Award Abstract #0535710
Collaborative Research: Cyberinfrastructure for Next Generation Biomolecular Modeling

NSF Org:	CHE Division of Chemistry
Initial Amendment Date:	August 10, 2005
Latest Amendment Date:	June 23, 2008
Award Number:	0535710
Award Instrument:	Continuing grant
Program Manager:	Robert L. Kuczkowski CHE Division of Chemistry MPS Directorate for Mathematical & Physical Sciences
Start Date:	August 15, 2005
Expires:	July 31, 2009 (Estimated)
Awarded Amount to Date:	$954552
Investigator(s):	Teresa Head-Gordon TLHead-Gordon@lbl.gov (Principal Investigator) Martin Head-Gordon (Co-Principal Investigator)
Sponsor:	University of California-Berkeley Sponsored Projects Office BERKELEY, CA 94704 510/642-8109
NSF Program(s):	SCI TESTBEDS, CHEMICAL INSTRUMENTATION
Field Application(s):
Program Reference Code(s):	OTHR, HPCC, 9217, 0000
Program Element Code(s):	7368, 1938

ABSTRACT

Teresa Head-Gordon and Martin Head-Gordon of the University of California at Berkeley, Vijay Pande of Stanford University, and Jay Ponder of Washington University are supported by the NSF Divisions of Chemistry and Shared Cyberinfrastructure, under the Cyberinfrastructure and Research Facilities Program. This collaborative project includes extensive development and validation of polarizable force fields for use in biomolecular simulations, public distribution of resulting software components and parallelized computer codes, and workshops to disseminate these tools to the research community.

Biomolecular simulations lie at the heart of physically-driven, atomistic approaches to protein/water dynamics. Empirical force fields are at the core of such simulations, and together with the computer programs that employ them, they define the central cyberinfrastructure in this field. Outcomes of this project include publicly available parameter sets and software, along with workshops for dissemination.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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J.M. Herbert and M. Head-Gordon.  "Charge penetration and the origin of large O-H vibrational redshifts in hydrated-electron clusters,"  J. Am. Chem. Soc.,  v.128,  2006,  p. 13932.

J.M. Herbert and M. Head-Gordon.  "First-principles, quantum mechanical simulation of electron solvation by a water cluster,,"  Proc. Natl. Acad. Sci.,  v.103,  2006,  p. 14282.

J.M. Herbert and M. Head-Gordon.  "Accuracy and limitations of second order many-body perturbation theory for predicting vertical detachment energies of solvated-electron clusters.,"  Phys. Chem. Chem. Phys.,  v.8,  2006,  p. 68.

M. J. Schnieders and J. W. Ponder.  "Polarizable atomic multipole solutes in a generalized kirkwood continuum,,"  J. Chem. Theory Comput.,  v.3,  2007,  p. 2083.

M. J. Schnieders, N. A. Baker, P. Ren and J. W. Ponder.  "Polarizable atomic multipole solutes in a poisson-boltzmann continuum,"  J. Chem. Phys.,  v.126,  2007,  p. 124114.

M. R. Shirts, D. Mobley, J. Chodera, and V. S. Pande.  "Accurately and efficiently correcting for missing dispersion due to cutoffs in molecular simulations,"  J. Phys. Chem. B.,  v.111,  2007,  p. 13052.

M. S. Lin and T. Head-Gordon.  "Improved energy selection of native loops from loop decoys,"  J. Chem. Theory Comput.,  v.4,  2008,  p. 515.

M. S. Lin, N. L. Fawzi, and T. Head-Gordon.  "Hydrophobic potential of mean force as a solvent function for protein structure prediction,"  Structure,  v.15,  2007,  p. 727.

N. Lux Fawzi, A. Phillips, J. Z. Ruscio, M. Doucleff, D. E. Wemmer & T. Head-Gordon.  "Structure and dynamics of the Alzheimer?s Ab21-30 peptide from the interplay of NMR experiments and simulation,"  J. Am. Chem. Soc. published online,  2008, 

R. M. Lynden-Bell and T. Head-Gordon.  "Solvation in modified water models: toward understanding hydrophobic solvation.,"  Mol. Phys.,  v.104,  2007,  p. 3593.

R.A. DiStasio Jr, G. Von Helden, R.P. Steele, and M. Head-Gordon.  "On the T-shaped structures of the benzene dimer,"  Chem. Phys. Lett.,  v.437,  2007,  p. 277.

R.A. DiStasio Jr, Y. Jung, and M. Head-Gordon.  "A Resolution-Of-The-Identity Implementation of the Local Triatomics-In-Molecules Model for Second Order Møller-Plesset Perturbation Theory with Application to Alanine Tetrapeptide Conformational Energies.,"  J. Chem. Theor. Comput.,  v.124,  2005,  p. 862.

R.A. DiStasio Jr., and M. Head-Gordon.  "Optimized spin-component scaled second order Moller-Plesset perturbation theory for intermolecular interaction energies,"  Mol. Phys.,  v.105,  2007,  p. 1073.

R.A. DiStasio Jr., R.P. Steele, and M. Head-Gordon.  "The analytical gradient of dual basis resolution-of-the-identity second order Moller-Plesset perturbation theory,"  Mol. Phys.,  v.105,  2007,  p. 2731.

R.A. DiStasio Jr., R.P. Steele, Y.M. Rhee, Y. Shao, and M. Head-Gordon.  "An improved algorithm for analytical gradient evaluation in resolution-of-the-identity second-order Møller-Plesset perturbation theory: Application to alanine tetrapeptide conformational analysis,"  J. Comput. Chem,  v.28,  2007,  p. 839.

R.P. Steele and M. Head-Gordon.  "Dual basis self-consistent field methods: 6-31G* calculations with a minimal 6-4G primary basis,"  Mol. Phys.,  v.105,  2007,  p. 2455.

R.P. Steele, R.A. Distasio Jr., Y. Shao, J. Kong and M. Head-Gordon,.  "Dual basis second order Møller-Plesset theory: a reduced cost reference for correlation calculations.,"  Journal Chemical Physics,  v.125,  2006,  p. 074108.

R.P. Steele, Y. Shao, R.A. Distasio Jr, and M. Head-Gordon.  "Dual basis analytic gradients I: Self-consistent field theory,,"  J. Phys. Chem. A,  v.110,  2006,  p. 13915.

R.Z. Khaliullin, E.A. Cobar, R.C. Lochan, A.T. Bell and M. Head-Gordon.  "Unravelling the origin of intermolecular interactions using absolutely localized molecular orbitals,"  J. Phys. Chem. A,  v.111,  2007,  p. 8753.

R.Z. Khaliullin, M. Head-Gordon and A.T. Bell.  "An efficient self-consistent field method for large systems of weakly interacting components,"  J. Chem. Phys.,  v.124,  2006,  p. 204105.


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