Related papers: Explicit formulas for reaction probability in reac…
Motivation: The design of enzymes is as challenging as it is consequential for making chemical synthesis in medical and industrial applications more efficient, cost-effective and environmentally friendly. While several aspects of this…
We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of…
The concept of an active zone in Laplacian transport is used to obtain an analytical approximation for the reactive effectiveness of a pore with an arbitrary rough geometry. We show that this approximation is in very good agreement with…
In this paper we consider the problem of calculating the quantiles of a risky position, the dynamic of which is described as a continuous time regime-switching jump-diffusion, by using Fourier Transform methods. Furthermore, we study a…
This is a study of localised structures in one-dimensional cellular automata, with the elementary cellular automaton Rule 54 as a guiding example. A formalism for particles on a periodic background is derived, applicable to all…
We consider a process in which there are p-species of particles, i.e. A_1,A_2,...,A_p, on an infinite one-dimensional lattice. Each particle $A_i$ can diffuse to its right neighboring site with rate $D_i$, if this site is not already…
In many biological situations, a species arriving from a remote source diffuses in a domain confined between two parallel surfaces until it finds a binding partner. Since such a geometric shape falls in between two- and three-dimensional…
We present a procedure for the determination of the interaction potential from the knowledge of the radial pair distribution function. The method, realized inside an inverse Monte Carlo simulation scheme, is based on the application of the…
This paper proposes to use probabilistic model checking to synthesize optimal robot policies in multi-tasking autonomous systems that are subject to human-robot interaction. Given the convincing empirical evidence that human behavior can be…
We investigate the diffusive motion of an overdamped classical particle in a 1D random potential using the mean first-passage time formalism and demonstrate the efficiency of this method in the investigation of the large-time dynamics of…
A computer program is presented aiming at the calculation of bound and continuum states, reduced transition probabilities, phase-shifts, photo-disintegration cross sections, radiative capture cross sections, and astrophysical S-factors, for…
In the recent years, high energy physics discoveries have been driven by the increasing of luminosity and/or detector granularity. This evolution gives access to bigger statistics and data samples, but can make it hard to process results…
Finding representative reaction pathways is necessary for understanding mechanisms of molecular processes, but is considered to be extremely challenging. We propose a new method to construct reaction paths based on mean first-passage times.…
The diffusion of particles trapped in long narrow channels occurs predominantly in one dimension. Here, molecular dynamics simulation is used to study the inertial dynamics of two-dimensional hard disks, confined to long, narrow,…
The diffusion of finite-size hard-core interacting particles in two- or three-dimensional confined domains is considered in the limit that the confinement dimensions become comparable to the particle's dimensions. The result is a nonlinear…
The emission of multi-MeV ($\gamma$-ray) photons from the interaction of a high-powered laser pulse with a dense plasma target is studied using particle-in-cell simulations. A new set of diagnostic techniques is presented and applied to…
Systems switching between different dynamical phases is an ubiquitous phenomenon. The general understanding of such a process is limited. To this end, we present a general expression that captures fluctuations of a system exhibiting a…
We study front propagation in the reversible reaction-diffusion system A + A <-> A on a 1-d lattice. Extending the idea of leading particle in studying the motion of the front we write a master equation in the stochastically moving frame…
Accurately modeling chemical reactions at the atomistic level requires high-level electronic structure theory due to the presence of unpaired electrons and the need to properly describe bond breaking and making energetics. Commonly used…
We consider two particles performing continuous-time nearest neighbor random walk on $\mathbb Z$ and interacting with each other when they are at neighboring positions. Typical examples are two particles in the partial exclusion process or…