NAME: Ross Walker
CONTACT ADDRESS: San Diego Supercomputer Center
University of California San Diego
9500 Gilman Drive #0505
La Jolla, California, 92093-0505
Work:  +1 858 822 0854
E-MAIL: ross 'at'
  • Imperial College of Science, Technology and Medicine
    (2000 - 2003)
     (PhD and Diploma of Imperial College - “The Development of a QM/MM Based Linear Response Method and its Application to Proteins.”)
  • Imperial College of Science, Technology and Medicine (Undergraduate Reading Chemistry) (1996 - 2000)
    1st Class Honors, summa cum laude.
  • BETHS Grant-Maintained Grammar School (1989 - 1996)


Experienced research scientist and manager of research team in computational chemistry, molecular biology and high performance and data intensive computing. Responsible for building high profile research group at a major US University with extensive experience writing proposals and managing federal and industrial funding. Lead developer of world-renowned molecular dynamics simulation software and key architect for multiple US supercomputers. Advisor to US Government on high performance computing and software development in the chemical sciences. Reviewer for major scientific journals and funding review panels in the fields of chemistry, biochemistry and molecular biology. Author of over 50 research papers and collected works in major international journals.


Jan 2008 - to date Associate Research Professor (Jul 13) / Assistant Research Professor, Walker Molecular Dynamics Lab, Biosciences lead, San Diego Supercomputer Center, UC San Diego, La Jolla, CA.

Built highly successful research lab of 10+ scientists specializing in computational chemistry, molecular biology and high performance and data intensive computing. Key research projects include enzyme reaction and activation path modeling; GPU acceleration of MD simulations; development of new algorithms for simulation of lipid membranes; quantification of drug interaction with membranes; automated multidimensional biological force field parameter refinement; enzyme optimization for bioethanol production; accelerated sampling algorithms and GPU accelerated binding free energy methods. Highlights include:

  • Successfully closed > $2.8 million in NSF, NIH, DOE and industry funding.
  • Authored over 50 research papers and collected works including articles in Nature Communications & Nature Methods.
  • Director SDSC/UCSD CUDA teaching center for GPU computing.
  • Director SDSC/UCSD Intel Center for Parallel Computing.
  • Principal author of the AMBER molecular dynamics software, over 1000 university and commercial site licenses, > 1,500 citations per year. World's fastest MD software on commodity hardware.
  • Key contributor to major research software including CHARMM and Rosetta.
  • Optimized key scientific software in serial and parallel on all major US supercomputers.
  • Conceived NVIDIA GPU test drive program (, now offered by all major computer hardware vendors in 30+ countries.
  • Designed custom MD simulation hardware program (AMBER MD SimCluster) with Exxact Corp and CirraScale to provide custom solutions for academic and industry research teams. Currently averaging > $2.0 million in new quotes per quarter, with installations in over 50 major US and international universities as well as multiple fortune 500 companies.
  • Advisor to US Government on high performance computing and software development in the chemical sciences.
  • Reviewer for major scientific journals and funding review panels in chemistry, biochemistry, molecular biology and HPC.
  • Lead designer of major US supercomputers including projects with hardware acquisition in excess of $30 million.
  • Authored tutorials on molecular dynamics simulation that are incorporated in undergraduate and graduate level courses in multiple universities worldwide.
  • Presented over 100 major research talks, including keynote presentations, and over 25 posters at multiple international conferences including Supercomputing, American Chemical Society, Royal Society of Chemistry, Gordon Research Conferences, Molecular Graphics and Modeling Society, World Association of Theoretically Oriented Chemists, Institute of Electrical and Electronic Engineers and NVIDIA Graphics Technology Conferences.
  • Organized conference symposiums at Supercomputing and American Chemical Society national meetings.

Major research collaborations have included: Memorial Sloan Kettering Cancer Center, National Renewable Energy Laboratory, Lawrence Livermore National Laboratory, Brookhaven National Laboratory, Imperial College London, University of Cambridge, Yale University, University of Florida, Rutgers University, University of Minnesota, The Scripps Research Institute, Harvard University, University of Washington, University of Bergen Norway, Howard Hughes Medical Institute, Intel Corp, NVIDIA Corp, Amazon Web Services, Microsoft, Takeda, Dart Neuroscience, Pfizer and Novartis.

Jun 2008 - Jun 2013 Adjunct Associate Professor (Jul 13) / Adjunct Assistant Professor, Department of Chemistry and Biochemistry, University of California San Diego.
  • Teaching of UCSD undergraduate and graduate level courses including Phys244 - Parallel programming, Chem185/285 - A practical introduction to computational chemistry and Chem113/213 - Physical chemistry of biological macromolecules.
  • Organized and taught week long workshops providing a practical introduction to molecular dynamics simulations with the AMBER software in multiple countries including USA, UK, Norway, Switzerland, Spain, France, Germany, South Africa, Israel, Brazil, Oman and China.
  • Conducted examinations for MSc and Ph.D. candidates in multiple countries.
  • Supervision and training of numerous high school, undergraduate and graduate students.
Apr 2015 - to date Scientific and Research Computing Consultant, Pfizer Inc., Cambridge, MA.
May 2014 - to date Scientific Consultant, Takeda Pharmaceuticals, San Diego, CA.
Jan 2014 - to date Scientific Consultant, Novartis Institutes for Biomedical Research, Cambridge, MA
Apr 2013 - to date Scientific Consultant, Dart Neurosciences, San Diego, CA.
Sep 2010 - to date NVIDIA CUDA fellow, NVIDIA Inc. Santa Clara, CA.

Project leader developing the world's fastest and fully featured molecular dynamics software using Graphics Cards running on workstation hardware. Incorporated within the AMBER MD software and used in all major US and international universities and multiple biotech and pharmaceutical companies. Performance to date has ultimately exceeded that of all traditional supercomputers and represents a reduction in cost of simulation for a typical sized enzyme from $7.50/ns to $0.25/ns.

Jan 2008 - Mar 2013 Computational Lead & Scientific Advisory Board Member, Incitor Inc, Albuquerque, NM

Developed custom simulation techniques to support bio-engineering team in the design and optimization of a novel and patent-pending nanoscale manufacturing platform aimed at making cost-effective renewable fuels a reality. Computational design of synthetic enzymes contributed to closure of $10 million contract with US Army and $5 million+ in venture funding. Sold to external investors Mar 2013.

Mar 2006 - Dec 2007 Staff Scientist and HPC Consultant, San Diego Supercomputer Center, UC San Diego, La Jolla, CA.

Biosciences lead of the Strategic Applications Computing group at the San Diego Supercomputer Center. Specialist in the migration and scale-up of scientific projects from the individual lab scale to leadership class HPC platforms. Primarily responsible for the recruitment and technical support of US faculty to HPC resources under the NSF TeraGrid program. Major projects included working with faculty from University of Washington, Rutgers University, NVIDIA, The Scripps Research Institute, Brookhaven National Laboratory, the National Renewable Energy Laboratory, the Howard Hughes Medical Institute, the University of Bergen, Norway and the University of Florida.

Oct 2003 - Mar 2006 Postdoctoral Fellow and Applications Scientist, The Scripps Research Institute, La Jolla, CA.

Research into direct computational simulation of reactions within enzyme active sites. Primary developer of molecular dynamics software including design and implementation of new Quantum Mechanical/Molecular Mechanical (QM/MM) algorithms for enzyme reaction modelling; hybrid OpenMP/MPI threading for multi-core CPUs and HPC clusters; development of methodology and software for prediction of low energy activation paths in enzymes; developed software for automated force field parameterisation via multi-dimensional fitting; designed the first implementation of a fully periodic particle mesh Ewald (PME) based QM/MM algorithm; authored the world's fastest semi-empirical QM/MM software.

Oct 2000 - Sep 2003 Scientific Computing Consultant, Imperial College of Science, Technology and Medicine, London, UK.

Scientific Computing Consultant, during graduate studies, for multiple research groups at Imperial College, London. Designed custom software solutions for specific scientific applications; Linux clustering and supercomputer construction from commodity components as well as providing a build-to-order service for scientific computer systems. University wide level I & II computer support for faculty, staff and students.

Jun 2000 - Sep 2000 Computer Software Engineer, Venners PLC. London, UK.

Developed work planning optimization software. Re-wrote DOS based invoice system as a Windows 2000 program; developed a distributed parallel system for indexing the distance, time, cost and route by road between all auditors and all jobs in the UK in a combination of C and Visual Basic combined with Microsoft SQL Server.

Jun 1999 - Sep 1999 Computer Software Engineer, National Assurance and Advisory Dept, Deloitte and Touche, London, UK.

Y2K compliance testing of in-house audit software; complete overhaul of departmental intranet; design, implementation and testing of automated tools for compliance risk analysis.

1998 - 2000 Project Manager, Imperial College of Science, Technology and Medicine.

Chemical Resource Discovery and Teaching project manager. The initial aim was to produce a CDROM with copies of all undergraduate chemistry lecture notes and past exam papers as well as copies of free chemistry related software that would be distributed to all IC chemistry undergraduates at the start of the 1998/99 academic year. This aim was successfully achieved and further work involved improving and updating the project for a further 2 years in succession.


  • National Science Foundation SI2-Scientific Software Elements Grant - "Collaborative Research SI2-SSE: Comprehensive Sustained Innovation in Acceleration of Molecular Dynamics Simulation and Analysis on Graphics Processing Units" [PI]
  • National Institutes of Heath R01 "Accounting for Water Structure and Thermodynamics in Computer-Aided Drug Design" [co-PI]
  • NVIDIA Foundation Compute the Cure - "Accelerating the cure: GPU-driven drug discovery for anti-cancer targets" [collaboration with Prof. Rommie Amaro, UCSD]
  • National Institutes of Health R01 "Quantum Chemistry of Proton Pumping by Cytochrome c Oxidases", [co-PI]
  • SDSC Collaborative Research Opportunities Grant "Development of Novel Antiviral Therapies for Influenza", [PI]
  • Microsoft Foundation Award, "Porting and Optimization of GPU Accelerated Molecular Dynamics Software on Microsoft HPC Clusters", [PI]
  • University of California Office of the President, UC Lab award - "Novel Approaches for Analysis of Large Scale MD Simulations." [PI]
  • Director of the UC  San Diego Intel Parallel Computing Center.
  • Director of the UC San Diego NVIDIA CUDA Teaching Center.
  • NVIDIA Fellowship.
  • UCSD Triton Resource Opportunities and Collaboration Grant - "TRO: Development and application of structure-based potentials for parallel simulation of a key transcriptional module." [PI]
  • National Renewable Energy Laboratory – Key member of Department of Energy Funded Targeted Biomass Conversion Research Task Force – Project aimed at the improvement of the efficiency of cellulose degrading enzymes for the cost effective and clean production of renewable bioethanol. (DOE Sci-DAC Grant [co-PI], NSF Supercomputer Grant).
  • National Renewable Energy Laboratory – Award to conduct simulations of the binding domain of the CBH-I cellulose degrading enzyme. [PI]
  • Brookhaven National Laboratory – Key collaborator on the development of advanced anti-viral drugs to target SARS and Bird-Flu pandemics. (NSF Supercomputer Grant SUs [PI]).
  • Howard Hughes Medical Institute – Key collaborator on development of highly parallel versions of the Rosetta protein structure and design software. (NSF Supercomputer Grant [co-PI], IBM Blue Gene Supercomputer Grant.)
  • University of Florida – Collaboration to develop highly scalable SCC-DFTB QM/MM/MD software. Integration into the AMBER suite of software. (NSF Supercomputer Grant [co-PI])


  • Member of the U.S. National Science Foundation Resource Allocations Committee Review Panel (Review grant proposals from leading U.S. scientists for supercomputer time) [2007-2011]

  • Reviewer of Grant Proposals to the National Science Foundation OCI Directorate.

  • Peer Review for the Journal of Computational Chemistry.

  • Peer Review for the Journal of Physical Chemistry.

  • Peer Review for the Journal of Molecular Graphics and Modelling.

  • Peer Review for the Royal Society of Chemistry Publishing Division (Books).

  • Peer Review for The Protein Journal.

  • Peer Review for Protein Science.

  • Peer Review for the Journal of Photochemistry and Photobiology A: Chemistry.

  • Adviser to the U.S. National Science Foundation and U.S. Department of Energy on high performance supercomputing policy for bio-molecular simulation.


  • Member of the American Chemical Society.

  • Affiliate Member of the International Union of Pure and Applied Chemistry.

  • Lifetime Associate of the Royal College of Science.


  Ph.D. and Diploma of Imperial College. 2003
Chemistry Master in Science 1st Class Honours
[summa cum laude]
Associateship of the Royal College of Science 2000
Chemistry A 1996
Physics A
Mathematics A
Engineering (Design & Technology (Technology)) A


RSA Internet Technologies Stage 1
Bronze Medallion and Award of Merit, Lifesaving, RLSS.
Preliminary Teachers Certificate Swimming, ASA
UK and CA(USA) Driving Licenses
IANTD Technical Trimix Diver and Advanced Gas Blender


1) Best paper, IEEE SE-CSE 2013 - Implementing continuous integration software in an established computational chemistry software package, May 2013
2) HP / ACS Outstanding junior faculty award, Mar 2011.
3) Schrodinger / ACS emerging technologies in computational chemistry, finalist, Aug 2010.
4) NVIDIA Fellowship, 2010, 2011, 2012, 2013
5) Electronic Visualization and Poster Night People's Choice Award, DOE SciDAC 2008, 2008. Cellobiohydrolase Action on Cellulose.
6) MGMS Young Modellers Forum.
Accelrys sponsored prize for best speaker, 2002.
7) Nominee for Royal Society of Chemistry Student of the Year Awards.
Imperial College Candidate for Chemistry, 2000.
8) Imperial College of Science, Technology & Medicine
SmithKline Beecham prize for Practical Physical Chemistry in 1999.
9) Imperial College of Science, Technology & Medicine sponsored prize for Best Chemistry related web pages, 1998 Taxol Project.
10) BETHS Grammar School for Boys.
Valedictorian 1996.
11) BETHS Grammar School for Boys.
The Webber Cup for best A-Level results in 1996.
12) BETHS Grammar School for Boys.
The Chubby Trophy for best engineer in 1996.



Over 15 years experience in both independent and collaborative research including experience writing and reviewing NSF, DOE and NIH grant applications. Over 9 years experience leading a team of graduate and postgraduate research scientists.

In-depth knowledge of all major computer operating systems including: Linux, Irix, Solaris, Tru64, OSX and Microsoft Windows. Experience in both serial and massively parallel computer programming for Desktop, Cluster, Supercomputer and Cloud resources running Unix and Windows environments in C, C++, Fortran, CUDA, Visual Basic + SQL Server.

Extensive experience designing and running in-house multi-user computational research environment including >1 PB fileservers, CPU and GPU clusters, incremental backup, 24/7 web servers, CVS, SVN and GIT servers and design of custom benchmark and continuous integration servers for research and commercial software projects. Considerable scripting experience in perl, awk, csh and bash.

Extensive experience in design and construction of extremely high performance workstation, clusters and leadership-class supercomputers utilizing all major interconnect technologies.

Experienced in the use and modification of the source code of multiple computational chemistry and molecular biology software packages including AMBER, CHARMM, Gromacs, NAMD, Gaussian, Gamess US and VMD.

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