Related papers: Remark on Protein Collapse from a Random Walk
We argue that the mean crossing number of a random polymer configuration is simply a measure of opacity, without being closely related to entanglement as claimed by several authors. We present an easy way of estimating its asymptotic…
The conformation and the phase diagram of a membrane protein are investigated via grand canonical ensemble approach using a homopolymer model. We discuss the nature and pathway of $\alpha$-helix integration into the membrane that results…
A particle subject to successive, random displacements is said to execute a random walk (in position or some other coordinate). The mathematical properties of random walks have been very thoroughly investigated, and the model is used in…
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…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
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…
We study a heteropolymer model with random contact interactions introduced some time ago as a simplified model for proteins. The model consists of self-avoiding walks on the simple cubic lattice, with contact interactions between nearest…
Chain-like macromolecules in solution, whether biological or synthetic, transform from an extended conformation to a compact one when temperature or other system parameters change. This collapse transition is relevant in various phenomena,…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Random walks with a general, nonlinear barrier have found recent applications ranging from reionization topology to refinements in the excursion set theory of halos. Here, we derive the first-crossing distribution of random walks with a…
We investigate the dynamics of the collapse of a single copolymer chain, when the solvent quality is suddenly quenched from good to poor. We employ Brownian dynamics simulations of a bead-spring chain model and incorporate fluctuating…
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…
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…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
We propose the quantitative mean-field theory of mechanical unfolding of a globule formed by long flexible homopolymer chain collapsed in poor solvent and subjected to an extensional force We show that with an increase in the applied force…
Collapse of the polymer chain upon the sharp decrease of solvent quality is studied. During collapse, any pair of polymer units appearing in a sufficiently close vicinity in space has the possibility with a certain probability to form an…
We investigate the internal structure of a polymer during collapse from an expanded coil to a compact globule. Collapse is more probable in local regions of high curvature, so a smoothing of the fractal polymer structure occurs that…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
We use a one-dimensional random walk on $D$-dimensional hyper-spheres to determine the critical behavior of statistical systems in hyper-spherical geometries. First, we demonstrate the properties of such walk by studying the phase diagram…