Related papers: Maximum Flux Transition Paths of Conformational Ch…
We study metastability and nucleation for the Blume-Capel model: a ferromagnetic nearest neighbour two-dimensional lattice system with spin variables taking values in -1,0,+1. We consider large but finite volume, small fixed magnetic field…
Macroscopic fluctuations have become an essential tool to understand physics far from equilibrium due to the link between their statistics and nonequilibrium ensembles. The optimal path leading to a fluctuation encodes key information on…
We consider the junction of multiple one-dimensional systems and study how conserved currents transport at the junction. To characterize the transport process, we introduce reflection/transmission coefficients by applying boundary conformal…
Transition pathways of stochastic dynamical systems are typically approximated by instantons. Here we show, using a dynamical system containing two competing pathways, that at low-to-intermediate temperatures, instantons can fail to capture…
We present a data-driven point of view for rare events, which represent conformational transitions in biochemical reactions modeled by over-damped Langevin dynamics on manifolds in high dimensions. We first reinterpret the transition state…
We investigate the maximum caliber variational principle as an inference algorithm used to predict dynamical properties of complex nonequilibrium, stationary, statistical systems in the presence of incomplete information. Specifically, we…
The committor constitutes the primary quantity of interest within chemical kinetics as it is understood to encode the ideal reaction coordinate for a rare reactive event. We show the generative utility of the committor, in that it can be…
Nonconvexity induced by the nonlinear AC power flow equations challenges solution algorithms for AC optimal power flow (OPF) problems. While significant research efforts have focused on reliably computing high-quality OPF solutions, it is…
The reaction coordinate describing a transition between reactant and product is a fundamental concept in the theory of chemical reactions. Within transition-path theory, a quantitative definition of the reaction coordinate is found in the…
For two canonical examples of driven mesoscopic systems - a harmonically-trapped Brownian particle and a quantum dot - we numerically determine the finite-time protocols that optimize the compromise between the standard deviation and the…
Transition path theory (TPT) offers a powerful formalism for extracting the rate and mechanism of rare dynamical transitions between metastable states. Most applications of TPT either focus on systems with modestly sized state spaces or use…
The steady, coaxial flow in which two immiscible, incompressible fluids move past each other in a cylindrical tube has a continuum of possibilities due to the arbitrariness of the interface between the fluids. By invoking the presence of…
Experimental and empirical observations on cell metabolism cannot be understood as a whole without their integration into a consistent systematic framework. However, the characterization of metabolic flux phenotypes is typically reduced to…
The Maximum Flow Problem with Conflict Constraints is a generalization that adds conflict constraints to a classical optimization problem on networks used to model several real-world applications. In the last few years several approaches,…
Rare transition events in meta-stable systems under noisy fluctuations are crucial for many non-equilibrium physical and chemical processes. In these processes, the primary contributions to reactive flux are predominantly near the…
For a transition between two stable states, the committor is the probability that the dynamics leads to one stable state before the other. It can be estimated from trajectory data by minimizing an expression for the transition rate that…
Biomolecular machines transduce between different forms of energy. These machines make directed progress and increase their speed by consuming free energy, typically in the form of nonequilibrium chemical concentrations. Machine dynamics…
An analysis of the network defined by the potential energy minima of multi-atomic systems and their connectivity via reaction pathways that go through transition states allows to understand important characteristics like thermodynamic,…
We perform a numeric study of the flux transitions in a superconducting ring at fixed temperature, while the applied field is swept at an ideally slow rate. The current around the ring and its free energy are evaluated. We partially explain…
Diffusion of a particle passing over the saddle point of a two-dimensional quadratic potential is studied via a set of coupled Langevin equations and the expression for the passing probability is obtained exactly. The passing probability is…