Related papers: Phase Diagram for Unzipping DNA Using a Bond-Force…
A model for filament buckling at finite temperatures is presented. Starting from the classical worm-like chain model under constant compression, we use a mean-field approach for filament inextensibility to find the complete partition…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
Using dissipative particle dynamics (DPD) simulation method, we study the phase separation dynamics in block copolymer (BCP) melt in $d=3$, subjected to external stimuli such as light. An initial homogeneous BCP melt is rapidly quenched to…
We study the force-induced unfolding of a homopolymer on the three dimensional Sierpinski gasket. The polymer is subject to a contact energy between nearest neighbour sites not consecutive along the chain and to a stretching force. The…
In the standard model of particle physics, the strong force is characterized by the theory of quantum chromodynamics (QCD). It is commonly understood from QCD properties that hadrons, at sufficiently high temperatures or densities, melt…
The dependence of the unfolding pathway of proteins on the pulling speed is investigated. This is done by introducing a simple one-dimensional chain comprising $N$ units, with different characteristic bistable free energies. These units…
A simple model for the "diamond graphitization" type of phase transition is proposed, leading to a good agreement with the experimental data. The phase transition temperature dependence on the external pressure is found. A new phenomenon in…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
The Quark Meson Coupling Model which describes nuclear matter as a collection of non-overlapping MIT bags interacting by the self-consistent exchange of scalar and vector mesons is used to study nuclear matter at finite temperature. In its…
The QCD phase diagram in the temperature versus quark chemical potential plane is studied in the presence of a magnetic field, using the linear sigma model coupled to quarks. It is shown that the decrease of the couplings with increasing…
Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter $x$ and effective self-attraction promoting…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
We test the validity of some widely used phenomenological criteria for the localization of the fluid-solid transition thresholds against the phase diagrams of particles interacting through the exp-6, inverse-power-law, and Gaussian…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
Most bacteriophages are known to inject their double-stranded DNA into bacteria upon receptor binding in an essentially spontaneous way. This downhill thermodynamic process from the intact virion toward the empty viral capsid plus released…
This work introduces a methodology for the statistical mechanical analysis of polymeric chains under tension controlled by optical or magnetic tweezers at thermal equilibrium with an embedding fluid medium. The response of single bonds…
A simple model for the force-dependent unwinding and rewinding rates of the nucleosome inner turn is constructed and quantitatively compared to the results of recent measurements [A. H. Mack et al., J. Mol. Biol. 423, 687 (2012)]. First, a…
Dynamics of nucleosomes, the building blocks of the chromatin, has crucial effects on expression, replication and repair of genomes in eukaryotes. Beside constant movements of nucleosomes by thermal fluctuations, ATP-dependent chromatin…