Coordination numbers as reaction coordinates in constrained molecular dynamics

1998 ◽  
Vol 110 ◽  
pp. 437-445 ◽  
Author(s):  
Michiel Sprik
Keyword(s):  
Molecular Dynamics ◽  
Coordination Numbers ◽  
Reaction Coordinates

scholarly journals Studies of the molecular dynamics in polyurethane networks with hyperbranched crosslinkers of different coordination numbers

2007 ◽  
Vol 105 (1) ◽  
pp. 89-98 ◽  
Author(s):  
Przemyslaw Czech ◽  
Lidia Okrasa ◽  
Jacek Ulanski ◽  
Gisele Boiteux ◽  
Francoise Mechin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Coordination Numbers ◽  
Polyurethane Networks

scholarly journals Low Dimensional Representations along Intrinsic Reaction Coordinates and Molecular Dynamics Trajectories Using Interatomic Distance Matrices

2019 ◽  
Author(s):  
Stephanie Hare ◽  
Lars Bratholm ◽  
David Glowacki ◽  
Barry Carpenter
Keyword(s):  
Molecular Dynamics ◽  
Principal Component Analysis ◽  
Dimensionality Reduction ◽  
Physical Meaning ◽  
Interatomic Distance ◽  
Dimensional Space ◽  
Principal Component ◽  
Reaction Pathways ◽  
Reaction Coordinates ◽  
Low Dimensional

Low dimensional representations along reaction pathways were produced using newly created Python software that utilises Principal Component Analysis (PCA) to do dimensionality reduction. Plots of these pathways in reduced dimensional space, as well as the physical meaning of the reduced dimensional axes, are discussed.

scholarly journals Atomistic Nodal Approach: a General Molecular Dynamics Method For Computing Local Thermal Conductance at Atomistic Resolution

2021 ◽  
Author(s):  
Mingxuan Jiang ◽  
Juan D. Olarte-Plata ◽  
Fernando Bresme
Keyword(s):  
Molecular Dynamics ◽  
Thermal Transport ◽  
Temperature Drop ◽  
Thermal Conductance ◽  
Fundamental Property ◽  
Lower Surface ◽  
Coordination Numbers ◽  
Interfacial Thermal Conductance ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations

The Interfacial Thermal Conductance (ITC) is a fundamental property of mate- rials and has particular relevance at the nanoscale. The ITC quanti�es the thermal resistance between materials of dierent compositions or between uids in contact with materials. Furthermore, the ITC determines the rate of cooling/heating of the materi- als and the temperature drop across the interface. Here we propose a method to com- pute local ITCs and temperature drops of nanoparticle- uid interfaces. Our approach resolves the ITC at the atomic level using the atomic coordinates of the nanomaterial as nodes to compute local thermal transport properties. We obtain high-resolution descriptions of the interfacial thermal transport by combining the atomistic nodal ap- proach, computational geometry techniques and \computational farming" using Non- Equilibrium Molecular Dynamics simulations. We illustrate our method by analyzing various nanoparticles as a function of their size and geometry, targeting experimentally relevant structures like capped octagonal rods, cuboctahedrons, decahedrons, rhombic dodecahedrons, cubes, icosahedrons, truncated octahedrons, octahedrons and spheres. We show that the ITC of these very dierent geometries can be accurately described in terms of the local coordination number of the atoms in the nanoparticle surface. Nanoparticle geometries with lower surface coordination numbers feature higher ITCs, and the ITC generally increases with decreasing particle size.

scholarly journals Boltzmann generators: Sampling equilibrium states of many-body systems with deep learning

Science ◽  
2019 ◽  
Vol 365 (6457) ◽  
pp. eaaw1147 ◽  
Author(s):  
Frank Noé ◽  
Simon Olsson ◽  
Jonas Köhler ◽  
Hao Wu
Keyword(s):  
Molecular Dynamics ◽  
Deep Learning ◽  
Statistical Mechanics ◽  
Equilibrium Distribution ◽  
Condensed Matter ◽  
Computational Effort ◽  
Equilibrium States ◽  
Many Body ◽  
Reaction Coordinates ◽  
Many Body Systems

Computing equilibrium states in condensed-matter many-body systems, such as solvated proteins, is a long-standing challenge. Lacking methods for generating statistically independent equilibrium samples in “one shot,” vast computational effort is invested for simulating these systems in small steps, e.g., using molecular dynamics. Combining deep learning and statistical mechanics, we developed Boltzmann generators, which are shown to generate unbiased one-shot equilibrium samples of representative condensed-matter systems and proteins. Boltzmann generators use neural networks to learn a coordinate transformation of the complex configurational equilibrium distribution to a distribution that can be easily sampled. Accurate computation of free-energy differences and discovery of new configurations are demonstrated, providing a statistical mechanics tool that can avoid rare events during sampling without prior knowledge of reaction coordinates.

Ion Hydration Under Pressure: A Molecular Dynamics Study

2013 ◽  
Vol 68 (1-2) ◽  
pp. 112-122 ◽  
Author(s):  
Maksym Druchok ◽  
Myroslav Holovko
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solutions ◽  
Dynamic Properties ◽  
Ion Hydration ◽  
Coordination Numbers ◽  
Self Diffusion ◽  
Velocity Autocorrelation ◽  
Hydration Behaviour ◽  
Hydration Shells ◽  
Dynamics Simulations

This study is intended to elucidate the role of pressure on the hydration behaviour of ions in aqueous solutions. Molecular dynamics simulations were performed for systems modelling CsF, CsCl, CsBr, and CsI aqueous solutions under ‘normal’ (105 Pa, 298 K) and ‘high pressure’ (4 ·109 Pa, 500 K) conditions. Structural details are discussed in terms of radial distributions functions, coordination numbers, and instantaneous configurations of the ionic hydration shells. The dynamic properties studied include the velocity autocorrelation functions and self-diffusion coefficients of the ions for both pressure regimes. The results indicate strong changes in the hydration behaviour and mobility of the ions.

Structural and Dynamical Correlations in Stishovite and High Density Silica Glass

1992 ◽  
Vol 293 ◽  
Author(s):  
Wei Jin ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Density Of States ◽  
Silica Glass ◽  
Bond Angle ◽  
Diffraction Peak ◽  
Static Structure Factor ◽  
Static Structure ◽  
Coordination Numbers ◽  
Intermediate Range Order ◽  
Vibrational Density

AbstractPressure-induced structural transformation from tetrahedral to octahedral coordination and the destruction of intermediate-range order (IRO) are studied in silica glass (a-SiO 2) using the molecular-dynamics (MD) method. Changes in the position and height of the first sharp diffraction peak (FSDP) in the static structure factor, bond lengths, coordination numbers, bond-angle distributions, and statistics of rings are investigated as a function of density. Modifications of the vibrational density of states and participation ratio are also discussed.

STRUCTURE AND DYNAMICAL PROPERTIES OF AuN, N = 12–14 CLUSTERS: MOLECULAR DYNAMICS SIMULATION

2005 ◽  
Vol 16 (01) ◽  
pp. 99-116 ◽  
Author(s):  
ERDEM K. YILDIRIM ◽  
MURAT ATİŞ ◽  
ZİYA B. GÜVENÇ
Keyword(s):  
Molecular Dynamics ◽  
Thermal Quenching ◽  
Melting Behavior ◽  
Dynamics Simulation ◽  
Embedded Atom Method ◽  
Coordination Numbers ◽  
Embedded Atom ◽  
Long Time ◽  
Time Average ◽  
Short Time

Using molecular dynamics and thermal quenching methods on the basis of Voter–Chen version of the embedded-atom method, we have studied the melting behavior of Au N (N = 12, 13, 14) clusters. This behavior is described in terms of overall and atom resolved root-mean-square bond-length fluctuations, specific-heat, short- and long-time average coordination numbers of each atom and short-time average temperatures of the clusters. The isomer sampling probabilities are obtained from the thermal quenching of the molten clusters, and their energy-spectrum widths are investigated. Phase change of a cluster takes place with the collective and simultaneous motion of all the atoms.

scholarly journals Comparing state-of-the-art approaches to back-calculate SAXS spectra from atomistic molecular dynamics simulations

2021 ◽  
Vol 94 (9) ◽  
Author(s):  
Mattia Bernetti ◽  
Giovanni Bussi
Keyword(s):  
Molecular Dynamics ◽  
Solvent Effects ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Implicit Solvent ◽  
Remarkable Effect ◽  
Rna Molecules ◽  
Reaction Coordinates ◽  
Effective Instrument ◽  
Dynamics Simulations

Abstract Small-angle X-ray scattering (SAXS) experiments are arising as an effective instrument in the structural characterization of biomolecules in solution. However, they suffer from limited resolution, and complementing them with molecular dynamics (MD) simulations can be a successful strategy to obtain information at a finer scale. To this end, tools that allow computing SAXS spectra from MD-sampled structures have been designed over the years, mainly differing in how the solvent contribution is accounted for. In this context, RNA molecules represent a particularly challenging case, as they can have a remarkable effect on the surrounding solvent. Herein, we provide a comparison of SAXS spectra computed through different available software packages for a prototypical RNA system. RNA conformational dynamics is intentionally neglected so as to focus on solvent effects. The results highlight that solvent effects are important also at relatively low scattering vector, suggesting that approaches explicitly modeling solvent contribution are advisable when comparing with experimental data, while more efficient implicit-solvent methods can be a better choice as reaction coordinates to improve MD sampling on-the-fly. Graphic abstract

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