Related papers: Force-Induced Unzipping Transitions in an Athermal…
The interior of cells is crowded thus making it important to assess the effects of macromolecules on the folding of proteins. Using the Self-Organized Polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we…
We investigate by Monte Carlo simulations the zipping and unzipping dynamics of two polymers connected by one end and subject to an attractive interaction between complementary monomers. In zipping, the polymers are quenched from a high…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
Depletion forces and macromolecular crowding govern the structure and function of biopolymers in biological cells and the properties of polymer nanocomposite materials. To isolate and analyze the influence of polymer shape fluctuations and…
We provide a unified theory for the high force elasticity of biopolymers solely in terms of the persistence length, $\xi_p$, and the monomer spacing, $a$. When the force $f>\fh \sim k_BT\xi_p/a^2$ the biopolymers behave as Freely Jointed…
We elucidate the structural transitions in a helical off-lattice homopolymer induced by crowding agents, as function of the number of monomers ($N$) and volume fraction ($\phi_c$) of crowding particles. At $\phi_c = 0$, the homopolymer…
Experiments and theories have shown that when steric interactions between crowding particles and proteins are dominant, which give rise to Asakura-Oosawa depletion forces, then the stabilities of the proteins increase compared to the…
We solve a two dimensional model for polymer chain folding in the presence of mechanical pulling force ($f$) exactly using equilibrium statistical mechanics. Using analytically derived expression for the partition function we determine the…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
The structural dynamics of a biopolymer is governed by a process of diffusion through its conformational energy landscape. In pulling experiments using optical tweezers, features of the energy landscape can be extracted from the probability…
Recent simulations have predicted that near jamming for collections of spherical particles, there will be a discontinuous increase in the mean contact number, Z, at a critical volume fraction, phi_c. Above phi_c, Z and the pressure, P are…
Force induced stretching of polymers is important in a variety of contexts. We have used theory and simulations to describe the response of homopolymers, with $N$ monomers, to force ($f$) in good and poor solvents. In good solvents and for…
We investigate the folding and forced-unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe biologically relevant phenomena that include adhesive interactions between proteins…
We investigate the force generation by polymerizing bundles of filaments, which form because of short-range attractive filament interactions. We show that bundles can generate forces by a zipping mechanism, which is not limited by buckling…
The entropic force exerted by the Brownian fluctuations of a grafted semiflexible polymer upon a rigid smooth wall are calculated both analytically and by Monte Carlo simulations. Such forces are thought to play an important role for…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
Using molecular dynamics simulations, we investigate the aggregation behavior of neutral stiff (rod-like) and flexible polymer chains mediated by attractive crowders. Attractive crowders serve as bridging agents, inducing aggregation…
The nonequilibrium dynamics of diffusion-mediated plasticity and creep in materials subjected to constant load at high homologous temperatures is studied atomistically using Phase Field Crystal (PFC) methods. Creep stress and grain size…
Using the criterion that the mechanical unzipping transition in a bound homopolymer is triggered when the average force exerted by the single unbound strands on the first base pair in the bound section exceeds the force binding the pair…