Related papers: Single-Trajectory Bayesian Modeling Reveals Multi-…
We provide a transmission line representation for channels exhibiting spin-momentum locking (SML) which can be used for both time-dependent and steady-state transport analysis on a wide variety of materials with spin-orbit coupling such as…
We develop methods for investigating protein drift-diffusion dynamics in heterogeneous cell membranes and the roles played by geometry, diffusion, chemical kinetics, and phase separation. Our hybrid stochastic numerical methods combine…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We found evidence of dynamic scaling in the spreading of MDCK monolayer, which can be characterized by the Hurst exponent ${\alpha} = 0.86$ and the growth exponent ${\beta} = 0.73$, and theoretically and experimentally clarified the…
In this short note, a correction is made to the recently proposed solution [1] to a 1D biased diffusion model for linear DNA translocation and a new analysis will be given to the data in [1]. It was pointed out [2] by us recently that this…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
Heterogeneous media diffusion is often described using position-dependent diffusion coefficients and estimated indirectly through mean squared displacement in experiments. This approach may overlook other mechanisms and their interaction…
Diffusion and flow matching approaches to generative modeling have shown promise in domains where the state space is continuous, such as image generation or protein folding & design, and discrete, exemplified by diffusion large language…
The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…
We study the mean velocity and diffusion constant in three related models of molecular Brownian ratchets. Brownian ratchets can be used to describe translocation of biopolymers like DNA through nanopores in cells in the presence of…
Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of…
Particle transport in complex environments such as the interior of living cells is often (transiently) non-Fickian or anomalous, that is, it deviates from the laws of Brownian motion. Such anomalies may be the result of small-scale…
Local diffusion coefficients in disordered systems such as spin glass systems and living cells are highly heterogeneous and may change over time. Such a time-dependent and spatially heterogeneous environment results in irreproducibility of…
We develop an general formalism of single enzyme kinetics in two dimension where substrates diffuse stochastically on a square lattice in presence of disorder. The dynamics of the model could be decoupled effectively to two stochastic…
In recent single-particle tracking (SPT) measurements on {\it Listeria monocytogenes} motility {\em in vitro}, the actin-based stochastic dynamics of the bacterium movement is analyzed statistically (Kuo and McGrath, 2000). The mean-square…
We analyse how the sampling dynamics of distributions evolve in score-based diffusion models using cross-fluctuations, a centered-moment statistic from statistical physics. Specifically, we show that starting from an unbiased isotropic…
Spiking Neural Networks (SNNs) currently face a critical bottleneck: while individual neurons exhibit dynamic biological properties, their macro-scopic architectures remain confined within conventional connectivity patterns that are static…
The diffusion motions of individual polymer aggregates in disordered porous media were visualized using the single particle tracking (SPT) method because the motions inside porous media play important roles in various fields of science and…
Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that…