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 ($T_C$~= 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 $T_C$ is thermally broadened. However, the anomaly changes to the characteristic sharp $\lambda$-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 $\lambda$-shape appeared in the absence of an external field. This effect enabled a determination of the critical exponents above and below $T_C$, and may be understood on the basis that the surface charge originating from the pyroelectric coefficient, $dP/dT$, 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 $C(\omega)$ and, in particular, its low frequency limit. This study indicates that in the $\omega \to 0$ limit $C(\omega)$ 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