Related papers: Point-particle method to compute diffusion-limited…
Modeling electronic systems is an important application for quantum computers. In the context of materials science, an important open problem is the computational description of chemical reactions on surfaces. In this work, we outline a…
When calculating the optical absorption spectra of molecular crystals from first principles, the influence of the crystalline environment on the excitations is of significant importance. For such systems, however, methods to describe the…
In this paper, we report a numerical method for analyzing optical radiation from a two-level atom. The proposed method can consistently consider the optical emission and absorption process of an atom, and also the interaction between atoms…
Absorbing boundary condition approach to nuclear breakup reactions is investigated. A key ingredient of the method is an absorbing potential outside the physical area, which simulates the outgoing boundary condition for scattered waves.…
With the rise of service-oriented computing, applications are more and more based on coordination of autonomous services. Envisioned over largely distributed and highly dynamic platforms, expressing this coordination calls for alternative…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
When recording the movement of individual animals, cells or molecules one will often observe changes in their diffusive behaviour at certain points in time along their trajectory. In order to capture the different diffusive modes assembled…
An extended thermal particle boundary condition is devised to more efficiently and accurately model laser-plasma interactions in overdense plasmas. Particle-in-cell simulations of such interactions require many particles per cell, and a…
An analytical soluble model based on a Continuous Time Random Walk (CTRW) scheme for the adsorption-desorption processes at interfaces, called bulk-mediated surface diffusion, is presented. The time evolution of the effective probability…
Light scattering patterns (LSP) of blood platelets were theoretically and experimentally analyzed. We used spicular spheroids as a model for the platelets with pseudopodia. The discrete dipole approximation was employed to simulate light…
We consider the problem of inference for nonlinear, multivariate diffusion processes, satisfying It\^o stochastic differential equations (SDEs), using data at discrete times that may be incomplete and subject to measurement error. Our…
In this paper, we develop an encounter-based model of partial surface adsorption for fractional diffusion in a bounded domain. We take the probability of adsorption to depend on the amount of particle-surface contact time, as specified by a…
Direct numerical simulation of diffusion through heterogeneous media can be difficult due to the computational cost of resolving fine-scale heterogeneities. One method to overcome this difficulty is to homogenize the model by replacing the…
We present a novel immersed boundary method that implements acoustic perturbation theory to model an acoustically levitated droplet. Instead of resolving sound waves numerically, our hybrid method solves acoustic scattering…
Stochastic chemical systems with diffusion are modeled with a reaction-diffusion master equation. On a macroscopic level, the governing equation is a reaction-diffusion equation for the averages of the chemical species. On a mesoscopic…
The analytical solution of the equation describing diffusion of intrinsic point defects has been obtained for a one-dimensional finite-length domain. This solution is intended for investigating and modeling the changes in defect…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
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…
Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics…
The kinetics of collective rearrangements in solution, such as protein folding and nanocrystal phase transitions, often involve free energy barriers that are both long and rough. Applying methods of transition path sampling to harvest…