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

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

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

Nanoparticle characterization: What to measure?

What to measure? is a key question in nanoscience, and it is not straightforward to address as different physicochemical properties define a nanoparticle sample. Most prominent among these properties are size, shape, surface charge, and porosity. Today researchers have an unprecedented variety of measurement techniques at their disposal to assign precise numerical values to those parameters. However, methods based on different physical principles probe different aspects, not only of the particles themselves, but also of their preparation history and their environment at the time of measurement. Understanding these connections can be of great value for interpreting characterization results and ultimately controlling the nanoparticle structure–function relationship. Here, the current techniques that enable the precise measurement of these fundamental nanoparticle properties are presented and their practical advantages and disadvantages are discussed. Some recommendations of how the physicochemical parameters of nanoparticles should be investigated and how to fully characterize these properties in different environments according to the intended nanoparticle use are proposed. The intention is to improve comparability of nanoparticle properties and performance to ensure the successful transfer of scientific knowledge to industrial real‐world applications

Accurate Structural Correlations from Maximum Likelihood Superpositions

The cores of globular proteins are densely packed, resulting in complicated networks of structural interactions. These interactions in turn give rise to dynamic structural correlations over a wide range of time scales. Accurate analysis of these complex correlations is crucial for understanding biomolecular mechanisms and for relating structure to function. Here we report a highly accurate technique for inferring the major modes of structural correlation in macromolecules using likelihood-based statistical analysis of sets of structures. This method is generally applicable to any ensemble of related molecules, including families of nuclear magnetic resonance (NMR) models, different crystal forms of a protein, and structural alignments of homologous proteins, as well as molecular dynamics trajectories. Dominant modes of structural correlation are determined using principal components analysis (PCA) of the maximum likelihood estimate of the correlation matrix. The correlations we identify are inherently independent of the statistical uncertainty and dynamic heterogeneity associated with the structural coordinates. We additionally present an easily interpretable method (“PCA plots”) for displaying these positional correlations by color-coding them onto a macromolecular structure. Maximum likelihood PCA of structural superpositions, and the structural PCA plots that illustrate the results, will facilitate the accurate determination of dynamic structural correlations analyzed in diverse fields of structural biology

Sol-Gel Prepared Nanoscopic Metal Fluorides - a New Class of Tunable Acid-Base Catalysts

In this article, the high potential of the fluorolytic sol-gel process to synthesise nanoscopic metal fluorides with different acid-base properties is shown. These nanoscopic materials exhibit high potential to be used as heterogeneous catalysts due to their high surface areas and their tunable surface properties. Thus, for each specific reaction the required surface properties of the catalysts can be ”adjusted” to achieve a high yield and selectivity of the desired product. As a consequence, a greener method of chemical production can be accomplished. Moreover the cheap and easy synthesis of the catalysts using basic chemicals makes them not only interesting for fundamental research but provides an easy transformation to industrial applications

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

Propylene Carbonate Reexamined: Mode-Coupling β\beta Scaling without Factorisation ?

The dynamic susceptibility of propylene carbonate in the moderately viscous regime above $T_{\rm c}$ is reinvestigated by incoherent neutron and depolarised light scattering, and compared to dielectric loss and solvation response. Depending on the strength of $\alpha$ relaxation, a more or less extended $\beta$ scaling regime is found. Mode-coupling fits yield consistently $\lambda=0.72$ and $T_{\rm c}=182$K, although different positions of the susceptibility minimum indicate that not all observables have reached the universal asymptotics

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