Related papers: Facilitated diffusion of DNA-binding proteins: Sim…
Extracting scientific results from high-energy collider data involves the comparison of data collected from the experiments with synthetic data produced from computationally-intensive simulations. Comparisons of experimental data and…
Microscopic processes on surfaces such as adsorption, desorption, diffusion and reaction of interacting particles can be simulated using kinetic Monte Carlo (kMC) algorithms. Even though kMC methods are accurate, they are computationally…
Reaction-diffusion processes are the foundational model for a diverse range of complex systems, ranging from biochemical reactions to social agent-based phenomena. The underlying dynamics of these systems occur at the individual…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Under dilute in vitro conditions transcription factors rapidly locate their target sequence on DNA by using the facilitated diffusion mechanism. However, whether this strategy of alternating between three-dimensional bulk diffusion and…
We consider a family of controlled reaction-diffusion equations, describing the spatial spreading of an invasive biological species. For a given propagation speed $c\in{I\!\!R}$, we seek a control with minimum cost, which achieves a…
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
The rare-event sampling problem has long been the central limiting factor in molecular dynamics (MD), especially in biomolecular simulation. Recently, diffusion models such as BioEmu have emerged as powerful equilibrium samplers that…
The stochastic motions of a diffusing particle contain information concerning the particle's interactions with binding partners and with its local environment. However, accurate determination of the underlying diffusive properties, beyond…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
Delayed processes are ubiquitous in biological systems and are often characterized by delay differential equations (DDEs) and their extension to include stochastic effects. DDEs do not explicitly incorporate intermediate states associated…
We study the approximation of a multiscale reaction-diffusion system posed on both macroscopic and microscopic space scales. The coupling between the scales is done via micro-macro flux conditions. Our target system has a typical structure…
In various chemical systems enthalpy-entropy compensation (EEC) is a well-known rule of behavior, although the physical roots of it are still not completely understood. It has been frequently questioned whether EEC is a truly physical…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
This paper presents an efficient method based on Evolutionary Center Algorithm (ECA) for accurately and efficiently determining the optimal reaction and diffusion parameters for Chemical-Diffusive Models (CDM) to simulate flame acceleration…
Recent masked diffusion models (MDMs) have shown competitive performance compared to autoregressive models (ARMs) for language modeling. While most literature has focused on performance enhancing sampling procedures, efficient sampling from…
In molecular simulations, efficient methods for investigating equilibration and slow relaxation in dense systems are crucial yet challenging. This study focuses on the diffusional characteristics of monodisperse hard disk systems at…