Related papers: Predicting Heteropolymer Phase Separation Using Tw…
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…
Intrinsically disordered proteins (IDPs) are typically low in nonpolar/hydrophobic but relatively high in polar, charged, and aromatic amino acid compositions. Some IDPs undergo liquid-liquid phase separation in the aqueous milieu of the…
Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of…
Liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is a major undergirding factor in the regulated formation of membraneless organelles in the cell. The phase behavior of an IDP is sensitive to its amino acid…
We present a theoretical model for predicting the phase behavior of polymer solutions in which phase separation competes with oligomerization. Specifically, we consider scenarios in which the assembly of polymer chains into stoichiometric…
A two-component system of penetrable particles interacting via a gaussian core potential is considered, which may serve as a crude model for binary polymer solutions. The pair structure and thermodynamic properties are calculated within the…
Synthetic copolymers and biopolymers, such as polypeptides and double-stranded DNA, often exhibit strong variations in bending stiffness along their contour, which can significantly impact conformational behavior at larger scales. To…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
Motivated by the idea that intrinsically disordered proteins (IDPs) condense into liquid-like droplets within cells, we carry out Monte Carlo simulations of a polymer lattice model to study the relationship between charge patterning and…
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex…
This paper studies a polymer chain in the vicinity of a linear interface separating two immiscible solvents. The polymer consists of random monomer types, while the interface carries random charges. Both the monomer types and the charges…
Large-scale Monte Carlo simulations of a phase-separating colloid-polymer mixture are performed and compared to recent experiments. The approach is based on effective interaction potentials in which the central monomers of self-avoiding…
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…
Using molecular dynamics simulation of a standard bead-spring model we investigate the density crossover scaling of strictly two-dimensional self-avoiding polymer chains focusing on properties related to the contact exponent set by the…
We apply the computational methodology of phase retrieval to the problem of folding heteropolymers. The ground state fold of the polymer is defined by the intersection of two sets in the configuration space of its constituent monomers: a…
A coarse-grained model for solutions of polymers in supercritical fluids is introduced and applied to the system of hexadecane and carbon dioxide as a representative example. Fitting parameters of the model to the gas-liquid critical point…
We present a generalized theory for studying phase separation in blends of polymers containing dipoles on their backbone. The theory is used to construct co-existence curves and to study the effects of dipolar interactions on interfacial…
Biologically functional liquid-liquid phase separation of intrinsically disordered proteins (IDPs) is driven by interactions encoded by their amino acid sequences. Little is currently known about the molecular recognition mechanisms for…
The phase structure of a homopolymer chain is investigated in terms of a universal theoretical model, designed to describe the infrared limit of slow spatial variations. The effects of chirality are studied and compared with the influence…
Motivation. Protein contact map describes the pairwise spatial and functional relationship of residues in a protein and contains key information for protein 3D structure prediction. Although studied extensively, it remains very challenging…