48 citations · 106 across the 14 of their papers we have counts for
13 papers
Accelerated Simulation Algorithms for Extreme First-Passage Problems with General Emission Profiles
Emmanuel Akame Mfoumou, David Holcman
Fastest arrival events, where the first among many diffusing particles reaches a target, are central in triggering signal initiation in molecular stochastic systems. Classical appr…
Single particle algorithms to reveal cellular nanodomain organization
Pierre Parutto, Jennifer Heck, Martin Heine +1
Formation, maintenance and physiology of high-density protein-enriched organized nanodomains, first observed in electron microscopy images, remains challenging to investigate due t…
Modeling ionic flow between small targets: insights from diffusion and electro-diffusion theory
Frédéric Paquin-Lefebvre, David Holcman
The flow of ions through permeable channels causes voltage drop in physiological nanodomains such as synapses, dendrites and dendritic spines, and other protrusions. How the voltag…
How large should be the redundant numbers of copy to make a rare event probable
Fred Paquin-Lefebvre, Suney Toste, David Holcman
The redundancy principle provides the framework to study how rare events are made possible with probability 1 in accelerated time, by making many copies of similar random searchers…
Extreme diffusion with point-sink killing field
Suney Toste, David Holcman
We study here the escape time for the fastest diffusing particle from the boundary of an interval with point-sink killing sources. Killing represents a degradation that leads to th…
Arrival time for the fastest among switching stochastic particles
Suney Toste, David Holcman
The first arrivals among Brownian particles is ubiquitous in the life sciences, as it often trigger cellular processes from the molecular level. We study here the case where st…
Modeling and asymptotic analysis of the concentration difference in a nanoregion between an influx and outflux diffusion across narrow windows
Frédéric Paquin-Lefebvre, David Holcman
When a flux of Brownian particles is injected in a narrow window located on the surface of a bounded domain, these particles diffuse and can eventually escape through a cluster of…
Encounter time of two loci governed by polymer de-condensation and local chromatin interaction
Assaf Amitai, David Holcman
The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first e…
Recovering a stochastic process from noisy ensembles of many single particle trajectories
Nathanael Hoze, David Holcman
Recovering a stochastic process from noisy ensembles of single particle trajectories (SPTs) is resolved here using the Langevin equation as a model. The massive redundancy containe…
Poisson-Nernst-Planck equations in a ball
Z. Schuss J. Cartailler, D. Holcman
The Poisson Nernst-Planck equations for charge concentration and electric potential in a ball is a model of electro-diffusion of ions in the head of a neuronal dendritic spine. We…
Oscillatory Survival Probability: Analytical, Numerical Study for oscillatory narrow escape and applications to neural network dynamics
K. Dao Duc, Z. Schuss, D. Holcman
We study the escape of Brownian motion from the domain of attraction of a stable focus with a strong drift. The boundary of is an unstable limit cycle of the d…
Computation of the Mean First-Encounter Time Between the Ends of a Polymer Chain
Assaf Amitai, Ivan Kupka, David Holcman
Using a novel theoretical approach, we study the mean first encounter time (MFET) between the two ends of a polymer. Previous approaches used various simplifications that reduced t…
Encounter dynamics of a small target by a polymer diffusing in a confined domain
A. Amitai, Carlo Amoruso, Avi Ziskind +1
We study the first passage time for a polymer, that we call the narrow encounter time (NETP), to reach a small target located on the surface of a microdomain. The polymer is modele…