650 research outputs found
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 at a
distance of three lattice spacings in two dimensions and one of depth about
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
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