相关论文: Nonlinear dynamic intertwining of rods with self-c…

It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…

The importance of nonlinearities in material constitutive relations has long been appreciated in the continuum mechanics of macroscopic rods. Although the moment (torque) response to bending is almost universally linear for small deflection…

Cellular biology abound with filaments interacting through fluids, from intracellular microtubules, to rotating flagella and beating cilia. While previous work has demonstrated the complexity of capturing nonlocal hydrodynamic interactions…

Aims: Our aim is to investigate the resistive relaxation of a magnetic loop that contains braided magnetic flux but no net current or helicity. The loop is subject to line-tied boundary conditions. We investigate the dynamical processes…

We had combined the Neukirch-Marko model that describes the extension, torque and supercoiling in single, stretched and twisted DNA of infinite contour length, with a form of the free energy suggested by Sinha and Samuels to describe short…

Large scale molecular dynamics simulations are used to investigate the structural and dynamical modifications of supercooled water when confined inside an hydrophilic nanopore. We then investigate the evolution of the auto-organization of…

Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…

Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…

We simulate the nonlinear dynamic responses in Kirchhoff rod by including the important effects due to inertia and kinematic coupling of tension and torsion. We begin by reviewing a dynamic rod model of a strand (length of cable or DNA) in…

The genomic DNA of most bacteria is significantly underwound, which constrains the DNA molecule to adopt a branched plectoneme geometry. Moreover, biological functions like replication and transcription require that the two DNA strands be…

Random tilings of very large domains will typically lead to a solid, a liquid, and a gas phase. In the two-phase case, the solid-liquid boundary (arctic curve) is smooth, possibly with singularities. At the point of tangency of the arctic…

Macromolecules can gain special properties by adopting knotted conformations, but engineering knotted macromolecules is a challenging task. Here we surprisingly observed that knotting can be very effectively produced in active polymers.…

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…

Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…

We examine the conformations of a model for under- and overwound DNA. The molecule is represented as a cylindrically symmetric elastic string subjected to a stretching force and to constraints corresponding to a specification of the link…

The transport of DNA polymers through nanoscale pores is central to many biological processes, from bacterial gene exchange to viral infection. In single-molecule nanopore sensing, the detection of nucleic acid and protein analytes relies…

Recent works on localized charge transport along DNA, based on a three--dimensional, tight--binding model (Eur. Phys. J. B 30:211, 2002; Phys. D 180:256, 2003), suggest that charge transport is mediated by the coupling of the radial and…

Hydrodynamic interactions can generate rich emergent structures in active matter systems. Using large-scale hydrodynamic simulations, we demonstrate that hydrodynamic coupling alone can drive spontaneous self-organization across a hierarchy…

Innovation and its complement exnovation describe the progression of realized possibilities from the past to the future, and the process depends on the structure of the underlying graph. For example, the phylogenetic tree represents the…

The success of DNA nanotechnology has been driven by the discovery of novel structural motifs with a wide range of shapes and uses. We present a comprehensive study of the T-motif, a 3-armed, planar, right-angled junction that has been used…