Related papers: Protein folding simulations with Interacting Growt…
The physics of glass has been a significant topic of interest for decades. Dynamical facilitation is widely believed to be an important characteristic of glassy dynamics, but the precise mechanism is still under debate. We propose a lattice…
There have been separate studies of the polymer collapse transition, where the collapse was induced by two different types of attraction. In each case, the configurations of the polymer were given by the same subset of random walks being…
A central goal of protein-folding theory is to predict the stochastic dynamics of transition paths --- the rare trajectories that transit between the folded and unfolded ensembles --- using only thermodynamic information, such as a…
We consider two types of Go models of a protein (crambin) and study their kinetics through molecular dynamics simulations. In the first model, the residue -- residue contact interactions are selected based on a cutoff distance, $R_c$,…
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…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
The self-avoiding walk on the square site-diluted correlated percolation lattice is considered. The Ising model is employed to realize the spatial correlations of the metric space. As a well-accepted result, the (generalized) Flory's mean…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Oriented self-avoiding walks (OSAWs) on a square lattice are studied, with binding energies between steps that are oriented parallel across a face of the lattice. By means of exact enumeration and Monte Carlo simulation, we reconstruct the…
Simple coarse-grained hydrophobic-polar models for heteropolymers as the lattice HP and the off-lattice AB model allow a general classification of characteristic behaviors for hydrophobic-core based tertiary folding. The strongly reduced…
A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…
Using the homogeneous electron gas (HEG) as a model, we investigate the sources of error in the `initiator' adaptation to Full Configuration Interaction Quantum Monte Carlo (i-FCIQMC), with a view to accelerating convergence. In particular…
We calculate thermodynamic quantities of HP lattice proteins by means of a multicanonical chain growth algorithm that connects the new variants of the Pruned-Enriched Rosenbluth Method (nPERM) and flat histogram sampling of the entire…
This paper presents a novel contact-implicit trajectory optimization method using an analytically solvable contact model to enable planning of interactions with hard, soft, and slippery environments. Specifically, we propose a novel contact…
In suitable environments, proteins, nucleic acids and certain synthetic polymers fold into unique conformations. This work shows that it is possible to construct lattice models of foldable heteropolymers by expressing the energy only in…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
In view of recent intense experimental and theoretical interests in the biophysics of liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), heteropolymer models with chain molecules configured as self-avoiding…
In two dimensions polymer collapse has been shown to be complex with multiple low temperature states and multi-critical points. Recently, strong numerical evidence has been provided for a long-standing prediction of universal scaling of…
With the aim to study the relationship between protein sequences and their native structures, we adopt vectorial representations for both sequence and structure. The structural representation is based on the Principal Eigenvector of the…
Scaling of folding properties of proteins is studied in a toy system -- the lattice Go model with various two- and three- dimensional geometries of the maximally compact native states. Characteristic folding times grow as power laws with…