Related papers: On Heteropolymer Shape Dynamics
We have developed a theory of polymer entanglement using an extended Cahn-Hilliard functional, with two extra terms. One is a nonlocal attractive term, operating over mesoscales, which is interpreted as giving rise to entanglement, and the…
We present a scaling theory describing the collapse of a homopolymer chain in poor solvent. At time t after the beginning of the collapse, the original Gaussian chain of length N is streamlined to form N/g segments of length R(t), each…
Molecular dynamic simulation enables one to correlate the evolution of the micro-structure with anisotropic stress when a material is subject to strain. The anisotropic stress due to a constant strain-rate load in a cross-linked polymer is…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
We extend classical Flory-Rehner theory for the expansion and compression of porous materials such as cross-linked polymer networks. The theory includes volume exclusion, affinity with the solvent, and finite stretching of the polymer…
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…
A vertex model introduced by M. Bowick, P. Di Francesco, O. Golinelli, and E. Guitter (cond-mat/9502063) describing the folding of the triangular lattice onto the face centered cubic lattice has been studied in the hexagon approximation of…
We study, using Monte Carlo simulations, the steady state properties of a system of particles interacting via hard core exclusion and moving in a discrete flashing disordered ratchet potential. Quenched disorder is introduced by breaking…
We study theoretically the entropic elasticity of a semi-flexible polymer, such as DNA, confined to two dimensions. Using the worm-like-chain model we obtain an exact analytical expression for the partition function of the polymer pulled at…
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…
A polymer network fractures by breaking covalent bonds, but the experimentally measured strength of the polymer network is orders of magnitude lower than the strength of covalent bonds. We investigate the effect of statistical variation of…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
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…
We address the general question of how the molecular weight dependence of chain dynamics in unentangled polymers is modified by blending. By dielectric spectroscopy we measure the normal mode relaxation of polyisoprene in blends with a slow…
The scaling behavior of a directed polymer in a two-dimensional (2D) random potential under confining force is investigated. The energy of a polymer with configuration $\{y(x)\}$ is given by $H\big(\{y(x)\}\big) = \sum_{x=1}^N \exyx +…
We theoretically investigate the kinetics of the folding transition of a single semiflexible polymer. In the folding transition, the growth rate decrease with an increase in the number of monomers in a collapsed domain, suggesting that the…
We investigate dimensional reduction, the property that the critical behavior of a system in the presence of quenched disorder in dimension d is the same as that of its pure counterpart in d-2, and its breakdown in the case of the…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
We use the variational approximation with double Gaussian type trial wave-functional approximation, in which we use the square root of the dispersion of the zero-mode wave-function as an order parameter, to study the out of equilibrium…