Related papers: Target finding in fibrous biological environments
Topic of the thesis is a theoretical description of the ultracold atomic gases in one- and two-dimensional optical lattices in the presence of the disorder leading to the Anderson localization. The disorder is created by interaction of the…
The first-passage time (FPT), i.e., the moment when a stochastic process reaches a given threshold value for the first time, is a fundamental mathematical concept with immediate applications. In particular, it quantifies the statistics of…
Intracellular processes often rely on the timely encounter of mobile reaction partners, including intermittently motor-driven organelles. The underlying cytoskeletal network presents a complex landscape that both directs particle movement…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
Studies of transient dynamics captures the time history of any dramatic changes in the dynamics of a system. The transient dynamics is investigated here in a classic ecological model of a bistable tri-trophic food chain. All the species in…
We study chemotaxis of a single {\sl E.coli} bacterium in a medium where the nutrient chemical is also undergoing diffusion and its concentration has the form of a Gaussian whose width increases with time. We measure the average first…
We determine the full distribution and moments of the first passage time for a wide class of stochastic search processes in the limit of frequent stochastic resetting. Our results apply to any system whose short-time behavior of the search…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
A variety of transport processes in natural and man-made systems are intrinsically random. To model their stochasticity, lattice random walks have been employed for a long time, mainly by considering Cartesian lattices. However, in many…
Brownian diffusion subject to stochastic resetting to a fixed position has been widely studied for applications to random search processes. In an unbounded domain, the mean first-passage time at a target site can be minimized for a…
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is…
Quantitative analysis of the dynamics of tiny cellular and sub-cellular structures, known as particles, in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous…
In many situations, simply finding a target during a search is not enough. It is equally important to be able to return to that target repeatedly or to enable a larger community to locate and utilize it. While first passage time is commonly…
We consider a problem of finding a target located in a finite $d$-dimensional domain, using $N$ independent random walkers, when partial information on the target location is given as a probability distribution. When $N$ is large, the…
We study competition of two non-motile bacterial strains in a three-dimensional channel numerically, and analyze how their configuration evolves in space and time. We construct a lattice model that takes into account self-replication,…
Driven lattice gases serve as canonical models for investigating collective transport phenomena and properties of non-equilibrium steady states (NESS). Here we study one-dimensional transport with nearest-neighbor interactions both in…
The traffic of molecular motors through open tube-like compartments is studied using lattice models. These models exhibit boundary-induced phase transitions related to those of the asymmetric simple exclusion process (ASEP) in one…
The time instant -- the first-passage time (FPT) -- when a diffusive particle (e.g., a ligand such as oxygen or a signalling protein) for the first time reaches an immobile target located on the surface of a bounded three-dimensional domain…
We consider the dynamics of lattice random walks with resetting. The walker moving randomly on a lattice of arbitrary dimensions resets at every time step to a given site with a constant probability $r$. We construct a discrete renewal…
Many events in biology are triggered when a diffusing searcher finds a target, which is called a first passage time (FPT). The overwhelming majority of FPT studies have analyzed the time it takes a single searcher to find a target. However,…