: Ben Madej, Davide Sabbadin


Group Leader

Dr Ross C. Walker

Ross Walker

Prof. Walker serves as an Associate Research Professor at the San Diego Supercomputer Center at the University of California, San Diego (UCSD), as an Adjunct Associate 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.


Academic Staff  
Andreas Goetz

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).


Postdoctoral Fellows  
Romelia Salomon-Ferrer

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.

   
Age Skjevik

Dr. Skjevik is a postdoctoral research associate jointly appointed with the University of Bergen in Norway. His research includes improved all atom force fields for simulations of phospholipids as well as the application of techniques developed in the Walker Lab for studying the transport and diffusion of small molecules, ligands and toxins across phospholipid membranes.

   

Graduate Researchers  

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.


Undergrad Researchers  

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.

   
 
   

High School Researchers  
 

Aditi Munshi

 

Aditi is a high school student from Torrey Pines High School. She is working in the lab under the SDSC Research Experience for High School Students program. She is working on developing optical character recognition (OCR) software and hardware for automating the reading of One Time Password (OTP) tokens to improve efficiency and accessibility.

   
 

Keshav Tadimete

 

Keshav is a high school student intern in the lab under the SDSC Research Experience for High School Students program. He is working on determining the power consumption of Molecular Dynamics simulations when run on a variety of hardware.

   

Academic Visitors  

Ju Xie

 

Prof. Xie is a visiting academic from Yangzhou University in China. She is visiting the Walker Lab for 6 months to learn Molecular Dynamics and QM/MM MD simulation techniques.

   

Alumni  
   

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 Frybarger

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.

   
Dong Xu

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 was a visiting undergraduate student from the Department of Bioengineering at UCSD. She worked 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. 

   

Matthew Clark

 

Matthew is a undergraduate student from Caltech who worked 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. His recent work included extending and benchmarking 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.

   

Manita Singh

 

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

   
 

Roger Ouyang

 

Roger was a high school student from Westview High School who worked in the lab for the summer of 2012 under the SDSC Research Experiences for High School Students program. He worked on developing interfaces 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 was a high school student from Westview High School who worked in the lab for the summer of 2012 under the SDSC Research Experiences for High School Students program. He worked on developing interfaces between the AMBER package and multiple Quantum packages including NWChem and Q-Chem programs to support ab initio based QM/MM MD simulations.

   
 

Mike Wu

 

Mike was a high school student from Torrey Pines High School working at SDSC as a visiting student, He participated in the summer (2011) SDSC Research Experiences for High School Students program and returned for a subsequent internship. Mike worked on testing the latest version of the GPU accelerated AMBER code. He is now a electrical engineering major at Yale University.

   
Sarah Witzke

Sarah is a graduate student at the University of Southern Denmark. She spent the early part of 2013 visiting the Walker Lab to learn advanced MD simulation techniques and force field fitting with an aim to fitting parameters for specific bacterial lipids.

   
Levi Pierce

Dr. Pierce was 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. Levi is now a development engineer at Schrodinger.

   
  Davide Sabbadin

Davide is a graduate student from the University of Padova in Italy. He spent 6 months in the lab in early 2013 as part of a joint research program looking at the interaction of key signaling enzymes with lipid bilayers. He also helped test developments in GPU accelerate molecular dynamics.

   
  Jian Yin

Dr. Yin was a postdoctoral research associate working on improving accelerated molecular dynamics and other advanced sampling techniques. She is now a postdoctoral research associate in the group of Prof. Mike Gilson at the UCSD School of Pharmacy.

 

 

The Walker Molecular Dynamics Lab
June 2009 (from left): Paul Frybarger, Parastou Sadatmousavi, Ross Walker, Andreas Goetz, Mark Williamson

 


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

 


the Walker Molecular Dynamics lab