相关论文: Revising Berg-Purcell for finite receptor kinetics
We develop a theory of reversible diffusion-controlled reactions with generalized binding/unbinding kinetics. In this framework, a diffusing particle can bind to the reactive substrate after a random number of arrivals onto it, with a given…
Recently, molecular communication (MC) has been studied as a micro-scale communication between cells or molecular robots. In previous works, the MC channels in unbounded environment was analyzed. However, many of the experimentally…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Cells use surface receptors to estimate the concentration of external ligands. Limits on the accuracy of such estimations have been well studied for pairs of ligand and receptor species. However, the environment typically contains many…
Molecular transport in living systems regulates numerous processes underlying biological function. Although many cellular components exhibit anomalous diffusion, only recently has the subdiffusive motion been associated with nonergodic…
A new mathematical model for complex neural networks of the partly diffusive Hindmasrh-Rose equations with boundary coupling is proposed. Through analysis of absorbing dynamics for the solution semiflow, the asymptotic synchronization of…
Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a…
In molecular dynamics simulations under periodic boundary conditions, particle positions are typically wrapped into a reference box. For diffusion coefficient calculations using the Einstein relation, the particle positions need to be…
The functional relevance of regulating proteins is often limited to specific binding sites such as the ends of microtubules or actin-filaments. A localization of proteins on these functional sites is of great importance. We present a…
In this paper we propose and validate a multiscale model for the description of particle diffusion in presence of trapping boundaries. We start from a drift-diffusion equation in which the drift term describes the effect of bubble traps,…
A new type of absorbing boundary conditions for molecular dynamics simulations are presented. The exact boundary conditions for crystalline solids with harmonic approximation are expressed as a dynamic Dirichlet- to-Neumann (DtN) map. It…
Every mathematical model describing physical phenomena is an approximation to model reality, hence has its limitations. Depending on characteristic values of the variables in the model, different aspects of the model and, e.g.,…
We develop a mesoscopic approach to model the non-equilibrium behavior of membranes at the cellular scale. Relying on lattice Boltzmann methods, we develop a solution procedure to recover the Nernst-Planck equations and Gauss's law. A…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
A simple multiscale approach to the diffusion-driven adsorption from a solution to a solid surface is presented. The model combines two important features of the adsorption process: (i) the kinetics of the chemical reaction between…
In this paper, a diffusion-based molecular communication channel between two nano-machines is considered. The effect of the amount of memory on performance is characterized, and a simple memory-limited decoder is proposed and its…
Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity…
For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…
Diffusion preserves the positivity of concentrations, therefore, multicomponent diffusion should be nonlinear if there exist non-diagonal terms. The vast variety of nonlinear multicomponent diffusion equations should be ordered and special…
Reaction rate equations are ordinary differential equations that are frequently used to describe deterministic chemical kinetics at the macroscopic scale. At the microscopic scale, the chemical kinetics is stochastic and can be captured by…