Related papers: Protein folding simulations with Interacting Growt…
A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
A simple approach is proposed to investigate the protein structure. Using a low complexity model, a simple pairwise interaction and the concept of global optimization, we are able to calculate ground states of proteins, which are in…
We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries.…
We present a semiclassical phase-space method to calculate thermal and ground states of large interacting spin systems. To this end, we extend the recently developed truncated Wigner approximation for spins (TWA) to the imaginary time,…
We report a numerical study of self-avoiding polymers on the square lattice, including an attractive potential between nonconsecutive monomers. Using Wang-Landau sampling (WLS) with adaptive windows, we obtain the density of states for…
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
The cluster state acquired by evolving the nearest-neighbor (NN) Ising model from a completely separable state is the resource for measurement-based quantum computation. Instead of an NN system, a variable-range power law interacting Ising…
Single linear polymer chains in dilute solutions under good solvent conditions are studied by Monte Carlo simulations with the pruned-enriched Rosenbluth method up to the chain length $N \sim {\cal O}(10^4)$. Based on the standard simple…
In this work, we present a simple and efficient generator of polymeric linear chains, based on a random self-avoiding walk process. The chains are generated using a discrete process of growth, in cubic networks and in a finite time, without…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
A linear polymer grafted to a hard wall and underneath an AFM tip can be modelled in a lattice as a grafted lattice polymer (or self-avoiding walk) compressed underneath a piston approaching the wall. As the piston approaches the wall the…
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…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
The Go model is extended to the case when the non-native contact energies may be either attractive or repulsive. The folding temperature is found to increase with the energy of non-native contacts. The repulsive non-native contact energies…
The WW domain of the human Pin1 protein for its simple topology and the large amount of experimental data is an ideal candidate to assess theoretical approaches to protein folding. The purpose of the present work is to compare the…
We study the performance of Monte Carlo simulations that sample a broad histogram in energy by determining the mean first-passage time to span the entire energy space of d-dimensional ferromagnetic Ising/Potts models. We first show that…