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 10 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.

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)

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)
 

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."

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)