Related papers: Enumerating Designing Sequences in the HP Model
We have constructed a model for the kinetics of rupture of membranes under tension, applying physical principles relevant to lipid bilayers held together by hydrophobic interactions. The membrane is characterized by the bulk compressibility…
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice ($d=3$ dimensions) and square lattice ($d=2$ dimensions), varying chain stiffness by an energy…
Phase separation of intrinsically disordered proteins is important for the formation of membraneless organelles, or biomolecular condensates, which play key roles in the regulation of biochemical processes within cells. In this work, we…
We investigate contact angle hysteresis on chemically patterned and superhydrophobic surfaces, as the drop volume is quasi-statically increased and decreased. We consider both two, and three, dimensions using analytical and numerical…
We present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible…
Interest in the protein folding problem has motivated a wide range of theoretical and experimental studies of the kinetics of the collapse of flexible homopolymers. In this Paper a phenomenological model is proposed for the kinetics of the…
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting…
Statistical models for families of evolutionary related proteins have recently gained interest: in particular pairwise Potts models, as those inferred by the Direct-Coupling Analysis, have been able to extract information about the…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
Wang-Landau sampling has been applied to investigate the thermodynamics and structural properties of a lattice hydrophobic-polar heteropolymer (the HP protein model) interacting with an attractive substrate. For simplicity, we consider a…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $\theta$-temperature is predicted to be sharp. For…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20 types or 20 letters). The reduced…
Ring, or cyclic, polymers have unique properties compared to linear polymers, due to their topologically closed structure that has no beginning or end. Experimental measurements on molecular ring polymers are challenging due to their…
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…
We present simulation results for the contact process on regular, cubic networks that are composed of a one-dimensional lattice and a set of long edges with unbounded length. Networks with different sets of long edges are considered, that…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…