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The inherent flexibility of soft robots offers numerous advantages, such as enhanced adaptability and improved safety. However, this flexibility can also introduce challenges regarding highly uncertain and nonlinear motion. These challenges…
We study several Fokker-Planck equations arising from a stochastic chemical kinetic system modeling a gene regulatory network in biology. The densities solving the Fokker-Planck equations describe the joint distribution of the messenger RNA…
Stochastic models of chemical systems are often analysed by solving the corresponding Fokker-Planck equation which is a drift-diffusion partial differential equation for the probability distribution function. Efficient numerical solution of…
Recently, the fractional Fokker-Planck equations (FFPEs) with multiple internal states are built for the particles undergoing anomalous diffusion with different waiting time distributions for different internal states, which describe the…
As a counterpoint to classical stochastic particle methods for linear diffusion equations, we develop a deterministic particle method for the weighted porous medium equation (WPME) and prove its convergence on bounded time intervals. This…
Experiments show that when a monolayer of cells cultured on an elastic substrate is subject to a cyclic stretch, cells tend to re-orient either perpendicularly or at an oblique angle with respect to the main direction of the stretch. Due to…
High-energy, multi-component plasmas in which pair creation and annihilation, lepton-lepton scattering, lepton-proton scattering, and Comptonization all contribute to establishing the particle and photon distributions, are present in a…
We derive methods for estimating the topology of the stationary probability current $\vec{j}_s$ of the two-species Fokker-Planck equation (FPE) without the need to solve the FPE. These methods are chosen such that they become exact in…
The modeling and simulation of stochastic reaction-diffusion processes is a topic of steady interest that is approached with a wide range of methods. \rev{At the level of particle-resolved descriptions, where chemical reactions are coupled…
The chemical diffusion master equation (CDME) describes the probabilistic dynamics of reaction--diffusion systems at the molecular level [del Razo et al., Lett. Math. Phys. 112:49, 2022]; it can be considered the master equation for…
When the complete understanding of a complex system is not available, as, e.g., for systems considered in the real-world, we need a top-down approach to complexity. In this approach one may start with the desire to understand general…
Populations of spiking neuron models have densities of their microscopic variables (e.g., single-cell membrane potentials) whose evolution fully capture the collective dynamics of biological networks, even outside equilibrium. Despite its…
We investigate the relation between the stationary probability distribution of chemical reaction systems and the convective field derived from the chemical Fokker-Planck equation (CFPE) by comparing predictions of the convective field to…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
Heterogeneity in gene expression across isogenic cell populations can give rise to phenotypic diversity, even when cells are in homogenous environments. This diversity arises from the discrete, stochastic nature of biochemical reactions,…
The concern of the present paper is the design of efficient numerical schemes for a specific Fokker-Planck equation describing the dynamics of energetic particles occurring in thermonuclear fusion plasmas (runaway electrons for example). In…
We present a control framework for stochastic compartmental models in epidemiology. In this framework, rather than directly controlling the stochastic system, we perform optimal control of an associated Fokker-Planck equation, with the goal…
We propose a model based on coupled multiplicative stochastic processes to understand the dynamics of competing species in an ecosystem. This process can be conveniently described by a Fokker-Planck equation. We provide an analytical…
We present a formulation of an optimal control problem for a two-dimensional diffusion process governed by a Fokker-Planck equation to achieve a nonequilibrium steady state with a desired circulation while accelerating convergence toward…
The Cellular Potts Model (CPM) has been used for simulating various biological phenomena such as differential adhesion, fruiting body formation of the slime mold Dictyostelium discoideum, angiogenesis, cancer invasion, chondrogenesis in…