相关论文: A Bell-Evans-Polanyi principle for molecular dynam…
In a series of essays, beginning with this article, we are going to develop a new formulation of micro-phenomena based on the principles of reality and causality. The new theory provides with us a new depiction of micro-phenomena assuming…
Most biochemical reactions in living cells are open systems interacting with environment through chemostats to exchange both energy and materials. At a mesoscopic scale, the number of each species in those biochemical reactions can be…
Theoretical design of global optimization algorithms can profitably utilize recent statistical mechanical treatments of potential energy surfaces (PES's). Here we analyze the basin-hopping algorithm to explain its success in locating the…
A mean-field model to describe electron transfer processes in ion-molecule collisions at the $\hbar =0$ level is presented and applied to collisions involving water and ammonia molecules. Multicenter model potentials account for the…
The energy-minimization multiscale (EMMS) principle of compromise in competition is believed to be generally applicable for all mesoscale problems at different levels in the real world, spanning from elementary particles to the universe.…
The predictive ability of stochastic chemical reactions is currently limited by the lack of closed form solutions to the governing chemical master equation. To overcome this limitation, this paper proposes a computational method capable of…
This paper presents a global optimization approach to quantum mechanics, which describes the most fundamental dynamics of the universe. It suggests that the wave-like behavior of (sub)atomic particles could be the critical characteristic of…
Within the mode-coupling theory for ideal glass-transitions, the mean-squared displacement and the correlation function for density fluctuations are evaluated for a colloidal liquid of particles interacting with a square-well potential for…
Extensive studies on thin films indicated a generic cubic current-voltage $I-V$ dependence as a salient feature of charge transport by tunneling. A quick glance at $I-V$ data for molecular junctions suggests a qualitatively similar…
Reaction-diffusion equations are widely used as the governing evolution equations for modeling many physical, chemical, and biological processes. Here we derive reaction-diffusion equations to model transport with reactions on a…
The thermal activation process by which a system passes from one local energy minimum to another is a recurring motif in physics, chemistry, and biology. For instance, biopolymer chains are typically modeled in terms of energy landscapes,…
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,…
Biological systems fundamentally exist out of equilibrium in order to preserve organized structures and processes. Many changing cellular conditions can be represented as transitions between nonequilibrium steady states, and organisms have…
We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are…
Dynamic properties of molecular motors whose motion is powered by interactions with specific lattice bonds are studied theoretically with the help of discrete-state stochastic "burnt-bridge" models. Molecular motors are depicted as random…
In this paper we compute quantum trajectories arising from Bohm's causal description of quantum mechanics. Our computational methodology is based upon a finite-element moving least-squares method (MWLS) presented recently by Wyatt and…
The transport behavior of a system of gravitationally driven colloidal particles is investigated. The particle interactions are determined by the superparamagnetic behavior of the particles. They can thus be arranged in a crystalline order…
Aim of this note is to analyse branching Brownian motion within the class of models introduced in the recent paper [4] and called chemical diffusion master equations. These models provide a description for the probabilistic evolution of…
All living cells transport molecules and ions across membranes, often against concentration gradients. This active transport requires continual energy expenditure and is clearly a nonequilibrium process for which standard equilibrium…
A generalization of the Gibbs entropy postulate is proposed based on the BBGKY hierarchy as the nonequilibrium entropy for a system of N interacting particles. This entropy satisfies the basic principles of thermodynamics in the sense that…