Direct generation of loop-erased transition paths in non-equilibrium reactions

2016 ◽  
Vol 195 ◽  
pp. 443-468 ◽  
Author(s):  
Ralf Banisch ◽  
Eric Vanden-Eijnden

A computational procedure is proposed to generate directly loop-erased transition paths in the context of non-equilibrium reactions, i.e. reactions that occur in systems whose dynamics is not in detailed balance. The procedure builds on results from Transition Path Theory (TPT), and it avoids altogether the need to generate reactive trajectories, either by brute-force calculations or using importance sampling schemes such as Transition Path Sampling (TPS). This is computationally advantageous since these reactive trajectories can themselves be very long and intricate in complex reactions. The loop-erased transition paths, on the other hand, are shorter and simpler because, by construction, they are pruned of all the detours typical reactive trajectories make and contain only their productive pieces that carry the effective current of the reaction. As a result they give direct access to the reaction rate and mechanism.

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Federico S. Gnesotto ◽  
Grzegorz Gradziuk ◽  
Pierre Ronceray ◽  
Chase P. Broedersz

Abstract Time-lapse microscopy imaging provides direct access to the dynamics of soft and living systems. At mesoscopic scales, such microscopy experiments reveal intrinsic thermal and non-equilibrium fluctuations. These fluctuations, together with measurement noise, pose a challenge for the dynamical analysis of these Brownian movies. Traditionally, methods to analyze such experimental data rely on tracking embedded or endogenous probes. However, it is in general unclear, especially in complex many-body systems, which degrees of freedom are the most informative about their non-equilibrium nature. Here, we introduce an alternative, tracking-free approach that overcomes these difficulties via an unsupervised analysis of the Brownian movie. We develop a dimensional reduction scheme selecting a basis of modes based on dissipation. Subsequently, we learn the non-equilibrium dynamics, thereby estimating the entropy production rate and time-resolved force maps. After benchmarking our method against a minimal model, we illustrate its broader applicability with an example inspired by active biopolymer gels.


2020 ◽  
Vol 33 (8) ◽  
pp. 2133-2145 ◽  
Author(s):  
Nikolay A. ELISOV ◽  
Sergey A. ISHKOV ◽  
Igor A. LOMAKA ◽  
Valentin G. SHAKHOV

2020 ◽  
Vol 30 (6) ◽  
pp. 3321-3366
Author(s):  
Luzie Helfmann ◽  
Enric Ribera Borrell ◽  
Christof Schütte ◽  
Péter Koltai

Abstract Given two distinct subsets A, B in the state space of some dynamical system, transition path theory (TPT) was successfully used to describe the statistical behavior of transitions from A to B in the ergodic limit of the stationary system. We derive generalizations of TPT that remove the requirements of stationarity and of the ergodic limit and provide this powerful tool for the analysis of other dynamical scenarios: periodically forced dynamics and time-dependent finite-time systems. This is partially motivated by studying applications such as climate, ocean, and social dynamics. On simple model examples, we show how the new tools are able to deliver quantitative understanding about the statistical behavior of such systems. We also point out explicit cases where the more general dynamical regimes show different behaviors to their stationary counterparts, linking these tools directly to bifurcations in non-deterministic systems.


Author(s):  
Marco A. Cruz-de la Rosa ◽  
Roberto Quezada

We study detailed balance and non-equilibrium steady states of a Markov generator of weak coupling limit type, modeling absorption and simultaneous emission of [Formula: see text]- and [Formula: see text]-photons, with [Formula: see text]. In the case [Formula: see text], under natural constraints on the absorption and emission rates, there exist infinitely many non-equilibrium steady states which are convex linear combination of even and odd states.


2012 ◽  
Vol 1383 ◽  
Author(s):  
Massimiliano Picciani ◽  
Manuel Athènes ◽  
Mihai-Cosmin Marinica

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.


2015 ◽  
Vol 137 (8) ◽  
pp. 3041-3050 ◽  
Author(s):  
Tang-Qing Yu ◽  
Mauro Lapelosa ◽  
Eric Vanden-Eijnden ◽  
Cameron F. Abrams

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