Related papers: A Bell-Evans-Polanyi principle for molecular dynam…
In this work, a many-body potential of Nb for radiation damage simulation was developed based on EAM, and most of the point defects of Nb can be predicted properly by this potential. By using the constructed potential, the…
Molecular motors convert chemical energy into mechanical work while operating in an environment dominated by Brownian motion. The aim of this paper is to explore the flow of energy between the molecular motors and its surroundings, in…
Individual components such as cells, particles, or agents within a larger system often require detailed understanding of their relative position to act accordingly, enabling the system as a whole to function in an organised and efficient…
We study merchant energy production modeled as a compound switching and timing option. The resulting Markov decision process is intractable. State-of-the-art approximate dynamic programming methods applied to realistic instances of this…
In mechanics, common energy principles are based on fixed boundary conditions. However, in bridge engineering structures, it is usually necessary to adjust the boundary conditions to make the structure's internal force reasonable and save…
Knowing if an optimal solution is local or global has always been a hard question to answer in more sophisticated situations of optimization problems. In this work, for finite-time and weak isothermal driving processes, we show the…
Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze a particular method to explain its success in locating global minima…
Travelling wave solutions of reaction-diffusion equations are widely used to model the spatial spread of populations and other phenomena in biology and physics. In this article, we reinterpret the classical variational principle approach…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Molecular optimization in drug discovery aims to discover molecules with improved target properties, but practical lead optimization often requires more than high predicted scores. A useful candidate should also be actionable: it should be…
In chemical or physical reaction dynamics, it is essential to distinguish precisely between reactants and products for all time. This task is especially demanding in time-dependent or driven systems because therein the dividing surface (DS)…
In the stochastic formulation of chemical kinetics, the stationary moments of the population count of species can be described via a set of linear equations. However, except for some specific cases such as systems with linear reaction…
Under temperature oscillation, cyclic molecular machines such as catalysts and enzymes could harness energy from the oscillatory bath and use it to drive other processes. Using a novel geometrical approach, under fast temperature…
We have a general knowledge of the principles by which catalysts accelerate the rate of chemical reactions but no precise understanding of the geometrical and physical constraints to which their design is subject. To analyze these…
The Poisson-Boltzmann equation is often presented via a variational formulation based on the electrostatic potential. However, the functional has the defect of being non-convex. It can not be used as a local minimization principle while…
L\'evy walks are continuous time random walks with spatio-temporal coupling of jump lengths and waiting times, often used to model superdiffusive spreading processes such as animals searching for food, tracer motion in weakly chaotic…
A new concept of the molecular structure optimization method based on quantum dynamics computations is presented. Nuclei are treated as quantum mechanical particles, as are electrons, and the many-body wave function of the system is…
Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant…
We develop a microscopic approach to the kinetic theory of many-particle systems with dissipative and potential interactions in presence of active fluctuations. The approach is based on a generalization of Bogolyubov--Peletminsky reduced…
We show that molecular dynamics based moves in the Minima Hopping (MH) method are more efficient than saddle point crossing moves which select the lowest possible saddle point. For binary systems we incorporate identity exchange moves in a…