Associate Research Professor &
High Performance Computing Consultant

San Diego Supercomputer Center &
AMBER Development Team
Leader: Walker Molecular Dynamics Lab

Ross Walker

My Curriculum Vitae is available here.

The Walker Molecular Dynamics Lab is here.

Work Address:
 San Diego Supercomputer Center
University of California San Diego
 9500 Gilman Drive #0505
La Jolla, CA, 92093-0505
USA

Telephone: +1 (858) 822 0854

Email: ross 'at' rosswalker.co.uk


Please note: In Nov 2016 Ross Walker joined GSK as Director of Scientific Research Computing and Analytics. This webpage will be updated in due course.

About me

I am currently an Associate Research Professor working at the San Diego Supercomputer Center (University of California San Diego) in La Jolla (San Diego), California, an Adjunct Associate Professor in the Department of Chemistry and Biochemistry at the University of California San Diego and an NVIDIA Fellow. Prior to this I worked as a research associate in the lab of Prof. David Case at The Scripps Research Institute.

Research Interests

My interests lie in the fields of computational chemistry and molecular biology. In particular I am interested in the development of efficient algorithms for parallel computation of Classical, Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM) techniques.  I am also interested in the use of MM and QM/MM Molecular Dynamics algorithms for the determination of physical and chemical properties of protein based systems. I am currently working as part of the AMBER development team integrating new features into AMBER 12 including the world's fastest GPU accelerated Moecular Dynamics engine (pmemd.cuda), a fast and feature rich modern QM/MM implementation, Nudged Elastic Band (NEB) methods for locating low energy reaction pathways in enzymes and RNA, improvements to the AMBER force fields for accurately modeling the structure of peptide linkages in proteins, an advanced pluggable force field for simulation of phospholipid membranes, development of accelerated MD algorithms and a new software module for performing automated multiple dimension parameter fitting to high level quantum data.

My current research is directed towards developing new molecular dynamics techniques for studying protein reactivity and reaction pathways with the goal of furthering the understanding of such complex mechanistic processes in order to aid the development of new drugs and to improve current biofuel technologies.

I currently have a number of ongoing collaborations with U.S. research groups including:


Cellobiohydrolaze I (CBH-I)
This artist's rendition shows the cellulase enzyme (CBH-I) pulling up a strand of cellulose which it hydrolyzes into dissacharides that can then be fermented to ethanol. (Image courtesy DOE & NREL)

  • NVIDIA Inc. Development of Accelerated Molecular Dynamics algorithms on NVIDIA GPUs using CUDA. Released as part of AMBER 11.

  • Prof. Walter Mangel at Brookhaven National Laboratory to develop techniques for studying the activation pathways of adenovirus proteases.

  • Prof. Adrian Roitberg at the University of Florida to develop advanced QM/MM techniques for modeling condensed phase biological systems. This includes their implementation within AMBER. Recent work has centered on work to produce a very efficient implementation of the Self Consistent Charge, Density Functional, Tight Binding (SCC-DFTB) method.

  • Prof. Knut Teigen at the University of Bergen, Norway to develop next generation comprehensive force fields for Molecular Dynamics Simulations of phospholipid membranes.

Memberships and Peer Review

I am member of the National Science Foundation Resource Allocations Review panel which is responsible for reviewing all applications for supercomputer time on NSF systems. In addition to this I perform peer review for a number of U.S. and International Journals. A complete list is provided on my curriculum vitae.

Education

I obtained my PhD from Imperial College London where my research work was directed towards investigating the ability of Molecular Dynamics (both MM and QM/MM) coupled with excited state quantum chemistry calculations to predict the stokes shift of the NADH coenzyme of horse liver alcohol dehydrogenase (LADH - pictured opposite) and subsequently offer an insight into hydride transfer within this system. A pdf of my thesis is available here. I continue to work in this field investigating new ways to improve the fidelity of molecular dynamics simulations.

Cartoon View of a Crystal structure (PDB-1LDY) of Liver Alcohol Dehydrogenase
Cartoon view of a crystal structure (PDB-1LDY) of Liver Alcohol Dehydrogenase showing the system consists of two dimers in close proximity when crystallised.

Training and Teaching

I currently provide both training and consultancy on the use of the AMBER molecular dynamics package and molecular dynamics simulations in general. In order to introduce new users to molecular dynamics simulations I have hosted a number of worldwide workshops, recent ones being based at the University of Duesseldorf, Germany, Sultan Qaboos University, Muscat, Oman, Pittsburgh Supercomputer Center, the University of California San Diego, the University of Bergen, Norway and Imperial College London. The latter being hosted as part of the EPSRC's National Service for Computational Chemistry Service. If you are interested in hosting a workshop on the AMBER software please contact me at ross 'at' rosswalker.co.uk.

As part of my work with the AMBER software I have developed a number of tutorials on running molecular dynamics simulations of both biomolecules and pharmocophores using the AMBER suite of programs. These tutorials are available here and here.

I also provide computer consultancy for scientific computing applications and have been involved with a number of high profile projects including the specification and installation of high performance and desktop computer equipment both in the offices and laboratories of the newly created Gene Therapy Centre at Imperial College, London.

Computational Experience

I have a large amount of experience running and administering various computer systems including Windows 95/98/ME/NT/2000/XP, Linux, OSX, MacOS, Irix, Tru64 etc.   I also have considerable experience in computer networking and the construction of high performance computer clusters using MPI/PVM with various interconnect technologies including Ethernet, Scali and Myrinet.  I have a great deal of expertise (some commercially) in computer programming with Visual Basic + SQL Server, Quick Basic, C, C++, Fortran 90, Fortran 77, Unix shell scripting and am confident in the use and modification of source code of several computational chemistry programs including Gaussian 98, AMBER, CHARMM, and Gamess US.  I am also well versed in the authoring of web pages and administering of web servers.

I also maintain the Amber Mailing List Archive which is available here.

Optimized Computational Solutions for Life Sciences and Machine Learning

 



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