scholarly journals A multiple replica approach to simulate reactive trajectories

2011 ◽  
Vol 134 (5) ◽  
pp. 054108 ◽  
Author(s):  
Frédéric Cérou ◽  
Arnaud Guyader ◽  
Tony Lelièvre ◽  
David Pommier
Keyword(s):  
Reactive Trajectories ◽  
Replica Approach

Active Learning Accelerates Ab Initio Molecular Dynamics on Pericyclic Reactive Energy Surfaces

2020 ◽  
Author(s):  
Shi Jun Ang ◽  
Wujie Wang ◽  
Daniel Schwalbe-Koda ◽  
Simon Axelrod ◽  
Rafael Gomez-Bombarelli
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy ◽  
Transition State ◽  
Potential Energy Surface ◽  
Ab Initio ◽  
Energy Surface ◽  
Computational Cost ◽  
Reactive Trajectories ◽  
Dynamics Simulations ◽  
Energy Surfaces

<div>Modeling dynamical effects in chemical reactions, such as post-transition state bifurcation, requires <i>ab initio</i> molecular dynamics simulations due to the breakdown of simpler static models like transition state theory. However, these simulations tend to be restricted to lower-accuracy electronic structure methods and scarce sampling because of their high computational cost. Here, we report the use of statistical learning to accelerate reactive molecular dynamics simulations by combining high-throughput ab initio calculations, graph-convolution interatomic potentials and active learning. This pipeline was demonstrated on an ambimodal trispericyclic reaction involving 8,8-dicyanoheptafulvene and 6,6-dimethylfulvene. With a dataset size of approximately</div><div>31,000 M062X/def2-SVP quantum mechanical calculations, the computational cost of exploring the reactive potential energy surface was reduced by an order of magnitude. Thousands of virtually costless picosecond-long reactive trajectories suggest that post-transition state bifurcation plays a minor role for the reaction in vacuum. Furthermore, a transfer-learning strategy effectively upgraded the potential energy surface to higher</div><div>levels of theory ((SMD-)M06-2X/def2-TZVPD in vacuum and three other solvents, as well as the more accurate DLPNO-DSD-PBEP86 D3BJ/def2-TZVPD) using about 10% additional calculations for each surface. Since the larger basis set and the dynamic correlation capture intramolecular non-covalent interactions more accurately, they uncover longer lifetimes for the charge-separated intermediate on the more accurate potential energy surfaces. The character of the intermediate switches from entropic to thermodynamic upon including implicit solvation effects, with lifetimes increasing with solvent polarity. Analysis of 2,000 reactive trajectories on the chloroform PES shows a qualitative agreement with the experimentally-reported periselectivity for this reaction. This overall approach is broadly applicable and opens a door to the study of dynamical effects in larger, previously-intractable reactive systems.</div>

scholarly journals Static replica approach to critical correlations in glassy systems

2013 ◽  
Vol 138 (12) ◽  
pp. 12A540 ◽  
Author(s):  
Silvio Franz ◽  
Hugo Jacquin ◽  
Giorgio Parisi ◽  
Pierfrancesco Urbani ◽  
Francesco Zamponi
Keyword(s):  
Glassy Systems ◽  
Replica Approach

Barriers and metastable states as saddle points in the replica approach

1993 ◽  
Vol 3 (8) ◽  
pp. 1819-1838 ◽  
Author(s):  
J. Kurchan ◽  
G. Parisi ◽  
M. A. Virasoro
Keyword(s):  
Saddle Points ◽  
Metastable States ◽  
Replica Approach

Calculation of migration rates of vacancies and divacancies in α-Iron using transition path sampling biased with a Lyapunov indicator

2012 ◽  
Vol 1383 ◽  
Author(s):  
Massimiliano Picciani ◽  
Manuel Athènes ◽  
Mihai-Cosmin Marinica
Keyword(s):  
Time Scales ◽  
Reaction Rates ◽  
Model Potential ◽  
Analysis Tool ◽  
Path Sampling ◽  
Transition Path ◽  
Stable States ◽  
Transition Path Sampling ◽  
Reaction Rate Constants ◽  
Reactive Trajectories

ABSTRACTPredicting the microstructural evolution of radiation damage in materials requires handling the physics of infrequent-events, in which several time scales are involved. The reactions rates characterizing these events are the main ingredient for simulating the kinetics of materials under irradiation over large time scales and high irradiation doses. We propose here an efficient, finite temperature method to compute reaction rate constants of thermally activated processes. The method consists of two steps. Firstly, rare reactive trajectories in phase-space are sampled using a transition path sampling (TPS) algorithm supplemented with a local Lyapunov bias favoring diverging trajectories. This enables the system to visit transition regions separating stable configurations more often, and thus enhances the probability of observing transitions between stable states during relatively short simulations. Secondly, reaction constants are estimated from the unbiased fraction of reactive trajectories, yielded by an appropriate statistical data analysis tool, the multistate Bennett acceptance ratio (MBAR) package. We apply our method to the calculation of reaction rates for vacancy and di-vacancy migration in α-Iron crystal, using an Embedded Atom Model potential, for temperatures ranging from 300 K to 800 K.

Thermodynamic non-additivity in disordered systems with extended phase space

Open Physics ◽  
2004 ◽  
Vol 2 (2) ◽  
Author(s):  
Eduard Vakarin ◽  
Jean Badiali
Keyword(s):  
Phase Space ◽  
Probability Distribution ◽  
Disordered Systems ◽  
Stochastic Systems ◽  
Extended Phase Space ◽  
Extended Phase ◽  
Thermodynamic Entropy ◽  
Dynamic Stochastic ◽  
Replica Approach ◽  
Dynamic Subsystem

AbstractNon-additivity effects in coupled dynamic-stochastic systems are investigated. It is shown that there is a mapping of the replica approach to disordered systems with finite replica indexn on Tsallis non-extensive statistics, if the average thermodynamic entropy of the dynamic subsystem differs from the information entropy for the probability distribution in the stochastic subsystem. The entropic indexq is determined by the entropy difference ΔS. In the case of incomplete information, the entropic indexq=1−n is shown to be related to the degree of lost information.

scholarly journals Determination of Kinetic Properties in Unimolecular Dissociation of Complex Systems from Graph-Theory Based Analysis of an Ensemble of Reactive Trajectories.

2021 ◽  
Author(s):  
Ariel F. Perez-Mellor ◽  
Riccardo Spezia
Keyword(s):  
Graph Theory ◽  
Complex Systems ◽  
Kinetic Properties ◽  
Unimolecular Dissociation ◽  
Theoretical Mass ◽  
Reactive Trajectories ◽  
Direct Counting ◽  
Dynamics Simulations ◽  
State Kinetic

<div>We describe and apply a general approach based on graph-theory to obtain kinetic and structural properties from direct dynamics simulations. In particular, we focus on the unimolecular fragmentation of complex systems in which, prior to dissociation, different events can take place, and notably isomerizations and formation of ion-molecule complex.</div><div>3-state and 4-state kinetic models are thus obtained and rate constants for global or specific pathways are obtained from direct counting and flux calculation, both being in agreement.<br />Finally, we show how a theoretical mass spectrum can also be obtained automatically.<br /></div>

scholarly journals Replica approach in random matrix theory

2018 ◽  
Author(s):  
Thomas Guhr
Keyword(s):  
Partition Function ◽  
Random Matrix Theory ◽  
Random Matrix ◽  
Matrix Theory ◽  
Field Theories ◽  
Partition Functions ◽  
Gaussian Unitary Ensemble ◽  
Integrable Theory ◽  
Unitary Ensemble ◽  
Replica Approach

This article examines the replica method in random matrix theory (RMT), with particular emphasis on recently discovered integrability of zero-dimensional replica field theories. It first provides an overview of both fermionic and bosonic versions of the replica limit, along with its trickery, before discussing early heuristic treatments of zero-dimensional replica field theories, with the goal of advocating an exact approach to replicas. The latter is presented in two elaborations: by viewing the β = 2 replica partition function as the Toda lattice and by embedding the replica partition function into a more general theory of τ functions. The density of eigenvalues in the Gaussian Unitary Ensemble (GUE) and the saddle point approach to replica field theories are also considered. The article concludes by describing an integrable theory of replicas that offers an alternative way of treating replica partition functions.

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