Related papers: Statistical physics of the melting of inhomogeneou…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
We study a one-dimensional spatial population model where the population sizes at each site are chosen according to a translation invariant and ergodic distribution and are uniformly bounded away from 0 and infinity. We suppose that the…
A method is proposed to select the suitable sets of potential parameters for a one-dimensional mesoscopic Hamiltonian model, first introduced to describe the DNA melting transition and later extended to investigate thermodynamic and…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
Using a simple analytic approach, we study the universal properties of second-order phase transition in holographic superconductor models. We explore a general model in arbitrary dimensions in which the condensation occurs via the…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…
It has recently been shown that in some DNA microarrays the time needed to reach thermal equilibrium may largely exceed the typical experimental time, which is about 15h in standard protocols (Hooyberghs et al. Phys. Rev. E 81, 012901…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
In the present work, we explore homogenization techniques for a class of switching diffusion processes whose drift and diffusion coefficients, and jump intensities are smooth, spatially periodic functions; we assume full coupling between…
We report a phase transition in the projected ensemble - the collection of post-measurement wavefunctions of a local subsystem obtained by measuring its complement. The transition emerges in systems undergoing random permutation dynamics, a…
Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work we employ…
How a closed system thermalizes, especially in the absence of global conservation laws but in the presence of disorder and interactions, is one of the central questions in non-equilibrium statistical mechanics. We explore this for a…
We study the influence of a THz field on thermal properties of DNA molecules. A Peyrard- Bishop-Dauxois model with the inclusion of a solvent interaction term is considered. The THz field is included as a sinusoidal driven force in the…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
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…
We present in this paper an approach for computing the homogenized behavior of a medium that is a small random perturbation of a periodic reference material. The random perturbation we consider is, in a sense made precise in our work, a…
During the melting transition of dimyristoyl phosphatidylglycerol (DMPG), the order of the lipid chains and the three-dimensional, vesicular structural arrangement change simultaneously. These changes result in peculiar heat capacity…
Phase transitions are ubiquitous across life, yet hard to quantify and describe accurately. In this work, we develop an approach for characterizing generic attributes of phase transitions from very limited observations made deep within…
This study examines anomalous diffusion and dynamical phase transitions in a nonlinear bouncer model with short-range interactions leading to velocity-dependent (adiabatic) collisions. By varying a control parameter, transitions between…
Systems of particles in a confining potential exhibit a spatially dependent density which fundamentally alters the nature of phase transitions that occur. A specific instance of this situation, which is being extensively explored currently,…