Search Results - "Asthagiri, Dilipkumar"

MD Simulation of Water Using a Rigid Body Description Requires a Small Time Step to Ensure Equipartition by Asthagiri, Dilipkumar N., Beck, Thomas L.

“…In simulations of aqueous systems, it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time step δt for…”
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All-Atom Biomolecular Simulation in the Exascale Era by Beck, Thomas L., Carloni, Paolo, Asthagiri, Dilipkumar N.

“…Exascale supercomputers have opened the door to dynamic simulations, facilitated by AI/ML techniques, that model biomolecular motions over unprecedented length…”
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Thermodynamics of Hydration from the Perspective of the Molecular Quasichemical Theory of Solutions by Asthagiri, Dilipkumar N, Paulaitis, Michael E, Pratt, Lawrence R

“…The quasichemical organization of the potential distribution theorem, molecular quasichemical theory (QCT), enables practical calculations and also provides a…”
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Hydrated Anions: From Clusters to Bulk Solution with Quasi-Chemical Theory by Gomez, Diego T., Pratt, Lawrence R., Asthagiri, Dilipkumar N., Rempe, Susan B.

“…Conspectus The interactions of hydrated ions with molecular and macromolecular solution and interface partners are strong on a chemical energy scale. Here, we…”
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Structural biology in the age of X-ray free-electron lasers and exascale computing by Mous, Sandra, Poitevin, Frédéric, Hunter, Mark S., Asthagiri, Dilipkumar N., Beck, Thomas L.

“…Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of…”
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Hydration Free Energies of Polypeptides from Popular Implicit Solvent Models versus All-Atom Simulation Results Based on Molecular Quasichemical Theory by Adhikari, Rohan S., Parambathu, Arjun Valiya, Chapman, Walter G., Asthagiri, Dilipkumar N.

“…Calculating the hydration free energy of a macromolecule in all-atom simulations has long remained a challenge, necessitating the use of models wherein the…”
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Polarizability Plays a Decisive Role in Modulating Association between Molecular Cations and Anions by Herman, Chase E., Valiya Parambathu, Arjun, Asthagiri, Dilipkumar N., Lenhoff, Abraham M.

“…Electrostatic interactions involving proteins depend on not only the ionic charges involved but also their chemical identities. Here we examine the origins of…”
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Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity by Tomar, Dheeraj S, Paulaitis, Michael E, Pratt, Lawrence R, Asthagiri, Dilipkumar N

“…We address the association of the hydrophobic driving forces in protein folding with the inverse temperature dependence of protein hydration, wherein…”
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Influence of Charge Block Length on Conformation and Solution Behavior of Polyampholytes by Shi, Winnie H., Adhikari, Rohan S., Asthagiri, Dilipkumar N., Marciel, Amanda B.

“…We investigate the effect of charge block length on polyampholyte chain conformation and phase behavior using small-angle X-ray scattering (SAXS) and…”
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Molecular Modes Elucidate the Nuclear Magnetic Resonance Relaxation of Viscous Fluids by Valiya Parambathu, Arjun, Pinheiro dos Santos, Thiago J., Chapman, Walter G., Hirasaki, George J., Asthagiri, Dilipkumar N., Singer, Philip M.

“…The Bloembergen, Purcell, and Pound (BPP) theory of nuclear magnetic resonance (NMR) relaxation in fluids dating back to 1948 continues to be the linchpin in…”
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Comment on “Calculation of Solid–Fluid Interfacial Free Energy with Consideration of Solid Deformation by Molecular Dynamics” by Valiya Parambathu, Arjun, Pinheiro dos Santos, Thiago J, Chapman, Walter G, Asthagiri, Dilipkumar N

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Solvation Free Energies of Alanine Peptides: The Effect of Flexibility by Kokubo, Hironori, Harris, Robert C, Asthagiri, Dilipkumar, Pettitt, B. Montgomery

“…The electrostatic (ΔG el), van der Waals cavity-formation (ΔG vdw), and total (ΔG) solvation free energies for 10 alanine peptides ranging in length (n) from 1…”
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Pressure Denaturation of Staphylococcal Nuclease Studied by Neutron Small-Angle Scattering and Molecular Simulation by Paliwal, Amit, Asthagiri, Dilipkumar, Bossev, Dobrin P., Paulaitis, Michael E.

“…We studied the pressure-induced folding/unfolding transition of staphylococcal nuclease (SN) over a pressure range of ∼1–3 kilobars at 25°C by small-angle…”
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System Size Dependence of Hydration-Shell Occupancy and Its Implications for Assessing the Hydrophobic and Hydrophilic Contributions to Hydration by Asthagiri, Dilipkumar, Tomar, Dheeraj Singh

“…The occupancy distribution of water molecules in the first hydration shell around a solute is intimately connected with solvent density fluctuations and is of…”
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Density Functional Study of the Mechanism of a Tyrosine Phosphatase:  I. Intermediate Formation by Asthagiri, Dilipkumar, Dillet, Valerie, Liu, Tiqing, Noodleman, Louis, Van Etten, Robert L, Bashford, Donald

“…The first step in the catalytic mechanism of a protein tyrosine phosphatase, the transfer of a phosphate group from the phosphotyrosine substrate to a cysteine…”
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Critical Role of Confinement in the NMR Surface Relaxation and Diffusion of n‑Heptane in a Polymer Matrix Revealed by MD Simulations by Valiya Parambathu, Arjun, Singer, Philip M, Hirasaki, George J, Chapman, Walter G, Asthagiri, Dilipkumar

“…The mechanism behind the NMR surface-relaxation times (T 1S,2S) and the large T 1S/T 2S ratio of light hydrocarbons confined in the nanopores of kerogen…”
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Effect of Nanoconfinement on NMR Relaxation of Heptane in Kerogen from Molecular Simulations and Measurements by Valiya Parambathu, Arjun, Chapman, Walter G., Hirasaki, George J., Asthagiri, Dilipkumar, Singer, Philip M.

“…Kerogen-rich shale reservoirs will play a key role during the energy transition, yet the effects of nanoconfinement on the NMR relaxation of hydrocarbons in…”
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Tribute to Lawrence R. Pratt by Ashbaugh, Henry S, Asthagiri, Dilipkumar, Beck, Thomas L, Rempe, Susan B

“…Lawrence Pratt’s career following completion of his Ph.D. at the University of Illinois Urbana Champaign has taken him from Harvard University, to the…”
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Solvation Free Energies of Alanine Peptides: The Effect of Flexibility by KOKUBO, Hironori, HARRIS, Robert C, ASTHAGIRI, Dilipkumar, PETTITT, B. Montgomery

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Equilibration between Translational and Rotational Modes in Molecular Dynamics Simulations of Rigid Water Requires a Smaller Integration Time-Step Than Often Used by Asthagiri, Dilipkumar N, Beck, Thomas L

“…In simulations of aqueous systems it is common to freeze the bond vibration and angle bending modes in water to allow for a longer time-step $\delta t$ for…”
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