3,388 research outputs found
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
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
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
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
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
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