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We propose a model for cell polarization as a response to an external signal which results in a system of PDEs for different variants of a protein on the cell surface and interior respectively. We study stationary states of this model in…
In vivo, eukaryotic cells are embedded in a matrix environment, where they grow and develop. Generally, this extracellular matrix (ECM) is an anisotropic fibrous structure, through which macromolecules and biochemical signaling molecules at…
This study concerns with singularly perturbed systems of second-order reaction-diffusion equations in ODE's. To handle this type of problems, a numerical-asymptotic hybrid method is employed. In this hybrid method, an efficient asymptotic…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through excluded volume effects. However the standard approach to…
We study the decay process for the reaction-diffusion process of three species on the small-world network. The decay process is manipulated from the deterministic rate equation of three species in the reaction-diffusion system. The particle…
We demonstrate and characterize a first-principles approach to modeling the mass action dynamics of metabolism. Starting from a basic definition of entropy expressed as a multinomial probability density using Boltzmann probabilities with…
Computational prediction of enzyme mechanism and protein function requires accurate physics-based models and suitable sampling. We discuss recent advances in large-scale quantum mechanical (QM) modeling of biochemical systems that have…
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…
We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales that are inaccessible in standard…
Pore-scale simulations accurately describe transport properties of fluids in the subsurface. These simulations enhance our understanding of applications such as assessing hydrogen storage efficiency and forecasting CO$_2$ sequestration…
Molecular dynamics simulation is used to study the time-scales involved in the homogeneous melting of a superheated crystal. The interaction model used is an embedded-atom model for Fe developed in previous work, and the melting process is…
Reaction-diffusion systems, which consist of the reacting particles subject to diffusion process, constitute one of the common examples of non-linear statistical systems. In low space dimensions $d \leq 2$ the usual description by means of…
Training diffusion models is always a computation-intensive task. In this paper, we introduce a novel speed-up method for diffusion model training, called, which is based on a closer look at time steps. Our key findings are: i) Time steps…
While energy-based models (EBMs) exhibit a number of desirable properties, training and sampling on high-dimensional datasets remains challenging. Inspired by recent progress on diffusion probabilistic models, we present a diffusion…
We study the long-time behavior of the solutions of a two-component reaction-diffusion system on the real line, which describes the basic chemical reaction $A <=> 2 B$. Assuming that the initial densities of the species $A, B$ are bounded…
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework, frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical…
Different relaxation approximations to partial differential equations, including conservation laws, Hamilton-Jacobi equations, convection-diffusion problems, gas dynamics problems, have been recently proposed. The present paper focuses onto…
In this paper we analyze the equilibrium properties of a large class of stochastic processes describing the fundamental biological process within bacterial cells, {\em the production process of proteins}. Stochastic models classically used…
Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for…