Related papers: Exactly Solvable Model for Helix-Coil-Sheet Transi…
The thermodynamic behavior of collapse transition in a fully flexible coarse-grained model of energy polydisperse polymer (EPP), a statistical model of random heteropolymer, is investigated in an implicit solvent by means of molecular…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Fluid dynamics plays a crucial role in various multiphysics applications, including energy systems, electronics cooling, and biomedical engineering. Developing models for complex coupled systems can be challenging and time-consuming. In…
We construct a Hamiltonian for a single domain protein where the contact enthalpy and the chain entropy decrease linearly with the number of native contacts. The hydration effect upon protein unfolding is included by modeling water as ideal…
An interacting lattice model describing the subspace spanned by a set of strongly-correlated bands is rigorously coupled to density functional theory to enable ab initio calculations of geometric and topological material properties. The…
A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
The helix-coil transition is modified by grafting to a surface. This modification is studied for short peptides capable of forming $\alpha$-helices. Three factors are involved: (i) the grafting can induced change of the boundary free energy…
The folding of a peptide chain into a three dimensional structure is a thermodynamically driven process such that the chain naturally evolves to form domains of similar amino acids. The formation of this domain occurs by curling the one…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
The Hamiltonian dynamics of chains of nonlinearly coupled particles is numerically investigated in two and three dimensions. Simple, off-lattice homopolymer models are used to represent the interparticle potentials. Time averages of…
A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Quantifying the effects of amino acid mutations in proteins presents a significant challenge due to the vast combinations of residue sites and amino acid types, making experimental approaches costly and time-consuming. The Potts model has…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
Conformational phases of a semiflexible off-lattice homopolymer model near an attractive substrate are investigated by means of multicanonical computer simulations. In our polymer-substrate model, nonbonded pairs of monomers as well as…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
Inverse statistical approaches to determine protein structure and function from Multiple Sequence Alignments (MSA) are emerging as powerful tools in computational biology. However the underlying assumptions of the relationship between the…
The melting transition of two-dimensional (2D) systems is a fundamental problem in condensed matter and statistical physics that has advanced significantly through the application of computational resources and algorithms. 2D systems…