Related papers: Stick-release pattern in stretching single condens…
Although the stretching of polymers and biomolecules is important in numerous settings, their response when confined to two-dimensions is relatively poorly-studied. In this paper, we derive closed-form analytical expressions for the…
Understanding how cells escape from embedded spheroids requires a mechanical framework linking stress generation within cells, across cells, and between cells and the surrounding extracellular matrix (ECM). We develop such a framework by…
When stressed sufficiently, solid materials yield and deform plastically via reorganization of microscopic constituents. Indeed, it is possible to alter the micro-structure of materials by judicious application of stress, an empirical pro-…
We propose a framework to model elastic properties of polycrystals by coupling crystal orientational degrees of freedom with elastic strains. Our model encodes crystal symmetries and takes into account explicitly the strain compatibility…
In this paper we consider a physical system in which two DNA molecules braid about each other. The distance between the two molecular ends, on either side of the braid, is held at a distance much larger than supercoiling radius of the…
We propose that semiflexible polymers in poor solvent collapse in two stages. The first stage is the well known formation of a dense toroidal aggregate. However, if the solvent is sufficiently poor, the condensate will undergo a second…
The buckling and twisting of slender, elastic fibers is a deep and well-studied field. A slender elastic rod that is twisted with respect to a fixed end will spontaneously form a loop, or hockle, to relieve the torsional stress that builds.…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
We report a computer simulation study of a model gel-former obtained by modifying the three-body interactions of the Stillinger-Weber potential for silicon. This modification reduces the average coordination number and consequently shifts…
The dynamic response of prestressed semiflexible biopolymers is characterized by the propagation and relaxation of tension, which arises due to the near inextensibility of a stiff backbone. It is coupled to the dynamics of contour length…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
An applied tension force changes the equilibrium conformations of a polymer chain tethered to a planar substrate and thus affects the adsorption transition as well as the coil-globule and crystallization transitions. Conversely, solvent…
To study the elastic properties of rod-like DNA nanostructures, we perform long simulations of these structure using the oxDNA coarse-grained model. By analysing the fluctuations in these trajectories we obtain estimates of the bend and…
One cannot pull an open, curved string along itself. This fact is clearly reflected in the unwrapping motion of a string or chain as it is dragged around an object, and implies strong consequences for slender structures in passive…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical…
Though often considered as one of the main driving process of the complexation of species of opposite charges, the release of counterions has never been experimentally directly measured on polyelectrolyte/proteins complexes. We present here…
Recently experiments showed that some adhesive receptor-ligand complexes increase their lifetimes when they are stretched by mechanical force, while the force increase beyond some thresholds their lifetimes decrease. Several specific…
The article presents a comprehensive study of counterion dynamics around a generic linear polyelectrolyte (PE) chain with the help of coarse-grained computer simulations. The ion-chain coupling is discussed in the form of binding time,…
The dynamic structure factor of semiflexible polymers in solution is derived from the wormlike chain model. Special attention is paid to the rigid constraint of an inextensible contour and to the hydrodynamic interactions. For the cases of…