Related papers: Phase Diagram for Unzipping DNA Using a Bond-Force…
Dynamics of a single stranded DNA, which can form a hairpin have been studied in the constant force ensemble. Using Langevin dynamics simulations, we obtained the force-temperature diagram, which differs from the theoretical prediction…
The onset of an "eye-phase" and its role during the DNA unzipping is studied when a force is applied to the interior of the chain. The directionality of the hydrogen bond introduced here shows oscillations in force-extension curve similar…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
Using theoretical arguments and extensive Monte Carlo (MC) simulations of a coarse-grained three-dimensional off-lattice model of a \beta-hairpin, we demonstrate that the equilibrium critical force, $F_c$, needed to unfold the biopolymer…
Single molecule force spectroscopy provide details of the underlying energy surfaces of proteins which are essential to the understanding of their unfolding process. Recently, it has been observed experimentally that by pulling proteins in…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the…
We consider two complementary polymer strands of length $L$ attached by a common end monomer. The two strands bind through complementary monomers and at low temperatures form a double stranded conformation (zipping), while at high…
We explore the temperature effects in the superconducting phases of a hybridized two-band system. We show that for zero hybridization between the bands, there are two different critical temperatures. However, for any finite hybridization…
Single molecule force spectroscopy reveals unfolding of domains in titin upon stretching. We provide a theoretical framework for these experiments by computing the phase diagrams for force-induced unfolding of single domain proteins using…
A field theory of frictionless grain packings in two dimensions is shown to exhibit a zero-temperature critical point at a non-zero value of the packing fraction. The zero-temperature constraint of force-balance plays a crucial role in…
A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram…
With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…
Within self-consistent field theory we study the phase behavior of a symmetrical binary AB polymer blend confined into a thin film. The film surfaces interact with the monomers via short range potentials. One surface attracts the A…
Using Monte Carlo simulations, we study the dynamic transitions in the unzipping of an adsorbed homogeneous polymer on a surface (or wall). We consider three different types of surfaces. One end of the polymer is always kept anchored, and…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
A DNA-protein complex modelled by a semiflexible chain and an attractive spherical core is studied in the situation when an external stretching force is acting on one end monomer of the chain while the other end monomer is kept fixed in…
It is shown that hadronic matter formed at high temperatures, according to the prescription of the statistical bootstrap principle, develops a critical point at nonzero baryon chemical potential. The location of the critical point in the…
We study the features on the unzipping process of a modified version of the Peyrard-Bishop- Dauxois model. We show that the inclusion of a barrier in the on-site potential allows for the existence of stable domain wall solutions between…
Thermodynamical features of Xe system is investigated as functions of temperature and freeze-out density in the frame of lattice gas model. The calculation shows different temperature dependence of physical observables at different…