CURRICULUM VITAE
NAME: |
Ross Walker |
CONTACT ADDRESS: |
San Diego Supercomputer Center
University of California San
Diego 9500 Gilman Drive #0505 La Jolla, California,
92093-0505 USA |
TEL: |
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E-MAIL: |
ross 'at' rosswalker.co.uk |
WEB PAGE: |
http://www.rosswalker.co.uk/ |
EDUCATION: |
- 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)
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SUMMARY
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.
PROFESSIONAL EXPERIENCE:
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 (http://www.nvidia.com/object/gpu-test-drive.html),
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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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MAJOR COLLABORATION HIGHLIGHTS:
- 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])
REVIEW AND ADVISORY PANELS:
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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]
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Reviewer of Grant Proposals to the National Science
Foundation OCI Directorate.
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Peer Review for the Journal of Computational
Chemistry.
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Peer Review for the Journal of Physical Chemistry.
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Peer Review for the Journal of Molecular Graphics
and Modelling.
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Peer Review for the Royal Society of Chemistry
Publishing Division (Books).
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Peer Review for The Protein Journal.
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Peer Review for Protein Science.
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Peer Review for the Journal of Photochemistry and
Photobiology A: Chemistry.
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Adviser to the U.S. National Science Foundation and
U.S. Department of Energy on high performance supercomputing policy
for bio-molecular simulation.
PROFESSIONAL SOCIETY MEMBERSHIPS:
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Member of the American Chemical Society.
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Affiliate Member of the International Union of Pure
and Applied Chemistry.
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Lifetime Associate of the Royal College of Science.
EDUCATION:
PHD |
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Ph.D. and Diploma of Imperial
College. |
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2003 |
DEGREE |
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Chemistry Master in Science |
1st Class Honours
[summa cum laude] |
2000 |
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Associateship of the Royal College of
Science |
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2000 |
A LEVELS |
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Grade |
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Chemistry |
A |
1996 |
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Physics |
A |
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Mathematics |
A |
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Engineering (Design & Technology
(Technology)) |
A |
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OTHER QUALIFICATIONS
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 |
AWARDS
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 ChemWeb.com 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. |
PUBLICATIONS AND PRESENTATIONS:
SKILLS:
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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