Related papers: Stochastic approach to DNA breathing dynamics
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Molecular search phenomena are observed in a variety of chemical and biological systems. During the search the participating particles frequently move in complex inhomogeneous environments with random transitions between different dynamic…
By means of the Brownian dynamics (BD) method of simulations we have developed, we study dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE), focusing on the relevance of the `defect' concept due to de Gennes in…
The authors present a new molecular dynamics algorithm for sampling the isothermal-isobaric ensemble. In this approach the velocities of all particles and volume degrees of freedom are rescaled by a properly chosen random factor. The…
A comprehensive study is presented on the short-time dynamics in suspensions of charged colloidal spheres. The explored parameter space covers the major part of the fluid-state regime, with colloid concentrations extending up to the…
We introduce a model of long-range interacting particles evolving under a stochastic Monte Carlo dynamics, in which possible increase or decrease in the values of the dynamical variables is accepted with preassigned probabilities. For…
We study the convergence of stochastic time-discretization schemes for evolution equations driven by random velocity fields, including examples like stochastic gradient descent and interacting particle systems. Using a unified framework…
Mouse-tracking recording techniques are becoming very attractive in experimental psychology. They provide an effective means of enhancing the measurement of some real-time cognitive processes involved in categorization, decision-making, and…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
The issue of the nucleation and slow closure mechanisms of non superhelical stress-induced denaturation bubbles in DNA is tackled using coarse-grained MetaDynamics and Brownian simulations. A minimal mesoscopic model is used where the…
Biological processes at the cellular level are stochastic in nature, and the immune response system is no different. Therefore, models that attempt to explain this system need to also incorporate noise or fluctuations that can account for…
We introduce a description of the collective transverse dynamics of charged (proton) beams in the stability regime by suitable classical stochastic fluctuations. In this scheme, the collective beam dynamics is described by time--reversal…
Motivated by recent DNA-pulling experiments, we revisit the Poland-Scheraga model of melting a double-stranded polymer. We include distinct bending rigidities for both the double-stranded segments, and the single-stranded segments forming a…
We study the diffusion process in a Heisenberg chain with correlated spatial disorder, with a power spectrum in the momentum space behaving as $k^{-\beta}$, using a stochastic description. It establishes a direct connection between the…
In ABP systems, phase separation is accompanied by the emergence of vapor bubbles within liquid domains. Using large-scale particle-based simulations, we study the stochastic dynamics of these bubbles and find that most nucleate, grow, and…
Condensed phase systems often exhibit a mixture of deterministic and stochastic dynamics at the nanoscale which are essential to understanding their function, but can be challenging to study directly using conventional imaging methods.…
We prove local (in space and time) well-posedness for a mildly regularised version of the stochastic quantisation of the Yukawa$_{2}$ Euclidean field theory with a self-interacting boson. Our regularised dynamic is still singular but avoids…
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics…
Open quantum systems theory is central to describing the dynamics and equilibration of dilute-gas Bose-Einstein condensates (BECs). We present an analysis of the linearized stochastic projected Gross-Pitaevskii equation (SPGPE) describing…