Related papers: Characterizing large scale base composition struct…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
We study a highly supercooled two-dimensional fluid mixture via molecular dynamics simulation. We follow bond breakage events among particle pairs, which occur on the scale of the $\alpha$ relaxation time $\tau_{\alpha}$. Large scale…
Systems driven far from equilibrium may exhibit anomalous density fluctuations: active matter with orientational order display giant density fluctuations at large scale, while systems of interacting particles close to an absorbing phase…
It is of great interest to quantify the contributions of genetic variation to brain structure and function, which are usually measured by high-dimensional imaging data (e.g., magnetic resonance imaging). In addition to the variance, the…
ds-RNA and standard ds-DNA show specific structural differences in their di-nucleotide steps, piled along the helical axis. Modeling the helices of short fragments by a 3D mesoscopic Hamiltonian model, I use path integral techniques to…
Four quantities are fundamental in homogenization of elliptic systems in divergence form and in its applications: the field and the flux of the solution operator (applied to a general deterministic right-hand side), and the field and the…
Genetic sequences are known to possess non-trivial composition together with symmetries in the frequencies of their components. Recently, it has been shown that symmetry and structure are hierarchically intertwined in DNA, suggesting a…
Using Bayesian inference, we determine probabilistic constraints on the parameters describing the fluctuating structure of protons at high energy. We employ the color glass condensate framework supplemented with a model for the spatial…
The complexity of the primary structure of human DNA is explored using methods from nonequilibrium statistical mechanics, dynamical systems theory and information theory. The use of chi-square tests shows that DNA cannot be described as a…
The understanding of inertial-scale dynamics in the heliosheath is not yet thorough. Magnetic field fluctuations across the inner heliosheath (IHS) and the local interstellar medium (LISM) are here considered to provide accurate and highly…
Twenty years of extensive research has yet to produce a general consensus on the origin of high temperature superconductivity (HTS). However, several generic characteristics of the cuprate superconductors have emerged as the essential…
We develop a formalism to discuss the properties of GENERIC systems in terms of corresponding Hamiltonians that appear in the characterization of large-deviation limits. We demonstrate how the GENERIC structure naturally arises from a…
Physical properties of the tiny scale structures in the cold neutral medium (CNM) of galaxies is a long-standing puzzle. Only a few lines of sights in our Galaxy have been studies with mixed results on the scale-invariant properties of such…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
Catalogues of galaxies, clusters of galaxies and superclusters - sources of information to study the large-scale structure of the Universe are reviewed. The power spectrum of density perturbations, and the correlation function are discussed…
Several differential equation models have been proposed to explain the formation of patterns characteristic of the grid cell network. Understanding the effect of noise on these models is one of the key open questions in computational…
We present a novel method for the accurate numerical determination of the phase behavior of fluid mixtures having large particle size asymmetries. By incorporating the recently developed geometric cluster algorithm within a restricted Gibbs…