相关论文: Thermodynamics of DNA loops with long-range correl…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Effects of sequence disorder on looping and cyclization of the double-stranded DNA are studied theoretically. Both random intrinsic curvature and inhomogeneous bending rigidity are found to result in a remarkably wide distribution of…
Inspired by the avalanche scenario for many-body localization (MBL) instability, we reverse the conventional set-up and ask whether a large weakly-disordered chain can thermalize a smaller, strongly-disordered chain when the composite…
We use first-principles calculations to study the effect of magnetic disorder and electron correlations on the structural and thermodynamic properties of CrN. We illustrate the usability of a special quasirandom structure supercell…
We explore how the thermodynamic properties and dynamics of a self-interstitial prismatic dislocation loop are affected by microscopic-scale variations in its geometric configuration, an aspect that rarely received attention in literature.…
The elastic properties of semiflexible polymers are of great importance in biology. There are experiments on biopolymers like double stranded DNA, which twist and stretch single molecules to probe their elastic properties. It is known that…
Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential…
In fluids under temperature gradients, long-range correlations (LRCs) emerge generically, leading to enhanced density fluctuations. This phenomenon, characterized by the $\boldsymbol{q}^{-4}$ divergence in the static structure factor (where…
In this paper, we propose a thermodynamic mechanism for the formation of transcriptional foci via the joint agglomeration of DNA-looping proteins and protein-binding domains on DNA: The competition between the gain in protein-DNA binding…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
The dynamics of short 1D nonlinear Hamiltonian chains is analyzed numerically at different temperatures (energy per particle). The boundary temperature $T_b$ separating the regular (quasiperiodic) and the stochastic (chaotic) chain motion…
Prominences show a surprising amount of fine structure and it is widely believed that their threads, as seen in H$\alpha$ observations, provide indirect information concerning magnetic field topology. We investigate the spontaneous…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
We study the interplay between quasi-periodic disorder and superconductivity in a 1D tight-binding model with the quasi-periodic modulation of on-site energies that follow the Fibonacci rule and all the eigenstates are multifractal. As a…
Short-range order in strongly disordered structures plays an important role in their heat conduction property. Using numerical and analytical methods, we show that short-range spatial correlation (with a correlation length of $\Lambda_{m}$)…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
The interplay of superconductivity and disorder generates a wealth of complex phenomena. In particular, the peculiar structure of diffusive electronic wavefunctions is predicted to increase the superconducting critical temperature in some…
In a one dimensional lattice thermal fluctuations destroy the long-range order making particles of the lattice move on a scale much larger than the lattice spacing. We discuss the assumption that this motion may be responsible for the…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…