Related papers: Single-Trajectory Bayesian Modeling Reveals Multi-…
We propose and study a one-dimensional model which consists of two cross-diffusion systems coupled via a moving interface. The motivation stems from the modelling of complex diffusion processes in the context of the vapor deposition of thin…
Constructing physical models of living cells and tissues is an extremely challenging task because of the high complexities of both intra- and intercellular processes. In addition, the force that a single cell generates vanishes in total due…
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…
Several enzymes exhibit enhanced diffusion in the presence of a substrate. One explanation of this enhancement arises from fluctuating dimer models, which suggest that enzymes have a higher diffusion constant when interacting with…
The momentum Schr\"odinger Bridge (mSB) has emerged as a leading method for accelerating generative diffusion processes and reducing transport costs. However, the lack of simulation-free properties inevitably results in high training costs…
In this work we probe the dynamics of the particle-hole symmetric many-body localized (MBL) phase. We provide numerical evidence that it can be characterized by an algebraic propagation of both entanglement and charge, unlike in the…
Masked diffusion language models (MDLMs) have emerged as a promising alternative to dominant autoregressive approaches. Although they achieve competitive performance on several tasks, a substantial gap remains in open-ended text generation.…
Here we implement microfabricated boomerang particles with unequal arm lengths as a model for non-symmetry particles and study their Brownian motion in a quasi-two dimensional geometry by using high precision single particle motion…
A novel approach to simulate simple protein-ligand systems at large time- and length-scales is to couple Markov state models (MSMs) of molecular kinetics with particle-based reaction-diffusion (RD) simulations, MSM/RD. Currently, MSM/RD…
Single molecule time trajectories of biomolecules provide glimpses into complex folding landscapes that are difficult to visualize using conventional ensemble measurements. Recent experiments and theoretical analyses have highlighted…
First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…
We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein…
To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…
The muscle contraction, operation of ATP synthase, maintaining the shape of a cell are believed to be secured by motor proteins, which can be modelled using the Brownian ratchet mechanism. We consider the randomly flashing ratchet model of…
In this paper we develop a probabilistic model of single-particle diffusion in 1D multi-layered media by constructing a multi-layered version of so-called snapping out Brownian motion (BM). The latter sews together successive rounds of…
The persistent motion of bacteria produces clusters with a stationary cluster size distribution (CSD). Here we develop a minimal model for bacteria in a narrow channel to assess the relative importance of motility diversity (i.e.…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Inherent stochasticity in gene expression leads to distributions of mRNA copy numbers in a population of identical cells. These distributions are determined primarily by the multitude of states of a gene promoter, each driving transcription…
We study the number entropy and quasiparticle width in one-dimensional quasiperiodic many-body localized (MBL) systems and observe slow dynamics that have previously been investigated in detail only in random systems. In contrast,…
In this short note we provide two extensions on the recent explicit results on the matrix-product ansatz for the non-equilibrium steady state of a markovianly boundary-driven anisotropic Heisenberg XXZ spin 1/2 chain. We write a…