Search Results - "Swenson, David W. H"

OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics by Swenson, David W. H, Prinz, Jan-Hendrik, Noe, Frank, Chodera, John D, Bolhuis, Peter G

“…Transition path sampling techniques allow molecular dynamics simulations of complex systems to focus on rare dynamical events, providing insight into…”
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OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes by Swenson, David W. H, Prinz, Jan-Hendrik, Noe, Frank, Chodera, John D, Bolhuis, Peter G

“…The OpenPathSampling (OPS) package provides an easy-to-use framework to apply transition path sampling methodologies to complex molecular systems with a…”
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The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids by Newton, Arthur C, Kools, Ramses, Swenson, David W H, Bolhuis, Peter G

“…The association and dissociation of particles via specific anisotropic interactions is a fundamental process, both in biology (proteins) and in soft matter…”
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Promoting transparency and reproducibility in enhanced molecular simulations by Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Tribello, Gareth A, Banáš, Pavel, Barducci, Alessandro, Bernetti, Mattia, Bolhuis, Peter G, Bottaro, Sandro, Branduardi, Davide, Capelli, Riccardo, Carloni, Paolo, Ceriotti, Michele, Cesari, Andrea, Chen, Haochuan, Chen, Wei, Colizzi, Francesco, De, Sandip, De La Pierre, Marco, Donadio, Davide, Drobot, Viktor, Ensing, Bernd, Ferguson, Andrew L, Filizola, Marta, Fraser, James S, Fu, Haohao, Gasparotto, Piero, Gervasio, Francesco Luigi, Giberti, Federico, Gil-Ley, Alejandro, Giorgino, Toni, Heller, Gabriella T, Hocky, Glen M, Iannuzzi, Marcella, Invernizzi, Michele, Jelfs, Kim E, Jussupow, Alexander, Kirilin, Evgeny, Laio, Alessandro, Limongelli, Vittorio, Lindorff-Larsen, Kresten, Löhr, Thomas, Marinelli, Fabrizio, Martin-Samos, Layla, Masetti, Matteo, Meyer, Ralf, Michaelides, Angelos, Molteni, Carla, Morishita, Tetsuya, Nava, Marco, Paissoni, Cristina, Papaleo, Elena, Parrinello, Michele, Pfaendtner, Jim, Piaggi, Pablo, Piccini, GiovanniMaria, Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Provasi, Davide, Quigley, David, Raiteri, Paolo, Raniolo, Stefano, Rydzewski, Jakub, Salvalaglio, Matteo, Gabriele Cesare Sosso, Spiwok, Vojtěch, Šponer, Jiří, Swenson, David W H, Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A, White, Andrew

“…The PLUMED consortium unifies developers and contributors to PLUMED, an open-source library for enhanced-sampling, free-energy calculations and the analysis of…”
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Transition Path Sampling as Markov Chain Monte Carlo of Trajectories: Recent Algorithms, Software, Applications, and Future Outlook by Bolhuis, Peter G., Swenson, David W. H.

“…The development of enhanced sampling methods to investigate rare but important events has always been a focal point in the molecular simulation field. Such…”
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Path Sampling Simulations Reveal How the Q61L Mutation Alters the Dynamics of KRas by Roet, Sander, Hooft, Ferry, Bolhuis, Peter G., Swenson, David W. H., Vreede, Jocelyne

“…Flexibility is essential for many proteins to function, but can be difficult to characterize. Experiments lack resolution in space and time, while the time…”
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Konnektor: A Framework for Using Graph Theory to Plan Networks for Free Energy Calculations by Ries, Benjamin, Gowers, Richard J., Baumann, Hannah M., Swenson, David W. H., Henry, Michael M., Eastwood, James R. B., Alibay, Irfan, Mobley, David

“…Alchemical free energy campaigns can be planned using graph theory by building networks that contain nodes representing molecules that are connected by…”
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Atomistic insight into the kinetic pathways for Watson–Crick to Hoogsteen transitions in DNA by Vreede, Jocelyne, Pérez de Alba Ortíz, Alberto, Bolhuis, Peter G, Swenson, David W H

“…Abstract DNA predominantly contains Watson–Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif…”
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Kartograf: A Geometrically Accurate Atom Mapper for Hybrid-Topology Relative Free Energy Calculations by Ries, Benjamin, Alibay, Irfan, Swenson, David W. H., Baumann, Hannah M., Henry, Michael M., Eastwood, James R. B., Gowers, Richard J.

“…Relative binding free energy (RBFE) calculations have emerged as a powerful tool that supports ligand optimization in drug discovery. Despite many successes,…”
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Remarkable Features in the Interactions of Quadrupolar Molecules by Jaeger, Heather M, Swenson, David W. H, Dykstra, Clifford E

“…Quadrupolar charge fields of molecules and of molecular fragments give rise to unique features in weakly interacting clusters and aggregations. Relative to…”
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A Cartesian Quasi-classical Model to Nonequilibrium Quantum Transport: The Anderson Impurity Model by Li, Bin, Levy, Tal J, Swenson, David W. H, Rabani, Eran, Miller, William H

“…We apply the recently proposed quasi-classical approach for a second quantized many-electron Hamiltonian in Cartesian coordinates [J. Chem. Phys. 137, 154107…”
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A semiclassical model for the non-equilibrium quantum transport of a many-electron Hamiltonian coupled to phonons by Swenson, David W.H., Cohen, Guy, Rabani, Eran

“…The semiclassical approach developed for non-equilibrium quantum transport in molecular junctions [J. Chem. Phys. 134, 164103 (2011)] is extended to include…”
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Application of a semiclassical model for the second-quantized many-electron Hamiltonian to nonequilibrium quantum transport: The resonant level model by Swenson, David W. H, Levy, Tal, Cohen, Guy, Rabani, Eran, Miller, William H

“…A semiclassical (SC) approach is developed for nonequilibrium quantum transport in molecular junctions. Following the early work of Miller and White [J. Chem…”
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Clustering of molecular hydrogen around benzene by Swenson, David W.H., Jaeger, Heather M., Dykstra, Clifford E.

“…Clustering of H 2 molecules around benzene shows a number of interesting features that are important for understanding the interaction of hydrogen with certain…”
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