490 research outputs found
Discovery and Assessment of New Target Sites for Anti-HIV Therapies
Human immunodeficiency virus (HIV) infects cells by endocytosis and takes over parts of the cell’s reaction pathways in order to reproduce itself and spread the infection. One such pathway taken over by HIV becomes the inflammatory pathway which uses Nuclear Factor κB (NF-κB) as the principal transcription factor. Therefore, knocking out the NF-κB pathway would prevent HIV from reproducing itself. In this report, our goal is to produce a simple model for this pathway with which we can identify potential targets for anti-HIV therapies and test out various hypotheses. We present a very simple model with four coupled first-order ODEs and see what happens if we treat IκK concentration as a parameter that can be controlled (by some unspecified means). In Section 3, we augment this model to account for activation and deactivation of IκK, which is controlled (again, by some unspecified means) by TNF
Self-avoiding walks crossing a square
We study a restricted class of self-avoiding walks (SAW) which start at the
origin (0, 0), end at , and are entirely contained in the square on the square lattice . The number of distinct
walks is known to grow as . We estimate as well as obtaining strict upper and lower bounds,
We give exact results for the number of SAW of
length for and asymptotic results for .
We also consider the model in which a weight or {\em fugacity} is
associated with each step of the walk. This gives rise to a canonical model of
a phase transition. For the average length of a SAW grows as ,
while for it grows as
. Here is the growth constant of unconstrained SAW in . For we provide numerical evidence, but no proof, that the
average walk length grows as .
We also consider Hamiltonian walks under the same restriction. They are known
to grow as on the same lattice. We give
precise estimates for as well as upper and lower bounds, and prove that
Comment: 27 pages, 9 figures. Paper updated and reorganised following
refereein
Equilibrium size of large ring molecules
The equilibrium properties of isolated ring molecules were investigated using
an off-lattice model with no excluded volume but with dynamics that preserve
the topological class. Using an efficient set of long range moves, chains of
more than 2000 monomers were studied. Despite the lack of any excluded volume
interaction, the radius of gyration scaled like that of a self avoiding walk,
as had been previously conjectured. However this scaling was only seen for
chains greater than 500 monomers.Comment: 11 pages, 3 eps figures, latex, psfi
A new transfer-matrix algorithm for exact enumerations: Self-avoiding polygons on the square lattice
We present a new and more efficient implementation of transfer-matrix methods
for exact enumerations of lattice objects. The new method is illustrated by an
application to the enumeration of self-avoiding polygons on the square lattice.
A detailed comparison with the previous best algorithm shows significant
improvement in the running time of the algorithm. The new algorithm is used to
extend the enumeration of polygons to length 130 from the previous record of
110.Comment: 17 pages, 8 figures, IoP style file
Determination of the exponent gamma for SAWs on the two-dimensional Manhattan lattice
We present a high-statistics Monte Carlo determination of the exponent gamma
for self-avoiding walks on a Manhattan lattice in two dimensions. A
conservative estimate is \gamma \gtapprox 1.3425(3), in agreement with the
universal value 43/32 on regular lattices, but in conflict with predictions
from conformal field theory and with a recent estimate from exact enumerations.
We find strong corrections to scaling that seem to indicate the presence of a
non-analytic exponent Delta < 1. If we assume Delta = 11/16 we find gamma =
1.3436(3), where the error is purely statistical.Comment: 24 pages, LaTeX2e, 4 figure
A Swendsen-Wang update algorithm for the Symanzik improved sigma model
We study a generalization of Swendsen-Wang algorithm suited for Potts models
with next-next-neighborhood interactions. Using the embedding technique
proposed by Wolff we test it on the Symanzik improved bidimensional non-linear
model. For some long range observables we find a little slowing down
exponent () that we interpret as an effect of the partial
frustration of the induced spin model.Comment: Self extracting archive fil
On the Dominance of Trivial Knots among SAPs on a Cubic Lattice
The knotting probability is defined by the probability with which an -step
self-avoiding polygon (SAP) with a fixed type of knot appears in the
configuration space. We evaluate these probabilities for some knot types on a
simple cubic lattice. For the trivial knot, we find that the knotting
probability decays much slower for the SAP on the cubic lattice than for
continuum models of the SAP as a function of . In particular the
characteristic length of the trivial knot that corresponds to a `half-life' of
the knotting probability is estimated to be on the cubic
lattice.Comment: LaTeX2e, 21 pages, 8 figur
Persistence length of a polyelectrolyte in salty water: a Monte-Carlo study
We address the long standing problem of the dependence of the electrostatic
persistence length of a flexible polyelectrolyte (PE) on the screening
length of the solution within the linear Debye-Huckel theory. The
standard Odijk, Skolnick and Fixman (OSF) theory suggests ,
while some variational theories and computer simulations suggest . In this paper, we use Monte-Carlo simulations to study the conformation
of a simple polyelectrolyte. Using four times longer PEs than in previous
simulations and refined methods for the treatment of the simulation data, we
show that the results are consistent with the OSF dependence . The linear charge density of the PE which enters in the coefficient of
this dependence is properly renormalized to take into account local
fluctuations.Comment: 7 pages, 6 figures. Various corrections in text and reference
Staircase polygons: moments of diagonal lengths and column heights
We consider staircase polygons, counted by perimeter and sums of k-th powers
of their diagonal lengths, k being a positive integer. We derive limit
distributions for these parameters in the limit of large perimeter and compare
the results to Monte-Carlo simulations of self-avoiding polygons. We also
analyse staircase polygons, counted by width and sums of powers of their column
heights, and we apply our methods to related models of directed walks.Comment: 24 pages, 7 figures; to appear in proceedings of Counting Complexity:
An International Workshop On Statistical Mechanics And Combinatorics, 10-15
July 2005, Queensland, Australi
Asymptotic Behavior of Inflated Lattice Polygons
We study the inflated phase of two dimensional lattice polygons with fixed
perimeter and variable area, associating a weight to a
polygon with area and bends. For convex and column-convex polygons, we
show that , where , and . The
constant is found to be the same for both types of polygons. We argue
that self-avoiding polygons should exhibit the same asymptotic behavior. For
self-avoiding polygons, our predictions are in good agreement with exact
enumeration data for J=0 and Monte Carlo simulations for . We also
study polygons where self-intersections are allowed, verifying numerically that
the asymptotic behavior described above continues to hold.Comment: 7 page
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