Related papers: Controlling the folding and substrate-binding of p…
Associative polymer networks have shown a major promise in fabrication of self-healing and responsive materials. The can also serve as simple models to study more complex biological systems where transient interactions play an important…
Planar brushes formed by end-grafted semiflexible polyampholyte chains, each chain containing equal number of positively and negatively charged monomers is studied using molecular dynamics simulations. Keeping the length of the chains…
We present Monte Carlo simulations of colloidal particles pulled into grafted polymer layers by external fields. The insertion free energy of a single colloid into the polymer layer is qualitatively different for surfaces with an ordered…
The folding vs. adsorption behaviour of a coarse-grained off-lattice protein model near an attractive surface is presented within the frame of a Multicanonical Monte Carlo simulations. In the polymer-surface model, the Lennard-Jones…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
Using three-dimensional Go lattice models with side chains for proteins, we investigate the dependence of folding times on protein length. In agreement with previous theoretical predictions, we find that the folding time grows as a power…
We introduce an efficient, scalable Monte Carlo algorithm to simulate cross-linked architectures of freely-jointed and discrete worm-like chains. Bond movement is based on the discrete tractrix construction, which effects conformational…
The structure of a polystyrene matrix filled with tightly cross-linked polystyrene nanoparticles, forming an athermal nanocomposite system, is investigated by means of a Monte Carlo sampling formalism. The polymer chains are represented as…
Many variants of RNA, DNA, and even proteins can be considered semiflexible polymers, where bending stiffness, as a type of energetic penalty, competes with attractive van der Waals forces in structure formation processes. Here, we…
We propose new polymer models for Monte Carlo simulation and apply them to a polymer chain confined in a relatively thin box which has both curved and flat sides, and show that either an ideal or an excluded-volume chain spends more time in…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…
We study folding dynamics of protein-like sequences on square lattice using physical move set that exhausts all possible conformational changes. By analytically solving the master equation, we follow the time-dependent probabilities of…
Semiflexible polymers are ubiquitous in natural and artificial systems, where their intermediate rigidity gives rise to rich structural and dynamical behavior. Confinement plays a central role in these behaviors, as spatial restrictions can…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
We study the Brownian dynamics of flexible and semiflexible polymer chains densely grafted on a flat substrate, upon rapid quenching of the system when the quality of solvent becomes poor and chains attempt collapse into a globular state.…
In this paper we study the phenomenon of kinetic partitioning when a polypeptide chain has two ground state conformations one of which is more kinetically reachable than the other. This question is relevant to understand the phenomenology…