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We undertake a detailed analysis of a reaction-advection-diffusion (RAD) equation from the viewpoint of pulse-response studies, with particular attention to effects due to the advection velocity. Our boundary-value problem is a mathematical…
We develop an analytical diffusion-equation-type approximation scheme for the one-dimensional coagulation reaction A+A->A with partial reaction probability on particle encounters which are otherwise hard-core. The new approximation…
Energy barriers for different moves of a single Rh adatom in the vicinity of steps on Rh(111) surface are studied with molecular statics. Interatomic interactions are modeled by the semi-empirical many-body Rosato-Guillope-Legrand…
Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events…
We present a real-time path integral theory for the rate of electron transfer reactions. Using graph theoretic techniques, the dynamics is expressed in a formally exact way as a set of integral equations. With a simple approximation for the…
Calculations of the diffusion of a Au adatom on the dimer reconstructed Si(100)-2x1 surface reveal an interesting mechanism that differs significantly from a direct path between optimal binding sites, which are located in between dimer…
The transport equation of active motion is generalised to consider time-fractional dynamics for describing the anomalous diffusion of self-propelled particles observed in many different systems. In the present study, we consider an…
The surface diffusion of Cu adatoms in the presence of an adisland at FCC or HCP sites on Cu(111) is studied using the EAM potential derived by Mishin {\it et al.} [Phys. Rev. B {\bf 63} 224106 (2001)]. The diffusion rates along straight…
In this paper we consider three classes of interacting particle systems on $\mathbb Z$: independent random walks, the exclusion process, and the inclusion process. We allow particles to switch their jump rate (the rate identifies the type…
Instanton theory is an established method to calculate rate constants of chemical reactions including atom tunneling. Technical and methodological improvements increased its applicability. Still, a large number of energy and gradient…
Using density-functional theory we investigate several properties of Al(111), Al(100), Al(110), and stepped Al(111) surfaces. We report results of formation energies of surfaces, steps, adatoms, and vacancies. For the adsorption and…
A formalism using a double Laplace Fourier transform of the transport equation yields the return probabilities of the vacancy in the vicinity of the tracer atom in the presence of solute-vacancy interactions of arbitrary extension. Studying…
Within the framework of quantization of the macroscopic electromagnetic field, equations of motion and an effective Hamiltonian for treating both the resonant dipole-dipole interaction between two-level atoms and the resonant atom-field…
We present models for prediction of activation energy barrier of diffusion process of adatom (1-4) islands obtained by using data-driven techniques. A set of easily accessible features, geometric and energetic, that are extracted by…
We study the non-Arrhenius behavior of surface diffusion near the second-order phase transition boundary of an adsorbate layer. In contrast to expectations based on macroscopic thermodynamic effects, we show that this behavior can be…
We consider the motion of an underdamped Brownian particle in a tilted periodic potential in a wide temperature range. Based on the previous data [1] and the new simulation results we show that the underdamped motion of particles in…
Biomolecular folding, at least in simple systems, can be described as a two state transition in a free energy landscape with two deep wells separated by a high barrier. Transition paths are the short part of the trajectories that cross the…
We introduce a rigorous method to microscopically compute the observables which characterize the thermodynamics and kinetics of rare macromolecular transitions for which it is possible to identify a priori a slow reaction coordinate. In…
The acceleration of charged particles (electrons and protons) in flaring solar active regions is analyzed by numerical experiments. The acceleration is modelled as a stochastic process taking place by the interaction of the particles with…
Atomic diffusion is usually understood as a succession of random, independent displacements of an adatom over the surface's potential energy landscape. Nevertheless, an analysis of Molecular Dynamics simulations of self-diffusion on Cu(111)…