Related papers: Enumerating Designing Sequences in the HP Model
We address the problem of inverse polymer swelling. This phenomenon, in which a collapsed polymer chain swells upon decreasing temperature, can be observed experimentally in so-called thermoreversible homopolymers in aqueous solution, and…
We present results from extensive molecular dynamics simulations of collapse transitions of hydrophobic polymers in explicit water focused on understanding effects of lengthscale of the hydrophobic surface and of attractive interactions on…
Hydrophobic interactions provide driving forces for protein folding, membrane formation, and oil-water separation. Motivated by information theory, the poorly understood nonpolar solute interactions in water are investigated. A simple…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Force induced stretching of polymers is important in a variety of contexts. We have used theory and simulations to describe the response of homopolymers, with $N$ monomers, to force ($f$) in good and poor solvents. In good solvents and for…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
The stability of model proteins with designed sequences is assessed in terms of the number of sequences (obtained from the designed sequence through mutations), which fold into 5the ``native'' conformation. By a complete enumeration of the…
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
Among the various features of amino acids, the hydrophobic property has most visible impact on stability of a sequence folding. This is mentioned in many protein folding related work, in this paper we more elaborately discuss the…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
Water and water-mediated interactions determine thermodynamic and kinetics of protein folding, protein aggregation and self-assembly in confined spaces. To obtain insights into the role of water in the context of folding problems, we…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
In this brief report, we revisit analytical calculation [Mishra, {\it et al.}, Physica A {\bf 323} (2003) 453 and Mishra, NewYork Sci. J. {\bf{3(1)}} (2010) 32.] of the persistent length of a semiflexible homopolymer chain in %the extremely…
We use a bath of chaotic surface waves in water to mechanically and macroscopically mimic the thermal behavior of a short articulated chain with only nearest-neighbor interactions. The chaotic waves provide isotropic and random agitation to…
Employing numerical linked-cluster expansions (NLCEs) along with exact diagonalizations of finite clusters with periodic boundary condition, we study the energy, specific heat, entropy, and various susceptibilities of the antiferromagnetic…
Motivation: Protein sequence world is discrete as 20 amino acids (AA) while its structure world is continuous, though can be discretized into structural alphabets (SA). In order to reveal the relationship between sequence and structure, it…
Protein structure prediction (PSP) is computationally a very challenging problem. The challenge largely comes from the fact that the energy function that needs to be minimised in order to obtain the native structure of a given protein is…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…