Scaling properties of the Penna model

We investigate the scaling properties of the Penna model, which has become a popular tool for the study of population dynamics and evolutionary problems in recent years. We find that the model generates a normalised age distribution for which a simple scaling rule is proposed, that is able to reproduce qualitative features for all genome sizes.Comment: 4 pages, 4 figure

Parallel computing and molecular dynamics of biological membranes

In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on the possible programming strategies. Liquids can be very satisfactorily simulated using the "systolic" method. For more complex systems, like the biological ones at which we are ultimately interested in, the "domain decomposition" approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of elementary components of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed.Comment: 4 pages LaTeX, 2 figures included, espcrc2.sty require

Ab initio simulations of Cu binding sites in the N-terminal region of PrP

The prion protein (PrP) binds Cu2+ ions in the octarepeat domain of the N-terminal tail up to full occupancy at pH=7.4. Recent experiments show that the HGGG octarepeat subdomain is responsible for holding the metal bound in a square planar coordination. By using first principle ab initio molecular dynamics simulations of the Car-Parrinello type, the Cu coordination mode to the binding sites of the PrP octarepeat region is investigated. Simulations are carried out for a number of structured binding sites. Results for the complexes Cu(HGGGW)+(wat), Cu(HGGG) and the 2[Cu(HGGG)] dimer are presented. While the presence of a Trp residue and a H2O molecule does not seem to affect the nature of the Cu coordination, high stability of the bond between Cu and the amide Nitrogens of deprotonated Gly's is confirmed in the case of the Cu(HGGG) system. For the more interesting 2[Cu(HGGG)] dimer a dynamically entangled arrangement of the two monomers, with intertwined N-Cu bonds, emerges. This observation is consistent with the highly packed structure seen in experiments at full Cu occupancy.Comment: 4 pages, conference proceedin

Sharp gene pool transition in a population affected by phenotype-based selective hunting

We use a microscopic model of population dynamics, a modified version of the well known Penna model, to study some aspects of microevolution. This research is motivated by recent reports on the effect of selective hunting on the gene pool of bighorn sheep living in the Ram Mountain region, in Canada. Our model finds a sharp transition in the structure of the gene pool as some threshold for the number of animals hunted is reached.Comment: 5 pages, 4 figure

Colloidal hard-rod fluids near geometrically structured substrates

Density functional theory is used to study colloidal hard-rod fluids near an individual right-angled wedge or edge as well as near a hard wall which is periodically patterned with rectangular barriers. The Zwanzig model, in which the orientations of the rods are restricted to three orthogonal orientations but their positions can vary continuously, is analyzed by numerical minimization of the grand potential. Density and orientational order profiles, excess adsorptions, as well as surface and line tensions are determined. The calculations exhibit an enrichment [depletion] of rods lying parallel and close to the corner of the wedge [edge]. For the fluid near the geometrically patterned wall, complete wetting of the wall -- isotropic liquid interface by a nematic film occurs as a two-stage process in which first the nematic phase fills the space between the barriers until an almost planar isotropic -- nematic liquid interface has formed separating the higher-density nematic fluid in the space between the barriers from the lower-density isotropic bulk fluid. In the second stage a nematic film of diverging film thickness develops upon approaching bulk isotropic -- nematic coexistence.Comment: 9 pages, 9 figure

A simple atomistic model for the simulation of the gel phase of lipid bilayers

In this paper we present the results of a large-scale numerical investigation of structural properties of a model of cell membrane, simulated as a bilayer of flexible molecules in vacuum. The study was performed by carrying out extensive Molecular Dynamics simulations, in the (NVE) micro-canonical ensemble, of two systems of different sizes (2x32 and 2x256 molecules), over a fairly large set of temperatures and densities, using parallel platforms and more standard serial computers. Depending on the dimension of the system, the dynamics was followed for physical times that go from few hundred of picoseconds for the largest system to 5--10 nanoseconds for the smallest one. We find that the bilayer remains stable even in the absence of water and neglecting Coulomb interactions in the whole range of temperatures and densities we have investigated. The extension of the region of physical parameters that we have explored has allowed us to study significant points in the phase diagram of the bilayer and to expose marked structural changes as density and temperature are varied, which are interpreted as the system passing from a crystal to a gel phase.Comment: 41 pages, 13 figure

Near-infrared photoluminescence of erbium tris(8-hydroxyquinoline) spin-coated thin films induced by low coherence light sources

Copyright 2007 AIP Publishing LLC. This article may be downloaded for personal use only. Any other use requires prior permission of the author and AIP Publishing. This article appeared in Applied Physics Letters [91, 021106 (2007)] and may be found at

Analytical solution of a generalized Penna model

In 1995 T.J.Penna introduced a simple model of biological aging. A modified Penna model has been demonstrated to exhibit behaviour of real-life systems including catastrophic senescence in salmon and a mortality plateau at advanced ages. We present a general steady-state, analytic solution to the Penna model, able to deal with arbitrary birth and survivability functions. This solution is employed to solve standard variant Penna models studied by simulation. Different Verhulst factors regulating both the birth rate and external death rate are considered.Comment: 6 figure

Mutant Resources and Mutagenomics in crop plants

Agricultural sustainability and food security are major challenges facing continued population growth. Integration of existing and new technologies for the induction and exploitation of genetic diversity towards developing healthier, nutritious and productive crops is the need of the hour. Mutagenesis is a proven technology for the development of improved or novel varieties with desirable traits. Several mutant genes have been successfully explored, either directly or indirectly, to complement crop productivity. The advent of genomics approaches and plant genome sequencing has benefitted mutation discovery and mutant characterization. Plant mutant repositories are being established to serve as platforms for basic and applied research in crop improvement. This review briefly outlines the impact and molecular/genomic characterization of induced mutations in crop improvement.Peer reviewe