Literature DB >> 23249062

Multiscale reactive molecular dynamics.

Chris Knight1, Gerrick E Lindberg, Gregory A Voth.   

Abstract

Many processes important to chemistry, materials science, and biology cannot be described without considering electronic and nuclear-level dynamics and their coupling to slower, cooperative motions of the system. These inherently multiscale problems require computationally efficient and accurate methods to converge statistical properties. In this paper, a method is presented that uses data directly from condensed phase ab initio simulations to develop reactive molecular dynamics models that do not require predefined empirical functions. Instead, the interactions used in the reactive model are expressed as linear combinations of interpolating functions that are optimized by using a linear least-squares algorithm. One notable benefit of the procedure outlined here is the capability to minimize the number of parameters requiring nonlinear optimization. The method presented can be generally applied to multiscale problems and is demonstrated by generating reactive models for the hydrated excess proton and hydroxide ion based directly on condensed phase ab initio molecular dynamics simulations. The resulting models faithfully reproduce the water-ion structural properties and diffusion constants from the ab initio simulations. Additionally, the free energy profiles for proton transfer, which is sensitive to the structural diffusion of both ions in water, are reproduced. The high fidelity of these models to ab initio simulations will permit accurate modeling of general chemical reactions in condensed phase systems with computational efficiency orders of magnitudes greater than currently possible with ab initio simulation methods, thus facilitating a proper statistical sampling of the coupling to slow, large-scale motions of the system.

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Year:  2012        PMID: 23249062      PMCID: PMC3432097          DOI: 10.1063/1.4743958

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  43 in total

1.  Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

Authors:  Stefan Grimme
Journal:  J Comput Chem       Date:  2006-11-30       Impact factor: 3.376

2.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.

Authors:  W G Noid; Pu Liu; Yanting Wang; Jhih-Wei Chu; Gary S Ayton; Sergei Izvekov; Hans C Andersen; Gregory A Voth
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

3.  Importance of van der Waals interactions in liquid water.

Authors:  I-Chun Lin; Ari P Seitsonen; Maurício D Coutinho-Neto; Ivano Tavernelli; Ursula Rothlisberger
Journal:  J Phys Chem B       Date:  2009-01-29       Impact factor: 2.991

4.  Isobaric-isothermal molecular dynamics simulations utilizing density functional theory: an assessment of the structure and density of water at near-ambient conditions.

Authors:  Jochen Schmidt; Joost VandeVondele; I-F William Kuo; Daniel Sebastiani; J Ilja Siepmann; Jürg Hutter; Christopher J Mundy
Journal:  J Phys Chem B       Date:  2009-09-03       Impact factor: 2.991

5.  A multistate empirical valence bond model for solvation and transport simulations of OH- in aqueous solutions.

Authors:  Ivan S Ufimtsev; Andrey G Kalinichev; Todd J Martinez; R James Kirkpatrick
Journal:  Phys Chem Chem Phys       Date:  2009-08-27       Impact factor: 3.676

6.  Communication: The effect of dispersion corrections on the melting temperature of liquid water.

Authors:  Soohaeng Yoo; Sotiris S Xantheas
Journal:  J Chem Phys       Date:  2011-03-28       Impact factor: 3.488

Review 7.  Computer simulation of proton solvation and transport in aqueous and biomolecular systems.

Authors:  Gregory A Voth
Journal:  Acc Chem Res       Date:  2006-02       Impact factor: 22.384

8.  Multiscale coarse-graining and structural correlations: connections to liquid-state theory.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Gregory A Voth
Journal:  J Phys Chem B       Date:  2007-03-30       Impact factor: 2.991

9.  Systematic coarse-graining of a multicomponent lipid bilayer.

Authors:  Lanyuan Lu; Gregory A Voth
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

10.  The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models.

Authors:  W G Noid; Jhih-Wei Chu; Gary S Ayton; Vinod Krishna; Sergei Izvekov; Gregory A Voth; Avisek Das; Hans C Andersen
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

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  23 in total

1.  Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase.

Authors:  Ruibin Liang; Jessica M J Swanson; Mårten Wikström; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-23       Impact factor: 11.205

2.  Reactive molecular dynamics models from ab initio molecular dynamics data using relative entropy minimization.

Authors:  Christopher Arntsen; Chen Chen; Gregory A Voth
Journal:  Chem Phys Lett       Date:  2017-04-22       Impact factor: 2.328

3.  Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale.

Authors:  Chenghan Li; Zhi Yue; L Michel Espinoza-Fonseca; Gregory A Voth
Journal:  Biophys J       Date:  2020-08-06       Impact factor: 4.033

4.  Acid activation mechanism of the influenza A M2 proton channel.

Authors:  Ruibin Liang; Jessica M J Swanson; Jesper J Madsen; Mei Hong; William F DeGrado; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-24       Impact factor: 11.205

5.  Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data.

Authors:  Chen Chen; Christopher Arntsen; Gregory A Voth
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

6.  Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase.

Authors:  Ruibin Liang; Jessica M J Swanson; Yuxing Peng; Mårten Wikström; Gregory A Voth
Journal:  Proc Natl Acad Sci U S A       Date:  2016-06-23       Impact factor: 11.205

7.  Computationally Efficient Multiconfigurational Reactive Molecular Dynamics.

Authors:  Takefumi Yamashita; Yuxing Peng; Chris Knight; Gregory A Voth
Journal:  J Chem Theory Comput       Date:  2012-12-11       Impact factor: 6.006

8.  Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter.

Authors:  Sangyun Lee; Jessica M J Swanson; Gregory A Voth
Journal:  Biophys J       Date:  2016-03-29       Impact factor: 4.033

9.  Understanding and Tracking the Excess Proton in Ab Initio Simulations; Insights from IR Spectra.

Authors:  Chenghan Li; Jessica M J Swanson
Journal:  J Phys Chem B       Date:  2020-06-24       Impact factor: 2.991

10.  Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules.

Authors:  Zhi Yue; Chenghan Li; Gregory A Voth; Jessica M J Swanson
Journal:  J Am Chem Soc       Date:  2019-08-16       Impact factor: 15.419

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