2016
64. S. Ou, Di Cui, S. Patel. Molecular Modeling of Ions At Interfaces: Exploring Similarities to Hydrophobic Solvation through the Lens of Induced Aqueous Interfacial Fluctuations. Accepted to Phys. Chem. Chem. Phys. (August 2016).
63. Y. Hu and S. Patel. Thermodynamics of Cell-Penetrating HIV1 TAT Peptide Insertion into PC/PS/CHOL Model Bilayers through Transmembrane Pore: the Roles of Cholesterol and Anionic Lipid. Accepted to Soft Matter (July 2016).
2015
62. S. Ou, D. Cui, M. Wesowicz, M. Taufer, and S. Patel. Free Energetics of Carbon Nanotube Assocation in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations and High-Performance Graphical Processing Unit Based Resources. Accepted. J. Comput. Chem.
61. Y. Hu, S. K. Sinha, and S. Patel. Exploring Hydrophilic Pores in Model Lipid Bilayers: Correlating Pore Formation Free Energetics and Lipid Bilayer Properties.. Langmuir. (invited Feature Article).
2014
60. D. Cui, S. Ou, and S. Patel. Protein Denaturants at Aqueous-Hydrophobic Interfaces: Self-Consistent Correlation Between Induced Interfacial Fluctuations and Denaturant Stability at the Interface. Accepted October 2014. J. Phys. Chem.
59. S. Ou, D. Cui, and S. Patel. Association of Alkanes with the Aqueous liquid-vapor Interface: A Reference
System for Interpreting Hydrophobicity Generally Through Interfacial Fluctuations. Accepted to Phys. Chem. Chem. Phys. October, 2014.
58. Y. Hu., S. K. Sinha, and S. Patel. Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation Into DMPC Bilayers. J. Phys. Chem. B. Accepted Sept. 2014
57. D. Cui, S. Ou, and S. Patel. Protein-Spanning Water Networks and Implications for Prediction of Ubiquitous, Weak Protein-Protein Interactions Mediated through Hydrophobic Effects. Proteins: Structure, Function, Bioinformatics. Accepted. August 2014.
56. Y. Hu and S. Patel. Structural and Thermodynamic Insight into Spontaneous Membrane-Translocating Peptides across Model PC/PG Lipid Bilayers. Accepted. Journal of Membrane Biology. (special issue on membrane protein structure and function)
55. D. Cui, S. Ou, E. R. Peters, and S. Patel. Ion-Specific Induced Fluctuations and Free Energetics of Aqueous Protein Hydrophobic Interfaces: Towards Connecting to Specific-Ion Behaviors at Aqueous Liquid-Vapor Interfaces. Accepted April, 2014. J. Phys. Chem. B.
54. S. Ou and S. Patel. Electrostatic Contribution from Solvent in Modulating Single-Walled Carbon Nanotube Association. J. Chemical Physics. Accepted July 2014.
2013
53. Y. Hu, S. Ou, and S. Patel. Free Energetics of Arginine Permeation into Model DMPC Lipid Bilayers: Coupling of Effective Counterion Concentration and Lateral Bilayer Dimensions. J. Phys. Chem. B. 2013. In press.
52. S. Ou, T. R. Lucas, Y. Zhong, B. A. Bauer, Y. Hu, and S. Patel. Free Energetics and the Role of Water in the Permeation of Methyl Guanidinium across the Bilayer–Water Interface: Insights from Molecular Dynamics Simulations Using Charge Equilibration Potentials. J. Phys. Chem. B. 117 (13), pp 3578–3592. 2013. DOI: 10.1021/jp400389z.
51. S. Ou. and S. Patel. Temperature Dependence and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface. J. Phys. Chem. B. 117 (21), pp 6512–6523. 2013. DOI: 10.1021/jp401243m
50. S. Ou, D. Cui, and S. Patel. Liquid-Vapor Interfacial Properties of Aqueous Solutions of Guanidinium and Methyl Guanidinium Chloride: Influence of Molecular Orientation on Interface Fluctuations. J. Phys. Chem. B. In press.
49. S. Ou, Y. Hu, H. Wan, and S. Patel. Spherical Monovalent Ions at Aqueous Liquid-Vapor Interfaces: Interfacial Stability and Induced Interface Fluctuations. J. Phys. Chem. B. In Press.
48. S. Schlachter, S. Herbein, S. Ou, J. S. Logan, S. Patel, and M. Taufer. Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-enabled Molecular Dynamics Simulations. IEEE Design and Test Magazine. Special Issue on Hardware Acceleration. Accepted. September 2013.
47. D. Cui, S. Ou, and S. Patel. Free Energetics of Rigid Body Association of Ubiquitin Binding Domains: A Biochemical Model for Binding Mediated by Hydrophobic Interaction. Accepted 12/2013, Proteins: Structure, Function, Bioinformatics.
46. Y. Hu, X. Liu, S. K. Sinha, and S. Patel. Translocation thermodynamics of linear and cyclic nona-arginine into model DPPC bilayer via coarse-grained molecular dynamics simulation: Implications of pore formation and non-additivity. Accepted. J. Phys. Chem. B.
2012
45. S. Ou, B. A. Bauer, and S. Patel. Free Energetics of Carbon Nanotube Association in Pure and Aqueous Ionic Solutions. Submitted to J. Phys. Chem. B. Accepted May 2012.
44. B. A. Bauer, S. Ou, K. Siva, and S. Patel. Dynamics and Energetics of Hydrophobically Confined Water. Accepted. Phys. Rev. E. April 2012.
43 . N. Ganesan, M. Taufer, S. Patel. GPU enabled Macromolecular Simulation: Challenges and Opportunities Accepted March 2012. Computing in Science and Engineering (CiSE). March 2012.
42. B. A. Bauer, S. Ou, and S. Patel. Role of Spatial Ionic Distribution on the Energetics of Hydrophobic Assembly and Properties of the Water/Hydrophobe Interface. Phys. Chem. Chem. Phys. 14, 1892-1906. 2012.
41. T. R. Lucas, B. A. Bauer, J. E. Davis, and S. Patel. Molecular Dynamics Simulation of Hydrated DPPC Monolayers Using Charge Equilibration Force Fields. J. Comp. Chem. 33(2):141-52. 2012.
40. B. A. Bauer, S. Ou, and S. Patel. Solvation Structure and Energetics of Single Ions at the Aqueous Liquid-Vapor Interface. Chem. Phys. Lett. Vol. 527, pp. 22–26.
39. B. A. Bauer and S. Patel. Recent Applications and Developments of Charge Equilibration Force Fields for Modeling Dynamical Charges in Classical Molecular Dynamics Simulations. In press Theoret. Chem. Acc. 2012 (invited).
38. T. R. Lucas, B. A. Bauer, and S. Patel. Charge Equilibration Force Fields for Molecular Dynamics Simulations of Lipids, Bilayers, and Integral Membrane Protein Systems. BBA:Biomembranes. Vol. 1818. pp. 318-329. 2012 (invited)
37. Y. Zhong and S. Patel. Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field. Accepted to . J. Comp. Chem. August 2012.
2011
36. B.A. Bauer, Y. Zhong, D. Meninger, J.E. Davis, S. Patel. Phase-Transfer Energetics of Small Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulations using Charge Equilibration Models. Journal of Molecular Graphics and Modeling. 29(6), 876-887. 2011.
35. Y. Zhong and S. Patel. Solvation Properties of N-acetyl-β-hexosaminides: A Molecular Dynamics Study Incorporating Electrostatic Polarization. J. Comp. Chem. Vol. 32. 3339–3353. 2011.
34. N. Ganesan, B.A. Bauer, T.R. Lucas, S. Patel, M. Taufer. Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers from Molecular Dynamics Simulations Accelerated with Graphical Processing Units. Accepted. Journal of Computational Chemistry. 2011.
33. B.A. Bauer, T.R. Lucas, D.J. Meninger, S. Patel. Water Permeation Through DMPC Lipid Bilayers using Polarizable Charge Equilibration Force Fields. Chem. Phys. Lett. 27;508(4-6):289-294. 2011.
2010
32. B. A. Bauer and S. Patel. Role of Electrostatics in Modulating Hydrophobic Interactions and Barriers to Hydrophobic Assembly. J. Phys. Chem. B. accepted April 2010.
31. B. A. Bauer, J. E. Davis, M. Taufer, S. Patel. Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors. J. Comp. Chem. accepted April 2010.
30. 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. 132(2):024713. 2010.
29. Y. Zhong and S. Patel. Non-Additive Empirical Force Fields for Short-Chain Linear Alcohols: Methanol to Butanol. Hydration Free Energetics and Kirkwood-Buff Analysis Using Charge Equilibration Models. J. Phys. Chem. B. accepted June, 2010.
28. B. Bauer, T. Lucas, A. Krishtal, C. van Alsenoy, S. Patel. Variation of Ion Polarizability From Vacuum to Hydration: Insights from Hirshfeld Partitioning J. Phys. Chem. A. accepted June, 2010.
27. B. Bauer, Y. Zhong, D. Meninger, J. Davis, S. Patel. Phase-Transfer Energetics of Small-Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulation Using Charge Equilibration Models. Journ. Mol. Graph. Model. accepted, September 2010.
2009
26. 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.
25. 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).
24. 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.
23. 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.
22. J. E. Davis and S. Patel. Revised Charge Equilibration Parameters for More Accurate Hydration Free Energies of Alkanes. Accepted Chem. Phys. Lett. September 2009.
21. 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.
2008
20. 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.
19. 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.
18. 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.
17. J. E. Davis, G. Lee Warren, and S. Patel*. A Revised Charge Equilibration Potential for Liquid Alkanes J. Phys. Chem. B. 112, 8298. 2008.
16. 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).
15. 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.
14. 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
13. 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
12. J. E. Davis, O. Rahaman, and S. Patel*. Molecular Dynamics Simulations of a DMPC Bilayer Using Non-Additive Interaction Models. Accepted. Biophysical Journal. 2008.
11. 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.
2007
10. 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
9. 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).
2000-2006
8. S. Patel and C. L. Brooks III. Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. The Journal of chemical physics 124 (20), 204706. 2006.
7. S. Patel and C. L. Brooks III. Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using non additive interactions. The Journal of chemical physics 123 (16), 164502. 2005.
6. S. Patel and C. L. Brooks III. A nonadditive methanol force field: Bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model The Journal of chemical physics 122 (2), 024508, 2005
5. S. Patel and C. L. Brooks III. Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems Molecular Simulation 32 (3-4), 231-249. 2006
4. S. Patel and C. L. Brooks III. CHARMM Fluctuating Charge Force Fields for Proteins: I Paramaterization and application to bulk organic liquid simulations. J. Comp. Chem. 25 (1). 1-16. 2004.
3. S. Patel. A. D. MacKerell, Jr., C. L. Brooks III. CHARMM Fluctuating Charge Force FIeld for Proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comp. Chem. 25 (12). 1504-1514. 2004.
1990-2000
2. Y. Wei, R. Hariharan, S. Patel. Chemical and electrochemical copolymerization of aniline with alkyl ring-substituted anilines. Macromolecules. 23 (3), 758-764. 1990.
1. Yen Wei, Guang Way Jang, Chi Cheung Chan, Kesyin F. Hsueh, Ramakrishnan Hariharan, Sandeep A. patel, Charles K. Whitecar. Polymerization of aniline and alkyl ring-substituted anilines in the presence of aromatic additives. Journal of Physical Chemistry. 94 (19). 7716-7721. 1990.
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.
2. E. Lyman and S. Patel. Molecular Dynamics of Lipid Bilayers: Standards, Successes, and Works in Progress. In Liposomes, Lipid Bilayers and Model Membranes. Georg Pabst (Ed.). CRC Press | Taylor & Francis Group. 2014.
