Related papers: Modeling force-induced bio-polymer unfolding
We study a model describing the force-extension curves of modular proteins, nucleic acids, and other biomolecules made out of several single units or modules. At a mesoscopic level of description, the configuration of the system is given by…
Using a coarse-grained bead-spring model for semi-flexible macromolecules forming a polymer brush, structure and dynamics of the polymers is investigated, varying chain stiffness and grafting density. The anchoring condition for the grafted…
This paper reports the force spectroscopy analysis of a polymer that translocates from one side of a membrane to the other side through an extended pore, pulled by a cantilever that moves with constant velocity against the damping and the…
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…
We revisit the classical problem of a polymer confined in a slit in both of its static and dynamic aspects. We confirm a number of well known scaling predictions and analyse their range of validity by means of comprehensive Molecular…
Exact solutions for the elastic and thermodynamic properties for the wormlike chain model are elaborated in terms of Mathieu functions. The smearing of the classical Euler buckling instability for clamped polymers is analyzed for the…
Equilibrium mechanical unfolding of a globule formed by long flexible homopolymer chain collapsed in a poor solvent and subjected to an extensional force f (force-clamp mode) or extensional deformation D (position-clamp mode) is studied…
Motivated by single molecule experiments on biopolymers we explore equilibrium morphologies and force-extension behavior of copolymers with hydrophobic segments using Langevin dynamics simulations. We find that the interplay between…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
We report on an extensive study of craze formation in glassy polymers. Molecular dynamics simulations of a coarse-grained bead-spring model were employed to investigate the molecular level processes during craze nucleation, widening, and…
Constitutive modeling of dielectric elastomers has been of long standing interest in mechanics. Over the last two decades rigorous constitutive models have been developed that couple the electrical response of these polymers with large…
Force-induced deformations of a self-avoiding chain confined inside a cylindrical cavity, with diameter $D$, are probed using molecular dynamics simulations, scaling analysis, and analytical calculations. We obtain and confirm a simple…
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…
Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecule due to the intricate interplay between their activity and topological constraints. This study focuses on…
The interplay of nematic order and phase separation in solutions of semiflexible polymers in solvents of variable quality is investigated by density functional theory (DFT) and molecular dynamics (MD) simulations. We studied coarse-grained…
We study the influence of some quenched disorder in the sequence of monomers on the entropic elasticity of long polymeric chains. Starting from the Kratky-Porod model, we show numerically that some randomness in the favoured angles between…
Several methods for preparing well equilibrated melts of long chains polymers are studied. We show that the standard method in which one starts with an ensemble of chains with the correct end-to-end distance arranged randomly in the…
The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $\rho$, via Monte Carlo and molecular…
Using molecular dynamics simulations, we provide chain-level insights into the dissimilarities in rearrangements of polymers under uniaxial tensile and compressive deformation in glassy and semicrystalline samples of varying chain lengths.…
The unfolding of a polymer below the $\theta$ point when pulled by an external force is studied both in d=2 on the lattice and in $d=3$ off lattice. A ground state analysis of finite length chains shows that the globule unfolds via multiple…