Related papers: Dynamics of DNA Bubble in Viscous Medium
This article deals with the issues of global-in-time existence and asymptotic analysis of a fluid-particle interaction model in the so-called bubbling regime. The mixture occupies the physical space $\Omega \subset \mathbb{R}^3$ which may…
We consider the dynamics of a population of organisms containing two mutually inhibitory gene regulatory networks, that can result in a bistable switch-like behaviour. We completely characterize their local and global dynamics in the…
Wave self-focusing in molecular systems subject to thermal effects, such as thin molecular films and long biomolecules, can be modeled by stochastic versions of the Discrete Self-Trapping equation of Eilbeck, Lomdahl and Scott, and this can…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…
Systems of the first order partial differential equations with singular solutions appear in many multiphysics problems and the weak formulation of solutions involve in many cases product of distributions. In this paper we study such a…
A novel theoretical model for bubble dynamics is established that simultaneously accounts for the liquid compressibility, phase transition, oscillation, migration, ambient flow field, etc. The bubble dynamics equations are presented in a…
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this…
We study the rising dynamics of a bubble driven into periodic volumetric oscillations by an external pressure driving within a highly viscous shear-thinning fluid. We perform axisymmetric direct numerical simulations employing the…
We study the discrete nonlinear Schr\"odinger equation (DNLS) in an annular geometry with on-site defects. The dynamics of a traveling plane-wave maps onto an effective ''non-rigid pendulum'' Hamiltonian. The different regimes include the…
We explore the melting of a lattice DNA in the presence of atmospheric disorder, which mimics the crowded environment inside the cell nucleus, using Monte Carlo simulations. The disorder is modeled by randomly retaining lattice sites with…
In a set of experiments, Couder et. al. demonstrate that an oscillating fluid bed may propagate a bouncing droplet through the guidance of the surface waves. We present a dynamical systems model, in the form of an iterative map, for a…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
By assuming that not only counter-ions but DNA molecules as well are thermally distributed according to a Boltzmann law, we propose a modified Poisson-Boltzmann equation at the classical level as starting point to compute the effects of…
Self-assembly and dynamical properties of Janus nanoparticles have been studied by molecular dynamic simulations. The nanoparticles are modeled as dimers and they are confined between two flat parallel plates to simulate a thin film. One…
We consider the influence of a terahertz field on the breathing dynamics of double-stranded DNA. We model the spontaneous formation of spatially localized openings of a damped and driven DNA chain, and find that linear instabilities lead to…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
The non-linear dynamics of driven oscillations in the size of a spherical bubble are mapped to the dynamics of a Newtonian particle in a potential within the incompressible liquid regime. The compressible liquid regime, which is important…
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and…
We investigate a higher order nonlinear Schr\"odinger equation with linear damping and weak viscosity, recently proposed as a model for deep water waves exhibiting frequency downshifting. Through analysis and numerical simulations, we…
Due to its polyionic character the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment and they are…