Related papers: Microscopic Reversibility or Detailed Balance in I…
The conduction and selectivity of calcium/sodium ion channels are described in terms of ionic Coulomb blockade, a phenomenon based on charge discreteness and an electrostatic model of an ion channel. This novel approach provides a unified…
Motivated by the study of reversal behaviour of myxobacteria, in this article we are interested in a kinetic model for reversal dynamics, in which particles with directions close to be opposite undergo binary collision resulting in…
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…
We study an irreversible Markov chain Monte Carlo method based on a skew detailed balance condition for an one-dimensional Ising model. Dynamical behavior of the magnetization density is analyzed in order to understand the properties of…
Many ion channels spontaneously switch between different levels of activity. Although this behaviour known as modal gating has been observed for a long time it is currently not well understood. Despite the fact that appropriately…
Time-reversal symmetry of microscopic laws dictates that the equilibrium distribution of a stochastic process must obey the detailed balance. On the other hand, cyclic Markov processes that do not admit equilibrium distributions with…
The behaviour of a system of ion channels formed across the cell membrane is presented. The infinite number of channels with an infinite coupling is introduced first as a reference point for the detailed derivation of the…
Switching between different levels of resolution is essential for multiscale modeling, but restoring details at higher resolution remains challenging. In our previous study we have introduced deepBackmap: a deep neural-network-based…
Stochastic thermodynamics has largely succeeded in characterizing both equilibrium and far-from-equilibrium phenomena. Yet many opportunities remain for application to mesoscopic complex systems -- especially biological ones -- whose…
We consider various modeling levels for spatially homogeneous chemical reaction systems, namely the chemical master equation, the chemical Langevin dynamics, and the reaction-rate equation. Throughout we restrict our study to the case where…
Integrating out fast degrees of freedom is known to yield, to a good approximation, memory-less, i.e. Markovian, dynamics. In the presence of such a time-scale separation local detailed balance is believed to emerge and to guarantee…
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 slow microstructural evolution of materials often plays a key role in determining material properties. When the unit steps of the evolution process are slow, direct simulation approaches such as molecular dynamics become prohibitive and…
In this work, we devise a model adaptation strategy for a class of model hierarchies consisting of two levels of model complexity. In particular, the fine model consists of a system of hyperbolic balance laws with stiff reaction terms and…
Transmembrane ion flow through channel proteins undergoing density fluctuations may cause lateral gradients of the electrical potential across the membrane giving rise to electrophoresis of charged channels. A model for the dynamics of the…
Recently a number of approaches has been developed to connect the microscopic dynamics of particle systems to the macroscopic properties of systems in nonequilibrium stationary states, via the theory of dynamical systems. This way a direct…
We consider a simple working hypothesis that all permeation properties of open ionic channels can be predicted by understanding electrodiffusion in fixed structures, without invoking conformation changes, or changes in chemical bonds. We…
A new model for the electrical conductivity of dense plasmas with a mixture of ion species, containing no adjustable parameters, is presented. The model takes the temperature, mass density and relative abundances of the species as input. It…
Catalytically active macromolecules are envisioned as key building blocks in development of artificial nanomotors. However, theory and experiments report conflicting findings regarding their dynamics. The lack of consensus is mostly caused…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…