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Interactions between biomolecules are ubiquitous in nature and crucial to many applications including vaccine development; environmentally friendly textile detergents; and food formulation. Using small angle X-ray scattering and structure-based molecular simulations, we explore protein-protein interactions in dilute to semi-concentrated protein solutions. We address the pertinent question, whether interaction models developed at infinite dilution can be extrapolated to concentrated regimes? Our analysis is based on measured and simulated osmotic second virial coefficients and solution structure factors at varying protein concentration and for different variants of the protein Thermomyces Lanuginosus Lipase (TLL). We show that in order to span the dilute and semi-concentrated regime, any model must carefully capture the balance between spatial and orientational correlations as the protein concentration is elevated. This requires consideration of the protein surface morphology, including possible patch interactions. Experimental data for TLL is most accurately described when assuming a patchy interaction, leading to dimer formation. Our analysis supports that the dimeric proteins predominantly exist in their open conformation where the active site is exposed, thereby maximising hydrophobic attractions that promote inter-protein alignment.(c) 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/).

Interactions between biomolecules are ubiquitous in nature and crucial to many applications including vaccine development; environmentally friendly textile detergents; and food formulation. Using small angle X-ray scattering and structure-based molecular simulations, we explore protein-protein interactions in dilute to semi-concentrated protein solutions. We address the pertinent question, whether interaction models developed at infinite dilution can be extrapolated to concentrated regimes? Our analysis is based on measured and simulated osmotic second virial coefficients and solution structure factors at varying protein concentration and for different variants of the protein Thermomyces Lanuginosus Lipase (TLL). We show that in order to span the dilute and semi-concentrated regime, any model must carefully capture the balance between spatial and orientational correlations as the protein concentration is elevated. This requires consideration of the protein surface morphology, including possible patch interactions. Experimental data for TLL is most accurately described when assuming a patchy interaction, leading to dimer formation. Our analysis supports that the dimeric proteins predominantly exist in their open conformation where the active site is exposed, thereby maximising hydrophobic attractions that promote inter-protein alignment.(c) 2022 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/).

Gasification of biomass allows for its efficient utilisation as a renewable fuel through syngas production. This work presents the different effects of gasifying agents (H2O, CO2 and H2O/CO2) on the pore structure evolution in biochar during gasification. The effects of temperature (700, 800 and 900 °C) and biomass particle size (up to 5.6 mm) were also studied. The pore structure of biochar was characterized using synchrotron small angle X-ray scattering (SAXS). The pore development in biochar during gasification in H2O/CO2 was close to that in H2O. Carbon removal is more selective in CO2 than H2O and the derived biochar displayed pore fractal features, whereas the biochars gasified in H2O and H2O/CO2 exhibited a surface fractal network due to the less selective carbon removal in the presence of H2O. The pore structure development produced by various gasifying agents was paralleled by the evolution of the aromatic structures characterized by Raman spectroscopy. The different pore structure features result from the different reactivity of carbon sites with H2O and CO2, which can be attributed to the different amounts of O-containing groups in biochar, as well as the different reactivity of H2O and CO2. Increasing temperature reduced the differences in pore structure between biochars gasified in H2O and CO2. Biomass particle size had little impact on the pore structure of biochar.

Apolipoproteins are vital to lipid metabolism and cholesterol transport in the human body. Here we present a structural study of the lipid-bound particles formed by ApoE3 in a full-length and a truncated version. The particles are formed with, respectively, POPC and DMPC and investigated by small-angle X-ray scattering and negative stain electron microscopy. We find that lipid-bound ApoE3 particles are elliptical, disc-shaped particles composed of a central lipid bilayer encircled by two amphipathic ApoE3 proteins. We went on to investigate a truncated form of ApoE3 containing only residue 80 to 255 (ApoE380-255), which is the central helical repeat segment of ApoE3. The lipid-bound ApoE380-255 particles are found to have the same morphology as the particles with full-length ApoE3. However, they are larger, and form more heterogeneous discoidal structures with four proteins per particle. This behavior is in contrast to ApoA1 where the highly similar helical repeat domain determines the size and stoichiometry of the formed particles both in the case of full-length and truncated ApoA1. Our data hence points towards different mechanisms for lipid bilayer structural modulation by ApoA1 and ApoE3 due to different roles of the non-repeat segments.

Small-angle X-ray and neutron scattering are widely used to investigate soft matter and biophysical systems. The experimental errors are essential when assessing how well a hypothesized model fits the data. Likewise, they are important when weights are assigned to multiple data sets used to refine the same model. Therefore, it is problematic when experimental errors are over- or underestimated. A method is presented, using Bayesian indirect Fourier transformation for small-angle scattering data, to assess whether or not a given small-angle scattering data set has over- or underestimated experimental errors. The method is effective on both simulated and experimental data, and can be used to assess and rescale the errors accordingly. Even if the estimated experimental errors are appropriate, it is ambiguous whether or not a model fits sufficiently well, as the `true' reduced chi(2) of the data is not necessarily unity. This is particularly relevant for approaches where overfitting is an inherent challenge, such as reweighting of a simulated molecular dynamics trajectory against small-angle scattering data or ab initio modelling. Using the outlined method, it is shown that one can determine what reduced chi(2) to aim for when fitting a model against small-angle scattering data. The method is easily accessible via the web interface BayesApp.

Apolipoproteins are vital to lipid metabolism and cholesterol transport in the human body. Here we present a structural study of the lipid-bound particles formed by ApoE3 in a full-length and a truncated version. The particles are formed with, respectively, POPC and DMPC and investigated by small-angle X-ray scattering and negative stain electron microscopy. We find that lipid-bound ApoE3 particles are elliptical, disc-shaped particles composed of a central lipid bilayer encircled by two amphipathic ApoE3 proteins. We went on to investigate a truncated form of ApoE3 containing only residue 80 to 255 (ApoE380-255), which is the central helical repeat segment of ApoE3. The lipid-bound ApoE380-255 particles are found to have the same morphology as the particles with full-length ApoE3. However, they are larger, and form more heterogeneous discoidal structures with four proteins per particle. This behavior is in contrast to ApoA1 where the highly similar helical repeat domain determines the size and stoichiometry of the formed particles both in the case of full-length and truncated ApoA1. Our data hence points towards different mechanisms for lipid bilayer structural modulation by ApoA1 and ApoE3 due to different roles of the non-repeat segments.

A recently reported approach to nanocrystallise encapsulated ciprofloxacin within liposomes has generated increased interest in the solid-state properties of drug nanocrystals within liposomal confinement. To explore the potential application of nanocrystallised drug liposomes in oral delivery, a liposomal ciprofloxacin formulation was used as a model system. An in vitro digestion model coupled to small angle X-ray scattering was used to analyse the solid-state properties of the drug nanocrystals during digestion of the liposomal ciprofloxacin nanocrystal formulations. Results showed a complete polymorphic transformation of the ciprofloxacin hydrate nanocrystals to a new salt form at a threshold sodium taurodeoxycholate to ciprofloxacin molar ratio of 0.6. The in vitro drug release from the nanocrystallised drug containing liposomes showed controlled drug release behaviour under non-digestive conditions, while a 3.5-fold increase in the drug release was seen when they were exposed to the simulated digestive environment. In conclusion, the solid state of the drug inside the liposomes is important in dictating the drug release behaviour from the liposomes. The identification of the solid state transformation during digestion in real time and the bile salt-induced polymorphic transformation of ciprofloxacin from nanocrystallised ciprofloxacin liposome are important to understand how the drug is released in vivo, as well as for future formulation design.

Aggregation processes are central features of many systems ranging from colloids and polymers to inorganic nanoparticles and biological systems. Some aggregated structures are controlled and desirable, e.g. in the design of size-controlled clustered nanoparticles or some protein-based drugs. In other cases, the aggregates are undesirable, e.g. protein aggregation involved in neurodegenerative diseases or in vitro studies of single protein structures. In either case, experimental and analytical tools are needed to cast light on the aggregation processes. Aggregation processes can be studied with small-angle scattering, but analytical descriptions of the aggregates are needed for detailed structural analysis. This paper presents a list of useful small-angle scattering structure factors, including a novel structure factor for a spherical cluster with local correlations between the constituent particles. Several of the structure factors were renormalized to get correct limit values in both the high- q and low-q limit, where q is the modulus of the scattering vector. The structure factors were critically evaluated against simulated data. Structure factors describing fractal aggregates provided approximate descriptions of the simulated data for all tested structures, from linear to globular aggregates. The addition of a correlation hole for the constituent particles in the fractal structure factors significantly improved the fits in all cases. Linear aggregates were best described by a linear structure factor and globular aggregates by the newly derived spherical cluster structure factor. As a central point, it is shown that the structure factors could be used to take aggregation contributions into account for samples of monomeric protein containing a minor fraction of aggregated protein. After applying structure factors in the analysis, the correct structure and oligomeric state of the protein were determined. Thus, by careful use of the presented structure factors, i

Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity.

Conditionally disordered proteins are either ordered or disordered depending on the environmental context. The substrates of the mitochondrial intermembrane space (IMS) oxidoreductase Mia40 are synthesized on cytosolic ribosomes and diffuse as intrinsically disordered proteins to the IMS, where they fold into their functional conformations; behaving thus as conditionally disordered proteins. It is not clear how the sequences of these polypeptides encode at the same time for their ability to adopt a folded structure and to remain unfolded. Here we characterize the disorder-to-order transition of a Mia40 substrate, the human small copper chaperone Cox17. Using an integrated real-time approach, including chromatography, fluorescence, CD, FTIR, SAXS, NMR, and MS analysis, we demonstrate that in this mitochondrial protein, the conformational switch between disordered and folded states is controlled by the formation of a single disulfide bond, both in the presence and in the absence of Mia40. We provide molecular details on how the folding of a conditionally disordered protein is tightly regulated in time and space, in such a way that the same sequence is competent for protein translocation and activity.

Fast concentration-induced diffusion-limited lyotropic phase transitions can be studied in situ with millisecond time resolution using continuous flow microfluidics in combination with microfocus small-angle X-ray scattering. The method was applied to follow a classical self-assembly sequence where amphiphiles assemble into micelles, which subsequently assemble into an ordered lattice via a disorder/order transition. As a model system we selected the self-assembly of an amphiphilic block copolymer induced by the addition of a nonsolvent. Using microchannel hydrodynamic flow-focusing, large concentration gradients can be generated, leading to a deep quench from the miscible to the microphase-separated state. Within milliseconds the block copolymers assembly via a spinodal microphase separation into micelles, followed by a disorder/order transition into an FCC liquid-crystalline phase with late-stage domain growth and shear-induced domain orientation into a mesocrystal. A comparison with a slow macroscopic near-equilibrium kinetic experiment shows that the fast structural transitions follow a direct pathway to the equilibrium structure without the trapping of metastable states., QC 2016-01-18

Meso-porous metal materials have enhanced surface energies offering unique surface properties with potential applications in chemical catalysis, molecular sensing and selective separation. In this paper, commercial 20 nm diameter metal nano-particles, including silver and copper were blended with 7 nm silica nano-particles by shear mixing. The resulted powders were cold-sintered to form dense, hybrid thin films. The sacrificial silica template was then removed by selective etching in 12 wt% hydrofluoric acid solutions for 15 min to reveal a purely metallic meso-porous thin film material. The impact of the initial silica nano-particle diameter (7–20 nm) as well as the sintering pressure (5–20 ton·m−2) and etching conditions on the morphology and properties of the final nano-porous thin films were investigated by porometry, pyknometery, gas and liquid permeation and electron microscopy. Furthermore, the morphology of the pores and particle aggregation during shear mixing were assessed through cross-sectioning by focus ion beam milling. It is demonstrated that meso-pores ranging between 50 and 320 nm in average diameter and porosities up to 47% can be successfully formed for the range of materials tested.

Supramolecular complexes of polystyrene-block-poly(4-vinylpyridine) (PS-b-P4VP) diblock copolymers and small molecules such as pentadecylphenol (PDP) have been studied extensively in recent years. In the present study, PS-b-P4VP(PDP) complexes with a minority P4VP(PDP) block are morphologically characterized focusing on the region between the lamellar and cylindrical phase. Dynamic mechanical measurements and small-angle X-ray scattering are used to follow the transitions between the ordered states upon heating/cooling. The self-assembled state at various temperatures is determined by small-angle X-ray scattering and transmission electron microscopy. In contrast to the opposite case of majority P4VP(PDP) blocks, where the transition from lamellar to cylindrical structures frequently occurs via the gyroid morphology, the complexes adopt the hexagonally perforated layered morphology in a broad range of compositions. Although known as a metastable phase in pure diblock copolymers, the hexagonally perforated layered phase appears as an equilibrium phase in PS-b-P4VP(PDP) complexes, being stabilized by the presence of the hydrogen-bonded PDP side chains in the minority component domains.

The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state lack a folded structure and fluctuate between many conformations. In its physiological state, tau helps nucleating and stabilizing the microtubules' (MTs) surfaces in the axons of the neurons. Tau is mainly composed by two domains: (i) the binding domain that tightly bounds the MT surfaces and (ii) the projection domain that exerts a long-range entropic repulsive force and thus provides the proper spacing between adjacent MTs. Tau is also involved in the genesis and in the development of the Alzheimer disease when it detaches from MT surfaces and aggregates in paired helical filaments. Unfortunately, the molecular mechanisms behind these phenomena are still unclear. Temperature variation, rarely considered in biological studies, is here used to provide structural information on tau correlated to its role as an entropic spacer between adjacent MTs surfaces. In this paper, by means of small-angle X-ray scattering and molecular dynamics simulation, we demonstrate that tau undergoes a counterintuitive collapse phenomenon with increasing temperature. A detailed analysis of our results, performed by the Ensemble Optimization Method, shows that the thermal collapse is coupled to the occurrence of a transient long-range contact between a region encompassing the end of the proline-rich domain P2 and the first part of the repeats domain, and the region of the N-terminal domain entailing residues 80-150. Interestingly these two regions involved in the tau temperature collapse belong to the flexible projection domain that acts as an entropic bristle and regulates the MTs' architecture. Our results show that temperature is an important parameter that influences the dynamics of the tau projection domain, and hence its entropic behavior.

© 2011 IOP Publishing Ltd and SISSA. We were partly supported by MICINN (Spain) through research contract nos. FIS2009-12648-C03-01 (VMM and PV) and FIS2008-01323 (PV)., Diagrammatic techniques to compute perturbatively the spectral properties of Euclidean random matrices (ERM) in the high-density regime are introduced and discussed in detail. Such techniques are developed in two alternative and very different formulations of the mathematical problem and are shown to give identical results up to second order in the perturbative expansion. One method, based on writing the so-called resolvent function as a Taylor series, allows to group the diagrams in a small number of topological classes, providing a simple way to determine the infrared (small momenta) behavior of the theory up to third order, which is of interest for the comparison with experiments. The other method, which reformulates the problem as a field theory, can instead be used to study the infrared behaviour at any perturbative order., Ministerio de Ciencia e Innovación (MICINN), Depto. de Física Teórica, Fac. de Ciencias Físicas, TRUE, pub

Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17-174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 x 10(-10) N-0.39 m(2) s(-1). The hydrodynamic radius R-H depended on N with R-H = 5.00 x 10(-10) N-0.38 m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 +/- 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size., QC 20110318

The preparation of carboxymethylated microfibrillated cellulose (MFC) films by dispersion-casting from aqueous dispersions and by surface coating on base papers is described. The oxygen permeability of MFC films were studied at different relative humidity (RH). At low RH (0%), the MFC films showed very low oxygen permeability as compared with films prepared from plasticized starch, whey protein and arabinoxylan and values in the same range as that of conventional synthetic films, e.g., ethylene vinyl alcohol. At higher RH's, the oxygen permeability increased exponentially, presumably due to the plasticizing and swelling of the carboxymethylated nanofibers by water molecules. The effect of moisture on the barrier and mechanical properties of the films was further studied using water vapor sorption isotherms and by humidity scans in dynamic mechanical analysis. The influences of the degree of nanofibrillation/dispersion on the microstructure and optical properties of the films were evaluated by field-emission scanning electron microscopy (FE-SEM) and light transmittance measurements, respectively. FE-SEM micrographs showed that the MFC films consisted of randomly assembled nanofibers with a thickness of 5-10 nm, although some larger aggregates were also formed. The use of MFC as surface coating on various base papers considerably reduced the air permeability. Environmental scanning electron microscopy (E-SEM) micrographs indicated that the MFC layer reduced sheet porosity, i.e., the dense structure formed by the nanofibers resulted in superior oil barrier properties., QC 20100623

Dynamic structure factors for a lipid bilayer have been calculated from molecular dynamics simulations. From trajectories of a system containing 1024 lipids we obtain wave vectors down to 0.34 nm(-1), which enables us to directly resolve the Rayleigh and Brillouin lines of the spectrum. The results confirm the validity of a model based on generalized hydrodynamics, but also improves the line widths and the position of the Brillouin lines. The improved resolution shows that the Rayleigh line is narrower than in earlier studies, which corresponds to a smaller thermal diffusivity. From a detailed analysis of the power spectrum, we can, in fact, distinguish two dispersive contributions to the elastic scattering. These translate to two exponential relaxation processes in separate time domains. Further, by including a first correction to the wave-vector-dependent position of the Brillouin lines, the results agree favorably to generalized hydrodynamics even up to intermediate wave vectors, and also yields a 20% higher adiabatic sound velocity. The width of the Brillouin lines shows a linear, not quadratic, dependence to low wave vectors., QC 20101006

We report lattice-dynamical measurements, made using neutron inelastic-scattering methods, of the relaxor perovskite PbMg1/3Nb2/3O3 (PMN) at momentum transfers near the edge of the Brillouin zone. Unusual "columns" of phonon scattering that are localized in momentum, but extended in energy, are seen at both high-symmetry points along the zone edge: (Q) over right arrowR= {1/2,1/2,1/2} and (Q) over right arrowM={1/2,1/2,0}. These columns soften at similar to 400 K which is similar to the onset temperature of the zone-center diffuse scattering, indicating a competition between ferroelectric and antiferroelectric distortions. We propose a model for the atomic displacements associated with these phonon modes that is based on a combination of structure factors and group theoretical analysis. This analysis suggests that the scattering is not from tilt modes (rotational modes of oxygen octahedra), but from zone-boundary optic modes that are associated with the displacement of Pb2+ and O2- ions. Whereas similar columns of scattering have been reported in metallic and (less commonly) molecular systems, they are unusual in insulating materials, particularly in ferroelectrics; therefore, the physical origin of this inelastic feature in PMN is unknown. We speculate that the underlying disorder contributes to this unique anomaly.

Crystalline-to-rotator phase transitions have been widely studied in bulk hydrocarbons, in particular in normal alkanes. But few studies of these transitions deal with molecularly thin films of pure n-alkanes on solid substrates. In this work, we were able to grow dotriacontane (n-C32H66) films without coexisting bulk particles, which allows us to isolate the contribution to the ellipsometric signal from a monolayer of molecules oriented with their long axis perpendicular to the SiO2 surface. For these submonolayer films, we found a step in the ellipsometer signal at similar to 331 K, which we identify with a solid-solid phase transition. At higher coverages, we observed additional steps in the ellipsometric signal that we identify with a solid-solid phase transition in multilayer islands (similar to 333 K) and with the transition to the rotator phase in bulk crystallites (similar to 337 K), respectively. After considering three alternative explanations, we propose that the step upward in the ellipsometric signal observed at similar to 331 K on heating the submonolayer film is the signature of a transition from a perpendicular monolayer phase to a denser phase in which the alkane chains contain on average one to two gauche defects per molecule. (C) 2009 American Institute of Physics. [doi: 10.1063/1.3213642]

We have studied mixtures of an anionic surfactant (deuterated sodium dodecyl sulfate, SDS-d) and cationic polyelectrolytes with different charge densities (10%, 30%, 60%, and 100%) using small-angle neutron scattering (SANS). Near compositions corresponding to charge neutralization, the solutions phase separate into a complex phase (precipitate) consisting of, in the cases of 30%, 60%, and 100% charge density, a two-dimensional (213) hexagonal lattice of close-packed cylindrical micelles and a clear liquid. When either polyelectrolyte with charge density less than 100% or SDS-d is present in sufficient excess, the solution becomes clear and isotropic, and from the scattering data we may conclude that prolate or rod-shaped micelles are present. The micelles are seen to grow in length with increasing SDS-d concentration and polyelectrolyte charge density from about 80 Angstrom to 550 Angstrom, whereas the cross-sectional radius is 15 Angstrom and approximately constant. The number of micelles per polyelectrolyte chain is found to be slightly larger than unity (1-6). In some of the (turbid) samples rod-shaped micelles are found to coexist with larger polyelectrolyte-surfactant complexes. Solutions consisting of 10% charged polyelectrolyte and SDS-d are very viscous and gellike, and the complex phase is much less defined with a much larger distance between adjacent aggregates in the complex phase., QC 20100525 QC 20111031

We have extended the transition-state theory to describe the dynamics of core hole excitation. This allows us to interpret the abnormally bland near-edge x-ray absorption fine structure spectrum of the gas phase benzonitrile molecule at the N 1s edge. We have brought to light different paths for the two most intensive resonances, going from the linear to the bent structure. The profile of each resonance consists of two different vibrational progressions corresponding to stretching modes and a broad continuum of bending excited states., QC 20100525 QC 20110923

The uptake of HCl on vapor-deposited ice is investigated for HCl partial pressure p from 2 x 10(-8) to 10(-5) Torr at temperatures of 190 and 203 K in an especially designed Knudsen cell experiment. Two kinetic regimes can be distinguished experimentally: a long-lasting tailing which accounts for the major amount of the overall uptake and follows diffusion-like kinetics, gamma(t) proportional to t(-1/2) (gamma, uptake coefficient; t, time), and an initial period, where the uptake is higher than predicted by diffusion-like kinetics. The uptake kinetics are analyzed using analytical equations and also by full numerical simulation of simultaneous adsorption onto the surface and diffusion into the bulk. We derive the quantity H-d*D-1/2 (H-d*, effective Henry's law constant, D diffusion constant) and find H-d*D-1/2 proportional to p(-1/2), which implies that HCl dissociates upon uptake. The results for both analysis methods closely coincide. We suggest the use of a semiempirical parametrization for the total HCl uptake (molecules per geometric surface area) on vapor-deposited ice films as time dependent function n(t, p) = n(resid)(P) + C(T)(tp)(1/2), where C(T) is a constant which depends on temperature only. The compatibility of the residual, nondiffusive uptake, n(resid), with various adsorption isotherms is discussed. The analysis suggests that the experimentally observed diffusion-like kinetics dominates the overall trace gas uptake after a brief initial period. The diffusion-like kinetics must be considered when analyzing uptake experiments and when making applications to natural ice., QC 20100525

We use resonant inelastic x-ray scattering to study the electronic structure of nickel oxide, the prototype charge-transfer insulator, as a function of pressure. At ambient pressure, we observe spectral features due to the charge-transfer excitation and the Coulomb correlation energy which progressively smear up to a pressure of 100 GPa. These changes are interpreted as due to increased dispersion of the concerned electronic bands. This opens new perspectives both for the study of electronic structure of correlated materials and for high-pressure research such as a deeper understanding of metal-insulator transitions, as well as the study of deep-earth chemistry.

© 2003 American Institute of Physics. We are indebted to Giancarlo Ruocco, Oreste Pilla, and Gabriele Viliani for helpful discussions. V.M.-M. is a Ramón y Cajal research fellow (MCyT, Spain). P.V. acknowledges financial support from the European Union through its Human Potential Program (Contract HPRN-CT-2002-00307, DYGLAGEMEM network). This work has been partly financially supported by MCyT Research Contracts FPA2001- 1813 and FPA2000-0956., A simple model of harmonic vibrations in topologically disordered systems, such as glasses and supercooled liquids, is studied analytically by extending Euclidean random matrix theory to include vector vibrations. Rather generally, it is found that (i) the dynamic structure factor shows soundlike Brillouin peaks whose longitudinal/transverse character can only be distinguished for small transferred momentum, p; (ii) the model presents a mechanical instability transition at small densities, for which scaling laws are analytically predicted and confirmed numerically; (iii) the Brillouin peaks persist deep into the unstable phase, the phase transition being noticeable mostly in their linewidth; (iv) the Brillouin linewidth scales like p^(2) in the stable phase, and like p in the unstable one. The analytical results are checked numerically for a simple potential. The main features of glassy vibrations previously deduced from scalar are not substantially altered by these new results., Ramón y Cajal research fellow (MCyT, Spain, European Union through its Human Potential Program, MCyT, Spain, Depto. de Física Teórica, Fac. de Ciencias Físicas, TRUE, pub

Shear-induced orientation and the relaxation of orientation after the cessation of shear in 45 and 50 wt% solutions of cholesteric hydroxypropylcellulose (HPC) in m-cresol have been studied in situ by infrared spectroscopy and polarised microscopy. The shearing experiments were conducted at 30-80 degreesC at shear rates of 1-300 s(-1), which covered the director tumbling, wagging and a small part of the steady-state shear rate regimes. The steady-state order parameter was proportional to the shear rate and the proportionality constant increased with increasing HPC concentration and decreasing temperature. The concentrated solutions studied showed steady-state alignment even in the tumbling regime. Three different shear-rate regions with different behaviours of the solutions after the cessation of shear were found in these concentrated HPC solutions. At low shear rates (1-5 s(-1), referring to the 50% HPC solution) the polymer remained isotropic during shear but became gradually more oriented a few minutes after the cessation of shear, an observation that was substantiated by polarized microscopy. The order parameter reached a final plateau value and stayed constant at this level for long periods of time (similar to24 h). At intermediate shear rates (from 5 to 50 s(-1) for the 50% HPC solution), a detectable order parameter was recorded at steady shear and, after the cessation of shear, the structure returned to an almost isotropic state within a few minutes, after which the orientation gradually started to increase to approach a plateau value after about 150 min. At even higher shear rates (similar to100 s(-1) for to the 50% HPC solution), the initial steady shear order parameter relaxed to an almost isotropic state and remained constant at this level for time periods extending up to 24 h., QC 20100525

The Cu-Fe-Ni system was reassessed taking into account new experimental data in particular in the region of the ordered phase (Cu,Ni)(3)Fe. Its thermodynamic description was assessed using a four sub-lattice model, while a random substitutional solution model was used for the disordered solution phases., QC 20100525

EXAFS studies of metal ions with hydration numbers higher than six in aqueous solution, often show asymmetric distribution of the metal-oxygen bond distances. The hydration number can be determined from a correlation with the bond distance. The mean Ca-O distance 2.46(1) Angstrom shows the calcium( II) ion to be eight-hydrated in a wide asymmetric distribution. Theoretically calculated EXAFS oscillations for individual snapshots from an MD simulation show large variations. The scandium( III) ion is surrounded by two groups of about eight water molecules, with the mean Sc-O distance 2.185(6) Angstrom. The yttrium( III) ion coordinates eight waters in an asymmetric distribution at 2.368(5) Angstrom, and the lanthanum( III) ion 6 + 3 water molecules at 2.52(2) and 2.65(3) Angstrom, respectively. For the the uranium( IV) and thorium(IV) ions, the M-O distances 2.42(1) and 2.45(1) Angstrom, respectively, indicate hydration numbers close to 10., QC 20100525

In situ ultrasonic measurements for the Pd40Cu30Ni10P20 bulk glass in three states: Glassy solid, supercooled liquid, and crystalline, have been performed. It is found that velocities of both longitudinal and transverse waves and elastic moduli (shear modulus, bulk modulus, Young's modulus, and Lame parameter), together with Debye temperature, gradually decrease with increasing temperature through the glass transition temperature as the Poisson's ratio increases. The behavior of the velocity of transverse wave vs. temperature in the supercooled liquid region could be explained by viscosity flow, rather than the two different crystallization processes in the region, suggested in the literature. No decomposition was detected at a temperature only 5 K below the crystallization temperature.

In situ ultrasonic measurements for the Pd40Cu30Ni10P20 bulk glass in three states: Glassy solid, supercooled liquid, and crystalline, have been performed. It is found that velocities of both longitudinal and transverse waves and elastic moduli (shear modulus, bulk modulus, Young's modulus, and Lame parameter), together with Debye temperature, gradually decrease with increasing temperature through the glass transition temperature as the Poisson's ratio increases. The behavior of the velocity of transverse wave vs. temperature in the supercooled liquid region could be explained by viscosity flow, rather than the two different crystallization processes in the region, suggested in the literature. No decomposition was detected at a temperature only 5 K below the crystallization temperature.

In situ ultrasonic measurements for the Pd40Cu30Ni10P20 bulk glass in three states: Glassy solid, supercooled liquid, and crystalline, have been performed. It is found that velocities of both longitudinal and transverse waves and elastic moduli (shear modulus, bulk modulus, Young's modulus, and Lame parameter), together with Debye temperature, gradually decrease with increasing temperature through the glass transition temperature as the Poisson's ratio increases. The behavior of the velocity of transverse wave vs. temperature in the supercooled liquid region could be explained by viscosity flow, rather than the two different crystallization processes in the region, suggested in the literature. No decomposition was detected at a temperature only 5 K below the crystallization temperature.

We have determined the kinetic scheme and the reaction rates of binding to microtubules of two fluorescent taxoids, 7-O-[N-(4'-fluoresceincarbonyl)-l-alanyl]Taxol (Flutax-1) and 7-O-[N-(2,7-difluoro-4'-fluoresceincarbonyl)-l-alanyl]Taxol (Flutax-2). Flutax-1 and Flutax-2 bind to microtubules with high affinity (K(a) approximately 10(7) m(-1), 37 degrees C). The binding mechanism consists of a fast bimolecular reaction followed by at least two monomolecular rearrangements, which were characterized with stopped-flow techniques. The kinetic constants of the bimolecular reaction were 6.10 +/- 0.22 x 10(5) m(-1) s(-1) and 13.8 +/- 1.8 x 10(5) m(-1) s(-1) at 37 degrees C, respectively. A second slow binding step has been measured employing the change of fluorescence anisotropy of the probe. The reversal of this reaction is the rate-limiting step of dissociation. A third step has been detected using small angle x-ray scattering and involves a 2-nm increase in the diameter of microtubules. It is suggested that the first step entails the binding of the Taxol moiety and the second a relative immobilization of the fluorescent probe. The equilibrium and some kinetic measurements required the use of stabilized cross-linked microtubules, which preserved taxoid binding. The results indicate that the Taxol binding site is directly accessible, in contrast with its location at lumen in the current model of microtubules. An alternative structural model is considered in which the binding site is located between protofilaments, accessible from the microtubule surface.

We have investigated the accessibility of the Taxol-binding site and the effects of Taxol binding on the structures of assembled microtubules. Taxol and docetaxel readily bind to and dissociate from microtubules, reaching 95% ligand exchange equilibrium in less than 3 min under our solution conditions (microtubules were previously assembled from GTP-tubulin, GTP-tubulin and microtubule-associated proteins, or GDP-tubulin and taxoid). Microtubules assembled from purified tubulin with Taxol are known to have typically one protofilament less than with the analogue docetaxel and control microtubules. Surprisingly, Taxol binding and exchange induce changes in the structure of preformed microtubules in a relatively short time scale. Cryoelectron microscopy shows changes toward the protofilament number distribution characteristic of Taxol or docetaxel, with a half-time of approximately 0.5 min, employing GDP-tubulin-taxoid microtubules. Correspondingly, synchrotron x-ray solution scattering shows a reduction in the mean microtubule diameter upon Taxol binding to microtubules assembled from GTP-tubulin in glycerol-containing buffer, with a structural relaxation half-time of approximately 1 min. These results imply that microtubules can exchange protofilaments upon Taxol binding, due to internal dynamics along the microtubule wall. The simplest interpretation of the relatively fast taxoid exchange observed and labeling of cellular microtubules with fluorescent taxoids, is that the Taxol-binding site is at the outer microtubule surface. On the contrary, if Taxol binds at the microtubule lumen in agreement with the electron crystallographic structure of tubulin dimers, our results suggest that the inside of microtubules is easily accessible from the outer solution. Large pores or moving lattice defects in microtubules might facilitate the binding of taxoids, as well as of possible endogenous cellular ligands of the inner microtubule wall.

© 1996 The American Physical Society. The authors express their appreciation to Dr. Kristl Hathaway (NRL) for valuable discussions concerning the magnetic and electronic properties of the Fe-Cu and Fe/Cu systems, and to Professor J. J. Rehr and associates (University of Washington) for providing us with the theoretical EXAFS simulation (i.e., FEFF) codes used here. This research was carried out in part at the National Synchrotron Light Source (Brookhaven National Laboratories, Upton, New York), which is sponsored by the U.S. Department of Energy. In addition, some of the samples included in this research were processed and characterized with support from the Spanish CICYT through projects Mat. 92-0491 and Mat. 92-0404. A.H. acknowledges support to the BBV Foundation and K.M.K. acknowledges support of the National Research Council during the time of this research., Extended x-ray-absorption fine-structure (EXAFS) measurements were used to obtain element- specific, structural, and chemical information of the local environments around Cu and Fe atoms in high-energy ballmilled Cu_Fe_(12-X) samples (x=0.50 and 0.70). Analysis of the EXAFS data shows both Fe and Cu atoms reside in face-centered-cubic sites where the first coordination sphere consists of a mixture of Fe and Cu atoms in a ratio which reflects the as-Prepared stoichiometry. The measured bond distances indicate a dilation in the bonds between unlike neighbors which accounts for the lattice expansion measured by x-ray diffraction. These results indicate that metastable alloys having a positive heat of mixing can be prepared via the high-energy ballmilling process., Spanish CICYT, Depto. de Física de Materiales, Fac. de Ciencias Físicas, TRUE, pub

The synchrotron x-ray solution scattering profiles of microtubules assembled from purified GDP- or GTP-tubulin with the antitumor drug docetaxel (Taxotere) are consistent with identical non-globular alpha and beta-tubulin monomers ordered within the known surface lattice of microtubules, with a center to center lateral spacing of 5.7 +/- 0.1 nm. The higher angle part of the scattering profile, and therefore the substructure of the microtubule wall is identical in Taxotere- and Taxol-induced microtubules, to the resolution of the measurements. However, Taxotere-induced microtubules have a mean diameter of 24.2 +/- 0.4 nm, which is 1.12 +/- 0.01 times larger than that of paclitaxel (Taxol) induced microtubules. The population of Taxotere microtubules has on average 13.4 protofilaments, which is similar to control microtubules assembled with glycerol but is in marked contrast with Taxol-induced microtubules, which have on average 12 protofilaments under identical solution conditions. Model populations of Taxotere and Taxol microtubules with the distributions of protofilament numbers determined by electron microscopy reproduce the positions and approximate intensities of the experimental x-ray scattering data. Comparison of the structures and activities of both taxoids strongly suggests that the change of the more frequent lateral bond angle between tubulin molecules from 152.3 degrees (13-protofilament microtubules) to 150 degrees (12-protofilament microtubules) is linked to the binding of the side chain of Taxol. Optimal microtubule formation is obtained with unitary Taxotere to tubulin heterodimer ratio; however, ligand molecules in excess over tubulin dimers cause a loss of cylindrical scattering features, consistent with microtubule opening. The results are compatible with the observed biochemical and thermodynamic properties of this ligand-induced microtubule assembly system and also with the simple working hypothesis that taxoids would bind between adjacent micro