Related papers: Folding and form: Insights from lattice simulation…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
A linear copolymer made of two reciprocally attracting N-monomer blocks collapses to a compact phase through a novel transition, whose exponents are determined with extensive MC simulations in two and three dimensions. In the former case,…
There is a growing interest, inspired by advances in technology, in the low temperature physics of thin films. These quasi-2D systems show a wide range of ordering effects including formation of striped states, reorientation transitions,…
We present a solvable model that predicts the folding kinetics of two-state proteins from their native structures. The model is based on conditional chain entropies. It assumes that folding processes are dominated by small-loop closure…
We derive a Kinetic Monte Carlo model for studying how contacts form between confined surfaces in an ideal solution. The model incorporates repulsive and attractive surface-surface forces between a periodic (2+1)-dimensional solid-on-solid…
We study polar molecules with long-range dipole-dipole interactions confined to move on a two-leg ladder for different orientations of the molecular dipole moments with respect to the ladder. Matrix product states are employed to calculate…
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential…
We introduce a 2-dimensional lattice model of granular matter. We use a combination of proof and simulation to demonstrate an order/disorder phase transition in the model, to which we associate the granular phenomenon of random close…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…
The folding of naturally occurring, single domain proteins is usually well-described as a simple, single exponential process lacking significant trapped states. Here we further explore the hypothesis that the smooth energy landscape this…
Simple two-state folding kinetics of many small single-domain proteins are characterized by chevron plots with linear folding and unfolding arms consistent with a two-state description of equilibrium thermodynamics. This phenomenon is…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Molecular building blocks interacting at the nanoscale organize spontaneously into stable mono- layers that display intriguing long-range ordering motifs on the surface of atomic substrates. The patterning process, if appropriately…
The contact of a hydrogel during the rotational shearing on glass surface in concentrated polymer solution was observed in situ. Dynamic contact patterns that rotate in-phase with the rotational shearing of the gel were observed for the…
Random sequential adsorption of binary mixtures of extended objects on a two-dimensional triangular lattice is studied numerically by means of Monte Carlo simulations. The depositing objects are formed by self-avoiding random walks on the…
Origami-based design holds promise for developing materials whose mechanical properties are tuned by crease patterns introduced to thin sheets. Although there has been heuristic developments in constructing patterns with desirable…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
The folding kinetics of three-dimensional lattice Go models with side chains is studied using two different Monte Carlo move sets. A flexible move set based on single, double and triple backbone moves is found to be far superior compared to…
Exact results for conformational statistics of compact polymers are derived from the two-flavour fully packed loop model on the square lattice. This loop model exhibits a two-dimensional manifold of critical fixed points each one…