Related papers: Protein folding, anisotropic collapse and blue pha…
We propose an experimental scheme to effectively assemble chains of dipolar gases with an uniform length in a multi-layer system. The obtained dipolar chains can form a chain crystal with the system temperature easily controlled by the…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
Homopolymer chain with beads forming pairwise reversible bonds is a well-known model in polymer physics. We studied kinetics of homopolymer chain collapse, which was induced by pairwise reversible bonds formation. We compared kinetic…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
Conformational transitions of a single macromolecule of finite size $N$ cannot be described within standard thermodynamic framework. Taking as a basis a simple model of homopolymer exhibiting a coil-globule transition, we show that a…
Using a phase field crystal model we study the structure and dynamics of a drop of colloidal suspension during evaporation of the solvent. We model an experimental system where contact line pinning of the drop on the substrate is…
We study how solidification of model freely rotating polymers under athermal quasistatic compression varies with their bond angle $\theta_0$. All systems undergo two discrete, first-order-like transitions: entanglement at $\phi =…
Structural transitions and the melting behavior of crystalline poly(ethylene oxide),(CH2-CH2-O)n, (PEO) has been investigated using fully atomistic, constant pressure-constant temperature (NPT) molecular dynamics (MD) simulations. Melting…
We present results of Monte Carlo computer simulations of a coarse-grained hydrophobic-polar Go-like heteropolymer model and discuss thermodynamic properties and kinetics of an exemplified heteropolymer, exhibiting two-state folding…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Folding of protein-like heteropolymers into unique 3D structures is investigated using Monte Carlo simulations on a cubic lattice. We found that folding time of chains of length $N$ scales as $N^\lambda$ at temperature of fastest folding.…
The dynamical behavior of a weakly damped harmonic chain in a spatially periodic potential (Frenkel-Kontorova model) under the subject of an external force is investigated. We show that the chain can be in a spatio-temporally chaotic state…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
We discuss some interesting physical features stemming from our previous analytical study of a simple model of a fluid with dipolar-like interactions of very short range in addition to the usual isotropic Baxter potential for adhesive…
We consider a two-letter self-avoiding (square) lattice heteropolymer model of N_H (out ofN) attracting sites. At zero temperature, permanent links are formed leading to collapse structures for any fraction rho_H=N_H/N. The average chain…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
The folding ability of a heteropolymer model for proteins subject to Monte Carlo dynamics on a simple cubic lattice is shown to be strongly correlated with the energy gap between the native state and the structurally dissimilar part of the…
The biopolymers actin and microtubules are often in an ongoing assembling/disassembling state far from thermal equilibrium. Above a critical density this leads to spatially periodic patterns, as shown by a scaling argument and in terms of a…
We present a simple analytical theory of flexible polymer chain dissolved in a good solvent, carrying permanent freely oriented dipoles on the monomers. We take into account the dipole correlations within the random phase approximation…