相关论文: Characterizing large scale base composition struct…

The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…

We aim to better understand how the spatial structure of molecular clouds is governed by turbulence. For that, we study the large-scale spatial distribution of low density molecular gas and search for characteristic length scales. We employ…

In this work we investigate the interplay between coherent and incoherent charge transport in cytosine-guanine (GC) rich DNA molecules. Our objective is to introduce physically grounded approach to dephasing in large molecules and to…

In condensed matter physics, simplified descriptions are obtained by coarse-graining the features of a system at a certain characteristic length, defined as the typical length beyond which some properties are no longer correlated. From a…

We perform three-dimensional (3D) compressible MHD simulations over many dynamical times for an extended range of sonic and Alfven Mach numbers and analyze the statistics of 3D density and 2D column density, which include probability…

We study big bang nucleosynthesis in the presence of large mass-scale, non-linear entropy fluctuations. Overdense regions, with masses above the local baryon-Jeans mass, are expected to collapse and form condensed objects. Surviving…

The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…

We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the…

Heterogeneity is classified in five categories---topologic, geometric, kinematic, static, and constitutive---and the first four categories are investigated in a numerical DEM simulation of biaxial compression. The simulation experiments…

High-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still…

Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…

Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…

The spectrum and scale of fluctuations in protein structures affect the range of cell phenomena, including stability of protein structures or their fragments, allosteric transitions and energy transfer. The study presents a…

It is shown that the nucleotide sequences in DNA molecules have cluster-scaling properties (discovered for the first time in turbulent processes: Sreenivasan and Bershadskii, 2006, J. Stat. Phys., 125, 1141-1153.). These properties are…

We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…

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…

A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…

We reexamine big bang nucleosynthesis with large-scale baryon density inhomogeneities when the length scale of the density fluctuations exceeds the neutron diffusion length ($\sim 10^7-10^8$ cm at BBN), and the amplitude of the fluctuations…

The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…

We study the effect of density fluctuations induced by turbulence on the HI/H$_2$ structure in photodissociation regions (PDRs) both analytically and numerically. We perform magnetohydrodynamic numerical simulations for both subsonic and…