Related papers: Melting of persistent double-stranded polymers
The Poland-Scheraga model for DNA denaturation, besides playing a central role in applications, has been widely studied in the physical and mathematical literature over the past decades. More recently a natural generalization has been…
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…
We introduce a simple geometric model for a double-stranded and double-helical polymer. We study the statistical mechanics of such polymers using both analytical techniques and simulation. Our model has a single energy-scale which…
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…
After crossing an initial barrier to break the first base-pair (bp) in double-stranded DNA, the disruption of further bps is characterized by free energies between less than one to a few kT. This causes the opening of intermittent…
Molecular dynamics simulation of a generic polymer model is applied to study melts of polymers with different types of intrinsic stiffness. Important static observables of the single chain such as gyration radius or persistence length are…
The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for…
Molecular dynamics simulations were performed for a polymer melt. In quiescent states, the inter-chain interaction energy supported by each particle takes relatively large values persistently for long times if the particle is close to an…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…
In this paper, a micro-mechanical model is introduce to characterize the stress softening phenomenon in double network hydrogels. Damage in polymer matrices under deformation, which appears as the rupture of cross-linking, is assumed to…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the binding (or hybridization) of two complementary strands of DNA of equal length, with the restriction that only bases with the…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
A barrier penetration model has been proposed to explain the spontaneous melting of the DNA oligomers into two separate single strands whereas the partially melted intermediate states are shown to be the bound state solution of the same…
The dynamical properties of double-stranded DNA are studied in the framework of the Peyrard-Bishop-Dauxois model using Langevin dynamics. Our simulations are analyzed in terms of two probability functions describing coherently localized…
The Poland-Scheraga model describes the denaturation transition of two complementary - in particular, equally long - strands of DNA, and it has enjoyed a remarkable success both for quantitative modeling purposes and at a more theoretical…
We generalize a recently investigated lattice model of semiflexible polymers formed under equilibrium polymerization in a solution and conduct a comprehensive investigation of its melting properties. The model is characterized by six…
We visualize entanglements in polymer melts using molecular dynamics simulation. A bead at an entanglement interacts persistently for long times with the non-bonded beads (those excluding the adjacent ones in the same chain). The…
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop-Daxuois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with…