127 research outputs found
Nature of vibrational eigenmodes in topologically disordered solids
We use a local projectional analysis method to investigate the effect of
topological disorder on the vibrational dynamics in a model glass simulated by
molecular dynamics. Evidence is presented that the vibrational eigenmodes in
the glass are generically related to the corresponding eigenmodes of its
crystalline counterpart via disorder-induced level-repelling and hybridization
effects. It is argued that the effect of topological disorder in the glass on
the dynamical matrix can be simulated by introducing positional disorder in a
crystalline counterpart.Comment: 7 pages, 6 figures, PRB, to be publishe
The vibrational dynamics of vitreous silica: Classical force fields vs. first-principles
We compare the vibrational properties of model SiO_2 glasses generated by
molecular-dynamics simulations using the effective force field of van Beest et
al. (BKS) with those obtained when the BKS structure is relaxed using an ab
initio calculation in the framework of the density functional theory. We find
that this relaxation significantly improves the agreement of the density of
states with the experimental result. For frequencies between 14 and 26 THz the
nature of the vibrational modes as determined from the BKS model is very
different from the one from the ab initio calculation, showing that the
interpretation of the vibrational spectra in terms of calculations using
effective potentials can be very misleading.Comment: 7 pages of Latex, 4 figure
Modelling the atomic structure of very high-density amorphous ice
The structure of very high-density amorphous (VHDA) ice has been modelled by
positionally disordering three crystalline phases, namely ice IV, VI and XII.
These phases were chosen because only they are stable or metastable in the
region of the ice phase diagram where VHDA ice is formed, and their densities
are comparable to that of VHDA ice. An excellent fit to the medium range of the
experimentally observed pair-correlation function g(r) of VHDA ice was obtained
by introducing disorder into the positions of the H2O molecules, as well as
small amounts of molecular rotational disorder, disorder in the O--H bond
lengths and disorder in the H--O--H bond angles. The low-k behaviour of the
experimental structure factor, S(k), is also very well reproduced by this
disordered-crystal model. The fraction of each phase present in the best-fit
disordered model is very close to that observed in the probable crystallization
products of VHDA ice. In particular, only negligible amounts of ice IV are
predicted, in accordance with experimental observation.Comment: 4 pages, 3 figures, 1 table, v2: changes made in response to
referees' comments, the justification for using certain ice phases is
improved, and ice IV is now disordered as wel
Mutations designed to modify the NS gene mRNA secondary structure affect influenza A pathogenicity in vivo
The influenza A virus genome consists of eight segments of negative-sense RNA that encode up to 18 proteins. During the process of viral replication, positive-sense (+)RNA (cRNA) or messenger RNA (mRNA) is synthesized. Today, there is only a partial understanding of the function of several secondary structures within vRNA and cRNA promoters, and splice sites in the M and NS genes. The most precise secondary structure of (+)RNA has been determined for the NS segment of influenza A virus. The influenza A virus NS gene features two regions with a conserved mRNA secondary structure located near splice sites. Here, we compared 4 variants of the A/Puerto Rico/8/1934 strain featuring different combinations of secondary structures at the NS segment (+)RNA regions 82-148 and 497-564. We found that RNA structures did not affect viral replication in cell culture. However, one of the viruses demonstrated lower NS1 and NEP expression levels during early stage cell infection as well as reduced pathogenicity in mice compared to other variants. In particular, this virus is characterized by an RNA hairpin in the 82-148 region and a stable hairpin in the 497-564 region.The influenza A virus genome consists of eight segments of negative-sense RNA that encode up to 18 proteins. During the process of viral replication, positive-sense (+)RNA (cRNA) or messenger RNA (mRNA) is synthesized. Today, there is only a partial understanding of the function of several secondary structures within vRNA and cRNA promoters, and splice sites in the M and NS genes. The most precise secondary structure of (+)RNA has been determined for the NS segment of influenza A virus. The influenza A virus NS gene features two regions with a conserved mRNA secondary structure located near splice sites. Here, we compared 4 variants of the A/Puerto Rico/8/1934 strain featuring different combinations of secondary structures at the NS segment (+)RNA regions 82-148 and 497-564. We found that RNA structures did not affect viral replication in cell culture. However, one of the viruses demonstrated lower NS1 and NEP expression levels during early stage cell infection as well as reduced pathogenicity in mice compared to other variants. In particular, this virus is characterized by an RNA hairpin in the 82-148 region and a stable hairpin in the 497-564 region
Vector vibrations and the Ioffe-Regel crossover in disordered lattices
The spectral density for vector vibrations in the f.c.c. lattice with
force-constant disorder is analysed within the coherent potential
approximation. The phase diagram showing the weak- and strong-scattering
regimes is presented and compared with that for electrons. The weak-scattering
regime for external long-wavelength vibrational plane waves is shown to be due
to sum-rule correlations in the dynamical matrix. A secondary peak below the
Brillouin peak for sufficiently large wavevectors is found for the lattice
models. The results obtained are supported by precise numerical solutions.Comment: 21 pages, 13 figure
The effect of heterogeneity on invasion in spatial epidemics: from theory to experimental evidence in a model system
Heterogeneity in host populations is an important factor affecting the ability of a pathogen to invade, yet the quantitative investigation of its effects on epidemic spread is still an open problem. In this paper, we test recent theoretical results, which extend the established “percolation paradigm” to the spread of a pathogen in discrete heterogeneous host populations. In particular, we test the hypothesis that the probability of epidemic invasion decreases when host heterogeneity is increased. We use replicated experimental microcosms, in which the ubiquitous pathogenic fungus Rhizoctonia solani grows through a population of discrete nutrient sites on a lattice, with nutrient sites representing hosts. The degree of host heterogeneity within different populations is adjusted by changing the proportion and the nutrient concentration of nutrient sites. The experimental data are analysed via Bayesian inference methods, estimating pathogen transmission parameters for each individual population. We find a significant, negative correlation between heterogeneity and the probability of pathogen invasion, thereby validating the theory. The value of the correlation is also in remarkably good agreement with the theoretical predictions. We briefly discuss how our results can be exploited in the design and implementation of disease control strategies
Structure and dynamics of a model glass: influence of long-range forces
We vary the amplitude of the long-range Coulomb forces within a classical
potential describing a model silica glass and study the consequences on the
structure and dynamics of the glass, via molecular dynamics simulations. This
model allows us to follow the variation of specific features such as the First
Sharp Diffraction Peak and the Boson Peak in a system going continuously from a
fragile (no Coulomb forces) to a strong (with Coulomb forces) glass. In
particular we show that the characteristic features of a strong glass
(existence of medium range order, bell-shaped ring size distribution, sharp
Boson peak) appear as soon as tetrahedral units are formed.Comment: 5 pages, 4 figures. To be published in J.Phys.: C
Heat Capacity in Magnetic and Electric Fields Near the Ferroelectric Transition in Tri-Glycine Sulfate
Specific-heat measurements are reported near the Curie temperature (~=
320 K) on tri-glycine sulfate. Measurements were made on crystals whose
surfaces were either non-grounded or short-circuited, and were carried out in
magnetic fields up to 9 T and electric fields up to 220 V/cm. In non-grounded
crystals we find that the shape of the specific-heat anomaly near is
thermally broadened. However, the anomaly changes to the characteristic sharp
-shape expected for a continuous transition with the application of
either a magnetic field or an electric field. In crystals whose surfaces were
short-circuited with gold, the characteristic -shape appeared in the
absence of an external field. This effect enabled a determination of the
critical exponents above and below , and may be understood on the basis
that the surface charge originating from the pyroelectric coefficient, ,
behaves as if shorted by external magnetic or electric fields.Comment: 4 Pages, 4 Figures. To Appear in Applied Physics Letters_ January
200
The Raman coupling function in amorphous silica and the nature of the long wavelength excitations in disordered systems
New Raman and incoherent neutron scattering data at various temperatures and
molecular dynamic simulations in amorphous silica, are compared to obtain the
Raman coupling coefficient and, in particular, its low frequency
limit. This study indicates that in the limit
extrapolates to a non vanishing value, giving important indications on the
characteristics of the vibrational modes in disordered materials; in particular
our results indicate that even in the limit of very long wavelength the local
disorder implies non-regular local atomic displacements.Comment: Revtex, 4 ps figure
Numerical study of anharmonic vibrational decay in amorphous and paracrystalline silicon
The anharmonic decay rates of atomic vibrations in amorphous silicon (a-Si)
and paracrystalline silicon (p-Si), containing small crystalline grains
embedded in a disordered matrix, are calculated using realistic structural
models. The models are 1000-atom four-coordinated networks relaxed to a local
minimum of the Stillinger-Weber interatomic potential. The vibrational decay
rates are calculated numerically by perturbation theory, taking into account
cubic anharmonicity as the perturbation. The vibrational lifetimes for a-Si are
found to be on picosecond time scales, in agreement with the previous
perturbative and classical molecular dynamics calculations on a 216-atom model.
The calculated decay rates for p-Si are similar to those of a-Si. No modes in
p-Si reside entirely on the crystalline cluster, decoupled from the amorphous
matrix. The localized modes with the largest (up to 59%) weight on the cluster
decay primarily to two diffusons. The numerical results are discussed in
relation to a recent suggestion by van der Voort et al. [Phys. Rev. B {\bf 62},
8072 (2000)] that long vibrational relaxation inferred experimentally may be
due to possible crystalline nanostructures in some types of a-Si.Comment: 9 two-column pages, 13 figure
- …