Related papers: Excluded Volume in Protein Sidechain Packing
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
We investigate the distribution of the volume and coordination number associated to each particle in a jammed packing of monodisperse hard sphere using the mesoscopic ensemble developed in Nature 453, 606 (2008). Theory predicts an…
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is…
The endpoint distribution and dynamics of semiflexible fibers is studied by numerical simulation. A brief overview is given over the analytical theory of flexible and semiflexible polymers. In particular, a closed expression is given for…
An off-lattice Monte Carlo algorithm for solutions of equilibrium polymers (EP) is proposed. At low and moderate densities this is shown to reproduce faithfully the (static) properties found recently for flexible linear EP using a lattice…
We perform Monte Carlo simulations to determine the average excluded volume <V_{ex}> of randomly oriented rectangular prisms, randomly oriented ellipsoids and randomly oriented capped cylinders in 3-D. There is agreement between the…
Using molecular dynamics simulation, we investigate the effect of confinement on a system that comprises several stiff segmented polymer chains where each chain has similar segments, but length and stiffness of the segments vary among the…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
Nanoscale and microscale confinement of biopolymers naturally occurs in cells and has been recently achieved in artificial structures designed for nanotechnological applications. Here, we present an extensive theoretical investigation of…
We obtain the entropy of flexible linear chains composed of M monomers placed on the square lattice using a transfer matrix approach. An excluded volume interaction is included by considering the chains to be self-and mutually avoiding, and…
We study entanglement properties of systems with spontaneously broken continuous symmetry. We find that in addition to the expected area law behavior, the entanglement entropy contains a subleading contribution which diverges…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
We use molecular dynamics simulations to study a semidilute, unentangled polymer solution containing well dispersed, weakly attractive nanoparticles (NP) of size ($\sigma_N$) smaller than the polymer radius of gyration $R_g$. We find that…
We show that an analogy between crowding in fluid and jammed phases of hard spheres captures the density dependence of the kissing number for a family of numerically generated jammed states. We extend this analogy to jams of mixtures of…
Conformations of partially or fully adsorbed semiflexible polymer chains are studied varying both contour length $L$, chain stiffness, $\kappa$, and the strength of the adsorption potential over a wide range. Molecular Dynamics simulations…
Through the consideration of spherically symmetric gravitating systems consisting of perfect fluids with linear equation of state constrained to be in a finite volume, an account is given of the properties of entropy at conditions in which…
As recently manifested , the quench dynamics of isolated quantum systems consisting of a finite number of particles, is characterized by an exponential spreading of wave packets in the many-body Hilbert space. This happens when the…
We develop a strong stretching approximation for a polymer brush made of self-avoiding polymer chains. The density profile of the brush and the distribution of the end monomer positions in stretching direction are computed and compared with…