相关论文: Torsional fluctuations in columnar DNA assemblies
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
The macroscopic properties, the properties of individual components and how those components interact with each other are three important aspects of a composited structure. An understanding of the interplay between them is essential in the…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
The elastic moduli of four numerical random isotropic packings of Hertzian spheres are studied. The four samples are assembled with different preparation procedures, two of which aim to reproduce experimental compaction by vibration and…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We examine the potential-energy curves and polarization of the dipole moments of two static polar molecules under the influence of an external dc electric field and their anisotropic dipole-dipole interaction. We model the molecules as…
The term active nematics designates systems in which apolar elongated particles spend energy to move randomly along their axis and interact by inelastic collisions in the presence of noise. Starting from a simple Vicsek-style model for…
The spatial organization of DNA involves DNA loop extrusion and the formation of protein-DNA condensates. While the significance of each process is increasingly recognized, their interplay remains unexplored. Using molecular dynamics…
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…
DNA supercoiling plays an important role in a variety of cellular processes. The torsional stress related with supercoiling may be also involved in gene regulation through the local structure and dynamics of the double helix. To check this…
DNA toroids are compact torus-shaped bundles formed by one or multiple DNA molecules being condensed from the solution due to various condensing agents. It has been shown that the DNA toroidal bundles are twisted. However, the global…
We examine the effects of thermal fluctuations on thin elastic filaments with non-circular cross-section and arbitrary spontaneous curvature and torsion. Analytical expressions for orientational correlation functions and for the persistence…
Molecular dynamics simulations were employed to investigate the phase separation process of a two-dimensional active Brownian dumbbell model. We evaluated the time dependence of the typical size of the dense component using the scaling…
DNA and other biopolymers differ from classical polymers due to their torsional stiffness. This property changes the statistical character of their conformations under tension from a classical random walk to a problem we call the `torsional…
Intermittent density fluctuations of nucleotide molecules (adenine, guanine, cytosine and thymine) along DNA sequences are studied in the framework of a hierarchical structure (HS) model originally proposed for the study of fully developed…
Turbulent motions due to flux-driven thermal convection is investigated by numerical simulations and stochastic modelling. Tilting of convection cells leads to the formation of sheared flows and quasi-periodic relaxation oscillations for…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…