Related papers: A Bell-Evans-Polanyi principle for molecular dynam…

Quasi-steady state reductions for the irreversible Michaelis--Menten reaction mechanism are of interest both from a theoretical and an experimental design perspective. A number of publications have been devoted to extending the parameter…

What is the path associated with the fastest Brownian particle that reaches a narrow window located on the boundary of a domain? Although the distribution of the fastest arrival times has been well studied in dimension 1, much less is known…

For the classical N-body problem, an approach is proposed based on the introduction of some natural in the physical sense optimization problems of mathematical programming for finding a conditional minimum for the characteristics of the…

Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…

Model reduction methods are relevant when the computation time of a full convection-diffusion-reaction simulation based on detailed chemical reaction mechanisms is too large. In this article, we review a model reduction approach based on…

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior…

Optimal prediction approximates the average solution of a large system of ordinary differential equations by a smaller system. We present how optimal prediction can be applied to a typical problem in the field of molecular dynamics, in…

Moment dynamics in stochastic chemical kinetics often involve an infinite chain of coupled equations, where lower-order moments depend on higher-order ones, making them analytically intractable. Moment bounding via semidefinite programming…

This work describes a geometric framework on molecular reaction dynamics based on the variational principle, where the Schr{\"o}dinger equation must be solved to ``see'' how a reaction occurs. First, the mathematical preliminaries are given…

Chemical kinetic models in terms of ordinary differential equations correspond to finite dimensional dissipative dynamical systems involving a multiple time scale structure. Most dimension reduction approaches aimed at a slow…

Discussed in the paper is the possibility of introducing the concept of Brownian motion of various mesoparticles in the ballistic regime. The case in point is the effect of collisions between thermal excitations in the liquid and the test…

Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…

We present a practical method to generate classical trajectories with fixed initial and final boundary conditions. Our method is based on the minimization of a suitably defined discretized action. The method finds its most natural…

The efficiency of minimum-energy configuration searching algorithms is closely linked to the energy landscape structure of complex systems. Here we characterize this structure by following the time evolution of two systems, vacancy…

How systems transit between different stable states under external perturbation is an important practical issue. We discuss here how a recently-developed energy optimization method for identifying the minimal disturbance necessary to reach…

We propose a new mechanism to alter the nature of the potential barriers when a biased Brownian particle under goes a constrained motion in narrow, periodic channel. By changing the angle of the external bias, the nature of the potential…

Owing to the Chapman-Kolmogorov equation for Markovian dynamics,any equilibrium trajectory of a Brownian particle in a solvent fluid can be viewed as the superposition of an uncountable number of non-equilibrium states. This property…

This paper is a continuation of a previous work about the study of the survival probability modelizing the molecular predissociation in the Born-Oppenheimer framework. Here we consider the critical case where the reference energy…

The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…

Bayesian optimization is a methodology to optimize black-box functions. Traditionally, it focuses on the setting where you can arbitrarily query the search space. However, many real-life problems do not offer this flexibility; in…