Related papers: Transition path theory for diffusive search with s…
We present an analytical description of the Alchemical Transfer Method (ATM) for molecular binding using the Potential Distribution Theory (PDT) formalism. ATM models the binding free energy by mapping the bound and unbound states of the…
We consider the problem of diffusion with stochastic resetting in a population of random walks where the diffusion coefficient is not constant, but behaves as a power-law of the average resetting rate of the population. Resetting occurs…
In this paper, we investigate the effects of stochastic resetting on diffusion in $\R^d\backslash \calU$, where $\calU$ is a bounded obstacle with a partially absorbing surface $\partial \calU$. We begin by considering a Robin boundary…
Anomalous subdiffusion characterizes transport in diverse physical systems and is especially prevalent inside biological cells. In cell biology, the prevailing model for chemical activation rates has recently changed from the first passage…
Determining the steady state of an open quantum system is crucial for characterizing quantum devices and studying various physical phenomena. Often, computing a single steady state is insufficient, and it is necessary to explore its…
In order to study transport in complex environments, it is extremely important to determine the physical mechanism underlying diffusion, and precisely characterize its nature and parameters. Often, this task is strongly impacted by data…
In this paper we consider a random search process with stochastic resetting and a partially accessible target $\calU$. That is, when the searcher finds the target by attaching to its surface $\partial \calU$ it does not have immediate…
Point processes often have a natural interpretation with respect to a continuous process. We propose a point process construction that describes arrival time observations in terms of the state of a latent diffusion process. In this…
Understanding the geometry of learned distributions is fundamental to improving and interpreting diffusion models, yet systematic tools for exploring their landscape remain limited. Standard latent-space interpolations fail to respect the…
Resetting is a strategy for boosting the speed of a target-searching process. Since its introduction over a decade ago, most studies have been carried out under the assumption that resetting takes place instantaneously. However, due to its…
Recent studies have identified plasma as a topological material. Yet, these researches often depict plasma as a fluid governed by electromagnetic fields, i.e., a classical wave system. Indeed, plasma transport can be characterized by a…
Will the strategy of resetting} help a stochastic process to reach its target efficiently, with its environment continually toggling between a strongly favourable and an unfavourable (or weakly favourable) state? A diffusive run-and-tumble…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to…
We consider diffusion in arbitrary spatial dimension d with the addition of a resetting process wherein the diffusive particle stochastically resets to a fixed position at a constant rate $r$. We compute the non-equilibrium stationary state…
Transition path sampling (TPS), which involves finding probable paths connecting two points on an energy landscape, remains a challenge due to the complexity of real-world atomistic systems. Current machine learning approaches use…
Aggregations are emergent features common to many biological systems. Mathematical models to understand their emergence are consequently widespread, with the aggregation-diffusion equation being a prime example. Here we study the…
For predicting the kinetics of nucleic acid reactions, continuous-time Markov chains (CTMCs) are widely used. The rate of a reaction can be obtained through the mean first passage time (MFPT) of its CTMC. However, a typical issue in CTMCs…
Processes controlled by stochastic synthesis and degradation (SSD) are widespread in biology but their reaction kinetics are not well understood. Using methods borrowed from the theory of resetting processes, we determine the first-passage…
Stochastic resetting has been a subject of considerable interest within statistical physics, both as means of improving completion times of complex processes such as searches and as a paradigm for generating nonequilibrium stationary…