Related papers: DNA melting in poor solvent
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
We present experimental evidence for a first-order freezing/melting phase transition in a nonequilibrium system -- an oscillated two-dimensional isobaric granular fluid. The steady-state transition occurs between a gas and a crystal and is…
The phase diagram and critical behaviour of a simple toy model for DNA zipping/unzipping is examined in the framework of the Bethe approximation. The effects of solvent quality are included, and found to lead to a variety of different…
This communication reports the effect of DNA conformation on fluorescence resonance energy transfer (FRET) efficiency between two laser dyes in layer by layer (LbL) self assembled film. The dyes Acraflavine and Rhodamine B were attached…
The temperature phase transition in the N-component scalar field theory with spontaneous symmetry breaking is investigated in the perturbative approach. The second Legendre transform is used together with the consideration of the gap…
A double-stranded DNA unravels thermally through intermediate denatured bubble segments. Intrinsically, fluctuations ensue at the bubble boundaries from non-equilibrium (NE) energy exchanges with the environment. However, such details gets…
Based on the Monte Carlo kinetic method, we investigated the formation mechanisms of periodical modulations arising along the length of one-dimensional structures. The evolution of initially cylindrical nanowires/slabs at temperatures lower…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
Diluted mean-field models are graphical models in which the geometry of interactions is determined by a sparse random graph or hypergraph. Based on a nonrigorous but analytic approach called the "cavity method", physicists have predicted…
A theory of condensation and resolubilization of a dilute DNA solution with growing concentration of multivalent cations, N is suggested. It is based on a new theory of screening of a macroion by multivalent cations, which shows that due to…
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…
Experiments on layered materials call for a study of the influence of short-range spin correlations on the Mott transition. To this end, we solve the cluster dynamical mean-field equations for the Hubbard model on a plaquette with…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
We present a theory of the melting of elemental solids as a dislocation-mediated phase transition. We model dislocations near melt as non-interacting closed strings on a lattice. In this framework we derive simple expressions for the…
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
We study the melting of a moving vortex lattice through numerical simulations with the current driven 3D XY model with disorder. We find that there is a first-order phase transition even for large disorder when the corresponding equilibrium…
Additive manufacturing and welding processes are highly sensitive to heat dissipation, where improper thermal management leads to residual stresses, distortions, and cracking. Existing heat transfer models, such as Rosenthal's solutions,…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…