Independent and collaborative research experience to date includes:

• A principal author of the AMBER Molecular Dynamics Software.

• Contributing author to the CHARMM Molecular Dynamics Software.

• Contributing author to the Rosetta Protein Structure Prediction and Design Software.

• The development and implementation of hybrid quantum mechanical and molecular mechanical based approaches for studying complex reaction dynamics across multiple time scales for biological systems.

• The development of Generalised Born implicit solvent models for use in QM/MM MD simulations.

• The implementation of a linear scaling PME Ewald sum based long range electrostatic model for QM/MM MD simulations.

• The development and implementation of a classical and QM/MM nudged elastic band method for locating low energy barrier transitions in biological systems.

• Serial and parallel (OpenMP/MPI) performance enhancements for AMBER 9.

• The development of software for performing automated multidimensional force field parameter fitting to high level ab initio quantum data.

• The creation of software based on linear response theory for processing the fluctuations of a system about equilibrium in order to generate predictions of steady state and non-linear spectra for direct comparison and interpretation with experiment; the development of a parallel version of this non-linear spectroscopy code via the use of MPI, and ultimately the use of this methodology for calculating free energy surfaces and activation energies.

• Continued studies of Cellulase Enzymes (CBH-I) for biofuel production.

• Interests include scientific computing and software development/optimisation, particularly simulations of complex chemical and biological systems with an aim to elucidating complex mechanistic processes.

MAJOR COLLABORATION HIGHLIGHTS:

1. 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]
2. University of California Office of the President, UC Lab award - "Novel Approaches for Analysis of Large Scale MD Simulations." [PI]
3. NVIDIA Fellowship.
4. UCSD Triton Resource Opportunities and Collaboration Grant - "TRO: Development and application of structure-based potentials for parallel simulation of a key transcriptional module." [PI]
5. 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).
6. National Renewable Energy Laboratory – Award to conduct simulations of the binding domain of the CBH-I cellulose degrading enzyme. 3 year renewable grant to start Aug 2007.
7. 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]).
8. 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.)
9. 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:

• Member of the U.S. National Science Foundation Resource Allocations Committee Review Panel (Review grant proposals from leading U.S. scientists for supercomputer time – app $100 million pa.)

• 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.

PROFESSIONAL SOCIETY MEMBERSHIPS: