Related papers: Protein folding simulations with Interacting Growt…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
We introduce a diffusion model for energetically inhomogeneous systems. A random walker moves on a spin-S Ising configuration, which generates the energy landscape on the lattice through the nearest-neighbors interaction. The underlying…
In this paper we introduce a novel method of deriving a pairwise potential for protein folding. The potential is obtained by optimization procedure, which simultaneously maximizes the energy gap for {\it all} proteins in the database. To…
Self-avoiding walk (SAW) represents linear polymer chain on a large scale, neglecting its chemical details and emphasizing the role of its conformational statistics. The role of the latter is important in formation of agglomerates and…
Prudent walks are self-avoiding walks which cannot step towards an already occupied vertex. We introduce a new model of adsorbing prudent walks on the square lattice, which start on an impenetrable surface and accrue a fugacity $a$ with…
Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
We propose a new way of looking at global optimization of off-lattice protein models. We present a dual optimization concept of predicting optimal sequences as well as optimal folds. We validate the utility of the recently introduced…
Path sampling allows the study of rare events like chemical reactions, nucleation and protein folding via a Monte Carlo (MC) exploration in path space. Instead of configuration points, this method samples short molecular dynamics (MD)…
Recent advances in the simulation of frictionally contacting elastodynamics with the Incremental Potential Contact (IPC) model have enabled inversion and intersection-free simulation via the application of mollified barriers, filtered…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
Self-avoiding walks and self-avoiding trails, two models of a polymer coil in dilute solution, have been shown to be governed by the same universality class. On the other hand, self-avoiding walks interacting via nearest-neighbour contacts…
In this paper we present a new Monte Carlo Search (MCS) algorithm for finding the ground state energy of proteins in the HP-model. We also compare it briefly to other MCS algorithms not usually used on the HP-model and provide an overview…
We offer simple solutions to three kinematic problems that occur in the folding of proteins. We show how to construct suitably local elementary Monte Carlo moves, how to close a loop, and how to fold a loop without breaking the bond that…
The quantitative description of model protein folding kinetics using a diffusive collective reaction coordinate is examined. Direct folding kinetics, diffusional coefficients and free energy profiles are determined from Monte Carlo…
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…
We propose a hybrid Molecular Dynamics/Multi-particle Collision Dynamics model to simulate a set of self-assembled semiflexible filaments and free monomers. Further, we introduce a Monte-Carlo scheme to deal with single monomer addition…
A reliable prediction of 3D protein structures from sequence data remains a big challenge due to both theoretical and computational difficulties. We have previously shown that our kinetostatic compliance method (KCM) implemented into the…
An efficient method for the simulation of strained heteroepitaxial growth with intermixing using kinetic Monte Carlo is presented. The model used is based on a solid-on-solid bond counting formulation in which elastic effects are…
Inspired by recent experimental observation of patterning at the membrane of a living cell, we propose a generic model for the dynamics of a fluctuating interface driven by particle-like inclusions which stimulate its growth. We find that…