Identification of drug resistance mutations in HIV from constraints on natural evolution

Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions, inferred from sequence data obtained prior to the use of antiretroviral drugs, can be used to identify clinically significant sites of resistance mutations. Successful predictions of the resistance sites indicate progress in the development of successful models of real viral evolution at the single residue level, and suggest that our approach may be applied to help design new therapies that are less prone to failure even where resistance data is not yet available.Comment: 5 pages, 3 figure

A new deterministic model of strange stars

The observed evidence for the existence of strange stars and the concomitant observed masses and radii are used to derive an interpolation formula for the mass as a function of the radial coordinate. The resulting general mass function becomes an effective model for a strange star. The analysis is based on the MIT bag model and yields the energy density, as well as the radial and transverse pressures. Using the interpolation function for the mass, it is shown that a mass-radius relation due to Buchdahl is satisfied in our model. We find the surface redshift ($Z$) corresponding to the compactness of the stars. Finally, from our results, we predict some characteristics of a strange star of radius 9.9 km.Comment: one new figures and minor revisions have been done. To appear in Eur.Phys.J.

Shell Crossing Singularities in Quasi-Spherical Szekeres Models

We investigate the occurrence of shell crossing singularities in quasi-spherical Szekeres dust models with or without a cosmological constant. We study the conditions for shell crossing singularity both from physical and geometrical point of view and they are in agreement.Comment: 10 latex pages, RevTex style, no figure

Composite Fermions in Quantum Dots

We demonstrate the formation of composite fermions in two-dimensional quantum dots under high magnetic fields. The composite fermion interpretation provides a simple way to understand several qualitative and quantitative features of the numerical results obtained earlier in exact diagonalization studies. In particular, the ground states are recognized as compactly filled quasi-Landau levels of composite fermions.Comment: Revtex. Postscript files of figures are appended the tex

For T Cell Receptors, Some Breakups Might Not Last Forever

Does the affinity or half-life of peptide-MHC-T cell receptor (TCR) interactions determine T cell activation? In this issue of Immunity, Aleksic et al. (2010) propose a role for the on rate through multiple rebindings to the same TCR

Static displacements and chemical correlations in alloys

Recent experiments in metallic solid solutions have revealed interesting correlations between static pair-displacements and the ordering behavior of these alloys. This paper discusses a simple theoretical model which successfully explains these observations and which provides a natural framework for analyzing experimental measurements of pair-displacements and chemical correlations in solid solutions. The utility and scope of this model is demonstrated by analyzing results of experiments on $Ni-Fe$ and $Cr-Fe$ alloys and results of simulations of $Cu-Au$ and $Cu-Ag$ alloys.Comment: 12 page

On two-dimensionalization of three-dimensional turbulence in shell models

Applying a modified version of the Gledzer-Ohkitani-Yamada (GOY) shell model, the signatures of so-called two-dimensionalization effect of three-dimensional incompressible, homogeneous, isotropic fully developed unforced turbulence have been studied and reproduced. Within the framework of shell models we have obtained the following results: (i) progressive steepening of the energy spectrum with increased strength of the rotation, and, (ii) depletion in the energy flux of the forward forward cascade, sometimes leading to an inverse cascade. The presence of extended self-similarity and self-similar PDFs for longitudinal velocity differences are also presented for the rotating 3D turbulence case