相关论文: Particle-based simulations of reaction-diffusion p…
The employment of nonlocal PDE models to describe biological aggregation and other phenomena has gained considerable traction in recent years. For cell populations, these methods grant a means of accommodating essential elements such as…
Conventional approaches for simulating steady-state distributions of particles under diffusive and advective transport at high P\'eclet numbers involve solving the diffusion and advection equations in at least two dimensions. Here, we…
Reaction-diffusion systems are used to represent many biological and physical phenomena. They model the random motion of particles (diffusion) and interactions between them (reactions). Such systems can be modelled at multiple scales with…
Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the assignment of partial…
The traditional methods of the biology, based on illustrative descriptions and linear logic explanations, are discussed. This work aims to improve this approach by introducing alternative tools to describe and represent complex biological…
We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially…
Inspired by a PDE-ODE system of aggregation developed in the biomathematical literature, an interacting particle system representing aggregation at the level of individuals is investigated. It is proved that the empirical density of the…
This paper presents a novel approach to the description and understanding of two-dimensional binary cellular automata with the Moore neighborhood that preserve the number of active cells. Such dynamical systems are known to successfully…
Computing reaction rates in biomolecular systems is a common goal of molecular dynamics simulations. The reactions considered often involve conformational changes in the molecule, either changes in the structure of a protein or the relative…
The long time dynamics of polymeric materials has been extensively studied in the past through various experimental techniques and computer simulations. While computer simulations typically treat generic, simplified models, experiments deal…
We propose a stochastic model for intracellular transport processes associated with the activity of molecular motors. This out-of-equilibrium model, based on a generalized Langevin equation, considers a particle immersed in a viscoelastic…
The vast majority of biochemical systems involve the exchange of information between different compartments, either in the form of transportation or via the intervention of membrane proteins which are able to transmit stimuli between…
This article introduces epidemia, an R package for Bayesian, regression-oriented modeling of infectious diseases. The implemented models define a likelihood for all observed data while also explicitly modeling transmission dynamics: an…
The role of memory and cognition in the movement of individuals (e.g. animals) within a population, is thought to play an important role in population dispersal. In response, there has been increasing interest in incorporating spatial…
We introduce expandable partial propensity direct method (EPDM) - a new exact stochastic simulation algorithm suitable for systems involving many interacting molecular species. The algorithm is especially efficient for sparsely populated…
We provide a review of recent advancements in nonlocal continuous models for migration, mainly from the perspective of its involvement in embryonal development and cancer invasion. Particular emphasis is placed on spatial nonlocality…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Ordinary differential equation models facilitate the understanding of cellular signal transduction and other biological processes. However, for large and comprehensive models, the computational cost of simulating or calibrating can be…
We study a non-conserved one-dimensional stochastic process which involves two species of particles $A$ and $B$. The particles diffuse asymmetrically and react in pairs as $A\emptyset\leftrightarrow AA\leftrightarrow BA \leftrightarrow…
We provide a numerical study of the macroscopic model of [3] derived from an agent-based model for a system of particles interacting through a dynamical network of links. Assuming that the network remodelling process is very fast, the…