934 research outputs found
Multiple-scattering effects on incoherent neutron scattering in glasses and viscous liquids
Incoherent neutron scattering experiments are simulated for simple dynamic
models: a glass (with a smooth distribution of harmonic vibrations) and a
viscous liquid (described by schematic mode-coupling equations). In most
situations multiple scattering has little influence upon spectral
distributions, but it completely distorts the wavenumber-dependent amplitudes.
This explains an anomaly observed in recent experiments
Vibrational States of Glassy and Crystalline Orthotherphenyl
Low-frequency vibrations of glassy and crystalline orthoterphenyl are studied
by means of neutron scattering. Phonon dispersions are measured along the main
axes of a single crystal, and the corresponding longitudinal and transversal
sound velocities are obtained. For glassy and polycrystalline samples, a
density of vibrational states is determined and cross-checked against other
dynamic observables. In the crystal, low-lying zone-boundary modes lead to an
excess over the Debye density of states. In the glass, the boson peak is
located at even lower frequencies. With increasing temperature, both glass and
crystal show anharmonicity.Comment: 7 pages of LaTeX (svjour), 2 tables, 10 figures accepted in Eur.
Phys. J.
Atomic Transport in Dense, Multi-Component Metallic Liquids
Pd43Ni10Cu27P0 has been investigated in its equilibrium liquid state with
incoherent, inelastic neutron scattering. As compared to simple liquids, liquid
PdNiCuP is characterized by a dense packing with a packing fraction above 0.5.
The intermediate scattering function exhibits a fast relaxation process that
precedes structural relaxation. Structural relaxation obeys a time-temperature
superposition that extends over a temperature range of 540K. The mode-coupling
theory of the liquid to glass transition (MCT) gives a consistent description
of the dynamics which governs the mass transport in liquid PdNiCuP alloys. MCT
scaling laws extrapolate to a critical temperature Tc at about 20% below the
liquidus temperature. Diffusivities derived from the mean relaxation times
compare well with Co diffusivities from recent tracer diffusion measurements
and diffsuivities calculated from viscosity via the Stokes-Einstein relation.
In contrast to simple metallic liquids, the atomic transport in dense, liquid
PdNiCuP is characterized by a drastical slowing down of dynamics on cooling, a
q^{-2} dependence of the mean relaxation times at intermediate q and a
vanishing isotope effect as a result of a highly collective transport
mechanism. At temperatures as high as 2Tc diffusion in liquid PdNiCuP is as
fast as in simple liquids at the melting point. However, the difference in the
underlying atomic transport mechanism indicates that the diffusion mechanism in
liquids is not controlled by the value of the diffusivity but rather by that of
the packing fraction
The Dynamic Transition of Protein Hydration Water
Thin layers of water on biomolecular and other nanostructured surfaces can be
supercooled to temperatures not accessible with bulk water. Chen et al. [PNAS
103, 9012 (2006)] suggested that anomalies near 220 K observed by quasi-elastic
neutron scattering can be explained by a hidden critical point of bulk water.
Based on more sensitive measurements of water on perdeuterated phycocyanin,
using the new neutron backscattering spectrometer SPHERES, and an improved data
analysis, we present results that show no sign of such a fragile-to-strong
transition. The inflection of the elastic intensity at 220 K has a dynamic
origin that is compatible with a calorimetric glass transition at 170 K. The
temperature dependence of the relaxation times is highly sensitive to data
evaluation; it can be brought into perfect agreement with the results of other
techniques, without any anomaly.Comment: 4 pages, 3 figures. Phys. Rev. Lett. (in press
YAC contigs of the Rab1 and wobbler (wr) spinal muscular atrophy gene region on proximal mouse chromosome 11 and of the homologous region on human chromosome 2p
powerful tool to advance the identi®cation of gene com-Despite rapid progress in the physical characteriza- plexes and of disease genes. In this respect, the analysis tion of murine and human genomes, little molecular in- of human chromosomes 16 and 19 (Nowak, 1995) and formation is available on certain regions, e.g., proximal mouse chromosomes 1 (Hunter et al., 1994) and 17 (Cox mouse chromosome 11 (Chr 11) and human chromosome et al., 1993) as well as of human and murine X chromo-2p (Chr 2p). We have localized the wobbler spinal atrophy somes is particularly far advanced (Hamvas et al., 1993). gene wr to proximal mouse Chr 11, tightly linked toRab1, On the other hand, such extensive information is not a gene coding for a small GTP-binding protein, and Glns- available for mouse proximal chromosome 11 (Chr 11) ps1, an intronless pseudogene of the glutamine synthe- and human chromosome 2p (Chr 2p) (Fig. 1; cf. Berry et tase gene. We have now used these markers to construct al., 1995; Nowak, 1995), known to share at least the genesa 1.3-Mb yeast arti®cial chromosome (YAC) contig of the for the reticuloendotheliosis oncogene (Brownell et al.,Rab1 region on mouse Chr 11. Four YAC clones isolated 1985), for a brain-speci®cb-spectrin isoform (Bloom et al.,from two independent YAC libraries were characterized 1992), and for cytoplasmic malate dehydrogenase (Ball etby rare-cutting analysis, ¯uorescence in situ hybridiza-al., 1994). However, comparing the segregation map oftion (FISH), and sequence-tagged site (STS) isolation and the mouse with the human cytogenetic map, a colinearmapping. Rab1 and Glns-ps1 were found to be only 20
Telomerase and Telomere-Associated Proteins: Structural Insights into Mechanism and Evolution
SummaryRecent advances in our structural understanding of telomerase and telomere-associated proteins have contributed significantly to elucidating the molecular mechanisms of telomere maintenance. The structures of telomerase TERT domains have provided valuable insights into how experimentally identified conserved motifs contribute to the telomerase reverse transcriptase reaction. Additionally, structures of telomere-associated proteins in a variety of organisms have revealed that, across evolution, telomere-maintenance mechanisms employ common structural elements. For example, the single-stranded 3′ overhang of telomeric DNA is specifically and tightly bound by an OB-fold in nearly all species, including ciliates (TEBP and Pot1a), fission yeast (SpPot1), budding yeast (Cdc13), and humans (hPOT1). Structures of the yeast Cdc13, Stn1, and Ten1 proteins demonstrated that telomere maintenance is regulated by a complex that bears significant similarity to the RPA heterotrimer. Similarly, proteins that specifically bind double-stranded telomeric DNA in divergent species use homeodomains to execute their functions (human TRF1 and TRF2 and budding yeast ScRap1). Likewise, the conserved protein Rap1, which is found in budding yeast, fission yeast, and humans, contains a structural motif that is known to be critical for protein-protein interaction. In addition to revealing the common underlying themes of telomere maintenance, structures have also elucidated the specific mechanisms by which many of these proteins function, including identifying a telomere-specific domain in Stn1 and how the human TRF proteins avoid heterodimerization. In this review, we summarize the high-resolution structures of telomerase and telomere-associated proteins and discuss the emergent common structural themes among these proteins. We also address how these high-resolution structures complement biochemical and cellular studies to enhance our understanding of telomere maintenance and function
Thermalization via Heat Radiation of an Individual Object Thinner than the Thermal Wavelength
Modeling and investigating the thermalization of microscopic objects with
arbitrary shape from first principles is of fundamental interest and may lead
to technical applications. Here, we study, over a large temperature range, the
thermalization dynamics due to far-field heat radiation of an individual,
deterministically produced silica fiber with a predetermined shape and a
diameter smaller than the thermal wavelength. The temperature change of the
subwavelength-diameter fiber is determined through a measurement of its optical
path length in conjunction with an ab initio thermodynamic model of the fiber
structure. Our results show excellent agreement with a theoretical model that
considers heat radiation as a volumetric effect and takes the emitter shape and
size relative to the emission wavelength into account
Harmonic behavior of metallic glasses up to the metastable melt
In two amorphous alloys ZrTiCuNiBe and ZrAlNiCu coherent neutron scattering has been measured over five decades in energy, including measurements in the metastable melt of a metallic alloy more than 80 K above Tg. In the vibrational spectra a pronounced "boson" peak is found: Even in crystallized samples the density of states exceeds the Debye ω2 model, and in the amorphous state low-frequency vibrations are further enhanced. The peak position shows no dispersion in q, while intensities are strongly correlated with the static structure factor. Over the full energy range the temperature dependence is strictly harmonic. From high-energy resolution measurements we establish lower bounds for the temperatures at which structural α and fast β relaxation become observable
Identification of the determinants for the specific recognition of single-strand telomeric DNA by Cdc13
The single-strand overhang present at telomeres plays a critical role in mediating both the capping and telomerase regulation functions of telomeres. The telomere end-binding proteins, Cdc13 in Saccharomyces cerevisiae, Pot1 in higher eukaryotes, and TEBP in the ciliated protozoan Oxytricha nova, exhibit sequence-specific binding to their respective single-strand overhangs. S. cerevisiae telomeres are composed of a heterogeneous mixture of GT-rich telomeric sequence, unlike in higher eukaryotes which have a simple repeat that is maintained with high fidelity. In yeast, the telomeric overhang is recognized by the essential protein Cdc13, which coordinates end-capping and telomerase activities at the telomere. The Cdc13 DNA-binding domain (Cdc13-DBD) binds these telomere sequences with high affinity (3 pM) and sequence specificity. To better understand the basis for this remarkable recognition, we have investigated the binding of the Cdc13-DBD to a series of altered DNA substrates. Although an 11-mer of GT-rich sequence is required for full binding affinity, only three of these 11 bases are recognized with high specificity. This specificity differs from that observed in the other known telomere end-binding proteins, but is well suited to the specific role of Cdc13 at yeast telomeres. These studies expand our understanding of telomere recognition by the Cdc13-DBD and of the unique molecular recognition properties of ssDNA binding. © 2006 American Chemical Society
Wavenumber dependence of structural alpha relaxation in a molecular liquid
Structural alpha relaxation in liquid orthoterphenyl is studied by means of
coherent neutron time-of-flight and backscattering spectroscopy over a large
temperature range. Not only amplitude and relaxation time but also the spectral
line shape show a significant variation with wavenumber. As expected from mode
coupling theory, these variations are correlated with the static structure
factor. Even far above the melting point, alpha relaxation remains
non-exponential.Comment: 6 pages of LaTeX, 4 figure
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