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 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 11 including a fast and feature rich modern QM/MM implementation, a Nudged Elastic Band (NEB) method for locating low energy reaction pathways in enzymes and RNA, improvements to the AMBER force fields for accurately modelling the structure of peptide linkages in proteins 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.

One of my recent publications, that was part of my collaboration with the National Renewable Energy Laboratory was featured on the front cover of the April 2007 edition of Journal Protein Engineering Design and Selection.

Zhong, L., Walker, R.C., Brady, J.W. et al., "Computational Simulations of the Trichoderma reesei Cellobiohydrolase I Acting on Microcrystalline Cellulose Iβ: The Enzyme-Substrate Complex", Carb. Res., 2009, 344, 1984-1992. (Full Text PDF)

Seabra, G.M., Walker, R.C., Roitberg, A.E., "Are Current Semi-Empirical Methods Better than Force Fields? A Study from the Thermodynamics Perspective", J. Phys. Chem. A., 2009, 113, 11938-11948. (Full Text PDF)

Bergonzo, C., Campbell, A.J., Walker, R.C., Simmerling, C., "A Partial Nudged Elastic Band Implementation for Use with Large or Explicitly Solvated Large Systems", Int. J. Quant. Chem., 2009, 109, 15, 3781-3790. (Full Text PDF)

Crowley, M.F., Williamson, M.J., Walker, R.C., "CHAMBER: Comprehensive Support for CHARMM Force Fields Within the AMBER Software", Int. J. Quant. Chem., 2009, 109, 15, 3767-3772. (Full Text PDF)

C. David Sherrill, Bobby G. Sumpter, Mutasem O. Sinnokrot, Michael S. Marshall, Edward G. Hohenstein, Ross C. Walker, Ian R. Gould, "Assessment of standard force field models against high-quality ab initio potential curves for prototypes of -, CH/, and SH/ interactions", J. Comput. Chem, 2009, 30, 2187-2193. (Full Text PDF)

Crowley, M. F.; Uberbacher, E. C.; Brooks, C. L., III; Walker, R. C.; Nimlos, M. R.; Himmel, M. E., "Developing improved MD codes for understanding processive cellulases", SCIDAC 2008: Scientific Discovery Through Advanced Computing, 2008, 125: 12049-12049. (Full Text PDF)

Sharikov, Y., Walker, R.C., Greenberg, J., Kouznetsova, V., Nigam, S., Miller, M.A.,  Masliah, E., Tsigelny, I.F., "MAPAS: a tool for prediction of membrane-contacting protein surfaces" Nature: Methods, 2008, 5(2), 119. (Full Text PDF, Supplemental Material PDF)

Case, D.A., Walker, R.C. et al. AMBER 10, 2008, University of California, San Francisco.

Walker, R.C., Crowley, M.F., Case, D.A., "The Implementation of a Fast and Accurate QM/MM Potential Method in AMBER." J. Comp. Chem. 2008, 29, 1019-1031. (Full Text PDF, Supplemental Material PDF)

Seabra, G.M., Torras-Costa, J., Walker, R.C., Roitberg, A.E. "Mixed QM/MM calculations in Biological Systems" John von Neumann Institut fur Computing, NIC Series, 2007, 34, 37-43 (Full Text PDF)

Zhong, L. Walker, R.C, Brady, J.W. et al. "Interactions of the Complete Cellobiohydrolase I from Trichodera reesei with Microcrystalline Cellulose IB.", Cellulose. 2008, 15, 261-273 (Full Text PDF)

Raman, S., Bin, Q., Baker, D., Walker, R.C. "Advances in Protein Structure Prediction on Massively Parallel Systems: Recent Successes with the Rosetta Software and Future Directions.", IBM Journal of R and D. 2008, 5, 7-17 (Full Text PDF)

Seabra, G.M, Walker, R.C., Elstner, M., Case, D.A., Roitberg, A.E., "Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package.", J. Phys. Chem A. 2007, 111, 5655-5664. (Full Text PDF)

Nimlos, M.R., Walker, R.C. Himmel, M. et al., "Molecular Modeling Suggests Induced Fit of Family I Carbohydrate Binding Modules with a Broken Chain Cellulose Surface.", Prot. Eng., Des and Sel. 2007, 20(4), 179-187. (Full Text PDF)

Walker, R.C., Gould, I.R., Klug, D.R. "A Comparison of the Performance of Ab Initio, DFT and Semi- Empirical Methods for Probing Equilibrium Fluctuations." J. Comp. Chem., 2007, 28(2), 478-490 (Full Text PDF)

Case, D.A., Walker, R.C. et al. AMBER 9, (2006), University of California, San Francisco.

Walker, R.C., Cho, B.M., Amer, H., Mercer, I.P., Gould, I.R., Klug, D.R., "The effect of adiabaticity on electron dynamics in Zinc Myoglobin." J. Phys. Chem. B., 2005, 109(12), 5954-5961. (Full Text PDF)

Case, D.A., Crowley, M.F., Walker, R.C. et al. "Computer Modeling of Proteins and Nucleic Acids", Sci. Rep. of The Scripps Research Institute. 2005, 189-190.

Case, D.A., Crowley, M.F., Walker, R.C. et al. "Computer Modeling of Proteins and Nucleic Acids", Sci. Rep. of The Scripps Research Institute. 2004, 182-184.

Walker, R.C., Klug, D.R. et al. "Large and fast relaxations inside a protein: Calculation and measurement of reorganisation energies in alcohol dehydrogenase.", J. Phys. Chem. B., 2002, 106(46). 11658-11665 (Full Text PDF)

Tsigelny, I.F., Sharikov, Y., Walker, R.C., Greenberg, J., Kouznetsova, V., Miller, M.A., Masliah, E., "Membrane-active peptides: methods and results on structure and function", Ed. M. Castanha, International University Line, La Jolla, CA, 2009.

Chapter entitled "Computer Simulations of Cellulase", in "Biomass Recalcitrance", Ed. Dr. M. Himmel, NREL, Blackwell Publishing, Oxford, UK, 2008, ISBN: 978-1405-16360-6 . (Purchase Here)

Seabra, G.M., Walker, R.C., Roitberg, A.E., "Quantifying Solvation Effects on Peptide Conformations: A QM/MM Replica Exchange Study.", Ed. Prof. Sylvio Canuto, Springer, 2008, ISBN: 978-1-4020-8269-6. (Purchase Here)
 

2009-05-18 Yale University, CT, "Applications of Semi-empirical Methods to the Study of Biological Molecules", Ross C. Walker

2009-05-18 Yale University, CT, "An Overview of the NSF TeraGrid Supercomputer Resources", Ross C. Walker

2009-03-24 237^th American Chemical Society National Meeting, Salt Lake City, UT, "A QM/MM study of the cis-trans isomerism in peptide bonds", Ross C. Walker, Gustavo de M. Seabra, Adrian E. Roitberg

2009-03-22 Michael Dewar Memorial Symposium, 237^th American Chemical Society National Meeting, Salt Lake City, UT, "Insights into the activation pathway of the adenovirus protease enzyme: Large scale nudged elastic band simulations on NSF supercomputers.", Ross C. Walker

2009-02-28 49^th Sanibel Meeting, St. Simon’s Island, GA. "Applications of Semi-Empirical Methods to the Study of Biological Molecules.", Gustavo de M. Seabra, Adrian E. Roitberg and Ross C. Walker

2009-02-27 AMBER Developers Meeting Feb 2009, Pre-AMBER 11 release. 49^th Sanibel Meeting, St. Simon’s Island, GA. "Implementation of support for variable 1-4 non-bond scaling in AMBER 11. Updates to topology files and impact for GLYCAM simulations.", Ross C. Walker

2009-02-27 AMBER Developers Meeting Feb 2009, Pre-AMBER 11 release. 49^th Sanibel Meeting, St. Simon’s Island, GA. "CHAMBER: A CHARMM to AMBER force field converter.", Ross C. Walker

2008-12-09 Quantum Theory Project, University of Florida, Invited Speaker, "Recent Progress in Determining the Activation Pathway of Adenovirus Proteases using Nudged Elastic Band Simulations.”, Ross C. Walker

2008-08-20 236^th American Chemical Society National Meeting, Philadelphia, PN, "Replica exchange QM/MM simulations of peptides in solution.", Ross C. Walker, Adrian E. Roitberg and Gustavo de M. Seabra.

2008-08-20 236^th American Chemical Society National Meeting, Philadelphia, PN, "Toward routine long timescale QM/MM/MD simulations: Improvements in AMBER’s QM/MM support.", Ross C. Walker

2008-04-21 University of Illinois at Urbana-Champaign, Beckman Institute Seminar, Invited Speaker, "Insights into the Activation Pathway of the Adenovirus Protease Enzyme using Nudged Elastic Band Simulations.", Ross C. Walker.  

2008-04-09 235th American Chemical Society National Meeting, New Orleans, VA, "Energetics of rearrangement of Family 1 carbohydrate-binding modules.", Mark Nimlos, Michael Crowley, Ross C. Walker et al.

2008-04-07 235th American Chemical Society National Meeting, New Orleans, VA, "Evaluating the accuracy of semi-empirical QM/MM methods using replica exchange and AMBER 10: Phi/Psi free energy calculations of peptides in solution.", Ross C. Walker, Gustavo de M. Seabra and Adrian Roitberg.

2008-04-07 235th American Chemical Society National Meeting, New Orleans, VA, "Recent progress in MD simulations of the CBH I cellulase from T. Reesei bound to cellulose microfibrils.", John W. Brady, Ross C. Walker, et al.

2008-04-06 235th American Chemical Society National Meeting, New Orleans, VA, "Novel QM/MM investigations of enzyme catalysis.", Mark Williamson, Ian R. Gould, David R Klug and Ross C Walker.

2008-03-31 Wright Patterson Air Force Base, Dayton, OH, Invited Speaker, "An overview of the AMBER Molecular Dynamics Software Suite: Capabilities, Performance and Example Calculations.", Ross C. Walker.

2008-03-12 SIAM National Meeting - Parallel Processing for Scientific Computing, Invited Speaker, "A summary of the performance and scaling of AMBER 10 and the challenges ahead", Ross C. Walker  

2008-01-25 Brookhaven National Lab, NY, Invited Speaker, "Modeling an Enzyme to Make Ethanol from Cellulose", Ross C. Walker

2007-12-11 Quantum Theory Project, University of Florida, Invited Speaker, "Modeling an Enzyme to Make Biofuels from Biomass", Ross C. Walker

2007-11-13 Supercomputing 2007, Reno, NV, "Molecular Dynamics on Next Generation HPC Resources", Ross C. Walker

2007-10-31 UCSD Chemistry Department Faculty Symposium. "An Overview of SDSC Collaborative Research Projects", Ross C. Walker

2007-10-23 AMBER Developers Meeting 2007 - Amber 10 pre-release - San Diego, CA, "QM/MM Support in AMBER 10 - New Features and Improved Performance", Ross C. Walker

2007-08-24 2nd CMM 'Users Meet Developers' Workshop, University of Pensylvania, Philidelphia, PA - "An overview of the QM/MM Molecular Dynamics Support in Amber 9.0", Ross C. Walker

2007-08-21 American Chemical Society National Meeting, Boston, MA - "Evaluation of different quantum mechanics methods applied to biological molecules: Potential and free energy surfaces of alanine and glycine dipeptides in vacuum and in water.", Gustavo D.M. Seabra, Ross C. Walker, Adrian E. Roitberg

2007-07-18 San Diego Supercomputer Center General Staff Meeting, Invited Speaker – “Modeling An Enzyme to Make Biofuels from Biomass” & “Molecular Dynamics Simulations of Cellobiohydrolase I”, Ross C. Walker

2007-07-17 San Diego Supercomputer Center Summer Institute 2007 La Jolla CA – Reducing Your Time to Solution – “Lies, Damn Lies, Statistics and Flops – Optimizing Scientific Codes for Maximum Productivity.”, Ross C. Walker

2007-04-25 San Diego Supercomputer Center - National Science Foundation Funded Student Summer Program for advanced Supercomputer use. "Workshop on Single Processor Performance Optimization"., Ross C. Walker

2007-04-11 IBM, Yorktown Research Site, NY, Invited Speaker - "Automated refinements of the AMBER force field parameters for peptides.", Ross C. Walker

2007-03-28 American Chemical Society National Meeting, Chicago, IL - "Beyond Force Fields: Sampling and Folding with QM and QM/MM Hamiltonians" Adrian E. Roitberg, Ross C.Walker, and Gustavo de Miranda Seabra

2007-02-28 AMBER Developers Meeting 2007, 47th Sanibel Symposium, St. Simons Island, GA. Invited Speaker - "QMMM Support in AMBER" Ross C. Walker

2006-12-11 Future of Biomolecular Simulations Workshop, Oak Ridge National Lab. Invited Speaker - "How can we make the most of Petascale Resources for Molecular Dynamics? : Rethinking the Problem" Ross C. Walker

2006-11-15 Supercomputing 2006, Tampa FL - "HPC for Protein Structure Prediction." Ross C. Walker

2006-09-13 American Chemical Society National Meeting, San Francisco CA - "Considerations for running long timescale semi-empirical QM/MM MD simulations: A QM/MM Implementation of the Particle Mesh Ewald Approach." Ross C. Walker, David A. Case

2006-07-27 Rosetta Con 2006, Sleeping Lady, Seattle, WA - "Improving Rosetta Single Processor Performance on SDSC Supercomputers - Tips for Developers." Ross C. Walker

2006-07-18 SDSC Summer Institute 2006, La Jolla CA - Taking Your Science to the Next Level: On the Path to Petascale Computing - "Single Processor Code Optimization for the Datastar (Power 4) Architecture"

2006-03-26 American Chemical Society National Meeting, Atlanta, GA - "Implementation of SCC-DFTB in AMBER" Gustavo de Miranda Seabra, Ross C. Walker and Adrian E. Roitberg

2005-12-07 SDSC Inverted Speaker, La Jolla CA - "The Implementation of a Fast and Efficient Hybrid QM/MM Potential Method within the AMBER 9.0 Sander Module."

2005-10-28 AMBER Developers Meeting 2005, Salt Lake City UT - "QMMM Support in Amber 9"

2005-09-21 Zymeworks Inc Invited Speaker, Vancouver BC - "Improvements to the Amber Force Field via the use of the Simplex Method for Multiple-Dimensional Parameter Fitting."

2004-11-08 La Jolla Interfaces in Science Joint Group Meeting, La Jolla, CA (McCammon, Brooks & Case) - "Refinements of the Amber Force Field via the use of Multi-Dimensional Parameter Fitting."

2004-10-24 AMBER Developers Meeting 2004, Stony Brook NY - "Improving the Support for QMMM in Amber 9 - What’s New."

2003-04-19 Imperial College London, Invited Speaker - "Lights, Computer, Action: Probing Protein Dynamics with QM/MM Techniques and Femtosecond Laser Spectroscopy."

2003-03-13 Theoretical Computing Group Meeting, Kings College London UK - "Probing Protein Dynamics: Simulating Femtosecond Spectroscopy Results"

2002-11-29 Young Modellers Forum 2002, Royal Institution, London UK (Prize Winner) - "Lights, Computer, Action: Probing Protein Dynamics with QM/MM Techniques."

2002-11-07 The Scripps Research Institute, La Jolla CA, Invited Speaker - "Lights, Computer, Action: Probing Protein Dynamics with QM/MM Techniques."

2002-11-02 Accelrys Inc, La Jolla CA, Invited Speaker - "Lights, Computer, Action: Probing Protein Dynamics with QM/MM Techniques."

Michael F. Crowley, Mark J. Williamson, Ross C. Walker et al. – "Cellobiohydrolase Processivity: Improved enzymes for bioethanol", SciDAC 2009, San Diego, CA, Jun 2009.

Michael F. Crowley, Mark J. Williamson, Ross C. Walker – "CHAMBER A CHARMM Format Convertor to Enable the use of CHARMM Force Fields in AMBER", 49^th Sanibel Symposium, St. Simon’s Island, GA, Feb 2009.

Ross C. Walker, Mark R. Nimlos, Michael F. Crowley, John W. Brady, James F. Matthews, Linghao Zhong, Michael E. Himmel - "Recent advances in understanding the mechanism of action of CBH I cellulase through advanced MD simulations.", 235th American Chemical Society National Meeting, New Orleans, LA, Apr 2008.

Gustavo D.M. Seabra, Ross C. Walker, Adrian E. Roitberg - "Evaluation of different quantum mechanics methods applied to biological molecules: Potential and free energy surfaces of alanine and glycine dipeptides in vacuum and in water.", American Chemical Society National Meeting, Boston, MA, Aug 2007.

Walker, R.C., Crowley, M.F., Case, D.A. - "An Efficient Particle Mesh Ewald Approach for Including Long-Range Electrostatics in QM/MM Molecular Dynamics Simulations", 47th Sanibel Symposium, 2007, St Simons Island, Georgia (PDF)

Walker, R.C., Raman, S., Baker, D. - "High Resolution, High Throughput Protein Structure Prediction using IBM Blue Gene Supercomputers: Predicting CASP Targets in Record Time", Supercomputing 2006, Tampa, FL. (PDF)

Walker, R.C., Mathews, D.H., Case, D.A. - "Calculating low energy reaction pathways in proteins and RNA: A QM/MM implementation of the nudged elastic band (NEB) method", Abst. Papers. Amer. Chem. Soc., 2005, 229: U791-U792 235-COMP Part 1 (PDF)

Walker, R.C., Klug, D.A., Gould, I.R. - "Large and Fast Relaxations Inside a Protein: Calculation and Measurement of Reorganisation Energies in Alcohol Dehydrogenase", MGMS Biomolecular Interactions Conference, Apr 2002, University of Bristol, Bristol UK. (PDF)

Walker, R.C., Klug, D.A., Gould, I.R. - "Successful Prediction of 1eV Stokes Shift from QMMM Application of Linear Response Theory" Royal Society of Chemistry: Biophysical Chemistry Conference, Sept 2001 (PDF)

08/2009 –Workshop: "An introduction to Molecular Dynamics Simulations using CHARMM, AMBER and the MMTSB Toolset.", NIH funded Center for Theorectical BioPhysics workshop, La Jolla, CA.

07/2009 – UC Course: "UC Merced Summer 2009 Computational Biology Course", UC Graduate Course, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA.

04/2009 – Workshop: "Modelling protein-carbohydrate recognition in-silico.", BBSRC & NGS sponsored Workshop, University of Westminster, London, UK.

07/2008 – Workshop: "Advanced workshop on AMBER Molecular Dynamics Simulations." EPSRC National Service for Computational Chemistry Software, Imperial College London, UK.

07/2008 – Workshop: "Introductory workshop on AMBER Molecular Dynamics Simulations." EPSRC National Service for Computational Chemistry Software, Imperial College London.

06/2008 – Workshop: "Advanced workshop on AMBER Molecular Dynamics Simulations." University of Bergen, Norway.

05/2008 – UCSD Physics 244, Parallel Computation - "Introduction to Parallel Processing in Molecular Dynamics", UCSD Graduate course.

01/2008 - "Advanced Simulation Using AMBER", Mitre Corp., McLean, VA, USA.

06/2007 - SDSC Summer Institute "Lies, Damn Lies, Statistics and FLOPS: Optimizing for performance on modern supercomputers." San Diego Supercomputer Center, University of California, San Diego.

05/2007 - "Molecular Dynamics Simulations for Beginners", University of Bergen, Norway.

04/2007 - SDSC Summer student SAC program "Single Processor Optimization", San Diego Supercomputer Center, University of California, San Diego.

06/2006 - SDSC Summer Institute "Single Processor Optimization for the Power 4 Architecture." San Diego Supercomputer Center, University of California, San Diego.

06/2006 - Workshop: "Advanced workshop on AMBER Molecular Dynamics Simulations." Imperial College London, London, UK.

06/2005 - Workshop: "Biomolecular Simulations using Amber, VMD and the MMTSB toolset." Pittsburgh Supercomputer Center, PA, USA.

09/2004 - Workshop: "An introduction to Molecular Dynamics using AMBER.", Imperial College London, London, UK. Invited host.

11/2008 Supercomputing 2008, Austin, TX – Birds of a Feather Session: "Requiring Open Source in Federal Grants.", Ross C. Walker & Laxmikant Kale.

03/2009 237^th American Chemical Society National Meeting, Salt Lake City, Utah. "Advancing Computational Chemistry through High-Performance Computing: From the Workstation to Petascale and Beyond: Michael Dewar Memorial Symposium", Ross C. Walker, Thomas E. Cheatham III. & Shawn Brown.

03/2009 237^th American Chemical Society National Meeting, Salt Lake City, Utah. "Connecting Computation to Experiment using Combined QM and MM Methods", Ross C. Walker & Brent P. Krueger.