Molecular Dynamics at Extended Timescales

Elber, Ron; Cárdenas, Alfredo E.

doi:10.1002/ijch.201400015

Cited by 3 publications

(2 citation statements)

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“…Methods to apply MD simulations to small peptides and biological macromolecules are reviewed by Doshi et al ( 76 ). The use of short time trajectory fragments to enhance sampling of kinetics is discussed in the review by Elber et al ( 77 ). These three review articles may be referred to for further information regarding methods, techniques, and theory of how one may apply MD simulations to biological systems.…”

Section: Simulation Methodsmentioning

confidence: 99%

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

2015

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In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

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Section: Simulation Methodsmentioning

confidence: 99%

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

2015

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“…Considering this ratio, we now understand that a "reaction" occurs in a highly infrequent, that is, rare event. 9 In the first decade of the 2000s, many simulation methods were developed to overcome this difficulty, such as generalized ensembles, 10 method of milestoning, 11 metadynamics, 12 transition path sampling, 13 and action-based path sampling, 14 which can deal with chemical reactions in an automatic or semi-automatic manner. Some have succeeded in performing effective statistical sampling 10 or searches for a minimum energy path for an elementary chemical reaction, 12 while others have included dynamical and thermal effects.…”

Section: Introductionmentioning

confidence: 99%

The computational molecular technology for complex reaction systems: The Red Moon approach

Nagaoka

2024

WIREs Comput Mol Sci

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For dealing with complex reaction (CR) systems that show typical chemical phenomena in molecular aggregation states, the Red Moon (RM) approach is introduced based on a new efficient and systematic RM methodology. First, the theoretical background with my motivation to develop the RM approach is presented from the recent necessity to perform ‘atomistic’ molecular simulation of large‐scale and long‐term phenomena of (i) complex chemical reactions, (ii) stereospecificity, and (iii) aggregation structures. The RM methodology uses both the molecular dynamics (MD) method for molecular motions (translation, rotation, and vibration of molecules) that frequently occur on a short‐time scale and the Monte Carlo (MC) method for rare events such as chemical reactions that hardly do on that time scale. Then, under the transition rate using both the potential energy difference before and after a rare event trial and its chemical kinetic probability, it is tested and judged by the MC method whether the trial is possible (Metropolis method). Next, typical applications of the RM approach are reviewed in two main research fields, (i) polymerization and (ii) storage battery (rechargeable battery or secondary cell), with various examples of our successful studies. Finally, we conclude that the RM approach using the RM methodology should become an efficient new‐generation approach as one promising computational molecular strategy (CMT). We believe it will play an essential role in surveying, at the multilevel resolution, various specificities of CR systems in molecular aggregation states.This article is categorized under: Theoretical and Physical Chemistry > Reaction Dynamics and Kinetics Structure and Mechanism > Reaction Mechanisms and Catalysis Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods

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Exploring the Molecular Theory of Complex Reaction Systems Toward a Deeper Understanding of Molecular Science

Nagaoka

2024

Mol. Sci.

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Molecular Dynamics at Extended Timescales

Cited by 3 publications

References 50 publications

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

The computational molecular technology for complex reaction systems: The Red Moon approach

Exploring the Molecular Theory of Complex Reaction Systems Toward a Deeper Understanding of Molecular Science

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