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 $t$ 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 $p$. At a critical value $p_c^{(1)}=1/2$ 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 $k = (2p-1)/t$. 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 $(L, L)$, and are entirely contained in the square $[0, L] \times [0, L]$ on the square lattice ${\mathbb Z}^2$. The number of distinct walks is known to grow as $\lambda^{L^2+o(L^2)}$. We estimate $\lambda = 1.744550 \pm 0.000005$ as well as obtaining strict upper and lower bounds, $1.628 < \lambda < 1.782.$ We give exact results for the number of SAW of length $2L + 2K$ for $K = 0, 1, 2$ and asymptotic results for $K = o(L^{1/3})$. We also consider the model in which a weight or {\em fugacity} $x$ is associated with each step of the walk. This gives rise to a canonical model of a phase transition. For $x < 1/\mu$ the average length of a SAW grows as $L$, while for $x > 1/\mu$ it grows as $L^2$. Here $\mu$ is the growth constant of unconstrained SAW in ${\mathbb Z}^2$. For $x = 1/\mu$ we provide numerical evidence, but no proof, that the average walk length grows as $L^{4/3}$. We also consider Hamiltonian walks under the same restriction. They are known to grow as $\tau^{L^2+o(L^2)}$ on the same $L \times L$ lattice. We give precise estimates for $\tau$ as well as upper and lower bounds, and prove that $\tau < \lambda.$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.

Multigrid Monte Carlo with higher cycles in the Sine Gordon model

We study the dynamical critical behavior of multigrid Monte Carlo for the two dimensional Sine Gordon model on lattices up to 128 x 128. Using piecewise constant interpolation, we perform a W-cycle (gamma=2). We examine whether one can reduce critical slowing down caused by decreasing acceptance rates on large blocks by doing more work on coarser lattices. To this end, we choose a higher cycle with gamma = 4. The results clearly demonstrate that critical slowing down is not reduced in either case.Comment: 7 pages, 1 figure, whole paper including figure contained in ps-file, DESY 93-00