Related papers: Path Integral Method for DNA Denaturation
Phase transitions impose topological constraints on thermodynamic state variables, masking energetic fluctuations at the phase boundary. This constraint is most apparent in melting systems, where temperature remains pinned despite continued…
The homochirality of the molecules of life has been a vexing problem with no generally accepted solution to date. Since a racemic mixture of chiral nucleotides frustrates the extension and replication of RNA and DNA, understanding the…
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 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…
Some lattice models having two conservation laws may display an equilibrium phase transition from a homogeneous (positive temperature - PT) to a condensed (negative temperature) phase, where a finite fraction of the energy is localized in a…
The kinetics of ordering and concurrent ordering and clustering is analyzed with an equation of motion initially developed to account for dissipative processes in quantum systems. A simplified energy eigenstructure, or…
The present work is devoted to the study of the thermostability of native DNA during binding to TiO$_{2}$ nanoparticles (NPs) at various concentrations under conditions close to physiological (0.1 M Na $^+$, pH 7) using thermal denaturation…
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…
Thermophoresis moves molecules along temperature gradients, typically from hot to cold. We superpose fluid flow with thermophoretic molecule flow under well defined microfluidic conditions, imaged by fluorescence microscopy. DNA is trapped…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
The denaturation transition which takes place in circular DNA is analyzed by extending the Poland-Scheraga model to include the winding degrees of freedom. We consider the case of a homopolymer whereby the winding number of the double…
The thermodynamics of phase transitions of binary solutions into spatially inhomogeneous one-dimensional states is studied theoretically with taking into account nonlinear effects. It is shown that below the spinodal decomposition…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
In a recent companion paper, we observed that the rules of ordinary thermodynamics generally fail to respect thermal duality, a symmetry of string theory under which the physics at temperature T is related to the physics at the inverse…
The decay rate for a particle in a metastable cubic potential is investigated in the quantum regime by the Euclidean path integral method in semiclassical approximation. The imaginary time formalism allows one to monitor the system as a…
Two temperature induced phase separation(2-TIPS) is a phenomenon observed in mixtures of active and passive particles modeled by scalar activity where the temperature of the particle is proportional to its activity. The binary mixture of…
The equilibrium thermodynamics of the two dimensional Su-Schrieffer-Heeger Model is derived by means of a path integral method which accounts for the variable range of the electronic hopping processes. While the lattice degrees of freedom…
We investigate a thermally isolated quantum many-body system with an external control represented by a step protocol of a parameter. The propagator at each step of the parameter change is described by thermodynamic quantities under some…