Related papers: Computing rates and understanding unbinding mechan…
A key factor influencing a drug's efficacy is its residence time in the binding pocket of the host protein. Using atomistic computer simulation to predict this residence time and the associated dissociation process is a desirable but…
One of the main applications of atomistic computer simulations is the calculation of ligand binding energies. The accuracy of these calculations depends on the force field quality and on the thoroughness of configuration sampling. Sampling…
The process of ligand-protein unbinding is crucial in biophysics. Water is an essential part of any biological system and yet, many aspects of its role remain elusive. Here, we simulate with state-of-the-art enhanced sampling techniques the…
A heuristic law widely used in fluid dynamics for steady flows states that the amount of a fluid in a control volume is the product of the fluid influx and the mean time that the particles of the fluid spend in the volume, or mean residence…
We present a method to learn mean residence time and escape probability from data modeled by stochastic differential equations. This method is a combination of machine learning from data (to extract stochastic differential equations as…
The aging phenomena occurring in the course of cycling processes in the insertion host-guest compounds are discussed in the framework of a simple model. It takes into account two types of effects. One can be attributed to modifications of…
A multi-patch and multi-group modeling framework describing the dynamics of a class of diseases driven by the interactions between vectors and hosts structured by groups is formulated. Hosts' dispersal is modeled in terms of patch-residence…
We discuss the properties of the residence time in presence of moving defects or obstacles for a particle performing a one dimensional random walk. More precisely, for a particle conditioned to exit through the right endpoint, we measure…
The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…
Motivated by the problem of predicting sleep states, we develop a mixed effects model for binary time series with a stochastic component represented by a Gaussian process. The fixed component captures the effects of covariates on the…
Binding kinetic parameters can be correlated with drug efficacy, which led to the development of various computational methods for predicting binding kinetic rates and gaining insight into protein-drug binding paths and mechanisms in recent…
In this work, we propose estimators for the uncertainty in mean residual times that require, for their evaluation, statistically independent individual residence times obtained from a discrete time process. We examine their performance…
Mixing timescales and residence times in reactive multiphase flows can be essential for product selectivity. For instance when a gas species is consumed e.g. by a competitive consecutive reaction with moderate reaction kinetics where…
The use of advanced sequential paging algorithms has been suggested as a means to reduce the signaling cost in future mobile cellular networks. In a proposed algorithm (Koukoutsidis and Theologou, 2003), the system can use the additional…
We provide a general thermodynamic framework for the understanding of guest-induced structural transitions in hybrid organic-inorganic materials. The method is based on the analysis of experimental adsorption isotherms. It allows the…
Many processes in chemistry and physics take place on timescales that cannot be explored using standard molecular dynamics simulations. This renders the use of enhanced sampling mandatory. Here we introduce an enhanced sampling method that…
This paper initiates the analysis of the relation between evacuation time and group size by applying an extended floor field cellular automaton model. Agents with various speeds, a group structure containing leaders and followers, and a…
The impact of droplets is a ubiquitous phenomenon, and reducing the residence time of the impact process is important for many potential applications. In this study of the impact dynamics on heated surfaces, we identify a mode of droplet…
We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly…
We present a theory of unbinding transitions for membranes that interact via short and long receptor/ligand bonds. The detail of unbinding behavior of the membranes is governed by the binding energies and concentrations of receptors and…