相关论文: Bubble Statistics and Dynamics in Double-Stranded …
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…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We study the unexpected high flexibility of short dsDNA which recently has been reported by a number of experiments. Via the Langevin dynamics simulation of our Breathing DNA model, first we observe the formation of bubbles within the…
We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the…
Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double…
Doubly diffusive convection is considered in a vertical slot where horizontal temperature and solutal variations provide competing effects to the fluid density while allowing the existence of a conduction state. In this configuration, the…
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
We study here the dynamics (and stability) of Probabilistic Population Protocols, via the differential equations approach. We provide a quite general model and we show that it includes the model of Angluin et. al. in the case of very large…
We present a numerical investigation of the Brownian motion and diffusion of a dumbbell in a two-dimensional periodic potential. Its dynamics is described by a Langevin model including the hydrodynamic interaction. With increasing values of…
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 investigate the coalescence of two DNA-bubbles initially located at weak domains and separated by a more stable barrier region in a designed construct of double-stranded DNA. In a continuum Fokker-Planck approach, the characteristic time…
We study dynamically coupled one-dimensional Bose-Hubbard models and solve for the wave functions and energies of two-particle eigenstates. Even though the wave functions do not directly follow the form of a Bethe Ansatz, we describe an…
DNA inside the cellular environment works under a confined space. An intense research of the transcription and replication of DNA in the confined state is structurally significant to command the self assembly of DNA in a chamber or channel.…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
We propose a formalism for describing two-strand systems of a DNA type by means of soliton von Neumann equations, and illustrate how it works on a simple example exactly solvably by a Darboux transformation. The main idea behind the…
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…
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 propose a stochastic Gillespie scheme to describe the temporal fluctuations of local denaturation zones in double-stranded DNA as a single molecule time series. It is demonstrated that the model recovers the equilibrium properties. We…
Motivated by the desire to understand complex transient behaviour in fluid flows, we study the dynamics of an air bubble driven by the steady motion of a suspending viscous fluid within a Hele-Shaw channel with a centred depth perturbation.…