265 research outputs found
High frequency sound waves in vitreous silica
We report a molecular dynamics simulation study of the sound waves in
vitreous silica in the mesoscopic exchanged momentum range. The calculated
dynamical structure factors are in quantitative agreement with recent
experimental inelastic neutron and x-ray scattering data. The analysis of the
longitudinal and transverse current spectra allows to discriminate between
opposite interpretations of the existing experimental data in favour of the
propagating nature of the high frequency sound waves.Comment: 4 pages, Revtex, 4 ps figures; to be published in Phys. Rev. Lett.,
February 198
The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: Impact on models for silencing
The subcellular three-dimensional distribution of three polycomb-group (PcG) proteins—polycomb, polyhomeotic and posterior sex combs—in fixed whole-mount Drosophila embryos was analyzed by multicolor confocal fluorescence microscopy. All three proteins are localized in complex patterns of 100 or more loci throughout most of the interphase nuclear volume. The rather narrow distribution of the protein intensities in the vast majority of loci argues against a PcG-mediated sequestration of repressed target genes by aggregation into subnuclear domains. In contrast to the case for PEV repression (Csink, A.K., and S. Henikoff. 1996. Nature. 381:529–531), there is a lack of correlation between the occurrence of PcG proteins and high concentrations of DNA, demonstrating that the silenced genes are not targeted to heterochromatic regions within the nucleus. There is a clear distinction between sites of transcription in the nucleus and sites of PcG binding, supporting the assumption that most PcG binding loci are sites of repressive complexes. Although the PcG proteins maintain tissue-specific repression for up to 14 cell generations, the proteins studied here visibly dissociate from the chromatin during mitosis, and disperse into the cytoplasm in a differential manner. Quantitation of the fluorescence intensities in the whole mount embryos demonstrate that the dissociated proteins are present in the cytoplasm. We determined that <2% of PH remains attached to late metaphase and anaphase chromosomes. Each of the three proteins that were studied has a different rate and extent of dissociation at prophase and reassociation at telophase. These observations have important implications for models of the mechanism and maintenance of PcG- mediated gene repression
The distribution of Polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing
The subcellular three-dimensional distribution of three polycomb-group (PcG) proteins-polycomb, polyhomeotic and posterior sex combs-in fixed whole-mount Drosophila embryos was analyzed by multicolor confocal fluorescence microscopy. All three proteins are localized in complex patterns of 100 or more loci throughout most of the interphase nuclear volume. The rather narrow distribution of the protein intensities in the vast majority of loci argues against a PcG-mediated sequestration of repressed target genes by aggregation into subnuclear domains. In contrast to the case for PEV repression (Csink, A.K., and S. Henikoff. 1996. Nature. 381:529-531), there is a lack of correlation between the occurrence of PcG proteins and high concentrations of DNA, demonstrating that the silenced genes are not targeted to heterochromatic regions within the nucleus. There is a clear distinction between sites of transcription in the nucleus and sites of PcG binding, supporting the assumption that most PcG binding loci are sites of repressive complexes. Although the PcG proteins maintain tissue-specific repression for up to 14 cell generations, the proteins studied here visibly dissociate from the chromatin during mitosis, and disperse into the cytoplasm in a differential manner. Quantitation of the fluorescence intensities in the whole mount embryos demonstrate that the dissociated proteins are present in the cytoplasm. We determined that <2% of PH remains attached to late metaphase and anaphase chromosomes. Each of the three proteins that were studied has a different rate and extent of dissociation at prophase and reassociation at telophase. These observations have important implications for models of the mechanism and maintenance of PcG-mediated gene repression
Phonons from neutron powder diffraction
The spherically averaged structure function \soq obtained from pulsed
neutron powder diffraction contains both elastic and inelastic scattering via
an integral over energy. The Fourier transformation of \soq to real space, as
is done in the pair density function (PDF) analysis, regularizes the data, i.e.
it accentuates the diffuse scattering. We present a technique which enables the
extraction of off-center phonon information from powder diffraction experiments
by comparing the experimental PDF with theoretical calculations based on
standard interatomic potentials and the crystal symmetry. This procedure
(dynamics from powder diffraction(DPD)) has been successfully implemented for
two systems, a simple metal, fcc Ni, and an ionic crystal, CaF. Although
computationally intensive, this data analysis allows for a phonon based
modeling of the PDF, and additionally provides off-center phonon information
from powder neutron diffraction
Fragility and compressibility at the glass transition
Isothermal compressibilities and Brillouin sound velocities from the
literature allow to separate the compressibility at the glass transition into a
high-frequency vibrational and a low-frequency relaxational part. Their ratio
shows the linear fragility relation discovered by x-ray Brillouin scattering
[1], though the data bend away from the line at higher fragilities. Using the
concept of constrained degrees of freedom, one can show that the vibrational
part follows the fragility-independent Lindemann criterion; the fragility
dependence seems to stem from the relaxational part. The physical meaning of
this finding is discussed. [1] T. Scopigno, G. Ruocco, F. Sette and G. Monaco,
Science 302, 849 (2003)Comment: 4 pages, 2 figures, 2 tables, 33 references. Slightly changed after
refereein
Energy landscape - a key concept for the dynamics of glasses and liquids
There is a growing belief that the mode coupling theory is the proper
microscopic theory for the dynamics of the undercooled liquid above a critical
temperature T_c. In addition, there is some evidence that the system leaves the
saddlepoints of the energy landscape to settle in the valleys at this critical
temperature. Finally, there is a microscopic theory for the entropy at the
calorimetric glass transition T_g by Mezard and Parisi, which allows to
calculate the Kauzmann temperature from the atomic pair potentials.
The dynamics of the frozen glass phase is at present limited to
phenomenological models. In the spirit of the energy landscape concept, one
considers an ensemble of independent asymmetric double-well potentials with a
wide distribution of barrier heights and asymmetries (ADWP or Gilroy-Phillips
model). The model gives an excellent description of the relaxation of glasses
up to about T_g/4. Above this temperature, the interaction between different
relaxation centers begins to play a role. One can show that the interaction
reduces the number of relaxation centers needed to bring the shear modulus down
to zero by a factor of three.Comment: Contribution to the III Workshop on Nonequilibrium Phenomena in
Supercooled Fluids, Glasses and Amorphous Materials, 22-27 September 2002,
Pisa; 14 pages, 3 figures; Version 3 takes criticque at Pisa into account;
final version 4 will be published in J.Phys.: Condens.Matte
A Solvable Model of a Glass
An analytically tractable model is introduced which exhibits both, a
glass--like freezing transition, and a collection of double--well
configurations in its zero--temperature potential energy landscape. The latter
are generally believed to be responsible for the anomalous low--temperature
properties of glass-like and amorphous systems via a tunneling mechanism that
allows particles to move back and forth between adjacent potential energy
minima. Using mean--field and replica methods, we are able to compute the
distribution of asymmetries and barrier--heights of the double--well
configurations {\em analytically}, and thereby check various assumptions of the
standard tunneling model. We find, in particular, strong correlations between
asymmetries and barrier--heights as well as a collection of single--well
configurations in the potential energy landscape of the glass--forming system
--- in contrast to the assumptions of the standard model. Nevertheless, the
specific heat scales linearly with temperature over a wide range of low
temperatures.Comment: 11 pages, latex, including 5 figures, talk presented at the XIV
Sitges Conferenc
Bosonic Excitations in Random Media
We consider classical normal modes and non-interacting bosonic excitations in
disordered systems. We emphasise generic aspects of such problems and parallels
with disordered, non-interacting systems of fermions, and discuss in particular
the relevance for bosonic excitations of symmetry classes known in the
fermionic context. We also stress important differences between bosonic and
fermionic problems. One of these follows from the fact that ground state
stability of a system requires all bosonic excitation energy levels to be
positive, while stability in systems of non-interacting fermions is ensured by
the exclusion principle, whatever the single-particle energies. As a
consequence, simple models of uncorrelated disorder are less useful for bosonic
systems than for fermionic ones, and it is generally important to study the
excitation spectrum in conjunction with the problem of constructing a
disorder-dependent ground state: we show how a mapping to an operator with
chiral symmetry provides a useful tool for doing this. A second difference
involves the distinction for bosonic systems between excitations which are
Goldstone modes and those which are not. In the case of Goldstone modes we
review established results illustrating the fact that disorder decouples from
excitations in the low frequency limit, above a critical dimension , which
in different circumstances takes the values and . For bosonic
excitations which are not Goldstone modes, we argue that an excitation density
varying with frequency as is a universal
feature in systems with ground states that depend on the disorder realisation.
We illustrate our conclusions with extensive analytical and some numerical
calculations for a variety of models in one dimension
Crystal-like high frequency phonons in the amorphous phases of solid water
The high frequency dynamics of low- (LDA) and high-density amorphous-ice
(HDA) and of cubic ice (I_c) has been measured by inelastic X-ray Scattering
(IXS) in the 1-15 nm^{-1} momentum transfer (Q) range. Sharp phonon-like
excitations are observed, and the longitudinal acoustic branch is identified up
to Q = 8nm^{-1} in LDA and I_c and up to 5nm^{-1} in HDA. The narrow width of
these excitations is in sharp contrast with the broad features observed in all
amorphous systems studied so far. The "crystal-like" behavior of amorphous
ices, therefore, implies a considerable reduction in the number of decay
channels available to sound-like excitations which is assimilated to low local
disorder.Comment: 4 pages, 3 figure
Anharmonicity, vibrational instability and Boson peak in glasses
We show that a {\em vibrational instability} of the spectrum of weakly
interacting quasi-local harmonic modes creates the maximum in the inelastic
scattering intensity in glasses, the Boson peak. The instability, limited by
anharmonicity, causes a complete reconstruction of the vibrational density of
states (DOS) below some frequency , proportional to the strength of
interaction. The DOS of the new {\em harmonic modes} is independent of the
actual value of the anharmonicity. It is a universal function of frequency
depending on a single parameter -- the Boson peak frequency, which
is a function of interaction strength. The excess of the DOS over the Debye
value is at low frequencies and linear in in the
interval . Our results are in an excellent
agreement with recent experimental studies.Comment: LaTeX, 8 pages, 6 figure
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