相关论文: Helix-coil Transition in Closed Circular DNA

A model which combines the perturbative behavior of QCD with low energy phenomenology in a unified framework is developed. This is achieved by applying a similarity transformation to the QCD Hamiltonian which removes interactions between…

We present a detailed analysis of the molecular kinetics of CHCl$_3$ in a range of temperatures covering the solid and liquid phases. Using nuclear quadrupolar resonance we determine the relaxation times for the molecular rotations in solid…

A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…

We present the first large-scale molecular dynamics simulations of hexane on graphite that completely reproduces all experimental features of the melting transition. The canonical ensemble simulations required and used the most realistic…

A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and…

The dynamics of loops at the DNA denaturation transition is studied. A scaling argument is used to evaluate the asymptotic behavior of the autocorrelation function of the state of complementary bases (either open or closed). The long-time…

This article proposes a model including thermal effects for closed supercoiled DNA. Existing models include an elastic rod. Euler's elastica, ideal elastic rods on a plane, have only two kinds of closed shapes, the circle and a…

Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…

The HeH$^+$ cation is the simplest molecular prototype of the indirect dissociative recombination (DR) process that proceeds through electron capture into Rydberg states of the corresponding neutral molecule. This Letter develops the first…

The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…

A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…

We introduce an analytical method to generate the pathway of a closed protein-bound DNA minicircle. This is a general method which can be used to connect any two open curves with well defined mathematical definitions as well as pairs of…

The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D…

Quantum theory of hydrogen atoms distribution between two complementary nucleotide bases in DNA double helix at moment of replication has been proposed in this work. It bases on two mechanisms of proton tunneling: the Andreev-Meyerovich…

Homogeneous nucleation of a new phase near a second, continuous, transition, is considered. The continuous transition is in the metastable region associated with the first-order phase transition, one of whose coexisting phases is…

We present the results of a series of calculations studying the collapse of molecular cloud cores performed using a three-dimensional smoothed particle hydr odynamics code with radiative transfer in the flux-limited diffusion approximation.…

The electrodynamic response of DNA in the millimeter wave range is investigated. By performing measurements under a wide range of humidity conditions and comparing the response of single strand DNA and double strand DNA, we show that the…

In the present paper we present results of calculations obtained with the use of the theoretical method described in our preceding paper [1] and perform detail analysis of alpha helix-random coil transition in alanine polypeptides of…