Related papers: Path Integral Method for DNA Denaturation
Materials with nanoscale phase separation are considered. These materials are formed by a mixture of several phases, so that inside one phase there exist nanosize inclusions of other phases, with random shapes and random spatial locations.…
Statistical models on infinite graphs may exhibit inhomogeneous thermodynamic behaviour at macroscopic scales. This phenomenon is of geometrical origin and may be properly described in terms of spectral partitions into subgraphs with well…
One of the most intriguing features of string thermodynamics is thermal duality, which relates the physics at temperature T to the physics at inverse temperature 1/T. Unfortunately, the traditional definitions of thermodynamic quantities…
Motivated by the notion that the mathematics of gravity can be reproduced from a statistical requirement of maximal entropy, we study the consequence of introducing an entropic source term in the Einstein-Hilbert action. For a spatially…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
We investigate the unified first law and the generalized second law in a modified holographic dark energy model. The thermodynamical analysis on the apparent horizon can work and the corresponding entropy formula is extracted from the…
In classical superconductors an energy gap and phase coherence appear simultaneously with pairing at the transition to the superconducting state. In high-temperature superconductors, the possibility that pairing and phase coherence are…
Development of thermodynamic induction up to second order gives a dynamical bifurcation for thermodynamic variables and allows for the prediction and detailed explanation of nonequilibrium phase transitions with associated spontaneous…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
We consider an isolated point defect embedded in a homogeneous crystalline solid. We show that, in the harmonic approximation, a periodic supercell approximation of the formation free energy as well as of the transition rate between two…
We introduce a novel model for DNA condensation (whip-toroid transition) using the path integral method in the framework of the non-linear sigma model on a line segment. We show that some of its classical configurations exhibit toroidal…
The dynamics of individual DNA molecules in semidilute solutions undergoing planar extensional flow is simulated using a multi-particle Brownian dynamics algorithm, which incorporates hydrodynamic and excluded volume interactions in the…
We investigate aggregation mechanism of two proteins in a thermodynamically unambiguous manner by considering the finite size effect of free energy landscape of HP lattice protein model. Multi-Self-Overlap-Ensemble Monte Carlo method is…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
We showed that quantum mechanical superposition can sustain in the process of ion transfer in protein membrane for a substantial period, in spite of the presence of the interactions with environmental modes of molecular vibration. The…
A model of self avoiding walks with suitable constraint has been developed to study the effect of temperature on a single stranded DNA (ssDNA) in the constant force ensemble. Our exact calculations for small chains show that the extension…
The thermodynamics of phase transitions between phases that are size-mismatched but coherent differs from conventional stress-free thermodynamics. Most notably, in open systems such phase transitions are always associated with hysteresis.…
Based on the direct method of molecular dynamics, the temperature dependence of energy, partition function, entropy and free energy, describing the first-order phase transition, is calculated for the classical Peyrard-Bishop-Dauxois model…
We have studied the separation of a double stranded DNA (dsDNA), which is driven either by the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends…