Related papers: Ideal-Chain Collapse in Biopolymers
By simulating the first order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics and Monte Carlo with non-kinetic moves, we show that the effective and the thermodynamic transition temperatures are…
Pull-in (or electro-mechanical) instability occurs when a drastic decrease in the thickness of a dielectric elastomer results in electrical breakdown, which limits the applications of dielectric devices. Here we derive the criteria for…
In recent years molecular elasticity has emerged as an active area of research: there are experiments that probe mechanical properties of single biomolecules such as DNA and Actin, with a view to understanding the role of elasticity of…
We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For…
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The elastic network (EN) is a prime model that describes the long-time dynamics of biomolecules. However, the use of harmonic potentials renders this model insufficient for studying large conformational changes of proteins (e.g. stretching…
Recent advances in single macromolecule experiments have sparked interest in the ensemble dependence of force-extension relations. The thermodynamic limit may not be attainable for such systems, that leads to inequivalence of the…
Folding and unfolding of biopolymers are often manipulated in experiment by tuning pH, temperature, single-molecule force or shear field. Here we carry out Brownian dynamics simulations to explore the behavior of a single self-attracting…
We study the elastic response of a worm-like polymer chain with reversible kink-like structural defects. This is a generic model for (a) the double-stranded DNA with sharp bends induced by binding of certain proteins, and (b) effects of…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, $\theta$-chains, i.e., chains at the transition from a swollen…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
A lattice model of the directed self-avoiding walk is used to estimate the possibility on the formation of an infinitely long linear semi-flexible copolymer chain. The copolymer chain is assumed to composed of four different types of the…
We show that when a self-avoiding polymer chain is pulled off a sticky surface by force applied to the end segment, it undergoes a first-order thermodynamic phase transition albeit without phase coexistence. This unusual feature is…
The mechanical resistance of a polyethylene strand subject to tension and the way its properties are affected by the presence of a knot is studied using first-principles molecular dynamics calculations. The distribution of strain energy for…
We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence…
This paper develops a damage model for unfilled cross-linked rubbers based on the concept of scission of polymer chains. The model is built up on the well-known Gent elastic potential complemented by a kinetic equation describing effects of…
Using analytic theory, numerical calculation and Langevin dynamics simulation we demonstrate the existence of a first order unraveling transition in the stretching of a polymer chain in a poor solvent. The chain suddenly unravels from a…
Scaling law for geometrical and dynamical quantities of biological molecules is an interesting topic. According to Flory's theory, a power law between radius of gyration and the length of homopolymer chain is found, with exponent 3/5 for…