2009

19. B. A. Bauer and S. Patel. Molecular Dynamics Simulations of Nonpolarizable Inorganic Salt Solution Interfaces: NaCl, NaBr, and NaI in TIP4P-QDP Water. J. Chem. Phys. acepted November 2009.

18. S. Patel, J. E. Davis, and B. A. Bauer. Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields. Accepted August 2009. JACS.

17. B. A. Bauer and S. Patel. Properties of Water Along the Liquid-Vapor Coexistence Curve via Molecular Dynamics Simulations Using the Polarizable TIP4P-QDP-LJ Water Model. Accepted July 2009. J. Chem. Phys. (selected for Virtual Journal of Biological Physics Researc, September 2009).

16. S. Patel*, Y. Zhong, B. A. Bauer, and J. E. Davis. Interfacial Structure, Thermodynamics, and Electrostatics of Methanol-Water Solutions via Molecular Dynamics Simulations Using Polarizable Charge Equilibration Models. Accepted. J. Phys. Chem. B. April 2009.

15. J. E. Davis and S. Patel. Charge Equilibration Force Fields for Lipid Environments: Applications to Fully Hydrated DPPC Bilayers and DMPC-Embedded Gramicidin A. Accepted J. Phys. Chem. B. April 2009.

14. J. E. Davis and S. Patel. Revised Charge Equilibration Parameters for More Accurate Hydration Free Energies of Alkanes. Accepted Chem. Phys. Lett. September 2009.

13. M. Taufer, P. Saponaro, O. Padron, and S. Patel. Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs. 24th IEEE International Parallel & Distributed Processing Symposium.

in prep: 

 J. E. Davis, B. A. Bauer, M. Taufer, S. Patel. Molecular Dynamics Simulations of Aqueous Ions at the liquid-vapor interface Accelerated Using Graphics Processors. Submitted to J. Computational Physics.

2008

12. J. E. Davis, A. Oszoy, S. Patel, M. Taufer.  Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. Accepted to 1st International Conference on Bioinformatics and Computational Biology, April 2009, New Orleans, Louisiana, USA.

11. B. Bauer, G. Lee. Warren, and S. Patel*.  Incorporating Phase-Dependent Polrizability in Non-Additive Electrostatic Models for Molecular Dynamics Simulations of Liquid-Vapor Interfacial Systems. Journal of Chemical Theory and Computation. Accepted November 2008.

10. Y. Zhong and S. Patel*. Studies of Ethanol-Water Mixtures Using Polarizable Charge Equilibration Force Fields: New Insights into Hydrophobic Hydration. Accepted. J. Phys. Chem. B. October 2008. 

9. J. E. Davis, G. Lee Warren, and S. Patel*. A Revised Charge Equilibration Potential for Liquid Alkanes J. Phys. Chem. B. 112, 8298.  2008. 

8.  G. Lee Warren, J. E. Davis, and S. Patel*. Origin and Control of Superlinear Polarizability Scaling in Chemical Potential Equalization Methods. J. Chem. Phys. 128, 44110. 2008. (accepted to Virtual Journal of Biophysics).

7.  B. Bauer and S. Patel*.  Condensed Phase Properties of n-Alkyl-Amines Calculated Using Fluctuating Charge Polarizable Force Fields. J. Mol. Liq. 142, 32. 2008.

6. G. Lee Warren and S. Patel*. A Comparison of the Solvation Structure of Polarizable and Non-Polarizable Ions in Bulk Water and Near the Aqueous Liquid-Vapor Interface. J. Phys. Chem. C. 112, 7455. 2008

5. G. Lee. Warren and S. Patel*. Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Non-Polarizable Ion Models . Accepted. J. Phys. Chem. B. 2008

4. J. E. Davis, O. Rahaman, and S. Patel*. Molecular Dynamics Simulations of a DMPC Bilayer Using Non-Additive Interaction Models. Accepted. Biophysical Journal. 2008.

3. S. Patel, Y. Zhong, B. A. Bauer, and J. E. Davis.*. Interfacial Structure, Thermodynamics, and Electrostatics of Methanol-Water Solutions via Molecular Dynamics Simulations Using Polarizable Charge Equilibration Models. in preparation.

Y. Zhong and S. Patel*. Novel Charge Equilibration Force Fields for Peptidoglycans: Application to N-Acetylglucosamines in Polarizable Solvent. in preparation.  

B. A. Bauer and S. Patel*. Effects of Phase-Dependent Polarizability on Electrostatic Properties of Nonpolarizable Inorganic Salt Solutions at the Aqueous Liquid-Vapor Interface. in preparation.

G. Lee Warren and S. Patel*. A Reference Charge Split Charge Equilibration Formalism for Modeling Charge Transfer Effects in Charged Systems: The Dissociation of LiH+, LiH, LiH-, and NaCl. Submitted to Chem. Phys. Lett. June 2008.

2007

2.    Y. Zhong, G. Lee Warren, and S. Patel*. Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models. Journal of Computational Chemistry. 2007

1.    G. L. Warren and S. Patel*. Hydration free energies of monovalent ions in TIP4P-FQ water: An assessment of simulation methodology and force field performance and transferability. Journal of Chemical Physics. 127, 6, pp. 064509-064509-19. 2007. (Selected for Virtual Journal of Biophysics).

Book Chapters

1. S. Patel. Polarizable Models of Aqueous and Non-Aqueous Solvent. in Modeling Solvent Environments. M. Feig (Ed.). Wiley-VCH Verlag GmbH & Co. 2009.  Accepted.