780 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
Elephants can always remember: Exact long-range memory effects in a non-Markovian random walk
We consider a discrete-time random walk where the random increment at time
step depends on the full history of the process. We calculate exactly the
mean and variance of the position and discuss its dependence on the initial
condition and on the memory parameter . At a critical value
where memory effects vanish there is a transition from a weakly localized
regime (where the walker returns to its starting point) to an escape regime.
Inside the escape regime there is a second critical value where the random walk
becomes superdiffusive. The probability distribution is shown to be governed by
a non-Markovian Fokker-Planck equation with hopping rates that depend both on
time and on the starting position of the walk. On large scales the memory
organizes itself into an effective harmonic oscillator potential for the random
walker with a time-dependent spring constant . The solution of
this problem is a Gaussian distribution with time-dependent mean and variance
which both depend on the initiation of the process.Comment: 10 page
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
What is the maximum rate at which entropy of a string can increase?
According to Susskind, a string falling toward a black hole spreads
exponentially over the stretched horizon due to repulsive interactions of the
string bits. In this paper such a string is modeled as a self-avoiding walk and
the string entropy is found. It is shown that the rate at which
information/entropy contained in the string spreads is the maximum rate allowed
by quantum theory. The maximum rate at which the black hole entropy can
increase when a string falls into a black hole is also discussed.Comment: 11 pages, no figures; formulas (18), (20) are corrected (the quantum
constant is added), a point concerning a relation between the Hawking and
Hagedorn temperatures is corrected, conclusions unchanged; accepted by
Physical Review D for publicatio
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
Current reversal and exclusion processes with history-dependent random walks
A class of exclusion processes in which particles perform history-dependent
random walks is introduced, stimulated by dynamic phenomena in some biological
and artificial systems. The particles locally interact with the underlying
substrate by breaking and reforming lattice bonds. We determine the
steady-state current on a ring, and find current-reversal as a function of
particle density. This phenomenon is attributed to the non-local interaction
between the walkers through their trails, which originates from strong
correlations between the dynamics of the particles and the lattice. We
rationalize our findings within an effective description in terms of
quasi-particles which we call front barriers. Our analytical results are
complemented by stochastic simulations.Comment: 5 pages, 6 figure
Existence of positive representations for complex weights
The necessity of computing integrals with complex weights over manifolds with
a large number of dimensions, e.g., in some field theoretical settings, poses a
problem for the use of Monte Carlo techniques. Here it is shown that very
general complex weight functions P(x) on R^d can be represented by real and
positive weights p(z) on C^d, in the sense that for any observable f, _P
= _p, f(z) being the analytical extension of f(x). The construction is
extended to arbitrary compact Lie groups.Comment: 9 pages, no figures. To appear in J.Phys.
Exact sampling of self-avoiding paths via discrete Schramm-Loewner evolution
We present an algorithm, based on the iteration of conformal maps, that
produces independent samples of self-avoiding paths in the plane. It is a
discrete process approximating radial Schramm-Loewner evolution growing to
infinity. We focus on the problem of reproducing the parametrization
corresponding to that of lattice models, namely self-avoiding walks on the
lattice, and we propose a strategy that gives rise to discrete paths where
consecutive points lie an approximately constant distance apart from each
other. This new method allows us to tackle two non-trivial features of
self-avoiding walks that critically depend on the parametrization: the
asphericity of a portion of chain and the correction-to-scaling exponent.Comment: 18 pages, 4 figures. Some sections rewritten (including title and
abstract), numerical results added, references added. Accepted for
publication in J. Stat. Phy
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