Search Results - "Noid, W. G"

Energetic and entropic considerations for coarse-graining by Kidder, Katherine M., Szukalo, Ryan J., Noid, W. G.

“…Molecular dynamics simulations often adopt coarse-grained (CG) models to investigate length- and time-scales that cannot be effectively addressed with…”
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The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models by Noid, W G, Chu, Jhih-Wei, Ayton, Gary S, Krishna, Vinod, Izvekov, Sergei, Voth, Gregory A, Das, Avisek, Andersen, Hans C

“…Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical…”
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The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models by Noid, W G, Liu, Pu, Wang, Yanting, Chu, Jhih-Wei, Ayton, Gary S, Izvekov, Sergei, Andersen, Hans C, Voth, Gregory A

“…The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a…”
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Perspective: Coarse-grained models for biomolecular systems by Noid, W G

“…By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual…”
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Perspective: Advances, Challenges, and Insight for Predictive Coarse-Grained Models by Noid, W. G.

“…By averaging over atomic details, coarse-grained (CG) models provide profound computational and conceptual advantages for studying soft materials. In…”
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Effective force coarse-graining by Wang, Yanting, Noid, W G, Liu, Pu, Voth, Gregory A

“…An effective force coarse-graining (EF-CG) method is presented in this paper that complements the more general multiscale coarse-graining (MS-CG) methodology…”
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Multiscale Coarse-Graining and Structural Correlations:  Connections to Liquid-State Theory by Noid, W. G, Chu, Jhih-Wei, Ayton, Gary S, Voth, Gregory A

“…A statistical mechanical framework elucidates the significance of structural correlations between coarse-grained (CG) sites in the multiscale coarse-graining…”
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Simple Simulation Model for Exploring the Effects of Solvent and Structure on Asphaltene Aggregation by Dunn, Nicholas J. H, Gutama, Besha, Noid, W. G

“…Asphaltenes are operationally defined as the fraction of crude oil that is soluble in toluene but insoluble in n-heptane. According to the Yen–Mullins model,…”
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Rigorous Progress in Coarse-Graining by Noid, W.G, Szukalo, Ryan J, Kidder, Katherine M, Lesniewski, Maria C

“…Low-resolution coarse-grained (CG) models provide remarkable computational and conceptual advantages for simulating soft materials. In principle, bottom-up CG…”
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Recovering physical potentials from a model protein databank by Mullinax, J. W., Noid, W. G., Scheraga, Harold A.

“…Knowledge-based approaches frequently employ empirical relations to determine effective potentials for coarse-grained protein models directly from protein…”
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Myoglobin-CO Substate Structures and Dynamics:  Multidimensional Vibrational Echoes and Molecular Dynamics Simulations by Merchant, Kusai A, Noid, W. G, Akiyama, Ryo, Finkelstein, Ilya J, Goun, Alexei, McClain, Brian L, Loring, Roger F, Fayer, M. D

“…Spectrally resolved infrared stimulated vibrational echo data were obtained for sperm whale carbonmonoxymyoglobin (MbCO) at 300 K. The measured dephasing…”
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Insight into the Density-Dependence of Pair Potentials for Predictive Coarse-Grained Models by Lesniewski, Maria C., Noid, W. G.

“…We investigate the temperature- and density-dependence of effective pair potentials for 1-site coarse-grained (CG) models of two industrial solvents,…”
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A simple theory for molecular chemotaxis driven by specific binding interactions by Krist, Kathleen T, Sen, Ayusman, Noid, W G

“…Recent experiments have suggested that enzymes and other small molecules chemotax toward their substrates. However, the physical forces driving this chemotaxis…”
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Exploring the landscape of model representations by Foley, Thomas T., Kidder, Katherine M., Shell, M. Scott, Noid, W. G.

“…The success of any physical model critically depends upon adopting an appropriate representation for the phenomenon of interest. Unfortunately, it remains…”
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Bottom-up coarse-grained models that accurately describe the structure, pressure, and compressibility of molecular liquids by Dunn, Nicholas J H, Noid, W G

“…The present work investigates the capability of bottom-up coarse-graining (CG) methods for accurately modeling both structural and thermodynamic properties of…”
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MD Simulations of the dsRBP DGCR8 Reveal Correlated Motions that May Aid pri-miRNA Binding by Wostenberg, Christopher, Noid, W.G., Showalter, Scott A.

“…Over the past decade, microRNAs (miRNAs) have been shown to affect gene regulation by basepairing with messenger RNA, and their misregulation has been directly…”
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A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials by Mullinax, J. W, Noid, W. G

“…The present work introduces a generalized-Yvon−Born−Green (YBG) theory for calculating coarse-grained (CG) force fields directly from structure ensembles. The…”
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Generalized Yvon-Born-Green theory for molecular systems by Mullinax, J W, Noid, W G

“…We employ a basis set representation for classical force fields to derive an original system of exact integral equations relating each mode in the force field…”
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Vibrational Echoes:  Dephasing, Rephasing, and the Stability of Classical Trajectories by Noid, W. G, Ezra, Gregory S, Loring, Roger F

“…The experimental observables in coherent, multiple pulse infrared spectroscopic measurements can be calculated from the nonlinear response functions describing…”
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BOCS: Bottom-up Open-source Coarse-graining Software by Dunn, Nicholas J. H, Lebold, Kathryn M, DeLyser, Michael R, Rudzinski, Joseph F, Noid, W.G

“…We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural…”
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