Related papers: Computing rates and understanding unbinding mechan…
We consider the exclusion process on segments of the integers in a site-dependent random environment. We assume to be in the ballistic regime in which a single particle has positive linear speed. Our goal is to study the mixing time of the…
Boolean network models of strongly connected modules are capable of capturing the high regulatory complexity of many biological gene regulatory circuits. We study numerically the previously introduced basin entropy, a parameter for the…
A relevant relation between the dwell time and the density of states for a three dimensional system of arbitrary shape with an arbitrary number of incoming channel is derived. This result extends the one obtained by Gasparian et al. for the…
Stochastic dynamical systems arise as models for fluid particle motion in geophysical flows with random velocity fields. Escape probability (from a fluid domain) and mean residence time (in a fluid domain) quantify fluid transport between…
In order to understand the long known anomalies in the composition dependence of diffusion and viscosity of binary mixtures, we introduce here two new models and carry out extensive molecular dynamic simulations. In these models, the two…
Stochastic systems characterised by a random driving in a form of the general stable noise are considered. The particle experiences long rests due to the traps the density of which is position-dependent and obeys a power-law form attributed…
Providing evidence that quantum computers can efficiently prepare low-energy or thermal states of physically relevant interacting quantum systems is a major challenge in quantum information science. A newly developed quantum Gibbs sampling…
The protein-ligand residence time, tau, influences molecular function in biological networks and has been recognized as an important determinant of drug efficacy. To predict tau, computational methods must overcome the problem that tau…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
The mean time for a diffusing ligand to activate a target protein located on the surface of a microdomain can regulate cellular signaling. When the ligand switches between various states induced by chemical interactions or conformational…
We introduce a family of local models of dynamics based on ``word problems'' from computer science and group theory, for which we can place rigorous lower bounds on relaxation timescales. These models can be regarded either as random…
A coupling of structural and thermodynamic fluctuations in the course of various-type insertion processes is investigated within a combination of Gibbsian statistics and the information theory approach. It is shown that the coupling makes…
Binary fluorescence time series obtained from single-molecule imaging experiments can be used to infer protein binding kinetics, in particular, association and dissociation rate constants from waiting time statistics of fluorescence…
We study the distribution of residence time or equivalently that of ``mean magnetization" for a family of Gaussian Markov processes indexed by a positive parameter $\alpha$. The persistence exponent for these processes is simply given by…
The relaxation time of a classical spin interacting with a large conduction-electron system is computed for a weak magnetic field, which initially drives the spin out of equilibrium. We trace the spin and the conduction-electron dynamics on…
We investigate the energy dependence of Jovian electron residence times, which allows for a deeper understanding of adiabatic energy changes that occur during charged particle transport, as well as of their significance for simulation…
As was shown in quant-ph/0405028, the state of a tunneling particle can be uniquely presented as a coherent superposition of two states to describe alternative sub-processes, transmission and reflection. In this paper, on the basis of the…
This article aims at discovering the unknown variables in the system through data analysis. The main idea is to use the time of data collection as a surrogate variable and try to identify the unknown variables by modeling gradual and sudden…
We study the effect of a large obstacle on the so called residence time, i.e., the time that a particle performing a symmetric random walk in a rectangular (2D) domain needs to cross the strip. We observe a complex behavior, that is we find…
Receptor-ligand interactions are essential for biological function and their binding strength is commonly explained in terms of static lock-and-key models based on molecular complementarity. However, detailed information of the full…