Related papers: Excluded volume effects in on- and off-lattice rea…
We propose a computational method to simulate anomalous self-diffusion in a simple liquid. The method is based on a molecular dynamics simulation on which we impose the following two conditions: firstly, the inter-particle interaction is…
We provide an overview of Monte Carlo algorithms based on Markovian stochastic dynamics of interacting and reacting many-particle systems not in thermal equilibrium. These agent-based simulations are an effective way of introducing students…
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding.…
Experiments have shown that self-propelled particles can slide along the surface of a circular obstacle without becoming trapped over long times. Using simulations and theory, we study the impact of boundary conditions on the diffusive…
Domain growth is a key process in many areas of biology, including embryonic development, the growth of tissue, and limb regeneration. As a result, mechanisms for incorporating it into traditional models for cell movement, interaction, and…
We investigate finite-size effects on diffusion in confined fluids using molecular dynamics simulations and hydrodynamic calculations. Specifically, we consider a Lennard-Jones fluid in slit pores without slip at the interface and show that…
Pattern formation in reaction-diffusion systems is of great importance in surface micro-patterning [Grzybowski et al. Soft Matter. 1, 114 (2005)], self-organization of cellular micro-organisms [Schulz et al. Annu. Rev. Microbiol. 55, 105…
Models invoking the chemical master equation are used in many areas of science, and, hence, their simulation is of interest to many researchers. The complexity of the problems at hand often requires considerable computational power, so a…
Gradient-driven diffusion in crowded, multicomponent mixtures is a topic of high interest because of its role in biological processes such as transport in cell membranes. In partially phase-separated solutions, gradient-driven diffusion…
Drift-diffusion plasma fluid models are commonly used to simulate electric discharges. Such models can computationally be very efficient if they are combined with explicit time integration. This paper deals with two issues that often arise…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
We present a dynamic model in which the weights are conditioned on an input sample x and are learned to match those that would be obtained by finetuning a base model on x and its label y. This mapping between an input sample and network…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
A one dimensional lattice model is formulated to study tapping dynamics and the long time steady distribution in granular media. The dynamics conserves the number of particles in the system, and density changes are associated to the…
The hydrodynamic effects of macromolecular crowding inside cells is often studied in vitro by using polymers as crowding reagents. Confinement of polymers inside cell-sized droplets has been shown to affect the diffusion of small molecules.…
This paper establishes existence, uniqueness, and an L^1-comparison principle for weak solutions of a PDE system modeling phase transition reaction-diffusion in congested crowd motion. We consider a general reaction term and mixed…
Physical systems with complex unsteady dynamics, such as fluid flows, are often poorly represented by a single mean solution. For many practical applications, it is crucial to access the full distribution of possible states, from which…
This study presents an innovative direct numerical simulation approach for complex particle systems with irregular shapes and large numbers. Using partially saturated methods, it accurately models arbitrary shapes, albeit at considerable…
In this work we discuss a modified version of Excluded Volume Hadron Resonance Gas model and also study the effect of Lorentz contraction of the excluded volume on scaled pressure and susceptibilities of conserved charges. We find that the…
The effects of particle discreteness in N-body simulations of Lambda Cold Dark Matter (LambdaCDM) are still an intensively debated issue. In this paper we explore such effects, taking into account the scatter caused by the randomness of the…