相关论文: Bubble Relaxation Dynamics in Double-Stranded DNA

The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…

We report on the statistics of bubble size, topology, and shape and on their role in the coarsening dynamics for foams consisting of bubbles compressed between two parallel plates. The design of the sample cell permits control of the liquid…

We consider two models of interacting DNA molecules: \textit{First} is (four parametric) bubble coalescence model in interacting DNAs (shortly: BCI-DNA). \textit{Second} is (three parametric) bubble coalescence model in a condensed DNA…

Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…

We study aging dynamics in two non-disordered spin models with multi-spin interactions, following a sudden quench to low temperature. The models are relevant to the physics of supercooled liquids. Their low temperature dynamics resemble…

We present a general stochastic dynamic model of a cluster of biological complexes with fluctuating dissociation and association rates. The master equation has analytical solutions in two limiting cases: the vanishing force with reflecting…

We study the BS model, which is a one-dimensional lattice field theory taking real values. Its dynamics is governed by coupled differential equations plus random nearest neighbor exchanges. The BS model has exactly two locally conserved…

We examine the density-density correlation function in a model recently proposed to study the effect of entropy barriers in glassy dynamics. We find that the relaxation proceeds in two steps with a fast beta process followed by alpha…

We present a theory for the steady-state dynamics of a two-dimensional system of spherically symmetric active Brownian particles. The derivation of the theory consists of two steps. First, we integrate out the self-propulsions and obtain a…

The paper presents an analytical description of the growth of a two-component bubble in a binary liquid-gas solution. We obtain asymptotic self-similar time dependence of the bubble radius and analytical expressions for the non-steady…

We consider the dynamics of diffusing particles in one space dimension with annihilation on collision and nucleation (creation of particles) with constant probability per unit time and length. The cases of nucleation of single particles and…

Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…

The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot…

Genetic feedback loops in cells break detailed balance and involve bimolecular reactions; hence exact solutions revealing the nature of the stochastic fluctuations in these loops are lacking. We here consider the master equation for a gene…

Advances in DNA nanotechnology have stimulated the search for simple motifs that can be used to control the properties of DNA nanostructures. One such motif, which has been used extensively in structures such as polyhedral cages,…

We develop theory for fluctuations in atom number and spin within finite-sized cells of a spinor Bose-Einstein condensate. This theory provides a model of measurements that can be performed in current experiments using finite resolution in…

The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…

We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…

The role of thermal pressure fluctuation excited within tightly packaged DNA prior to ejection from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a…

A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…