Related papers: Thermodynamics of DNA loops with long-range correl…
Equiatomic TaNbHfZr and TaNbHfZrTi high-entropy alloys (HEAs) have been investigated for their phase stability, short-range clustering (SRC) type chemical ordering, other structural phenomena and and the effects on strengthening. Ab-initio…
We investigate the characteristic length scales associated with the glass transition phenomenon. By studying an atomic glass-forming liquid in negatively curved space, for which the local order is well identified and the amount of…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Dynamic facilitation theory assumes short-ranged dynamic constraints to be the essential feature of supercooled liquids and draws much of its conclusions from the study of kinetically constrained models. While deceptively simple, these…
The effect of topology on the collapse transition and instantaneous shape of an energy polydisperse polymer (a model heteropolymer) is studied by means of computer simulations. In particular, we consider three different chain topology,…
We investigate the role of disorder on the superconducting (SC) fluctuation in short coherence length d-wave superconductors. The particular intetest is focused on the disorder-induced microscopic inhomogeneity of SC fluctuation and its…
Nonequilibrium dynamics in isolated quantum many-body systems displays a number of intriguing features, such as many-body localization (MBL) and prethermalization. Here we investigate a simple ladder system with disorder, in which various…
We discuss general thermodynamic properties of molecular structure formation processes like protein folding by means of simplified, coarse-grained models. The conformational transitions accompanying these processes exhibit similarities to…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
Thermodynamic and dynamical properties of systems with long-range pairwise interactions (LRI), which decay as $1/r^{d+\sigma}$ at large distances $r$ in $d$ dimensions, are reviewed. Two broad classes of such systems are discussed. (i)…
If a liquid is cooled rapidly to form a glass, its structural relaxation becomes retarded, producing a drastic increase in viscosity. In two dimensions, strong long-wavelength fluctuations persist, even at low temperature, making it…
Based on the theory of the thermodynamic equilibrium in a system of quantum vortices in superfluids in the presence of a counterflow, the influence of a vortex tangle on various thermodynamic phenomena in quantum liquids is studied. Using…
The lattice gas model of condensation in a heterogeneous pore system, represented by a random graph of cells, is studied using an exact analytical solution. A binary mixture of pore cells with different coordination numbers is shown to…
The short time behavior of a disturbed system is influenced by off-shell motion and best characterized by the reduced density matrix possessing high energetic tails. We present analytically the formation of correlations due to collisions in…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
We analyze a one dimensional quantum model with off-diagonal disorder, consisting of a sequence of potential energy barriers whose width is a random variable either uniformly or normally distributed. We investigate how the disorder and the…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
We investigate by means of computer simulations the effect of structural disorder on the statistics of cracking for a thin layer of material under uniform and isotropic drying. The layer is discretized into a triangular lattice of springs.…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…