Related papers: Chain reconfiguration in active noise
Molecular dynamics simulations were employed to investigate the phase separation process of a two-dimensional active Brownian dumbbell model. We evaluated the time dependence of the typical size of the dense component using the scaling…
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded…
A prime example of non-equilibrium or active environment is a biological cell. In order to understand in-vivo functioning of biomolecules such as proteins, chromatins, a description beyond equilibrium is absolutely necessary. In this…
We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyse their range of validity by means of comprehensive Molecular…
We investigate configuration dynamics of a flexible polymer chain in a bath of active particles with dynamic chirality, i.e., particles rotate with a deterministic angular velocity $\omega$ besides self-propulsion,by Langevin dynamics…
We investigate the nonequilibrium dynamics of semiflexible polymers driven by motor proteins (MPs) in two-dimensional motility assays under harmonic confinement. Using a coarse-grained agent-based model that incorporates stochastic motor…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
Background: Recent studies have indicated that functional connectivity is dynamic even during rest. A common approach to modeling the dynamic functional connectivity in whole-brain resting-state fMRI is to compute the correlation between…
We examine the thermally-induced fracture of an unstrained polymer chain of discrete segments coupled by an anharmonic potential by means of Molecular Dynamics simulation with a Langevin thermostat. Cases of both under- and over-damped…
Macroscale chains have been proposed to give insight into the physics of molecular polymer systems. Nevertheless, understanding the rheological response of systems of quasi-one-dimensional semiflexible materials, such as bead-chain…
We investigate, using numerical simulations and analytical arguments, a simple one dimensional model for the swelling or the collapse of a closed polymer chain of size N, representing the dynamical evolution of a polymer in a \Theta-solvent…
We examine motility-induced phase separation (MIPS) in two-dimensional run and tumble disk systems using both machine learning and noise fluctuation analysis. Our measures suggest that within the MIPS state there are several distinct…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
We study the emergence of correlations between $N$ components of the position of a diffusive walker in $N$ dimensions that starts at the origin and resets to previously visited sites with certain probabilities. This is equivalent to $N$…
When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
We use flicker-noise spectroscopy (FNS), a phenomenological method for the analysis of time and spatial series operating on structure functions and power spectrum estimates, to identify and study harmful chatter vibrations in a regenerative…
Noise can shape the firing behaviors of neurons. Here, we show that noise acting on the fast variable of the Hedgehog burster can tune the spike counts of bursts via the self-induced stochastic resonance (SISR) phenomenon. Using the…