Related papers: Single-Trajectory Bayesian Modeling Reveals Multi-…
Well-mixed chemical reaction networks (CRNs) contain many distinct chemical species with copy numbers that fluctuate in correlated ways. While those correlations are typically monitored via Monte Carlo sampling of stochastic trajectories,…
Theoretical understanding of strongly correlated systems in one spatial dimension (1D) has been greatly advanced by the density-matrix renormalization group (DMRG) algorithm, which is a variational approach using a class of…
The dynamics of short-lived mRNA results in bursts of protein production in gene regulatory networks. We investigate the propagation of bursting noise between different levels of mathematical modelling, and demonstrate that conventional…
In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…
We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…
Anomalous diffusion has been widely observed by single particle tracking microscopy in complex systems such as biological cells. The resulting time series are usually evaluated in terms of time averages. Often anomalous diffusion is…
The study of Brownian ratchets has taught how time-periodic driving supports a time-periodic steady state that generates nonequilibrium transport. When a single particle is transported in one dimension, it is possible to rationalize the…
We use a large single particle tracking data set to analyze the short time and small spatial scale motion of quantum dots labeling proteins in cell membranes. Our analysis focuses on the jumps which are the changes in the position of the…
The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to the specific sites on the DNA and regulating transcription, the ability of the proteins to…
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense…
Nonequilibrium dynamics of biomembranes with active inclusions is considered. The inclusions represent protein molecules which perform cyclic internal conformational motions driven by the energy brought with ATP ligands. As protein…
We consider the dynamics of a single shock in a partially asymmetric simple exclusion process (PASEP) on a finite lattice with open boundaries in the sublattice-parallel updating scheme. We then construct the steady state of the system by…
The transport of macromolecules, such as DNA, through the cytoskeleton is critical to wide-ranging cellular processes from cytoplasmic streaming to transcription. The rigidity and steric hindrances imparted by the network of filaments…
Under appropriate conditions, mixtures of cationic and neutral lipids and DNA in water condense into complexes in which DNA strands form local 2D smectic lattices intercalated between lipid bilayer membranes in a lamellar stack. These…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
Three-dimensional (3D) multi-slab imaging is a promising approach for high-resolution in vivo diffusion MRI (dMRI) due to its compatibility with short TR (1-2 s), providing optimal signal-to-noise ratio (SNR) efficiency. A major challenge,…
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…
A discrete nonlinear Schrodinger (NLS) model with long-range dispersive interactions describing the dynamical structure of DNA is proposed. Dispersive interactions of two types: the power dependence $r^{-s}$ and the exponential dependence…
Continuous diffusion is a natural framework for non-autoregressive generation but has generally lagged behind masked discrete diffusion models (MDMs) on discrete sequence generation. We argue that the bottleneck is not continuity itself,…
Continuous diffusion is a natural framework for non-autoregressive generation but has generally lagged behind masked discrete diffusion models (MDMs) on discrete sequence generation. We argue that the bottleneck is not continuity itself,…