Model of Hydrophobic Attraction in Two and Three Dimensions

An earlier one-dimensional lattice model of hydrophobic attraction is extended to two and three dimensions and studied by Monte Carlo simulation. The solvent-mediated contribution to the potential of mean force between hydrophobic solute molecules and the solubility of the solute are determined. As in the earlier model, an inverse relation is observed between the strength and range of the hydrophobic attraction. The mean force no longer varies monotonically with distance, as it does in one dimension, but has some oscillations, reflecting the greater geometrical complexity of the lattice in the higher dimensions. In addition to the strong attraction at short distances, there is now also a local minimum in the potential of depth about $kT$ at a distance of three lattice spacings in two dimensions and one of depth about $2kT$ at a distance of two lattice spacings in three dimensions. The solubility of the solute is found to decrease with increasing temperature at low temperatures, which is another signature of the hydrophobic effect and also agrees with what had been found in the one-dimensional model.Comment: 4 pages, 4 figures, submitted to J. Chem. Phy

Magnetophoresis of Tagged Polymers

We present quantitative results for the drift velocity of a polymer in a gel if a force (e.g. through an electric or magnetic field) acts on a tag, attached to one of its ends. This is done by introducing a modification of the Rubinstein-Duke model for electrophoresis of DNA. We analyze this modified model with exact and Monte Carlo calculations. Tagged magnetophoresis does not show band collapse, a phenomenon that limits the applicability of traditional electrophoresis to short polymers.Comment: 10 pages revtex, 3 PostScript figure

Identification of relaxation and diffusion mechanisms in amorphous silicon

The dynamics of amorphous silicon at low temperatures can be characterized by a sequence of discrete activated events, through which the topological network is locally reorganized. Using the activation-relaxation technique, we create more than 8000 events, providing an extensive database of relaxation and diffusion mechanisms. The generic properties of these events - size, number of atoms involved, activation energy, etc. - are discussed and found to be compatible with experimental data. We introduce a complete and unique classification of defects based on their topological properties and apply it to study of events involving only four-fold coordinated atoms. For these events, we identify and present in detail three dominant mechanisms.Comment: 4 pages, three figures, submitted to PR

Long-time dynamics of de Gennes' model for reptation

Diffusion of a polymer in a gel is studied within the framework of de Gennes' model for reptation. Our results for the scaling of the diffusion coefficient D and the longest relaxation time tau are markedly different from the most recently reported results, and are in agreement with de Gennes' reptation arguments: D ~ 1/N^2 and tau ~ N^3. The leading exponent of the finite-size corrections to the diffusion coefficient is consistent with the value of -2/3 that was reported for the Rubinstein model. This agreement suggests that its origin might be physical rather than an artifact of these models.Comment: 5 pages, 5 figures, submitted to J. Chem. Phy

Reaching large lengths and long times in polymer dynamics simulations

A lattice model is presented for the simulation of dynamics in polymeric systems. Each polymer is represented as a chain of monomers, residing on a sequence of nearest-neighbor sites of a face-centered-cubic lattice. The polymers are self- and mutually avoiding walks: no lattice site is visited by more than one polymer, nor revisited by the same polymer after leaving it. The dynamics occurs through single-monomer displacements over one lattice spacing. To demonstrate the high computational efficiency of the model, we simulate a dense binary polymer mixture with repelling nearest-neighbor interactions between the two types of polymers, and observe the phase separation over a long period of time. The simulations consist of a total of 46,080 polymers, 100 monomers each, on a lattice with 13,824,000 sites, and an interaction strength of 0.1 kT. In the final two decades of time, the domain-growth is found to be d(t) ~ t^1/3, as expected for a so-called "Model B" system.Comment: 6 pages, 4 eps figure