Related papers: On Heteropolymer Shape Dynamics
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…
We present a unified scaling theory for the dynamics of monomers for dilute solutions of semiflexible polymers under good solvent conditions in the free draining limit. Our theory encompasses the well-known regimes of mean square…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
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…
A kinetic model for the nucleation mechanism of protein folding is proposed. A protein is modeled as a heteropolymer consisting of hydrophobic and hydrophilic beads with equal constant bond lengths and bond angles. The total energy of the…
The dynamics of two 12-monomer heteropolymers on the square lattice is studied exactly within the master equation approach. The time evolution of the occupancy of the native state is determined. At low temperatures, the median folding time…
The kinetic behavior of a three-dimensional off-lattice heteropolymer model is studied in terms of the time dependence of the average mean-square displacement between configurations. It is found that at short time-scales similar behavior is…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
We present a model for semiflexible polymers in Hamiltonian formulation which interpolates between a Rouse chain and worm-like chain. Both models are realized as limits for the parameters. The model parameters can also be chosen to match…
We study the conformational properties of heteropolymers containing two types of monomers A and B, modeled as self-avoiding random walks on a regular lattice. Such a model can describe in particular the sequences of hydrophobic and…
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…
We perform a time-dependent study of the driven dynamics of overdamped particles which are placed in a one-dimensional, piecewise linear random potential. This set-up of spatially quenched disorder then exerts a dichotomous varying random…
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
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…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
The extension elasticity of rod-coil mutliblock copolymers is analyzed for two experimentally accessible situations. In the quenched case, when the architecture is fixed by the synthesis, the force law is distinguished by a sharp change in…
The phenomenology from the time of the quench to the asymptotic behavior in the phase-ordering kinetics of a system with conserved order parameter is investigated in the Bray-Humayun model and in the Cahn-Hilliard-Cook model. From the…
The conformational complexity of linear polymers far exceeds that of point-like atoms and molecules. Polymers can bend, twist, even become knotted. Thus they may also display a much richer phase structure than point particles. But it is not…