Related papers: Duplex-single strand denaturing transition in DNA …
The dynamics of flexible polymers in dilute solution is usually described in terms of the pure Rouse or Zimm bead-spring models assuming continuous distribution of the internal relaxation modes. We show that this approach may lead to…
Directed polymers on 1+1 dimensional lattices coupled to a heat bath at temperature $T$ are studied numerically for three ensembles of the site disorder. In particular correlations of the disorder as well as fractal patterning are…
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…
We study the structure and melting of a classical bilayer system of dipoles, in a setup where the dipoles are oriented perpendicular to the planes of the layers and the density of dipoles is the same in each layer. Due to the anisotropic…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
Peptide Nucleic Acids (PNA) are non-natural oligonucleotides mimics. {\gamma}-PNA backbone are formed by standard nucleic acids nucleobases connected by a neutral N-(2-aminoethyl)glycine backbone linked by a peptide bond. In this study, we…
We consider two parallel layers of dipolar ultracold Fermi gases at different temperatures and calculate the heat transfer between them. The effective interactions describing screening and correlation effects between the dipoles in a single…
We have studied structure formation in a confined block copolymer melt by means of dynamic density functional theory (DDFT). The confinement is two-dimensional, and the confined geometry is that of a cylindrical nanopore. Although the…
We investigate - with Monte Carlo computer simulations - the phase behaviour of dimeric colloidal molecules on periodic substrates with square symmetry. The molecules are formed in a two-dimensional suspension of like charged colloids…
DNA melting and hybridization is a fundamental biological process as well as a crucial step in many modern biotechnology applications. DNA confined on surfaces exhibits different behavior from that in free solutions. The system of…
As a prototype of systems bearing a localization-delocalization transition, the strand-separation (melting) process in a double-stranded biopolymer is studied by a mapping to a quantum-mechanical problem with short-ranged potentials. Both…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
In this work we have used extensive Monte Carlo simulations and finite size scaling theory to study the phase transition in the dipolar Planar Rotator model (dPRM), also known as dipolar XY model. The true long-range character of the…
We investigate thermodynamic properties of a one-dimensional S=1/2 antiferromagnetic Heisenberg model coupled to a lattice distortion by a quantum Monte Carlo method. In particular we study how spin and lattice dimerize as a function of the…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
During the melting transition of dimyristoyl phosphatidylglycerol (DMPG), the order of the lipid chains and the three-dimensional, vesicular structural arrangement change simultaneously. These changes result in peculiar heat capacity…
We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the…
Equations that govern the temperature-dependence of the rate constants, Gibbs energies,enthalpies, entropies and heat capacities of activation for folding and unfolding of spontaneously-folding fixed two-state systems have been derived…
Recent advances in operating and manipulating DNA have provided unique experimental possibilities in many fields of DNA research, especially in gene therapy. Researchers have deployed many techniques, experimental and theoretical, to study…