Related papers: Critical dynamics of DNA denaturation
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…
We study heat conduction in a one-dimensional chain of particles with longitudinal as well as transverse motions. The particles are connected by two-dimensional harmonic springs together with bending angle interactions. The problem is…
The concept of local symmetry dynamics has recently been used to demonstrate the evolution of discrete symmetries in one-dimensional chains leading to emergent periodicity. Here we go one step further and show that the unboundedness of this…
We theoretically study the molecular-weight dependence of DNA thermophoresis, which arises from mutual advection of the n repeat units of the molecular chain. As a main result we find that the dominant driving forces, i.e., the thermally…
We generate point configurations (PCs) by thresholding the local energy of the Ashkin-Teller model in two dimensions (2D) and study the percolation transition at different values of $\lambda$ along the critical Baxter line by varying the…
The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D…
We consider a new model which consists of a DNA together with a RNA. Here we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model we use methods of statistical mechanics,…
We show that in a decay of the form B_d or B_s-> P_1 P_2 gamma (where P_1 and P_2 are pseudoscalar mesons), through a flavor changing dipole transition, time dependent oscillations can reveal the presence of physics beyond the Standard…
We propose a phonon-assisted tunnelling model for explanation of conductivity dependence on temperature and temperature-dependent I-V characteristics in deoxyribonucleic acid (DNA) molecules. The capability of this model for explanation of…
We numerically study the binary disordered Poland-Scheraga model of DNA denaturation, in the regime where the pure model displays a first order transition (loop exponent $c=2.15>2$). We use a Fixman-Freire scheme for the entropy of loops…
Following upon our recent work on vector correlations in the Ar-NO collisions [PCCP 12, 1038 (2010)], we compare model results with close-coupling calculations for a range of channels and collision energies for the He-NO system. The…
At zero temperature the lowest part of the spectrum of the QCD Dirac operator is known to consist of delocalized modes that are described by random matrix statistics. In the present paper we show that the nature of these eigenmodes changes…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
We study the finite temperature localization transition in the spectrum of the overlap Dirac operator. Simulating the quenched approximation of QCD, we calculate the mobility edge, separating localized and delocalized modes in the spectrum.…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
In the demanding biosensing environment, improving selection efficiency strategies has become an issue of great significance. DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, are representative of the…
We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We…
We study dynamical properties of strongly coupled chiral matter by using holographic method. We demonstrate, at both linear and nonlinear levels, that perturbations on thermodynamically unstable backgrounds within the spinodal region of…
We review the background, theory and general equations for the analysis of equilibrium protein unfolding experiments, focusing on denaturant and heat-induced unfolding. The primary focus is on the thermodynamics of reversible…
We theoretically investigate the subradiance dynamics in a nonreciprocal chiral-coupled atomic chain, in which infinite-range dipole-dipole interaction emerges in the dissipation. We find that super- and subradiance are both present in the…