Sandeep Patel

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Papers by Sandeep Patel

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Pursuing Coordinated Trajectory Progression and Efficient Resource Utilization of GPU-Enabled Molecular Dynamics Simulations

IEEE Design & Test, 2014

ABSTRACT To address the challenge of pursuing coordinated trajectory progression and efficient re... more ABSTRACT To address the challenge of pursuing coordinated trajectory progression and efficient resource utilization of GPU-enabled molecular dynamics (MD) simulations on nondedicated high-end clusters, our work aims to supplement, rather than rewrite, existing workflow and resource managers. To this end, we propose a companion module that complements workflow managers and a wrapper module that supports resource managers. We model the maximum utilization of our approach in comparison to the traditional common approach for two molecular simulations: a sodium dodecyl sulfate (SDS) system with dynamically variable job runtimes and a carbon nanotube system with hardware and application failures. In light of our solution, we estimate increased utilization in both simulations. These findings implicitly assure a more coordinated progression of long trajectories across GPUs on a cluster&#39;s nodes.

Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction

Proteins: Structure, Function, and Bioinformatics, 2014

ABSTRACTWeak intermolecular interactions, such as hydrophobic associations, underlie numerous bio... more ABSTRACTWeak intermolecular interactions, such as hydrophobic associations, underlie numerous biomolecular recognition processes. Ubiquitin is a small protein that represents a biochemical model for exploring thermodynamic signatures of hydrophobic association as it is widely held that a major component of ubiquitin's binding to numerous partners is mediated by hydrophobic regions on both partners. Here, we use atomistic molecular dynamics simulations in conjunction with the Adaptive Biasing Force sampling method to compute potentials of mean force (the reversible work, or free energy, associated with the binding process) to investigate the thermodynamic signature of complexation in this well‐studied biochemical model of hydrophobic association. We observe that much like in the case of a purely hydrophobic solute (i.e., graphene, carbon nanotubes), association is favored by entropic contributions from release of water from the interprotein regions. Moreover, association is disfa...

Condensed-phase properties of n-alkyl-amines from molecular dynamics simulations using charge equilibration force fields

Journal of Molecular Liquids, 2008

... Compared to previous MD simulations [T. Kosztolanyi, I. Bako, and G. Palinkas, Hydrogen Bondi... more

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, 2005

We study the bulk and interfacial properties of methanol via molecular dynamics simulations using... more We study the bulk and interfacial properties of methanol via molecular dynamics simulations using a CHARMM (Chemistry at HARvard Molecular Mechanics) fluctuating charge force field. We discuss the parametrization of the electrostatic model as part of the ongoing CHARMM development for polarizable protein force fields. The bulk liquid properties are in agreement with available experimental data and competitive with existing fixed-charge and polarizable force fields. The liquid density and vaporization enthalpy are determined to be 0.809 g/cm3 and 8.9 kcal/mol compared to the experimental values of 0.787 g/cm3 and 8.94 kcal/mol, respectively. The liquid structure as indicated by radial distribution functions is in keeping with the most recent neutron diffraction results; the force field shows a slightly more ordered liquid, necessarily arising from the enhanced condensed phase electrostatics (as evidenced by an induced liquid phase dipole moment of 0.7 D), although the average coordin...

Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials

The Journal of Chemical Physics, 2006

We present results addressing properties of a polarizable force field for hexane based on the flu... more We present results addressing properties of a polarizable force field for hexane based on the fluctuating charge (FQ) formalism and developed in conjunction with the Chemistry at Harvard Molecular Mechanics (CHARMM) potential function. Properties of bulk neat hexane, its liquid-vapor interface, and its interface with a polarizable water model (TIP4P-FQ) are discussed. The FQ model is compared to a recently modified alkane model, C27r, also based on the CHARMM potential energy function. With respect to bulk properties, both models predict bulk density within 1%; the FQ model predicts the liquid vaporization enthalpy within 2%, while the C27r force field underestimates the property by roughly 20% (and in this sense reflects the quality of the C27r force field across the spectrum of linear and branched alkanes). The FQ hexane model realistically captures the dielectric properties of the bulk in terms of a dielectric constant of 1.94, in excellent agreement with experimental values in t...

Exploring Ion Permeation Energetics in Gramicidin A Using Polarizable Charge Equilibration Force Fields

Journal of the American Chemical Society, 2009

All-atom molecular dynamics simulations have been applied in the recent past to explore the free ... more All-atom molecular dynamics simulations have been applied in the recent past to explore the free energetics underlying ion transport processes in biological ion channels. Roux and co-workers, Kuyucak and coworkers, Busath and coworkers, and others have performed rather elegant and extended timescale molecular dynamics simulations using current state-of-the-art fixed-charge (nonpolarizable) force fields in order to calculate the potential of mean force defining the equilibrium flux of ions through prototypical channels such as Gramicidin A. An inescapable conclusion of such studies has been the gross overestimation of the equilibrium free energy barrier, generally predicted to be from 10-20 kcal/mole depending on the force field and simulation protocol used in the calculation; this translates to an underestimation of experimentally measurable single channel conductances by several orders of magnitude. Next-generation polarizable force fields have been suggested as possible alternatives for more quantitative predictions of the underlying free energy surface in such systems 1. Presently, we consider ion permeation energetics in the gramicidin A channel using a novel polarizable force field. Our results predict a peak barrier height of 6 kcal/mole relative to the channel entrance; this is significantly lower than the uncorrected value of 12 kcal/mol for non-polarizable force fields such as GROMOS and CHARMM27 which do not account for electronic polarization. These results provide promising initial indications substantiating the longconjectured importance of polarization effects in describing ion-protein interactions in narrow biological channels.

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Molecular dynamics simulations of nonpolarizable inorganic salt solution interfaces: NaCl, NaBr, and NaI in transferable intermolecular potential 4-point with charge dependent polarizability (TIP4P-QDP) water

The Journal of Chemical Physics, 2010

We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of n... more We present molecular dynamics simulations of the liquid-vapor interface of 1M salt solutions of nonpolarizable NaCl, NaBr, and NaI in polarizable transferable intermolecular potential 4-point with charge dependent polarizability water ͓B. A. Bauer et al., J. Chem. Theory Comput. 5, 359 ͑2009͔͒; this water model accommodates increased solvent polarizability ͑relative to the condensed phase͒ in the interfacial and vapor regions. We employ fixed-charge ion models developed in conjunction with the TIP4P-QDP water model to reproduce ab initio ion-water binding energies and ion-water distances for isolated ion-water pairs. The transferability of these ion models to the condensed phase was validated with hydration free energies computed using thermodynamic integration ͑TI͒ and appropriate energy corrections. Density profiles of Cl − , Br − , and I − exhibit charge layering in the interfacial region; anions and cation interfacial probabilities show marked localization, with the anions penetrating further toward the vapor than the cations. Importantly, in none of the cases studied do anions favor the outermost regions of the interface; there is always an aqueous region between the anions and vapor phase. Observed interfacial charge layering is independent of the strength of anion-cation interactions as manifest in anion-cation contact ion pair peaks and solvent separated ion pair peaks; by artificially modulating the strength of anion-cation interactions ͑independent of their interactions with solvent͒, we find little dependence on charge layering particularly for the larger iodide anion. The present results reiterate the widely held view of the importance of solvent and ion polarizability in mediating specific anion surface segregation effects. Moreover, due to the higher parametrized polarizability of the TIP4P-QDP condensed phase ͕1.31 Å 3 for TIP4P-QDP versus 1.1 Å 3 ͑TIP4P-FQ͒ and 0.87 Å 3 ͑POL3͒ ͓Ponder and Case, Adv. Protein Chem. 66, 27 ͑2003͔͖͒ based on ab initio calculations of the condensed-phase polarizability reduction in liquid water, the present simulations highlight the role of water polarizability in inducing water molecular dipole moments parallel to the interface normal ͑and within the interfacial region͒ so as to favorably oppose the macrodipole generated by the separation of anion and cation charge. Since the TIP4P-QDP water polarizability approaches that of the experimental vapor phase value for water, the present results suggest a fundamental role of solvent polarizability in accommodating the large spatial dipole generated by the separation of ion charges. The present results draw further attention to the question of what exact value of condensed phase water polarizability to incorporate in classical polarizable water force fields.

format_quoteInterfacial charge layering remains constant despite varying anion-cation interactions, underscoring the role of solvent polarizability.format_quote

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