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Schiro G.,University of Palermo | Caronna C.,SLAC | Natali F.,CNR Institute of Materials | Koza M.M.,ILL | Cupane A.,University of Palermo
Journal of Physical Chemistry Letters | Year: 2011

We give experimental evidence that the main features of protein dynamics revealed by neutron scattering, i.e., the "protein dynamical transition" and the "boson peak", do not need the protein polypeptide chain. We show that a rapid increase of hydrogen atoms fluctuations at about 220 K, analogous to the one observed in hydrated myoglobin powders, is also observed in a hydrated amino acids mixture with the chemical composition of myoglobin but lacking the polypeptide chain; in agreement with the protein behavior, the transition is abolished in the dry mixture. Further, an excess of low-frequency vibrational modes around 3 meV, typically observed in protein powders, is also observed in our mixture. Our results confirm that the dynamical transition is a water-driven onset and indicate that it mainly involves the amino acid side chains. Taking together the present data and recent results on the dynamics of a protein in denatured conformation and on the activity of dehydrated proteins, it can be concluded that the "protein dynamical transition" is neither a necessary nor a sufficient condition for active protein conformation and function. © 2011 American Chemical Society.

Bruno G.,Corning Inc. | Efremov A.M.,Corning Inc. | An C.P.,Corning Inc. | Wheaton B.R.,Corning Inc. | Hughes D.J.,ILL
Journal of Materials Science | Year: 2012

Following previous study on non-microcracked porous ceramics (SiC and alumina), we studied the micro and macrostrain response of honeycomb porous microcracked ceramics under applied uniaxial compressive stress. Cordierites of different porosities were compared. Both macroscopic and microscopic strains were measured, by extensometry and neutron diffraction, respectively. Lattice strains were determined using a single diffraction peak (steady-state neutron source) in both the axial and the transverse sample directions. Complementarily, we measured the macroscopic Young's modulus of these materials as a function of temperature, at zero load, using high-temperature laser ultrasound spectroscopy. This allowed having a non-microcracked reference state for all the materials investigated. Confirming our previous study, we observed that macrostrain relaxation occurs at constant load, which is not observed in non-microcracked compounds, such as SiC. This relaxation effect increases as a function of porosity. Moreover, we generally observed a linear dependence of the diffraction modulus on porosity. However, for low and very high applied stress, the lattice strain behavior versus stress seems to be influenced by microcracking and shows considerable strain release, as already observed in other porous microcracked ceramics. We extended to microcracked porous ceramics (cordierite) the macro to microstrain and stress relations previously developed for non-microcracked ceramics, making use of the integrity factor (IF) model. Using the whole set of data available, the IF could also be calculated as a function of applied stress. It was confirmed that highly porous microcracked materials have great potential to become stiffer and more connected. © 2012 Springer Science+Business Media, LLC.

Cuypers M.G.,Keele University | Mason S.A.,ILL | Blakeley M.P.,ILL | Mitchell E.P.,Keele University | And 3 more authors.
Angewandte Chemie - International Edition | Year: 2013

Neutron crystallographic analyses at near-atomic resolution are presented for both reduced and oxidized forms of perdeuterated Pyrococcus furiosus rubredoxin, a small iron-sulfur redox protein with remarkable thermostability. Hydronium ions may play a key role in the protonation and charge-transfer processes associated with the oxidized and reduced forms of the protein. Picture: overall structure showing D3O+ ions (red and gray molecules). Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bruno G.,Corning Inc. | Efremov A.M.,Corning Inc. | Levandovskiy A.N.,Corning Inc. | Pozdnyakova I.,French National Center for Scientific Research | And 2 more authors.
Materials Science Forum | Year: 2010

In this study, the mechanical behavior of porous thermally microcracked ceramics has been compared with that of solely porous materials, under compressive applied stress. The different aspects of the micro and macroscopic stress-strain curves have been inserted into a coherent analytical model and compared with finite element modeling calculations. The agreement between experiments and models is very good. It is shown that mechanical microcracking, as opposed to thermal, introduces an irreversible aspect in the deformation mechanisms of porous ceramics. In this concern, mechanical loads differentiate themselves from thermal cycling. This leads for instance to a change of the Young's modulus as a function of applied load, which qualifies those materials as visco-elastic. © (2010) Trans Tech Publications.

Willendrup P.,Technical University of Denmark | Farhi E.,ILL | Knudsen E.,Technical University of Denmark | Filges U.,PSI | Lefmann K.,Copenhagen University
Journal of Neutron Research | Year: 2014

The McStas neutron ray-tracing simulation package is a collaboration between Risø DTU, ILL, University of Copenhagen and the PSl. During its lifetime, McStas has evolved to become the world leading software in the area of neutron scattering simulations for instrument design, optimisation, virtual experiments. McStas is being actively used for the design-update of the European Spallation Source (ESS) in Lund. This paper includes an introduction to the McStas package, recent and ongoing simulation projects. Further, new features in releases McStas 1.12c and 2.0 are discussed. © 2014 - IOS Press and the authors. All rights reserved.

Codau C.,ILL | Nesvizhevsky V.V.,ILL | Fertl M.,ILL | Fertl M.,Paul Scherrer Institute | And 2 more authors.
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment | Year: 2012

The probability of transition between levels of a quantum bouncer, induced by a noise-like perturbation, is calculated. The results are applied to two sources of noise (vibrations and mirror surface waviness) which might play an important role in future GRANIT experiment, aiming at precision studies of/with the neutron quantum bouncer. © 2012 Elsevier B.V. All rights reserved.

Liu Y.,U.S. National Institute of Standards and Technology | Liu Y.,University of Delaware | Porcar L.,ILL | Chen J.,Sloan Kettering Cancer Center | And 8 more authors.
Journal of Physical Chemistry B | Year: 2011

The formation of equilibrium clusters has been studied in both a prototypical colloidal system and protein solutions. The appearance of a low-Q correlation peak in small angle scattering patterns of lysozyme solution was attributed to the cluster-cluster correlation. Consequently, the presence of long-lived clusters has been established. By quantitatively analyzing both the SANS (small angle neutron scattering) and NSE (neutron spin echo) data of lysozyme solution using statistical mechanics models, we conclusively show in this paper that the appearance of a low-Q peak is not a signature of the formation of clusters. Rather, it is due to the formation of an intermediate range order structure governed by a short-range attraction and a long-range repulsion. We have further studied dynamic features of a sample with high enough concentration at which clusters are formed in solution. From the estimation of the mean square displacement by using short-time and long-time diffusion coefficient measured by NSE and NMR, we find that these clusters are not permanent but have a finite lifetime longer than the time required to diffuse over a distance of a monomer diameter. © 2010 American Chemical Society.

Shen H.-H.,Physical and Theoretical Chemistry Laboratory | Thomas R.K.,Physical and Theoretical Chemistry Laboratory | Penfold J.,ISIS | Fragneto G.,ILL
Langmuir | Year: 2010

The lipopeptide surfactin from Bacillus subtilis strains exhibits strong surface and biological activity, the latter probably because of its interaction with biological membranes. We have investigated the interaction of aqueous solutions of surfactin with supported bilayers of diphosphatidylcholine (DPPC) on silica using neutron reflectometry. We have also used small-angle neutron scattering (SANS) to study the solubilized aggregates formed as a result of the destruction of the supported membrane by surfactin. Although surfactin on its own does not attach to the silica supporting surface, it is taken up from solution by the membrane, confirming that there is an attractive interaction between DPPC and surfactin. The surfactin concentration in the layer can reach up to about 20 mol % relative to DPPC. The membrane is stable provided that the surfactin concentration is below its critical micelle concentration (cmc, 5×10-5 M). Above the cmc, however, the membrane is solubilized and removed from the surface, though not always completely, over a period of hours. There are signs that there is an induction period while the surfactin concentration builds up in the membrane. This would be consistent with the need for a threshold concentration of surfactin in the bilayer. The presence of a surfactin correlation peak in the SANS showed that in the bulk solution, at the same concentrations as used for the deposition, surfactin forms aggregates that must be localized in the DPPC multilamellar vesicles at a separation of about 160 Å. The structure could be fitted with an approximate model where the surfactin has an aggregation number of 50 ± 10 with a radius of about 27 Å. Given the very small water thicknesses in the DPPC lamellar aggregates, the surfactin must exist as aggregates in the phospholipid bilayer, and these structures are responsible for solubilizing the DPPC. © 2010 American Chemical Society.

Neutron spectroscopy provides experimental data on time-dependent trajectories, which can be directly compared to molecular dynamics simulations. Its importance in helping us to understand biological macromolecules at a molecular level is demonstrated by the results of a literature survey over the last two to three decades. Around 300 articles in refereed journals relate to neutron scattering studies of biological macromolecular dynamics, and the results of the survey are presented here. The scope of the publications ranges from the general physics of protein and solvent dynamics, to the biologically relevant dynamics-function relationships in live cells. As a result of the survey we are currently setting up a neutron Dynamics Data Bank (nDDB) with the aim to make the neutron data on biological systems widely available. This will benefit, in particular, the MD simulation community to validate and improve their force fields. The aim of the database is to expose and give easy access to a body of experimental data to the scientific community. The database will be populated with as much of the existing data as possible. In the future it will give value, as part of a bigger whole, to high throughput data, as well as more detailed studies. A range and volume of experimental data will be of interest in determining how quantitatively MD simulations can reproduce trends across a range of systems and to what extent such trends may depend on sample preparation and data reduction and analysis methods. In this context, we strongly encourage researchers in the field to deposit their data in the nDDB.

PubMed | Keele University and ILL
Type: | Journal: Scientific reports | Year: 2016

In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences.

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