Pluridirectional High-Energy Agile Scanning Electron Radiotherapy (PHASER): Extremely Rapid Treatment for Early Lung Cancer

DTIC Science & Technology

2014-06-01

BEAMnrc Monte Carlo (MC) codes were used to simulate 50- 150MeV VHEE beam dose deposition and its effects on steel and titanium (Ti) heterogeneities in a...performed on water-only geometry and water with segmented prostheses ( steel and Ti) geometries with 100MeV and 150MeV beams...8 Results: 100MeV PDD 5cm behind steel /Ti heterogeneity was 51% less than in the

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

PubMed

Lee, Jonas; Kim, Sung Hou

2009-04-01

The Protein Data Bank file format is the format most widely used by protein crystallographers and biologists to disseminate and manipulate protein structures. Despite this, there are few user-friendly software packages available to efficiently edit and extract raw information from PDB files. This limitation often leads to many protein crystallographers wasting significant time manually editing PDB files. PDB Editor, written in Java Swing GUI, allows the user to selectively search, select, extract and edit information in parallel. Furthermore, the program is a stand-alone application written in Java which frees users from the hassles associated with platform/operating system-dependent installation and usage. PDB Editor can be downloaded from http://sourceforge.net/projects/pdbeditorjl/.

Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank

PubMed Central

Joosten, Robbie P.; Joosten, Krista; Cohen, Serge X.; Vriend, Gert; Perrakis, Anastassis

2011-01-01

Motivation: Macromolecular crystal structures in the Protein Data Bank (PDB) are a key source of structural insight into biological processes. These structures, some >30 years old, were constructed with methods of their era. With PDB_REDO, we aim to automatically optimize these structures to better fit their corresponding experimental data, passing the benefits of new methods in crystallography on to a wide base of non-crystallographer structure users. Results: We developed new algorithms to allow automatic rebuilding and remodeling of main chain peptide bonds and side chains in crystallographic electron density maps, and incorporated these and further enhancements in the PDB_REDO procedure. Applying the updated PDB_REDO to the oldest, but also to some of the newest models in the PDB, corrects existing modeling errors and brings these models to a higher quality, as judged by standard validation methods. Availability and Implementation: The PDB_REDO database and links to all software are available at http://www.cmbi.ru.nl/pdb_redo. Contact: r.joosten@nki.nl; a.perrakis@nki.nl Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22034521

Pressure Studies of Protein Dynamics

DTIC Science & Technology

1989-02-26

infrared flash photolysis system with the monitoring light produced by a Spectra-Physics/ Laser Analytics tunable- diode laser and detected by a liquid...refrigerator. Time range extends from about 100 ms to 100 s. The diode laser current is modulated at 10 kHz and the signal is amplified with a PAR 5101...Photolysis is obtained with a Phase-R D 121OOC dye laser using rhodamine 6G (pulse 4 width 500 ns, 0.3 J). Kinetic spectra are obtained from about 10

Pluridirectional High-Energy Agile Scanning Electron Radiotherapy (PHASER): Extremely Rapid Treatment for Early Lung Cancer

DTIC Science & Technology

2015-09-01

used to simulate 50- 150MeV VHEE beam dose deposition and its effects on steel and titanium (Ti) heterogeneities in a water phantom. Heterogeneities of...and water with segmented prostheses ( steel and Ti) geometries with 100MeV and 150MeV beams. Results: 100MeV PDD 5cm behind steel /Ti heterogeneity...in steel and 18% in Ti heterogeneities. The dose immediately behind steel heterogeneity decreased by an average of 6%, although for 150MeV, the

Non-Lethal Weapons: Setting Our Phasers on Stun? Potential Stratetgic Blessings and Curses of Non-Lethal Weapons on the Battlefield

DTIC Science & Technology

2003-08-01

improve our ability to verify compliance with the treaty’s global ban on biological weapons and would put national security and confidential business ...he was Assistant Professor of Aeronautics at the U.S. Air Force Academy, Colorado, where he was also instructor pilot in the T - 41 flight-screening...fielded on a greater scale are explored. The ability of non-lethal weapons to positively influence the global war on terrorism is also assessed. It

Fatty Acid Synthase Inhibitors Engage the Cell Death Program Through the Endoplasmic Reticulum

DTIC Science & Technology

2007-12-01

suite26 (Table 1). The structure was solved by molecular replacement using PHASER27 with the native, uncomplexed structure of the thioesterase domain ( PDB ...groups and molecular weight. Using a 96-well format, we screened compounds at 10 μM and used 40% inhibition at a single time point as our threshold for...thioesterase domain of human fatty acid synthase inhibited by Orlistat. (2007) Nature Structural and Molecular Biology 14(8): 704-709. (Article of the

Automated crystallographic system for high-throughput protein structure determination.

PubMed

Brunzelle, Joseph S; Shafaee, Padram; Yang, Xiaojing; Weigand, Steve; Ren, Zhong; Anderson, Wayne F

2003-07-01

High-throughput structural genomic efforts require software that is highly automated, distributive and requires minimal user intervention to determine protein structures. Preliminary experiments were set up to test whether automated scripts could utilize a minimum set of input parameters and produce a set of initial protein coordinates. From this starting point, a highly distributive system was developed that could determine macromolecular structures at a high throughput rate, warehouse and harvest the associated data. The system uses a web interface to obtain input data and display results. It utilizes a relational database to store the initial data needed to start the structure-determination process as well as generated data. A distributive program interface administers the crystallographic programs which determine protein structures. Using a test set of 19 protein targets, 79% were determined automatically.

DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs.

PubMed

Chodkiewicz, Michał L; Migacz, Szymon; Rudnicki, Witold; Makal, Anna; Kalinowski, Jarosław A; Moriarty, Nigel W; Grosse-Kunstleve, Ralf W; Afonine, Pavel V; Adams, Paul D; Dominiak, Paulina Maria

2018-02-01

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This comes, however, at the cost of increased complexity of the underlying calculations. In order to facilitate the adoption of this more advanced electron density model by the broader community of crystallographers, a new software implementation called DiSCaMB , 'densities in structural chemistry and molecular biology', has been developed. It addresses the challenge of providing for high performance on modern computing architectures. With parallelization options for both multi-core processors and graphics processing units (using CUDA), the library features calculation of X-ray scattering factors and their derivatives with respect to structural parameters, gives access to intermediate steps of the scattering factor calculations (thus allowing for experimentation with modifications of the underlying electron density model), and provides tools for basic structural crystallographic operations. Permissively (MIT) licensed, DiSCaMB is an open-source C++ library that can be embedded in both academic and commercial tools for X-ray structure refinement.

Sharing electronic structure and crystallographic data with ETSF_IO

NASA Astrophysics Data System (ADS)

Caliste, D.; Pouillon, Y.; Verstraete, M. J.; Olevano, V.; Gonze, X.

2008-11-01

We present a library of routines whose main goal is to read and write exchangeable files (NetCDF file format) storing electronic structure and crystallographic information. It is based on the specification agreed inside the European Theoretical Spectroscopy Facility (ETSF). Accordingly, this library is nicknamed ETSF_IO. The purpose of this article is to give both an overview of the ETSF_IO library and a closer look at its usage. ETSF_IO is designed to be robust and easy to use, close to Fortran read and write routines. To facilitate its adoption, a complete documentation of the input and output arguments of the routines is available in the package, as well as six tutorials explaining in detail various possible uses of the library routines. Catalogue identifier: AEBG_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEBG_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Gnu Lesser General Public License No. of lines in distributed program, including test data, etc.: 63 156 No. of bytes in distributed program, including test data, etc.: 363 390 Distribution format: tar.gz Programming language: Fortran 95 Computer: All systems with a Fortran95 compiler Operating system: All systems with a Fortran95 compiler Classification: 7.3, 8 External routines: NetCDF, http://www.unidata.ucar.edu/software/netcdf Nature of problem: Store and exchange electronic structure data and crystallographic data independently of the computational platform, language and generating software Solution method: Implement a library based both on NetCDF file format and an open specification (http://etsf.eu/index.php?page=standardization)

Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

ERIC Educational Resources Information Center

Battle, Gary M.; Allen, Frank H.; Ferrence, Gregory M.

2011-01-01

Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

Development of Pantothenate Analogs That Can Treat Combat-Related Infections

DTIC Science & Technology

2014-04-01

determined by the molecular replacement method using the structure of S. aureus PanK excluding bound AMPPNP as a search model ( PDB code 2EWS). The...were solved by molecular replacement using the program PHASER11 and the EcPanK structure as a search model ( PDB : 1SQ5). The models went through...aureus PanK (SaPanK) complexed with N5- Pan (months 1-3) We solved the structure of the SaPanK�N5-Pan complex by the molecular replacement method

Human Error as an Emergent Property of Action Selection and Task Place-Holding.

PubMed

Tamborello, Franklin P; Trafton, J Gregory

2017-05-01

A computational process model could explain how the dynamic interaction of human cognitive mechanisms produces each of multiple error types. With increasing capability and complexity of technological systems, the potential severity of consequences of human error is magnified. Interruption greatly increases people's error rates, as does the presence of other information to maintain in an active state. The model executed as a software-instantiated Monte Carlo simulation. It drew on theoretical constructs such as associative spreading activation for prospective memory, explicit rehearsal strategies as a deliberate cognitive operation to aid retrospective memory, and decay. The model replicated the 30% effect of interruptions on postcompletion error in Ratwani and Trafton's Stock Trader task, the 45% interaction effect on postcompletion error of working memory capacity and working memory load from Byrne and Bovair's Phaser Task, as well as the 5% perseveration and 3% omission effects of interruption from the UNRAVEL Task. Error classes including perseveration, omission, and postcompletion error fall naturally out of the theory. The model explains post-interruption error in terms of task state representation and priming for recall of subsequent steps. Its performance suggests that task environments providing more cues to current task state will mitigate error caused by interruption. For example, interfaces could provide labeled progress indicators or facilities for operators to quickly write notes about their task states when interrupted.

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

PubMed Central

Pothineni, Sudhir Babu; Venugopalan, Nagarajan; Ogata, Craig M.; Hilgart, Mark C.; Stepanov, Sergey; Sanishvili, Ruslan; Becker, Michael; Winter, Graeme; Sauter, Nicholas K.; Smith, Janet L.; Fischetti, Robert F.

2014-01-01

The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates a collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce. PMID:25484844

Tightly integrated single- and multi-crystal data collection strategy calculation and parallelized data processing in JBluIce beamline control system

DOE PAGES

Pothineni, Sudhir Babu; Venugopalan, Nagarajan; Ogata, Craig M.; ...

2014-11-18

The calculation of single- and multi-crystal data collection strategies and a data processing pipeline have been tightly integrated into the macromolecular crystallographic data acquisition and beamline control software JBluIce. Both tasks employ wrapper scripts around existing crystallographic software. JBluIce executes scripts through a distributed resource management system to make efficient use of all available computing resources through parallel processing. The JBluIce single-crystal data collection strategy feature uses a choice of strategy programs to help users rank sample crystals and collect data. The strategy results can be conveniently exported to a data collection run. The JBluIce multi-crystal strategy feature calculates amore » collection strategy to optimize coverage of reciprocal space in cases where incomplete data are available from previous samples. The JBluIce data processing runs simultaneously with data collection using a choice of data reduction wrappers for integration and scaling of newly collected data, with an option for merging with pre-existing data. Data are processed separately if collected from multiple sites on a crystal or from multiple crystals, then scaled and merged. Results from all strategy and processing calculations are displayed in relevant tabs of JBluIce.« less

Construction of hydrodynamic bead models from high-resolution X-ray crystallographic or nuclear magnetic resonance data.

PubMed Central

Byron, O

1997-01-01

Computer software such as HYDRO, based upon a comprehensive body of theoretical work, permits the hydrodynamic modeling of macromolecules in solution, which are represented to the computer interface as an assembly of spheres. The uniqueness of any satisfactory resultant model is optimized by incorporating into the modeling procedure the maximal possible number of criteria to which the bead model must conform. An algorithm (AtoB, for atoms to beads) that permits the direct construction of bead models from high resolution x-ray crystallographic or nuclear magnetic resonance data has now been formulated and tested. Models so generated then act as informed starting estimates for the subsequent iterative modeling procedure, thereby hastening the convergence to reasonable representations of solution conformation. Successful application of this algorithm to several proteins shows that predictions of hydrodynamic parameters, including those concerning solvation, can be confirmed. PMID:8994627

Gyre and gimble: a maximum-likelihood replacement for Patterson correlation refinement.

PubMed

McCoy, Airlie J; Oeffner, Robert D; Millán, Claudia; Sammito, Massimo; Usón, Isabel; Read, Randy J

2018-04-01

Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. Gyre refinement helps to lower the root-mean-square atomic displacements between model and target molecular-replacement solutions for the test case of antibody Fab(26-10) and improves structure solution with ARCIMBOLDO_SHREDDER.

Firefighter health and fitness assessment: a call to action.

PubMed

Storer, Thomas W; Dolezal, Brett A; Abrazado, Marlon L; Smith, Denise L; Batalin, Maxim A; Tseng, Chi-Hong; Cooper, Christopher B

2014-03-01

Sudden cardiac deaths experienced by firefighters in the line of duty account for the largest proportion of deaths annually. Several fire service standards for fitness and wellness have been recommended but currently only 30% of U.S. fire departments are implementing programs for this purpose. The Department of Homeland Security Science and Technology Directorate has initiated the Physiological Health Assessment System for Emergency Responders (PHASER) program aiming to reduce these line-of-duty deaths through an integration of medical science and sensor technologies. Confirming previous reports, PHASER comprehensive risk assessment has identified lack of physical fitness with propensity for overexertion as a major modifiable risk factor. We sought to determine if current levels of fitness and cardiovascular disease (CVD) risk factors in a contemporary cohort of firefighters were better than those reported over the past 30 years. Fifty-one firefighters from a Southern California department were characterized for physical fitness and CVD risk factors using standard measures. Overall, physical fitness and risk factors were not different from previous reports of firefighter fitness and most subjects did not achieve recommended fitness standards. Considering the lack of widespread implementation of wellness/fitness programs in the U.S. fire service together with our findings that low physical fitness and the presence of CVD risk factors persist, we issue a call to action among health and fitness professionals to assist the fire service in implementing programs for firefighters that improve fitness and reduce CVD risk factors. Fitness professionals should be empowered to work with fire departments lending their expertise to guide programs that achieve these objectives, which may then lead to reduced incidence of sudden cardiac death or stroke.

Fitmunk: improving protein structures by accurate, automatic modeling of side-chain conformations.

PubMed

Porebski, Przemyslaw Jerzy; Cymborowski, Marcin; Pasenkiewicz-Gierula, Marta; Minor, Wladek

2016-02-01

Improvements in crystallographic hardware and software have allowed automated structure-solution pipelines to approach a near-`one-click' experience for the initial determination of macromolecular structures. However, in many cases the resulting initial model requires a laborious, iterative process of refinement and validation. A new method has been developed for the automatic modeling of side-chain conformations that takes advantage of rotamer-prediction methods in a crystallographic context. The algorithm, which is based on deterministic dead-end elimination (DEE) theory, uses new dense conformer libraries and a hybrid energy function derived from experimental data and prior information about rotamer frequencies to find the optimal conformation of each side chain. In contrast to existing methods, which incorporate the electron-density term into protein-modeling frameworks, the proposed algorithm is designed to take advantage of the highly discriminatory nature of electron-density maps. This method has been implemented in the program Fitmunk, which uses extensive conformational sampling. This improves the accuracy of the modeling and makes it a versatile tool for crystallographic model building, refinement and validation. Fitmunk was extensively tested on over 115 new structures, as well as a subset of 1100 structures from the PDB. It is demonstrated that the ability of Fitmunk to model more than 95% of side chains accurately is beneficial for improving the quality of crystallographic protein models, especially at medium and low resolutions. Fitmunk can be used for model validation of existing structures and as a tool to assess whether side chains are modeled optimally or could be better fitted into electron density. Fitmunk is available as a web service at http://kniahini.med.virginia.edu/fitmunk/server/ or at http://fitmunk.bitbucket.org/.

SLAC All Access: Laser Labs

ScienceCinema

Minitti, Mike; Woods, Mike

2018-05-23

From supermarket checkouts to video game consoles, lasers are ubiquitous in our lives. Here at SLAC, high-power lasers are critical to the cutting-edge research conducted at the laboratory. But, despite what you might imagine, SLAC's research lasers bear little resemblance to the blasters and phasers of science fiction. In this edition of All Access we put on our safety goggles for a peek at what goes on inside some of SLAC's many laser labs. LCLS staff scientist Mike Minitti and SLAC laser safety officer Mike Woods detail how these lasers are used to study the behavior of subatomic particles, broaden our understanding of cosmic rays and even unlock the mysteries of photosynthesis.

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models.

PubMed

Keegan, Ronan M; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D; Rigden, Daniel J

2015-02-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected.

The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results

PubMed Central

Rosenbaum, Gerd; Alkire, Randy W.; Evans, Gwyndaf; Rotella, Frank J.; Lazarski, Krzystof; Zhang, Rong-Guang; Ginell, Stephan L.; Duke, Norma; Naday, Istvan; Lazarz, Jack; Molitsky, Michael J.; Keefe, Lisa; Gonczy, John; Rock, Larry; Sanishvili, Ruslan; Walsh, Martin A.; Westbrook, Edwin; Joachimiak, Andrzej

2008-01-01

The 19ID undulator beamline of the Structure Biology Center has been designed and built to take full advantage of the high flux, brilliance and quality of X-ray beams delivered by the Advanced Photon Source. The beamline optics are capable of delivering monochromatic X-rays with photon energies from 3.5 to 20 keV (3.5–0.6 Å wavelength) with fluxes up to 8–18 × 1012 photons s−1 (depending on photon energy) onto cryogenically cooled crystal samples. The size of the beam (full width at half-maximum) at the sample position can be varied from 2.2 mm × 1.0 mm (horizontal × vertical, unfocused) to 0.083 mm × 0.020 mm in its fully focused configuration. Specimen-to-detector distances of between 100 mm and 1500 mm can be used. The high flexibility, inherent in the design of the optics, coupled with a κ-geometry goniometer and beamline control software allows optimal strategies to be adopted in protein crystallographic experiments, thus maximizing the chances of their success. A large-area mosaic 3 × 3 CCD detector allows high-quality diffraction data to be measured rapidly to the crystal diffraction limits. The beamline layout and the X-ray optical and endstation components are described in detail, and the results of representative crystallographic experiments are presented. PMID:16371706

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov; Bricogne, Gerard, E-mail: terwilliger@lanl.gov; Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray datamore » continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

SLAC All Access: Laser Labs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minitti, Mike; Woods, Mike

2013-03-01

From supermarket checkouts to video game consoles, lasers are ubiquitous in our lives. Here at SLAC, high-power lasers are critical to the cutting-edge research conducted at the laboratory. But, despite what you might imagine, SLAC's research lasers bear little resemblance to the blasters and phasers of science fiction. In this edition of All Access we put on our safety goggles for a peek at what goes on inside some of SLAC's many laser labs. LCLS staff scientist Mike Minitti and SLAC laser safety officer Mike Woods detail how these lasers are used to study the behavior of subatomic particles, broadenmore » our understanding of cosmic rays and even unlock the mysteries of photosynthesis.« less

Exploring the speed and performance of molecular replacement with AMPLE using QUARK ab initio protein models

PubMed Central

Keegan, Ronan M.; Bibby, Jaclyn; Thomas, Jens; Xu, Dong; Zhang, Yang; Mayans, Olga; Winn, Martyn D.; Rigden, Daniel J.

2015-01-01

AMPLE clusters and truncates ab initio protein structure predictions, producing search models for molecular replacement. Here, an interesting degree of complementarity is shown between targets solved using the different ab initio modelling programs QUARK and ROSETTA. Search models derived from either program collectively solve almost all of the all-helical targets in the test set. Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. Taken together, the results show the potential for AMPLE to run more quickly and successfully solve more targets than previously suspected. PMID:25664744

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

PubMed

Terwilliger, Thomas C; Bricogne, Gerard

2014-10-01

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

DOE PAGES

Terwilliger, Thomas C.; Bricogne, Gerard

2014-09-30

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

PubMed Central

Terwilliger, Thomas C.; Bricogne, Gerard

2014-01-01

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering. PMID:25286839

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: The dual role of deposited experimental data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Terwilliger, Thomas C.; Bricogne, Gerard

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when itmore » was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.« less

Exploiting distant homologues for phasing through the generation of compact fragments, local fold refinement and partial solution combination.

PubMed

Millán, Claudia; Sammito, Massimo Domenico; McCoy, Airlie J; Nascimento, Andrey F Ziem; Petrillo, Giovanna; Oeffner, Robert D; Domínguez-Gil, Teresa; Hermoso, Juan A; Read, Randy J; Usón, Isabel

2018-04-01

Macromolecular structures can be solved by molecular replacement provided that suitable search models are available. Models from distant homologues may deviate too much from the target structure to succeed, notwithstanding an overall similar fold or even their featuring areas of very close geometry. Successful methods to make the most of such templates usually rely on the degree of conservation to select and improve search models. ARCIMBOLDO_SHREDDER uses fragments derived from distant homologues in a brute-force approach driven by the experimental data, instead of by sequence similarity. The new algorithms implemented in ARCIMBOLDO_SHREDDER are described in detail, illustrating its characteristic aspects in the solution of new and test structures. In an advance from the previously published algorithm, which was based on omitting or extracting contiguous polypeptide spans, model generation now uses three-dimensional volumes respecting structural units. The optimal fragment size is estimated from the expected log-likelihood gain (LLG) values computed assuming that a substructure can be found with a level of accuracy near that required for successful extension of the structure, typically below 0.6 Å root-mean-square deviation (r.m.s.d.) from the target. Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser's gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser's LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. Phase combination among consistent partial solutions is performed in reciprocal space with ALIXE. Finally, density modification and main-chain autotracing in SHELXE serve to expand to the full structure and identify successful solutions. The performance on test data and the solution of new structures are described.

Stennis hosts NASA Night in Oxford

NASA Technical Reports Server (NTRS)

2010-01-01

A young visitor to the Powerhouse Community Arts and Cultural Center in Oxford, Miss., enjoys a balloon rocket transportation activity during a NASA Night in the Neighborhood on March 29. NASA's John C. Stennis Space Center near Bay St. Louis visited the center with a variety of space-related displays and educational activities. Events targeted for children included moon phasers and build-your-own rocket transportation exercises, as well as an astronaut ice cream tasting station. Visitors also were able to take photos in the astronaut suit display. Displays focused on the 40th anniversaries of the Apollo 11 and Apollo 13 lunar missions, the International Space Station, and various aspects of Stennis work. The event was sponsored by the NASA Office of External Affairs and Education at Stennis.

Digital phase-lock loop

NASA Technical Reports Server (NTRS)

Thomas, Jr., Jess B. (Inventor)

1991-01-01

An improved digital phase lock loop incorporates several distinctive features that attain better performance at high loop gain and better phase accuracy. These features include: phase feedback to a number-controlled oscillator in addition to phase rate; analytical tracking of phase (both integer and fractional cycles); an amplitude-insensitive phase extractor; a more accurate method for extracting measured phase; a method for changing loop gain during a track without loss of lock; and a method for avoiding loss of sampled data during computation delay, while maintaining excellent tracking performance. The advantages of using phase and phase-rate feedback are demonstrated by comparing performance with that of rate-only feedback. Extraction of phase by the method of modeling provides accurate phase measurements even when the number-controlled oscillator phase is discontinuously updated.

Data to knowledge: how to get meaning from your result.

PubMed

Berman, Helen M; Gabanyi, Margaret J; Groom, Colin R; Johnson, John E; Murshudov, Garib N; Nicholls, Robert A; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated 'Big Data' technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB 'super' laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results.

Macromolecular ab initio phasing enforcing secondary and tertiary structure.

PubMed

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors' approach relies on the combination of locating model fragments such as polyalanine α-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a 'still-life', but some are correct enough for density modification and main-chain tracing to reveal the protein's true portrait. Beyond α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2 Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases.

Optically driven self-oscillations of a silica nanospike at low gas pressures

NASA Astrophysics Data System (ADS)

Xie, Shangran; Pennetta, Riccardo; Noskov, Roman E.; Russell, Philip St. J.

2016-09-01

We report light-driven instability and optomechanical self-oscillation of a fused silica "nanospike" at low gas pressures. The nanospike (tip diameter 400 nm), fabricated by thermally tapering and HF-etching a single mode fiber (SMF), was set pointing at the endface of a hollow-core photonic crystal fiber (HC-PCF) into the field created by the fundamental optical mode emerging from the HC-PCF. At low pressures, the nanospike became unstable and began to self-oscillate for optical powers above a certain threshold, acting like a phonon laser or "phaser". Because the nanospike is robustly connected to the base, direct measurement of the temporal dynamics of the instability is possible. The experiment sheds light on why particles escape from optical traps at low pressures.

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Hongxing; Fang, Hengrui; Miller, Mitchell D.

2016-07-15

An iterative transform algorithm is proposed to improve the conventional molecular-replacement method for solving the phase problem in X-ray crystallography. Several examples of successful trial calculations carried out with real diffraction data are presented. An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationshipmore » of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.« less

The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites

PubMed Central

2013-01-01

Background Many Protein Data Bank (PDB) users assume that the deposited structural models are of high quality but forget that these models are derived from the interpretation of experimental data. The accuracy of atom coordinates is not homogeneous between models or throughout the same model. To avoid basing a research project on a flawed model, we present a tool for assessing the quality of ligands and binding sites in crystallographic models from the PDB. Results The Validation HElper for LIgands and Binding Sites (VHELIBS) is software that aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e., users with little or no crystallography knowledge). Using a convenient graphical user interface, it allows one to check how ligand and binding site coordinates fit to the electron density map. VHELIBS can use models from either the PDB or the PDB_REDO databank of re-refined and re-built crystallographic models. The user can specify threshold values for a series of properties related to the fit of coordinates to electron density (Real Space R, Real Space Correlation Coefficient and average occupancy are used by default). VHELIBS will automatically classify residues and ligands as Good, Dubious or Bad based on the specified limits. The user is also able to visually check the quality of the fit of residues and ligands to the electron density map and reclassify them if needed. Conclusions VHELIBS allows inexperienced users to examine the binding site and the ligand coordinates in relation to the experimental data. This is an important step to evaluate models for their fitness for drug discovery purposes such as structure-based pharmacophore development and protein-ligand docking experiments. PMID:23895374

Data to knowledge: how to get meaning from your result

PubMed Central

Berman, Helen M.; Gabanyi, Margaret J.; Groom, Colin R.; Johnson, John E.; Murshudov, Garib N.; Nicholls, Robert A.; Reddy, Vijay; Schwede, Torsten; Zimmerman, Matthew D.; Westbrook, John; Minor, Wladek

2015-01-01

Structural and functional studies require the development of sophisticated ‘Big Data’ technologies and software to increase the knowledge derived and ensure reproducibility of the data. This paper presents summaries of the Structural Biology Knowledge Base, the VIPERdb Virus Structure Database, evaluation of homology modeling by the Protein Model Portal, the ProSMART tool for conformation-independent structure comparison, the LabDB ‘super’ laboratory information management system and the Cambridge Structural Database. These techniques and technologies represent important tools for the transformation of crystallographic data into knowledge and information, in an effort to address the problem of non-reproducibility of experimental results. PMID:25610627

Crystal Symmetry Algorithms in a High-Throughput Framework for Materials

NASA Astrophysics Data System (ADS)

Taylor, Richard

The high-throughput framework AFLOW that has been developed and used successfully over the last decade is improved to include fully-integrated software for crystallographic symmetry characterization. The standards used in the symmetry algorithms conform with the conventions and prescriptions given in the International Tables of Crystallography (ITC). A standard cell choice with standard origin is selected, and the space group, point group, Bravais lattice, crystal system, lattice system, and representative symmetry operations are determined. Following the conventions of the ITC, the Wyckoff sites are also determined and their labels and site symmetry are provided. The symmetry code makes no assumptions on the input cell orientation, origin, or reduction and has been integrated in the AFLOW high-throughput framework for materials discovery by adding to the existing code base and making use of existing classes and functions. The software is written in object-oriented C++ for flexibility and reuse. A performance analysis and examination of the algorithms scaling with cell size and symmetry is also reported.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

PubMed

Hiraki, Masahiko; Kato, Ryuichi; Nagai, Minoru; Satoh, Tadashi; Hirano, Satoshi; Ihara, Kentaro; Kudo, Norio; Nagae, Masamichi; Kobayashi, Masanori; Inoue, Michio; Uejima, Tamami; Oda, Shunichiro; Chavas, Leonard M G; Akutsu, Masato; Yamada, Yusuke; Kawasaki, Masato; Matsugaki, Naohiro; Igarashi, Noriyuki; Suzuki, Mamoru; Wakatsuki, Soichi

2006-09-01

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

Crystallographic, magnetic, and electronic structures of ferromagnetic shape memory alloys Ni2XGa (X=Mn,Fe,Co) from first-principles calculations

NASA Astrophysics Data System (ADS)

Bai, J.; Raulot, J. M.; Zhang, Y. D.; Esling, C.; Zhao, X.; Zuo, L.

2011-01-01

The crystallographic, magnetic and electronic structures of the ferromagnetic shape memory alloys Ni2XGa (X=Mn, Fe, and Co), are systematically investigated by means of the first-principles calculations within the framework of density functional theory using the VIENNA AB INITIO SOFTWARE PACKAGE. The lattice parameters of both austenitic and martensitic phases in Ni2MnGa have been calculated. The formation energies of the cubic phase of Ni2XGa are estimated, and show a destabilization tendency if Mn atom is substituted by Fe or Co. From Ni2MnGa to Ni2CoGa, the down spin total density of states (DOS) at Fermi level is gradually increasing, whereas that of the up spin part remains almost unchanged. This is the main origin of the difference of the magnetic moment in these alloys. The partial DOS is dominated by the Ni and Mn 3d states in the bonding region below EF. There are two bond types existing in Ni2XGa: one is between neighboring Ni atoms in Ni2MnGa; the other is between Ni and X atoms in Ni2FeGa and Ni2CoGa alloys.

Method for removing atomic-model bias in macromolecular crystallography

DOEpatents

Terwilliger, Thomas C [Santa Fe, NM

2006-08-01

Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

Crystallographically Anisotropic Shape of Forsterite: New Probe for Evaluating Dust Formation History from Infrared Spectroscopy

NASA Astrophysics Data System (ADS)

Takigawa, Aki; Tachibana, Shogo

2012-05-01

Crystalline dust has been observed by infrared spectroscopy around dust-enshrouded asymptotic giant branch stars, in protoplanetary disks, and from some comets. Crystalline materials often have a specific shape related to a specific crystallographic orientation (crystallographically anisotropic shape), which reflects the anisotropic nature of crystals, and their infrared spectral features depend on crystallographically anisotropic shapes. The crystallographically anisotropic shape is thus a potentially powerful probe to evaluate circumstellar dust-forming conditions quantitatively. In order to assess the possibility to determine the crystallographically anisotropic shape from infrared spectra, we calculated mass absorption coefficients for ellipsoidal forsterite particles, the most abundant circumstellar crystalline silicate, elongated and flattened along the crystallographic a-, b-, and c-axes with various aspect ratios in the wavelength range of 9-70 μm. It was found that differences in infrared features caused by various crystallographicaly anisotropic shapes are distinguishable from each other irrespective of the effects of temperature, size, chemical composition, and grain edges of forsterite in the range of 9-12 μm and 15-20 μm. We thus concluded that the crystallographically anisotropic shape of forsterite can be deduced from peak features in infrared spectra. We also showed that the crystallographically anisotropic shapes formed by evaporation and condensation of forsterite can be distinguished from each other and the temperature condition for evaporation can be evaluated from the peak features. We applied the present results to the infrared spectrum of a protoplanetary disk HD100546 and found that a certain fraction (~25%) of forsterite dust may have experienced high-temperature evaporation (>1600 K).

The Phenix Software for Automated Determination of Macromolecular Structures

PubMed Central

Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

2011-01-01

X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

Stennis hosts Gulf Pine Council's NASA Brownie Day

NASA Image and Video Library

2007-10-13

Tori Williams, of Brownie Girl Scout Troop 313, builds her own `stomp rocket' with the help of adult chaperone Pamela Cottrell. The two, of Gulfport, participated in NASA Brownie Day on Oct. 13 at Stennis Space Center. They were among nearly 200 members of Brownie Girl Scout Troops within the Gulf Pines Council who took part in the day of educational activities at SSC. Brownie Day used NASA curriculum support materials to teach about the sun and its significance in our solar system. In addition to building and launching their own model rockets, the girls toured the center's portable Starlab planetarium; viewed demonstrations about living and working in space; played games of `Moon Phasers' that teach about the rotation of the moon around the earth; made bracelets with ultraviolet-sensitive beads; and other activities that celebrated Earth's very own star. They also toured StenniSphere and were able to earn their Earth and Sky and Space Explorer `Try-Its.'

Prototype Holographic Atmospheric Scanner for Environmental Remote Sensing (PHASERS)

NASA Technical Reports Server (NTRS)

Guerra, David V.; Schwemmer, Geary K.; Wooten, Albert D., Jr.; Chaudhuri, Sandipan S.; Wilkerson, Thomas D.

1995-01-01

A ground-based atmospheric lidar system that utilizes a Holographic Optical Telescope and Scanner has been developed and successfully operated to obtain atmospheric backscatter profiles. The Prototype Holographic Atmospheric Scanner for Environmental Remote Sensing is built around a volume phase reflection Holographic Optical Element. This single optical element both directs and collimates the outgoing laser beam as well as collects, focuses, and filters the atmospheric laser backscatter, while offering significant weight savings over existing telescope mirror technology. Conical scanning is accomplished as the HOE rotates on a turntable sweeping the 1.2 mrad field of view around a 42deg cone. During this technology demonstration, atmospheric aerosol and cloud return signals have been received in both stationary and scanning modes. The success of this program has led to the further development of this technology for integration into airborne and eventually satellite earth observing scanning lidar telescopes.

Stennis hosts Gulf Pine Council's NASA Brownie Day

NASA Technical Reports Server (NTRS)

2007-01-01

Tori Williams, of Brownie Girl Scout Troop 313, builds her own `stomp rocket' with the help of adult chaperone Pamela Cottrell. The two, of Gulfport, participated in NASA Brownie Day on Oct. 13 at Stennis Space Center. They were among nearly 200 members of Brownie Girl Scout Troops within the Gulf Pines Council who took part in the day of educational activities at SSC. Brownie Day used NASA curriculum support materials to teach about the sun and its significance in our solar system. In addition to building and launching their own model rockets, the girls toured the center's portable Starlab planetarium; viewed demonstrations about living and working in space; played games of `Moon Phasers' that teach about the rotation of the moon around the earth; made bracelets with ultraviolet-sensitive beads; and other activities that celebrated Earth's very own star. They also toured StenniSphere and were able to earn their Earth and Sky and Space Explorer `Try-Its.'

Low Resolution Refinement of Atomic Models Against Crystallographic Data.

PubMed

Nicholls, Robert A; Kovalevskiy, Oleg; Murshudov, Garib N

2017-01-01

This review describes some of the problems encountered during low-resolution refinement and map calculation. Refinement is considered as an application of Bayes' theorem, allowing combination of information from various sources including crystallographic experimental data and prior chemical and structural knowledge. The sources of prior knowledge relevant to macromolecules include basic chemical information such as bonds and angles, structural information from reference models of known homologs, knowledge about secondary structures, hydrogen bonding patterns, and similarity of non-crystallographically related copies of a molecule. Additionally, prior information encapsulating local conformational conservation is exploited, keeping local interatomic distances similar to those in the starting atomic model. The importance of designing an accurate likelihood function-the only link between model parameters and observed data-is emphasized. The review also reemphasizes the importance of phases, and describes how the use of raw observed amplitudes could give a better correlation between the calculated and "true" maps. It is shown that very noisy or absent observations can be replaced by calculated structure factors, weighted according to the accuracy of the atomic model. This approach helps to smoothen the map. However, such replacement should be used sparingly, as the bias toward errors in the model could be too much to avoid. It is in general recommended that, whenever a new map is calculated, map quality should be judged by inspection of the parts of the map where there is no atomic model. It is also noted that it is advisable to work with multiple blurred and sharpened maps, as different parts of a crystal may exhibit different degrees of mobility. Doing so can allow accurate building of atomic models, accounting for overall shape as well as finer structural details. Some of the results described in this review have been implemented in the programs REFMAC5, ProSMART and LORESTR, which are available as part of the CCP4 software suite.

Parmodel: a web server for automated comparative modeling of proteins.

PubMed

Uchôa, Hugo Brandão; Jorge, Guilherme Eberhart; Freitas Da Silveira, Nelson José; Camera, João Carlos; Canduri, Fernanda; De Azevedo, Walter Filgueira

2004-12-24

Parmodel is a web server for automated comparative modeling and evaluation of protein structures. The aim of this tool is to help inexperienced users to perform modeling, assessment, visualization, and optimization of protein models as well as crystallographers to evaluate structures solved experimentally. It is subdivided in four modules: Parmodel Modeling, Parmodel Assessment, Parmodel Visualization, and Parmodel Optimization. The main module is the Parmodel Modeling that allows the building of several models for a same protein in a reduced time, through the distribution of modeling processes on a Beowulf cluster. Parmodel automates and integrates the main softwares used in comparative modeling as MODELLER, Whatcheck, Procheck, Raster3D, Molscript, and Gromacs. This web server is freely accessible at .

SAD phasing: History, current impact and future opportunities.

PubMed

Rose, John P; Wang, Bi-Cheng

2016-07-15

Single wavelength anomalous diffraction (SAD) can trace its beginnings to the early 1950s. Researchers at the time recognized that SAD offers some unique features that might be advantageous for crystallographic phasing, despite the fact that at that time recording accurate SAD data was problematic. In this review we will follow the trail from those early days, highlighting key advances in the field and interpreting them in terms on how they stimulated continued phasing development that produced the theoretical foundation for the routine macromolecular structure determination by SAD today. The technological advances over the past three decades in both hardware and software, which played a significant role in making SAD phasing a 'first choice method', will also be described. Copyright © 2016 Elsevier Inc. All rights reserved.

Weak hydrogen bonding interactions influence slip system activity and compaction behavior of pharmaceutical powders.

PubMed

Khomane, Kailas S; Bansal, Arvind K

2013-12-01

Markedly different mechanical behavior of powders of polymorphs, cocrystals, hydrate/anhydrate pairs, or structurally similar molecules has been attributed to the presence of active slip planes system in their crystal structures. Presence of slip planes in the crystal lattice allows easier slip under the applied compaction pressure. This allows greater plastic deformation of the powder and results into increased interparticulate bonding area and greater tensile strength of the compacts. Thus, based on this crystallographic feature, tableting performance of the active pharmaceutical ingredients can be predicted. Recently, we encountered a case where larger numbers of CH···O type interactions across the proposed slip planes hinder the slip and thus resist plastic deformation of the powder under the applied compaction pressure. Hence, attention must be given to these types of interactions while identifying slip planes by visualization method. Generally, slip planes are visualized as flat layers often strengthened by a two-dimensional hydrogen-bonding network within the layers or planes. No hydrogen bonding should exist between these layers to consider them as slip planes. Moreover, one should also check the presence of CH···O type interactions across these planes. Mercury software provides an option for visualization of these weak hydrogen bonding interactions. Hence, caution must be exercised while selecting appropriate solid form based on this crystallographic feature. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

PubMed

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2013-11-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. © 2013 FEBS.

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

PubMed Central

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2014-01-01

The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

Cambridge Crystallographic Data Centre. II. Structural Data File

ERIC Educational Resources Information Center

Allen, F. H.; And Others

1973-01-01

The Cambridge Crystallographic Data Centre is concerned with the retrieval, evaluation, synthesis, and dissemination of structural data obtained by diffraction methods. This article (Part I is EJ053033) describes the work of the center and deals with the organization and maintenance of a computerized file of numeric crystallographic structural…

Reconstruction of 3d grain boundaries from rock thin sections, using polarised light

NASA Astrophysics Data System (ADS)

Markus Hammes, Daniel; Peternell, Mark

2016-04-01

Grain boundaries affect the physical and chemical properties of polycrystalline materials significantly by initiating reactions and collecting impurities (Birchenall, 1959), and play an essential role in recrystallization (Doherty et al. 1997). In particular, the shape and crystallographic orientation of grain boundaries reveal the deformation and annealing history of rocks (Kruhl and Peternell 2002, Kuntcheva et al. 2006). However, there is a lack of non-destructive and easy-to-use computer supported methods to determine grain boundary geometries in 3D. The only available instrument using optical light to measure grain boundary angles is still the polarising microscope with attached universal stage; operated manually and time-consuming in use. Here we present a new approach to determine 3d grain boundary orientations from 2D rock thin sections. The data is recorded by using an automatic fabric analyser microscope (Peternell et al., 2010). Due to its unique arrangement of 9 light directions the highest birefringence colour due to each light direction and crystal orientation (retardation) can be determined at each pixel in the field of view. Retardation profiles across grain boundaries enable the calculation of grain boundary angle and direction. The data for all positions separating the grains are combined and further processed. In combination with the lateral position of the grain boundary, acquired using the FAME software (Hammes and Peternell, in review), the data is used to reconstruct a 3d grain boundary model. The processing of data is almost fully automatic by using MATLAB®. Only minor manual input is required. The applicability was demonstrated on quartzite samples, but the method is not solely restricted on quartz grains and other birefringent polycrystalline materials could be used instead. References: Birchenall, C.E., 1959: Physical Metallurgy. McGraw-Hill, New York. Doherty, R.D., Hughes, D.A., Humphreys, F.J., Jonas, J.J., Juul Jensen, D., Kassner, M.E., King, W.E., McNelley, T.R., McQueen, H.J., Rollett, A.D., 1997: Current issues in recrystallization: a review. Materials Science and Engineering A 238, 219-274. Hammes, D.M., Peternell, M., in review. FAME: Software for analysing rock microstructures. Computers & Geoscience. Kruhl, J.H., Peternell, M., 2002. The equilibration of high-angle grain boundaries in dynamically recrystallized quartz: the effect of crystallography and temperature. Journal of Structural Geology 24, 1125-1137. Kuntcheva, B., Kruhl, J.H. & Kunze, K., 2006. Crystallographic orientation of high-angle grain boundaries in dynamically recrystallized quartz: First results. Tectonophysics 421, 331-346. Peternell, M., Hasalová, P., Wilson, J.L., Piaziolo, S., Schulmann, K., 2010. Evaluating quartz crystallographic preferred orientations and the role of deformation partitioning using EBSD and fabric analyser techniques. Journal of Structural Geology 32, 803-817.

Non-crystallographic nets: characterization and first steps towards a classification.

PubMed

Moreira de Oliveira, Montauban; Eon, Jean Guillaume

2014-05-01

Non-crystallographic (NC) nets are periodic nets characterized by the existence of non-trivial bounded automorphisms. Such automorphisms cannot be associated with any crystallographic symmetry in realizations of the net by crystal structures. It is shown that bounded automorphisms of finite order form a normal subgroup F(N) of the automorphism group of NC nets (N, T). As a consequence, NC nets are unstable nets (they display vertex collisions in any barycentric representation) and, conversely, stable nets are crystallographic nets. The labelled quotient graphs of NC nets are characterized by the existence of an equivoltage partition (a partition of the vertex set that preserves label vectors over edges between cells). A classification of NC nets is proposed on the basis of (i) their relationship to the crystallographic net with a homeomorphic barycentric representation and (ii) the structure of the subgroup F(N).

What's New in GSAS-II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Toby, Brian H.; Von Dreele, Robert B.

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select anymore » version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered. © 2014 International Centre for Diffraction Data.« less

MrGrid: A Portable Grid Based Molecular Replacement Pipeline

PubMed Central

Reboul, Cyril F.; Androulakis, Steve G.; Phan, Jennifer M. N.; Whisstock, James C.; Goscinski, Wojtek J.; Abramson, David; Buckle, Ashley M.

2010-01-01

Background The crystallographic determination of protein structures can be computationally demanding and for difficult cases can benefit from user-friendly interfaces to high-performance computing resources. Molecular replacement (MR) is a popular protein crystallographic technique that exploits the structural similarity between proteins that share some sequence similarity. But the need to trial permutations of search models, space group symmetries and other parameters makes MR time- and labour-intensive. However, MR calculations are embarrassingly parallel and thus ideally suited to distributed computing. In order to address this problem we have developed MrGrid, web-based software that allows multiple MR calculations to be executed across a grid of networked computers, allowing high-throughput MR. Methodology/Principal Findings MrGrid is a portable web based application written in Java/JSP and Ruby, and taking advantage of Apple Xgrid technology. Designed to interface with a user defined Xgrid resource the package manages the distribution of multiple MR runs to the available nodes on the Xgrid. We evaluated MrGrid using 10 different protein test cases on a network of 13 computers, and achieved an average speed up factor of 5.69. Conclusions MrGrid enables the user to retrieve and manage the results of tens to hundreds of MR calculations quickly and via a single web interface, as well as broadening the range of strategies that can be attempted. This high-throughput approach allows parameter sweeps to be performed in parallel, improving the chances of MR success. PMID:20386612

Three sets of crystallographic sub-planar structures in quartz formed by tectonic deformation

NASA Astrophysics Data System (ADS)

Derez, Tine; Pennock, Gill; Drury, Martyn; Sintubin, Manuel

2016-05-01

In quartz, multiple sets of fine planar deformation microstructures that have specific crystallographic orientations parallel to planes with low Miller-Bravais indices are commonly considered as shock-induced planar deformation features (PDFs) diagnostic of shock metamorphism. Using polarized light microscopy, we demonstrate that up to three sets of tectonically induced sub-planar fine extinction bands (FEBs), sub-parallel to the basal, γ, ω, and π crystallographic planes, are common in vein quartz in low-grade tectonometamorphic settings. We conclude that the observation of multiple (2-3) sets of fine scale, closely spaced, crystallographically controlled, sub-planar microstructures is not sufficient to unambiguously distinguish PDFs from tectonic FEBs.

Crystallographic Orientation Identification in Multicrystalline Silicon Wafers Using NIR Transmission Intensity

NASA Astrophysics Data System (ADS)

Skenes, Kevin; Kumar, Arkadeep; Prasath, R. G. R.; Danyluk, Steven

2018-02-01

Near-infrared (NIR) polariscopy is a technique used for the non-destructive evaluation of the in-plane stresses in photovoltaic silicon wafers. Accurate evaluation of these stresses requires correct identification of the stress-optic coefficient, a material property which relates photoelastic parameters to physical stresses. The material stress-optic coefficient of silicon varies with crystallographic orientation. This variation poses a unique problem when measuring stresses in multicrystalline silicon (mc-Si) wafers. This paper concludes that the crystallographic orientation of silicon can be estimated by measuring the transmission of NIR light through the material. The transmission of NIR light through monocrystalline wafers of known orientation were compared with the transmission of NIR light through various grains in mc-Si wafers. X-ray diffraction was then used to verify the relationship by obtaining the crystallographic orientations of these assorted mc-Si grains. Variation of transmission intensity for different crystallographic orientations is further explained by using planar atomic density. The relationship between transmission intensity and planar atomic density appears to be linear.

Dependence of Crystallographic Orientation on Pitting Corrosion Behavior of Ni-Fe-Cr Alloy 028

NASA Astrophysics Data System (ADS)

Zhang, LiNa; Szpunar, Jerzy A.; Dong, JianXin; Ojo, Olanrewaju A.; Wang, Xu

2018-06-01

The influence of crystallographic orientation on the pitting corrosion behavior of Ni-Fe-Cr alloy 028 was studied using a combination of X-ray diffraction (XRD), electron backscatter diffraction (EBSD), potentiodynamic polarization technique, and atomic force microscopy (AFM). The results show that there is anisotropy of pitting corrosion that strongly depends on crystallographic orientation of the surface plane. The distribution of pit density in a standard stereographic triangle indicates that the crystallographic planes close to {100} are more prone to pitting corrosion compared to planes {110} and {111}. The surface energy calculation of (001) and (111) shows that the plane with a high atomic packing density has a low surface energy with concomitant strong resistance to pitting corrosion. A correlation function between crystallographic orientation and pitting corrosion susceptibility suggests a method that not only predicts the pitting resistance of known textured materials, but also could help to improve corrosion resistance by controlling material texture.

Surface Crystallographic Dependence of Voltammetric Oxidation of Polyhydric Alcohols and Related Systems at Monocrystalline Gold-Acidic Aqueous Interfaces

DTIC Science & Technology

1992-02-01

Crystallographic Dependence of Voltaumetric Oxidation of Polyhydric Alcohols and Related Systems at Monocrystalline Gold -Acidic Aqueous Interfaces by...Crystallographic Dependence of Voltamnnetric Oxidation )f Polyhydric Alcohols and Related Systems at onocrystalline Gold -Acidic Aqueous [nterfaces...mannitol, on seven oriented gold surfaces, Au(lll), 100), (110), (221), (533), (311), and (210), is reported with the objective of assessing the ole of

Crystallographic interpretation of Galois symmetries for magnetic pentagonal ring

NASA Astrophysics Data System (ADS)

Milewski, J.; Lulek, T.; Łabuz, M.

2017-03-01

Galois symmetry of exact Bethe Ansatz eigenstates for the magnetic pentagonal ring within the XXX model are investigated by a comparison with crystallographic constructions of space groups. It follows that the arithmetic symmetry of Bethe parameters for the interior of the Brillouin zone admits crystallographic interpretation, in terms of the periodic square Z2 ×Z2 , that is the two-dimensional crystal lattice with Born-Karman period two in both directions.

A Journey into Reciprocal Space; A crystallographer's perspective

NASA Astrophysics Data System (ADS)

Glazer, A. M.

2017-10-01

This book introduces undergraduate and graduate students to a crystallographer's view of real and reciprocal space, a concept that has been of particular use by crystallographers to understand the patterns of spots when x-rays are diffracted by crystals. It then proceeds to develop the concept in a form suitable for physics applications; such as how solid-state physicists use reciprocal space to explain various solid-state properties such as thermal and electrical phenomena.

Influence of different kinds of rolling on the crystallographic texture and magnetic induction of a NOG 3 wt% Si steel

NASA Astrophysics Data System (ADS)

Silva, J. M.; Baêta Júnior, E. S.; Moraes, N. R. D. C.; Botelho, R. A.; Felix, R. A. C.; Brandao, L.

2017-01-01

The purpose of this work was to study the influence of different kinds of rolling on the magnetic properties of NOG steel, an electric steel widely used in electrical motors. These properties are highly correlated with the crystallographic texture of the material, which can be changed by rolling. Three kinds of rolling were examined: conventional rolling, cross-rolling and asymmetrical rolling. The crystallographic texture was determined by X-ray diffraction and the magnetic properties were calculated from a theoretical model that related the magnetic induction to crystallographic texture through the anisotropy energy. The results show that cross-rolling yields higher values of magnetic induction than the other processes.

Native SAD is maturing.

PubMed

Rose, John P; Wang, Bi-Cheng; Weiss, Manfred S

2015-07-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow 'highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a 'first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

Crystallographic orientation mapping with an electron backscattered diffraction technique in (Bi, Pb)2Sr2Ca2Cu3O10 superconductor tapes

NASA Astrophysics Data System (ADS)

Tan, T. T.; Li, S.; Oh, J. T.; Gao, W.; Liu, H. K.; Dou, S. X.

2001-02-01

It is believed that grain boundaries act as weak links in limiting the critical current density (Jc) of bulk high-Tc superconductors. The weak-link problem can be greatly reduced by elimination or minimization of large-angle grain boundaries. It has been reported that the distribution of the Jc in (Bi, Pb)2Sr2Ca2Cu3O10+x (Bi2223) superconductor tapes presents a parabolic relationship in the transverse cross section of the tapes, with the lowest currents occurring at the centre of the tapes. It was proposed that the Jc distribution is strongly dependent on the local crystallographic orientation distribution of the Bi2223 oxides. However, the local three-dimensional crystallographic orientation distribution of Bi2223 crystals in (Bi, Pb)2Sr2Ca2Cu3O10+x superconductor tapes has not yet been experimentally determined. In this work, the electron backscattered diffraction technique was employed to map the crystallographic orientation distribution, determine the misorientation of grain boundaries and also map the misorientation distribution in Bi2223 superconductor tapes. Through crystallographic orientation mapping, the relationship between the crystallographic orientation distribution, the boundary misorientation distribution and the fabrication parameters may be understood. This can be used to optimize the fabrication processes thus increasing the critical current density in Bi2223 superconductor tapes.

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent

PubMed Central

Dahanayake, Jayangika N.; Gautam, Devaki N.; Verma, Rajni; Mitchell-Koch, Katie R.

2016-01-01

The use of enzymes in non-aqueous solvents expands the use of biocatalysts to hydrophobic substrates, with the ability to tune selectivity of reactions through solvent selection. Non-aqueous enzymology also allows for fundamental studies on the role of water and other solvents in enzyme structure, dynamics, and function. Molecular dynamics simulations serve as a powerful tool in this area, providing detailed atomic information about the effect of solvents on enzyme properties. However, a common protocol for non-aqueous enzyme simulations does not exist. If you want to simulate enzymes in non-aqueous solutions, how many and which crystallographic waters do you keep? In the present work, this question is addressed by determining which crystallographic water molecules lead most quickly to an equilibrated protein structure. Five different methods of selecting and keeping crystallographic waters are used in order to discover which crystallographic waters lead the protein structure to reach an equilibrated structure more rapidly in organic solutions. It is found that buried waters contribute most to rapid equilibration in organic solvent, with slow-diffusing waters giving similar results. PMID:27403032

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miao, Yinbin; Mo, Kun; Yao, Tiankai

Here coordinated experimental efforts to quantitatively correlate crystallographic orientation and surface faceting features in UO2 are reported upon. A sintered polycrystalline UO2 sample was thermally etched to induce the formation of surface faceting features. Synchrotron Laue microdiffraction was used to obtain a precise crystallographic orientation map for the UO2 surface grains. Scanning electron microscopy (SEM) was utilized to collect the detailed information on the surface morphology of the sample. The surface faceting features were found to be highly dependent on the crystallographic orientation. In most cases, Triple-plane structures containing one {100} plane and two {111} planes were found to dominatemore » the surface of UO2. The orientation-faceting relationship established in this study revealed a practical and efficient method of determining crystallographic orientation based on the surface features captured by SEM images.« less

Crystallographic Topology 2: Overview and Work in Progress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, C.K.

1999-08-01

This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.

Open Access Internet Resources for Nano-Materials Physics Education

NASA Astrophysics Data System (ADS)

Moeck, Peter; Seipel, Bjoern; Upreti, Girish; Harvey, Morgan; Garrick, Will

2006-05-01

Because a great deal of nano-material science and engineering relies on crystalline materials, materials physicists have to provide their own specific contributions to the National Nanotechnology Initiative. Here we briefly review two freely accessible internet-based crystallographic databases, the Nano-Crystallography Database (http://nanocrystallography.research.pdx.edu) and the Crystallography Open Database (http://crystallography.net). Information on over 34,000 full structure determinations are stored in these two databases in the Crystallographic Information File format. The availability of such crystallographic data on the internet in a standardized format allows for all kinds of web-based crystallographic calculations and visualizations. Two examples of which that are dealt with in this paper are: interactive crystal structure visualizations in three dimensions and calculations of lattice-fringe fingerprints for the identification of unknown nanocrystals from their atomic-resolution transmission electron microscopy images.

Tunable and laser-reconfigurable 2D heterocrystals obtained by epitaxial stacking of crystallographically incommensurate Bi2Se3 and MoS2 atomic layers

PubMed Central

Vargas, Anthony; Liu, Fangze; Lane, Christopher; Rubin, Daniel; Bilgin, Ismail; Hennighausen, Zachariah; DeCapua, Matthew; Bansil, Arun; Kar, Swastik

2017-01-01

Vertical stacking is widely viewed as a promising approach for designing advanced functionalities using two-dimensional (2D) materials. Combining crystallographically commensurate materials in these 2D stacks has been shown to result in rich new electronic structure, magnetotransport, and optical properties. In this context, vertical stacks of crystallographically incommensurate 2D materials with well-defined crystallographic order are a counterintuitive concept and, hence, fundamentally intriguing. We show that crystallographically dissimilar and incommensurate atomically thin MoS2 and Bi2Se3 layers can form rotationally aligned stacks with long-range crystallographic order. Our first-principles theoretical modeling predicts heterocrystal electronic band structures, which are quite distinct from those of the parent crystals, characterized with an indirect bandgap. Experiments reveal striking optical changes when Bi2Se3 is stacked layer by layer on monolayer MoS2, including 100% photoluminescence (PL) suppression, tunable transmittance edge (1.1→0.75 eV), suppressed Raman, and wide-band evolution of spectral transmittance. Disrupting the interface using a focused laser results in a marked the reversal of PL, Raman, and transmittance, demonstrating for the first time that in situ manipulation of interfaces can enable “reconfigurable” 2D materials. We demonstrate submicrometer resolution, “laser-drawing” and “bit-writing,” and novel laser-induced broadband light emission in these heterocrystal sheets. PMID:28740860

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

How to assign a (3 + 1)-dimensional superspace group to an incommensurately modulated biological macromolecular crystal

PubMed Central

2017-01-01

Periodic crystal diffraction is described using a three-dimensional (3D) unit cell and 3D space-group symmetry. Incommensurately modulated crystals are a subset of aperiodic crystals that need four to six dimensions to describe the observed diffraction pattern, and they have characteristic satellite reflections that are offset from the main reflections. These satellites have a non-integral relationship to the primary lattice and require q vectors for processing. Incommensurately modulated biological macromolecular crystals have been frequently observed but so far have not been solved. The authors of this article have been spearheading an initiative to determine this type of crystal structure. The first step toward structure solution is to collect the diffraction data making sure that the satellite reflections are well separated from the main reflections. Once collected they can be integrated and then scaled with appropriate software. Then the assignment of the superspace group is needed. The most common form of modulation is in only one extra direction and can be described with a (3 + 1)D superspace group. The (3 + 1)D superspace groups for chemical crystallographers are fully described in Volume C of International Tables for Crystallography. This text includes all types of crystallographic symmetry elements found in small-molecule crystals and can be difficult for structural biologists to understand and apply to their crystals. This article provides an explanation for structural biologists that includes only the subset of biological symmetry elements and demonstrates the application to a real-life example of an incommensurately modulated protein crystal. PMID:28808437

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

NASA Astrophysics Data System (ADS)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

On the retrieval of crystallographic information from atom probe microscopy data via signal mapping from the detector coordinate space.

PubMed

Wallace, Nathan D; Ceguerra, Anna V; Breen, Andrew J; Ringer, Simon P

2018-06-01

Atom probe tomography is a powerful microscopy technique capable of reconstructing the 3D position and chemical identity of millions of atoms within engineering materials, at the atomic level. Crystallographic information contained within the data is particularly valuable for the purposes of reconstruction calibration and grain boundary analysis. Typically, analysing this data is a manual, time-consuming and error prone process. In many cases, the crystallographic signal is so weak that it is difficult to detect at all. In this study, a new automated signal processing methodology is demonstrated. We use the affine properties of the detector coordinate space, or the 'detector stack', as the basis for our calculations. The methodological framework and the visualisation tools are shown to be superior to the standard method of crystallographic pole visualisation directly from field evaporation images and there is no requirement for iterations between a full real-space initial tomographic reconstruction and the detector stack. The mapping approaches are demonstrated for aluminium, tungsten, magnesium and molybdenum. Implications for reconstruction calibration, accuracy of crystallographic measurements, reliability and repeatability are discussed. Copyright © 2018 Elsevier B.V. All rights reserved.

Reorientations, relaxations, metastabilities, and multidomains of skyrmion lattices

NASA Astrophysics Data System (ADS)

Bannenberg, L. J.; Qian, F.; Dalgliesh, R. M.; Martin, N.; Chaboussant, G.; Schmidt, M.; Schlagel, D. L.; Lograsso, T. A.; Wilhelm, H.; Pappas, C.

2017-11-01

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both Cu2OSeO3 and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history of the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Furthermore, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.

A kinetic model for the characteristic surface morphologies of thin films by directional vapor deposition

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Huang, Po-Yu

2017-12-01

In order to simulate a process of directional vapor deposition, in this study, a numerical approach was applied to model the growth and evolution of surface morphologies for the crystallographic structures of thin films. The critical factors affecting the surface morphologies in a deposition process, such as the crystallographic symmetry, anisotropic interfacial energy, shadowing effect, and deposition rate, were all enclosed in the theoretical model. By altering the parameters of crystallographic symmetry in the structures, the faceted nano-columns with rectangular and hexagonal shapes were established in the simulation results. Furthermore, for revealing the influences of the anisotropic strength and the deposition rate theoretically on the crystallographic structure formations, various parameters adjusted in the numerical calculations were also investigated. Not only the morphologies but also the surface roughnesses for different processing conditions were distinctly demonstrated with the quantitative analysis of the simulations.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bannenberg, L. J.; Qian, F.; Dalgliesh, R. M.

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both Cu 2OSeO 3 and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history ofmore » the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Moreover, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.« less

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

PubMed Central

Kern, Jan; Hattne, Johan; Tran, Rosalie; Alonso-Mori, Roberto; Laksmono, Hartawan; Gul, Sheraz; Sierra, Raymond G.; Rehanek, Jens; Erko, Alexei; Mitzner, Rolf; Wernet, Phillip; Bergmann, Uwe; Sauter, Nicholas K.; Yachandra, Vittal; Yano, Junko

2014-01-01

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL. PMID:24914169

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coquelle, Nicolas; CNRS, IBS, 38044 Grenoble; CEA, IBS, 38044 Grenoble

A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able tomore » read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

Grain-scale investigations of deformation heterogeneities in aluminum alloys

NASA Astrophysics Data System (ADS)

Güler, Baran; Şimşek, Ülke; Yalçınkaya, Tuncay; Efe, Mert

2018-05-01

The anisotropic deformation of Aluminum alloys at micron scale exhibits localized deformation, which has negative implications on the macroscale mechanical and forming behavior. The scope of this work is twofold. Firstly, micro-scale deformation heterogeneities affecting forming behavior of aluminum alloys is investigated through experimental microstructure analysis at large strains and various strain paths. The effects of initial texture, local grain misorientation, and strain paths on the strain localizations are established. In addition to uniaxial tension condition, deformation heterogeneities are also investigated under equibiaxial tension condition to determine the strain path effects on the localization behavior. Secondly, the morphology and the crystallographic data obtained from the experiments is transferred to Abaqus software, in order to predict both macroscopic response and the microstructure evolution though crystal plasticity finite element simulations. The model parameters are identified through the comparison with experiments and the capability of the model to capture real material response is discussed as well.

Serial femtosecond crystallography datasets from G protein-coupled receptors

PubMed Central

White, Thomas A.; Barty, Anton; Liu, Wei; Ishchenko, Andrii; Zhang, Haitao; Gati, Cornelius; Zatsepin, Nadia A.; Basu, Shibom; Oberthür, Dominik; Metz, Markus; Beyerlein, Kenneth R.; Yoon, Chun Hong; Yefanov, Oleksandr M.; James, Daniel; Wang, Dingjie; Messerschmidt, Marc; Koglin, Jason E.; Boutet, Sébastien; Weierstall, Uwe; Cherezov, Vadim

2016-01-01

We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data. PMID:27479354

Auto-rickshaw: an automated crystal structure determination platform as an efficient tool for the validation of an X-ray diffraction experiment.

PubMed

Panjikar, Santosh; Parthasarathy, Venkataraman; Lamzin, Victor S; Weiss, Manfred S; Tucker, Paul A

2005-04-01

The EMBL-Hamburg Automated Crystal Structure Determination Platform is a system that combines a number of existing macromolecular crystallographic computer programs and several decision-makers into a software pipeline for automated and efficient crystal structure determination. The pipeline can be invoked as soon as X-ray data from derivatized protein crystals have been collected and processed. It is controlled by a web-based graphical user interface for data and parameter input, and for monitoring the progress of structure determination. A large number of possible structure-solution paths are encoded in the system and the optimal path is selected by the decision-makers as the structure solution evolves. The processes have been optimized for speed so that the pipeline can be used effectively for validating the X-ray experiment at a synchrotron beamline.

Native SAD is maturing

PubMed Central

Rose, John P.; Wang, Bi-Cheng; Weiss, Manfred S.

2015-01-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow ‘highly accurate data’ to be routinely collected. Today, native SAD sits on the verge of becoming a ‘first-choice’ method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development. PMID:26175902

Applied and implied semantics in crystallographic publishing

PubMed Central

2012-01-01

Background Crystallography is a data-rich, software-intensive scientific discipline with a community that has undertaken direct responsibility for publishing its own scientific journals. That community has worked actively to develop information exchange standards allowing readers of structure reports to access directly, and interact with, the scientific content of the articles. Results Structure reports submitted to some journals of the International Union of Crystallography (IUCr) can be automatically validated and published through an efficient and cost-effective workflow. Readers can view and interact with the structures in three-dimensional visualization applications, and can access the experimental data should they wish to perform their own independent structure solution and refinement. The journals also layer on top of this facility a number of automated annotations and interpretations to add further scientific value. Conclusions The benefits of semantically rich information exchange standards have revolutionised the scholarly publishing process for crystallography, and establish a model relevant to many other physical science disciplines. PMID:22932420

Serial femtosecond crystallography datasets from G protein-coupled receptors.

PubMed

White, Thomas A; Barty, Anton; Liu, Wei; Ishchenko, Andrii; Zhang, Haitao; Gati, Cornelius; Zatsepin, Nadia A; Basu, Shibom; Oberthür, Dominik; Metz, Markus; Beyerlein, Kenneth R; Yoon, Chun Hong; Yefanov, Oleksandr M; James, Daniel; Wang, Dingjie; Messerschmidt, Marc; Koglin, Jason E; Boutet, Sébastien; Weierstall, Uwe; Cherezov, Vadim

2016-08-01

We describe the deposition of four datasets consisting of X-ray diffraction images acquired using serial femtosecond crystallography experiments on microcrystals of human G protein-coupled receptors, grown and delivered in lipidic cubic phase, at the Linac Coherent Light Source. The receptors are: the human serotonin receptor 2B in complex with an agonist ergotamine, the human δ-opioid receptor in complex with a bi-functional peptide ligand DIPP-NH2, the human smoothened receptor in complex with an antagonist cyclopamine, and finally the human angiotensin II type 1 receptor in complex with the selective antagonist ZD7155. All four datasets have been deposited, with minimal processing, in an HDF5-based file format, which can be used directly for crystallographic processing with CrystFEL or other software. We have provided processing scripts and supporting files for recent versions of CrystFEL, which can be used to validate the data.

Experimental determination of spin-dependent electron density by joint refinement of X-ray and polarized neutron diffraction data.

PubMed

Deutsch, Maxime; Claiser, Nicolas; Pillet, Sébastien; Chumakov, Yurii; Becker, Pierre; Gillet, Jean Michel; Gillon, Béatrice; Lecomte, Claude; Souhassou, Mohamed

2012-11-01

New crystallographic tools were developed to access a more precise description of the spin-dependent electron density of magnetic crystals. The method combines experimental information coming from high-resolution X-ray diffraction (XRD) and polarized neutron diffraction (PND) in a unified model. A new algorithm that allows for a simultaneous refinement of the charge- and spin-density parameters against XRD and PND data is described. The resulting software MOLLYNX is based on the well known Hansen-Coppens multipolar model, and makes it possible to differentiate the electron spins. This algorithm is validated and demonstrated with a molecular crystal formed by a bimetallic chain, MnCu(pba)(H(2)O)(3)·2H(2)O, for which XRD and PND data are available. The joint refinement provides a more detailed description of the spin density than the refinement from PND data alone.

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry

PubMed Central

2017-01-01

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations. PMID:28094977

Crystallographic Mapping of Guided Nanowires by Second Harmonic Generation Polarimetry.

PubMed

Neeman, Lior; Ben-Zvi, Regev; Rechav, Katya; Popovitz-Biro, Ronit; Oron, Dan; Joselevich, Ernesto

2017-02-08

The growth of horizontal nanowires (NWs) guided by epitaxial and graphoepitaxial relations with the substrate is becoming increasingly attractive owing to the possibility of controlling their position, direction, and crystallographic orientation. In guided NWs, as opposed to the extensively characterized vertically grown NWs, there is an increasing need for understanding the relation between structure and properties, specifically the role of the epitaxial relation with the substrate. Furthermore, the uniformity of crystallographic orientation along guided NWs and over the substrate has yet to be checked. Here we perform highly sensitive second harmonic generation (SHG) polarimetry of polar and nonpolar guided ZnO NWs grown on R-plane and M-plane sapphire. We optically map large areas on the substrate in a nondestructive way and find that the crystallographic orientations of the guided NWs are highly selective and specific for each growth direction with respect to the substrate lattice. In addition, we perform SHG polarimetry along individual NWs and find that the crystallographic orientation is preserved along the NW in both polar and nonpolar NWs. While polar NWs show highly uniform SHG along their axis, nonpolar NWs show a significant change in the local nonlinear susceptibility along a few micrometers, reflected in a reduction of 40% in the ratio of the SHG along different crystal axes. We suggest that these differences may be related to strain accumulation along the nonpolar wires. We find SHG polarimetry to be a powerful tool to study both selectivity and uniformity of crystallographic orientations of guided NWs with different epitaxial relations.

Crystallographic Information Resources

ERIC Educational Resources Information Center

Glasser, Leslie

2016-01-01

Crystallographic information provides the fundamental basis for understanding the properties and behavior of materials. This data, such as chemical composition, unit cell dimensions, space group, and atomic positions, derives from the primary literature--that is, from published experimental measurement or theoretical calculation. Although the…

A crystallographic investigation of GaN nanostructures by reciprocal space mapping in a grazing incidence geometry.

PubMed

Lee, Sanghwa; Sohn, Yuri; Kim, Chinkyo; Lee, Dong Ryeol; Lee, Hyun-Hwi

2009-05-27

Reciprocal space mapping with a two-dimensional (2D) area detector in a grazing incidence geometry was applied to determine crystallographic orientations of GaN nanostructures epitaxially grown on a sapphire substrate. By using both unprojected and projected reciprocal space mapping with a proper coordinate transformation, the crystallographic orientations of GaN nanostructures with respect to that of a substrate were unambiguously determined. In particular, the legs of multipods in the wurtzite phase were found to preferentially nucleate on the sides of tetrahedral cores in the zinc blende phase.

Crystallization and preliminary X-ray crystallographic analysis of agkicetin-C from Deinagkistrodon acutus venom

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Gufeng; Departments of Molecular and Cell Biology, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026; Huang, Qingqiu

2005-01-01

The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. The crystallization and preliminary crystallographic analysis of agkicetin-C, a well known platelet glycoprotein Ib (GPIb) antagonist from the venom of Deinagkistrodon acutus found in Anhui Province, China is reported. Crystals of agkicetin-C suitable for structure determination were obtained from 1.8 M ammonium sulfate, 40 mM MES pH 6.5 with 2%(v/v) PEG 400. Interestingly, low buffer concentrations of MES seem to be necessary for crystal growth. The crystals of agkicetin-C belong tomore » space group C2, with unit-cell parameters a = 177.5, b = 97.7, c = 106.8 Å, β = 118.5°, and diffract to 2.4 Å resolution. Solution of the phase problem by the molecular-replacement method shows that there are four agkicetin-C molecules in the asymmetric unit, with a V{sub M} value of 3.4 Å{sup 3} Da{sup −1}, which corresponds to a high solvent content of approximately 64%. Self-rotation function calculations show a single well defined non-crystallographic twofold axis with features that may represent additional elements of non-crystallographic symmetry.« less

A synthesis, X-ray crystallographic and vibrational studies of guanidinium o-nitrobenzoate hydrate. New NLO crystal in guanidinium nitrobenzoate family

NASA Astrophysics Data System (ADS)

Drozd, Marek; Daszkiewicz, Marek

2018-06-01

According to literature data the two crystals are known: guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate. Both compounds belong to noncetrosymmetric crystallographic systems are consider as second order generators in nonlinear optic (NLO). For each of these crystals the detailed crystallographic, theoretical calculations and vibrational studies were performed. It is interesting that nitrobenzoic acid create tree variety of compounds ((2) ortho-, (3) meta- and (4) para-) what any data for third member of guanidinium nitrobenzoate crystal were not known. The guanidinium o-nitrobenzoate hydrate crystal was synthesized first time. The performed X-ray crystallographic study shown that crystal belongs to space group without macroscopic symmetry center. Additionally, the vibrational spectra (intensities, frequencies and PED analysis) of investigated compound are presented. These results are compared with theoretical calculations for equilibrium geometry and vibrational properties. Furthermore, the results of the theoretical approach include HOMO and LUMO energies and first order hyperpolarizability were obtained, also. On the basis of these data the crystal was classified as second order generator. All obtained results are compared with previous literature data of guanidinium m-nitrobenzoate and guanidinium p-nitrobenzoate compounds. Surprisingly, each of examined crystal belongs to different crystallographic system and shows different vibrational properties.

Final Report from The University of Texas at Austin for DEGAS: Dynamic Global Address Space programming environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erez, Mattan; Yelick, Katherine; Sarkar, Vivek

The Dynamic, Exascale Global Address Space programming environment (DEGAS) project will develop the next generation of programming models and runtime systems to meet the challenges of Exascale computing. Our approach is to provide an efficient and scalable programming model that can be adapted to application needs through the use of dynamic runtime features and domain-specific languages for computational kernels. We address the following technical challenges: Programmability: Rich set of programming constructs based on a Hierarchical Partitioned Global Address Space (HPGAS) model, demonstrated in UPC++. Scalability: Hierarchical locality control, lightweight communication (extended GASNet), and ef- ficient synchronization mechanisms (Phasers). Performance Portability:more » Just-in-time specialization (SEJITS) for generating hardware-specific code and scheduling libraries for domain-specific adaptive runtimes (Habanero). Energy Efficiency: Communication-optimal code generation to optimize energy efficiency by re- ducing data movement. Resilience: Containment Domains for flexible, domain-specific resilience, using state capture mechanisms and lightweight, asynchronous recovery mechanisms. Interoperability: Runtime and language interoperability with MPI and OpenMP to encourage broad adoption.« less

X-ray crystallographic data for minerals

USGS Publications Warehouse

Robie, Richard A.; Bethke, Philip M.; Toulmin, M.S.; Edwards, Jerry L.

1963-01-01

X-ray crystallographic data are of particular importance to the mineralogist. Beyond the considerations of structural chemistry they provide. one of the most accurate methods for phase and/or compositional determination and for obtaining _the molar volumes and densities of minerals {Robie and Bethke, 1962).

Crystallographic and Spectroscopic Symmetry Notations.

ERIC Educational Resources Information Center

Sharma, B. D.

1982-01-01

Compares Schoenflies and Hermann-Mauguin notations of symmetry. Although the former (used by spectroscopists) and latter (used by crystallographers) both describe the same symmetry, there are distinct differences in the manner of description which may lead to confusion in correlating the two notations. (Author/JN)

Recovery of Crystallographic Texture in Remineralized Dental Enamel

PubMed Central

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain structural integrity. PMID:25360532

Recovery of crystallographic texture in remineralized dental enamel.

PubMed

Siddiqui, Samera; Anderson, Paul; Al-Jawad, Maisoon

2014-01-01

Dental caries is the most prevalent disease encountered by people of all ages around the world. Chemical changes occurring in the oral environment during the caries process alter the crystallography and microstructure of dental enamel resulting in loss of mechanical function. Little is known about the crystallographic effects of demineralization and remineralization. The motivation for this study was to develop understanding of the caries process at the crystallographic level in order to contribute towards a long term solution. In this study synchrotron X-ray diffraction combined with scanning electron microscopy and scanning microradiography have been used to correlate enamel crystallography, microstructure and mineral concentration respectively in enamel affected by natural caries and following artificial demineralization and remineralization regimes. In particular, the extent of destruction and re-formation of this complex structure has been measured. 2D diffraction patterns collected at the European Synchrotron Radiation Facility were used to quantify changes in the preferred orientation (crystallographic texture) and position of the (002) Bragg reflection within selected regions of interest in each tooth slice, and then correlated with the microstructure and local mineral mass. The results revealed that caries and artificial demineralization cause a large reduction in crystallographic texture which is coupled with the loss of mineral mass. Remineralization restores the texture to the original level seen in healthy enamel and restores mineral density. The results also showed that remineralization promotes ordered formation of new crystallites and growth of pre-existing crystallites which match the preferred orientation of healthy enamel. Combining microstructural and crystallographic characterization aids the understanding of caries and erosion processes and assists in the progress towards developing therapeutic treatments to allow affected enamel to regain structural integrity.

Orientation relationship between diamond and magnesiochromite inclusions

NASA Astrophysics Data System (ADS)

Alvaro, Matteo; Angel, Ross; Nimis, Paolo; Milani, Sula; Harris, Jeff; Nestola, Fabrizio

2017-04-01

The correct determination of the relative crystallographic orientations of single crystals has many applications. When single crystals undergo phase transitions, especially at high pressures, the relative orientations of the two phases yields insights into transition mechanisms (Dobson et al 2013). On the other hand, determination of the crystallographic orientations of minerals included in diamonds can provide insights into the mechanisms of their entrapment and the timing of their formation relative to the host diamond (e.g. Nestola et al. 2014, Milani et al. 2016). The reported occurrence of non-trivial orientations for some minerals in diamonds, suggesting an epitaxial relationship, has long been considered to reflect contemporaneous growth of the diamond and the inclusion (e.g. syngenesis). Correct interpretation of such orientations requires (i) a statistically significant crystallographic data set for single and multiple inclusions in a large number of diamonds, and (ii) a robust data-processing method, capable of removing ambiguities derived from the high symmetry of the diamond and the inclusion. We have developed a software to perform such processing (OrientXplot, Angel et al. 2015), starting from crystallographic orientation matrixes obtained by X-ray diffractometry or EBSD data. Previous studies of inclusions in lithospheric diamonds, by single-crystal X-ray diffraction and EBSD, indicate a wide variety in the orientations of different inclusion phases with respect to their diamond host (Futergendler & Frank-Kamenetsky 1961; Frank-Kamenetsky 1964; Wiggers de Vries et al. 2011; Nestola et al. 2014, Milani et al. 2016). For example, olivine inclusions in lithospheric diamonds from Udachnaya do not show any preferred orientations with respect to their diamond hosts, but multiple inclusions in a single diamond often show very similar orientations within few degrees. In the present work on magnesiochromite inclusions in diamonds from Udachnaya, there is a partial orientation between inclusion and host. A (111) plane of each inclusion is sub-parallel to a {111} plane of their diamond host, but with random orientations of the magnesiochromite [100], [010] and [001] relative to the diamond. In one case, where a single inclusion comprised a magnesiochromite-olivine touching pair, the magnesiochromite was oriented as noted above and the olivine showed a random orientation. The implications of these observations for the mechanisms of diamond growth will be explored and the results will be compared and combined with previous work. This work was supported by ERC starting grant "INDIMEDEA" (307322) to F. Nestola and by the MIUR-SIR grant "MILE DEEp" (RBSI140351) to M. Alvaro. References Angel R. J. et al., J. Appl. Crystallogr. 48, 1330-1334 (2015). Wiggers de Vries D.F. et al., Contrib Mineral Petr 161, 565-579 (2011). Dobson D. P. et al., Nat. Geosci. 6, 575-578 (2013). Frank-Kamenetsky V.A. The nature of structural impurities and inclusions in minerals. Leningrad, Gos. Univ. (1964) Futergendler S.I. and Frank-Kamenetsky V.A. Zap Vsesoyuzn Mineral Obs 90, 230 (1961). Nestola F. et al., Int. Geol. Rev. 56(13), 1658-1667 (2014).

Crystallographic Data Centre Services and Publications.

ERIC Educational Resources Information Center

Cambridge Univ. (England). Chemical Lab.

The Cambridge Crystallographic Data Centre is concerned with the retrieval, evaluation, synthesis, and dissemination of structural data based on diffraction methods. The source of input is almost entirely primary journals. Bibliographic information and numeric data on crystal and molecular structures are on magnetic tapes. The bibliographic file…

Reorientations, relaxations, metastabilities, and multidomains of skyrmion lattices

DOE PAGES

Bannenberg, L. J.; Qian, F.; Dalgliesh, R. M.; ...

2017-11-13

Magnetic skyrmions are nanosized topologically protected spin textures with particlelike properties. They can form lattices perpendicular to the magnetic field, and the orientation of these skyrmion lattices with respect to the crystallographic lattice is governed by spin-orbit coupling. By performing small-angle neutron scattering measurements, we investigate the coupling between the crystallographic and skyrmion lattices in both Cu 2OSeO 3 and the archetype chiral magnet MnSi. The results reveal that the orientation of the skyrmion lattice is primarily determined by the magnetic field direction with respect to the crystallographic lattice. In addition, it is also influenced by the magnetic history ofmore » the sample, which can induce metastable lattices. Kinetic measurements show that these metastable skyrmion lattices may or may not relax to their equilibrium positions under macroscopic relaxation times. Moreover, multidomain lattices may form when two or more equivalent crystallographic directions are favored by spin-orbit coupling and oriented perpendicular to the magnetic field.« less

Inheritance of Crystallographic Orientation during Lithiation/Delithiation Processes of Single-Crystal α-Fe2O3 Nanocubes in Lithium-Ion Batteries.

PubMed

Ma, Xiaowei; Zhang, Manyu; Liang, Chongyun; Li, Yuesheng; Wu, Jingjing; Che, Renchao

2015-11-04

Iron oxides are very promising anode materials based on conversion reactions for lithium-ion batteries (LIBs). During conversion processes, the crystal structure and composition of the electrode material are drastically changed. Surprisingly, in our study, inheritance of a crystallographic orientation was found during lithiation/delithiation processes of single-crystal α-Fe2O3 nanocubes by ex situ transmission electron microscopy. Single-crystal α-Fe2O3 was first transformed into numerous Fe nanograins embedded in a Li2O matrix, and then the conversion between Fe and FeO nanograins became the main reversible electrochemical reaction for energy storage. Interestingly, these Fe/FeO nanograins had almost the same crystallographic orientation, indicating that the lithiated/delithiated products can inherit the crystallographic orientation of single-crystal α-Fe2O3. This finding is important for understanding the detailed electrochemical conversion processes of iron oxides, and this feature may also exist during lithiation/delithiation processes of other transition-metal oxides.

Equiaxed and columnar dendrite growth simulation in Al-7Si- Mg ternary alloys using cellular automaton method

NASA Astrophysics Data System (ADS)

Chen, Rui; Xu, Qingyan; Liu, Baicheng

2015-06-01

In this paper, a modified cellular automaton (MCA) model allowing for the prediction of dendrite growth of Al-Si-Mg ternary alloys in two and three dimensions is presented. The growth kinetic of S/L interface is calculated based on the solute equilibrium approach. In order to describe the dendrite growth with arbitrarily crystallographic orientations, this model introduces a modified decentered octahedron algorithm for neighborhood tracking to eliminate the effect of mesh dependency on dendrite growth. The thermody namic and kinetic data needed for dendrite growth is obtained through coupling with Pandat software package in combination with thermodynamic/kinetic/equilibrium phase diagram calculation databases. The effect of interactions between various alloying elements on solute diffusion coefficient is considered in the model. This model has first been used to simulate Al-7Si (weight percent) binary dendrite growth followed by a validation using theoretical predictions. For ternary alloy, Al-7Si-0.5Mg dendrite simulation has been carried out and the effects of solute interactions on diffusion matrix as well as the differences of Si and Mg in solute distribution have been analyzed. For actual application, this model has been applied to simulate the equiaxed dendrite growth with various crystallographic orientations of Al-7Si-0.36Mg ternary alloy, and the predicted secondary dendrite arm spacing (SDAS) shows a reasonable agreement with the experimental ones. Furthermore, the columnar dendrite growth in directional solidification has also been simulated and the predicted primary dendrite arm spacing (PDAS) is in good agreement with experiments. The simulated results effectively demonstrate the abilities of the model in prediction of dendritic microstructure of Al-Si-Mg ternary alloy.

Outcome of the First wwPDB/CCDC/D3R Ligand Validation Workshop.

PubMed

Adams, Paul D; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A; Berman, Helen M; Bhat, Talapady N; Blaney, Jeff M; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K; Case, David A; Clark, Kirk L; Darden, Tom; Emsley, Paul; Feher, Victoria A; Feng, Zukang; Groom, Colin R; Harris, Seth F; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E; Markley, John L; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T; Padyana, Anil K; Peishoff, Catherine E; Pieniazek, Susan; Read, Randy J; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna C; Warren, Gregory L; Westbrook, John D; Williams, Pamela; Yang, Huanwang; Young, Jasmine

2016-04-05

Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank (PDB) archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Outcome of the first wwPDB/CCDC/D3R Ligand Validation Workshop

PubMed Central

Adams, Paul D.; Aertgeerts, Kathleen; Bauer, Cary; Bell, Jeffrey A.; Berman, Helen M.; Bhat, Talapady N.; Blaney, Jeff; Bolton, Evan; Bricogne, Gerard; Brown, David; Burley, Stephen K.; Case, David A.; Clark, Kirk L.; Darden, Tom; Emsley, Paul; Feher, Victoria A.; Feng, Zukang; Groom, Colin R.; Harris, Seth F.; Hendle, Jorg; Holder, Thomas; Joachimiak, Andrzej; Kleywegt, Gerard J.; Krojer, Tobias; Marcotrigiano, Joseph; Mark, Alan E.; Markley, John L.; Miller, Matthew; Minor, Wladek; Montelione, Gaetano T.; Murshudov, Garib; Nakagawa, Atsushi; Nakamura, Haruki; Nicholls, Anthony; Nicklaus, Marc; Nolte, Robert T.; Padyana, Anil K.; Peishoff, Catherine E.; Pieniazek, Susan; Read, Randy J.; Shao, Chenghua; Sheriff, Steven; Smart, Oliver; Soisson, Stephen; Spurlino, John; Stouch, Terry; Svobodova, Radka; Tempel, Wolfram; Terwilliger, Thomas C.; Tronrud, Dale; Velankar, Sameer; Ward, Suzanna; Warren, Gregory L.; Westbrook, John D.; Williams, Pamela; Yang, Huanwang; Young, Jasmine

2016-01-01

Summary Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. PMID:27050687

On the control of the crystallographic texture in cladding tubes from Zr-based alloys for nuclear reactor

NASA Astrophysics Data System (ADS)

Isaenkova, M.; Perlovich, Yu.; Fesenko, V.

2016-10-01

This paper summarizes researches of authors, directed to the development of the methodological basis of X-ray studies as applied to zirconium alloys and on the systematization of new experimental results obtained using developed methods. The paper describes regularities of crystallographic texture formation in cladding tubes from zirconium alloys and their substructure inhomogeneity at various stages of manufacture, i.e. at hot and cold deformation, recrystallization, phase transformations and interaction of the above processes. The special attention is payed to possibilities of control the crystallographic texture of tubes at successive stages of their technological treatment.

Crystallographic texture in oxide-dispersion-strengthened alloys

NASA Technical Reports Server (NTRS)

Whittenberger, J. D.

1982-01-01

Crystallographic and elastic moduli data are presented which document the degree of texture in several oxide dispersion-strengthened (ODS) nickel-base alloys. The existence of strong crystallographic textures in such multicrystalline alloys is considered important, since the small angle grain boundaries may be partially responsible for creep threshold stresses. Gleiter (1979) has shown that ideal, low energy boundaries will act as vacancy sources only when the applied stress is greater than a threshold stress, while large angle grain boundaries will emit vacancies at all stress levels. The continued operation of a net vacancy in an ODS alloy must be avoided, since it will lead to a localized disruption of the microstructure.

Constitutive Modeling of Superalloy Single Crystals and Directionally Solidified Materials

NASA Technical Reports Server (NTRS)

Walker, K. P.; Jordan, E. H.

1985-01-01

A unified viscoplastic constitutive relation based on crystallographic slip theory was developed for the deformation analysis of nickel base face centered cubic superalloy single crystals at elevated temperature. The single crystal theory is embedded in a self consistent method to derive a constitutive relation for a directionally solidified material comprised of a polycrystalline aggregate of columnar cylindrical grains. One of the crystallographic axes of the cylindrical crystals points in the columnar direction while the remaining crystallographic axes are oriented at random in the basal plane perpendicular to the columnar direction. These constitutive formulations are coded in FORTRAN for use in nonlinear finite element and boundary element programs.

Metrics for comparison of crystallographic maps

DOE PAGES

Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; ...

2014-10-01

Numerical comparison of crystallographic contour maps is used extensively in structure solution and model refinement, analysis and validation. However, traditional metrics such as the map correlation coefficient (map CC, real-space CC or RSCC) sometimes contradict the results of visual assessment of the corresponding maps. This article explains such apparent contradictions and suggests new metrics and tools to compare crystallographic contour maps. The key to the new methods is rank scaling of the Fourier syntheses. The new metrics are complementary to the usual map CC and can be more helpful in map comparison, in particular when only some of their aspects,more » such as regions of high density, are of interest.« less

Tutorial: Crystal orientations and EBSD — Or which way is up?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Britton, T.B., E-mail: b.britton@imperial.ac.uk; Jiang, J.; Guo, Y.

2016-07-15

Electron backscatter diffraction (EBSD) is an automated technique that can measure the orientation of crystals in a sample very rapidly. There are many sophisticated software packages that present measured data. Unfortunately, due to crystal symmetry and differences in the set-up of microscope and EBSD software, there may be accuracy issues when linking the crystal orientation to a particular microstructural feature. In this paper we outline a series of conventions used to describe crystal orientations and coordinate systems. These conventions have been used to successfully demonstrate that a consistent frame of reference is used in the sample, unit cell, pole figuremore » and diffraction pattern frames of reference. We establish a coordinate system rooted in measurement of the diffraction pattern and subsequently link this to all other coordinate systems. A fundamental outcome of this analysis is to note that the beamshift coordinate system needs to be precisely defined for consistent 3D microstructure analysis. This is supported through a series of case studies examining particular features of the microscope settings and/or unambiguous crystallographic features. These case studies can be generated easily in most laboratories and represent an opportunity to demonstrate confidence in use of recorded orientation data. Finally, we include a simple software tool, written in both MATLAB® and Python, which the reader can use to compare consistency with their own microscope set-up and which may act as a springboard for further offline analysis. - Highlights: • Presentation of conventions used to describe crystal orientations • Three case studies that outline how conventions are consistent • Demonstrates a pathway for calibration and validation of EBSD based orientation measurements • EBSD computer code supplied for validation by the reader.« less

Lunar and Planetary Science XXXV: Undergraduate Education and Research Programs, Facilities, and Information Access

NASA Technical Reports Server (NTRS)

2004-01-01

The titles in this section include: 1) GRIDVIEW: Recent Improvements in Research and Education Software for Exploring Mars Topography; 2) Software and Hardware Upgrades for the University of North Dakota Asteroid and Comet Internet Telescope (ACIT); 3) Web-based Program for Calculating Effects of an Earth Impact; 4) On-Line Education, Web- and Virtual-Classes in an Urban University: A Preliminary Overview; 5) Modelling Planetary Material's Structures: From Quasicrystalline Microstructure to Crystallographic Materials by Use of Mathematica; 6) How We Used NASA Lunar Set in Planetary and Material Science Studies: Textural and Cooling Sequences in Sections of Lava Column from a Thin and a Thick Lava-Flow, from the Moon and Mars with Terrestrial Analogue and Chondrule Textural Comparisons; 7) Classroom Teaching of Space Technology and Simulations by the Husar Rover Model; 8) New Experiments (In Meteorology, Aerosols, Soil Moisture and Ice) on the New Hunveyor Educational Planetary Landers of Universities and Colleges in Hungary; 9) Teaching Planetary GIS by Constructing Its Model for the Test Terrain of the Hunveyor and Husar; 10) Undergraduate Students: An Untapped Resource for Planetary Researchers; 11) Analog Sites in Field Work of Petrology: Rock Assembly Delivered to a Plain by Floods on Earth and Mars; 12) RELAB (Reflectance Experiment Laboratory): A NASA Multiuser Spectroscopy Facility; 13) Full Text Searching and Customization in the NASA ADS Abstract Service.

Crystallographic Study of Itokawa Particle, RA-QD02-0127 by Using Energy-Scanning X-Ray Diffraction Method with Synchrotron Radiation

NASA Astrophysics Data System (ADS)

Hagiya, K.; Ohsumi, K.; Komatsu, M.; Mikouchi, T.; Zolensky, M. E.; Hirata, A.; Yamaguchi, S.; Kurokawa, A.

2016-08-01

Crystallographic study of Itokawa particle, RA-QD02-0127 by using new X-ray diffraction method was performed. The purpose of this study is to understand better the metamorphic and impact shock history of asteroid Itokawa, and other S-class asteroids.

A general way for quantitative magnetic measurement by transmitted electrons

NASA Astrophysics Data System (ADS)

Song, Dongsheng; Li, Gen; Cai, Jianwang; Zhu, Jing

2016-01-01

EMCD (electron magnetic circular dichroism) technique opens a new door to explore magnetic properties by transmitted electrons. The recently developed site-specific EMCD technique makes it possible to obtain rich magnetic information from the Fe atoms sited at nonequivalent crystallographic planes in NiFe2O4, however it is based on a critical demand for the crystallographic structure of the testing sample. Here, we have further improved and tested the method for quantitative site-specific magnetic measurement applicable for more complex crystallographic structure by using the effective dynamical diffraction effects (general routine for selecting proper diffraction conditions, making use of the asymmetry of dynamical diffraction for design of experimental geometry and quantitative measurement, etc), and taken yttrium iron garnet (Y3Fe5O12, YIG) with more complex crystallographic structure as an example to demonstrate its applicability. As a result, the intrinsic magnetic circular dichroism signals, spin and orbital magnetic moment of iron with site-specific are quantitatively determined. The method will further promote the development of quantitative magnetic measurement with high spatial resolution by transmitted electrons.

A preliminary neutron crystallographic study of thaumatin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Teixeira, Susana C. M.; Institut Laue Langevin, 6 Rue Jules Horowitz, 38042 Grenoble; EPSAM and ISTM, Keele University, Staffordshire ST5 5BG

2008-05-01

Preliminary neutron crystallographic data from the sweet protein thaumatin have been recorded using the LADI-III diffractometer at the Institut Laue Langevin (ILL). The results illustrate the feasibility of a full neutron structural analysis aimed at further understanding the molecular basis of the perception of sweet taste. Such an analysis will exploit the use of perdeuterated thaumatin. A preliminary neutron crystallographic study of the sweet protein thaumatin is presented. Large hydrogenated crystals were prepared in deuterated crystallization buffer using the gel-acupuncture method. Data were collected to a resolution of 2 Å on the LADI-III diffractometer at the Institut Laue Langevin (ILL).more » The results demonstrate the feasibility of a full neutron crystallographic analysis of this structure aimed at providing relevant information on the location of H atoms, the distribution of charge on the protein surface and localized water in the structure. This information will be of interest for understanding the specificity of thaumatin–receptor interactions and will contribute to further understanding of the molecular mechanisms underlying the perception of taste.« less

The localization and crystallographic dependence of Si suboxide species at the SiO2/Si interface

NASA Technical Reports Server (NTRS)

Grunthaner, P. J.; Hecht, M. H.; Grunthaner, F. J.; Johnson, N. M.

1987-01-01

X-ray photoemission spectroscopy has been used to examine the localization and crystallographic dependence of Si(+), Si(2+), and Si(3+) suboxide states at the SiO2/Si interface for (100)and (111)-oriented substrates with gate oxide quality thermal oxides. The Si(+) and Si(2+) states are localized within 6-10 A of the interface while the Si(3+) state extends about 30 A into the bulk SiO2. The distribution of Si(+) and Si(2+) states shows a strong crystallographic dependence with Si(2+) dominating on (100) substrates and Si(+) dominating on (111) substrates. This crystallographic dependence is anticipated from consideration of ideal unreconstructed (100) and (111) Si surfaces, suggesting that (1) the Si(+) and Si(2+) states are localized immediately within the first monolayer at the interface and (2) the first few monolayers of substrate Si atoms are not significantly displaced from the bulk. The total number of suboxide states observed at the SiO2/Si interface corresponds to 94 and 83 percent of a monolayer for these (100) and (111) substrates, respectively.

Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures

PubMed Central

Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

2015-01-01

The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45 000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered. PMID:18034855

Structure evolution of zinc oxide thin films deposited by unbalance DC magnetron sputtering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aryanto, Didik, E-mail: didi027@lipi.go.id; Materials Research Group, Physics Department, Universitas Negeri Semarang, Gunungpati, Semarang 50229 Jawa Tengah; Marwoto, Putut

Zinc oxide (ZnO) thin films are deposited on corning glass substrates using unbalanced DC magnetron sputtering. The effect of growth temperature on surface morphology and crystallographic orientation of ZnO thin film is studied using atomic force microscopy (AFM) and X-ray diffraction (XRD) techniques. The surface morphology and crystallographic orientation of ZnO thin film are transformed against the increasing of growth temperature. The mean grain size of film and the surface roughness are inversely and directly proportional towards the growth temperature from room temperature to 300 °C, respectively. The smaller grain size and finer roughness of ZnO thin film are obtainedmore » at growth temperature of 400 °C. The result of AFM analysis is in good agreement with the result of XRD analysis. ZnO thin films deposited in a series of growth temperatures have hexagonal wurtzite polycrystalline structures and they exhibit transformations in the crystallographic orientation. The results in this study reveal that the growth temperature strongly influences the surface morphology and crystallographic orientation of ZnO thin film.« less

Determining crystal structures through crowdsourcing and coursework

NASA Astrophysics Data System (ADS)

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-09-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

The X-ray system of crystallographic programs for any computer having a PIDGIN FORTRAN compiler

NASA Technical Reports Server (NTRS)

Stewart, J. M.; Kruger, G. J.; Ammon, H. L.; Dickinson, C.; Hall, S. R.

1972-01-01

A manual is presented for the use of a library of crystallographic programs. This library, called the X-ray system, is designed to carry out the calculations required to solve the structure of crystals by diffraction techniques. It has been implemented at the University of Maryland on the Univac 1108. It has, however, been developed and run on a variety of machines under various operating systems. It is considered to be an essentially machine independent library of applications programs. The report includes definition of crystallographic computing terms, program descriptions, with some text to show their application to specific crystal problems, detailed card input descriptions, mass storage file structure and some example run streams.

Determining crystal structures through crowdsourcing and coursework.

PubMed

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

2016-09-16

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

On three-dimensional misorientation spaces.

PubMed

Krakow, Robert; Bennett, Robbie J; Johnstone, Duncan N; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J; Einsle, Joshua F; Midgley, Paul A; Rae, Catherine M F; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

Preferred crystallographic orientation in the ice I ← II transformation and the flow of ice II

USGS Publications Warehouse

Bennett, K.; Wenk, H.-R.; Durham, W.B.; Stern, L.A.; Kirby, S.H.

1997-01-01

The preferred crystallographic orientation developed during the ice I ← II transformation and during the plastic flow of ice II was measured in polycrystalline deuterium oxide (D2O) specimens using low-temperature neutron diffraction. Samples partially transformed from ice I to II under a non-hydrostatic stress developed a preferred crystallographic orientation in the ice II. Samples of pure ice II transformed from ice I under a hydrostatic stress and then when compressed axially, developed a strong preferred orientation of compression axes parallel to (1010). A match to the observed preferred orientation using the viscoplastic self-consistent theory was obtained only when (1010) [0001] was taken as the predominant slip system in ice II.

On three-dimensional misorientation spaces

NASA Astrophysics Data System (ADS)

Krakow, Robert; Bennett, Robbie J.; Johnstone, Duncan N.; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J.; Einsle, Joshua F.; Midgley, Paul A.; Rae, Catherine M. F.; Hielscher, Ralf

2017-10-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance.

Crystallographic changes in lead zirconate titanate due to neutron irradiation

DOE PAGES

Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; ...

2014-11-17

Piezoelectric and ferroelectric materials are useful as the active element in non-destructive monitoring devices for high-radiation areas. Here, crystallographic structural refinement (i.e., the Rietveld method) is used to quantify the type and extent of structural changes in PbZr 0 .5Ti 0 .5O 3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 10 15 neutrons/cm 2. The results show a measurable decrease in the occupancy of Pb and O due to irradiation, with O vacancies in the tetragonal phase being created preferentially on one of the two O sites. The results demonstrate a method by which themore » effects of radiation on crystallographic structure may be investigated.« less

Crystallographic Characterization on Polycrystalline Ni-Mn-Ga Alloys with Strong Preferred Orientation.

PubMed

Li, Zongbin; Yang, Bo; Zou, Naifu; Zhang, Yudong; Esling, Claude; Gan, Weimin; Zhao, Xiang; Zuo, Liang

2017-04-27

Heusler type Ni-Mn-Ga ferromagnetic shape memory alloys can demonstrate excellent magnetic shape memory effect in single crystals. However, such effect in polycrystalline alloys is greatly weakened due to the random distribution of crystallographic orientation. Microstructure optimization and texture control are of great significance and challenge to improve the functional behaviors of polycrystalline alloys. In this paper, we summarize our recent progress on the microstructure control in polycrystalline Ni-Mn-Ga alloys in the form of bulk alloys, melt-spun ribbons and thin films, based on the detailed crystallographic characterizations through neutron diffraction, X-ray diffraction and electron backscatter diffraction. The presented results are expected to offer some guidelines for the microstructure modification and functional performance control of ferromagnetic shape memory alloys.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

Carbohydrate structure: the rocky road to automation.

PubMed

Agirre, Jon; Davies, Gideon J; Wilson, Keith S; Cowtan, Kevin D

2017-06-01

With the introduction of intuitive graphical software, structural biologists who are not experts in crystallography are now able to build complete protein or nucleic acid models rapidly. In contrast, carbohydrates are in a wholly different situation: scant automation exists, with manual building attempts being sometimes toppled by incorrect dictionaries or refinement problems. Sugars are the most stereochemically complex family of biomolecules and, as pyranose rings, have clear conformational preferences. Despite this, all refinement programs may produce high-energy conformations at medium to low resolution, without any support from the electron density. This problem renders the affected structures unusable in glyco-chemical terms. Bringing structural glycobiology up to 'protein standards' will require a total overhaul of the methodology. Time is of the essence, as the community is steadily increasing the production rate of glycoproteins, and electron cryo-microscopy has just started to image them in precisely that resolution range where crystallographic methods falter most. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Cambridge Structural Database in retrospect and prospect.

PubMed

Groom, Colin R; Allen, Frank H

2014-01-13

The Cambridge Crystallographic Data Centre (CCDC) was established in 1965 to record numerical, chemical and bibliographic data relating to published organic and metal-organic crystal structures. The Cambridge Structural Database (CSD) now stores data for nearly 700,000 structures and is a comprehensive and fully retrospective historical archive of small-molecule crystallography. Nearly 40,000 new structures are added each year. As X-ray crystallography celebrates its centenary as a subject, and the CCDC approaches its own 50th year, this article traces the origins of the CCDC as a publicly funded organization and its onward development into a self-financing charitable institution. Principally, however, we describe the growth of the CSD and its extensive associated software system, and summarize its impact and value as a basis for research in structural chemistry, materials science and the life sciences, including drug discovery and drug development. Finally, the article considers the CCDC's funding model in relation to open access and open data paradigms. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bioactive focus in conformational ensembles: a pluralistic approach

NASA Astrophysics Data System (ADS)

Habgood, Matthew

2017-12-01

Computational generation of conformational ensembles is key to contemporary drug design. Selecting the members of the ensemble that will approximate the conformation most likely to bind to a desired target (the bioactive conformation) is difficult, given that the potential energy usually used to generate and rank the ensemble is a notoriously poor discriminator between bioactive and non-bioactive conformations. In this study an approach to generating a focused ensemble is proposed in which each conformation is assigned multiple rankings based not just on potential energy but also on solvation energy, hydrophobic or hydrophilic interaction energy, radius of gyration, and on a statistical potential derived from Cambridge Structural Database data. The best ranked structures derived from each system are then assembled into a new ensemble that is shown to be better focused on bioactive conformations. This pluralistic approach is tested on ensembles generated by the Molecular Operating Environment's Low Mode Molecular Dynamics module, and by the Cambridge Crystallographic Data Centre's conformation generator software.

Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning System

NASA Astrophysics Data System (ADS)

Nagy, Julia; Eilert, Tobias; Michaelis, Jens

2018-03-01

Modern hybrid structural analysis methods have opened new possibilities to analyze and resolve flexible protein complexes where conventional crystallographic methods have reached their limits. Here, the Fast-Nano-Positioning System (Fast-NPS), a Bayesian parameter estimation-based analysis method and software, is an interesting method since it allows for the localization of unknown fluorescent dye molecules attached to macromolecular complexes based on single-molecule Förster resonance energy transfer (smFRET) measurements. However, the precision, accuracy, and reliability of structural models derived from results based on such complex calculation schemes are oftentimes difficult to evaluate. Therefore, we present two proof-of-principle benchmark studies where we use smFRET data to localize supposedly unknown positions on a DNA as well as on a protein-nucleic acid complex. Since we use complexes where structural information is available, we can compare Fast-NPS localization to the existing structural data. In particular, we compare different dye models and discuss how both accuracy and precision can be optimized.

First Results from a Microfocus X-Ray System for Macromolecular Crystallography

NASA Technical Reports Server (NTRS)

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

1999-01-01

The design and performance of a 40 Watt laboratory crystallography system optimized for the structure determination of small protein crystals are described. This system combines a microfocus x-ray generator (40 microns FWHM spot size at a power level of 40 Watts) and a short focal length (F = 2.6 mm) polycapillary collimating optic, and produces a small diameter quasi-parallel x-ray beam. Measurements of x-ray flux, divergence and spectral purity of the resulting x-ray beam are presented. The x-ray flux in a 250 microns diameter aperture produced by the microfocus system is 14.7 times higher .than that from a 3.15 kW rotating anode generator equipped with graphite monochromator. Crystallography data taken with the microfocus system are presented, and indicate that the divergence and spectral purity of the x-ray are sufficient to refine the diffraction data using a standard crystallographic software. Significant additional improvements in flux and beam divergence are possible, and plans for achieving these coals are discussed.

Mini-beam collimator applications at the Advanced Photon Source

NASA Astrophysics Data System (ADS)

Xu, Shenglan; Keefe, Lisa J.; Mulichak, Anne; Yan, Lifen; Alp, Ercan E.; Zhao, Jiyong; Fischetti, Robert F.

2011-09-01

In 2007, the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA CAT, Sector 23, Advanced Photon Source) began providing mini-beam collimators to its users. These collimators contained individual, 5- or 10-μm pinholes and were rapidly exchangeable, thereby allowing users to tailor the beam size to their experimental needs. The use of these collimators provided a reduction in background noise, and thus improved the signal-to-noise ratio [1,2]. Recent improvements in the collimator design include construction of the device from a monolithic piece of molybdenum with multiple pinholes mounted inside [3]. This allows users to select from various size options from within the beamline control software without the realignment that was previously necessary. In addition, a new, 20-μm pinhole has been added to create a "quad-collimator", resulting in greater flexibility for the users. The mini-beam collimator is now available at multiple crystallographic beamlines and also is a part of the first Mössbauer Microscopic system at sector 3-ID.

Defect formation energy and magnetic structure of shape memory alloys Ni-X-Ga (X=Mn, Fe, Co) by first principle calculation

NASA Astrophysics Data System (ADS)

Bai, J.; Raulot, J. M.; Zhang, Y. D.; Esling, C.; Zhao, X.; Zuo, L.

2010-09-01

The crystallographic and magnetic structures of the Ni2XGa (X=Mn, Fe, Co), are systematically investigated by means of the first-principles calculations within the framework of density functional theory using the VIENNA AB INITIO SOFTWARE PACKAGE. The formation energies of several kinds of defects (atomic exchange, antisite, vacancy) are estimated. The Ga atoms stabilize the cubic structure, and the effect of X atoms on the structural stability is opposite. For most cases of the site occupation, the excess atoms of the rich component directly occupy the site(s) of the deficient one(s), except for Ga-rich Ni-deficient type. The magnitude of the variation in Ni moments is much larger than that of Mn in defective Ni2XGa. The value of Ni magnetic moment sensitively depends on the distance between Ni and X. Excess Mn could be ferromagnetic or antiferromagnetic, depending on the distance between the neighboring Mn atoms.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum.

PubMed

Brunger, Axel T; Das, Debanu; Deacon, Ashley M; Grant, Joanna; Terwilliger, Thomas C; Read, Randy J; Adams, Paul D; Levitt, Michael; Schröder, Gunnar F

2012-04-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence.

Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum

PubMed Central

Brunger, Axel T.; Das, Debanu; Deacon, Ashley M.; Grant, Joanna; Terwilliger, Thomas C.; Read, Randy J.; Adams, Paul D.; Levitt, Michael; Schröder, Gunnar F.

2012-01-01

Phasing by molecular replacement remains difficult for targets that are far from the search model or in situations where the crystal diffracts only weakly or to low resolution. Here, the process of determining and refining the structure of Cgl1109, a putative succinyl-diaminopimelate desuccinylase from Corynebacterium glutamicum, at ∼3 Å resolution is described using a combination of homology modeling with MODELLER, molecular-replacement phasing with Phaser, deformable elastic network (DEN) refinement and automated model building using AutoBuild in a semi-automated fashion, followed by final refinement cycles with phenix.refine and Coot. This difficult molecular-replacement case illustrates the power of including DEN restraints derived from a starting model to guide the movements of the model during refinement. The resulting improved model phases provide better starting points for automated model building and produce more significant difference peaks in anomalous difference Fourier maps to locate anomalous scatterers than does standard refinement. This example also illustrates a current limitation of automated procedures that require manual adjustment of local sequence misalignments between the homology model and the target sequence. PMID:22505259

Effect of impurities and post-experimental purification in SAD phasing with serial femtosecond crystallography data.

PubMed

Zhang, Tao; Gu, Yuanxin; Fan, Haifu

2016-06-01

In serial crystallography (SX) with either an X-ray free-electron laser (XFEL) or synchrotron radiation as the light source, huge numbers of micrometre-sized crystals are used in diffraction data collection. For a SAD experiment using a derivative with introduced heavy atoms, it is difficult to completely exclude crystals of the native protein from the sample. In this paper, simulations were performed to study how the inclusion of native crystals in the derivative sample could affect the result of SAD phasing and how the post-experimental purification proposed by Zhang et al. [(2015), Acta Cryst. D71, 2513-2518] could be used to remove the impurities. A gadolinium derivative of lysozyme and the corresponding native protein were used in the test. Serial femtosecond crystallography (SFX) diffraction snapshots were generated by CrystFEL. SHELXC/D, Phaser, DM, ARP/wARP and REFMAC were used for automatic structure solution. It is shown that a small amount of impurities (snapshots from native crystals) in the set of derivative snapshots can strongly affect the SAD phasing results. On the other hand, post-experimental purification can efficiently remove the impurities, leading to results similar to those from a pure sample.

A Contribution to the Kinetic Study of the Metatectic Reaction U+U$sub 3$Si$sub 2$$Yields$U$sub 3$Si; CONTRIBUTION AL ESTUDIO CINETICO DE LA REACCION METATECTICA U+U$sub 3$Si$sub 2$$Yields$U$sub 3$Si

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruiperez, J.A.; Hernandez, J.A.E.

1962-01-01

An experimental study was made to decide upon the advantages and drawbacks of the different methods and reagents employed in the metallography of U-Si alloys. It has been observed that all samples thermally treated to the epsilon-phase undergo a coalescence of the U/sub 3/Si/sub 2/ particles. The coalescence decreases the surface available for reaction and consequently the reaction rate. The growth of the U/sub 3/Si/sub 2/ phase particles was determined as a function of time and temperature. To obtain samples with nuclei sufficiently isolated so that the U/sub 3/Si rings will not interfere their respective growth, the conditions that regulatemore » coalescence, Si content and thermal treatment, were determined. Data rel1tive to the growth of the U/sub 3/ Si phase-rings were obtained. Curves relating growth, time, and temperature are presented. The parameters that define the diffusion regulated reaction can be deduced from these curves. (auth)« less

Fragon: rapid high-resolution structure determination from ideal protein fragments.

PubMed

Jenkins, Huw T

2018-03-01

Correctly positioning ideal protein fragments by molecular replacement presents an attractive method for obtaining preliminary phases when no template structure for molecular replacement is available. This has been exploited in several existing pipelines. This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. The reliable scoring algorithm provided by ACORN identifies success. In these cases, the resulting phases are usually of sufficient quality to enable automated model building of the entire structure. Fragon was evaluated against two test sets comprising mixed α/β folds and all-β folds at resolutions between 1.0 and 1.7 Å. Success rates of 61% for the mixed α/β test set and 30% for the all-β test set were achieved. In almost 70% of successful runs, fragment placement and density modification took less than 30 min on relatively modest four-core desktop computers. In all successful runs the best set of phases enabled automated model building with ARP/wARP to complete the structure.

Large Aperture Scanning Lidar Based on Holographic Optical Elements

NASA Technical Reports Server (NTRS)

Schwemmer, Geary K.; Miller, David O.; Wilkerson, Thomas D.; Andrus, Ionio; Guerra, David V.; Einaudi, Franco (Technical Monitor)

2001-01-01

Lidar remote sensing instruments can make a significant contribution to satisfying many of the required measurements of atmospheric and surface parameters for future spaceborne platforms, including topographic altimeters, atmospheric profiles of, wind, humidity, temperature, trace molecules, aerosols, and clouds. It is highly desirable to have wide measurement swaths for rapid coverage rather than just the narrow ribbon of data that is obtained with a nadir only observation. For most applications global coverage is required, and for wind measurements scanning or pointing is required in order to retrieve the full 3-D wind vector from multiple line-of-sight Doppler measurements. Conventional lidar receivers make up a substantial portion of the instrument's size and weight. Wide angle scanning typically requires a large scanning mirror in front of the receiver telescope, or pointing the entire telescope and aft optics assembly, Either of these methods entails the use of large bearings, motors, gearing and their associated electronics. Spaceborne instruments also need reaction wheels to counter the torque applied to the spacecraft by these motions. NASA has developed simplified conical scanning telescopes using Holographic Optical Elements (HOEs) to reduce the size, mass, angular momentum, and cost of scanning lidar systems. NASA has developed two operating lidar systems based on 40 cm diameter HOEs. The first such system, named Prototype Holographic Atmospheric Scanner for Environmental Remote Sensing (PHASERS) was a joint development between NASA Goddard Space Flight Center (GSFC) and the University of Maryland College Park. PHASERS is based on a reflection HOE for use at the doubled Nd:YAG laser wavelength of 532 nm and has recently undergone a number of design changes in a collaborative effort between GSFC and Saint Anselm College in New Hampshire. The next step was to develop IR transmission HOEs for use with the Nd:YAG fundamental in the Holographic Airborne Rotating Lidar Instrument Experiment (HARLIE). The HOE spins like a compact disk in a large ring ball bearing. In an aircraft the HOE faces down, looking out through a window at an angle of 45 degrees off-nadir. The HOE diffracts 85% of the incident 532 nm light into a 160 micron spot at a focal length of 1 meter. HARLIE is a field deployable lidar measuring aerosol, cloud, and boundary layer backscatter for atmospheric research. It has flown several times and is also used from a ground-based trailer in an upward-looking mode. The HOE generates a 45 degree conical scan pattern by rotating at speeds up to 30 rpm. Like PHASERS, the HOE in HARLIE serves both as the laser collimating lens as well as the receiver telescope primary optic. The telescope is coupled to the receiver package via fiber optic. The transmitter is a diode pumped Nd:YAG laser operating at 1064 nm, delivering 1 mJ pulses at a 5 KHz rep-rate. The receiver has a 200 microradian field-of-view and a 0.5 nm optical bandpass. The photon counting data system utilizes a single Geiger-mode silicon avalanche photodiode detector, This new technology has also presented us with new data visualization challenges as well as new measurement techniques. The backscatter data obtained from a stationary (i.e. ground-based) scanning HOE lidar is on the surface of a cone, which when viewed over many consecutive scans can reveal atmospheric motions on this surface over time as the atmosphere advects over the site. In a moving platform such as an airplane or satellite, the data from consecutive scans cover different areas under the flight path, revealing atmospheric structure in 3-dimensions. An example of a visualization of HARLIE ground-based data is presented, showing aerosol backscatter on a 90 degree conical surface generated from one 360 degree scan of the lidar during the HOLO-1 field campaign on the afternoon of 10 March 1999. Higher backscatter levels are rendered as lighter signal against a dark background. Breaking Kelvin-Helmholtz waves are evident on the north side of the scan at an altitude of 10-11 km. Time series of successive scans made at regular intervals render unique views of atmospheric motions, from which vertical profiles of atmospheric wind vectors can be obtained using a unique data analysis approach. Wind vectors obtained from the lidar were compared with co-located radiosonde wind profiles during an intensive operating period in September-October 2000 at the Atmospheric Radiation Measurement Program's Southern Great Plains Central Facility.

Microstructure, crystallographic texture and mechanical properties of friction stir welded AA2017A

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, M.M.Z., E-mail: mohamed_ahmed4@s-petrol.suez.edu.eg; Department of Metallurgical and Materials Engineering, Suez Canal University, Suez 43721; Wynne, B.P.

2012-02-15

In this study a thick section (20 mm) friction stir welded AA2017A-T451 has been characterized in terms of microstructure, crystallographic texture and mechanical properties. For microstructural analysis both optical and scanning electron microscopes have been used. A detailed crystallographic texture analysis has been carried out using the electron back scattering diffraction technique. Crystallographic texture has been examined in both shoulder and probe affected regions of the weld NG. An entirely weak texture is observed at the shoulder affected region which is mainly explained by the effect of the sequential multi pass deformation experienced by both tool probe and tool shoulder.more » The texture in the probe dominated region at the AS side of the weld is relatively weak but still assembles the simple shear texture of FCC metals with B/B{sup Macron} and C components existing across the whole map. However, the texture is stronger at the RS than at the AS of the weld, mainly dominated byB/B{sup Macron} components and with C component almost absent across the map. An alternating bands between (B) components and (B{sup Macron }) component are observed only at the AS side of the weld. - Highlights: Black-Right-Pointing-Pointer Detailed investigation of microstructure and crystallographic texture. Black-Right-Pointing-Pointer The grain size is varied from the top to the bottom of the NG. Black-Right-Pointing-Pointer An entirely weak texture is observed at the shoulder affected region. Black-Right-Pointing-Pointer The texture in the probe affected region is dominated by simple shear texture.« less

Microfocus/Polycapillary-Optic Crystallographic X-Ray System

NASA Technical Reports Server (NTRS)

Joy, Marshall; Gubarev, Mikhail; Ciszak, Ewa

2005-01-01

A system that generates an intense, nearly collimated, nearly monochromatic, small-diameter x-ray beam has been developed for use in macromolecular crystallography. A conventional x-ray system for macromolecular crystallography includes a rotating-anode x-ray source, which is massive (.500 kg), large (approximately 2 by 2 by 1 m), and power-hungry (between 2 and 18 kW). In contrast, the present system generates a beam of the required brightness from a microfocus source, which is small and light enough to be mounted on a laboratory bench, and operates at a power level of only tens of watts. The figure schematically depicts the system as configured for observing x-ray diffraction from a macromolecular crystal. In addition to the microfocus x-ray source, the system includes a polycapillary optic . a monolithic block (typically a bundle of fused glass tubes) that contains thousands of straight or gently curved capillary channels, along which x-rays propagate with multiple reflections. This particular polycapillary optic is configured to act as a collimator; the x-ray beam that emerges from its output face consists of quasi-parallel subbeams with a small angular divergence and a diameter comparable to the size of a crystal to be studied. The gap between the microfocus x-ray source and the input face of the polycapillary optic is chosen consistently with the focal length of the polycapillary optic and the need to maximize the solid angle subtended by the optic in order to maximize the collimated x-ray flux. The spectrum from the source contains a significant component of Cu K (photon energy is 8.08 keV) radiation. The beam is monochromatized (for Cu K ) by a nickel filter 10 m thick. In a test, this system was operated at a power of 40 W (current of 897 A at an accelerating potential of 45 kV), with an anode x-ray spot size of 41+/-2 microns. Also tested, in order to provide a standard for comparison, was a commercial rotating-anode x-ray crystallographic system with a pyrolytic graphite monochromator and a 250-micron pinhole collimator, operating at a power of 3.15 kW (current of 70 mA at an accelerating potential of 45 kV). The flux of collimated Cu K radiation in this system was found to be approximately 16 times that in the rotatinganode system. Data on x-ray diffraction from crystals of tetragonal form of lysozyme (protein) in this system were found to be of high quality and to be reducible by use of standard crystallographic software.

Discovery of novel inhibitors for DHODH via virtual screening and X-ray crystallographic structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLean, Larry R.; Zhang, Ying; Degnen, William

2010-10-28

Amino-benzoic acid derivatives 1-4 were found to be inhibitors for DHODH by virtual screening, biochemical, and X-ray crystallographic studies. X-ray structures showed that 1 and 2 bind to DHODH as predicted by virtual screening, but 3 and 4 were found to be structurally different from the corresponding compounds initially identified by virtual screening.

Investigation of grain-scale microstructural variability in tantalum using crystal plasticity-finite element simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, Hojun; Dingreville, Rémi; Deibler, Lisa A.

In this research, a crystal plasticity-finite element (CP-FE) model is used to investigate the effects of microstructural variability at a notch tip in tantalum single crystals and polycrystals. It is shown that at the macroscopic scale, the mechanical response of single crystals is sensitive to the crystallographic orientation while the response of polycrystals shows relatively small susceptibility to it. However, at the microscopic scale, the local stress and strain fields in the vicinity of the crack tip are completely determined by the local crystallographic orientation at the crack tip for both single and polycrystalline specimens with similar mechanical field distributions.more » Variability in the local metrics used (maximum von Mises stress and equivalent plastic strain at 3% deformation) for 100 different realizations of polycrystals fluctuates by up to a factor of 2–7 depending on the local crystallographic texture. Comparison with experimental data shows that the CP model captures variability in stress–strain response of polycrystals that can be attributed to the grain-scale microstructural variability. In conclusion, this work provides a convenient approach to investigate fluctuations in the mechanical behavior of polycrystalline materials induced by grain morphology and crystallographic orientations.« less

Mechanical properties of niobium radio-frequency cavities

DOE PAGES

Ciovati, Gianluigi; Dhakal, Pashupati; Matalevich, Joseph R.; ...

2015-07-02

Radio-frequency cavities made of bulk niobium are one of the components used in modern particle accelerators. The mechanical stability is an important aspect of cavity design, which typically relies on finite-element analysis simulations using material properties from tensile tests on sample. This contribution presents the results of strain and resonant frequency measurements as a function of a uniform pressure up to 722 kPa, applied to single-cell niobium cavities with different crystallographic structure, purity and treatments. In addition, burst tests of high-purity multi-cell cavities with different crystallographic structure have been conducted up to the tensile strength of the material. Finite-element analysismore » of the single-cell cavity geometry is in good agreement with the observed behavior in the elastic regime assuming a Young's modulus value of 88.5 GPa and a Poisson's ratio of 0.4, regardless of crystallographic structure, purity or treatment. However, the measured yield strength and tensile strength depend on crystallographic structure, material purity and treatment. In particular, the results from this study show that the mechanical properties of niobium cavities with large crystals are comparable to those of cavities made of fine-grain niobium.« less

Investigation of grain-scale microstructural variability in tantalum using crystal plasticity-finite element simulations

DOE PAGES

Lim, Hojun; Dingreville, Rémi; Deibler, Lisa A.; ...

2016-02-27

In this research, a crystal plasticity-finite element (CP-FE) model is used to investigate the effects of microstructural variability at a notch tip in tantalum single crystals and polycrystals. It is shown that at the macroscopic scale, the mechanical response of single crystals is sensitive to the crystallographic orientation while the response of polycrystals shows relatively small susceptibility to it. However, at the microscopic scale, the local stress and strain fields in the vicinity of the crack tip are completely determined by the local crystallographic orientation at the crack tip for both single and polycrystalline specimens with similar mechanical field distributions.more » Variability in the local metrics used (maximum von Mises stress and equivalent plastic strain at 3% deformation) for 100 different realizations of polycrystals fluctuates by up to a factor of 2–7 depending on the local crystallographic texture. Comparison with experimental data shows that the CP model captures variability in stress–strain response of polycrystals that can be attributed to the grain-scale microstructural variability. In conclusion, this work provides a convenient approach to investigate fluctuations in the mechanical behavior of polycrystalline materials induced by grain morphology and crystallographic orientations.« less

Quantum crystallographic charge density of urea

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c =more » 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.« less

Mineralogical, crystallographic and morphological characteristics of natural kaolins from the Ivory Coast (West Africa)

NASA Astrophysics Data System (ADS)

Sei, J.; Morato, F.; Kra, G.; Staunton, S.; Quiquampoix, H.; Jumas, J. C.; Olivier-Fourcade, J.

2006-10-01

Thirteen clay samples from four deposits in the Ivory Coast (West Africa) were studied using X-ray diffraction, thermogravimetric analysis and chemical analysis. Mineralogical, crystallographic and morphological characteristics of these samples are given. Kaolinite is the principal mineral but other minerals are present in small quantities: illite, quartz, anatase and iron oxides (oxides and oxyhydroxides). The crystallographic, morphological and surface characteristics are influenced by the presence of these impurities. In particular, the presence of iron oxides was associated with reduced structural ordering and thermal stability of kaolinite and increased specific surface area. These clays could be used in the ceramics industry to make tiles and bricks, and also in agronomy as supports for chemical fertilizers or for environmental protection by immobilising potentially toxic waste products.

Identification, display, and use of symmetry elements in atomic and electronic structure models.

PubMed

Khosrovani, N; Kung, P W; Freeman, C M; Gorman, A M; Kölmel, C M; Levine, S M; Newsam, J M

1999-01-01

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Determining crystal structures through crowdsourcing and coursework

PubMed Central

Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

2016-01-01

We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

On three-dimensional misorientation spaces

PubMed Central

Bennett, Robbie J.; Vukmanovic, Zoja; Solano-Alvarez, Wilberth; Lainé, Steven J.; Einsle, Joshua F.; Midgley, Paul A.; Rae, Catherine M. F.; Hielscher, Ralf

2017-01-01

Determining the local orientation of crystals in engineering and geological materials has become routine with the advent of modern crystallographic mapping techniques. These techniques enable many thousands of orientation measurements to be made, directing attention towards how such orientation data are best studied. Here, we provide a guide to the visualization of misorientation data in three-dimensional vector spaces, reduced by crystal symmetry, to reveal crystallographic orientation relationships. Domains for all point group symmetries are presented and an analysis methodology is developed and applied to identify crystallographic relationships, indicated by clusters in the misorientation space, in examples from materials science and geology. This analysis aids the determination of active deformation mechanisms and evaluation of cluster centres and spread enables more accurate description of transformation processes supporting arguments regarding provenance. PMID:29118660

Role of Different Kinds of Boundaries Against Cleavage Crack Propagation in Low-Temperature Embrittlement of Low-Carbon Martensitic Steel

NASA Astrophysics Data System (ADS)

Tsuboi, Mizuki; Shibata, Akinobu; Terada, Daisuke; Tsuji, Nobuhiro

2017-07-01

The present paper investigated the relationship between low-temperature embrittlement and microstructure of lath martensite in a low-carbon steel from both microstructural and crystallographic points of view. The fracture surface of the specimen after the miniaturized Charpy impact test at 98 K (-175 °C) mainly consisted of cleavage fracture facets parallel to crystallographic {001} planes of martensite. Through the crystallographic orientation analysis of micro-crack propagation, we found that the boundaries which separated different martensite variants having large misorientation angles of {001} cleavage planes could inhibit crack propagation. It was then concluded that the size of the aggregations of martensite variants belonging to the same Bain deformation group could control the low-temperature embrittlement of martensitic steels.

Crystallographic Characterization on Polycrystalline Ni-Mn-Ga Alloys with Strong Preferred Orientation

PubMed Central

Li, Zongbin; Yang, Bo; Zou, Naifu; Zhang, Yudong; Esling, Claude; Gan, Weimin; Zhao, Xiang; Zuo, Liang

2017-01-01

Heusler type Ni-Mn-Ga ferromagnetic shape memory alloys can demonstrate excellent magnetic shape memory effect in single crystals. However, such effect in polycrystalline alloys is greatly weakened due to the random distribution of crystallographic orientation. Microstructure optimization and texture control are of great significance and challenge to improve the functional behaviors of polycrystalline alloys. In this paper, we summarize our recent progress on the microstructure control in polycrystalline Ni-Mn-Ga alloys in the form of bulk alloys, melt-spun ribbons and thin films, based on the detailed crystallographic characterizations through neutron diffraction, X-ray diffraction and electron backscatter diffraction. The presented results are expected to offer some guidelines for the microstructure modification and functional performance control of ferromagnetic shape memory alloys. PMID:28772826

A crystallographic perspective on sharing data and knowledge

NASA Astrophysics Data System (ADS)

Bruno, Ian J.; Groom, Colin R.

2014-10-01

The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices.

Crystallization and preliminary crystallographic study of 3 alpha, 20 beta-hydroxysteroid dehydrogenase from Streptomyces hydrogenans.

PubMed

Fitzgerald, P M; Duax, W L; Punzi, J S; Orr, J C

1984-05-15

3 alpha, 20 beta-Hydroxysteroid dehydrogenase, an NADH-dependent oxidoreductase isolated from Streptomyces hydrogenans , is a tetramer containing four subunits each of Mr 25,000. The enzyme has been crystallized by the vapor diffusion technique using either phosphate or borate buffered ammonium sulfate (pH between 6.0 and 8.7) as the precipitant. The crystals are hexagonal bipyramids ; they have the symmetry of space group P6(4)22 (or P6(2)22), with unit cell dimensions a = 127.3 A, c = 112.2 A. Volume and density considerations imply that the crystallographic asymmetric unit contains two monomers, and therefore that the tetramer possesses a 2-fold axis of symmetry that is coincident with a crystallographic 2-fold symmetry element.

Crystallographic Stability of Metastable Phase Formed by Containerless Processing in REFeO3 (RE: Rare-Earth Element)

NASA Technical Reports Server (NTRS)

Kuribayashi, Kazuhiko; Kumar, M. S. Vijaya

2012-01-01

Undercooling a melt often facilitates a metastable phase to nucleate preferentially. Although the classical nucleation theory shows that the most critical factor for forming a metastable phase is the interface free energy, the crystallographic stability is also indispensable for the phase to be frozen at ambient temperature. In compound materials such as oxides, authors have suggested that the decisive factors for forming a critical nucleus are not only the free energy difference but also the difference of the entropy of fusion between stable and metastable phases. In the present study, using REFeO3 (RE: rare-earth element) as a model material, we investigate the formation of a metastable phase from undercooled melts with respect to the competitive nucleation and crystallographical stabilities of both phases.

Conventional and Eccentric Uses of Crystallographic Databases in Practical Materials Identification Problems

PubMed Central

Kaduk, James A.

1996-01-01

The crystallographic databases are powerful and cost-effective tools for solving materials identification problems, both individually and in combination. Examples of the conventional and unconventional use of the databases in solving practical problems involving organic, coordination, and inorganic compounds are provided. The creation and use of fully-relational versions of the Powder Diffraction File and NIST Crystal Data are described. PMID:27805165

Displacive Transformation in Ceramics

DTIC Science & Technology

1994-02-28

product However, the evidence here is thin because no other interface which, during transformation movement, pro - crystallographic data were used other... con - and the parent phase. stants c and a change abruptly and the structure becomles The phenomenological crystallographic theory of cubic. Since the...detectable negative volume change near T,, PbTiO3 Pro * vides a more sensitve indication of the role of lattice vari- Department of Matcrials Science

Crystallography of refractory metal nuggets in carbonaceous chondrites: A transmission Kikuchi diffraction approach

NASA Astrophysics Data System (ADS)

Daly, Luke; Bland, Phil A.; Dyl, Kathryn A.; Forman, Lucy V.; Saxey, David W.; Reddy, Steven M.; Fougerouse, Denis; Rickard, William D. A.; Trimby, Patrick W.; Moody, Steve; Yang, Limei; Liu, Hongwei; Ringer, Simon P.; Saunders, Martin; Piazolo, Sandra

2017-11-01

Transmission Kikuchi diffraction (TKD) is a relatively new technique that is currently being developed for geological sample analysis. This technique utilises the transmission capabilities of a scanning electron microscope (SEM) to rapidly and accurately map the crystallographic and geochemical features of an electron transparent sample. TKD uses a similar methodology to traditional electron backscatter diffraction (EBSD), but is capable of achieving a much higher spatial resolution (5-10 nm) (Trimby, 2012; Trimby et al., 2014). Here we apply TKD to refractory metal nuggets (RMNs) which are micrometre to sub-micrometre metal alloys composed of highly siderophile elements (HSEs) found in primitive carbonaceous chondrite meteorites. TKD allows us to analyse RMNs in situ, enabling the characterisation of nanometre-scale variations in chemistry and crystallography, whilst preserving their spatial and crystallographic context. This provides a complete representation of each RMN, permitting detailed interpretation of their formation history. We present TKD analysis of five transmission electron microscopy (TEM) lamellae containing RMNs coupled with EBSD and TEM analyses. These analyses revealed textures and relationships not previously observed in RMNs. These textures indicate some RMNs experienced annealing, forming twins. Some RMNs also acted as nucleation centres, and formed immiscible metal-silicate fluids. In fact, each RMN analysed in this study had different crystallographic textures. These RMNs also had heterogeneous compositions, even between RMNs contained within the same inclusion, host phase and even separated by only a few nanometres. Some RMNs are also affected by secondary processes at low temperature causing exsolution of molybdenite. However, most RMNs had crystallographic textures indicating that the RMN formed prior to their host inclusion. TKD analyses reveal most RMNs have been affected by processing in the protoplanetary disk. Despite this alteration, RMNs still preserve primary crystallographic textures and heterogeneous chemical signatures. This heterogeneity in crystallographic relationships, which mostly suggest that RMNs pre-date their host, is consistent with the idea that there is not a dominant RMN forming process. Each RMN has experienced a complex history, supporting the suggestion of Daly et al. (2017), that RMNs may preserve a diverse pre-solar chemical signature inherited from the Giant Molecular Cloud.

Sparkle/AM1 Parameters for the Modeling of Samarium(III) and Promethium(III) Complexes.

PubMed

Freire, Ricardo O; da Costa, Nivan B; Rocha, Gerd B; Simas, Alfredo M

2006-01-01

The Sparkle/AM1 model is extended to samarium(III) and promethium(III) complexes. A set of 15 structures of high crystallographic quality (R factor < 0.05 Å), with ligands chosen to be representative of all samarium complexes in the Cambridge Crystallographic Database 2004, CSD, with nitrogen or oxygen directly bonded to the samarium ion, was used as a training set. In the validation procedure, we used a set of 42 other complexes, also of high crystallographic quality. The results show that this parametrization for the Sm(III) ion is similar in accuracy to the previous parametrizations for Eu(III), Gd(III), and Tb(III). On the other hand, promethium is an artificial radioactive element with no stable isotope. So far, there are no promethium complex crystallographic structures in CSD. To circumvent this, we confirmed our previous result that RHF/STO-3G/ECP, with the MWB effective core potential (ECP), appears to be the most efficient ab initio model chemistry in terms of coordination polyhedron crystallographic geometry predictions from isolated lanthanide complex ion calculations. We thus generated a set of 15 RHF/STO-3G/ECP promethium complex structures with ligands chosen to be representative of complexes available in the CSD for all other trivalent lanthanide cations, with nitrogen or oxygen directly bonded to the lanthanide ion. For the 42 samarium(III) complexes and 15 promethium(III) complexes considered, the Sparkle/AM1 unsigned mean error, for all interatomic distances between the Ln(III) ion and the ligand atoms of the first sphere of coordination, is 0.07 and 0.06 Å, respectively, a level of accuracy comparable to present day ab initio/ECP geometries, while being hundreds of times faster.

Ensemble MD simulations restrained via crystallographic data: Accurate structure leads to accurate dynamics

PubMed Central

Xue, Yi; Skrynnikov, Nikolai R

2014-01-01

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD simulation of protein crystal is essentially an ensemble simulation involving multiple protein molecules in a crystal unit cell (or a block of unit cells). To ensure that average protein coordinates remain correct during the simulation, we introduced crystallography-based restraints into the MD protocol. Because these restraints are aimed at the ensemble-average structure, they have only minimal impact on conformational dynamics of the individual protein molecules. So long as the average structure remains reasonable, the proteins move in a native-like fashion as dictated by the original force field. To validate this approach, we have used the data from solid-state NMR spectroscopy, which is the orthogonal experimental technique uniquely sensitive to protein local dynamics. The new method has been tested on the well-established model protein, ubiquitin. The ensemble-restrained MD simulations produced lower crystallographic R factors than conventional simulations; they also led to more accurate predictions for crystallographic temperature factors, solid-state chemical shifts, and backbone order parameters. The predictions for 15N R1 relaxation rates are at least as accurate as those obtained from conventional simulations. Taken together, these results suggest that the presented trajectories may be among the most realistic protein MD simulations ever reported. In this context, the ensemble restraints based on high-resolution crystallographic data can be viewed as protein-specific empirical corrections to the standard force fields. PMID:24452989

Microstructure and crystallographic texture of pure titanium parts generated by laser additive manufacturing

NASA Astrophysics Data System (ADS)

Arias-González, Felipe; del Val, Jesús; Comesaña, Rafael; Penide, Joaquín; Lusquiños, Fernando; Quintero, Félix; Riveiro, Antonio; Boutinguiza, Mohamed; Gil, Francisco Javier; Pou, Juan

2018-01-01

In this paper, the microstructure and crystallographic texture of pure Ti thin walls generated by Additive Manufacturing based on Laser Cladding (AMLC) are analyzed in depth. From the results obtained, it is possible to better understand the AMLC process of pure titanium. The microstructure observed in the samples consists of large elongated columnar prior β grains which have grown epitaxially from the substrate to the top, in parallel to the building direction. Within the prior β grains, α-Ti lamellae and lamellar colonies are the result of cooling from above the β-transus temperature. This transformation follows the Burgers relationship and the result is a basket-weave microstructure with a strong crystallographic texture. Finally, a thermal treatment is proposed to transform the microstructure of the as-deposited samples into an equiaxed microstructure of α-Ti grains.

Surface crystallographic structures of cellulose nanofiber films and overlayers of pentacene

NASA Astrophysics Data System (ADS)

Nakayama, Yasuo; Mori, Toshiaki; Tsuruta, Ryohei; Yamanaka, Soichiro; Yoshida, Koki; Imai, Kento; Koganezawa, Tomoyuki; Hosokai, Takuya

2018-03-01

Cellulose nanofibers or nanocellulose is a promising recently developed biomass and biodegradable material used for various applications. In order to utilize this material as a substrate in organic electronic devices, thorough understanding of the crystallographic structures of the surfaces of the nanocellulose composites and of their interfaces with organic semiconductor molecules is essential. In this work, surface crystallographic structures of nanocellulose films (NCFs) and overlayers of pentacene were investigated by two-dimensional grazing-incidence X-ray diffraction. The NCFs are found to crystallize on solid surfaces with the crystal lattice preserving the same structure of the known bulk phase, whereas distortion of interchain packing toward the surface normal direction is suggested. The pentacene overlayers on the NCFs are found to form the thin-film phase with an in-plane mean crystallite size of over 10 nm.

Impact of the Crystallite Orientation Distribution on Exciton Transport in Donor-Acceptor Conjugated Polymers.

PubMed

Ayzner, Alexander L; Mei, Jianguo; Appleton, Anthony; DeLongchamp, Dean; Nardes, Alexandre; Benight, Stephanie; Kopidakis, Nikos; Toney, Michael F; Bao, Zhenan

2015-12-30

Conjugated polymers are widely used materials in organic photovoltaic devices. Owing to their extended electronic wave functions, they often form semicrystalline thin films. In this work, we aim to understand whether distribution of crystallographic orientations affects exciton diffusion using a low-band-gap polymer backbone motif that is representative of the donor/acceptor copolymer class. Using the fact that the polymer side chain can tune the dominant crystallographic orientation in the thin film, we have measured the quenching of polymer photoluminescence, and thus the extent of exciton dissociation, as a function of crystal orientation with respect to a quenching substrate. We find that the crystallite orientation distribution has little effect on the average exciton diffusion length. We suggest several possibilities for the lack of correlation between crystallographic texture and exciton transport in semicrystalline conjugated polymer films.

Orientational anisotropy and interfacial transport in polycrystals

NASA Astrophysics Data System (ADS)

Moghadam, M. M.; Rickman, J. M.; Harmer, M. P.; Chan, H. M.

2016-04-01

Interfacial diffusion is governed to a large degree by geometric parameters that are determined by crystallographic orientation. In this study, we assess the impact of orientational anisotropy on mass transport at internal interfaces, focusing on the role of preferred crystallographic orientation (i.e., texture) on mass diffusion in a polycrystal. More specifically, we perform both numerical and analytical studies of steady-state diffusion for polycrystals having various grain-orientation distributions. By relating grain misorientation to grain-boundary energies and, via the Borisov relation, to the diffusivity, we link microstructure variability to kinetics. Our aim is to correlate shape features of the orientation distribution, such as the location and shapes of peaks, with the calculated effective diffusivity. Finally, we discuss the role of crystallographic constraints, such as those associated with grain junctions, in determining the effective diffusivity of a polycrystal.

Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.

PubMed

Huschmann, Franziska U; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S; Mueller, Uwe

2016-05-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein-ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin-fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity.

Structures of endothiapepsin–fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library

PubMed Central

Huschmann, Franziska U.; Linnik, Janina; Sparta, Karine; Ühlein, Monika; Wang, Xiaojie; Metz, Alexander; Schiebel, Johannes; Heine, Andreas; Klebe, Gerhard; Weiss, Manfred S.; Mueller, Uwe

2016-01-01

Crystallographic screening of the binding of small organic compounds (termed fragments) to proteins is increasingly important for medicinal chemistry-oriented drug discovery. To enable such experiments in a widespread manner, an affordable 96-compound library has been assembled for fragment screening in both academia and industry. The library is selected from already existing protein–ligand structures and is characterized by a broad ligand diversity, including buffer ingredients, carbohydrates, nucleotides, amino acids, peptide-like fragments and various drug-like organic compounds. When applied to the model protease endothiapepsin in a crystallographic screening experiment, a hit rate of nearly 10% was obtained. In comparison to other fragment libraries and considering that no pre-screening was performed, this hit rate is remarkably high. This demonstrates the general suitability of the selected compounds for an initial fragment-screening campaign. The library composition, experimental considerations and time requirements for a complete crystallographic fragment-screening campaign are discussed as well as the nine fully refined obtained endothiapepsin–fragment structures. While most of the fragments bind close to the catalytic centre of endothiapepsin in poses that have been observed previously, two fragments address new sites on the protein surface. ITC measurements show that the fragments bind to endothiapepsin with millimolar affinity. PMID:27139825

Ensembles generated from crystal structures of single distant homologues solve challenging molecular-replacement cases in AMPLE.

PubMed

Rigden, Daniel J; Thomas, Jens M H; Simkovic, Felix; Simpkin, Adam; Winn, Martyn D; Mayans, Olga; Keegan, Ronan M

2018-03-01

Molecular replacement (MR) is the predominant route to solution of the phase problem in macromolecular crystallography. Although routine in many cases, it becomes more effortful and often impossible when the available experimental structures typically used as search models are only distantly homologous to the target. Nevertheless, with current powerful MR software, relatively small core structures shared between the target and known structure, of 20-40% of the overall structure for example, can succeed as search models where they can be isolated. Manual sculpting of such small structural cores is rarely attempted and is dependent on the crystallographer's expertise and understanding of the protein family in question. Automated search-model editing has previously been performed on the basis of sequence alignment, in order to eliminate, for example, side chains or loops that are not present in the target, or on the basis of structural features (e.g. solvent accessibility) or crystallographic parameters (e.g. B factors). Here, based on recent work demonstrating a correlation between evolutionary conservation and protein rigidity/packing, novel automated ways to derive edited search models from a given distant homologue over a range of sizes are presented. A variety of structure-based metrics, many readily obtained from online webservers, can be fed to the MR pipeline AMPLE to produce search models that succeed with a set of test cases where expertly manually edited comparators, further processed in diverse ways with MrBUMP, fail. Further significant performance gains result when the structure-based distance geometry method CONCOORD is used to generate ensembles from the distant homologue. To our knowledge, this is the first such approach whereby a single structure is meaningfully transformed into an ensemble for the purposes of MR. Additional cases further demonstrate the advantages of the approach. CONCOORD is freely available and computationally inexpensive, so these novel methods offer readily available new routes to solve difficult MR cases.

Validation studies of the site-directed docking program LibDock.

PubMed

Rao, Shashidhar N; Head, Martha S; Kulkarni, Amit; LaLonde, Judith M

2007-01-01

The performance of the site-features docking algorithm LibDock has been evaluated across eight GlaxoSmithKline targets as a follow-up to a broad validation study of docking and scoring software (Warren, G. L.; Andrews, W. C.; Capelli, A.; Clarke, B.; Lalonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Walls, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. J. Med. Chem. 2006, 49, 5912-5931). Docking experiments were performed to assess both the accuracy in reproducing the binding mode of the ligand and the retrieval of active compounds in a virtual screening protocol using both the DJD (Diller, D. J.; Merz, K. M., Jr. Proteins 2001, 43, 113-124) and LigScore2 (Krammer, A. K.; Kirchoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. J. Mol. Graphics Modell. 2005, 23, 395-407) scoring functions. This study was conducted using DJD scoring, and poses were rescored using all available scoring functions in the Accelrys LigandFit module, including LigScore2. For six out of eight targets at least 30% of the ligands were docked within a root-mean-square difference (RMSD) of 2.0 A for the crystallographic poses when the LigScore2 scoring function was used. LibDock retrieved at least 20% of active compounds in the top 10% of screened ligands for four of the eight targets in the virtual screening protocol. In both studies the LigScore2 scoring function enhanced the retrieval of crystallographic poses or active compounds in comparison with the results obtained using the DJD scoring function. The results for LibDock accuracy and ligand retrieval in virtual screening are compared to 10 other docking and scoring programs. These studies demonstrate the utility of the LigScore2 scoring function and that LibDock as a feature directed docking method performs as well as docking programs that use genetic/growing and Monte Carlo driven algorithms.

Combined Near and Far Field High Energy Diffraction Microscopy Dataset for Ti-7Al Tensile Specimen Elastically Loaded In Situ

DOE Data Explorer

Turner, Todd J.; Shade, Paul A; Bernier, Joel V.; Li, Shiu Fai; Schuren, Jay C.; Lind, Jonathan F.; Lienert, Ulrich; Kenesei, Peter; Suter, Robert; Blank, Basil; Almer, Jonathan

2016-01-01

We present both near-field HEDM data that maps out the grain morphology and intragranular crystallographic orientations and far-field HEDM data that provides the grain centroid, grain average crystallographic orientation, and grain average elastic strain tensor for each grain. Finally, we provide a finite element mesh that can be utilized to simulate deformation in the volume of this Ti-7Al specimen.

Crystallographic data processing for free-electron laser sources

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, Thomas A., E-mail: taw@physics.org; Barty, Anton; Stellato, Francesco

2013-07-01

A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A processing pipeline for diffraction data acquired using the ‘serial crystallography’ methodology with a free-electron laser source is described with reference to the crystallographic analysis suite CrystFEL and the pre-processing program Cheetah. A detailed analysis of the nature and impact of indexing ambiguities is presented. Simulations of the Monte Carlo integration scheme, which accounts for the partially recorded nature of the diffraction intensities, are presented and show thatmore » the integration of partial reflections could be made to converge more quickly if the bandwidth of the X-rays were to be increased by a small amount or if a slight convergence angle were introduced into the incident beam.« less

Crystal Quality, the Long and the Short of It

NASA Technical Reports Server (NTRS)

Snell, Eddie H.

2004-01-01

The term "crystal quality" is ambiguous and implies different meanings to different crystallographers. For the physical crystallographer who aims to understand long-range aspects of crystal growth mosaicity is one of the leading measures of perfection. For the structural crystallographer and those seeking to understand growth at a short-range, molecular level, the detail in the resulting structure is a key goal. Different quality measures have been developed due to different needs. Each of the measures has advantages and each has limitations. In this talk a sample of these measures will be discussed with particular emphasis applied to their application in the analysis of microgravity grown crystals. The advantages and limitations of each will be discussed. Ultimately, the choice of crystal quality measurement lies in the nature of the question asked. It is scfill to remember that beauty is often in the eye of the beholder.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 7

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan

2007-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids have been produced which diffract X-rays to ∼3.0 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 7 capsids diffract X-rays to ∼3.0 Å resolution. The crystals belong to the rhombohedral space group R3, with unit-cell parameters a = 252.4, c = 591.2 Å in the hexagonal setting. The diffraction data were processed and reduced to an overall completeness of 79.0% and an R{sub merge} of 12.0%. There are three viral capsids in the unit cell. The icosahedral threefold axis is coincident with the crystallographic threefold axis, resulting in one third of amore » capsid (20 monomers) per crystallographic asymmetric unit. The orientation of the viral capsid has been determined by rotation-function searches and is positioned at (0, 0, 0) by packing considerations.« less

Distributed computing for macromolecular crystallography

PubMed Central

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Ballard, Charles

2018-01-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community. PMID:29533240

Distributed computing for macromolecular crystallography.

PubMed

Krissinel, Evgeny; Uski, Ville; Lebedev, Andrey; Winn, Martyn; Ballard, Charles

2018-02-01

Modern crystallographic computing is characterized by the growing role of automated structure-solution pipelines, which represent complex expert systems utilizing a number of program components, decision makers and databases. They also require considerable computational resources and regular database maintenance, which is increasingly more difficult to provide at the level of individual desktop-based CCP4 setups. On the other hand, there is a significant growth in data processed in the field, which brings up the issue of centralized facilities for keeping both the data collected and structure-solution projects. The paradigm of distributed computing and data management offers a convenient approach to tackling these problems, which has become more attractive in recent years owing to the popularity of mobile devices such as tablets and ultra-portable laptops. In this article, an overview is given of developments by CCP4 aimed at bringing distributed crystallographic computations to a wide crystallographic community.

Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

PubMed

Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

2016-01-01

Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

Strain-Detecting Composite Materials

NASA Technical Reports Server (NTRS)

Wallace, Terryl A. (Inventor); Smith, Stephen W. (Inventor); Piascik, Robert S. (Inventor); Horne, Michael R. (Inventor); Messick, Peter L. (Inventor); Alexa, Joel A. (Inventor); Glaessgen, Edward H. (Inventor); Hailer, Benjamin T. (Inventor)

2016-01-01

A composite material includes a structural material and a shape-memory alloy embedded in the structural material. The shape-memory alloy changes crystallographic phase from austenite to martensite in response to a predefined critical macroscopic average strain of the composite material. In a second embodiment, the composite material includes a plurality of particles of a ferromagnetic shape-memory alloy embedded in the structural material. The ferromagnetic shape-memory alloy changes crystallographic phase from austenite to martensite and changes magnetic phase in response to the predefined critical macroscopic average strain of the composite material. A method of forming a composite material for sensing the predefined critical macroscopic average strain includes providing the shape-memory alloy having an austenite crystallographic phase, changing a size and shape of the shape-memory alloy to thereby form a plurality of particles, and combining the structural material and the particles at a temperature of from about 100-700.degree. C. to form the composite material.

From direct-space discrepancy functions to crystallographic least squares.

PubMed

Giacovazzo, Carmelo

2015-01-01

Crystallographic least squares are a fundamental tool for crystal structure analysis. In this paper their properties are derived from functions estimating the degree of similarity between two electron-density maps. The new approach leads also to modifications of the standard least-squares procedures, potentially able to improve their efficiency. The role of the scaling factor between observed and model amplitudes is analysed: the concept of unlocated model is discussed and its scattering contribution is combined with that arising from the located model. Also, the possible use of an ancillary parameter, to be associated with the classical weight related to the variance of the observed amplitudes, is studied. The crystallographic discrepancy factors, basic tools often combined with least-squares procedures in phasing approaches, are analysed. The mathematical approach here described includes, as a special case, the so-called vector refinement, used when accurate estimates of the target phases are available.

The effects of deposition parameters on surface morphology and crystallographic orientation of electroless Ni-B coatings

NASA Astrophysics Data System (ADS)

Bulbul, Ferhat

2011-02-01

Electroless Ni-B coatings were deposited on AISI 304 stainless steels by electroless deposition method, which was performed for nine different test conditions at various levels of temperature, concentration of NaBH4, concentration of NiCl2, and time, using the Taguchi L9(34) experimental method. The effects of deposition parameters on the crystallographic orientation of electroless Ni-B coatings were investigated using SEM and XRD equipment. SEM analysis revealed that the Ni-B coatings developed six types (pea-like, maize-like, primary nodular, blackberry-like or grapes-like, broccoli-like, and cauliflower-like) of morphological structures depending on the deposition parameters. XRD results also showed that these structures exhibited different levels of amorphous character. The concentration of NaBH4 had the most dominant effect on the morphological and crystallographic development of electroless Ni-B coatings.

Epitaxial growth of CZT(S,Se) on silicon

DOEpatents

Bojarczuk, Nestor A.; Gershon, Talia S.; Guha, Supratik; Shin, Byungha; Zhu, Yu

2016-03-15

Techniques for epitaxial growth of CZT(S,Se) materials on Si are provided. In one aspect, a method of forming an epitaxial kesterite material is provided which includes the steps of: selecting a Si substrate based on a crystallographic orientation of the Si substrate; forming an epitaxial oxide interlayer on the Si substrate to enhance wettability of the epitaxial kesterite material on the Si substrate, wherein the epitaxial oxide interlayer is formed from a material that is lattice-matched to Si; and forming the epitaxial kesterite material on a side of the epitaxial oxide interlayer opposite the Si substrate, wherein the epitaxial kesterite material includes Cu, Zn, Sn, and at least one of S and Se, and wherein a crystallographic orientation of the epitaxial kesterite material is based on the crystallographic orientation of the Si substrate. A method of forming an epitaxial kesterite-based photovoltaic device and an epitaxial kesterite-based device are also provided.

Crystallographic control and texture inheritance during mylonitization of coarse grained quartz veins

NASA Astrophysics Data System (ADS)

Ceccato, Alberto; Pennacchioni, Giorgio; Menegon, Luca; Bestmann, Michel

2017-10-01

Quartz veins within Rieserferner pluton underwent deformation during post-magmatic cooling at temperature around 450 °C. Different crystallographic orientations of cm-sized quartz vein crystals conditioned the evolution of microstructures and crystallographic preferred orientations (CPO) during vein-parallel simple shear up to high shear strains (γ ≈ 10). For γ < 2, crystals stretched to ribbons of variable aspect ratios. The highest aspect ratios resulted from {m} glide in ribbons with c-axis sub-parallel to the shear zone vorticity Y-axis. Ribbons with c-axis orthogonal to Y (XZ-type ribbons) were stronger and hardened more quickly: they show lower aspect ratios and fine (grain size 10-20 μm) recrystallization along sets of microshear zones (μSZs) exploiting crystallographic planes. Distortion of XZ-type ribbons and recrystallization preferentially exploited the slip systems with misorientation axis close to Y. New grains of μSZs initiated by subgrain rotation recrystallization (SGR) and thereupon achieved high angle misorientations by a concurrent process of heterogeneous rigid grain rotation around Y associated with the confined shear within the μSZ. Dauphiné twinning occurred pervasively, but did not play a dominant role on μSZ nucleation. Recrystallization became widespread at γ > 2 and pervasive at γ ≈ 10. Ultramylonitic quartz veins are fine grained ( 10 μm, similar to new grains of μSZ) and show a CPO banding resulting in a bulk c-axis CPO with a Y-maximum, as part of a single girdle about orthogonal to the foliation, and orientations at the pole figure periphery at moderate to high angle to the foliation. This bulk CPO derives from steady-state SGR associated with preferential activity, in the different CPO bands, of slip systems generating subgrain boundaries with misorientation axes close to Y. The CPO of individual recrystallized bands is largely inherited from the original crystallographic orientation of the ribbons (and therefore vein crystals) from which they derived. High strain and pervasive recrystallization were not enough to reset the initial crystallographic heterogeneity and this CPO memory is explained by the dominance of SGR. This contrast with experimental observation of a rapid erasure of a pristine CPO by cannibalism from grains with the most favourably oriented slip system under dominant grain boundary migration recrystallization.

Evolution of the viscosity of Earth's upper mantle: Grain-boundary sliding and the role of microstructure in olivine deformation

NASA Astrophysics Data System (ADS)

Hansen, Lars N.

Many features of plate tectonics cannot be explained with standard rheological models of the upper mantle. In particular, the localization of deformation at plate boundaries requires the viscosity of the constituent rocks to evolve spatially and temporally. Such rheological complexity may arise from changing microstructural state variables (e.g., grain size and crystallographic-fabric strength), but the degree to which microstructure contributes to the evolution of viscosity is unclear given our current understanding of deformation mechanisms in mantle minerals. Dislocation-accommodated grain-boundary sliding (GBS) is a potentially critical mechanism for localizing deformation in olivine because it imparts a sensitivity of the viscosity to the state of the microstructure while simultaneously providing mechanisms for changing the microstructure. However, many details of GBS in olivine are currently unknown including 1) the magnitude of the sensitivity of strain rate to crystallographic fabric and grain size, 2) the strength of the crystallographic fabrics produced, and 3) the anisotropy in viscosity of polycrystalline aggregates. Detailed knowledge of these unknowns is necessary to assess the importance of microstructural evolution in the operation of plate tectonics. This dissertation investigates the details of GBS in olivine through four sets of laboratory-based experiments. In Chapter 2, triaxial compressive creep experiments on aggregates of San Carlos olivine are used to develop a flow law for olivine deforming by GBS. Extrapolations of strain rate to geological conditions using the derived flow law indicate that GBS is the dominant deformation mechanism throughout the uppermost mantle. Crystallographic fabrics observed in deformed samples are consistent with upper-mantle seismic anisotropy. In Chapter 3, torsion experiments on iron-rich olivine are used to determine the rheological behavior of olivine deforming by GBS at large strains. The sensitivity of the strain rate to grain size and stress is demonstrated to be consistent with low-strain experiments. Additionally, the sensitivity of strain rate to the development of a crystallographic fabric is determined. Constitutive relationships including microstructural evolution are developed that accurately predict the observed stress as a function of strain. The results of Chapter 3 confirm that significant weakening is associated with both grain-size reduction and crystallographic-fabric development. In Chapter 4, torsion experiments on iron-rich olivine are used to determine if microstructural evolution can lead to strain localization. Experiments were conducted with either constant-strain-rate or constant-stress boundary conditions. Localization is only observed in samples deformed at constant-stress, which suggests boundary conditions affect the critical size of strength perturbation necessary for localization to occur. Strain localization is correlated with fine-grained regions, and a feedback mechanism between grain-size reduction and strain rate is proposed. In Chapter 5, both torsion and tension experiments are used to assess the mechanical anisotropy of previously deformed samples. Based on the direction of the applied stress relative to the orientation of a pre-existing crystallographic fabric, the viscosity is demonstrated to vary by over an order of magnitude. This observation suggests deformation can localize in regions that were previously deformed and retained a strong crystallographic fabric. The results of this dissertation elucidate the interplay between microstructure and deformation of olivine in the GBS regime. Because the viscosity of olivine-rich rocks deforming by GBS is dependent on both grain size and crystallographic fabric, heterogeneities in these microstructural parameters can lead to spatial and temporal variations in viscosity, possibly explaining the large-scale patterns of deformation in the upper mantle. Future numerical simulations can test the importance of microstructure in geodynamic processes by incorporating the constitutive relationships outlined in this dissertation.

A numerical investigation of grain shape and crystallographic texture effects on the plastic strain localization in friction stir weld zones

NASA Astrophysics Data System (ADS)

Romanova, V.; Balokhonov, R.; Batukhtina, E.; Shakhidjanov, V.

2015-10-01

Crystal plasticity approaches were adopted to build models accounting for the microstructure and texture observed in different friction stir weld zones. To this end, a numerical investigation of crystallographic texture and grain shape effects on the plastic strain localization in a friction stir weld of an aluminum-base alloy was performed. The presence of texture was found to give rise to pronounced mesoscale plastic strain localization.

Data-driven high-throughput prediction of the 3-D structure of small molecules: review and progress. A response to the letter by the Cambridge Crystallographic Data Centre.

PubMed

Baldi, Pierre

2011-12-27

A response is presented to sentiments expressed in "Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress. A Response from The Cambridge Crystallographic Data Centre", recently published in the Journal of Chemical Information and Modeling, (1) which may give readers a misleading impression regarding significant impediments to scientific research posed by the CCDC.

Corrosion in drinking water pipes: the importance of green rusts.

PubMed

Swietlik, Joanna; Raczyk-Stanisławiak, Urszula; Piszora, Paweł; Nawrocki, Jacek

2012-01-01

Complex crystallographic composition of the corrosion products is studied by diffraction methods and results obtained after different pre-treatment of samples are compared. The green rusts are found to be much more abundant in corrosion scales than it has been assumed so far. The characteristic and crystallographic composition of corrosion scales and deposits suspended in steady waters were analyzed by X-ray diffraction (XRD). The necessity of the examination of corrosion products in the wet conditions is indicated. The drying of the samples before analysis is shown to substantially change the crystallographic phases originally present in corrosion products. On sample drying the unstable green rusts is converted into more stable phases such as goethite and lepidocrocite, while the content of magnetite and siderite decreases. Three types of green rusts in wet materials sampled from tubercles are identified. Unexpectedly, in almost all corrosion scale samples significant amounts of the least stable green rust in chloride form was detected. Analysis of corrosion products suspended in steady water, which remained between tubercles and possibly in their interiors, revealed complex crystallographic composition of the sampled material. Goethite, lepidocrocite and magnetite as well as low amounts of siderite and quartz were present in all samples. Six different forms of green rusts were identified in the deposits separated from steady waters and the most abundant was carbonate green rust GR(CO(3)(2-))(I). Copyright © 2011 Elsevier Ltd. All rights reserved.

Study on the crystallographic orientation relationship and formation mechanism of reversed austenite in economical Cr12 super martensitic stainless steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ye, Dong; Li, Shaohong; Li, Jun

Effect of carbides and crystallographic orientation relationship on the formation mechanism of reversed austenite of economical Cr12 super martensitic stainless steel (SMSS) has been investigated mainly by transmission electron microscopy (TEM) and electron backscatter diffraction (EBSD). The results indicate that the M{sub 23}C{sub 6} precipitation and the formation of the reversed austenite have the interaction effect during tempering process in SMSS. The reversed austenite forms intensively at the sub-block boundary and the lath boundary within a misorientation range of 0–60°. M{sub 23}C{sub 6} has the same crystallographic orientation relationship with reversed austenite. There are two different kinds of formation modesmore » for reversed austenite. One is a nondiffusional shear reversion; the other is a diffusion transformation. Both are strictly limited by crystallographic orientation relationship. The austenite variants are limited to two kinds within one packet and five kinds within one prior austenite grain. - Highlights: • Reversed austenite forms at martensite boundaries with misorientation of 0–60° • M{sub 23}C{sub 6} precipitation and reversed austenite formation have the interaction effect. • Two austenite variants with different orientations can be formed inside a packet. • Two reversed austenite formation modes: shear reversion; diffusion transformation.« less

Homology‐based hydrogen bond information improves crystallographic structures in the PDB

PubMed Central

van Beusekom, Bart; Touw, Wouter G.; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L.; Perrakis, Anastassis

2017-01-01

Abstract The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H‐bond) distances as a source of information. However, H‐bond restraints can improve structures at low resolution where diffraction data are limited. To improve low‐resolution structure refinement, we present methods for deriving H‐bond information either globally from well‐refined high‐resolution structures from the PDB‐REDO databank, or specifically from on‐the‐fly constructed sets of homologous high‐resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low‐resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB‐REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. PMID:29168245

Homology-based hydrogen bond information improves crystallographic structures in the PDB.

PubMed

van Beusekom, Bart; Touw, Wouter G; Tatineni, Mahidhar; Somani, Sandeep; Rajagopal, Gunaretnam; Luo, Jinquan; Gilliland, Gary L; Perrakis, Anastassis; Joosten, Robbie P

2018-03-01

The Protein Data Bank (PDB) is the global archive for structural information on macromolecules, and a popular resource for researchers, teachers, and students, amassing more than one million unique users each year. Crystallographic structure models in the PDB (more than 100,000 entries) are optimized against the crystal diffraction data and geometrical restraints. This process of crystallographic refinement typically ignored hydrogen bond (H-bond) distances as a source of information. However, H-bond restraints can improve structures at low resolution where diffraction data are limited. To improve low-resolution structure refinement, we present methods for deriving H-bond information either globally from well-refined high-resolution structures from the PDB-REDO databank, or specifically from on-the-fly constructed sets of homologous high-resolution structures. Refinement incorporating HOmology DErived Restraints (HODER), improves geometrical quality and the fit to the diffraction data for many low-resolution structures. To make these improvements readily available to the general public, we applied our new algorithms to all crystallographic structures in the PDB: using massively parallel computing, we constructed a new instance of the PDB-REDO databank (https://pdb-redo.eu). This resource is useful for researchers to gain insight on individual structures, on specific protein families (as we demonstrate with examples), and on general features of protein structure using data mining approaches on a uniformly treated dataset. © 2017 The Protein Society.

Five-parameter crystallographic characteristics of the interfaces formed during ferrite to austenite transformation in a duplex stainless steel

NASA Astrophysics Data System (ADS)

Haghdadi, N.; Cizek, P.; Hodgson, P. D.; Tari, V.; Rohrer, G. S.; Beladi, H.

2018-05-01

The crystallography of interfaces in a duplex stainless steel having an equiaxed microstructure produced through the ferrite to austenite diffusive phase transformation has been studied. The five-parameter interface character distribution revealed a high anisotropy in habit planes for the austenite-ferrite and austenite-austenite interfaces for different lattice misorientations. The austenite and ferrite habit planes largely terminated on (1 1 1) and (1 1 0) planes, respectively, for the austenite-ferrite interfaces associated with Kurdjumov-Sachs (K-S) and Nishiyama-Wasserman (N-W) orientation relationships. This was mostly attributed to the crystallographic preference associated with the phase transformation. For the austenite-ferrite interfaces with orientation relationships which are neither K-S nor N-W, both austenite and ferrite habit planes had (1 1 1) orientations. Σ3 twin boundaries comprised the majority of austenite-austenite interfaces, mostly showing a pure twist character and terminating on (1 1 1) planes due to the minimum energy configuration. The second highest populated austenite-austenite boundary was Σ9, which tended to have grain boundary planes in the tilt zone due to the geometrical constraints. Furthermore, the intervariant crystallographic plane distribution associated with the K-S orientation relationship displayed a general tendency for the austenite habit planes to terminate with the (1 1 1) orientation, mainly due to the crystallographic preference associated with the phase transformation.

Automated side-chain model building and sequence assignment by template matching.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

PubMed Central

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

2015-01-01

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering. PMID:25945583

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

DOE Office of Scientific and Technical Information (OSTI.GOV)

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams.

PubMed

Coquelle, Nicolas; Brewster, Aaron S; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques Philippe

2015-05-01

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

DOE PAGES

Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; ...

2015-04-25

High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Åmore » resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.« less

Structure-based virtual screening efforts against HIV-1 reverse transcriptase to introduce the new potent non-nucleoside reverse transcriptase inhibitor

NASA Astrophysics Data System (ADS)

Hosseini, Yaser; Mollica, Adriano; Mirzaie, Sako

2016-12-01

The human immunodeficiency virus (HIV) which is strictly related to the development of AIDS, is treated by a cocktail of drugs, but due its high propensity gain drug resistance, the rational development of new medicine is highly desired. Among the different mechanism of action we selected the reverse transcriptase (RT) inhibition, for our studies. With the aim to identify new chemical entities to be used for further rational drug design, a set of 3000 molecules from the Zinc Database have been screened by docking experiments using AutoDock Vina software. The best ranked compounds with respect of the crystallographic inhibitor MK-4965 resulted to be five compounds, and the best among them was further tested by molecular dynamics (MD) simulation. Our results indicate that comp1 has a stronger interaction with the subsite p66 of RT than MK-4965 and that both are able to stabilize specific conformational changes of the RT 3D structure, which may explain their activity as inhibitors. Therefore comp1 could be a good candidate for biological tests and further development.

Virtual screening and pharmacophore design for a novel theoretical inhibitor of macrophage stimulating factor as a metastatic agent.

PubMed

Torktaz, Ibrahim; Mohamadhashem, Faezeh; Esmaeili, Abolghasem; Behjati, Mohaddeseh; Sharifzadeh, Sara

2013-01-01

Metastasis is a crucial aspect of cancer. Macrophage stimulating protein (MSP) is a single chain protein and can be cleaved by serum proteases. MSP has several roles in metastasis. In this in silico study, MSP as a metastatic agent was considered as a drug target. Crystallographic structure of MSP was retrieved from protein data bank. To find a chemical inhibitor of MSP, a library of KEGG compounds was screened and 1000 shape complemented ligands were retrieved with FindSite algorithm. Molegro Virtual Docker (MVD) software was used for docking simulation of shape complemented ligands against MSP. Moldock score was used as scoring function for virtual screening and potential inhibitors with more negative binding energy were obtained. PLANS scoring function was used for revaluation of virtual screening data. The top found chemical had binding affinity of -183.55 based on MolDock score and equal to -66.733 PLANTs score to MSP structure. Based on pharmacophore model of potential inhibitor, this study suggests that the chemical which was found in this research and its derivate can be used for subsequent laboratory studies.

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Specific features of electron scattering in uniaxially deformed n-Ge single crystals in the presence of radiation defects

NASA Astrophysics Data System (ADS)

Luniov, S. V.; Zimych, A. I.; Nazarchuk, P. F.; Maslyuk, V. T.; Megela, I. G.

2016-12-01

Temperature dependencies for concentration of electrons and the Hall mobility for unirradiated and irradiated by the flow of electrons ? single crystals ?, with the energy of ?, for different values of uniaxial pressures along the crystallographic directions ?, ? and ? are obtained on the basis of piezo-Hall effect measurements. Non-typical growth of the Hall mobility of electrons for irradiated single crystals ? in comparison with unirradiated with the increasing of value of uniaxial pressures along the crystallographic directions ? (for the entire range of the investigated temperatures) and ? (to temperatures ?) has been revealed. Such an effect of the Hall mobility increase for uniaxially deformed single crystals ? is explained by the reduction of gradients of a resistance as a result of reduction in the amplitude of a large-scale potential with deformation and concentration of charged A-centers in the process of their recharge by the increasing of uniaxial pressure and consequently the probability of scattering on these centers. Theoretical calculations for temperature dependencies of the Hall mobility for uniaxially deformed single crystals ? in terms of the electrons scattering on the ions of shallow donors, acoustic, optical and intervalley phonons, regions of disordering and large-scale potential is good conformed to the corresponding experimental results at temperatures T<220 K for the case of uniaxial pressures along the crystallographic directions ? and ? and for temperatures ? when the uniaxial pressure is directed along the crystallographic directions ?. The mechanism of electron scattering on a charged radiation defects (which correspond to the deep energy levels of A-centers) 'is turned off' for the given temperatures due to the uniaxial pressure. Reduction of the Hall mobility in transition through a maximum of dependence ? with the increasing temperature for cases of the uniaxial deformation of the irradiated single crystals ? along the crystallographic directions ? and ? is explained by the deforming redistribution of electrons between the minima of conduction band of germanium with different mobility.

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

DOE PAGES

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler; ...

2017-03-31

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Low Loss Substrates for Microwave Applications and Sol-Gel Processing of Superconductors

DTIC Science & Technology

1994-03-31

crystallographic axis normal to solid state technology, in the growth of ferrimagnetic garnets the substrate plane) or. better, in "epitaxial" films (i.e...hay- by liquid phase epitaxy ( LPE ). is from a melt using a para- ing their three crystallographic axes related to those of a magnetic garnet structure...yttrium barium cuprate (YBCO) films and their microwave applications have been carried out. Several promising new hosts such as Sr(All/2Tal/2)03, Sr(Al1

Evidence for Coordination and Redox Changes of Iron in Shocked Feldspar from Synchrotron MicroXANES

NASA Technical Reports Server (NTRS)

Delaney, J. S.; Dyar, M. D.; Hoerz, F.; Johnson, J. R.

2003-01-01

Shock modification of feldspar has been documented and experimentally reproduced in many studies since the recognition of maskelynite in Shergotty. Experimentally shocked feldspar samples have been well studied using chemical and crystallographic techniques. The crystallographic, site-specific characterization of major and minor elements is less well documented. We present early x-ray absorption (XAS) spectral data for a suite of albitite samples that were experimentally shocked at pressures between 17 and 50 Gpa.

Development of Specific Inhibitors for Breast Cancer-Associated Variants of ErbB2

DTIC Science & Technology

2015-10-01

Produce ErbB2 structures for drug-lead identification Months 1-12 Milestone #2: Production of computationally-derived pdb files of the structures of...crystallographic structures of the kinase domain of ErbB2 and its close relative EGFR (ErbB1). The kinase domains of ErbB2 and EGFR are highly...homologous as indicated by a sequence identity of ~ 78%. There are two currently available crystallographic structures of the ErbB2 kinase domain. One is

XAS Characterization of the Zn Site of Non-structural Protein 3 (NS3) from Hepatitis C Virus

NASA Astrophysics Data System (ADS)

Ascone, I.; Nobili, G.; Benfatto, M.; Congiu-Castellano, A.

2007-02-01

XANES spectra of non structural protein 3 (NS3) have been calculated using 4 Zn coordination models from three crystallographic structures in the Protein Data Base (PDB): 1DY9, subunit B, 1CU1 subunit A and B, and 1JXP subunit B. Results indicate that XANES is an appropriate tool to distinguish among them. Experimental XANES spectra have been simulated refining crystallographic data. The model obtained by XAS is compared with the PDB models.

The effect of crystal orientation on the aluminum anodes of the aluminum-air batteries in alkaline electrolytes

NASA Astrophysics Data System (ADS)

Fan, Liang; Lu, Huimin; Leng, Jing; Sun, Zegao; Chen, Chunbo

2015-12-01

Recently, aluminum-air (Al-air) batteries have received attention from researchers as an exciting option for safe and efficient batteries. The electrochemical performance of Aluminum anode remains an active area of investigation. In this paper, the electrochemical properties of polycrystalline Al, Al (001), (110) and (111) single crystals are investigated using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS) in 4 M NaOH and KOH. Hydrogen corrosion rates of the Al anodes are determined by hydrogen collection. Battery performance using the anodes is tested by constant current discharge at 10 mA cm-2. This is the first report showing that the electrochemical properties of Al are closely related to the crystallographic orientation in alkaline electrolytes. The (001) crystallographic plane has good corrosion resistance but (110) is more sensitive. Al (001) single crystals display higher anode efficiency and capacity density. Controlling the crystallographic orientation of the Al anode is another way to improve the performance of Al-air batteries in alkaline electrolytes.

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Angkawidjaja, Clement; You, Dong-Ju; Matsumura, Hiroyoshi

2007-03-01

A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. A family I.3 lipase from Pseudomonas sp. MIS38 was secreted from Escherichia coli cells to the external medium, purified and crystallized and preliminary crystallographic studies were performed. The crystal was grown at 277 K by the hanging-drop vapour-diffusion method. Native X-ray diffraction data were collected to 1.7 Å resolution using synchrotron radiation at station BL38B1, SPring-8. The crystal belongs to space group P2{sub 1}, with unit-cell parameters a = 48.79, b = 84.06,more » c = 87.04 Å. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V{sub M} was calculated to be 2.73 Å{sup 3} Da{sup −1} and the solvent content was 55%.« less

Production, purification, crystallization and preliminary X-ray analysis of adeno-associated virus serotype 8

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lane, Michael Douglas; Nam, Hyun-Joo; Padron, Eric

2005-06-01

The production, purification, crystallization and preliminary X-ray crystallographic analysis of adeno-associated virus serotype 8 is reported. Adeno-associated viruses (AAVs) are actively being developed for clinical gene-therapy applications and the efficiencies of the vectors could be significantly improved by a detailed understanding of their viral capsid structures and the structural determinants of their tissue-transduction interactions. AAV8 is ∼80% identical to the more widely studied AAV2, but its liver-transduction efficiency is significantly greater than that of AAV2 and other serotypes. The production, purification, crystallization and preliminary X-ray crystallographic analysis of AAV8 viral capsids are reported. The crystals diffract X-rays to 3.0 Åmore » resolution using synchrotron radiation and belong to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = 257.5, c = 443.5 Å. The unit cell contains two viral particles, with ten capsid viral protein monomers per crystallographic asymmetric unit.« less

First-principles study of crystallographic slip modes in ω-Zr.

PubMed

Kumar, Anil; Kumar, M Arul; Beyerlein, Irene J

2017-08-21

We use first-principles density functional theory to study the preferred modes of slip in the high-pressure ω phase of Zr. The generalized stacking fault energy surfaces associated with shearing on nine distinct crystallographic slip modes in the hexagonal ω-Zr crystal are calculated, from which characteristics such as ideal shear stress, the dislocation Burgers vector, and possible accompanying atomic shuffles, are extracted. Comparison of energy barriers and ideal shear stresses suggests that the favorable modes are prismatic 〈c〉, prismatic-II [Formula: see text] and pyramidal-II 〈c + a〉, which are distinct from the ground state hexagonal close packed α phase of Zr. Operation of these three modes can accommodate any deformation state. The relative preferences among the identified slip modes are examined using a mean-field crystal plasticity model and comparing the calculated deformation texture with the measurement. Knowledge of the basic crystallographic modes of slip is critical to understanding and analyzing the plastic deformation behavior of ω-Zr or mixed α-ω phase-Zr.

Effect of the sample annealing temperature and sample crystallographic orientation on the charge kinetics of MgO single crystals subjected to keV electron irradiation.

PubMed

Boughariou, A; Damamme, G; Kallel, A

2015-04-01

This paper focuses on the effect of sample annealing temperature and crystallographic orientation on the secondary electron yield of MgO during charging by a defocused electron beam irradiation. The experimental results show that there are two regimes during the charging process that are better identified by plotting the logarithm of the secondary electron emission yield, lnσ, as function of the total trapped charge in the material QT. The impact of the annealing temperature and crystallographic orientation on the evolution of lnσ is presented here. The slope of the asymptotic regime of the curve lnσ as function of QT, expressed in cm(2) per trapped charge, is probably linked to the elementary cross section of electron-hole recombination, σhole, which controls the trapping evolution in the reach of the stationary flow regime. © 2014 The Authors Journal of Microscopy © 2014 Royal Microscopical Society.

Detailed characterization of thermal expansion tensor in monoclinic K Re(WO 4) 2 (where Re = Gd, Y, Lu, Yb)

NASA Astrophysics Data System (ADS)

Loiko, P. A.; Yumashev, K. V.; Kuleshov, N. V.; Rachkovskaya, G. E.; Pavlyuk, A. A.

2011-11-01

Linear thermal expansion coefficients αT were measured in monoclinic potassium (rare-earth) double tungstates K Re(WO 4) 2 ( Re = Gd, Y, Lu, Yb) by a dilatometric technique in the directions of a1, b1, c1∗ crystallographic axes (I2/c space group) and optical indicatrix axes Nm and Ng. Thermal expansion tensor αij was evaluated in the { Nm, Np, Ng} frame and then diagonalized. The orientation of corresponding frame {Xi'} with respect to crystallographic and optical indicatrix frames was determined, considering two different crystallographic settings (C2/c and I2/c). Potassium lutetium tungstate KLu(WO 4) 2 was found to possess the lower thermal expansion anisotropy among K Re(WO 4) 2 family. Athermal orientations of laser elements were proposed for K Re(WO 4) 2-based lasers under diode pumping, taking into account temperature dependence of the refractive index and bulging of crystal end faces.

Microstructural evolution and rheology of quartz in a mid-crustal shear zone

NASA Astrophysics Data System (ADS)

Rahl, Jeffrey M.; Skemer, Philip

2016-06-01

We present microstructural and crystallographic preferred orientation (CPO) data on quartz deformed in the middle crust to explore the interaction and feedback between dynamic recrystallization, deformation processes, and CPO evolution. The sample investigated here is a moderately deformed quartz-rich mylonite from the Blue Ridge in Virginia. We have created high-resolution crystallographic orientation maps using electron backscatter diffraction (EBSD) of 51 isolated quartz porphyroclasts with recrystallized grain fractions ranging from 10 to 100%. Recrystallized grains are internally undeformed and display crystallographic orientations dispersed around the orientation of the associated parent porphyroclast. We document a systematic decrease in fabric intensity with recrystallization, suggesting that progressive deformation of the recrystallized domains involves processes that can weaken a pre-existing CPO. Relationships between recrystallization fraction and shear strain suggest that complete microstructural re-equilibration requires strains in excess of γ = 5. Variation in the degree of recrystallization implies that strain was accumulated heterogeneously, and that a steady-state microstructure and rheology were not achieved.

Crystallographic studies of gas sorption in metal–organic frameworks

PubMed Central

Carrington, Elliot J.; Vitórica-Yrezábal, Iñigo J.; Brammer, Lee

2014-01-01

Metal–organic frameworks (MOFs) are a class of porous crystalline materials of modular design. One of the primary applications of these materials is in the adsorption and separation of gases, with potential benefits to the energy, transport and medical sectors. In situ crystallography of MOFs under gas atmospheres has enabled the behaviour of the frameworks under gas loading to be investigated and has established the precise location of adsorbed gas molecules in a significant number of MOFs. This article reviews progress in such crystallographic studies, which has taken place over the past decade, but has its origins in earlier studies of zeolites, clathrates etc. The review considers studies by single-crystal or powder diffraction using either X-rays or neutrons. Features of MOFs that strongly affect gas sorption behaviour are discussed in the context of in situ crystallographic studies, specifically framework flexibility, and the presence of (organic) functional groups and unsaturated (open) metal sites within pores that can form specific interactions with gas molecules. PMID:24892587

Atomically Resolved STM Characterization of the 3-D Dirac Semimetal Cd3As2

NASA Astrophysics Data System (ADS)

Butler, Christopher; Tseng, Yi; Hsing, Cheng-Rong; Wu, Yu-Mi; Sankar, Raman; Wang, Mei-Fang; Wei, Ching-Ming; Chou, Fang-Cheng; Lin, Minn-Tsong

Dirac semimetals such as Cd3As2 are a recently discovered class of materials which host three-dimensional linear dispersion around point-like band crossings in the bulk Brillouin zone, and hence represent three-dimensional analogues of graphene. This electronic phase is enabled by specific crystal symmetries: In the case of Cd3As2, a C4 rotational symmetry associated with its peculiar corkscrew arrangement of systematic Cd vacancies. Although this arrangement underpins the current crystallographic understanding of Cd3As2, and all its theoretical implications, it is strangely absent in surface microscopic investigations reported previously. Here we use a combined approach of scanning tunneling microscopy and ab initio calculations to show that the currently held crystallographic model of Cd3As2 is indeed predictive of a periodic zig-zag superstructure at the (112) surface, which we observe in scanning tunneling microscopy images. This helps to reconcile the current state of microscopic surface observations with the prevailing crystallographic and theoretical models.

You are lost without a map: Navigating the sea of protein structures.

PubMed

Lamb, Audrey L; Kappock, T Joseph; Silvaggi, Nicholas R

2015-04-01

X-ray crystal structures propel biochemistry research like no other experimental method, since they answer many questions directly and inspire new hypotheses. Unfortunately, many users of crystallographic models mistake them for actual experimental data. Crystallographic models are interpretations, several steps removed from the experimental measurements, making it difficult for nonspecialists to assess the quality of the underlying data. Crystallographers mainly rely on "global" measures of data and model quality to build models. Robust validation procedures based on global measures now largely ensure that structures in the Protein Data Bank (PDB) are largely correct. However, global measures do not allow users of crystallographic models to judge the reliability of "local" features in a region of interest. Refinement of a model to fit into an electron density map requires interpretation of the data to produce a single "best" overall model. This process requires inclusion of most probable conformations in areas of poor density. Users who misunderstand this can be misled, especially in regions of the structure that are mobile, including active sites, surface residues, and especially ligands. This article aims to equip users of macromolecular models with tools to critically assess local model quality. Structure users should always check the agreement of the electron density map and the derived model in all areas of interest, even if the global statistics are good. We provide illustrated examples of interpreted electron density as a guide for those unaccustomed to viewing electron density. Copyright © 2014 Elsevier B.V. All rights reserved.

Electron tomography and 3D molecular simulations of platinum nanocrystals

NASA Astrophysics Data System (ADS)

Florea, Ileana; Demortière, Arnaud; Petit, Christophe; Bulou, Hervé; Hirlimann, Charles; Ersen, Ovidiu

2012-07-01

This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface.This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30990d

Size and Crystallographic Orientation Effects on the Mechanical Behavior of 4H-SiC Micro-/nano-pillars

NASA Astrophysics Data System (ADS)

Guo, Xiaolei; Guo, Qiang; Li, Zhiqiang; Fan, Genlian; Xiong, Ding-Bang; Su, Yishi; Zhang, Jie; Tan, Zhanqiu; Guo, Cuiping; Zhang, Di

2018-02-01

Single crystalline 4H-SiC micro-/nano-pillars of various sizes and different crystallographic orientations were fabricated and tested by uniaxial compression. The pillars with zero shear stress resolved on the basal slip system were found to fracture in a brittle manner without showing significant size dependence, while the pillars with non-zero resolved shear stress showed a "smaller is stronger" behavior and a jerky plastic flow. These observations were interpreted by homogeneous dislocation nucleation and dislocation glide on the basal plane.

Role of stresses in annealing of ion-implantation damage in Si

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seshan, K.; EerNisse, E.P.

Recent results showing a crystallographic orientation dependence of growth kinetics, secondary defects, and stress relief in annealing of ion-implanted Si are shown to be self-consistent if interpreted in terms of the influence of stresses upon annealing processes. The stress influence proposed is microplastic shear which is induced in (112) directions on (111) planes inclined to the implant surface by the biaxial stress created in the implant region by ion-implantation damage. The shear stresses are shown to be dependent on crystallographic orientation in a manner consistent with the model.

Three phase crystallography and solute distribution analysis during residual austenite decomposition in tempered nanocrystalline bainitic steels

DOE Office of Scientific and Technical Information (OSTI.GOV)

Caballero, F.G.; Yen, Hung-Wei; Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006

2014-02-15

Interphase carbide precipitation due to austenite decomposition was investigated by high resolution transmission electron microscopy and atom probe tomography in tempered nanostructured bainitic steels. Results showed that cementite (θ) forms by a paraequilibrium transformation mechanism at the bainitic ferrite–austenite interface with a simultaneous three phase crystallographic orientation relationship. - Highlights: • Interphase carbide precipitation due to austenite decomposition • Tempered nanostructured bainitic steels • High resolution transmission electron microscopy and atom probe tomography • Paraequilibrium θ with three phase crystallographic orientation relationship.

Al-doped ZnO seed layer-dependent crystallographic control of ZnO nanorods by using electrochemical deposition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Son, Hyo-Soo; Choi, Nak-Jung; Kim, Kyoung-Bo

Highlights: • Polar and semipolar ZnO NRs were successfully achieved by hydrothermal synthesis. • Semipolar and polar ZnO NRs were grown on ZnO and AZO/m-sapphire, respectively. • Al % of AZO/m-sapphire enhanced the lateral growth rate of polar ZnO NRs. - Abstract: We investigated the effect of an Al-doped ZnO film on the crystallographic direction of ZnO nanorods (NRs) using electrochemical deposition. From high-solution X-ray diffraction measurements, the crystallographic plane of ZnO NRs grown on (1 0 0) ZnO/m-plane sapphire was (1 0 1). The surface grain size of the (100) Al-doped ZnO (AZO) film decreased with increasing Al contentmore » in the ZnO seed layer, implying that the Al dopant accelerated the three-dimensional (3D) growth of the AZO film. In addition, it was found that with increasing Al doping concentration of the AZO seed layer, the crystal orientation of the ZnO NRs grown on the AZO seed layer changed from [1 0 1] to [0 0 1]. With increasing Al content of the nonpolar (1 0 0) AZO seed layer, the small surface grains with a few crystallographic planes of the AZO film changed from semipolar (1 0 1) ZnO NRs to polar (0 0 1) ZnO NRs due to the increase of the vertical [0 0 1] growth rate of the ZnO NRs owing to excellent electrical properties.« less

Cluster Analysis of Time-Dependent Crystallographic Data: Direct Identification of Time-Independent Structural Intermediates

PubMed Central

Kostov, Konstantin S.; Moffat, Keith

2011-01-01

The initial output of a time-resolved macromolecular crystallography experiment is a time-dependent series of difference electron density maps that displays the time-dependent changes in underlying structure as a reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which these intermediates interconvert; and thereby to elucidate a chemical kinetic mechanism. One strategy toward achieving this goal is to use cluster analysis, a statistical method that groups objects based on their similarity. If the difference electron density at a particular voxel in the time-dependent difference electron density (TDED) maps is sensitive to the presence of one and only one intermediate, then its temporal evolution will exactly parallel the concentration profile of that intermediate with time. The rationale is therefore to cluster voxels with respect to the shapes of their TDEDs, so that each group or cluster of voxels corresponds to one structural intermediate. Clusters of voxels whose TDEDs reflect the presence of two or more specific intermediates can also be identified. From such groupings one can then infer the number of intermediates, obtain their time-independent difference density characteristics, and refine the structure of each intermediate. We review the principles of cluster analysis and clustering algorithms in a crystallographic context, and describe the application of the method to simulated and experimental time-resolved crystallographic data for the photocycle of photoactive yellow protein. PMID:21244840

Effet de l'anisotropie élastique cristalline sur la distribution des facteurs de Schmid à la surface des polycristaux

NASA Astrophysics Data System (ADS)

Sauzay, Maxime

2006-06-01

Experimental studies of the plasticity mechanisms of polycrystals are usually based on the Schmid factor distribution supposing crystalline elasticity isotropy. A numerical evaluation of the effect of crystalline elasticity anisotropy on the apparent Schmid factor distribution at the free surface of polycrystals is presented. Cubic elasticity is considered. Order II stresses (averaged on all grains with the same crystallographic orientation) as well as variations between averages computed on grains with the same crystallographic orientation but with different neighbour grains are computed. The Finite Element Method is used. Commonly studied metals presenting an increasing anisotropy degree are considered (aluminium, nickel, austenite, copper). Concerning order II stresses in strongly anisotropic metals, the apparent Schmid factor distribution is drifted towards small Schmid factor values (the maximum Schmid factor is equal to 0.43 instead of 0.5) and the slip activation order between characteristic orientations of the crystallographic standard triangle is modified. The computed square deviations of the stresses averaged on grains with the same crystallographic orientation but with different neighbour grains are a bit higher than the second order ones (inter-orientation scatter). Our numerical evaluations agree quantitatively with several observations and measures of the literature concerning stress and strain distribution in copper and austenite polycrystals submitted to low amplitude loadings. Hopefully, the given apparent Schmid factor distributions could help to better understand the observations of the plasticity mechanisms taking place at the free surface of polycrystals. To cite this article: M. Sauzay, C. R. Mecanique 334 (2006).

Crystallographic Analysis of a Japanese Sword by using Bragg Edge Transmission Spectroscopy

NASA Astrophysics Data System (ADS)

Shiota, Yoshinori; Hasemi, Hiroyuki; Kiyanagi, Yoshiaki

Neutron imaging using a pulsed neutron source can give crystallographic information over wide area of a sample by analysing position dependent transmission spectra. With the use of a Bragg edge imaging method we non-destructively obtained crystallographic information of a Japanese sword, signed by Bishu Osafune Norimitsu, in order to know position dependent crystallographic characteristics and to check usefulness of the method for the Japanese sword investigation. Strong texture appeared on the back side. On the other hand in the middle area almost isotropic feature appeared and edge side showed feature between them. Rather isotropic area in the centre area gradually reduced from the grip side to the tip side. The crystallite size was smaller near the edge and became larger towards the back side. The smaller crystallite size will be due to quenching around the edge and this trend disappeared in the grip (nakago) area. The larger crystallite size will be due to strong hammering. Coarse grains were also observed directly as transmission images with the use of a high spatial resolution detector. The spatial distribution of the grains was not uniform but the reason have not been understood. Furthermore, a white area around a tip area was proved to be a void by looking at the Brag edge transmission spectra. This void may be formed during forging process of two kinds of steel. It is suggested that consideration on differences in the texture and the crystallite size depending on position will give information to clarify the manufacturing process, and Bragg edge analysis will be a profitable tool for research of Japanese sword.

Absorption Efficiencies of Forsterite. I: DDA Explorations in Grain Shape and Size

NASA Technical Reports Server (NTRS)

Lindsay, Sean S.; Wooden, Diane; Harker, David E.; Kelley, Michael S.; Woodward, Charles E.; Murphy, Jim R.

2013-01-01

We compute the absorption efficiency (Q(sub abs)) of forsterite using the discrete dipole approximation (DDA) in order to identify and describe what characteristics of crystal grain shape and size are important to the shape, peak location, and relative strength of spectral features in the 8 - 40 micron wavelength range. Using the DDSCAT code, we compute Q(sub abs) for non-spherical polyhedral grain shapes with a(sub eff) = 0.1 micron. The shape characteristics identified are: 1) elongation/reduction along one of three crystallographic axes; 2) asymmetry, such that all three crystallographic axes are of different lengths; and 3) the presence of crystalline faces that are not parallel to a specific crystallographic axis, e.g., non-rectangular prisms and (di)pyramids. Elongation/reduction dominates the locations and shapes of spectral features near 10, 11, 16, 23.5, 27, and 33.5 micron, while asymmetry and tips are secondary shape effects. Increasing grain sizes (0.1 - 1.0 micron) shifts the 10, 11 micron features systematically towards longer wavelengths and relative to the 11 micron feature increases the strengths and slightly broadens the longer wavelength features. Seven spectral shape classes are established for crystallographic a-, b-, and c-axes and include columnar and platelet shapes plus non-elongated or equant grain shapes. The spectral shape classes and the effects of grain size have practical application in identifying or excluding columnar, platelet or equant forsterite grain shapes in astrophysical environs. Identification of the shape characteristics of forsterite from 8 - 40 micron spectra provides a potential means to probe the temperatures at which forsterite formed.

Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

DOE PAGES

Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

2016-12-21

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating differentmore » magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.« less

Texture evolution and mechanical behaviour of irradiated face-centred cubic metals

NASA Astrophysics Data System (ADS)

Chen, L. R.; Xiao, X. Z.; Yu, L.; Chu, H. J.; Duan, H. L.

2018-02-01

A physically based theoretical model is proposed to investigate the mechanical behaviour and crystallographic texture evolution of irradiated face-centred cubic metals. This model is capable of capturing the main features of irradiated polycrystalline materials including irradiation hardening, post-yield softening and plasticity localization. Numerical results show a good agreement with experimental data for both unirradiated and irradiated stress-strain relationships. The study of crystallographic texture reveals that the initial randomly distributed texture of unirradiated metals under tensile loading can evolve into a mixture of [111] and [100] textures. Regarding the irradiated case, crystallographic texture develops in a different way, and an extra part of [110] texture evolves into [100] and [111] textures. Thus, [100] and [111] textures become dominant more quickly compared with those of the unirradiated case for the reason that [100] and [111]-oriented crystals have higher strength, and their plastic deformation behaviours are more active than other oriented crystals. It can be concluded that irradiation-induced defects can affect both the mechanical behaviour and texture evolution of metals, both of which are closely related to irradiation hardening.

Characterization of the carbides and the martensite phase in powder-metallurgy high-speed steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Godec, Matjaz, E-mail: matjaz.godec@imt.si; Batic, Barbara Setina; Mandrino, Djordje

2010-04-15

A microstructural characterization of the powder-metallurgy high-speed-steel S390 Microclean was performed based on an elemental distribution of the carbide phase as well as crystallographic analyses. The results showed that there were two types of carbides present: vanadium-rich carbides, which were not chemically homogeneous and exhibited a tungsten-enriched or tungsten-depleted central area; and chemically homogeneous tungsten-rich M{sub 6}C-type carbides. Despite the possibility of chemical inhomogenities, the crystallographic orientation of each of the carbides was shown to be uniform. Using electron backscatter diffraction the vanadium-rich carbides were determined to be either cubic VC or hexagonal V{sub 6}C{sub 5}, while the tungsten-rich carbidesmore » were M{sub 6}C. The electron backscatter diffraction results were also verified using X-ray diffraction. Several electron backscatter diffraction pattern maps were acquired in order to define the fraction of each carbide phase as well as the amount of martensite phase. The fraction of martensite was estimated using band-contrast images, while the fraction of carbides was calculated using the crystallographic data.« less

Production, purification, crystallization and preliminary X-ray structural studies of adeno-associated virus serotype 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiMattia, Michael; Govindasamy, Lakshmanan; Levy, Hazel C.

2005-10-01

The production, purification, crystallization and preliminary crystallographic analysis of empty adeno-associated virus serotype 5 capsids are reported. Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Å resolution using synchrotron radiation and belong to the orthorhombicmore » space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c = 629.7 Å. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

First-principles study of crystallographic slip modes in ω-Zr

DOE PAGES

Kumar, Anil; Kumar, M. Arul; Beyerlein, Irene Jane

2017-08-21

We use first-principles density functional theory to study the preferred modes of slip in the high-pressure ω phase of Zr. The generalized stacking fault energy surfaces associated with shearing on nine distinct crystallographic slip modes in the hexagonal ω-Zr crystal are calculated, from which characteristics such as ideal shear stress, the dislocation Burgers vector, and possible accompanying atomic shuffles, are extracted. Comparison of energy barriers and ideal shear stresses suggests that the favorable modes are prismatic < c >, prismatic-II <101¯0> and pyramidal-II < c+a >, which are distinct from the ground state hexagonal close packed α phase of Zr.more » Operation of these three modes can accommodate any deformation state. The relative preferences among the identified slip modes are examined using a mean-field crystal plasticity model and comparing the calculated deformation texture with the measurement. In conclusion, knowledge of the basic crystallographic modes of slip is critical to understanding and analyzing the plastic deformation behavior of ω-Zr or mixed α-ω phase-Zr.« less

Magnetic transition temperatures follow crystallographic symmetry in Samarium under high-pressures and low-temperatures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vohra, Yogesh K.; Tsoi, Georgiy M.; Johnson, Craig R.

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating differentmore » magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm → dhcp → fcc/dist.fcc → hP3 structure sequence at high-pressures and low-temperatures.« less

Effect of crystallographic orientations of grains on the global mechanical properties of steel sheets by depth sensing indentation

NASA Astrophysics Data System (ADS)

Burik, P.; Pesek, L.; Kejzlar, P.; Andrsova, Z.; Zubko, P.

2017-01-01

The main idea of this work is using a physical model to prepare a virtual material with required properties. The model is based on the relationship between the microstructure and mechanical properties. The macroscopic (global) mechanical properties of steel are highly dependent upon microstructure, crystallographic orientation of grains, distribution of each phase present, etc... We need to know the local mechanical properties of each phase separately in multiphase materials. The grain size is a scale, where local mechanical properties are responsible for the behavior. Nanomechanical testing using depth sensing indentation (DSI) provides a straightforward solution for quantitatively characterizing each of phases in microstructure because it is very powerful technique for characterization of materials in small volumes. The aim of this experimental investigation is: (i) to prove how the mixing rule works for local mechanical properties (indentation hardness HIT) in microstructure scale using the DSI technique on steel sheets with different microstructure; (ii) to compare measured global properties with properties achieved by mixing rule; (iii) to analyze the effect of crystallographic orientations of grains on the mixing rule.

Crystallographic Orientation Effect on Electromigration in Ni-Sn Microbump

NASA Astrophysics Data System (ADS)

Huang, Yi-Ting; Chen, Chih-Hao; Chakroborty, Subhendu; Wu, Albert T.

2017-09-01

This article addresses the reliability challenges regarding electromigration in developing three-dimensional integrated circuits (3D-ICs). The line-type sandwich structure of Ni/Sn3.5Ag(15 μm)/Ni was used to simulate microbumps to examine the reliability of electromigration in 3D-IC technology. The solder strip of Ni/Sn3.5Ag(15 μm)/Ni was stressed with a current density of 1.0 × 104 A/cm2 at 150°C. The current stressing enhanced the reaction between the solder and Ni to form Ni3Sn4, which occupied the entire joint and transformed into a Ni/Ni3Sn4/Ni structure when the solder was completely consumed. Electron backscatter diffraction was used to analyze the crystallographic characteristics of Sn and Ni3Sn4 as related to the electromigration effect. The results indicated that the crystallographic orientation of Sn plays a significant role in the Ni/Sn3.5Ag/Ni, whereas the orientation of Ni3Sn4 is the dominant factor of diffusion behavior in the Ni/Ni3Sn4/Ni.

NMR crystallography of oxybuprocaine hydrochloride, Modification II degrees.

PubMed

Harris, Robin K; Cadars, Sylvian; Emsley, Lyndon; Yates, Jonathan R; Pickard, Chris J; Jetti, Ram K R; Griesser, Ulrich J

2007-01-21

The (13)C CPMAS spectrum is presented for the polymorph of oxybuprocaine hydrochloride which is stable at room temperature, i.e. Mod. II degrees . It shows crystallographic splittings arising from the fact that there are two molecules, with substantially different conformations, in the asymmetric unit. An INADEQUATE two-dimensional experiment was used to link signals for the same independent molecule. The chemical shifts are discussed in relation to the crystal structure. Of the four ethyl groups attached to NH(+) nitrogens, one gives rise to unusually low chemical shifts, very different from those of the other three ethyl groups. This is attributed empirically to gamma-gauche conformational effects, as is confirmed by shielding computations. These considerations allow (13)C signals to be assigned to specific carbons in the two crystallographically inequivalent molecules in the crystal structure. Indeed, information about the conformations is inherent in the NMR spectrum, which thus provides data of crystallographic significance. A (13)C/(1)H HETCOR experiment enabled resolution to be obtained in the (1)H dimension and allowed (1)H and (13)C signals for the same independent molecule to be linked.

Fundamental piezo-Hall coefficients of single crystal p-type 3C-SiC for arbitrary crystallographic orientation

NASA Astrophysics Data System (ADS)

Qamar, Afzaal; Dao, Dzung Viet; Phan, Hoang-Phuong; Dinh, Toan; Dimitrijev, Sima

2016-08-01

Piezo-Hall effect in a single crystal p-type 3C-SiC, grown by LPCVD process, has been characterized for various crystallographic orientations. The quantified values of the piezo-Hall effect in heavily doped p-type 3C-SiC(100) and 3C-SiC(111) for different crystallographic orientations were used to obtain the fundamental piezo-Hall coefficients, P 12 = ( 5.3 ± 0.4 ) × 10 - 11 Pa - 1 , P 11 = ( - 2.6 ± 0.6 ) × 10 - 11 Pa - 1 , and P 44 = ( 11.42 ± 0.6 ) × 10 - 11 Pa - 1 . Unlike the piezoresistive effect, the piezo-Hall effect for (100) and (111) planes is found to be independent of the angle of rotation of the device within the crystal plane. The values of fundamental piezo-Hall coefficients obtained in this study can be used to predict the piezo-Hall coefficients in any crystal orientation which is very important for designing of 3C-SiC Hall sensors to minimize the piezo-Hall effect for stable magnetic field sensitivity.

Advantages of Crystallographic Fragment Screening: Functional and Mechanistic Insights from a Powerful Platform for Efficient Drug Discovery

PubMed Central

Patel, Disha; Bauman, Joseph D.; Arnold, Eddy

2015-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this “chemical interrogation” of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. PMID:25117499

Fine refinement of solid-state molecular structures of Leu- and Met-enkephalins by NMR crystallography.

PubMed

Pawlak, Tomasz; Potrzebowski, Marek J

2014-03-27

This paper presents a methodology that allows the fine refinement of the crystal and molecular structure for compounds for which the data deposited in the crystallographic bases are of poor quality. Such species belong to the group of samples with molecular disorder. In the Cambridge Crystallographic Data Center (CCDC), there are approximately 22,000 deposited structures with an R-factor over 10. The powerful methodology we present employs crystal data for Leu-enkephalin (two crystallographic forms) with R-factor values of 14.0 and 8.9 and for Met-enkephalin (one form) with an R-factor of 10.5. NMR crystallography was employed in testing the X-ray data and the quality of the structure refinement. The GIPAW (gauge invariant projector augmented wave) method was used to optimize the coordinates of the enkephalins and to compute NMR parameters. As we reveal, this complementary approach makes it possible to generate a reasonable set of new coordinates that better correlate to real samples. This methodology is general and can be employed in the study of each compound possessing magnetically active nuclei.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Magnetic transition temperatures follow crystallographic symmetry in samarium under high-pressures and low-temperatures

NASA Astrophysics Data System (ADS)

Johnson, Craig R.; Tsoi, Georgiy M.; Vohra, Yogesh K.

2017-02-01

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm  →  dhcp  →  fcc/dist.fcc  →  hP3 structure sequence at high-pressures and low-temperatures.

Magnetic transition temperatures follow crystallographic symmetry in samarium under high-pressures and low-temperatures.

PubMed

Johnson, Craig R; Tsoi, Georgiy M; Vohra, Yogesh K

2017-02-15

Magnetic ordering temperatures in rare earth metal samarium (Sm) have been studied using an ultrasensitive electrical transport measurement technique in a designer diamond anvil cell to high-pressure up to 47 GPa and low-temperature to 10 K. The two magnetic transitions at 106 K and 14 K in the α-Sm phase, attributed to antiferromagnetic ordering on hexagonal and cubic layers respectively, collapse in to one magnetic transition near 10 GPa when Sm assumes a double hexagonal close packed (dhcp) phase. On further increase in pressure above 34 GPa, the magnetic transitions split again as Sm adopts a hexagonal-hP3 structure indicating different magnetic transition temperatures for different crystallographic sites. A model for magnetic ordering for the hexagonal-hP3 phase in samarium has been proposed based on the experimental data. The magnetic transition temperatures closely follow the crystallographic symmetry during α-Sm  →  dhcp  →  fcc/dist.fcc  →  hP3 structure sequence at high-pressures and low-temperatures.

Advantages of crystallographic fragment screening: functional and mechanistic insights from a powerful platform for efficient drug discovery.

PubMed

Patel, Disha; Bauman, Joseph D; Arnold, Eddy

2014-01-01

X-ray crystallography has been an under-appreciated screening tool for fragment-based drug discovery due to the perception of low throughput and technical difficulty. Investigators in industry and academia have overcome these challenges by taking advantage of key factors that contribute to a successful crystallographic screening campaign. Efficient cocktail design and soaking methodologies have evolved to maximize throughput while minimizing false positives/negatives. In addition, technical improvements at synchrotron beamlines have dramatically increased data collection rates thus enabling screening on a timescale comparable to other techniques. The combination of available resources and efficient experimental design has resulted in many successful crystallographic screening campaigns. The three-dimensional crystal structure of the bound fragment complexed to its target, a direct result of the screening effort, enables structure-based drug design while revealing insights regarding protein dynamics and function not readily obtained through other experimental approaches. Furthermore, this "chemical interrogation" of the target protein crystals can lead to the identification of useful reagents for improving diffraction resolution or compound solubility. Copyright © 2014. Published by Elsevier Ltd.

Modeling the Flow Behavior, Recrystallization, and Crystallographic Texture in Hot-Deformed Fe-30 Wt Pct Ni Austenite

NASA Astrophysics Data System (ADS)

Abbod, M. F.; Sellars, C. M.; Cizek, P.; Linkens, D. A.; Mahfouf, M.

2007-10-01

The present work describes a hybrid modeling approach developed for predicting the flow behavior, recrystallization characteristics, and crystallographic texture evolution in a Fe-30 wt pct Ni austenitic model alloy subjected to hot plane strain compression. A series of compression tests were performed at temperatures between 850 °C and 1050 °C and strain rates between 0.1 and 10 s-1. The evolution of grain structure, crystallographic texture, and dislocation substructure was characterized in detail for a deformation temperature of 950 °C and strain rates of 0.1 and 10 s-1, using electron backscatter diffraction and transmission electron microscopy. The hybrid modeling method utilizes a combination of empirical, physically-based, and neuro-fuzzy models. The flow stress is described as a function of the applied variables of strain rate and temperature using an empirical model. The recrystallization behavior is predicted from the measured microstructural state variables of internal dislocation density, subgrain size, and misorientation between subgrains using a physically-based model. The texture evolution is modeled using artificial neural networks.

Anisotropic magnetocrystalline coupling of the skyrmion lattice in MnSi

NASA Astrophysics Data System (ADS)

Luo, Yongkang; Lin, Shi-Zeng; Fobes, D. M.; Liu, Zhiqi; Bauer, E. D.; Betts, J. B.; Migliori, A.; Thompson, J. D.; Janoschek, M.; Maiorov, B.

2018-03-01

We investigate the anisotropic nature of magnetocrystalline coupling between the crystallographic and skyrmion crystal (SKX) lattices in the chiral magnet MnSi by magnetic field-angle resolved resonant ultrasound spectroscopy. Abrupt changes are observed in the elastic moduli and attenuation when the magnetic field is parallel to the [011] crystallographic direction. These observations are interpreted in a phenomenological Ginzburg-Landau theory that identifies switching of the SKX orientation to be the result of an anisotropic magnetocrystalline coupling potential. Our paper sheds new light on the nature of magnetocrystalline coupling potential relevant to future spintronic applications.

Copper-based alloys, crystallographic and crystallochemical parameters of alloys in binary systems Cu-Me (Me=Co, Rh, Ir, Cu, Ag, Au, Ni, Pd, Pt)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Porobova, Svetlana, E-mail: porobova.sveta@yandex.ru; Loskutov, Oleg, E-mail: lom58@mail.ru; Markova, Tat’jana, E-mail: patriot-rf@mail.ru

2016-01-15

The article presents the results of the analysis of phase equilibrium of ordered phases in binary systems based on copper Cu- Me (where Me - Co, Rh, Ir, Ag, Au, Ni, Pd, Pt) to find correlations of crystallochemical and crystallographic factors. It is established that the packing index in disordered solid solutions in binary systems based on copper is close to the value of 0.74 against the background of an insignificant deviation of atomic volumes from the Zen’s law.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bodenheimer, Annette M.; Meilleur, Flora

Trichoderma reesei Cel7A efficiently hydrolyses cellulose. We report here the crystallographic structures of the wild-type TrCel7A catalytic domain (CD) in an open state and, for the first time, in a closed state. Molecular dynamics (MD) simulations indicate that the loops along the CD tunnel move in concerted motions. Together, the crystallographic and MD data suggest that the CD cycles between the tense and relaxed forms that are characteristic of work producing enzymes. Analysis of the interactions formed by R251 provides a structural rationale for the concurrent decrease in product inhibition and catalytic efficiency measured for product-binding site mutants.

Anisotropic magnetocrystalline coupling of the skyrmion lattice in MnSi

DOE PAGES

Luo, Yongkang; Lin, Shi-Zeng; Fobes, D. M.; ...

2018-03-26

In this paper, we investigate the anisotropic nature of magnetocrystalline coupling between the crystallographic and skyrmion crystal (SKX) lattices in the chiral magnet MnSi by magnetic field-angle resolved resonant ultrasound spectroscopy. Abrupt changes are observed in the elastic moduli and attenuation when the magnetic field is parallel to the [011] crystallographic direction. These observations are interpreted in a phenomenological Ginzburg-Landau theory that identifies switching of the SKX orientation to be the result of an anisotropic magnetocrystalline coupling potential. Finally, our paper sheds new light on the nature of magnetocrystalline coupling potential relevant to future spintronic applications.

Crystallographic tile

NASA Astrophysics Data System (ADS)

Kartono; Heri Sulistyo Utomo, R.; Priyo, Sidik S.; Titi Ujiani, SRRM

2018-05-01

A symmetry operation is a rigid motion that include reflection, rotation, translation and their combinations. These motions determine orderly repetition, that can have aesthetic appeal. So, the symmetry is often found in art, and the decorative tiles are wonderful sources of examples of symmetry. In this article, we introduce and describe the crystallographic tile (CT). Ornament decorative motif on the CT is designed with consider the symmetry operations. Surprisingly, orderly repetition of this CT can generate many variant patterns. The result of this research, orderly repetition of one motif can produce 14 patterns. Finally, we conclude that an application of the crystallography theory can increase the product competitiveness.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Qi; Zhu, Fang-Yuan; Cheng, Li-Qian

Crystallographic structure of sol-gel-processed lead-free (K,Na)NbO{sub 3} (KNN) epitaxial films on [100]-cut SrTiO{sub 3} single-crystalline substrates was investigated for a deeper understanding of its piezoelectric response. Lattice parameter measurement by high-resolution X-ray diffraction and transmission electron microscopy revealed that the orthorhombic KNN films on SrTiO{sub 3} (100) surfaces are [010] oriented (b-axis-oriented) rather than commonly identified c-axis orientation. Based on the crystallographic orientation and corresponding ferroelectric domain structure investigated by piezoresponse force microscopy, the superior piezoelectric property along b-axis of epitaxial KNN films than other orientations can be explained.

Twilight reloaded: the peptide experience.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2017-03-01

The de facto commoditization of biomolecular crystallography as a result of almost disruptive instrumentation automation and continuing improvement of software allows any sensibly trained structural biologist to conduct crystallographic studies of biomolecules with reasonably valid outcomes: that is, models based on properly interpreted electron density. Robust validation has led to major mistakes in the protein part of structure models becoming rare, but some depositions of protein-peptide complex structure models, which generally carry significant interest to the scientific community, still contain erroneous models of the bound peptide ligand. Here, the protein small-molecule ligand validation tool Twilight is updated to include peptide ligands. (i) The primary technical reasons and potential human factors leading to problems in ligand structure models are presented; (ii) a new method used to score peptide-ligand models is presented; (iii) a few instructive and specific examples, including an electron-density-based analysis of peptide-ligand structures that do not contain any ligands, are discussed in detail; (iv) means to avoid such mistakes and the implications for database integrity are discussed and (v) some suggestions as to how journal editors could help to expunge errors from the Protein Data Bank are provided.

Specific noncovalent interactions at protein-ligand interface: implications for rational drug design.

PubMed

Zhou, P; Huang, J; Tian, F

2012-01-01

Specific noncovalent interactions that are indicative of attractive, directional intermolecular forces have always been of key interest to medicinal chemists in their search for the "glue" that holds drugs and their targets together. With the rapid increase in the number of solved biomolecular structures as well as the performance enhancement of computer hardware and software in recent years, it is now possible to give more comprehensive insight into the geometrical characteristics and energetic landscape of certain sophisticated noncovalent interactions present at the binding interface of protein receptors and small ligands based on accumulated knowledge gaining from the combination of two quite disparate but complementary approaches: crystallographic data analysis and quantum-mechanical ab initio calculation. In this perspective, we survey massive body of published works relating to structural characterization and theoretical investigation of three kinds of strong, specific, direct, enthalpy-driven intermolecular forces, including hydrogen bond, halogen bond and salt bridge, involved in the formation of protein-ligand complex architecture in order to characterize their biological functions in conferring affinity and specificity for ligand recognition by host protein. In particular, the biomedical implications of raised knowledge are discussed with respect to potential applications in rational drug design.

Binding cooperativity between a ligand carbonyl group and a hydrophobic side chain can be enhanced by additional H-bonds in a distance dependent manner: A case study with thrombin inhibitors.

PubMed

Said, Ahmed M; Hangauer, David G

2015-01-01

One of the underappreciated non-covalent binding factors, which can significantly affect ligand-protein binding affinity, is the cooperativity between ligand functional groups. Using four different series of thrombin inhibitors, we reveal a strong positive cooperativity between an H-bond accepting carbonyl functionality and the adjacent P3 hydrophobic side chain. Adding an H-bond donating amine adjacent to the P3 hydrophobic side chain further increases this positive cooperativity thereby improving the Ki by as much as 546-fold. In contrast, adding an amidine multiple H-bond/salt bridge group in the distal S1 pocket does not affect this cooperativity. An analysis of the crystallographic B-factors of the ligand groups inside the binding site indicates that the strong cooperativity is mainly due to a significant mutual reduction in the residual mobility of the hydrophobic side chain and the H-bonding functionalities that is absent when the separation distance is large. This type of cooperativity is important to encode in binding affinity prediction software, and to consider in SAR studies. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

A Practical Approach to Protein Crystallography.

PubMed

Ilari, Andrea; Savino, Carmelinda

2017-01-01

Macromolecular crystallography is a powerful tool for structural biology. The resolution of a protein crystal structure is becoming much easier than in the past, thanks to developments in computing, automation of crystallization techniques and high-flux synchrotron sources to collect diffraction datasets. The aim of this chapter is to provide practical procedures to determine a protein crystal structure, illustrating the new techniques, experimental methods, and software that have made protein crystallography a tool accessible to a larger scientific community.It is impossible to give more than a taste of what the X-ray crystallographic technique entails in one brief chapter and there are different ways to solve a protein structure. Since the number of structures available in the Protein Data Bank (PDB) is becoming ever larger (the protein data bank now contains more than 100,000 entries) and therefore the probability to find a good model to solve the structure is ever increasing, we focus our attention on the Molecular Replacement method. Indeed, whenever applicable, this method allows the resolution of macromolecular structures starting from a single data set and a search model downloaded from the PDB, with the aid only of computer work.

Virtual Screening and Pharmacophore Design for a Novel Theoretical Inhibitor of Macrophage Stimulating Factor as a Metastatic Agent

PubMed Central

Torktaz, Ibrahim; Mohamadhashem, Faezeh; Esmaeili, Abolghasem; Behjati, Mohaddeseh; Sharifzadeh, Sara

2013-01-01

Introduction: Metastasis is a crucial aspect of cancer. Macrophage stimulating protein (MSP) is a single chain protein and can be cleaved by serum proteases. MSP has several roles in metastasis. In this in silico study, MSP as a metastatic agent was considered as a drug target. Methods: Crystallographic structure of MSP was retrieved from protein data bank. To find a chemical inhibitor of MSP, a library of KEGG compounds was screened and 1000 shape complemented ligands were retrieved with FindSite algorithm. Molegro Virtual Docker (MVD) software was used for docking simulation of shape complemented ligands against MSP. Moldock score was used as scoring function for virtual screening and potential inhibitors with more negative binding energy were obtained. PLANS scoring function was used for revaluation of virtual screening data. Results: The top found chemical had binding affinity of -183.55 based on MolDock score and equal to -66.733 PLANTs score to MSP structure. Conclusion: Based on pharmacophore model of potential inhibitor, this study suggests that the chemical which was found in this research and its derivate can be used for subsequent laboratory studies. PMID:24163807

Reliability analysis of a phaser measurement unit using a generalized fuzzy lambda-tau(GFLT) technique.

PubMed

Komal

2018-05-01

Nowadays power consumption is increasing day-by-day. To fulfill failure free power requirement, planning and implementation of an effective and reliable power management system is essential. Phasor measurement unit(PMU) is one of the key device in wide area measurement and control systems. The reliable performance of PMU assures failure free power supply for any power system. So, the purpose of the present study is to analyse the reliability of a PMU used for controllability and observability of power systems utilizing available uncertain data. In this paper, a generalized fuzzy lambda-tau (GFLT) technique has been proposed for this purpose. In GFLT, system components' uncertain failure and repair rates are fuzzified using fuzzy numbers having different shapes such as triangular, normal, cauchy, sharp gamma and trapezoidal. To select a suitable fuzzy number for quantifying data uncertainty, system experts' opinion have been considered. The GFLT technique applies fault tree, lambda-tau method, fuzzified data using different membership functions, alpha-cut based fuzzy arithmetic operations to compute some important reliability indices. Furthermore, in this study ranking of critical components of the system using RAM-Index and sensitivity analysis have also been performed. The developed technique may be helpful to improve system performance significantly and can be applied to analyse fuzzy reliability of other engineering systems. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Influence of grain orientation on the incipient oxidation behavior of Haynes 230 at 900 °C

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xu, E-mail: xuw388@mail.usask.ca; Fan, Fan; Szpunar, Jerzy A.

Ni-based superalloy Haynes 230 is used in many applications such as very high temperature reactor (VHTR) or solid oxide fuel cells (SOFCs) where it is exposed to high temperature service environment. In order to improve the resistance for high temperature oxidation, the effect of crystallographic orientation on the early stage oxidation was investigated. It was demonstrated that different oxide thicknesses are formed on grains having different orientations. Comparison of electron backscatter diffraction (EBSD) orientation maps before and after oxidation at 900 °C indicates that grains near (111) orientation, especially with the deviation angle from <111> that is smaller than 20°,more » are more oxidation resistant than grains of other orientations. Correlation between the results of electron backscatter diffraction (EBSD) and atomic force microscopy (AFM) was used to compare the oxidation rate of grains having different crystallographic orientation. The oxidation rate was found to change with the crystallographic orientation as follows (111) < (110) < (100), also it was demonstrated that the oxidation rate changes are a nearly linear function of the angle of deviation from <111> direction. The morphology of surface oxide also depends on the orientation of grains. - Highlights: • Comparison of EBSD maps before and after oxidation allows to investigate the effect of orientation on oxidation in a more direct way; • Effect of crystallographic orientation on oxidation behavior of alloy 230 is studied by combination of EBSD and AFM; • Different thickness of oxide is formed on grain with different orientation and dependence of anisotropic oxidation behavior is discussed; • The morphology of grains is also orientation dependence.« less

Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling

NASA Astrophysics Data System (ADS)

Rosenfeld, Robin J.; Goodsell, David S.; Musah, Rabi A.; Morris, Garrett M.; Goodin, David B.; Olson, Arthur J.

2003-08-01

The W191G cavity of cytochrome c peroxidase is useful as a model system for introducing small molecule oxidation in an artificially created cavity. A set of small, cyclic, organic cations was previously shown to bind in the buried, solvent-filled pocket created by the W191G mutation. We docked these ligands and a set of non-binders in the W191G cavity using AutoDock 3.0. For the ligands, we compared docking predictions with experimentally determined binding energies and X-ray crystal structure complexes. For the ligands, predicted binding energies differed from measured values by ± 0.8 kcal/mol. For most ligands, the docking simulation clearly predicted a single binding mode that matched the crystallographic binding mode within 1.0 Å RMSD. For 2 ligands, where the docking procedure yielded an ambiguous result, solutions matching the crystallographic result could be obtained by including an additional crystallographically observed water molecule in the protein model. For the remaining 2 ligands, docking indicated multiple binding modes, consistent with the original electron density, suggesting disordered binding of these ligands. Visual inspection of the atomic affinity grid maps used in docking calculations revealed two patches of high affinity for hydrogen bond donating groups. Multiple solutions are predicted as these two sites compete for polar hydrogens in the ligand during the docking simulation. Ligands could be distinguished, to some extent, from non-binders using a combination of two trends: predicted binding energy and level of clustering. In summary, AutoDock 3.0 appears to be useful in predicting key structural and energetic features of ligand binding in the W191G cavity.

Petrofabrics of high-pressure rocks exhumed at the slab-mantle interface from the "point of no return" in a subduction zone (Sivrihisar, Turkey)

NASA Astrophysics Data System (ADS)

Whitney, Donna L.; Teyssier, Christian; Seaton, Nicholas C. A.; Fornash, Katherine F.

2014-12-01

The highest pressure recorded by metamorphic rocks exhumed from oceanic subduction zones is 2.5 GPa, corresponding to the maximum decoupling depth (MDD) (80 ± 10 km) identified in active subduction zones; beyond the MDD (the "point of no return") exhumation is unlikely. The Sivrihisar massif (Turkey) is a coherent terrane of lawsonite eclogite and blueschist facies rocks in which assemblages and fabrics record P-T-fluid-deformation conditions during exhumation from 80 to 45 km. Crystallographic fabrics and other features of high-pressure metasedimentary and metabasaltic rocks record transitions during exhumation. In quartzite, microstructures and crystallographic fabrics record deformation in the dislocation creep regime, including dynamic recrystallization during decompression, and a transition from prism slip to activation of rhomb and basal slip that may be related to a decrease in water fugacity during decompression ( 2.5 to 1.5 GPa). Phengite, lawsonite, and omphacite or glaucophane in quartzite and metabasalt remained stable during deformation, and omphacite developed an L-type crystallographic fabric. In marble, aragonite developed columnar textures with strong crystallographic fabrics that persisted during partial to complete dynamic recrystallization that was likely achieved in the stability field of aragonite (P > 1.2 GPa). Results of kinematic vorticity analysis based on lawsonite shape fabrics are consistent with shear criteria in quartzite and metabasalt and indicate a large component of coaxial deformation in the exhuming channel beneath a simple shear dominated interface. This large coaxial component may have multiplied the exhuming power of the subduction channel and forced deeply subducted rocks to flow back from the point of no return.

Rheed Investigation of Pd/Al Bimetallic System on KCl(001) Substrate

NASA Astrophysics Data System (ADS)

Masek, K.; Moroz, V.; Matolín, V.

Pd/Al alloys have very interesting properties from the point of view of their possible application in heterogeneous catalysis. Preparation of small heteroepitaxial Pd/Al alloy particles opens a new way in studies of the influence of Pd/Al crystallographic structure on the alloy catalytic properties. Pd/Al alloy particles were grown by the molecular beam epitaxy method. Their crystallographical structure was controlled by reflection high energy electron diffraction (RHEED). It was found that Pd deposited on epitaxial 3D Al particles grown on KCl is intermixing with Al. This process is accompanied by the variation of lattice parameter from the Al value to the Pd one.

A CPU benchmark for protein crystallographic refinement.

PubMed

Bourne, P E; Hendrickson, W A

1990-01-01

The CPU time required to complete a cycle of restrained least-squares refinement of a protein structure from X-ray crystallographic data using the FORTRAN codes PROTIN and PROLSQ are reported for 48 different processors, ranging from single-user workstations to supercomputers. Sequential, vector, VLIW, multiprocessor, and RISC hardware architectures are compared using both a small and a large protein structure. Representative compile times for each hardware type are also given, and the improvement in run-time when coding for a specific hardware architecture considered. The benchmarks involve scalar integer and vector floating point arithmetic and are representative of the calculations performed in many scientific disciplines.

Inverse analysis of giant macroscopic negative thermal expansion of Ca2RuO4‑ y ceramics based on elasticity and structural topology optimization

NASA Astrophysics Data System (ADS)

Takezawa, Akihiro; Takenaka, Koshi; Zhang, Xiaopeng

2018-05-01

Ca2RuO4‑ y ceramics exhibit a large volumetric negative thermal expansions (NTE), although the crystallographic volume contraction on heating is much smaller than the NTE. Therefore, we examine the differences in the mechanisms underlying the volumetric thermal expansion for ruthenate ceramics and crystals in the context of the elasticity. We identify the possible microstructure of ruthenate ceramics composed of crystal grains and cavities using structural topology optimization. We conclude that the measured large volumetric NTE of ruthenate ceramics is certainly possible via anisotropic crystallographic thermal expansion through an elastic mechanism.

N-(2-Chloro­eth­yl)morpholine-4-carbox­amide

PubMed Central

Ujam, Oguejiofo T.; Asegbeloyin, Jonnie N.; Nicholson, Brian K.; Ukoha, Pius O.; Ukwueze, Nkechi N.

2014-01-01

The title compound, C7H13ClN2O2, synthesized by the reaction of 2-chloro­ethyl iso­cyanate and morpholine, crystallizes with four molecules in the asymmetric unit, which have similar conformations and comprise two pairs each related by approximate non-crystallographic inversion centres. Two of them have a modest orientational disorder of the 2-chloro­ethyl fragments [occupancy ratio of 0.778 (4):0.222 (4)]. In the crystal, mol­ecules are linked by N—H⋯O=C hydrogen bonds, forming three crystallographically different kinds of infinite hydrogen-bonded chains extending along [001]. PMID:24826162

Crystallographic phases in heavy rare earth metals under megabar pressures

NASA Astrophysics Data System (ADS)

Samudrala, G. K.; Vohra, Y. K.

2012-07-01

Experiments aimed at understanding the crystallographic phases of heavy rare earth metals were carried out in a diamond anvil cell at the Advanced Photon Source, Argonne National Laboratory. Heavy rare earth metals dysprosium (Dy), holmium (Ho), erbium (Er) and thulium (Tm) were compressed to multi-megabar pressures. The rare earth crystal sequence hcp→Sm-type→dhcp→distorted-fcc (dfcc) is observed in all four elements. Upon further compression, a structural transformation to a monoclinic C2/m phase has been observed. We summarize the results from these experiments and present Rietveld structural refinements on high pressure phases for the specific case of dysprosium.

The crystalline sponge method: MOF terminal ligand effects† †Electronic supplementary information (ESI) available: Experimental and crystallographic procedures, and data tables. CCDC 1063685 and 1063686. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5cc03840e Click here for additional data file. Click here for additional data file.

PubMed Central

Ramadhar, Timothy R.; Zheng, Shao-Liang; Chen, Yu-Sheng

2015-01-01

Bromide and chloride analogs of the commonly used zinc iodide-based metal organic framework for the crystalline sponge method were synthesized and evaluated. Inclusion of (1R)-(–)-menthyl acetate into these MOFs was analysed using third-generation synchrotron radiation, and the effects and potential benefits of varying the MOF terminal ligand are discussed. PMID:26081991

Modeling the characteristic etch morphologies along specific crystallographic orientations by anisotropic chemical etching

NASA Astrophysics Data System (ADS)

Li, Kun-Dar; Miao, Jin-Ru

2018-02-01

To improve the advanced manufacturing technology for functional materials, a sophisticated control of chemical etching process is highly demanded, especially in the fields of environment and energy related applications. In this study, a phase-field-based model is utilized to investigate the etch morphologies influenced by the crystallographic characters during anisotropic chemical etching. Three types of etching modes are inspected theoretically, including the isotropic, <100> and <111> preferred oriented etchings. Owing to the specific etching behavior along the crystallographic directions, different characteristic surface structures are presented in the simulations, such as the pimple-like, pyramidal hillock and ridge-like morphologies. In addition, the processing parameters affecting the surface morphological formation and evolution are also examined systematically. According to the numerical results, the growth mechanism of surface morphology in a chemical etching is revealed distinctly. While the etching dynamics plays a dominant role on the surface formation, the characteristic surface morphologies corresponding to the preferred etching direction become more apparent. As the atomic diffusion turned into a determinative factor, a smoothened surface would appear, even under the anisotropic etching conditions. These simulation results provide fundamental information to enhance the development and application of anisotropic chemical etching techniques.

In-situ neutron diffraction of LaCoO3 perovskite under uniaxial compression. I. Crystal structure analysis and texture development

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aman, Amjad; Chen, Yan; Lugovy, Mykola

2014-01-01

The dynamics of texture formation, changes in crystal structure and stress accommodation mechanisms are studied in R3c rhombohedral LaCoO3 perovskite during in-situ uniaxial compression experiment by neutron diffraction. The neutron diffraction revealed the complex crystallographic changes causing the texture formation and significant straining along certain crystallographic directions during in-situ compression, which are responsible for the appearance of hysteresis and non-linear ferroelastic deformation in LaCoO3 perovskite. The irreversible strain after the first loading was connected with the appearance of non-recoverable changes in the intensity ratio of certain crystallographic peaks, causing non-reversible texture formation. However in the second loading/unloading cycle the hysteresismore » loop was closed and no irreversible strain appears after deformation. The significant texture formation is responsible for increase in the Young s modulus of LaCoO3 at high compressive loads, where the reported values of Young s modulus increase from 76 GPa measured at the very beginning of the loading to 194 GPa at 900 MPa applied compressive stress measured at the beginning of the unloading curve.« less

The fourth crystallographic closest packing unveiled in the gold nanocluster crystal

NASA Astrophysics Data System (ADS)

Gan, Zibao; Chen, Jishi; Wang, Juan; Wang, Chengming; Li, Man-Bo; Yao, Chuanhao; Zhuang, Shengli; Xu, An; Li, Lingling; Wu, Zhikun

2017-03-01

Metal nanoclusters have recently attracted extensive interest not only for fundamental scientific research, but also for practical applications. For fundamental scientific research, it is of major importance to explore the internal structure and crystallographic arrangement. Herein, we synthesize a gold nanocluster whose composition is determined to be Au60S6(SCH2Ph)36 by using electrospray ionization mass spectrometry and single crystal X-ray crystallography (SCXC). SCXC also reveals that Au60S6(SCH2Ph)36 consists of a fcc-like Au20 kernel protected by a pair of giant Au20S3(SCH2Ph)18 staple motifs, which contain 6 tetrahedral-coordinate μ4-S atoms not previously reported in the Au-S interface. Importantly, the fourth crystallographic closest-packed pattern, termed 6H left-handed helical (6HLH) arrangement, which results in the distinct loss of solid photoluminescence of amorphous Au60S6(SCH2Ph)36, is found in the crystals of Au60S6(SCH2Ph)36. The solvent-polarity-dependent solution photoluminescence is also demonstrated. Overall, this work provides important insights about the structure, Au-S bonding and solid photoluminescence of gold nanoclusters.

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel

PubMed Central

Gyhlesten Back, Jessica; Engberg, Göran

2017-01-01

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample. PMID:28772813

Crystallographic alignment of high-density gallium nitride nanowire arrays.

PubMed

Kuykendall, Tevye; Pauzauskie, Peter J; Zhang, Yanfeng; Goldberger, Joshua; Sirbuly, Donald; Denlinger, Jonathan; Yang, Peidong

2004-08-01

Single-crystalline, one-dimensional semiconductor nanostructures are considered to be one of the critical building blocks for nanoscale optoelectronics. Elucidation of the vapour-liquid-solid growth mechanism has already enabled precise control over nanowire position and size, yet to date, no reports have demonstrated the ability to choose from different crystallographic growth directions of a nanowire array. Control over the nanowire growth direction is extremely desirable, in that anisotropic parameters such as thermal and electrical conductivity, index of refraction, piezoelectric polarization, and bandgap may be used to tune the physical properties of nanowires made from a given material. Here we demonstrate the use of metal-organic chemical vapour deposition (MOCVD) and appropriate substrate selection to control the crystallographic growth directions of high-density arrays of gallium nitride nanowires with distinct geometric and physical properties. Epitaxial growth of wurtzite gallium nitride on (100) gamma-LiAlO(2) and (111) MgO single-crystal substrates resulted in the selective growth of nanowires in the orthogonal [1\\[Evec]0] and [001] directions, exhibiting triangular and hexagonal cross-sections and drastically different optical emission. The MOCVD process is entirely compatible with the current GaN thin-film technology, which would lead to easy scale-up and device integration.

Coupling of Crystal Structure and Magnetism in the Layered, Ferromagnetic Insulator CrI 3

DOE PAGES

McGuire, Michael A.; Dixit, Hemant; Cooper, Valentino R.; ...

2014-12-23

Here, we examine the crystallographic and magnetic properties of single crystals of CrI 3, an easily cleavable, layered and insulating ferromagnet with a Curie temperature of 61 K. Our X-ray diffraction studies reveal a first-order crystallographic phase transition occurring near 210–220 K upon warming, with significant thermal hysteresis. The low-temperature structure is rhombohedral (Rmore » $$\\bar{3}$$, BiI 3-type) and the high-temperature structure is monoclinic (C2/m, AlCl 3-type). Evidence for coupling between the crystallographic and magnetic degrees of freedom in CrI 3 was found; we observed an anomaly in the interlayer spacing at the Curie temperature and an anomaly in the magnetic susceptibility at the structural transition. First-principles calculations reveal the importance of proper treatment of the long-ranged interlayer forces, and van der Waals density functional theory does an excellent job of predicting the crystal structures and their relative stability. Our calculations suggest that the ferromagnetic order found in the bulk material may persist into monolayer form, suggesting that CrI 3 and other chromium trihalides may be promising materials for spintronic and magnetoelectronic research.« less

Aragonite pseudomorphs in high-pressure marbles of Syros, Greece

NASA Astrophysics Data System (ADS)

Brady, John B.; Markley, Michelle J.; Schumacher, John C.; Cheney, John T.; Bianciardi, Grace A.

2004-01-01

Numerous rod-shaped calcite crystals occur in the blueschist to eclogite facies marbles of Syros, Greece. The rods show a shape-preferred orientation, and the long axes of the rods are oriented at a large angle to foliation. The crystals also have a crystallographic-preferred orientation: calcite c-axes are oriented parallel to the long axes of the rods. Based on their chemical composition, shape, and occurrence in high-pressure marbles, these calcite crystals are interpreted as topotactic pseudomorphs after aragonite that developed a crystallographic-preferred orientation during peak metamorphism. This interpretation is consistent with deformation of aragonite by dislocation creep, which has been observed in laboratory experiments but has not been previously reported on the basis of field evidence. Subsequent to the high-pressure deformation of the aragonite marbles, the aragonite recrystallized statically into coarse rod-shaped crystals, maintaining the crystallographic orientation developed during deformation. During later exhumation, aragonite reverted to calcite, and the marbles experienced little further deformation, at least in the pseudomorph-rich layers. Some shearing of pseudomorph-bearing marble layers did occur and is indicated by twinning of calcite and by a variable inclination of the pseudomorphs relative to foliation.

Investigation of Parent Austenite Grains from Martensite Structure Using EBSD in a Wear Resistant Steel.

PubMed

Gyhlesten Back, Jessica; Engberg, Göran

2017-04-26

Crystallographic reconstruction of parent austenite grain boundaries from the martensitic microstructure in a wear resistant steel was carried out using electron backscattered diffraction (EBSD). The present study mainly aims to investigate the parent austenite grains from the martensitic structure in an as-rolled (reference) steel sample and samples obtained by quenching at different cooling rates with corresponding dilatometry. Subsequently, this study is to correlate the nearest cooling rate by the dilatometer which yields a similar orientation relationship and substructure as the reference sample. The Kurdjumov-Sachs orientation relationship was used to reconstruct the parent austenite grain boundaries from the martensite boundaries in both reference and dilatometric samples using EBSD crystallographic data. The parent austenite grain boundaries were successfully evaluated from the EBSD data and the corresponding grain sizes were measured. The parent austenite grain boundaries of the reference sample match the sample quenched at 100 °C/s (CR100). Also the martensite substructures and crystallographic textures are similar in these two samples. The results from hardness measurements show that the reference sample exhibits higher hardness than the CR100 sample due to the presence of carbides in the reference sample.

Quantitative Phase Composition of TiO 2-Coated Nanoporous-Au Monoliths by X-ray Absorption Spectroscopy and Correlations to Catalytic

DOE PAGES

Bagge-Hansen, Michael; Wichmann, Andre; Wittstock, Arne; ...

2014-02-03

Porous titania/metal composite materials have many potential applications in the fields of green catalysis, energy harvesting, and storage in which both the overall morphology of the nanoporous host material and the crystallographic phase of the titania (TiO 2) guest determine the material’s performance. New insights into the structure–function relationships of these materials were obtained by near-edge X-ray absorption fine structure (NEXAFS) spectroscopy that, for example, provides quantitative crystallographic phase composition from ultrathin, nanostructured titania films, including sensitivity to amorphous components. We demonstrate that crystallographic phase, morphology, and catalytic activity of TiO 2-functionalized nanoporous gold (np-Au) can be controlled by amore » simple annealing procedure (T < 1300 K). The material was prepared by atomic layer deposition of ~2 nm thick TiO 2 on millimeter-sized samples of np-Au (40–50 nm mean ligament size) and catalytically investigated with respect to aerobic CO oxidation. Moreover, the annealing-induced changes in catalytic activity are correlated with concurrent morphology and phase changes as provided by cross-sectional scanning electron microscopy, transmission electron microscopy, and near-edge X-ray absorption fine structure (NEXAFS) spectroscopy.« less

Three-Dimensional Mantle Flow Near an Oceanic Paleotransform Fault System: Geological Constraints From the Bogota Peninsula, New Caledonia

NASA Astrophysics Data System (ADS)

Chatzaras, V.; Kruckenberg, S. C.; Titus, S.; Tikoff, B.; Teyssier, C. P.; Drury, M. R.

2016-12-01

We provide geological constraints on mantle deformation across a system of two oceanic paleotransform faults exposed in the Bogota Peninsula area, New Caledonia. Mantle deformation occurred at depths corresponding to temperatures of 900 oC and is highly heterogeneous. The paleotransform faults consist of mylonitic shear zones ( 1 km wide), and are surrounded by broader areas in which rotation of both the shape fabric (foliation and lineation) and olivine crystallographic preferred orientation (CPO) takes place. Outside the plaeotransform faults, mantle flows oblique to the strike of the mylonitic zones and is characterized by lateral variations in the flow direction. To further constrain the kinematics and type of deformation, we determine the orientation of the crystallographic vorticity axes as an independent tool for constraining deformation geometry (e.g., simple shear, transpression, transtension). The observed mantle flow is associated to lateral variations in: 1) the geometry and degree of anisotropy of spinel shape fabric; 2) olivine CPO type; 3) amount of stretching; and 4) the orientation of the crystallographic vorticity axes. Upper mantle in the vicinity of oceanic transform faults may be characterized by complex, three-dimensional flow patterns and deformation geometries deviating from simple shear.

Crystallographic control of surface structure on the sectoral zoning of iron in a diopside from Orford nickel mine (Quebec), Canada

NASA Astrophysics Data System (ADS)

Paquette, J.; Zangooi, A.; Thornton, K.

2004-05-01

The influence of surface structure on partitioning between mineral and melt (or solution) has been noted by other workers in a handful of minerals, including calcite, dolomite, apatite, topaz and diamond. Each one of these minerals displays at least one crystallographic face where steps present during crystal growth are not equivalent by symmetry. When this is the case, sectors grown at the edge of these steps commonly show differential incorporation of minor or trace elements. In the diopside investigated here, electron probe microanalyses performed on the as-grown (100) surface of several crystals show concentric and sectoral zoning defined by variations in Fe content. Atomic force microscopy (AFM) was used to study the surfaces of the three crystallographic forms present on the diopside crystals, with the goal of relating the compositional zoning to the surface structure of the faces. The dominant {100} faces are covered with growth hillocks consisting of four vicinal faces defined by steps parallel to [010] and [001]. The steps are often bunched into macrosteps and the resulting hillocks are visible optically. The steps along the two crystallographic directions show significant differences in straightness and smoothness that indicate non-equivalent kinetics. The wavier steps correspond to Fe-enriched areas within the {100} sectors. The {010} faces, next in morphological importance, are dominated by a single step orientation and show no differential incorporation. They display topography related to polysynthetic twinning. The {110} faces are much smaller and very few show resolvable steps. Sector zoning (i.e. diffential partitioning among non-equivalent crystallographic faces) has been described in the past from pyroxenes. Explanations have invoked either differences in surface structure among non-equivalent faces or their unequal growth rates. This particular occurrence indicates that trace element incorporation is, in fact, highly site-specific and that significant compositioinal zoning can be induced on a single face without invoking the effect of growth rate. The natural diopside crystals from the Orford nickel mine (Brompton, Quebec) show a unusual bladed habit flattened on {100} faces. Exceptional fluid chemistry during crystallization may therefore be required for the persistence of steps responsible for differential incorporation. Nevertheless, whenever this zoning is present, the trace element involved cannot be expected to reflect thermodynamic equilibrium between the solid and the fluid from which it crystallized.

Development and Processing Improvement of Aerospace Aluminum Alloys

NASA Technical Reports Server (NTRS)

Lisagor, W. Barry; Bales, Thomas T.

2007-01-01

This final report, in multiple presentation format, describes a comprehensive multi-tasked contract study to improve the overall property response of selected aerospace alloys, explore further a newly-developed and registered alloy, and correlate the processing, metallurgical structure, and subsequent properties achieved with particular emphasis on the crystallographic orientation texture developed. Modifications to plate processing, specifically hot rolling practices, were evaluated for Al-Li alloys 2195 and 2297, for the recently registered Al-Cu-Ag alloy, 2139, and for the Al-Zn-Mg-Cu alloy, 7050. For all of the alloys evaluated, the processing modifications resulted in significant improvements in mechanical properties. Analyses also resulted in an enhanced understanding of the correlation of processing, crystallographic texture, and mechanical properties.

Effect of crystallographic orientation on the anodic formation of nanoscale pores/tubes in TiO 2 films

NASA Astrophysics Data System (ADS)

Kalantar-zadeh, K.; Sadek, A. Z.; Zheng, H.; Partridge, J. G.; McCulloch, D. G.; Li, Y. X.; Yu, X. F.; Wlodarski, W.

2009-10-01

Self-organized nanopores and nanotubes have been produced in thin films of titanium (Ti) prepared using filtered cathodic vacuum arc (FCVA), DC- and RF-sputter deposition systems. The anodization process was performed using a neutral electrolyte containing fluoride ions with an applied potential between 2 and 20 V (for clarity the results are only presented for 5 V). Scanning electron microscopy (SEM), atomic force microscopy (AFM) and X-ray diffraction (XRD) techniques were used to characterise the films. It was found that the crystallographic orientation of the Ti films played a significant role in determining whether pores or tubes were formed during the anodic etching process.

Crystal structure and magnetic properties of Mn substituted ludwigite Co 3O 2BO 3

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Ivanova, N. B.; Kazak, N. V.; Platunov, M. S.; Bezmaternykh, L. N.; Velikanov, D. А.; Vasiliev, А. D.; Ovchinnikov, S. G.; Yurkin, G. Yu.

2012-03-01

The needle shape single crystals Co3-x MnxO2BO3 with ludwigite structure have been prepared. According to the X-ray diffraction data the preferable character of distinct crystallographic positions occupation by Mn ions is established. Magnetization field and temperature dependencies are measured. Paramagnetic Curie temperature value Θ=-100 K points out the predominance of antiferromagnetic interactions. Spin-glass magnetic ordering takes the onset at TN=41 K. The crystallographic and magnetic properties of Co3O2BO3:Mn are compared with the same for the isostructural analogs Co3O2BO3 and CoO2BO3:Fe.

Dissolution of quartz in aqueous basic solution, 106-236 C - Surface kinetics of 'perfect' crystallographic faces

NASA Technical Reports Server (NTRS)

Gratz, Andrew J.; Bird, Peter; Quiro, Glenn B.

1990-01-01

A highly accurate method, called the negative crystal method, for determining the rate of dissolution on specific crystallographic faces of crystals was developed, in which the dissolution rates of nominally perfect crystal faces are obtained by measuring the size of individual negative crystals during a sequence of dissolution steps. The method was applied to determine the apparent activation energy and rate constants for the dissolution of quartz in 0.01 M KOH solutions at temperatures from 106 to 236 C. Also investigated were the effects of hydroxyl activity and ionic strength. The apparent activation energies for the dissolution of the prism and of the rhomb were determined.

Crystallographic analysis of the solid-state dewetting of polycrystalline gold film using automated indexing in a transmission electron microscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jang, S. A.; Lee, H. J.; Oh, Y. J., E-mail: yjoh@hanbat.ac.kr

We analyzed the effect of crystallographic anisotropy on the morphological evolution of a 12-nm-thick gold film during solid-state dewetting at high temperatures using automated indexing tool in a transmission electron microscopy. Dewetting initiated at grain-boundary triple junctions adjacent to large grains resulting from abnormal grain growth driven by (111) texture development. Voids at the junctions developed shapes with faceted edges bounded by low-index crystal planes. The kinetic mobility of the edges varied with the crystal orientation normal to the edges, with a predominance of specific edges with the slowest retraction rates as the annealing time was increased.

The effect of crystallographic misorientation and interfacial separation on jump-to-contact behavior and defect generation in aluminum

NASA Astrophysics Data System (ADS)

Khajehvand, Milad; Sepehrband, Panthea

2018-07-01

The jump-to-contact (JC) phenomenon for (111)-oriented surfaces in aluminum at room temperature is studied via molecular dynamics simulations. The effect of crystallographic misorientation and interfacial distance on the JC behavior and distribution of the resultant defects at the interface is investigated. The effect of misorientation on the critical distance for JC is found to be negligible. However, when JC occurs, different distribution of defects is observed for various misorientation angles. The density of defects is shown to be a function of interfacial distance for low misorientation angles, but independent of it for misorientation angles of ∼30 ± 10°.

Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis

PubMed Central

Fancher, Chris M.; Han, Zhen; Levin, Igor; Page, Katharine; Reich, Brian J.; Smith, Ralph C.; Wilson, Alyson G.; Jones, Jacob L.

2016-01-01

A Bayesian inference method for refining crystallographic structures is presented. The distribution of model parameters is stochastically sampled using Markov chain Monte Carlo. Posterior probability distributions are constructed for all model parameters to properly quantify uncertainty by appropriately modeling the heteroskedasticity and correlation of the error structure. The proposed method is demonstrated by analyzing a National Institute of Standards and Technology silicon standard reference material. The results obtained by Bayesian inference are compared with those determined by Rietveld refinement. Posterior probability distributions of model parameters provide both estimates and uncertainties. The new method better estimates the true uncertainties in the model as compared to the Rietveld method. PMID:27550221

Nanoparticle Superlattice Engineering with DNA

NASA Astrophysics Data System (ADS)

Macfarlane, Robert J.; Lee, Byeongdu; Jones, Matthew R.; Harris, Nadine; Schatz, George C.; Mirkin, Chad A.

2011-10-01

A current limitation in nanoparticle superlattice engineering is that the identities of the particles being assembled often determine the structures that can be synthesized. Therefore, specific crystallographic symmetries or lattice parameters can only be achieved using specific nanoparticles as building blocks (and vice versa). We present six design rules that can be used to deliberately prepare nine distinct colloidal crystal structures, with control over lattice parameters on the 25- to 150-nanometer length scale. These design rules outline a strategy to independently adjust each of the relevant crystallographic parameters, including particle size (5 to 60 nanometers), periodicity, and interparticle distance. As such, this work represents an advance in synthesizing tailorable macroscale architectures comprising nanoscale materials in a predictable fashion.

Phasing via pure crystallographic least squares: an unexpected feature.

PubMed

Burla, Maria Cristina; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Polidori, Giampiero

2018-03-01

Crystallographic least-squares techniques, the main tool for crystal structure refinement of small and medium-size molecules, are for the first time used for ab initio phasing. It is shown that the chief obstacle to such use, the least-squares severe convergence limits, may be overcome by a multi-solution procedure able to progressively recognize and discard model atoms in false positions and to include in the current model new atoms sufficiently close to correct positions. The applications show that the least-squares procedure is able to solve many small structures without the use of important ancillary tools: e.g. no electron-density map is calculated as a support for the least-squares procedure.

A crystallographic model for the tensile and fatigue response for Rene N4 at 982 C

NASA Technical Reports Server (NTRS)

Sheh, M. Y.; Stouffer, D. C.

1990-01-01

An anisotropic constitutive model based on crystallographic slip theory was formulated for nickel-base single-crystal superalloys. The current equations include both drag stress and back stress state variables to model the local inelastic flow. Specially designed experiments have been conducted to evaluate the existence of back stress in single crystals. The results showed that the back stress effect of reverse inelastic flow on the unloading stress is orientation-dependent, and a back stress state variable in the inelastic flow equation is necessary for predicting inelastic behavior. Model correlations and predictions of experimental data are presented for the single crystal superalloy Rene N4 at 982 C.

Dielectric and Piezoelectric Properties of Barium-substituted Sr1.9Ca0.1NaNb5O15 Ceramics

NASA Astrophysics Data System (ADS)

Xie, Rong-Jun; Akimune, Yoshio; Wang, Ruiping; Hirosaki, Naoto; Nishimura, Toshiyuki

2003-12-01

Highly dense piezoelectric ceramics of tungsten bronze-type (Sr1.9Ca0.1)1-0.5xBaxNaNb5O15 (where x=0.1--0.8) were prepared by spark plasma sintering. The crystallographic parameters, dielectric behaviors and piezoelectric properties of the sintered ceramics were investigated, and the effects of the Ba substitution on these electrical properties were discussed. The structural analysis and the electrical property measurements indicate a morphotropic phase boundary (MPB)-like phenomenon at x=0.4--0.5. In all compositions, a diffuse phase transition and a relaxor behavior are observed. The electrical properties are found to be crystallographically dependent.

The effect of grooves in amorphous substrates on the orientation of metal deposits. I - Carbon substrates

NASA Technical Reports Server (NTRS)

Anton, R.; Poppa, H.; Flanders, D. C.

1982-01-01

The graphoepitaxial alignment of vapor-deposited discrete metal crystallites is investigated in the nucleation and growth stages and during annealing by in situ UHV/TEM techniques. Various stages of nucleation, growth and coalescence of vapor deposits of Au, Ag, Pb, Sn, and Bi on amorphous, topographically structured C substrates are analyzed by advanced dark-field techniques to detect preferred local orientations. It is found that the topography-induced orientation of metal crystallites depends strongly on their mobility and their respective tendency to develop pronounced crystallographic shapes. Lowering of the average surface free energies and increasing the crystallographic surface energy anisotropies cause generally improved graphoepitaxial alignments.

Anisotropic constitutive modeling for nickel base single crystal superalloys using a crystallographic approach

NASA Technical Reports Server (NTRS)

Stouffer, D. C.; Sheh, M. Y.

1988-01-01

A micromechanical model based on crystallographic slip theory was formulated for nickel-base single crystal superalloys. The current equations include both drag stress and back stress state variables to model the local inelastic flow. Specially designed experiments have been conducted to evaluate the effect of back stress in single crystals. The results showed that (1) the back stress is orientation dependent; and (2) the back stress state variable in the inelastic flow equation is necessary for predicting anelastic behavior of the material. The model also demonstrated improved fatigue predictive capability. Model predictions and experimental data are presented for single crystal superalloy Rene N4 at 982 C.

Structure-Guided Design and Optimization of Dipeptidyl Inhibitors of Norovirus 3CL Protease. Structure–Activity Relationships and Biochemical, X-ray Crystallographic, Cell-Based, and In Vivo Studies

DOE PAGES

Galasiti Kankanamalage, Anushka C.; Kim, Yunjeong; Weerawarna, Pathum M.; ...

2015-04-09

Norovirus infection constitutes the primary cause of acute viral gastroenteritis. There are currently no vaccines or norovirus-specific antiviral therapeutics available for the management of norovirus infection. Norovirus 3C-like protease is essential for viral replication, consequently, inhibition of this enzyme is a fruitful avenue of investigation that may lead to the emergence of antinorovirus therapeutics. We describe herein the optimization of dipeptidyl inhibitors of norovirus 3C-like protease using iterative SAR, X-ray crystallographic, and enzyme and cell-based studies. We also demonstrate herein in vivo efficacy of an inhibitor using the murine model of norovirus infection.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan

2006-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cellmore » volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.« less

Simultaneously enhanced strength and ductility for 3D-printed stainless steel 316L by selective laser melting

NASA Astrophysics Data System (ADS)

Sun, Zhongji; Tan, Xipeng; Tor, Shu Beng; Chua, Chee Kai

2018-04-01

Laser-based powder-bed fusion additive manufacturing or three-dimensional printing technology has gained tremendous attention due to its controllable, digital, and automated manufacturing process, which can afford a refined microstructure and superior strength. However, it is a major challenge to additively manufacture metal parts with satisfactory ductility and toughness. Here we report a novel selective laser melting process to simultaneously enhance the strength and ductility of stainless steel 316L by in-process engineering its microstructure into a <011> crystallographic texture. We find that the tensile strength and ductility of SLM-built stainless steel 316L samples could be enhanced by 16% and 40% respectively, with the engineered <011> textured microstructure compared to the common <001> textured microstructure. This is because the favorable nano-twinning mechanism was significantly more activated in the <011> textured stainless steel 316L samples during plastic deformation. In addition, kinetic simulations were performed to unveil the relationship between the melt pool geometry and crystallographic texture. The new additive manufacturing strategy of engineering the crystallographic texture can be applied to other metals and alloys with twinning-induced plasticity. This work paves the way to additively manufacture metal parts with high strength and high ductility.

Refolding, crystallization and preliminary X-ray crystallographic studies of the β-barrel domain of BamA, a membrane protein essential for outer membrane protein biogenesis.

PubMed

Ni, Dongchun; Yang, Kun; Huang, Yihua

2014-03-01

In Gram-negative bacteria, the assembly of outer membrane proteins (OMPs) requires a five-protein β-barrel assembly machinery (BAM) complex, of which BamA is an essential and evolutionarily conserved integral outer membrane protein. Here, the refolding, crystallization and preliminary X-ray crystallographic characterization of the β-barrel domain of BamA from Escherichia coli (EcBamA) are reported. Native and selenomethionine-substituted EcBamA proteins were crystallized at 16°C and X-ray diffraction data were collected to 2.6 and 3.7 Å resolution, respectively. The native crystals belonged to space group P21212, with unit-cell parameters a = 118.492, b = 159.883, c = 56.000 Å and two molecules in one asymmetric unit; selenomethionine-substituted protein crystals belonged to space group P4322, with unit-cell parameters a = b = 163.162, c = 46.388 Å and one molecule in one asymmetric unit. Initial phases for EcBamA β-barrel domain were obtained from a SeMet SAD data set. These preliminary X-ray crystallographic studies paved the way for further structural determination of the β-barrel domain of EcBamA.

Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening.

PubMed

Amano, Yasushi; Tanabe, Eiki; Yamaguchi, Tomohiko

2015-05-15

Soluble epoxide hydrolase (sEH) is a potential target for the treatment of inflammation and hypertension. X-ray crystallographic fragment screening was used to identify fragment hits and their binding modes. Eight fragment hits were identified via soaking of sEH crystals with fragment cocktails, and the co-crystal structures of these hits were determined via individual soaking. Based on the binding mode, N-ethylmethylamine was identified as a promising scaffold that forms hydrogen bonds with the catalytic residues of sEH, Asp335, Tyr383, and Tyr466. Compounds containing this scaffold were selected from an in-house chemical library and assayed. Although the starting fragment had a weak inhibitory activity (IC50: 800μM), we identified potent inhibitors including 2-({[2-(adamantan-1-yl)ethyl]amino}methyl)phenol exhibiting the highest inhibitory activity (IC50: 0.51μM). This corresponded to a more than 1500-fold increase in inhibitory activity compared to the starting fragment. Co-crystal structures of the hit compounds demonstrate that the binding of N-ethylmethylamine to catalytic residues is similar to that of the starting fragment. We therefore consider crystallographic fragment screening to be appropriate for the identification of weak but promising fragment hits. Copyright © 2015 Elsevier Ltd. All rights reserved.

Solution NMR and molecular dynamics reveal a persistent alpha helix within the dynamic region of PsbQ from photosystem II of higher plants.

PubMed

Rathner, Petr; Rathner, Adriana; Horničáková, Michaela; Wohlschlager, Christian; Chandra, Kousik; Kohoutová, Jaroslava; Ettrich, Rüdiger; Wimmer, Reinhard; Müller, Norbert

2015-09-01

The extrinsic proteins of photosystem II of higher plants and green algae PsbO, PsbP, PsbQ, and PsbR are essential for stable oxygen production in the oxygen evolving center. In the available X-ray crystallographic structure of higher plant PsbQ residues S14-Y33 are missing. Building on the backbone NMR assignment of PsbQ, which includes this "missing link", we report the extended resonance assignment including side chain atoms. Based on nuclear Overhauser effect spectra a high resolution solution structure of PsbQ with a backbone RMSD of 0.81 Å was obtained from torsion angle dynamics. Within the N-terminal residues 1-45 the solution structure deviates significantly from the X-ray crystallographic one, while the four-helix bundle core found previously is confirmed. A short α-helix is observed in the solution structure at the location where a β-strand had been proposed in the earlier crystallographic study. NMR relaxation data and unrestrained molecular dynamics simulations corroborate that the N-terminal region behaves as a flexible tail with a persistent short local helical secondary structure, while no indications of forming a β-strand are found. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

DOE PAGES

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian; ...

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Raw diffraction data preservation and reuse: overview, update on practicalities and metadata requirements

PubMed Central

Kroon-Batenburg, Loes M. J.

2017-01-01

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an ‘Open Science’ model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education and training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction data via different types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromol­ecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. A number of specific case studies are presented, including an example research thread that provides complete open access to raw data. PMID:28250944

Biomineral shell formation under ocean acidification: a shift from order to chaos.

PubMed

Fitzer, Susan C; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S; Kamenos, Nicholas A; Phoenix, Vernon R; Cusack, Maggie

2016-02-15

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Biomineral shell formation under ocean acidification: a shift from order to chaos

PubMed Central

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-01-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments. PMID:26876022

The role of crystallographic texture in achieving low friction zinc oxide nanolaminate films

NASA Astrophysics Data System (ADS)

Mojekwu, Nneoma

Metal oxide nanolaminate films are potential high temperature solid lubricants due to their ability to exhibit significant plasticity when grain size is reduced to the nanometer scale, and defective growth structure is achieved by condensation of oxygen vacancies to form intrinsic stacking faults. This is in contrast to conventional microcrystalline and single crystal oxides that exhibit brittle fracture during loading in a sliding contact. This study emphasizes the additional effect of growth orientation, in particular crystallographic texture, on determining the sliding friction behavior in nanocolumnar grain zinc oxide films grown by atomic layer deposition. It was determined that zinc oxide low (0002) versus higher (101¯3) surface energy crystallographic planes influenced the sliding friction coefficient. Texturing of the (0002) grains resulted in a decreased adhesive component of friction thereby lowering the sliding friction coefficient to ˜0.25, while the friction coefficient doubled to ˜0.5 with increasing contribution of surface (101¯3) grains. In addition, the variation of the x-ray grazing incident angle from 0.5° to 5° was studied to better understand the surface grain orientation as a function of ZnO layer thickness in one versus four bilayer nanolaminates where the under layer (seed layer) was load-bearing Zn(Ti,Zr)O3.

Raw diffraction data preservation and reuse: Overview, update on practicalities and metadata requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kroon-Batenburg, Loes M. J.; Helliwell, John R.; McMahon, Brian

A topical review is presented of the rapidly developing interest in and storage options for the preservation and reuse of raw data within the scientific domain of the IUCr and its Commissions, each of which operates within a great diversity of instrumentation. A résumé is included of the case for raw diffraction data deposition. An overall context is set by highlighting the initiatives of science policy makers towards an `Open Science' model within which crystallographers will increasingly work in the future; this will bring new funding opportunities but also new codes of procedure within open science frameworks. Skills education andmore » training for crystallographers will need to be expanded. Overall, there are now the means and the organization for the preservation of raw crystallographic diffraction dataviadifferent types of archive, such as at universities, discipline-specific repositories (Integrated Resource for Reproducibility in Macromolecular Crystallography, Structural Biology Data Grid), general public data repositories (Zenodo, ResearchGate) and centralized neutron and X-ray facilities. Formulation of improved metadata descriptors for the raw data types of each of the IUCr Commissions is in progress; some detailed examples are provided. Lastly, a number of specific case studies are presented, including an example research thread that provides complete open access to raw data.« less

Biomineral shell formation under ocean acidification: a shift from order to chaos

NASA Astrophysics Data System (ADS)

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-02-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Crystallographic and theoretical studies of an inclusion complex of β-cyclodextrin with fentanyl.

PubMed

Ogawa, Noriko; Nagase, Hiromasa; Loftsson, Thorsteinn; Endo, Tomohiro; Takahashi, Chisato; Kawashima, Yoshiaki; Ueda, Haruhisa; Yamamoto, Hiromitsu

2017-10-15

The crystal structure of an inclusion complex of β-cyclodextrin (β-CD) with fentanyl was determined by single crystal X-ray diffraction analysis. The crystal belongs to the triclinic space group P1 and the complex comprises one fentanyl, two β-CD, and several water molecules. β-CD and fentanyl form a host-guest inclusion complex at a ratio of 2:1 and the asymmetric unit of the complex contains two host molecules (β-CDs) in a head-to-head arrangement that form dimers through hydrogen bonds between the secondary hydroxyl groups of β-CD and one guest molecule. Fentanyl is totally contained within the β-CD cavity and the structure of the phenylethyl part of fentanyl inside the dimeric cavity of the complex is disordered. Furthermore, theoretical molecular conformational calculations were conducted to clarify the mobility of the guest molecule in the β-CD cavity using CONFLEX software. Crystal optimization and crystal energy calculations were also conducted. The results of the theoretical calculations confirmed that the conformation of disorder part 1, which was high in occupancy by crystal structure analysis, was more stable. The phenylethyl part of fentanyl existed in several stable conformations. Copyright © 2017 Elsevier B.V. All rights reserved.

Room Temperature Antiferromagnetic Ordering of Nanocrystalline Tb1.90Ni0.10O3

NASA Astrophysics Data System (ADS)

Mandal, J.; Dalal, M.; Sarkar, B. J.; Chakrabarti, P. K.

2017-02-01

Nanocrystalline Ni-doped terbium oxide (Tb1.90Ni0.10O3) has been synthesized by the co-precipitation method followed by annealing at 700°C for 6 h in vacuum. The crystallographic phase and the substitution of Ni2+ ions in the lattice of Tb2O3 are confirmed by Rietveld analysis of the x-ray diffraction pattern using the software MAUD. High-resolution transmission electron microscopy is also carried out to study the morphology of the sample. Magnetic measurements are carried out at different temperatures from 5 K to 300 K using a superconducting quantum interference device (SQUID) magnetometer. The dependence of the magnetization of Tb1.90Ni0.10O3 as a function of temperature ( M- T) and magnetic field ( M- H) suggests the presence of both paramagnetic and antiferromagnetic phase at room temperature, but antiferromagnetic phase dominates below ˜120 K. The lack of saturation in the M- H curve and good fitting of the M- T curve by the Johnston formula also indicate the presence of both paramagnetic and antiferromagnetic phase at room temperature. Interestingly, an antiferromagnetic to ferromagnetic phase transition is observed below ˜40 K. The result also shows a high value of magnetization at 5 K.

EPICS controlled sample mounting robots at the GM/CA CAT.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Makarov, O. A.; Benn, R.; Corcoran, S.

2007-11-11

GM/CA CAT at Sector 23 of the advanced photon source (APS) is an NIH funded facility for crystallographic structure determination of biological macromolecules by X-ray diffraction [R.F. Fischetti, et al., GM/CA canted undulator beamlines for protein crystallography, Acta Crystallogr. A 61 (2005) C139]. The facility consists of three beamlines; two based on canted undulators and one on a bending magnet. The scientific and technical goals of the CAT emphasize streamlined, efficient throughput for a variety of sample types, sizes and qualities, representing the cutting edge of structural biology research. For this purpose all three beamlines are equipped with the ALS-stylemore » robots [C.W.Cork, et al. Status of the BCSB automated sample mounting and alignment system for macromolecular crystallography at the Advanced Light Source, SRI-2003, San-Francisco, CA, USA, August 25-29, 2003] for an automated mounting of cryo-protected macromolecular crystals. This report summarizes software and technical solutions implemented with the first of the three operational robots at beamline 23-ID-B. The automounter's Dewar can hold up to 72 or 96 samples residing in six Rigaku ACTOR magazines or ALS-style pucks, respectively. Mounting of a crystal takes approximately 2 s, during which time the temperature of the crystal is maintained near that of liquid nitrogen.« less

Structural similarities in tetraaryltins described by virtual non-crystallographic rotations or translations: Kitaigorodskii's morphotropism is revisited.

PubMed

Kálmán, Alajos; Fábián, László

2007-06-01

Recently Kálmán [(2005), Acta Cryst. B61, 536-547] revealed that semirigid molecules or their patterns held together e.g. by hydrogen bonds may perform non-crystallographic rotations (through 180, 90 degrees etc.) around themselves whenever a substitution, ring enlargement or isomerization destroys the existing close packing, i.e. the novel substituent or the enlarged ring can no longer fit in the hollows formed between the molecules. In other words, the old and new arrangements of such chemically similar molecules can be converted into each other by virtual rotations. However, when a semirigid molecule without substitution, but under the influence of solvents, temperature etc., is fully or partly rearranged in the solid state, the corresponding non-crystallographic rotation (hereinafter ncr) is real and gives rise to polymorphism. Such polymorphs are hallmarked by full or partial isostructurality and show that ncrs always occur together with isostructurality. First Kitaigorodskii [(1961), Organic Chemical Crystallography, New York: Consultants Bureau] reported on the structural similarity of three tetraaryltins, (p-RC(6)H(4))(4)Sn, R = H, CH(3), CH(3)O, which is terminated by the larger C(2)H(5)O group. A revisit to these structures revealed that the tetragonal --> monoclinic conversion termed by Kitaigorodskii as a ;morphotropic step' is also performed by an ncr. Similarly, other tetraaryltins in the literature are related by ncrs or the nc translation of the semirigid tetrahedra, or they remain isostructural. Since one of the definitions of morphotropism, a word of Greek origin, is 'turn of form', the ncrs of semirigid molecules can be denoted--following Kitaigorodskii--by this word, whereas its alternative definition in the morphological crystallography of ;unidirectional changes' [applied by Groth (1870). Ber. Chem. Ges. 3, 449-457] covers the non-crystallographic translations described first in this work.

Modelling of deformation and recrystallisation microstructures in rocks and ice

NASA Astrophysics Data System (ADS)

Bons, Paul D.; Evans, Lynn A.; Gomez-Rivas, Enrique; Griera, Albert; Jessell, Mark W.; Lebensohn, Ricardo; Llorens, Maria-Gema; Peternell, Mark; Piazolo, Sandra; Weikusat, Ilka; Wilson, Chris J. L.

2015-04-01

Microstructures both record the deformation history of a rock and strongly control its mechanical properties. As microstructures in natural rocks only show the final "post-mortem" state, geologists have attempted to simulate the development of microstructures with experiments and later numerical models. Especially in-situ experiments have given enormous insight, as time-lapse movies could reveal the full history of a microstructure. Numerical modelling is an alternative approach to simulate and follow the change in microstructure with time, unconstrained by experimental limitations. Numerical models have been applied to a range of microstructural processes, such as grain growth, dynamic recrystallisation, porphyroblast rotation, vein growth, formation of mylonitic fabrics, etc. The numerical platform "Elle" (www.elle.ws) in particular has brought progress in the simulation of microstructural development as it is specifically designed to include the competition between simultaneously operating processes. Three developments significantly improve our capability to simulate microstructural evolution: (1) model input from the mapping of crystallographic orientation with EBSD or the automatic fabric analyser, (2) measurement of grain size and crystallographic preferred orientation evolution using neutron diffraction experiments and (3) the implementation of the full-field Fast Fourier Transform (FFT) solver for modelling anisotropic crystal-plastic deformation. The latter enables the detailed modelling of stress and strain as a function of local crystallographic orientation, which has a strong effect on strain localisation such as, for example, the formation of shear bands. These models can now be compared with the temporal evolution of crystallographic orientation distributions in in-situ experiments. In the last decade, the possibility to combine experiments with numerical simulations has allowed not only verification and refinement of the numerical simulation technique but also increased significantly the ability to predict and/or interpret natural microstructures. This contribution will present the most recent developments in in-situ and numerical modelling of deformation and recrystallisation microstructures in rocks and in ice.

CIF2Cell: Generating geometries for electronic structure programs

NASA Astrophysics Data System (ADS)

Björkman, Torbjörn

2011-05-01

The CIF2Cell program generates the geometrical setup for a number of electronic structure programs based on the crystallographic information in a Crystallographic Information Framework (CIF) file. The program will retrieve the space group number, Wyckoff positions and crystallographic parameters, make a sensible choice for Bravais lattice vectors (primitive or principal cell) and generate all atomic positions. Supercells can be generated and alloys are handled gracefully. The code currently has output interfaces to the electronic structure programs ABINIT, CASTEP, CPMD, Crystal, Elk, Exciting, EMTO, Fleur, RSPt, Siesta and VASP. Program summaryProgram title: CIF2Cell Catalogue identifier: AEIM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU GPL version 3 No. of lines in distributed program, including test data, etc.: 12 691 No. of bytes in distributed program, including test data, etc.: 74 933 Distribution format: tar.gz Programming language: Python (versions 2.4-2.7) Computer: Any computer that can run Python (versions 2.4-2.7) Operating system: Any operating system that can run Python (versions 2.4-2.7) Classification: 7.3, 7.8, 8 External routines: PyCIFRW [1] Nature of problem: Generate the geometrical setup of a crystallographic cell for a variety of electronic structure programs from data contained in a CIF file. Solution method: The CIF file is parsed using routines contained in the library PyCIFRW [1], and crystallographic as well as bibliographic information is extracted. The program then generates the principal cell from symmetry information, crystal parameters, space group number and Wyckoff sites. Reduction to a primitive cell is then performed, and the resulting cell is output to suitably named files along with documentation of the information source generated from any bibliographic information contained in the CIF file. If the space group symmetries is not present in the CIF file the program will fall back on internal tables, so only the minimal input of space group, crystal parameters and Wyckoff positions are required. Additional key features are handling of alloys and supercell generation. Additional comments: Currently implements support for the following general purpose electronic structure programs: ABINIT [2,3], CASTEP [4], CPMD [5], Crystal [6], Elk [7], exciting [8], EMTO [9], Fleur [10], RSPt [11], Siesta [12] and VASP [13-16]. Running time: The examples provided in the distribution take only seconds to run.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kish, Kevin; McDonnell, Patricia A.; Goldfarb, Valentina

Protein tyrosine phosphatase {gamma} is a membrane-bound receptor and is designated RPTP{gamma}. RPTP{gamma} and two mutants, RPTP{gamma}(V948I, S970T) and RPTP{gamma}(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form wasmore » only obtained in the presence of a particularly elaborated inhibitor.« less

Friction and wear of single-crystal manganese-zinc ferrite

NASA Technical Reports Server (NTRS)

Miyoshi, K.; Buckley, D. H.

1979-01-01

Sliding friction experiments were conducted with single crystal manganese-zinc ferrite in contact with itself and with transition metals. Results indicate mating highest atomic density directions (110) on matched crystallographic planes exhibit the lowest coefficient of friction, indicating that direction is important in the friction behavior of ferrite. Matched parallel high atomic density planes and crystallographic directions at the interface exhibit low coefficients of friction. The coefficients of friction for ferrite in contact with various metals are related to the relative chemical activity of these metals. The more active the metal, the higher the coefficient of friction. Cracking and the formation of hexagon- and rectangular-shaped platelet wear debris due to cleavages of (110) planes are observed on the ferrite surfaces as a result of sliding.

Automating tasks in protein structure determination with the clipper python module

PubMed Central

McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M.; Hoh, Soon Wen; Jenkins, Huw T.; Dodson, Eleanor

2017-01-01

Abstract Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine‐independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo‐microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. PMID:28901669

Mechanical properties of hydroxyapatite single crystals from nanoindentation data

PubMed Central

Zamiri, A.; De, S.

2011-01-01

In this paper we compute elasto-plastic properties of hydroxyapatite single crystals from nanindentation data using a two-step algorithm. In the first step the yield stress is obtained using hardness and Young’s modulus data, followed by the computation of the flow parameters. The computational approach is first validated with data from existing literature. It is observed that hydroxyapatite single crystals exhibit anisotropic mechanical response with a lower yield stress along the [1010] crystallographic direction compared to the [0001] direction. Both work hardening rate and work hardening exponent are found to be higher for indentation along the [0001] crystallographic direction. The stress-strain curves extracted here could be used for developing constitutive models for hydroxyapatite single crystals. PMID:21262492

A spherical electron-channelling pattern map for use in quartz petrofabric analysis

USGS Publications Warehouse

Lloyd, G.E.; Ferguson, C.C.

1986-01-01

Electron channelling patterns (ECP's) are formed in the scanning electron microscope (SEM) by the interaction between the incident electrons and the lattice of crystalline specimens. The patterns are unique for a particular crystallographic orientation and are therefore of considerable potential in petrofabric studies provided they can be accurately indexed. Indexing requires an ECP-map of the crystallographic stereogram or unit triangle covering all possible orientations and hence ECP patterns. Due to the presence of long-range distortions in planar ECP-maps, it is more convenient to construct the maps over a spherical surface. This also facilitates the indexing of individual ECP's. A spherical ECP-map for quartz is presented together with an example of its use in petrofabric analysis. ?? 1986.

Giant voltage-controlled magnetic anisotropy effect in a crystallographically strained CoFe system

NASA Astrophysics Data System (ADS)

Kato, Yushi; Yoda, Hiroaki; Saito, Yoshiaki; Oikawa, Soichi; Fujii, Keiko; Yoshiki, Masahiko; Koi, Katsuhiko; Sugiyama, Hideyuki; Ishikawa, Mizue; Inokuchi, Tomoaki; Shimomura, Naoharu; Shimizu, Mariko; Shirotori, Satoshi; Altansargai, Buyandalai; Ohsawa, Yuichi; Ikegami, Kazutaka; Tiwari, Ajay; Kurobe, Atsushi

2018-05-01

We experimentally demonstrate a giant voltage-controlled magnetic anisotropy (VCMA) coefficient in a crystallographically strained CoFe layer (∼15 monolayers in thickness) in a MgO/CoFe/Ir system. We observed a strong applied voltage dependence of saturation field and an asymmetric concave behavior with giant VCMA coefficients of ‑758 and 1043 fJ V‑1 m‑1. The result of structural analysis reveals epitaxial growth in MgO/CoFe/Ir layers and the orientation relationship MgO(001)[110] ∥ CoFe(001)[100] ∥ Ir(001)[110]. The CoFe layer has a bcc structure and a tetragonal distortion due to the lattice mismatch; therefore, the CoFe layer has a large perpendicular magnetic anisotropy.

Thermal expansion and elastic anisotropy in single crystal Al2O3 and SiC reinforcements

NASA Technical Reports Server (NTRS)

Salem, Jonathan A.; Li, Zhuang; Bradt, Richard C.

1994-01-01

In single crystal form, SiC and Al2O3 are attractive reinforcing components for high temperature composites. In this study, the axial coefficients of thermal expansion and single crystal elastic constants of SiC and Al2O3 were used to determine their coefficients of thermal expansion and Young's moduli as a function of crystallographic orientation and temperature. SiC and Al2O3 exhibit a strong variation of Young's modulus with orientation; however, their moduli and anisotropies are weak functions of temperature below 1000 C. The coefficients of thermal expansion exhibit significant temperature dependence, and that of the non-cubic Al2O3 is also a function of crystallographic orientation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aagesen, Larry K.; Thornton, Katsuyo, E-mail: kthorn@umich.edu; Coltrin, Michael E.

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. The model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. The model provides a route to optimize masks and processing conditions during materialsmore » synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

High resolution electron backscatter diffraction (EBSD) data from calcite biominerals in recent gastropod shells.

PubMed

Pérez-Huerta, Alberto; Dauphin, Yannicke; Cuif, Jean Pierre; Cusack, Maggie

2011-04-01

Electron backscatter diffraction (EBSD) is a microscopy technique that reveals in situ crystallographic information. Currently, it is widely used for the characterization of geological materials and in studies of biomineralization. Here, we analyze high resolution EBSD data from biogenic calcite in two mollusk taxa, Concholepas and Haliotis, previously used in the understanding of complex biomineralization and paleoenvironmental studies. Results indicate that Concholepas has less ordered prisms than in Haliotis, and that in Concholepas the level of order is not homogenous in different areas of the shell. Overall, the usefulness of data integration obtained from diffraction intensity and crystallographic orientation maps, and corresponding pole figures, is discussed as well as its application to similar studies. © 2010 Elsevier Ltd. All rights reserved.

Crystallographic identification of an unexpected by-product in an Ullman's reaction toward biphenyls: 1-(4-hexyloxy-3-hydroxyphenyl)ethanone.

PubMed

Manzano, Veronica E; Baggio, Ricardo; Cukiernik, Fabio D

2015-11-01

The synthesis of 3,3'-diacetoxy-4,4'-bis(hexyloxy)biphenyl following the nickel-modified Ullmann reaction yielded a by-product which was identified successfully by crystallographic analysis as 1-(4-hexyloxy-3-hydroxyphenyl)ethanone, C14H20O3. This unexpected nonbiphenyl by-product exhibited IR, (1)H NMR, (13)C NMR and COSY (correlation spectroscopy) spectra fully consistent with the proposed structure. The compound crystallized in the orthorombic Pbca space group, with two independent formula units in the asymmetric unit (one of which was slightly disordered), and showed a supramolecular architecture in which molecules linked by hydroxy-ethanone O-H···O interactions are organized in columns separated by the aliphatic tails.

Characterization of Localized Corrosion in an Al-Cu-Li Alloy

NASA Astrophysics Data System (ADS)

Luo, Chen; Zhang, Xinxin; Zhou, Xiaorong; Sun, Zhihua; Zhang, Xiaoyun; Tang, Zhihui; Lu, Feng; Thompson, George E.

2016-05-01

Corrosion behaviors of recently developed 2A97-T6 aluminum-copper-lithium alloy in sodium chloride solution are investigated using scanning electron and transmission electron microscopies in conjunction with electron backscatter diffraction. It has been found that corrosion product rings were established on the alloy surface as early as 5 min during immersion in sodium chloride solution. Meanwhile, hydrogen continuously evolved from within the rings. Pitting corrosion is evident with crystallographic dependant corrosion channel facets mainly parallel to {100} planes. Non-uniform distribution of misorientation in the 2A97 aluminum alloy results in a portion of grains of relatively high stored energy. Such grains were preferentially attacked, serving as local anodes, during the development of crystallographic pitting.

Synthesis, crystal structures and luminescence properties of the Eu 3+-doped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13

NASA Astrophysics Data System (ADS)

Höss, Patrick; Osvet, Andres; Meister, Frank; Batentschuk, Miroslaw; Winnacker, Albrecht; Schleid, Thomas

2008-10-01

Y 2Te 4O 11:Eu 3+ and Y 2Te 5O 13:Eu 3+ single crystals in sub-millimeter scale were synthesized from the binary oxides (Y 2O 3, Eu 2O 3 and TeO 2) using CsCl as fluxing agent. Crystallographic structures of the undoped yttrium oxotellurates(IV) Y 2Te 4O 11 and Y 2Te 5O 13 have been determined and refined from single-crystal X-ray diffraction data. In Y 2Te 4O 11, a layered structure is present where the reticulated sheets consisting of edge-sharing [YO 8] 13- polyhedra are interconnected by the oxotellurate(IV) units, whereas in Y 2Te 5O 13 only double chains of condensed yttrium-oxygen polyhedra with coordination numbers of 7 and 8 are left, now linked in two crystallographic directions by the oxotellurate(IV) entities. The Eu 3+ luminescence spectra and the decay time from different energy levels of the doped compounds were investigated and all detected emission levels were identified. Luminescence properties of the Eu 3+ cations have been interpreted in consideration of the now accessible detailed crystallographic data of the yttrium compounds, providing the possibility to examine the influence of the local symmetry of the oxygen coordination spheres.

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

Spherulitic Growth of Hematite Under Hydrothermal Conditions: Insights into the Growth Mechanism of Hematite Spherules at Meridiani Planum Mars.

NASA Technical Reports Server (NTRS)

Ming, Douglas W.; Golden, D. C.; Morris, R. V.

2010-01-01

Hematite-rich spherules were discovered embedded in sulfate-rich outcrop rock and as lag deposits of whole and broken spherules by the Opportunity rover at Meridiani Planem [1-6]. The Mars Global Surveyor (MGS) Thermal Emission Spectrometer (TES), which has a wider spectral range compared to the Mars Exploration Rover Mini-TES, provided an important constraint that hematite-rich spherules are dominated by emission along the crystallographic c-axis [7-10]. We have previously synthesized hematite spherules whose mineralogic, chemical, and crystallographic properties are strikingly similar to those for the hematite-rich spherules at Meridiani Planum [11]. The spherules were synthesized in the laboratory along with hydronium jarosite and minor hydronium alunite from Fe-Al-Mg-S-Cl acid sulfate solutions under hydrothermal conditions. The reaction sequence was (1) precipitation of hydronium jarosite, (2) jarosite dissolution and precipitation of hematite spherules, and (3) precipitation of hydronium alunite upon depletion of hydronium jarosite. The spherules exhibit a radial growth texture with the crystallographic c-axis aligned along the radial direction, so that thermal emission spectra have no hematite emissivity minimum at approx.390/cm similar to the emission spectra returned by MGS TES. The objective of this paper is to expand on our initial studies [11] to examine the morphological evolution during growth of spherules starting from sub-micrometer crystals to spherules many orders of magnitude in size.

Expression, limited proteolysis and preliminary crystallographic analysis of IpaD, a component of the Shigella flexneri type III secretion system

PubMed Central

Johnson, Steven; Roversi, Pietro; Espina, Marianela; Deane, Janet E.; Birket, Susan; Picking, William D.; Blocker, Ariel; Picking, Wendy L.; Lea, Susan M.

2006-01-01

IpaD, the putative needle-tip protein of the Shigella flexneri type III secretion system, has been overexpressed and purified. Crystals were grown of the native protein in space group P212121, with unit-cell parameters a = 55.9, b = 100.7, c = 112.0 Å, and data were collected to 2.9 Å resolution. Analysis of the native Patterson map revealed a peak at 50% of the origin on the Harker section v = 0.5, suggesting twofold non-crystallographic symmetry parallel to the b crystallographic axis. As attempts to derivatize or grow selenomethionine-labelled protein crystals failed, in-drop proteolysis was used to produce new crystal forms. A trace amount of subtilisin Carlsberg was added to IpaD before sparse-matrix screening, resulting in the production of several new crystal forms. This approach produced SeMet-labelled crystals and diffraction data were collected to 3.2 Å resolution. The SeMet crystals belong to space group C2, with unit-cell parameters a = 139.4, b = 45.0, c = 99.5 Å, β = 107.9°. An anomalous difference Patterson map revealed peaks on the Harker section v = 0, while the self-rotation function indicates the presence of a twofold noncrystallographic symmetry axis, which is consistent with two molecules per asymmetric unit. PMID:16946465

Expression, limited proteolysis and preliminary crystallographic analysis of IpaD, a component of the Shigella flexneri type III secretion system.

PubMed

Johnson, Steven; Roversi, Pietro; Espina, Marianela; Deane, Janet E; Birket, Susan; Picking, William D; Blocker, Ariel; Picking, Wendy L; Lea, Susan M

2006-09-01

IpaD, the putative needle-tip protein of the Shigella flexneri type III secretion system, has been overexpressed and purified. Crystals were grown of the native protein in space group P2(1)2(1)2(1), with unit-cell parameters a = 55.9, b = 100.7, c = 112.0 A, and data were collected to 2.9 A resolution. Analysis of the native Patterson map revealed a peak at 50% of the origin on the Harker section v = 0.5, suggesting twofold non-crystallographic symmetry parallel to the b crystallographic axis. As attempts to derivatize or grow selenomethionine-labelled protein crystals failed, in-drop proteolysis was used to produce new crystal forms. A trace amount of subtilisin Carlsberg was added to IpaD before sparse-matrix screening, resulting in the production of several new crystal forms. This approach produced SeMet-labelled crystals and diffraction data were collected to 3.2 A resolution. The SeMet crystals belong to space group C2, with unit-cell parameters a = 139.4, b = 45.0, c = 99.5 A, beta = 107.9 degrees . An anomalous difference Patterson map revealed peaks on the Harker section v = 0, while the self-rotation function indicates the presence of a twofold noncrystallographic symmetry axis, which is consistent with two molecules per asymmetric unit.

Crystal Structure Prediction via Deep Learning.

PubMed

Ryan, Kevin; Lengyel, Jeff; Shatruk, Michael

2018-06-06

We demonstrate the application of deep neural networks as a machine-learning tool for the analysis of a large collection of crystallographic data contained in the crystal structure repositories. Using input data in the form of multi-perspective atomic fingerprints, which describe coordination topology around unique crystallographic sites, we show that the neural-network model can be trained to effectively distinguish chemical elements based on the topology of their crystallographic environment. The model also identifies structurally similar atomic sites in the entire dataset of ~50000 crystal structures, essentially uncovering trends that reflect the periodic table of elements. The trained model was used to analyze templates derived from the known binary and ternary crystal structures in order to predict the likelihood to form new compounds that could be generated by placing elements into these structural templates in combinatorial fashion. Statistical analysis of predictive performance of the neural-network model, which was applied to a test set of structures never seen by the model during training, indicates its ability to predict known elemental compositions with a high likelihood of success. In ~30% of cases, the known compositions were found among top-10 most likely candidates proposed by the model. These results suggest that the approach developed in this work can be used to effectively guide the synthetic efforts in the discovery of new materials, especially in the case of systems composed of 3 or more chemical elements.

Production, Purification and Preliminary X-ray Crystallographic Studies of Adeno-Associated Virus Serotype 9

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mitchell, M.; Nam, H; Carter, A

2009-01-01

Adeno-associated virus (AAV) serotype 9, which is under development for gene-delivery applications, shows significantly enhanced capsid-associated transduction efficiency in muscle compared with other AAV serotypes. With the aim of characterizing the structural determinants of this property, the purification, crystallization and preliminary X-ray crystallographic analyses of the AAV9 viral capsid are reported. The crystals diffracted X-rays to 2.8 A resolution using synchrotron radiation and belonged to the trigonal space group P32, with unit-cell parameters a = b = 251.0, c = 640.0 A. There are three complete viral capsids in the crystal unit cell. The orientation and position of the asymmetricmore » unit capsid have been determined by molecular-replacement methods and structure determination is in progress.« less

Constitutive modeling of superalloy single crystals with verification testing

NASA Technical Reports Server (NTRS)

Jordan, Eric; Walker, Kevin P.

1985-01-01

The goal is the development of constitutive equations to describe the elevated temperature stress-strain behavior of single crystal turbine blade alloys. The program includes both the development of a suitable model and verification of the model through elevated temperature-torsion testing. A constitutive model is derived from postulated constitutive behavior on individual crystallographic slip systems. The behavior of the entire single crystal is then arrived at by summing up the slip on all the operative crystallographic slip systems. This type of formulation has a number of important advantages, including the prediction orientation dependence and the ability to directly represent the constitutive behavior in terms which metallurgists use in describing the micromechanisms. Here, the model is briefly described, followed by the experimental set-up and some experimental findings to date.

Persistent four-coordinate iron-centered radical stabilized by π-donation† †Electronic supplementary information (ESI) available: Experimental, crystallographic, computational details, and crystal data for 2, 4, 5 and 8. CCDC 1057111–1057113 and 1425703. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc02601f Click here for additional data file. Click here for additional data file.

PubMed Central

Ishida, Shintaro; Hirakawa, Fumiya; Shiota, Yoshihito; Yoshizawa, Kazunari; Kanegawa, Shinji; Sato, Osamu; Nagashima, Hideo

2016-01-01

Dinuclear iron carbonyl complex 2, which contains an elongated unsupported Fe–Fe bond, was synthesized by the reaction between Fe2(CO)9 and phosphinyl radical 1. Thermal Fe–Fe bond homolysis led to the generation of a four-coordinate carbonyl-based iron-centered radical, 3, which is stabilized by π-donation. Complex 3 exhibited high reactivity toward organic radicals to form diamagnetic five-coordinate Fe(ii) complexes. PMID:28758000

Neutron and X-ray Microbeam Diffraction Studies around a Fatigue-Crack Tip after Overload

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sooyeol; Barabash, Rozaliya; Chung, Jin-Seok

2008-01-01

An in-situ neutron diffraction technique was used to investigate the lattice-strain distributions and plastic deformation around a crack tip after overload. The lattice-strain profiles around a crack tip were measured as a function of the applied load during the tensile loading cycles after overload. Dislocation densities calculated from the diffraction peak broadening were presented as a function of the distance from the crack tip. Furthermore, the crystallographic orientation variations were examined near a crack tip using polychromatic X-ray microdiffraction combined with differential aperture microscopy. Crystallographic tilts are considerably observed beneath the surface around a crack tip, and these are consistentmore » with the high dislocation densities near the crack tip measured by neutron peak broadening.« less

Stress dependence of the Raman spectrum of polycrystalline barium titanate in presence of localized domain texture

NASA Astrophysics Data System (ADS)

Sakashita, Tatsuo; Deluca, Marco; Yamamoto, Shinsuke; Chazono, Hirokazu; Pezzotti, Giuseppe

2007-06-01

The stress dependence of the Raman spectrum of polycrystalline barium titanate (BaTiO3, BT) ceramics has been examined with microprobe polarized Raman spectroscopy. The angular dependence of the Raman spectrum of the tetragonal BT crystal has been theoretically established, enabling us to assess the stress dependence of selected spectral modes without the influence of crystallographic domain orientation. Upon considering the frequency shift of selected Raman modes as a function of orientation between the crystallographic axis and the polarization vector of incident and scattered light, a suitable instrumental configuration has been selected, which allowed a direct residual stress measurement according to a modified piezospectroscopic procedure. The analysis is based on the selection of mixed photostimulated spectral modes in two perpendicular angular orientations.

Controllable Modular Growth of Hierarchical MOF-on-MOF Architectures.

PubMed

Gu, Yifan; Wu, Yi-Nan; Li, Liangchun; Chen, Wei; Li, Fengting; Kitagawa, Susumu

2017-12-04

Fabrication of hybrid MOF-on-MOF heteroarchitectures can create novel and multifunctional platforms to achieve desired properties. However, only MOFs with similar crystallographic parameters can be hybridized by the classical epitaxial growth method (EGM), which largely suppressed its applications. A general strategy, called internal extended growth method (IEGM), is demonstrated for the feasible assembly of MOFs with distinct crystallographic parameters in an MOF matrix. Various MOFs with diverse functions could be introduced in a modular MOF matrix to form 3D core-satellite pluralistic hybrid system. The number of different MOF crystals interspersed could be varied on demand. More importantly, the different MOF crystals distributed in individual domains could be used to further incorporate functional units or enhance target functions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Redox-promoted associative assembly of metal–organic materials† †Electronic supplementary information (ESI) available: Experimental procedures, compound characterization data, and X-ray crystallographic data for compounds 3–7 and 9–11. CCDC 1405641–1405645, 1429643, 1405647 and 1405648. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c5sc02214b Click here for additional data file. Click here for additional data file.

PubMed Central

Glavinović, Martin; Qi, Feng; Katsenis, Athanassios D.

2016-01-01

We develop an associative synthesis of metal–organic materials that combines solid-state metal oxidation and coordination-driven self-assembly into a one-step, waste-free transformation. The methodology hinges on the unique reactivity of ortho-quinones, which we introduce as versatile oxidants for mechanochemical synthesis. Our strategy opens a previously unexplored route to paramagnetic metal–organic materials from elementary metals. PMID:28791114

The transformation of magnetite to hematite and its influence on the rheology of iron oxide rock

NASA Astrophysics Data System (ADS)

Lagoeiro, Leonardo; Barbosa, Paola; Goncalves, Fabio; Rodrigues, Carlos

2013-04-01

Phase transformation is an important process for strain localization after the initiation of ductile shear zones. In polyphase aggregates one important aspect to consider is likely to be the interconnectivity of weak phase after the transformation of the load-bearing framework grains. However the physical processes involved in that transition is not well understood, partially because the microstructures of the initial weakening are generally obliterated by subsequent deformation. Iron oxide-quartz rocks from paleoproterozoic Iron Formations in southern Brazil preserve microstructures that allow a good insight into the evolution of the deformation mechanisms and fabrics during the transition from a load-bearing framework (magnetite) to an interconnected weak phase (hematite). We conducted microstructural and textural analyses of aggregates of magnetite and hematite combining observations in an optical microscope and measurements in the electron back-scatter diffraction (EBSD). The samples were cut parallel to the mineral lineation (the X-axis) and perpendicular to the foliation. Our goal was to understand the evolution of fabric and texture of the iron oxide aggregates caused by the change in deformation behavior resulting from the phase transformation. The studied samples consist mainly of aggregates of magnetite and hematite in a varied proportions. Samples that preserve the early microstructures consist in aggregate of magnetite grains of varied sizes. The grains are partially transformed to hematite along {111} planes but no foliation is observed in the samples. Basically the samples consist of grains of irregular shapes and a weak or absent crystallographic preferred orientation. The newly transformed hematite crystals share the (0001) planes and directions <11-20> with planes {111} and directions <110> of magnetite grains. Other samples present relicts of initial magnetite grains surrounded by a matrix of tabular to platy hematite crystals. The matrix show a preferred orientation of hematite grains. Close to the magnetite, hematite crystals show crystallographic relationship similar to those observed inside the magnetite crystals showing a good match in crystallographic planes and directions. However away from the magnetite crystals hematite of the matrix tend to show a more independent crystallographic orientation with respect to the magnetite grains. The poles to the basal planes of hematite distributed in a small circle centered around the Z-axis and the crystallographic directions <11-20> spread in a wide angle along the foliation plane. In samples where no crystal of magnetite grains is observed only platy hematite with a strong shape preferred orientation occur. Their basal planes show a strong concentration around the foliation pole contrasting to the more dispersed distribution around the Z-axis found in the samples with magnetite relicts.The directions <11-20> also distributed along the foliation planes in platy hematite samples but with a narrower angles than those of samples with magnetite relicts. The progressive transformation of magnetite to hematite led to a change in the iron formation rock fabrics from an isotropic distribution of a load-supporting magnetite to an interconnected weak platy hematite forming a strongly anisotropic fabric. The hard magnetite behaves in a brittle manner with a very limited operation of slip along the main crystallographic planes. The microfracturing creates an easy path for oxidation and transformation of magnetite. The newly formed hematite grains behave in a ductile manner and form a matrix of strongly oriented crystals. The deformation mechanisms change from the microfracturing of the harder magnetite phase to a crystal plastic deformation of the softer hematite platy grains through slip along their basal planes.

A matrix of heterobimetallic complexes for interrogation of hydrogen evolution reaction electrocatalysts† †Electronic supplementary information (ESI) available: Experimental, spectroscopic, additional electrochemical and computational details, X-ray crystallographic data (CIF) from the structure of the complexes [Ni–Fe]0, [Ni2–Fe2]2+, [Ni2–Fe]+, and computational coordinates are available. CCDC crystallographic data for the complexes [Ni–Fe]0, [Ni2–Fe2]2+ and [Ni2–Fe]+ were deposited in the Cambridge Crystallographic Data Centre. CCDC [Ni–Fe]0 (CCDC 1045461), [Ni2–Fe2]2+ (CCDC 1045460) and [Ni2–Fe]+ (CCDC 1565539). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c7sc03378h

PubMed Central

Ghosh, Pokhraj; Ding, Shengda; Chupik, Rachel B.; Quiroz, Manuel; Hsieh, Chung-Hung; Bhuvanesh, Nattami; Hall, Michael B.

2017-01-01

Experimental and computational studies address key questions in a structure–function analysis of bioinspired electrocatalysts for the HER. Combinations of NiN2S2 or [(NO)Fe]N2S2 as donors to (η5-C5H5)Fe(CO)+ or [Fe(NO)2]+/0 generate a series of four bimetallics, gradually “softened” by increasing nitrosylation, from 0 to 3, by the non-innocent NO ligands. The nitrosylated NiFe complexes are isolated and structurally characterized in two redox levels, demonstrating required features of electrocatalysis. Computational modeling of experimental structures and likely transient intermediates that connect the electrochemical events find roles for electron delocalization by NO, as well as Fe–S bond dissociation that produce a terminal thiolate as pendant base well positioned to facilitate proton uptake and transfer. Dihydrogen formation is via proton/hydride coupling by internal S–H+···–H–Fe units of the “harder” bimetallic arrangements with more localized electron density, while softer units convert H–···H–via reductive elimination from two Fe–H deriving from the highly delocalized, doubly reduced [Fe2(NO)3]– derivative. Computational studies also account for the inactivity of a Ni2Fe complex resulting from entanglement of added H+ in a pinched –Sδ–···H+···δ–S– arrangement. PMID:29619175

Structural characterization of framework–gas interactions in the metal–organic framework Co2(dobdc) by in situ single-crystal X-ray diffraction† †Electronic supplementary information (ESI) available: Supplementary figures, crystallographic information, adsorption isotherms and fits, CCDC 1530119–1530126. For ESI and crystallographic data in CIF or other electronic format. See DOI: 10.1039/c7sc00449d Click here for additional data file. Click here for additional data file.

PubMed Central

Gonzalez, Miguel I.; Mason, Jarad A.; Bloch, Eric D.; Teat, Simon J.; Gagnon, Kevin J.; Morrison, Gregory Y.; Queen, Wendy L.

2017-01-01

The crystallographic characterization of framework–guest interactions in metal–organic frameworks allows the location of guest binding sites and provides meaningful information on the nature of these interactions, enabling the correlation of structure with adsorption behavior. Here, techniques developed for in situ single-crystal X-ray diffraction experiments on porous crystals have enabled the direct observation of CO, CH4, N2, O2, Ar, and P4 adsorption in Co2(dobdc) (dobdc4– = 2,5-dioxido-1,4-benzenedicarboxylate), a metal–organic framework bearing coordinatively unsaturated cobalt(ii) sites. All these molecules exhibit such weak interactions with the high-spin cobalt(ii) sites in the framework that no analogous molecular structures exist, demonstrating the utility of metal–organic frameworks as crystalline matrices for the isolation and structural determination of unstable species. Notably, the Co–CH4 and Co–Ar interactions observed in Co2(dobdc) represent, to the best of our knowledge, the first single-crystal structure determination of a metal–CH4 interaction and the first crystallographically characterized metal–Ar interaction. Analysis of low-pressure gas adsorption isotherms confirms that these gases exhibit mainly physisorptive interactions with the cobalt(ii) sites in Co2(dobdc), with differential enthalpies of adsorption as weak as –17(1) kJ mol–1 (for Ar). Moreover, the structures of Co2(dobdc)·3.8N2, Co2(dobdc)·5.9O2, and Co2(dobdc)·2.0Ar reveal the location of secondary (N2, O2, and Ar) and tertiary (O2) binding sites in Co2(dobdc), while high-pressure CO2, CO, CH4, N2, and Ar adsorption isotherms show that these binding sites become more relevant at elevated pressures. PMID:28966783

Characterization of the mechanomyographic signal of three different muscles and at different levels of isometric contractions.

PubMed

Jotta, Bruno; Cavalcanti Garcia, Marco Antonio; Visintainer Pino, Alexandre; De Souza, Marcio Nogueira

2015-01-01

Lateral (X) and longitudinal (Y) mechanical oscillations of muscle fibers that take place during muscular contraction seem to contain information additionally to the myoelectric activity, which can contribute to the interpretation of some muscle gradation force mechanisms. However, no previous study was found that had investigated the relationship between the muscle force and features associated to the mechanomyographic (MMG) signal obtained by means of a biaxial accelerometer in three different muscles. Therefore, the aim of this study was to evaluate the relationship between the force output at different load levels (20% to 100%) of the maximum voluntary isometric contraction (%MVIC) and the two signals supplied by a biaxial accelerometer and, in addition, the so-called resultant (R) acceleration signal derived from the two signals mentioned previously. Twenty seven male volunteers participated in this study. The force output related to the right biceps brachii, soleus and gastrocnemius medialis muscles was studied by means of linear regression models fit to log-transformed of the root mean square (RMS) values of the MMG signals in X, Y, and R axes versus each %MVIC. The phase angle of R acceleration (PhaseR) and anthropometric data were also considered. The angular coefficient a and the antilog of y-intercept b from the log-transformed of MMG data values versus force output were able to distinguish partially motor unit strategies during isometric contractions in the three muscles studied. The findings suggest that biaxial accelerometer seems to be an interesting approach in the assessment of muscle contraction properties.

Likelihood-based molecular-replacement solution for a highly pathological crystal with tetartohedral twinning and sevenfold translational noncrystallographic symmetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sliwiak, Joanna; Jaskolski, Mariusz, E-mail: mariuszj@amu.edu.pl; A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznan

With the implementation of a molecular-replacement likelihood target that accounts for translational noncrystallographic symmetry, it became possible to solve the crystal structure of a protein with seven tetrameric assemblies arrayed translationally along the c axis. The new algorithm found 56 protein molecules in reduced symmetry (P1), which was used to resolve space-group ambiguity caused by severe twinning. Translational noncrystallographic symmetry (tNCS) is a pathology of protein crystals in which multiple copies of a molecule or assembly are found in similar orientations. Structure solution is problematic because this breaks the assumptions used in current likelihood-based methods. To cope with such cases,more » new likelihood approaches have been developed and implemented in Phaser to account for the statistical effects of tNCS in molecular replacement. Using these new approaches, it was possible to solve the crystal structure of a protein exhibiting an extreme form of this pathology with seven tetrameric assemblies arrayed along the c axis. To resolve space-group ambiguities caused by tetartohedral twinning, the structure was initially solved by placing 56 copies of the monomer in space group P1 and using the symmetry of the solution to define the true space group, C2. The resulting structure of Hyp-1, a pathogenesis-related class 10 (PR-10) protein from the medicinal herb St John’s wort, reveals the binding modes of the fluorescent probe 8-anilino-1-naphthalene sulfonate (ANS), providing insight into the function of the protein in binding or storing hydrophobic ligands.« less

Holographic Airborne Rotating Lidar Instrument Experiment (HARLIE)

NASA Technical Reports Server (NTRS)

Schwemmer, Geary K.

1998-01-01

Scanning holographic lidar receivers are currently in use in two operational lidar systems, PHASERS (Prototype Holographic Atmospheric Scanner for Environmental Remote Sensing) and now HARLIE (Holographic Airborne Rotating Lidar Instrument Experiment). These systems are based on volume phase holograms made in dichromated gelatin (DCG) sandwiched between 2 layers of high quality float glass. They have demonstrated the practical application of this technology to compact scanning lidar systems at 532 and 1064 nm wavelengths, the ability to withstand moderately high laser power and energy loading, sufficient optical quality for most direct detection systems, overall efficiencies rivaling conventional receivers, and the stability to last several years under typical lidar system environments. Their size and weight are approximately half of similar performing scanning systems using reflective optics. The cost of holographic systems will eventually be lower than the reflective optical systems depending on their degree of commercialization. There are a number of applications that require or can greatly benefit from a scanning capability. Several of these are airborne systems, which either use focal plane scanning, as in the Laser Vegetation Imaging System or use primary aperture scanning, as in the Airborne Oceanographic Lidar or the Large Aperture Scanning Airborne Lidar. The latter class requires a large clear aperture opening or window in the aircraft. This type of system can greatly benefit from the use of scanning transmission holograms of the HARLIE type because the clear aperture required is only about 25% larger than the collecting aperture as opposed to 200-300% larger for scan angles of 45 degrees off nadir.

CASIS PCG 6

NASA Image and Video Library

2017-06-06

iss052e000508 (June 6, 2017) --- View of astronaut Jack Fischer working with the Neutron Crystallographic Studies of Human Acetylcholinesterase for the Design of Accelerated Reactivators (CASIS PCG 6) experiment in the Japanese Experiment Module

On the water promoted reaction of titanium isopropoxide with carbon dioxide.

PubMed

Ghosh, Rajshekhar; Nethaji, Munirathinam; Samuelson, Ashoka G

2003-10-21

Insertion of carbon dioxide into titanium isopropoxide takes place only in the presence of trace quantities of water to give an isopropyl carbonato cluster which has been crystallographically characterised.

Preliminary crystallographic analysis of ADP-glucose pyrophosphorylase from Agrobacterium tumefaciens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cupp-Vickery, Jill R., E-mail: jvickery@uci.edu; Igarashi, Robert Y.; Meyer, Christopher R.

2005-03-01

Crystallization and X-ray diffraction methods for native A. tumefaciens ADP-glucose pyrophosphorylase and its selenomethionyl derivative are described. Two crystal forms are identified, both of which diffract to 2 Å.

Homology modeling of Homo sapiens lipoic acid synthase: Substrate docking and insights on its binding mode.

PubMed

Krishnamoorthy, Ezhilarasi; Hassan, Sameer; Hanna, Luke Elizabeth; Padmalayam, Indira; Rajaram, Rama; Viswanathan, Vijay

2017-05-07

Lipoic acid synthase (LIAS) is an iron-sulfur cluster mitochondrial enzyme which catalyzes the final step in the de novo pathway for the biosynthesis of lipoic acid, a potent antioxidant. Recently there has been significant interest in its role in metabolic diseases and its deficiency in LIAS expression has been linked to conditions such as diabetes, atherosclerosis and neonatal-onset epilepsy, suggesting a strong inverse correlation between LIAS reduction and disease status. In this study we use a bioinformatics approach to predict its structure, which would be helpful to understanding its role. A homology model for LIAS protein was generated using X-ray crystallographic structure of Thermosynechococcus elongatus BP-1 (PDB ID: 4U0P). The predicted structure has 93% of the residues in the most favour region of Ramachandran plot. The active site of LIAS protein was mapped and docked with S-Adenosyl Methionine (SAM) using GOLD software. The LIAS-SAM complex was further refined using molecular dynamics simulation within the subsite 1 and subsite 3 of the active site. To the best of our knowledge, this is the first study to report a reliable homology model of LIAS protein. This study will facilitate a better understanding mode of action of the enzyme-substrate complex for future studies in designing drugs that can target LIAS protein. Copyright © 2017 Elsevier Ltd. All rights reserved.

The collection of MicroED data for macromolecular crystallography.

PubMed

Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

2016-05-01

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

Macromolecular crystallography with a large format CMOS detector

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nix, Jay C., E-mail: jcnix@lbl.gov

Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can bemore » obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.« less

Supersaturation of aqueous species and hydrothermal crystal growth of ZnO

NASA Astrophysics Data System (ADS)

Gelabert, M. C.

2015-05-01

Synthesis of ZnO crystals prepared with zinc acetate or chloride, disodium dihydrogen ethylenediaminetetraacetate (EDTA), potassium hydroxide and sodium triflate at 200 °C and variable pH 8-12 is reported. Crystals were imaged and size-analyzed with optical microscopy. Using aqueous speciation modeling software, supersaturation dependence on pH was calculated for five zinc species-Zn2+, Zn(OH)+, Zn(OH)2, Zn(OH)3- and Zn(OH)42- -to investigate connections between predominate crystal habits at different pH and dominant aqueous species. For zinc acetate and chloride systems, the zinc species with highest supersaturation was Zn(OH)42- throughout the pH 8-12 range, and the second highest was Zn2+ or Zn(OH)3-, with a crossover pH of 10.2-10.4 depending on counterion. The prominence of the tetrahydroxyl zinc species in ZnO crystal growth is supported by these calculations, and total supersaturation is inversely proportional to average crystal sizes, as expected. Optical microscopy and size analysis on products revealed crystals with a needle or prismatic habit throughout the studied pH range, and the change in aspect ratio correlates with supersaturation changes for the Zn2+ in this pH range, thus suggesting that growth rates along the [001] crystallographic direction are affected by small concentration changes of this ion.

Conserved water molecules in bacterial serine hydroxymethyltransferases.

PubMed

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano

2015-10-01

Water molecules occurring in the interior of protein structures often are endowed with key structural and functional roles. We report the results of a systematic analysis of conserved water molecules in bacterial serine hydroxymethyltransferases (SHMTs). SHMTs are an important group of pyridoxal-5'-phosphate-dependent enzymes that catalyze the reversible conversion of l-serine and tetrahydropteroylglutamate to glycine and 5,10-methylenetetrahydropteroylglutamate. The approach utilized in this study relies on two programs, ProACT2 and WatCH. The first software is able to categorize water molecules in a protein crystallographic structure as buried, positioned in clefts or at the surface. The other program finds, in a set of superposed homologous proteins, water molecules that occur approximately in equivalent position in each of the considered structures. These groups of molecules are referred to as 'clusters' and represent structurally conserved water molecules. Several conserved clusters of buried or cleft water molecules were found in the set of 11 bacterial SHMTs we took into account for this work. The majority of these clusters were not described previously. Possible structural and functional roles for the conserved water molecules are envisaged. This work provides a map of the conserved water molecules helpful for deciphering SHMT mechanism and for rational design of molecular engineering experiments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

In vitro and in silico Studies of Mangiferin from Aphloia theiformis on Key Enzymes Linked to Diabetes Type 2 and Associated Complications.

PubMed

Picot, Marie C N; Zengin, Gokhan; Mollica, Adriano; Stefanucci, Azzurra; Carradori, Simone; Mahomoodally, Mohamad F

2017-01-01

Mangiferin, was identified in the crude methanol extract, ethyl acetate, and n-butanol fractions of Aphloia theiformis (Vahl.) Benn. This study aimed to analyze the plausible binding modes of mangiferin to key enzymes linked to diabetes type 2 (DT2), obesity, hypertension, Alzheimer's disease, and urolithiasis using molecular docking. Crystallographic structures of α-amylase, α-glucosidase, glycogen phosphorylase (GP), pancreatic lipase, cholesterol esterase (CEase), angiotensin-I-converting enzyme (ACE), acetyl cholinesterase (AChE), and urease available on the Protein Databank database were docked to mangiferin using Gold 6.0 software. We showed that mangiferin bound to all enzymes by π-π and hydrogen bonds mostly. Mangiferin was docked to both allosteric and orthosteric sites of α-glucosidase by π-π interactions. However, several hydrogen bonds were observed at the orthosteric position, suggesting a preference for this site. The docking of mangiferin on AChE with the catalytic pocket occupied by paraoxon could be attributed to π-π stacking involving amino acid residues, Trp341 and Trp124. This study provided an insight of the molecular interaction of mangiferin with the studied enzymes and can be considered as a valuable tool for designing new drugs for better management of these diseases. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

NASA Tech Briefs, April 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Gas-Tolerant Device Senses Electrical Conductivity of Liquid Nanoactuators Based on Electrostatic Forces on Dielectrics Replaceable Microfluidic Cartridges for a PCR Biosensor CdZnTe Image Detectors for Hard-X-Ray Telescopes High-Aperture-Efficiency Horn Antenna Full-Circle Resolver-to-Linear-Analog Converter Continuous, Full-Circle Arctangent Circuit Advanced Three-Dimensional Display System Automatic Focus Adjustment of a Microscope Topics covered include: FastScript3D - A Companion to Java 3D; Generating Mosaics of Astronomical Images; Simulating Descent and Landing of a Spacecraft; Simulating Vibrations in a Complex Loaded Structure; Rover Sequencing and Visualization Program; Software Template for Instruction in Mathematics; Support for User Interfaces for Distributed Systems; Nanostructured MnO2-Based Cathodes for Li-Ion/Polymer Cells; Multi-Layer Laminated Thin Films for Inflatable Structures; Two-Step Laser Ranging for Precise Tracking of a Spacecraft; Growing Aligned Carbon Nanotubes for Interconnections in ICs; Multilayer Composite Pressure Vessels; Texturing Blood-Glucose-Monitoring Optics Using Oxygen Beams; Fault-Tolerant Heat Exchanger; Atomic Clock Based on Opto-Electronic Oscillator; Microfocus/Polycapillary-Optic Crystallographic X-Ray Sys; Depth-Penetrating Luminescence Thermography of Thermal- Barrier Coatings; One-Dimensional Photonic Crystal Superprisms; Measuring Low-Order Aberrations in a Segmented Telescope; Mapping From an Instrumented Glove to a Robot Hand; Application of the Hilbert-Huang Transform to Financial Data; Optimizing Parameters for Deep-Space Optical Communication; and Low-Shear Microencapsulation and Electrostatic Coating.

Solvent-induced chirality control in the enantioseparation of 1-phenylethylamine via diastereomeric salt formation.

PubMed

Kodama, Koichi; Kimura, Yuria; Shitara, Hiroaki; Yasutake, Mikio; Sakurai, Rumiko; Hirose, Takuji

2011-04-01

Solvent-induced chirality control in the enantioseparation of 1-phenylethylamine 1 by N-(p-toluenesulfonyl)-(S)-phenylalanine 2 via diastereomeric salt formation was studied. (S)-1·(S)-2 was preferentially crystallized as a less-soluble salt from aqueous alcohol, while (R)-1·(S)-2 salt was mainly obtained by addition of solvents with a six-membered ring such as dioxane, cyclohexane, tetrahydropyran, and cyclohexene to 2-propanol. Further investigations were carried out from the viewpoints of molecular structures, optical rotation measurement, and X-ray crystallographic analyses. Crystallographic analyses have revealed that incorporation of the six-membered ring solvent molecule in (R)-1·(S)-2 without hydrogen bonds changed the molecular conformation of (S)-2 to stabilize the salt, which changed the selectivity of 1 in the enantioseparation. Copyright © 2010 Wiley-Liss, Inc.

Preferred orientation in experimentally deformed stishovite: implications for deformation mechanisms

DOE PAGES

Kaercher, Pamela M.; Zepeda-Alarcon, Eloisa; Prakapenka, Vitali B.; ...

2014-11-07

Although the crystal structure of the high pressure SiO 2 polymorph stishovite has been studied in detail, little is known about the development of crystallographic preferred orientation (CPO) during deformation in stishovite. Insight into CPO and associated deformation mechanics of stishovite would provide important information for understanding subduction of quartz-bearing crustal rocks into the mantle. To study CPO development, we converted a natural sample of flint to stishovite in a laser heated diamond anvil cell and compressed the stishovite aggregate up to 38 GPa. We collected diffraction patterns in radial geometry to examine in situ development of crystallographic preferred orientationmore » and find that (001) poles preferentially align with the compression direction. Viscoplastic self-consistent modeling suggests the most likely slip systems at high pressure and ambient temperature are pyramidal and basal slip.« less

5,11,17,23-Tetra-tert-butyl-25,26,27,28-tetra­methoxy­calix[4]arene dichloro­methane hemisolvate

PubMed Central

Fischer, Conrad; Gruber, Tobias; Seichter, Wilhelm; Schindler, Diana; Weber, Edwin

2008-01-01

In the title compound, C48H64O4·0.5CH2Cl2, both crystallographically independent calixarene mol­ecules display a partial cone conformation. Their crystal packing is stabilized by C—H⋯π contacts involving the meth­oxy groups. The solvent mol­ecule is located inter­stitially between two calixarene units with C—H⋯Cl contacts to meth­oxy and tert-butyl groups. One tert-butyl residue of each calixarene mol­ecule is disordered over two positions (occupancies 0.60/0.40 and 0.63/0.37), resulting in bond distances that deviate from ideal values. The tetra­mer calixarene mol­ecules present models with approximate non-crystallographic Cs symmetry. PMID:21202066

Automating tasks in protein structure determination with the clipper python module.

PubMed

McNicholas, Stuart; Croll, Tristan; Burnley, Tom; Palmer, Colin M; Hoh, Soon Wen; Jenkins, Huw T; Dodson, Eleanor; Cowtan, Kevin; Agirre, Jon

2018-01-01

Scripting programming languages provide the fastest means of prototyping complex functionality. Those with a syntax and grammar resembling human language also greatly enhance the maintainability of the produced source code. Furthermore, the combination of a powerful, machine-independent scripting language with binary libraries tailored for each computer architecture allows programs to break free from the tight boundaries of efficiency traditionally associated with scripts. In the present work, we describe how an efficient C++ crystallographic library such as Clipper can be wrapped, adapted and generalized for use in both crystallographic and electron cryo-microscopy applications, scripted with the Python language. We shall also place an emphasis on best practices in automation, illustrating how this can be achieved with this new Python module. © 2017 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms.

PubMed

Balasubramanian, M; Moorthy, Pon Sathya; Neelagandan, K; Ponnuswamy, M N

2009-03-01

Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (alpha(2)beta(2)), respectively, in the asymmetric unit.

Mosaic structure in epitaxial thin films having large lattice mismatch

NASA Astrophysics Data System (ADS)

Srikant, V.; Speck, J. S.; Clarke, D. R.

1997-11-01

Epitaxial films having a large lattice mismatch with their substrate invariably form a mosaic structure of slightly misoriented sub-grains. The mosaic structure is usually characterized by its x-ray rocking curve on a surface normal reflection but this is limited to the out-of-plane component unless off-axis or transmission experiments are performed. A method is presented by which the in-plane component of the mosaic misorientation can be determined from the rocking curves of substrate normal and off-axis reflections. Results are presented for two crystallographically distinct heteroepitaxial systems, ZnO, AlN, and GaN (wurtzite crystal structure) on c-plane sapphire and MgO (rock salt crystal structure) on (001) GaAs. The differences in the mosaic structure of these films are attributed to the crystallographic nature of their lattice dislocations.

Phase-field simulations of GaN growth by selective area epitaxy on complex mask geometries

DOE PAGES

Aagesen, Larry K.; Coltrin, Michael Elliott; Han, Jung; ...

2015-05-15

Three-dimensional phase-field simulations of GaN growth by selective area epitaxy were performed. Furthermore, this model includes a crystallographic-orientation-dependent deposition rate and arbitrarily complex mask geometries. The orientation-dependent deposition rate can be determined from experimental measurements of the relative growth rates of low-index crystallographic facets. Growth on various complex mask geometries was simulated on both c-plane and a-plane template layers. Agreement was observed between simulations and experiment, including complex phenomena occurring at the intersections between facets. The sources of the discrepancies between simulated and experimental morphologies were also investigated. We found that the model provides a route to optimize masks andmore » processing conditions during materials synthesis for solar cells, light-emitting diodes, and other electronic and opto-electronic applications.« less

Deformation induced microtwins and stacking faults in aluminum single crystal.

PubMed

Han, W Z; Cheng, G M; Li, S X; Wu, S D; Zhang, Z F

2008-09-12

Microtwins and stacking faults in plastically deformed aluminum single crystal were successfully observed by high-resolution transmission electron microscope. The occurrence of these microtwins and stacking faults is directly related to the specially designed crystallographic orientation, because they were not observed in pure aluminum single crystal or polycrystal before. Based on the new finding above, we propose a universal dislocation-based model to judge the preference or not for the nucleation of deformation twins and stacking faults in various face-centered-cubic metals in terms of the critical stress for dislocation glide or twinning by considering the intrinsic factors, such as stacking fault energy, crystallographic orientation, and grain size. The new finding of deformation induced microtwins and stacking faults in aluminum single crystal and the proposed model should be of interest to a broad community.

Angle-dependent electron spin resonance of YbRh2Si2 measured with planar microwave resonators and in-situ rotation

NASA Astrophysics Data System (ADS)

Bondorf, Linda; Beutel, Manfred; Thiemann, Markus; Dressel, Martin; Bothner, Daniel; Sichelschmidt, Jörg; Kliemt, Kristin; Krellner, Cornelius; Scheffler, Marc

2018-05-01

We present a new experimental approach to investigate the magnetic properties of the anisotropic heavy-fermion system YbRh2Si2 as a function of crystallographic orientation. Angle-dependent electron spin resonance (ESR) measurements are performed at a low temperature of 1.6 K and at an ESR frequency of 4.4 GHz utilizing a superconducting planar microwave resonator in a 4He-cryostat in combination with in-situ sample rotation. The obtained ESR g-factor of YbRh2Si2 as a function of the crystallographic angle is consistent with results of previous measurements using conventional ESR spectrometers at higher frequencies and fields. Perspectives to implement this experimental approach into a dilution refrigerator and to reach the magnetically ordered phase of YbRh2Si2 are discussed.

Production, crystallization and preliminary crystallographic analysis of Allochromatium vinosum thiosulfate dehydrogenase TsdA, an unusual acidophilic c-type cytochrome

PubMed Central

Brito, José A.; Gutierres, André; Denkmann, Kevin; Dahl, Christiane; Archer, Margarida

2014-01-01

The ability to perform the very simple oxidation of two molecules of thiosulfate to tetrathionate is widespread among prokaryotes. Despite the prevalent occurrence of tetrathionate formation and its well documented significance within the sulfur cycle, little is known about the enzymes that catalyze the oxidative condensation of two thiosulfate anions. To fill this gap, the thiosulfate dehydrogenase (TsdA) enzyme from the purple sulfur bacterium Allochromatium vinosum was recombinantly expressed in Escherichia coli, purified and crystallized, and a crystallographic data set was collected. The crystals belonged to the monoclinic space group C2, with unit-cell parameters a = 79.2, b = 69.9, c = 57.9 Å, β = 129.3°, contained one monomer per asymmetric unit and diffracted to a resolution of 1.98 Å. PMID:25286955

Thermomechanical processing of HAYNES alloy No. 188 sheet to improve creep strength

NASA Technical Reports Server (NTRS)

Klarstrom, D. L.

1978-01-01

Improvements in the low strain creep strength of HAYNES alloy No. 188 thin gauge sheet by means of thermomechanical processing were developed. Processing methods designed to develop a sheet with strong crystallographic texture after recrystallization and to optimize grain size were principally studied. The effects of thickness-to-grain diameter ratio and prestrain on low strain creep strength were also briefly examined. Results indicate that the most significant improvements were obtained in the sheets having a strong crystallographic texture. The low strain creep strength of the textured sheets was observed to be superior to that of standard production sheets in the 922 K to 1255 K temperature range. Tensile, stress rupture, fabricability, and surface stability properties of the experimental sheets were also measured and compared to property values reported for the baseline production sheets.

Constitutive and life modeling of single crystal blade alloys for root attachment analysis

NASA Technical Reports Server (NTRS)

Meyer, T. G.; Mccarthy, G. J.; Favrow, L. H.; Anton, D. L.; Bak, Joe

1988-01-01

Work to develop fatigue life prediction and constitutive models for uncoated attachment regions of single crystal gas turbine blades is described. At temperatures relevant to attachment regions, deformation is dominated by slip on crystallographic planes. However, fatigue crack initiation and early crack growth are not always observed to be crystallographic. The influence of natural occurring microporosity will be investigated by testing both hot isostatically pressed and conventionally cast PWA 1480 single crystal specimens. Several differnt specimen configurations and orientations relative to the natural crystal axes are being tested to investigate the influence of notch acuity and the material's anisotropy. Global and slip system stresses in the notched regions were determined from three dimensional stress analyses and will be used to develop fatigue life prediction models consistent with the observed lives and crack characteristics.

Crystallographic and magnetic structure of UCu{sub 1.5}Sn{sub 2}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purwanto, A.; Robinson, R.A.; Nakotte, H.

1996-04-01

We report on the crystallographic and magnetic structures of the antiferromagnet UCu{sub 1.5}Sn{sub 2}, as determined by x-ray and neutron powder diffraction. It crystallizes in the tetragonal CaBe{sub 2}Ge{sub 2} structure type, with space group P/4nmm, and we find no site disorder between two different Sn2{ital c} sites, in contrast with a previous report. UCu{sub 1.5}Sn{sub 2} orders antiferromagnetically with a N{acute e}el temperature of about 110 K. This is unusually high among uranium intermetallics. The uranium moments align along the {ital c} axis in a collinear arrangement but alternating along the {ital c} axis. The low-temperature uranium moment ismore » 2.01{mu}{sub {ital B}}. {copyright} {ital 1996 American Institute of Physics.}« less

Improving Protocols for Protein Mapping through Proper Comparison to Crystallography Data

PubMed Central

Lexa, Katrina W.; Carlson, Heather A.

2013-01-01

Computational approaches to fragment-based drug design (FBDD) can complement experiments and facilitate the identification of potential hot spots along the protein surface. However, the evaluation of computational methods for mapping binding sites frequently focuses upon the ability to reproduce crystallographic coordinates to within a low RMSD threshold. This dependency on the deposited coordinate data overlooks the original electron density from the experiment, thus techniques may be developed based upon subjective - or even erroneous - atomic coordinates. This can become a significant drawback in applications to systems where the location of hot spots is unknown. Based on comparison to crystallographic density, we previously showed that mixed-solvent molecular dynamics (MixMD) accurately identifies the active site for HEWL, with acetonitrile as an organic solvent. Here, we concentrated on the influence of protic solvent on simulation and refined the optimal MixMD approach for extrapolation of the method to systems without established sites. Our results establish an accurate approach for comparing simulations to experiment. We have outlined the most efficient strategy for MixMD, based on simulation length and number of runs. The development outlined here makes MixMD a robust method which should prove useful across a broad range of target structures. Lastly, our results with MixMD match experimental data so well that consistency between simulations and density may be a useful way to aid the identification of probes vs waters during the refinement of future MSCS crystallographic structures. PMID:23327200

Crystal structure and electronic properties of a thiolate-protected Au24 nanocluster

NASA Astrophysics Data System (ADS)

Das, Anindita; Li, Tao; Li, Gao; Nobusada, Katsuyuki; Zeng, Chenjie; Rosi, Nathaniel L.; Jin, Rongchao

2014-05-01

Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''.Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''. Electronic supplementary information (ESI) available: Experimental and supporting Fig. S1-S3. CCDC NUMBER(1000102). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4nr01350f

Orientational Glass Formation in Substituted Hybrid Perovskites

DOE PAGES

Mozur, Eve M.; Maughan, Annalise E.; Cheng, Yongqiang; ...

2017-11-07

Hybrid organic-inorganic perovskites have gained notoriety in the photovoltaic community for their composition-tunable band gaps and long-lived electronic excited states, which are known to be related to the crystalline phase. While indirect evidence suggests that coupling between polar organic cations affects the phase behavior, it remains unclear how the coupling manifests in hybrid perovskites such as methylammonium lead halides (CH 3NH 3PbX 3). Here, we present crystallographic and spectroscopic data for the series (CH 3NH 3) 1-xCs xPbBr 3. CH 3NH 3PbBr 3 behaves as a plastic crystal in the high temperature cubic phase, and substitution of CH 3NH 3more » + with Cs + leads to the formation of an orientational glass. While the organic molecule exhibits slow, glassy reorientational dynamics, the inorganic framework continues to undergo crystallographic phase transitions. These crystallographic transitions occur in the absence of thermodynamic signatures in the specific heat, which suggests that the phase transitions result from underlying instabilities intrinsic to the inorganic lattice. However, these transitions are not decoupled from the reorientations of the organic molecule, as indicated by inelastic and quasielastic neutron scattering. Observation of a reentrant phase transition in (CH 3NH 3) 0.8Cs 0.2PbBr 3 permits the resolution of these complex behaviors within the context of strain mediated interactions. Lastly, together, these results provide critical insight into the coupled phase behavior and dynamics in hybrid perovskites.« less

Stress generated modifications of epitaxial ferroelectric SrTiO3 films on sapphire

NASA Astrophysics Data System (ADS)

Hollmann, E.; Schubert, J.; Kutzner, R.; Wördenweber, R.

2009-06-01

The effect of lattice-mismatch induced stress upon the crystallographic structure, strain, strain relaxation, and the generation of different types of defects in heteroepitaxially grown SrTiO3 films on CeO2 buffered sapphire is examined. Depending on the thickness of the SrTiO3 layer, characteristic changes in the structural perfection of the layers, their crystallographic orientation with respect to the substrate system, and their strain is observed. For thin films misfit dislocations partially compensate the stress in the SrTiO3 layer, whereas cracks develop in thicker SrTiO3 films. The cracks are orientated along two predominant crystallographic orientations of the sapphire. The structural modifications and the formation of misfit defects and cracks are explained in a model based on lattice misfit induced stress, on the one hand, and energy considerations taking into account the stress release due to crack formation and the energy necessary for the formation of new surfaces at the crack, on the other hand. The impact of lattice misfit is discussed in two steps, i.e., intrinsic and thermal induced misfits during heteroepitaxial film growth at a given temperature and the subsequent cooling of the sample, respectively. The comparison of the theoretical predictions and the experimental observations demonstrate that intrinsic mismatch and thermal mismatch have to be considered in order to explain strain dependent effects in complex heteroepitaxial layer systems such as induced ferroelectricity of SrTiO3 on sapphire.

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

DOE PAGES

McGuire, Michael A.; Clark, Genevieve; KC, Santosh; ...

2017-06-19

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mozur, Eve M.; Maughan, Annalise E.; Cheng, Yongqiang

Hybrid organic-inorganic perovskites have gained notoriety in the photovoltaic community for their composition-tunable band gaps and long-lived electronic excited states, which are known to be related to the crystalline phase. While indirect evidence suggests that coupling between polar organic cations affects the phase behavior, it remains unclear how the coupling manifests in hybrid perovskites such as methylammonium lead halides (CH 3NH 3PbX 3). Here, we present crystallographic and spectroscopic data for the series (CH 3NH 3) 1-xCs xPbBr 3. CH 3NH 3PbBr 3 behaves as a plastic crystal in the high temperature cubic phase, and substitution of CH 3NH 3more » + with Cs + leads to the formation of an orientational glass. While the organic molecule exhibits slow, glassy reorientational dynamics, the inorganic framework continues to undergo crystallographic phase transitions. These crystallographic transitions occur in the absence of thermodynamic signatures in the specific heat, which suggests that the phase transitions result from underlying instabilities intrinsic to the inorganic lattice. However, these transitions are not decoupled from the reorientations of the organic molecule, as indicated by inelastic and quasielastic neutron scattering. Observation of a reentrant phase transition in (CH 3NH 3) 0.8Cs 0.2PbBr 3 permits the resolution of these complex behaviors within the context of strain mediated interactions. Lastly, together, these results provide critical insight into the coupled phase behavior and dynamics in hybrid perovskites.« less

AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

2002-01-01

Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

Crystallographic tilt and in-plane anisotropies of an a-plane InGaN/GaN layered structure grown by MOCVD on r-plane sapphire using a ZnO buffer

NASA Astrophysics Data System (ADS)

Liu, H. F.; Liu, W.; Guo, S.; Chi, D. Z.

2016-03-01

High-resolution x-ray diffraction (HRXRD) was used to investigate the crystallographic tilts and structural anisotropies in epitaxial nonpolar a-plane InGaN/GaN grown by metal-organic chemical vapor deposition on r-plane sapphire using a ZnO buffer. The substrate had an unintentional miscut of 0.14° towards its [-4 2 2 3] axis. However, HRXRD revealed a tilt of 0.26° (0.20°) between the ZnO (GaN) (11-20) and the Al2O3 (1-102) atomic planes, with the (11-20) axis of ZnO (GaN) tilted towards its c-axis, which has a difference of 163° in azimuth from that of the substrate’s miscut. Excess broadenings in the GaN/ZnO (11-20) rocking curves (RCs) were observed along its c-axis. Specific analyses revealed that partial dislocations and anisotropic in-plane strains, rather than surface-related effects, wafer curvature or stacking faults, are the dominant factors for the structural anisotropy. The orientation of the partial dislocations is most likely affected by the miscut of the substrate, e.g. via tilting of the misfit dislocation gliding planes created during island coalescences. Their Burgers vector components in the growth direction, in turn, gave rise to crystallographic tilts in the same direction as that of the excess RC-broadenings.

Location-Control of Large Si Grains by Dual-Beam Excimer-Laser and Thick Oxide Portion

NASA Astrophysics Data System (ADS)

Ishihara, Ryoichi; Burtsev, Artyom; Alkemade, Paul F. A.

2000-07-01

An array of large Si grains was placed at a predetermined position by dual excimer-laser irradiation of a multi-layer structure of silicon (Si), silicon dioxide (SiO2) with an array of bumps and metal on a glass substrate. We have investigated the effects of irradiating energy density and the topology of the structure on the grain size and crystallographic structure by scanning electron microscopy (SEM) and electron back-scattering pattern (EBSP) analysis. In the low-energy-density regime, numerous small grains and petal shaped grains formed on top of the SiO2 bumps. The number of small grains on the bumps decreased with increasing irradiating energy density. At sufficiently high energy densities, one single Si grain as large as 3.5 μm was positioned at the center of the bumps. Although most of the area of the large Si grain has a single crystallographic orientation, twins and low-angle grain boundaries are often formed at the periphery of the grain. There was no preferred crystallographic orientation in the center of the location-controlled Si grain. Numerical analysis of the temperature profile showed that a temperature drop occurs at the center of the bump, during and immediately after laser irradiation. The diameter of the location-controlled Si grain increased with total thickness of the intermediate SiO2 layer, and took the maximum value of 6.2 μm.

Comparison of the NCI open database with seven large chemical structural databases.

PubMed

Voigt, J H; Bienfait, B; Wang, S; Nicklaus, M C

2001-01-01

Eight large chemical databases have been analyzed and compared to each other. Central to this comparison is the open National Cancer Institute (NCI) database, consisting of approximately 250 000 structures. The other databases analyzed are the Available Chemicals Directory ("ACD," from MDL, release 1.99, 3D-version); the ChemACX ("ACX," from CamSoft, Version 4.5); the Maybridge Catalog and the Asinex database (both as distributed by CamSoft as part of ChemInfo 4.5); the Sigma-Aldrich Catalog (CD-ROM, 1999 Version); the World Drug Index ("WDI," Derwent, version 1999.03); and the organic part of the Cambridge Crystallographic Database ("CSD," from Cambridge Crystallographic Data Center, 1999 Version 5.18). The database properties analyzed are internal duplication rates; compounds unique to each database; cumulative occurrence of compounds in an increasing number of databases; overlap of identical compounds between two databases; similarity overlap; diversity; and others. The crystallographic database CSD and the WDI show somewhat less overlap with the other databases than those with each other. In particular the collections of commercial compounds and compilations of vendor catalogs have a substantial degree of overlap among each other. Still, no database is completely a subset of any other, and each appears to have its own niche and thus "raison d'être". The NCI database has by far the highest number of compounds that are unique to it. Approximately 200 000 of the NCI structures were not found in any of the other analyzed databases.

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGuire, Michael A.; Clark, Genevieve; KC, Santosh

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

Human TTR conformation altered by rhenium tris-carbonyl derivatives.

PubMed

Ciccone, Lidia; Policar, Clotilde; Stura, Enrico A; Shepard, William

2016-09-01

Transthyretin (TTR) is a 54 kDa homotetrameric serum protein that transports thyroxine (T4) and retinol. TTR is potentially amyloidogenic due to homotetramer dissociation into monomeric intermediates that self-assemble as amyloid deposits and insoluble fibrils. Most crystallographic structures, including those of amyloidogenic variants show the same tetramer without major variations in the monomer-monomer interface nor in the volume of the interdimeric cavity. Soaking TTR crystals in a solution containing rhenium tris-carbonyl derivatives yields a TTR conformer never observed before. Only one of the two monomers of the crystallographic dimer is significantly altered, and the inner part of the T4 binding cavity is expanded at one end and shrunk at the other. The result redefines the mechanism of allosteric communication between the two sites, suggesting that negative cooperativity is a function of dimer asymmetry, which can be induced through internal or external binding. An aspect that remains unexplained is why the conformational changes are ubiquitous throughout the crystal although the heavy metal content of the derivatized crystals is relatively low. The conformational changes observed, which include Leu(82), may represent a form of TTR better at scavenging β-Amyloid. At a resolution of 1.69Å, with excellent refinement statistics and well defined electron density for all parts of the structure, it is possible to envisage answering important questions that range from protein cooperative behavior to heavy atom induced protein conformational modifications that can result in crystallographic non-isomorphism. Copyright © 2016 Elsevier Inc. All rights reserved.

Computational materials science: Think locally, act globally

NASA Astrophysics Data System (ADS)

Rabe, Karin M.

2002-11-01

New first-principles calculations reveal the range of atomic arrangements underlying the average crystallographic structure of a perovskite oxide, PZT. This work opens the door to understanding the exceptional physical behaviour of PZT and related systems.

TEXTURES IN EXTRUDED URANIUM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Russell, R.B.

The preferred orientation or texture of alpha-extruded, cold-swaged, recrystallized, and beta-quenched uranium has been determined. An attempt is made to predict the mean thermal expansion coefficients from the texture and principal crystallographic thermal expansion coefficients. (auth)

Oriented attachment by enantioselective facet recognition in millimeter-sized gypsum crystals.

PubMed

Viedma, Cristóbal; Cuccia, Louis A; McTaggart, Alicia; Kahr, Bart; Martin, Alexander T; McBride, J Michael; Cintas, Pedro

2016-09-22

Crystal growth by oriented attachment involves the spontaneous self-assembly of adjoining crystals with common crystallographic orientations. Herein, we report the oriented attachment of gypsum crystals on agitation to form stereoselective mesoscale aggregates.

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE PAGES

Chandra, Vikas; Wu, Dalei; Li, Sheng; ...

2017-10-11

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

HRTEM Analysis of Crystallographic Defects in CdZnTe Single Crystal

NASA Astrophysics Data System (ADS)

Yasar, Bengisu; Ergunt, Yasin; Kabukcuoglu, Merve Pinar; Parlak, Mehmet; Turan, Rasit; Kalay, Yunus Eren

2018-01-01

In recent years, CdZnTe has attracted much attention due to its superior electrical and structural properties for room-temperature operable gamma and x-ray detectors. However, CdZnTe (CZT) material has often suffered from crystallographic defects encountered during the growth and post-growth processes. The identification and structural characterization of these defects is crucial to synthesize defect-free CdZnTe single crystals. In this study, Cd0.95 Zn0.05 Te single crystals were grown using a three-zone vertical Bridgman system. The single crystallinity of the material was ensured by using x-ray diffraction measurements. High-resolution electron microscopy (HRTEM) was used to characterize the nano-scale defects on the CdZnTe matrix. The linear defects oriented along the ⟨211⟩ direction were examined by transmission electron microscopy (TEM) and the corresponding HRTEM image simulations were performed by using a quantitative scanning TEM simulation package.

3D Microstructural Architectures for Metal and Alloy Components Fabricated by 3D Printing/Additive Manufacturing Technologies

NASA Astrophysics Data System (ADS)

Martinez, E.; Murr, L. E.; Amato, K. N.; Hernandez, J.; Shindo, P. W.; Gaytan, S. M.; Ramirez, D. A.; Medina, F.; Wicker, R. B.

The layer-by-layer building of monolithic, 3D metal components from selectively melted powder layers using laser or electron beams is a novel form of 3D printing or additive manufacturing. Microstructures created in these 3D products can involve novel, directional solidification structures which can include crystallographically oriented grains containing columnar arrays of precipitates characteristic of a microstructural architecture. These microstructural architectures are advantageously rendered in 3D image constructions involving light optical microscopy and scanning and transmission electron microscopy observations. Microstructural evolution can also be effectively examined through 3D image sequences which, along with x-ray diffraction (XRD) analysis in the x-y and x-z planes, can effectively characterize related crystallographic/texture variances. This paper compares 3D microstructural architectures in Co-base and Ni-base superalloys, columnar martensitic grain structures in 17-4 PH alloy, and columnar copper oxides and dislocation arrays in copper.

Study of Initial Stages of Ball-Milling of Cu Powder Using X-ray Diffraction

NASA Astrophysics Data System (ADS)

Gayathri, N.; Mukherjee, Paramita

2018-04-01

The initial stage of size refinement of Cu powder is studied using detailed X-ray diffraction (XRD) analysis to understand the mechanism of formation of nanomaterials during the ball-milling process. The study was restricted to samples obtained for milling time up to 240 min to understand the deformation mechanism at the early stages of ball milling. Various model based approaches for the analysis of the XRD were used to study the evolution of the microstructural parameters such as domain size and microstrain along the different crystallographic planes. It was seen that the domain size saturates at a low value along the (311) plane whereas the size along the (220) and (200) plane is still higher. The r.m.s microstrain showed a non-monotonic change along the different crystallographic directions up to the milling time of 240 min.

RCrane: semi-automated RNA model building.

PubMed

Keating, Kevin S; Pyle, Anna Marie

2012-08-01

RNA crystals typically diffract to much lower resolutions than protein crystals. This low-resolution diffraction results in unclear density maps, which cause considerable difficulties during the model-building process. These difficulties are exacerbated by the lack of computational tools for RNA modeling. Here, RCrane, a tool for the partially automated building of RNA into electron-density maps of low or intermediate resolution, is presented. This tool works within Coot, a common program for macromolecular model building. RCrane helps crystallographers to place phosphates and bases into electron density and then automatically predicts and builds the detailed all-atom structure of the traced nucleotides. RCrane then allows the crystallographer to review the newly built structure and select alternative backbone conformations where desired. This tool can also be used to automatically correct the backbone structure of previously built nucleotides. These automated corrections can fix incorrect sugar puckers, steric clashes and other structural problems.

Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M., E-mail: dinakar@nii.res.in

The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presencemore » of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 150.7, c = 164.9 Å.« less

Preliminary crystallographic analysis of the oxidized form of a two mono-nuclear iron centres protein from Desulfovibrio desulfuricans ATCC 27774.

PubMed Central

Coelho, A. V.; Matias, P. M.; Carrondo, M. A.; Tavares, P.; Moura, J. J.; Moura, I.; Fülop, V.; Hajdu, J.; Le Gall, J.

1996-01-01

Crystals of the fully oxidized form of desulfoferrodoxin were obtained by vapor diffusion from a solution containing 20% PEG 4000, 0.1 M HEPES buffer, pH 7.5, and 0.2 M CaCl2. Trigonal and/or rectangular prisms could be obtained, depending on the temperature used for the crystal growth. Trigonal prisms belong to the rhombohedral space group R32, with a = 112.5 A and c = 63.2 A; rectangular prisms belong to the monoclinic space group C2, with a = 77.7 A, b = 80.9 A, c = 53.9 A, and beta = 98.1 degrees. The crystallographic asymmetric unit of the rhombohedral crystal form contains one molecule. There are two molecules in the asymmetric unit of the monoclinic form, in agreement with the self-rotation function. PMID:8762151

The quaternary architecture of RARβ–RXRα heterodimer facilitates domain–domain signal transmission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandra, Vikas; Wu, Dalei; Li, Sheng

Assessing the physical connections and allosteric communications in multi-domain nuclear receptor (NR) polypeptides has remained challenging, with few crystal structures available to show their overall structural organizations. Here we report the quaternary architecture of multi-domain retinoic acid receptor beta-retinoic X receptor alpha (RAR beta-RXR alpha) heterodimer bound to DNA, ligands and coactivator peptides, examined through crystallographic, hydrogen-deuterium exchange mass spectrometry, mutagenesis and functional studies. The RAR beta ligand-binding domain (LBD) and DNA-binding domain (DBD) are physically connected to foster allosteric signal transmission between them. Direct comparisons among all the multi-domain NRs studied crystallographically to date show significant variations within theirmore » quaternary architectures, rather than a common architecture adhering to strict rules. RXR remains flexible and adaptive by maintaining loosely organized domains, while its hetero-dimerization partners use a surface patch on their LBDs to form domain-domain interactions with DBDs.« less

A transmission Kikuchi diffraction study of cementite in a quenched and tempered steel

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saleh, Ahmed A., E-mail: asaleh@uow.edu.au; Casillas, Gilberto; Pereloma, Elena V.

2016-04-15

This is the first transmission Kikuchi diffraction (TKD) study to report the indexing of nano-sized cementite as distinct structures and its orientation relationship with the body-centered cubic matrix in a quenched and tempered steel. Crystallographic analysis via TKD and selected area diffraction returned the well-known Bagaryatskii and Isaichev orientation relationships. However, the indexing of nano-sized cementite via TKD was sensitive to the thickness of the electron transparent region such that TEM remains the most precise method to characterise such precipitates. - Highlights: • Nano-sized cementite in a QT steel has been investigated by TKD and TEM. • Cementite has beenmore » indexed as distinct structures via TKD. • Crystallographic analysis returned the Bagaryatskii and Isaichev ORs. • Success of TKD is sensitive to the thickness of the electron transparent region. • TEM remains the most precise technique to characterise nano-sized precipitates.« less

The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive

PubMed Central

Gilliland, Gary L.; Tung, Michael; Ladner, Jane

1996-01-01

The NIST/NASA/CARB Biological Macromolecule Crystallization Database (BMCD), NIST Standard Reference Database 21, contains crystal data and crystallization conditions for biological macromolecules. The database entries include data abstracted from published crystallographic reports. Each entry consists of information describing the biological macromolecule crystallized and crystal data and the crystallization conditions for each crystal form. The BMCD serves as the NASA Protein Crystal Growth Archive in that it contains protocols and results of crystallization experiments undertaken in microgravity (space). These database entries report the results, whether successful or not, from NASA-sponsored protein crystal growth experiments in microgravity and from microgravity crystallization studies sponsored by other international organizations. The BMCD was designed as a tool to assist x-ray crystallographers in the development of protocols to crystallize biological macromolecules, those that have previously been crystallized, and those that have not been crystallized. PMID:11542472

Low temperature dielectric relaxation in ordinary perovskite ferroelectrics: enlightenment from high-energy x-ray diffraction

NASA Astrophysics Data System (ADS)

Ochoa, D. A.; Levit, R.; Fancher, C. M.; Esteves, G.; Jones, J. L.; E García, J.

2017-05-01

Ordinary ferroelectrics exhibit a second order phase transition that is characterized by a sharp peak in the dielectric permittivity at a frequency-independent temperature. Furthermore, these materials show a low temperature dielectric relaxation that appears to be a common behavior of perovskite systems. Tetragonal lead zirconate titanate is used here as a model system in order to explore the origin of such an anomaly, since there is no consensus about the physical phenomenon involved in it. Crystallographic and domain structure studies are performed from temperature dependent synchrotron x-ray diffraction measurement. Results indicate that the dielectric relaxation cannot be associated with crystallographic or domain configuration changes. The relaxation process is then parameterized by using the Vogel-Fulcher-Tammann phenomenological equation. Results allow us to hypothesize that the observed phenomenon is due to changes in the dynamic behavior of the ferroelectric domains related to the fluctuation of the local polarization.

Catalytic, Enantioselective Sulfenofunctionalisation of Alkenes: Mechanistic, Crystallographic, and Computational Studies

PubMed Central

Denmark, Scott E.; Hartmann, Eduard; Kornfilt, David J. P.; Wang, Hao

2015-01-01

The stereocontrolled introduction of vicinal heteroatomic substituents into organic molecules is one of the most powerful ways of adding value and function. Whereas many methods exist for the introduction of oxygen- and nitrogen-containing substituents, the number stereocontrolled methods for the introduction of sulfur-containing substituents pales by comparison. Previous reports from these laboratories have described the sulfenofunctionalization of alkenes that construct vicinal carbon-sulfur and carbon-oxygen, carbon-nitrogen as well as carbon-carbon bonds with high levels of diastereospecificity and enantioselectivity. This process is enabled by the concept of Lewis base activation of Lewis acids that provides activation of Group 16 electrophiles. To provide a foundation for expansion of substrate scope and improved selectivities, we have undertaken a comprehensive study of the catalytically active species. Insights gleaned from kinetic, crystallographic and computational methods have led to the introduction of a new family of sulfenylating agents that provide significantly enhanced selectivities. PMID:25411883

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beste, Ariana; Overbury, Steven H.

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed productmore » selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Ultimately, subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.« less

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces

DOE PAGES

Beste, Ariana; Overbury, Steven H.

2016-03-09

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed productmore » selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Ultimately, subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.« less

Dehydrogenation of methanol to formaldehyde catalyzed by pristine and defective ceria surfaces.

PubMed

Beste, Ariana; Overbury, Steven H

2016-04-21

We have explored the dehydrogenation of methoxy on pristine and defective (111), (100), and (110) ceria surfaces with density functional methods. Methanol conversion is used as a probe reaction to understand structure sensitivity of the oxide catalysis. Differences in reaction selectivity have been observed experimentally as a function of crystallographically exposed faces and degree of reduction. We find that the barrier for carbon-hydrogen cleavage in methoxy is similar for the pristine and defective (111), (100), and (110) surfaces. However, there are large differences in the stability of the surface intermediates on the different surfaces. The variations in experimentally observed product selectivities are a consequence of the interplay between barrier controlled bond cleavage and desorption processes. Subtle differences in activation energies for carbon-hydrogen cleavage on the different crystallographic faces of ceria could not be correlated with structural or electronic descriptors.

Electrical properties of NiAs-type MnTe films with preferred crystallographic plane of (110)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, L.; Wang, Z. H., E-mail: zhwang@imr.ac.cn; Zhang, Z. D.

2016-01-28

NiAs-type manganese telluride (MnTe) films with preferred crystallographic plane of (110) were prepared on Si/SiO{sub 2} substrates by pulsed laser deposition. X-ray diffraction (XRD) of the films was studied at different temperatures. The XRD peak of MnTe (110) films shifts to higher angle with decreasing temperature, showing the decrease of the lattice parameter. Resistivity of the films was studied in the temperature range of 2–350 K. The bump between 150 and 250 K was observed in the films, which may be related to the special s-d and p-d overlaps induced by the compressed lattice. The magnon drag effect near its Néel temperaturemore » T{sub N} and enlarged magnetic-elastic coupling below 100 K were observed and analyzed in details.« less

Local atomic and magnetic structure of dilute magnetic semiconductor (Ba ,K ) (Zn,Mn ) 2As2

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; Banerjee, Soham; Chen, Bijuan; Jin, Changqing; Feygenson, Mikhail; Uemura, Yasutomo J.; Billinge, Simon J. L.

2016-09-01

We have studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba ,K )(Zn ,Mn )2As2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. We detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5 Å , resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment of Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. We discuss these results in the context of other experiments and theoretical studies on this system.

Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

PubMed

Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

2015-05-01

The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples.

Rapid experimental SAD phasing and hot-spot identification with halogenated fragments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bauman, Joseph D.; Harrison, Jerry Joe E. K.; Arnold, Eddy

2016-01-01

Through X-ray crystallographic fragment screening, 4-bromopyrazole was discovered to be a `magic bullet' that is capable of binding at many of the ligand `hot spots' found in HIV-1 reverse transcriptase (RT). The binding locations can be in pockets that are `hidden' in the unliganded crystal form, allowing rapid identification of these sites forin silicoscreening. In addition to hot-spot identification, this ubiquitous yet specific binding provides an avenue for X-ray crystallographic phase determination, which can be a significant bottleneck in the determination of the structures of novel proteins. The anomalous signal from 4-bromopyrazole or 4-iodopyrazole was sufficient to determine the structuresmore » of three proteins (HIV-1 RT, influenza A endonuclease and proteinase K) by single-wavelength anomalous dispersion (SAD) from single crystals. Both compounds are inexpensive, readily available, safe and very soluble in DMSO or water, allowing efficient soaking into crystals.« less

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide

NASA Astrophysics Data System (ADS)

Saravanan, R. R.; Seshadri, S.; Gunasekaran, S.; Mendoza-Meroño, R.; Garcia-Granda, S.

2015-03-01

Conformational analysis, X-ray crystallographic, FT-IR, FT-Raman, DFT, MEP and molecular docking studies on 1-(1-(3-methoxyphenyl) ethylidene) thiosemicarbazide (MPET) are investigated. From conformational analysis the examination of the positions of a molecule taken and the energy changes is observed. The docking studies of the ligand MPET with target protein showed that this is a good molecule which docks well with target related to HMG-CoA. Hence MPET can be considered for developing into a potent anti-cholesterol drug. MEP assists in optimization of electrostatic interactions between the protein and the ligand. The MEP surface displays the molecular shape, size and electrostatic potential values. The optimized geometry of the compound was calculated from the DFT-B3LYP gradient calculations employing 6-31G (d, p) basis set and calculated vibrational frequencies are evaluated via comparison with experimental values.

Supervised machine learning techniques to predict binding affinity. A study for cyclin-dependent kinase 2.

PubMed

de Ávila, Maurício Boff; Xavier, Mariana Morrone; Pintro, Val Oliveira; de Azevedo, Walter Filgueira

2017-12-09

Here we report the development of a machine-learning model to predict binding affinity based on the crystallographic structures of protein-ligand complexes. We used an ensemble of crystallographic structures (resolution better than 1.5 Å resolution) for which half-maximal inhibitory concentration (IC 50 ) data is available. Polynomial scoring functions were built using as explanatory variables the energy terms present in the MolDock and PLANTS scoring functions. Prediction performance was tested and the supervised machine learning models showed improvement in the prediction power, when compared with PLANTS and MolDock scoring functions. In addition, the machine-learning model was applied to predict binding affinity of CDK2, which showed a better performance when compared with AutoDock4, AutoDock Vina, MolDock, and PLANTS scores. Copyright © 2017 Elsevier Inc. All rights reserved.

On the relationship between cumulative correlation coefficients and the quality of crystallographic data sets.

PubMed

Wang, Jimin; Brudvig, Gary W; Batista, Victor S; Moore, Peter B

2017-12-01

In 2012, Karplus and Diederichs demonstrated that the Pearson correlation coefficient CC 1/2 is a far better indicator of the quality and resolution of crystallographic data sets than more traditional measures like merging R-factor or signal-to-noise ratio. More specifically, they proposed that CC 1/2 be computed for data sets in thin shells of increasing resolution so that the resolution dependence of that quantity can be examined. Recently, however, the CC 1/2 values of entire data sets, i.e., cumulative correlation coefficients, have been used as a measure of data quality. Here, we show that the difference in cumulative CC 1/2 value between a data set that has been accurately measured and a data set that has not is likely to be small. Furthermore, structures obtained by molecular replacement from poorly measured data sets are likely to suffer from extreme model bias. © 2017 The Protein Society.

Fine refinement of solid state structure of racemic form of phospho-tyrosine employing NMR Crystallography approach.

PubMed

Paluch, Piotr; Pawlak, Tomasz; Oszajca, Marcin; Lasocha, Wieslaw; Potrzebowski, Marek J

2015-02-01

We present step by step facets important in NMR Crystallography strategy employing O-phospho-dl-tyrosine as model sample. The significance of three major techniques being components of this approach: solid state NMR (SS NMR), X-ray diffraction of powdered sample (PXRD) and theoretical calculations (Gauge Invariant Projector Augmented Wave; GIPAW) is discussed. Each experimental technique provides different set of structural constraints. From the PXRD measurement the size of the unit cell, space group and roughly refined molecular structure are established. SS NMR provides information about content of crystallographic asymmetric unit, local geometry, molecular motion in the crystal lattice and hydrogen bonding pattern. GIPAW calculations are employed for validation of quality of elucidation and fine refinement of structure. Crystal and molecular structure of O-phospho-dl-tyrosine solved by NMR Crystallography is deposited at Cambridge Crystallographic Data Center under number CCDC 1005924. Copyright © 2014 Elsevier Inc. All rights reserved.

In-plane isotropic magnetic and electrical properties of MnAs/InAs/GaAs (111) B hybrid structure

NASA Astrophysics Data System (ADS)

Islam, Md. Earul; Akabori, Masashi

2018-03-01

We characterized in-plane magnetic and electrical properties of MnAs/InAs/GaAs (111) B hybrid structure grown by molecular beam epitaxy (MBE). We observed isotropic easy magnetization in two crystallographic in-plane directions, [ 2 ̅ 110 ] and [ 0 1 ̅ 10 ] of hexagonal MnAs i.e. [ 1 ̅ 10 ] and [ 11 2 ̅ ] of cubic InAs. We also fabricated transmission line model (TLM) devices, and observed almost isotropic electrical properties in two crystallographic in-plane directions, [ 1 ̅ 10 ] and [ 11 2 ̅ ] of cubic InAs. Also we tried to fabricate and characterize lateral spin-valve (LSV) devices from the hybrid structure. We could roughly estimate the spin injection efficiency and the spin diffusion length at room temperature in [ 11 2 ̅ ] direction. We believe that the hybrid structures are helpful to design spintronic device with good flexibility in-plane.

Understanding pre-mRNA splicing through crystallography.

PubMed

Espinosa, Sara; Zhang, Lingdi; Li, Xueni; Zhao, Rui

2017-08-01

Crystallography is a powerful tool to determine the atomic structures of proteins and RNAs. X-ray crystallography has been used to determine the structure of many splicing related proteins and RNAs, making major contributions to our understanding of the molecular mechanism and regulation of pre-mRNA splicing. Compared to other structural methods, crystallography has its own advantage in the high-resolution structural information it can provide and the unique biological questions it can answer. In addition, two new crystallographic methods - the serial femtosecond crystallography and 3D electron crystallography - were developed to overcome some of the limitations of traditional X-ray crystallography and broaden the range of biological problems that crystallography can solve. This review discusses the theoretical basis, instrument requirements, troubleshooting, and exciting potential of these crystallographic methods to further our understanding of pre-mRNA splicing, a critical event in gene expression of all eukaryotes. Copyright © 2017 Elsevier Inc. All rights reserved.

A high-throughput technique for determining grain boundary character non-destructively in microstructures with through-thickness grains

DOE PAGES

Seita, Matteo; Volpi, Marco; Patala, Srikanth; ...

2016-06-24

Grain boundaries (GBs) govern many properties of polycrystalline materials. However, because of their structural variability, our knowledge of GB constitutive relations is still very limited. We present a novel method to characterise the complete crystallography of individual GBs non-destructively, with high-throughput, and using commercially available tools. This method combines electron diffraction, optical reflectance and numerical image analysis to determine all five crystallographic parameters of numerous GBs in samples with through-thickness grains. We demonstrate the technique by measuring the crystallographic character of about 1,000 individual GBs in aluminum in a single run. Our method enables cost- and time-effective assembly of crystallography–propertymore » databases for thousands of individual GBs. Furthermore, such databases are essential for identifying GB constitutive relations and for predicting GB-related behaviours of polycrystalline solids.« less

Signatures of unfolding in the early stages of protein denaturation

NASA Astrophysics Data System (ADS)

Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2012-04-01

A comparative study of the early stages of unfolding of five proteins: cyt c, c-b 562, cyt c‧, azurin, and lysozyme is reported. From crystallographic data, helical regions and intervening non-helical (or 'turning') regions are identified in each. Exploiting a previously introduced geometrical model, the paper describes quantitatively the stepwise extension of a polypeptide chain subject to the geometrical constraint that the spatial relationship among the residues of each triplet is fixed by native-state crystallographic data. Despite differences among the above-cited proteins, remarkable universality of behavior is found in the early stages of unfolding. At the very earliest stages, internal residues in each helical region have a common unfolding history; the terminal residues, however, are extraordinarily sensitive to structural perturbations. Residues in non-helical sections of the polypeptide unfold after residues in the internal helical regions, but with increasing steric perturbation playing a dominant role in advancing denaturation.

Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko

2007-10-01

Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two moleculesmore » per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.« less

Texture analysis of Napoleonic War Era copper bolts

NASA Astrophysics Data System (ADS)

Malamud, Florencia; Northover, Shirley; James, Jon; Northover, Peter; Kelleher, Joe

2016-04-01

Neutron diffraction techniques are suitable for volume texture analyses due to high penetration of thermal neutrons in most materials. We have implemented a new data analysis methodology that employed the spatial resolution achievable by a time-of-flight neutron strain scanner to non-destructively determine the crystallographic texture at selected locations within a macroscopic sample. The method is based on defining the orientation distribution function of the crystallites from several incomplete pole figures, and it has been implemented on ENGIN-X, a neutron strain scanner at the Isis Facility in the UK. Here, we demonstrate the application of this new texture analysis methodology in determining the crystallographic texture at selected locations within museum quality archaeological objects up to 1 m in length. The results were verified using samples of similar, but less valuable, objects by comparing the results of applying this method with those obtained using both electron backscatter diffraction and X-ray diffraction on their cross sections.

Levers for Thermoelectric Properties in Titania-Based Ceramics

NASA Astrophysics Data System (ADS)

Backhaus-Ricoult, Monika; Rustad, James R.; Vargheese, Deenamma; Dutta, Indrajit; Work, Kim

2012-06-01

While the beneficial impact of nanostructural engineering on thermoelectric performance has been demonstrated for many semiconducting materials (SiGe, skutterudites, PbTe2, etc.), no significant advantages have been reported for oxide nanomaterials. In this study, titania is used as a model material to compare the impact of grain size, doping and substitution, second-phase nanodispersion, and crystallographic defects on the electronic and thermal properties. It is shown that the lattice thermal conductivity can be most efficiently reduced by high densities of crystallographic planar defects in the Magnéli phases, while modification of grain size or introduction of second phases on length scales of 20 nm to 100 nm introduces only minor improvement. For the electronic properties, donor dopants such as niobium provide improvement of the power factor, but are not able to compete with the enhanced carrier concentration that is reached through oxygen vacancy introduction.

Polarized Neutron Study of Ni-Mn-Ga Alloys: Site-Specific Spin Density Affected by Martensitic Transformation.

PubMed

Lázpita, P; Barandiarán, J M; Gutiérrez, J; Mondelli, C; Sozinov, A; Chernenko, V A

2017-10-13

Polarized neutron scattering has been used to obtain the magnetic moment at specific crystallographic sites of the austenitic and martensitic phases of two nonstoichiometric Ni-Mn-Ga single crystals with close composition. These alloys have been chosen because they exhibit different structures in the paramagnetic state and inverse positions of the respective martensitic transformation and Curie temperature. The diffraction analysis revealed a remarkable result: Despite the similar alloy composition, the magnetic moments of Mn are quite different for the two alloys at the same crystallographic position. Furthermore, such a difference enabled us to assess that the exchange coupling between Mn atoms switches from ferro- to antiferromagnetic at a distance between 2.92 and 3.32 Å in the martensite. These results are of great importance to guide first principles calculations that, up to now, have not been contrasted with experiments at the atomic level.

Crystallographic evidence for noncoplanar catalytic aspartic acids in plasmepsin II resides in the Protein Data Bank.

PubMed

Robbins, Arthur H; Dunn, Ben M; Agbandje-McKenna, Mavis; McKenna, Robert

2009-03-01

The carboxylate atoms of the two catalytic aspartic acid residues in aspartic proteases are nearly coplanar and in the uncomplexed form share an in-plane nucleophilic water molecule that is central to the mechanism of these enzymes. This note reports that while reviewing the electron-density maps derived from the deposited data for uncomplexed plasmepsin II from Plasmodium falciparum [Asojo et al. (2003), J. Mol. Biol. 327, 173-181; PDB code 1lf4], it was discovered that the aspartic acid residues in this structure should in fact be distinctly noncoplanar. The crystallographic model from the deposited coordinates has been re-refined against the 1.9 A resolution published diffraction data to an R(cryst) of 21.2% and an R(free) of 22.2%. The catalytic water molecule is present, but the plane of the carboxylate group of Asp214 is rotated by 66 degrees from its original position.

A crystallographic model for nickel base single crystal alloys

NASA Technical Reports Server (NTRS)

Dame, L. T.; Stouffer, D. C.

1988-01-01

The purpose of this research is to develop a tool for the mechanical analysis of nickel-base single-crystal superalloys, specifically Rene N4, used in gas turbine engine components. This objective is achieved by developing a rate-dependent anisotropic constitutive model and implementing it in a nonlinear three-dimensional finite-element code. The constitutive model is developed from metallurgical concepts utilizing a crystallographic approach. An extension of Schmid's law is combined with the Bodner-Partom equations to model the inelastic tension/compression asymmetry and orientation-dependence in octahedral slip. Schmid's law is used to approximate the inelastic response of the material in cube slip. The constitutive equations model the tensile behavior, creep response and strain-rate sensitivity of the single-crystal superalloys. Methods for deriving the material constants from standard tests are also discussed. The model is implemented in a finite-element code, and the computed and experimental results are compared for several orientations and loading conditions.

Optical third harmonic generation in the magnetic semiconductor EuSe

NASA Astrophysics Data System (ADS)

Lafrentz, M.; Brunne, D.; Kaminski, B.; Pavlov, V. V.; Pisarev, R. V.; Henriques, A. B.; Yakovlev, D. R.; Springholz, G.; Bauer, G.; Bayer, M.

2012-01-01

Third harmonic generation (THG) has been studied in europium selenide EuSe in the vicinity of the band gap at 2.1-2.6 eV and at higher energies up to 3.7 eV. EuSe is a magnetic semiconductor crystalizing in centrosymmetric structure of rock-salt type with the point group m3m. For this symmetry the crystallographic and magnetic-field-induced THG nonlinearities are allowed in the electric-dipole approximation. Using temperature, magnetic field, and rotational anisotropy measurements, the crystallographic and magnetic-field-induced contributions to THG were unambiguously separated. Strong resonant magnetic-field-induced THG signals were measured at energies in the range of 2.1-2.6 eV and 3.1-3.6 eV for which we assign to transitions from 4f7 to 4f65d1 bands, namely involving 5d(t2g) and 5d(eg) states.

Polarized Neutron Study of Ni-Mn-Ga Alloys: Site-Specific Spin Density Affected by Martensitic Transformation

NASA Astrophysics Data System (ADS)

Lázpita, P.; Barandiarán, J. M.; Gutiérrez, J.; Mondelli, C.; Sozinov, A.; Chernenko, V. A.

2017-10-01

Polarized neutron scattering has been used to obtain the magnetic moment at specific crystallographic sites of the austenitic and martensitic phases of two nonstoichiometric Ni-Mn-Ga single crystals with close composition. These alloys have been chosen because they exhibit different structures in the paramagnetic state and inverse positions of the respective martensitic transformation and Curie temperature. The diffraction analysis revealed a remarkable result: Despite the similar alloy composition, the magnetic moments of Mn are quite different for the two alloys at the same crystallographic position. Furthermore, such a difference enabled us to assess that the exchange coupling between Mn atoms switches from ferro- to antiferromagnetic at a distance between 2.92 and 3.32 Å in the martensite. These results are of great importance to guide first principles calculations that, up to now, have not been contrasted with experiments at the atomic level.

Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate.

PubMed

Zhang, Zhihong; Smart, Tristan J; Choi, Hwanho; Hardy, Florence; Lohans, Christopher T; Abboud, Martine I; Richardson, Melodie S W; Paton, Robert S; McDonough, Michael A; Schofield, Christopher J

2017-05-02

Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, but via the four-electron oxidation of 2-oxoglutarate to give ethylene in an arginine-dependent reaction. Crystallographic and biochemical studies on the Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide. Crystallographic and quantum chemical studies reveal that fragmentation to give ethylene is promoted by binding of l-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation.

Investigation of rail wheel steel crystallographic texture changes due to modification and thermomechanical treatment

NASA Astrophysics Data System (ADS)

Lychagina, T.; Nikolayev, D.; Sanin, A.; Tatarko, J.; Ullemeyer, K.

2015-04-01

In this work crystallographic texture for a set of rail wheel steel samples with different regimes of thermo-mechanical treatment and with and without modification by system Al-Mg-Si- Fe-C-Ca-Ti-Ce was measured by neutron diffraction. The texture measurements were carried out by using time-of-flight technique at SKAT diffractometer situated at IBR-2 reactor (Dubna, JINR, Russia). The three complete pole figures (110), (200), (211) of α-Fe phase in 5°×5°grid were extracted from a set of 1368 spectra measured for each sample. The samples were cut from rail wheel rim and from transitional zone (between rail wheel hub and wheel disk). It was concluded that the steel modification and some changes in the heat treatment modes of the rail wheels from the experimental (modified) and the conventional (non-modified) steel lead to reorientation of texture component.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nazareth, A.S.; Sood, D.K.; Zmood, R.B.

A focusing grid broad beam Kaufman source, using argon ions on a target of nominal composition Nd{sub 2}Fe{sub 14}B has been employed to sputter deposit magnetic thin films of thicknesses ranging from 800 {angstrom} to 1300 {angstrom} on silicon-(111) substrates at room temperature. These films were characterized for their composition depth profile by Rutherford Backscattering Spectroscopy, while x-ray diffraction was used to study the crystallographic structure. Due to a close match between (111) Si with (220) Nd{sub 2}Fe{sub 14}B lattice spacings, preferred crystallographic texturing was expected, and experimental results showed a greatly enhanced (220) texture. The degradation in magnetic propertiesmore » was attributed to the presence of oxygen in the films as indicated by concentration depth profiles. It is premised that another significant role of oxygen may be to relieve the misfit strain across the interface by its incorporation within the Nd{sub 2}Fe{sub 14}B phase.« less

Protein stability: a crystallographer’s perspective

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deller, Marc C., E-mail: mdeller@stanford.edu; Kong, Leopold; Rupp, Bernhard

An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhatmore » practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.« less

High quality factor GaAs-based photonic crystal microcavities by epitaxial re-growth.

PubMed

Prieto, Ivan; Herranz, Jesús; Wewior, Lukasz; González, Yolanda; Alén, Benito; González, Luisa; Postigo, Pablo A

2013-12-16

We investigate L7 photonic crystal microcavities (PCMs) fabricated by epitaxial re-growth of GaAs pre-patterned substrates, containing InAs quantum dots. The resulting PCMs show hexagonal shaped nano-holes due to the development of preferential crystallographic facets during the re-growth step. Through a careful control of the fabrication processes, we demonstrate that the photonic modes are preserved throughout the process. The quality factor (Q) of the photonic modes in the re-grown PCMs strongly depends on the relative orientation between photonic lattice and crystallographic directions. The optical modes of the re-grown PCMs preserve the linear polarization and, for the most favorable orientation, a 36% of the Q measured in PCMs fabricated by the conventional procedure is observed, exhibiting values up to ~6000. The results aim to the future integration of site-controlled QDs with high-Q PCMs for quantum photonics and quantum integrated circuits.

Experimental and first principle studies on electronic structure of BaTiO{sub 3}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sagdeo, Archna, E-mail: archnaj@rrcat.gov.in; Ghosh, Haranath, E-mail: archnaj@rrcat.gov.in; Chakrabarti, Aparna, E-mail: archnaj@rrcat.gov.in

2014-04-24

We have carried out photoemission experiments to obtain valence band spectra of various crystallographic symmetries of BaTiO{sub 3} system which arise as a function of temperature. We also present results of a detailed first principle study of these symmetries of BaTiO{sub 3} using generalized gradient approximation for the exchange-correlation potential. Here we present theoretical results of density of states obtained from DFT based simulations to compare with the experimental valence band spectra. Further, we also perform calculations using post density functional approaches like GGA + U method as well as non-local hybrid exchange-correlation potentials like PBE0, B3LYP, HSE in ordermore » to understand the extent of effect of correlation on band gaps of different available crystallographic symmetries (5 in number) of BaTiO{sub 3}.« less

Molecular dynamics simulations of polarizable DNA in crystal environment

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Baucom, Jason; Darden, Thomas A.; Sagui, Celeste

We have investigated the role of the electrostatic description and cell environment in molecular dynamics (MD) simulations of DNA. Multiple unrestrained MD simulations of the DNA duplex d(CCAACGTTGG)2 have been carried out using two different force fields: a traditional description based on atomic point charges and a polarizable force field. For the time scales probed, and given the ?right? distribution of divalent ions, the latter performs better than the nonpolarizable force field. In particular, by imposing the experimental unit cell environment, an initial configuration with ideal B-DNA duplexes in the unit cell acquires sequence-dependent features that very closely resemble the crystallographic ones. Simultaneously, the all-atom root-mean-square coordinates deviation (RMSD) with respect to the crystallographic structure is seen to decay. At later times, the polarizable force field is able to maintain this lower RMSD, while the nonpolarizable force field starts to drift away.

Texture-Induced Anisotropy in an Inconel 718 Alloy Deposited Using Electron Beam Freeform Fabrication

NASA Technical Reports Server (NTRS)

Tayon, W.; Shenoy, R.; Bird, R.; Hafley, R.; Redding, M.

2014-01-01

A test block of Inconel (IN) 718 was fabricated using electron beam freeform fabrication (EBF(sup 3)) to examine how the EBF(sup 3) deposition process affects the microstructure, crystallographic texture, and mechanical properties of IN 718. Tests revealed significant anisotropy in the elastic modulus for the as-deposited IN 718. Subsequent tests were conducted on specimens subjected to a heat treatment designed to decrease the level of anisotropy. Electron backscatter diffraction (EBSD) was used to characterize crystallographic texture in the as-deposited and heat treated conditions. The anisotropy in the as-deposited condition was strongly affected by texture as evidenced by its dependence on orientation relative to the deposition direction. Heat treatment resulted in a significant improvement in modulus of the EBF(sup 3) product to a level nearly equivalent to that for wrought IN 718 with reduced anisotropy; reduction in texture through recrystallization; and production of a more homogeneous microstructure.

Direct observation of grain rotations during coarsening of a semisolid Al–Cu alloy

PubMed Central

Dake, Jules M.; Oddershede, Jette; Sørensen, Henning O.; Werz, Thomas; Shatto, J. Cole; Uesugi, Kentaro; Schmidt, Søren; Krill, Carl E.

2016-01-01

Sintering is a key technology for processing ceramic and metallic powders into solid objects of complex geometry, particularly in the burgeoning field of energy storage materials. The modeling of sintering processes, however, has not kept pace with applications. Conventional models, which assume ideal arrangements of constituent powders while ignoring their underlying crystallinity, achieve at best a qualitative description of the rearrangement, densification, and coarsening of powder compacts during thermal processing. Treating a semisolid Al–Cu alloy as a model system for late-stage sintering—during which densification plays a subordinate role to coarsening—we have used 3D X-ray diffraction microscopy to track the changes in sample microstructure induced by annealing. The results establish the occurrence of significant particle rotations, driven in part by the dependence of boundary energy on crystallographic misorientation. Evidently, a comprehensive model for sintering must incorporate crystallographic parameters into the thermodynamic driving forces governing microstructural evolution. PMID:27671639

Crystallization and preliminary crystallographic analysis of l-asparaginase from Erwinia carotovora

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wikman, Linnea E. K.; Krasotkina, Julya; Kuchumova, Anastasia

2005-04-01

Er. carotovoral-asparaginase, a potential antileukaemic agent, has been crystallized. Crystals diffract to 2.6 Å using a rotating-anode source and belong to space group P2{sub 1}, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. Bacterial l-asparaginases have been used as therapeutic agents in the treatment of acute childhood lymphoblastic leukaemia for over 30 y. However, their use is limited owing to the glutaminase activity of the administered enzymes, which results in serious side effects. In contrast, l-asparaginase from Erwinia carotovora exhibits low glutaminase activity atmore » physiological concentrations of l-asparagine and l-glutamine in the blood. Recombinant Er. carotovoral-asparaginase was crystallized in the presence of l-glutamate by the hanging-drop vapour-diffusion method using 10 mg ml{sup −1} purified enzyme, 16–18%(w/v) PEG 3350 and 0.2 M NaF. X-ray diffraction data were collected to 2.6 Å at 293 K using an in-house rotating-anode generator. The crystals belong to the monoclinic P2{sub 1} space group, with unit-cell parameters a = 78.0, b = 112.3, c = 78.7 Å, β = 101.9° and a homotetramer in the crystallographic asymmetric unit. A molecular-replacement solution has been found and refinement is currently in progress. The crystal structure may provide leads towards protein-engineering efforts aimed at safer asparaginase administration in leukaemia treatment.« less

Crystallographic analysis of human hemoglobin elucidates the structural basis of the potent and dual antisickling activity of pyridyl derivatives of vanillin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abdulmalik, Osheiza; Ghatge, Mohini S.; Musayev, Faik N.

2011-11-01

Pyridyl derivatives of vanillin increase the fraction of the more soluble oxygenated sickle hemoglobin and/or directly increase the solubility of deoxygenated sickle hemoglobin. Crystallographic analysis reveals the structural basis of the potent and dual antisickling activity of these derivatives. Vanillin has previously been studied clinically as an antisickling agent to treat sickle-cell disease. In vitro investigations with pyridyl derivatives of vanillin, including INN-312 and INN-298, showed as much as a 90-fold increase in antisickling activity compared with vanillin. The compounds preferentially bind to and modify sickle hemoglobin (Hb S) to increase the affinity of Hb for oxygen. INN-312 also ledmore » to a considerable increase in the solubility of deoxygenated Hb S under completely deoxygenated conditions. Crystallographic studies of normal human Hb with INN-312 and INN-298 showed that the compounds form Schiff-base adducts with the N-terminus of the α-subunits to constrain the liganded (or relaxed-state) Hb conformation relative to the unliganded (or tense-state) Hb conformation. Interestingly, while INN-298 binds and directs its meta-positioned pyridine-methoxy moiety (relative to the aldehyde moiety) further down the central water cavity of the protein, that of INN-312, which is ortho to the aldehyde, extends towards the surface of the protein. These studies suggest that these compounds may act to prevent sickling of SS cells by increasing the fraction of the soluble high-affinity Hb S and/or by stereospecific inhibition of deoxygenated Hb S polymerization.« less

X-ray crystallographic and tungsten-183 nuclear magnetic resonance structural studies of the [M4(H2O)2(XW9O34) 2]10- heteropolyanions (M = COII or Zn, X = P or As)

USGS Publications Warehouse

Evans, H.T.; Tourne, C.M.; Tourne, G.F.; Weakley, T.J.R.

1986-01-01

The crystal structures of K10[Co4(H2O)2(PW9O 34)2]??22H2O (1) and isomorphous K10[Zn4(H2O)2(AsW9O 34)2]??23H2O (2) have been determined {Mo-K?? radiation, space group P21/n, Z = 2; (1) a = 15.794(2), b = 21.360(2), c = 12.312(1) A??, ?? = 91.96??, R = 0.084 for 3 242 observed reflections [I ??? 3??(I)]; (2) a = 15.842(4), b = 21.327(5), c = 12.308(4) A??, ?? = 92.42(4)??, R = 0.066 for 4 675 observed reflections [F ??? 3??(F)]}. The anions have crystallographic symmetry 1 and non-crystallographic symmetry very close to 2/m (C2h). Each consists of two [XW9O34]9- moieties [??-B isomers; X = P (1) or As (2)] linked via four CoIIO6 or ZnO6 groups. Two Co or Zn atoms each carry a water ligand. The 183W n.m.r. spectra of the anions [Zn4(H2O)2(XW9O34) 2]10- (X = P or As) confirm that the anions retain 2/m symmetry in aqueous solution. Homonuclear coupling constants between 183W atoms are 5.8-9.0 Hz for adjacent WO6 octahedra sharing edges, and 19.6-25.0 Hz for octahedra sharing corners.

Controlling the opto-electronic properties of nc-SiOx:H films by promotion of 〈220〉 orientation in the growth of ultra-nanocrystallites at the grain boundary

NASA Astrophysics Data System (ADS)

Das, Debajyoti; Samanta, Subhashis

2018-01-01

A systematic development of undoped nc-SiOx:H thin films from (SiH4 + CO2) plasma diluted by a combination of H2 and He has been investigated through structural, optical and electrical characterization and correlation. Gradual inclusion of O into a highly crystalline silicon network progressively produces a two-phase structure where Si-nanocrystals (Si-nc) are embedded into the a-SiOx:H matrix. However, at the intermediate grain boundary region the growth of ultra-nanocrystallites controls the effectiveness of the material. The ultra-nanocrystallites are the part and portion of crystallinity accommodating the dominant fraction of thermodynamically preferred 〈220〉 crystallographic orientation, most favourable for stacked layer device performance. Atomic H plays a dominant role in maintaining an improved nanocrystalliny in the network even during O inclusion, while He in its excited state (He*) maintains a good energy balance at the grain boundary and produces a significant fraction of ultra-nanocrystalline component which has been demonstrated to organize the energetically favourable 〈220〉 crystallographic orientation in the network. The nc-SiOx:H films, maintaining proportionally good electrical conductivity over an wide range of optical band gap, remarkably low microstructure factor and simultaneous high crystalline volume fraction dominantly populated by ultra-nanocrystallites of 〈220〉 crystallographic orientation mostly at the grain boundary, have been obtained in technologically most popular 13.56 MHz PECVD SiH4 plasma even at a low substrate temperature ∼250 °C, convenient for device fabrication.

Tiopronin Gold Nanoparticle Precursor Forms Aurophilic Ring Tetramer

PubMed Central

Simpson, Carrie A.; Farrow, Christopher L.; Tian, Peng; Billinge, Simon J.L.; Huffman, Brian J.; Harkness, Kellen M.; Cliffel, David E.

2010-01-01

In the two step synthesis of thiolate-monolayer protected clusters (MPCs), the first step of the reaction is a mild reduction of gold(III) by thiols that generates gold(I) thiolate complexes as intermediates. Using tiopronin (Tio) as the thiol reductant, the characterization of the intermediate Au4Tio4 complex was accomplished with various analytical and structural techniques. Nuclear magnetic resonance (NMR), elemental analysis, thermogravimetric analysis (TGA), and matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) were all consistent with a cyclic gold(I)-thiol tetramer structure, and final structural analysis was gathered through the use of powder diffraction and pair distribution functions (PDF). Crystallographic data has proved challenging for almost all previous gold(I)-thiolate complexes. Herein, a novel characterization technique when combined with standard analytical assessment to elucidate structure without crystallographic data proved invaluable to the study of these complexes. This in conjunction with other analytical techniques, in particular mass spectrometry, can elucidate a structure when crystallographic data is unavailable. In addition, luminescent properties provided evidence of aurophilicity within the molecule. The concept of aurophilicity has been introduced to describe a select group of gold-thiolate structures, which possess unique characteristics, mainly red photoluminescence and a distinct Au-Au intramolecular distance indicating a weak metal-metal bond as also evidenced by the structural model of the tetramer. Significant features of both the tetrameric and aurophilic properties of the intermediate gold(I) tiopronin complex are retained after borohydride reduction to form the MPC, including gold(I) tiopronin partial rings as capping motifs, or “staples”, and weak red photoluminescence that extends into the Near Infrared region. PMID:21067183

Resolving the cofactor-binding site in the proline biosynthetic enzyme human pyrroline-5-carboxylate reductase 1

PubMed Central

Christensen, Emily M.; Patel, Sagar M.; Korasick, David A.; Campbell, Ashley C.; Krause, Kurt L.; Becker, Donald F.; Tanner, John J.

2017-01-01

Pyrroline-5-carboxylate reductase (PYCR) is the final enzyme in proline biosynthesis, catalyzing the NAD(P)H-dependent reduction of Δ1-pyrroline-5-carboxylate (P5C) to proline. Mutations in the PYCR1 gene alter mitochondrial function and cause the connective tissue disorder cutis laxa. Furthermore, PYCR1 is overexpressed in multiple cancers, and the PYCR1 knock-out suppresses tumorigenic growth, suggesting that PYCR1 is a potential cancer target. However, inhibitor development has been stymied by limited mechanistic details for the enzyme, particularly in light of a previous crystallographic study that placed the cofactor-binding site in the C-terminal domain rather than the anticipated Rossmann fold of the N-terminal domain. To fill this gap, we report crystallographic, sedimentation-velocity, and kinetics data for human PYCR1. Structures of binary complexes of PYCR1 with NADPH or proline determined at 1.9 Å resolution provide insight into cofactor and substrate recognition. We see NADPH bound to the Rossmann fold, over 25 Å from the previously proposed site. The 1.85 Å resolution structure of a ternary complex containing NADPH and a P5C/proline analog provides a model of the Michaelis complex formed during hydride transfer. Sedimentation velocity shows that PYCR1 forms a concentration-dependent decamer in solution, consistent with the pentamer-of-dimers assembly seen crystallographically. Kinetic and mutational analysis confirmed several features seen in the crystal structure, including the importance of a hydrogen bond between Thr-238 and the substrate as well as limited cofactor discrimination. PMID:28258219

Crystallographic education in the 21st century

PubMed Central

Gražulis, Saulius; Sarjeant, Amy Alexis; Moeck, Peter; Stone-Sundberg, Jennifer; Snyder, Trevor J.; Kaminsky, Werner; Oliver, Allen G.; Stern, Charlotte L.; Dawe, Louise N.; Rychkov, Denis A.; Losev, Evgeniy A.; Boldyreva, Elena V.; Tanski, Joseph M.; Bernstein, Joel; Rabeh, Wael M.; Kantardjieff, Katherine A.

2015-01-01

There are many methods that can be used to incorporate concepts of crystallography into the learning experiences of students, whether they are in elementary school, at university or part of the public at large. It is not always critical that those who teach crystallography have immediate access to diffraction equipment to be able to introduce the concepts of symmetry, packing or molecular structure in an age- and audience-appropriate manner. Crystallography can be used as a tool for teaching general chemistry concepts as well as general research techniques without ever having a student determine a crystal structure. Thus, methods for younger students to perform crystal growth experiments of simple inorganic salts, organic compounds and even metals are presented. For settings where crystallographic instrumentation is accessible (proximally or remotely), students can be involved in all steps of the process, from crystal growth, to data collection, through structure solution and refinement, to final publication. Several approaches based on the presentations in the MS92 Microsymposium at the IUCr 23rd Congress and General Assembly are reported. The topics cover methods for introducing crystallography to undergraduate students as part of a core chemistry curriculum; a successful short-course workshop intended to bootstrap researchers who rely on crystallography for their work; and efforts to bring crystallography to secondary school children and non-science majors. In addition to these workshops, demonstrations and long-format courses, open-format crystallographic databases and three-dimensional printed models as tools that can be used to excite target audiences and inspire them to pursue a deeper understanding of crystallography are described. PMID:26664347

Molecular driving forces defining lipid positions around aquaporin-0

PubMed Central

Aponte-Santamaría, Camilo; Briones, Rodolfo; Schenk, Andreas D.; Walz, Thomas; de Groot, Bert L.

2012-01-01

Lipid–protein interactions play pivotal roles in biological membranes. Electron crystallographic studies of the lens-specific water channel aquaporin-0 (AQP0) revealed atomistic views of such interactions, by providing high-resolution structures of annular lipids surrounding AQP0. It remained unclear, however, whether these lipid structures are representative of the positions of unconstrained lipids surrounding an individual protein, and what molecular determinants define the lipid positions around AQP0. We addressed these questions by using molecular dynamics simulations and crystallographic refinement, and calculated time-averaged densities of dimyristoyl-phosphatidylcholine lipids around AQP0. Our simulations demonstrate that, although the experimentally determined crystallographic lipid positions are constrained by the crystal packing, they appropriately describe the behavior of unconstrained lipids around an individual AQP0 tetramer, and thus likely represent physiologically relevant lipid positions.While the acyl chains were well localized, the lipid head groups were not. Furthermore, in silico mutations showed that electrostatic interactions do not play a major role attracting these phospholipids towards AQP0. Instead, the mobility of the protein crucially modulates the lipid localization and explains the difference in lipid density between extracellular and cytoplasmic leaflets. Moreover, our simulations support a general mechanism in which membrane proteins laterally diffuse accompanied by several layers of localized lipids, with the positions of the annular lipids being influenced the most by the protein surface. We conclude that the acyl chains rather than the head groups define the positions of dimyristoyl-phosphatidylcholine lipids around AQP0. Lipid localization is largely determined by the mobility of the protein surface, whereas hydrogen bonds play an important but secondary role. PMID:22679286

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

Ocean acidification reduces the crystallographic control in juvenile mussel shells.

PubMed

Fitzer, Susan C; Cusack, Maggie; Phoenix, Vernon R; Kamenos, Nicholas A

2014-10-01

Global climate change threatens the oceans as anthropogenic carbon dioxide causes ocean acidification and reduced carbonate saturation. Future projections indicate under saturation of aragonite, and potentially calcite, in the oceans by 2100. Calcifying organisms are those most at risk from such ocean acidification, as carbonate is vital in the biomineralisation of their calcium carbonate protective shells. This study highlights the importance of multi-generational studies to investigate how marine organisms can potentially adapt to future projected global climate change. Mytilus edulis is an economically important marine calcifier vulnerable to decreasing carbonate saturation as their shells comprise two calcium carbonate polymorphs: aragonite and calcite. M. edulis specimens were cultured under current and projected pCO2 (380, 550, 750 and 1000μatm), following 6months of experimental culture, adults produced second generation juvenile mussels. Juvenile mussel shells were examined for structural and crystallographic orientation of aragonite and calcite. At 1000μatm pCO2, juvenile mussels spawned and grown under this high pCO2 do not produce aragonite which is more vulnerable to carbonate under-saturation than calcite. Calcite and aragonite were produced at 380, 550 and 750μatm pCO2. Electron back scatter diffraction analyses reveal less constraint in crystallographic orientation with increased pCO2. Shell formation is maintained, although the nacre crystals appear corroded and crystals are not so closely layered together. The differences in ultrastructure and crystallography in shells formed by juveniles spawned from adults in high pCO2 conditions may prove instrumental in their ability to survive ocean acidification. Copyright © 2014 Elsevier Inc. All rights reserved.

Shock Condition Forensics and Cryptic Phase Transformations from Crystallographic Orientation Relationships in Zircon

NASA Astrophysics Data System (ADS)

Timms, N. E.; Erickson, T. M.; Cavosie, A. J.; Pearce, M. A.; Reddy, S. M.; Zanetti, M.; Tohver, E.; Schmieder, M.; Nemchin, A. A.; Wittmann, A.

2016-08-01

We present an approach to constrain pressure and temperature conditions during impact events involving identification of cryptic histories of phase transformations from orientation relationships in shocked zircon, linked to new P-T phase diagrams.

Highly aligned vertical GaN nanowires using submonolayer metal catalysts

DOEpatents

Wang, George T [Albuquerque, NM; Li, Qiming [Albuquerque, NM; Creighton, J Randall [Albuquerque, NM

2010-06-29

A method for forming vertically oriented, crystallographically aligned nanowires (nanocolumns) using monolayer or submonolayer quantities of metal atoms to form uniformly sized metal islands that serve as catalysts for MOCVD growth of Group III nitride nanowires.

Study of nickel hydroxide electrodes. 2: Oxidation products of nickel (2) hydroxides

NASA Technical Reports Server (NTRS)

Bode, H.; Demelt, K.; White, J.

1986-01-01

Pure phases of some oxidized Ni oxides were prepared galvanimetrically with the Ni(2) hydroxide electrode of an alkaline battery. The crystallographic data of these phases, their chemical behavior, and conditions of transition were studied.

Experimentally determined isotope effect during Mg-Fe interdiffusion in olivine

NASA Astrophysics Data System (ADS)

Sio, C. K. I.; Roskosz, M.; Dauphas, N.; Bennett, N.; Mock, T. D.; Shahar, A.

2017-12-01

Isotopic fractionation provides the most direct means to investigate the nature of chemical zoning in minerals, which can be produced by either diffusive transport or crystal growth. Misinterpreting the nature of chemical zoning can result in erroneous conclusions regarding magmatic cooling rates and diffusion timescales. Isotopes are useful in this regard because the light isotopes diffuse faster than their heavier counterparts. As a result, isotopic fractionations should be associated with chemical zoning profiles if they are diffusion-driven. In contrast, little isotopic fractionation is associated with crystal growth during slow cooling at magmatic temperatures. The isotope effect for diffusion is described by β and is related to the mass (m) and diffusivity (D) of isotopes i and j of an element via: Di/Dj = (mj/mi)β. To model isotopic profiles, knowledge of β is required. Several estimates of β for Mg and Fe diffusion in olivine have been reported using natural samples but these estimates are uncertain because they depend on the choice of modeling parameters (Sio et al., 2013; Oeser et al., 2015; Collinet et al., 2017). We have experimentally determined β for Fe (βFe) in olivine as a function of crystallographic orientation, composition, and temperature. Thirty experiments have been conducted by juxtaposing crystallographically oriented olivine crystals to make Fo83.4-Fo88.8 and Fo88.8-Fo100 diffusion couples. These diffusion couples were annealed in a 1 atm gas mixing furnace at 1200 °C, 1300 °C or 1400 °C at QFM - 1.5 for up to 15 days. Chemical profiles were characterized using an electron microprobe and isotopic analyses were done using laser ablation MC-ICPMS. We found a crystallographic dependence of βFe for the Fo88.8-Fo100 couple where βFe [100] ≈ βFe [010] > βFe [001]. For the Fo83.4-Fo88.8 couple, βFe is 0.16 ± 0.09 (2σ) for all 3 major crystallographic axes. A temperature dependence of βFe could not be resolved. These experimentally determined β-values can be used in conjunction with the Mg-Fe diffusivities given in Dohmen and Chakraborty (2007) to simultaneously model the chemical-isotopic profiles of olivine to retrieve cooling and crystallization histories of magmatic rocks.

Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chon, Hyongi; Matsumura, Hiroyoshi; Koga, Yuichi

2005-03-01

A thermostable ribonuclease HIII from B. stearothermophilus (Bst RNase HIII) was crystallized and preliminary crystallographic studies were performed. Plate-like overlapping polycrystals were grown by the sitting-drop vapour-diffusion method at 283 K.

Crystallization screening: the influence of history on current practice.

PubMed

Luft, Joseph R; Newman, Janet; Snell, Edward H

2014-07-01

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed.

Three-dimensional Structures of Carotenoids by X-ray Crystallography

NASA Astrophysics Data System (ADS)

Helliwell, Madeleine

The number of crystal structures of carotenoid molecules and carotenoid derivatives deposited in the Cambridge Crystallographic Data Centre [1] is still relatively small, but has increased compared with the previous survey [2]. The list is summarized in Table 1.

Comparison of illumina and 454 deep sequencing in participants failing raltegravir-based antiretroviral therapy.

PubMed

Li, Jonathan Z; Chapman, Brad; Charlebois, Patrick; Hofmann, Oliver; Weiner, Brian; Porter, Alyssa J; Samuel, Reshmi; Vardhanabhuti, Saran; Zheng, Lu; Eron, Joseph; Taiwo, Babafemi; Zody, Michael C; Henn, Matthew R; Kuritzkes, Daniel R; Hide, Winston; Wilson, Cara C; Berzins, Baiba I; Acosta, Edward P; Bastow, Barbara; Kim, Peter S; Read, Sarah W; Janik, Jennifer; Meres, Debra S; Lederman, Michael M; Mong-Kryspin, Lori; Shaw, Karl E; Zimmerman, Louis G; Leavitt, Randi; De La Rosa, Guy; Jennings, Amy

2014-01-01

The impact of raltegravir-resistant HIV-1 minority variants (MVs) on raltegravir treatment failure is unknown. Illumina sequencing offers greater throughput than 454, but sequence analysis tools for viral sequencing are needed. We evaluated Illumina and 454 for the detection of HIV-1 raltegravir-resistant MVs. A5262 was a single-arm study of raltegravir and darunavir/ritonavir in treatment-naïve patients. Pre-treatment plasma was obtained from 5 participants with raltegravir resistance at the time of virologic failure. A control library was created by pooling integrase clones at predefined proportions. Multiplexed sequencing was performed with Illumina and 454 platforms at comparable costs. Illumina sequence analysis was performed with the novel snp-assess tool and 454 sequencing was analyzed with V-Phaser. Illumina sequencing resulted in significantly higher sequence coverage and a 0.095% limit of detection. Illumina accurately detected all MVs in the control library at ≥0.5% and 7/10 MVs expected at 0.1%. 454 sequencing failed to detect any MVs at 0.1% with 5 false positive calls. For MVs detected in the patient samples by both 454 and Illumina, the correlation in the detected variant frequencies was high (R2 = 0.92, P<0.001). Illumina sequencing detected 2.4-fold greater nucleotide MVs and 2.9-fold greater amino acid MVs compared to 454. The only raltegravir-resistant MV detected was an E138K mutation in one participant by Illumina sequencing, but not by 454. In participants of A5262 with raltegravir resistance at virologic failure, baseline raltegravir-resistant MVs were rarely detected. At comparable costs to 454 sequencing, Illumina demonstrated greater depth of coverage, increased sensitivity for detecting HIV MVs, and fewer false positive variant calls.

Electromagnetic characterization of photo-definable ferrite loaded polymers and their applications in micro-rectangular coaxial phase shifters

NASA Astrophysics Data System (ADS)

Sholiyi, Olusegun Samuel

As the demand for smaller size, lighter weight, lower loss and cost of communications transmit and receive (T/R) modules increases, there is an urgent need to focus investigation to the major subsystem or components that can improve these parameters. Phase shifters contribute greatly to the cost of T/R modules, and thus this research investigation examines a new way to reduce the weight and cost by miniaturizing the phaser design. Characterization of hexaferrite powders compatible with the sequential multilayer micro-fabrication technology and numerical simulations of a novel rectangular micro-coaxial phase shifter are investigated. This effort aims to integrate ferrite material into a rectangular micro-coaxial waveguide at Ka-band using electromagnetic finite element numerical tools. The proposed technique exploits rectangular coaxial waveguide with a symmetrically placed inner signal conductor inside an outer conductor connected to the ground. Strontium ferrite-SU8 composite is used as an anisotropic material of choice in the modelled design. Numerical modeling is employed using High Frequency Structure Simulator, HFSS, a 3-D full wave electromagnetic solver for analyzing the performance of the device. Two model structures were designed for reciprocal and non-reciprocal applications. The first model (Model A) produced a tunable phase shift of almost 60 degrees /cm across 0 to 400 kA/m applied field and at 1800 Gauss. In model B, a non-reciprocal phase shift performance of 20 degrees /cm from a reference phase of 24 degrees at 0 A/m was realized at the same saturation magnetization. A return loss better than 20 dB and an insertion loss less than 1.5 dB were obtained for both models.

Structural, magnetothermal, and magnetotransport properties of single crystal terbium silicon germanide and spontaneous generation of voltage in single crystal gadolinium silicon germanide and gadolinium

NASA Astrophysics Data System (ADS)

Zou, Min

A systematic study of single crystalline Tb5Si2.2Ge1.8, including magnetic field induced crystallographic and magnetic phase transformations, magnetocaloric effect, ferromagnetic short-range correlations, electrical resistivity, magnetoresistance, and spontaneous generation of voltage (SGV) has been presented. A study of SGV in single crystalline Gd5Si2Ge2 and Gd has also been included. The metamagnetic-like transitions and giant magnetocaloric effect were observed with the magnetic field applied parallel to the a- and c-axes, but not the b-axis in a Tb5Si 2.2Ge1.8 single crystal. The in-situ x-ray powder diffraction study indicates that these metamagnetic-like transitions are coupled to a crystallographic phase transformation occurring via strong magnetoelastic interactions. The magnetocrystalline anisotropy plays an important role in this system. Magnetic fields less than 40 kOe can not drive either the magnetic or the crystallographic phase transition to completion for Tb5Si2.2Ge1.8 powder due to the strong single ion anisotropy of Tb. Magnetic field dependencies of the critical temperatures of magnetic phase transitions of Tb5Si2.2Ge1.8 are highly anisotropic for both the main magnetic ordering process occurring around 120 K and a spin reorientation transition at ~70 K. Magnetic-field-induced phase transitions occur with the magnetic field applied isothermally along the a-and b-axes (but not along the c-axis) between 1.8 and 70 K in fields below 70 kOe. Strongly anisotropic thermal irreversibility is observed in the Griffiths phase regime between 120 and 200 K with applied fields ranging from 10 to 1000 Oe. Our data: (1) show that the magnetic and structural phase transitions around 120 K are narrowly decoupled; (2) uncover the anisotropy of ferromagnetic short-range order in the Griffiths phase; and (3) reveal some unusual magnetic domain effects in the long-range ordered state of the Tb5Si2.2Ge1.8 compound. The temperature-magnetic field phase diagrams with field applied along the three major crystallographic directions have been constructed. The positive colossal magnetoresistance (CMR) with a magnitude of ~150% was observed with the magnetic field applied parallel to the a-axis, but not the b- and c-axes in Tb5Si 2.2Ge1.8 single crystals. The electrical resistivity shows a low-temperature high-resistivity behavior (i.e. the resistivity at low temperature is higher after the transformation to the low temperature phase than the resistivity of the phase before the transition) along the a-axis, contrary to those along the b- and c-axes. The positive CMR effect originates from an intrinsic crystallographic phase coexistence state frozen below the Curie Temperature (TC). The differences in the temperature dependencies of electrical resistivities and longitudinal magnetoresistance along the a-axis and those along the b- and c-axes can be explained by the geometry of the phase boundaries at low temperatures, and the inability of the external magnetic field to induce the crystallographic phase transformation along the b- and c-axes. Temperature-induced SGVs were observed along all three principal crystallographic axes of Tb5Si2.2Ge1.8, but not in Gd. Field-induced SGVs were observed with magnetic fields less than 40 kOe applied along the a-axis of Tb5Si2.2Ge1.8, and the c-axis of Gd. The absence of the temperature induced SGV in Gd indicates the key role first-order phase transformations play in the appearance of the effect when temperature varies. The anisotropy of magnetic field induced SGV in Tb5Si2.2Ge1.8 and the existence of field induced SGV in Gd, highlight the importance of the magnetocaloric effect in bringing about the SGV. In single crystal and polycrystalline Gd5Si 2Ge2 during the coupled magneto-structural transformations, reversible and repeatable SGV responses of the materials to the temperature and magnetic field have been observed. The parameters of the response and the magnitude of the signal are anisotropic and rate dependent. The magnitude of the SGV signal, and the critical temperatures and critical magnetic fields at which the SGV occurs vary with the rate of temperature and magnetic field changes.

ESP Toolbox: A Computational Framework for Precise, Scale-Independent Analysis of Bulk Elastic and Seismic Properties

NASA Astrophysics Data System (ADS)

Johnson, S. E.; Vel, S. S.; Cook, A. C.; Song, W. J.; Gerbi, C. C.; Okaya, D. A.

2014-12-01

Owing to the abundance of highly anisotropic minerals in the crust, the Voigt and Reuss bounds on the seismic velocities can be separated by more than 1 km/s. These bounds are determined by modal mineralogy and crystallographic preferred orientations (CPO) of the constituent minerals, but where the true velocities lie between these bounds is determined by other fabric parameters such as the shapes, shape-preferred orientations, and spatial arrangements of grains. Thus, the calculation of accurate bulk stiffness relies on explicitly treating the grain-scale heterogeneity, and the same principle applies at larger scales, for example calculating accurate bulk stiffness for a crustal volume with varying proportions and distributions of folds or shear zones. We have developed stand-alone GUI software - ESP Toolbox - for the calculation of 3D bulk elastic and seismic properties of heterogeneous and polycrystalline materials using image or EBSD data. The GUI includes a number of different homogenization techniques, including Voigt, Reuss, Hill, geometric mean, self-consistent and asymptotic expansion homogenization (AEH) methods. The AEH method, which uses a finite element mesh, is most accurate since it explicitly accounts for elastic interactions of constituent minerals/phases. The user need only specify the microstructure and material properties of the minerals/phases. We use the Toolbox to explore changes in bulk elasticity and related seismic anisotropy caused by specific variables, including: (a) the quartz alpha-beta phase change in rocks with varying proportions of quartz, (b) changes in modal mineralogy and CPO fabric that occur during progressive deformation and metamorphism, and (c) shear zones of varying thickness, abundance and geometry in continental crust. The Toolbox allows rapid sensitivity analysis around these and other variables, and the resulting bulk stiffness matrices can be used to populate volumes for synthetic wave propagation experiments that allow direct visualization of how variables of interest might affect propagation at a variety of scales. Sensitivity analyses also illustrate the value of the more precise AEH method. The ESP Toolbox can be downloaded here: http://umaine.edu/mecheng/faculty-and-staff/senthil-vel/software/

Genesis of diamond inclusions: An integrated cathodoluminescence (CL) and Electron backscatter diffraction (EBSD) study on eclogitic and peridotitic inclusions and their diamond host.

NASA Astrophysics Data System (ADS)

van den Heuvel, Quint; Matveev, Sergei; Drury, Martyn; Gress, Michael; Chinn, Ingrid; Davies, Gareth

2017-04-01

Diamond inclusions are potentially fundamental to understanding the formation conditions of diamond and the volatile cycles in the deep mantle. In order to fully understand the implications of the compositional information recorded by inclusions it is vital to know whether the inclusions are proto-, syn-, or epigenetic and the extent to which they have equilibrated with diamond forming fluids. In previous studies, the widespread assumption was made that the majority of diamond inclusions are syngenetic, based upon observation of cubo-octahedral morphology imposed on the inclusions. Recent work has reported the crystallographic relationship between inclusions and the host diamond to be highly complex and the lack of crystallographic relationships between inclusions and diamonds has led some to question the significance of imposed cubo-octahedral morphology. This study presents an integrated EBSD and CL study of 9 diamonds containing 20 pyropes, 2 diopsides, 1 forsterite and 1 rutile from the Jwaneng and Letlhakane kimberlite clusters, Botswana. A new method was developed to analyze the crystallographic orientation of the host diamond and the inclusions with EBSD. Diamonds plates were sequentially polished to expose inclusions at different levels in the diamond. CL imaging at different depths was performed in order to produce a 3D view of diamond growth zones around the inclusions. Standard diamond polishing techniques proved too aggressive for silicate inclusions as they were damaged to such a degree that EBSD measurements on the inclusions were impossible. The inclusions were milled with a Ga+ focused ion beam (FIB) at a 12° angle to clean the surface for EBSD measurements. Of the 24 inclusions, 9 have an imposed cubo-octahedral morphology. Of these inclusions, 6 have faces orientated parallel to diamond growth zones and/or appear to have nucleated on a diamond growth surface, implying syngenesis. In contrast, other diamonds record resorption events such that inclusions now cut diamond growth zones. In most cases, the growth zonation around inclusions is not well defined due to CL haloes but some inclusions clearly disrupt diamond growth. Crystallographic orientations of diamond and the inclusions, determined using EBSD, revealed that each inclusion has a homogeneous orientation and record no compositional zonation. The diamonds also showed no angular deviations despite many having multiple growth and resorption zones; implying epitaxial growth of diamond. Crystallographic alignment between diamond and inclusions was not recorded for the principle planes and limited to 3 possible coincidences on minor planes from the 24 inclusions studied. The CL data show no evidence of syngenesis for these 3 inclusions. Analyses of two diamonds with inclusion clusters in different growth zones, 400 µm apart, revealed the same chemical composition and orientation, potentially implying they originated from an original larger inclusion. Combined EBSD and CL data suggest that there is no direct orientational correlation (epitaxial growth) between silicate inclusions and the host diamond, even when the mineral phases are of the same symmetry group. The presentation will provide a detailed evaluation of the genesis of individual inclusions.

The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.

PubMed

Krojer, Tobias; Talon, Romain; Pearce, Nicholas; Collins, Patrick; Douangamath, Alice; Brandao-Neto, Jose; Dias, Alexandre; Marsden, Brian; von Delft, Frank

2017-03-01

XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein-ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallographic software packages such as CCP4 [Winn et al. (2011), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), Acta Cryst. D66, 213-221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

Models of protein–ligand crystal structures: trust, but verify

PubMed Central

Deller, Marc C.

2015-01-01

X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

Models of protein-ligand crystal structures: trust, but verify.

PubMed

Deller, Marc C; Rupp, Bernhard

2015-09-01

X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Raymond, Amy; Lovell, Scott; Lorimer, Don

2009-12-01

With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38{alpha}), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. colimore » and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.« less

Luminescence in Sr2MgAl22O36:Eu2+ phosphor

NASA Astrophysics Data System (ADS)

Tawalare, P. K.; Bhatkar, V. B.; Talewar, R. A.; Joshi, C. P.; Moharil, S. V.

2018-05-01

New results on luminescence of Eu2+ are reported in Sr2MgAl22O36 host prepared by combustion synthesis. Different emission and excitation spectra are observed for Eu2+ ions occupying two crystallographically non-equivalent sites.

Crystallization screening: the influence of history on current practice

PubMed Central

Luft, Joseph R.; Newman, Janet; Snell, Edward H.

2014-01-01

While crystallization historically predates crystallography, it is a critical step for the crystallographic process. The rich history of crystallization and how that history influences current practices is described. The tremendous impact of crystallization screens on the field is discussed. PMID:25005076

The Workshop on Conductive Polymers: Final Report

DOE R&D Accomplishments Database

1985-10-01

Reports are made by groups on: polyacetylene, polyphenylene, polyaniline, and related systems; molecular, crystallographic, and defect structures in conducting polymers; heterocyclic polymers; synthesis of new and improved conducting polymers; future applications possibilities for conducting polymers; and challenges for improved understanding of properties. (DLC)

Spatially Resolved Mid-IR Spectra from Meteorites; Linking Composition, Crystallographic Orientation and Spectra on the Micro-Scale

NASA Astrophysics Data System (ADS)

Stephen, N. R.

2016-08-01

IR spectroscopy is used to infer composition of extraterrestrial bodies, comparing bulk spectra to databases of separate mineral phases. We extract spatially resolved meteorite-specific spectra from achondrites with respect to zonation and orientation.

Observation of a re-entrant phase transition in the molecular complex tris(μ 2-3,5-diisopropyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) under high pressure

DOE PAGES

Woodall, Christopher H.; Christensen, Jeppe; Skelton, Jonathan M.; ...

2016-08-18

We report a molecular crystal that exhibits four successive phase transitions under hydro­static pressure, driven by aurophilic interactions, with the ground-state structure re-emerging at high pressure. The effect of pressure on two polytypes of tris(μ 2-3,5-diiso­propyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) (denoted Form-I and Form-II) has been analysed using luminescence spectroscopy, single-crystal X-ray diffraction and first-principles computation. A unique phase behaviour was observed in Form-I, with a complex sequence of phase transitions between 1 and 3.5 GPa. The ambient C2/c mother cell transforms to a P2 1/n phase above 1 GPa, followed by a P2 1/a phase above 2 GPamore » and a large-volume C2/c supercell at 2.70 GPa, with the previously observed P2 1/n phase then reappearing at higher pressure. The observation of crystallographically identical low- and high-pressure P2 1/n phases makes this a rare example of a re-entrant phase transformation. The phase behaviour has been characterized using detailed crystallographic theory and modelling, and rationalized in terms of molecular structural distortions. The dramatic changes in conformation are correlated with shifts of the luminescence maxima, from a band maximum at 14040 cm –1 at 2.40 GPa, decreasing steeply to 13550 cm –1 at 3 GPa. A similar study of Form-II displays more conventional crystallographic behaviour, indicating that the complex behaviour observed in Form-I is likely to be a direct consequence of the differences in crystal packing between the two polytypes.« less

Deformation microstructures and magnetite texture development in synthetic shear zones

NASA Astrophysics Data System (ADS)

Till, Jessica L.; Moskowitz, Bruce M.

2014-08-01

We present observations of deformation features in magnetite from synthetic magnetite-bearing silicate aggregates deformed between 1000 °C and 1200 °C in transpressional shear experiments with strains of up to 300%. Anisotropy of magnetic susceptibility and shape preferred orientation (SPO) analysis were combined with electron backscatter diffraction (EBSD) to characterize the magnetite deformation fabrics and intragrain microstructures. Crystallographic preferred orientation (CPO) in magnetite is very weak in all deformed samples and does not vary as a function of either temperature or shear strain. Magnetic anisotropy and SPO increase strongly with both strain and deformation temperature and indicate that strain partitioning between magnetite and the plagioclase matrix decreases at higher temperatures. EBSD orientation mapping of individual magnetite particles revealed substantial dispersions in intragrain orientation, analogous to undulose extinction, after deformation at 1000 and 1100 °C, indicating that dislocation creep processes were active in magnetite despite the lack of a well-developed CPO. Geometrical analysis of crystallographic orientation dispersions from grain map data indicates that low-angle grain boundary formation in magnetite could have been accommodated by slip on {110} or {100} planes, but no evidence for dominant slip on the expected {111} planes was found. Evidence for activation of multiple slip systems was seen in some magnetite grains and could be partially responsible for the lack of CPO in magnetite. These results suggest that, at least in polyphase rocks, crystallographic textures in magnetite may be inherently weak or slow to develop and CPO alone is not an adequate indicator of magnetite deformation mechanisms. These results may aid in the interpretation of deformation textures in other spinel-structured phases such as chromite and ringwoodite.

Tuning fluorocarbon adsorption in new isoreticular porous coordination frameworks for heat transformation applications† †Electronic supplementary information (ESI) available: Experimental section, PXRD patterns, crystallographic tables and characterization details, and X-ray crystallographic files in CIF format. CCDC 1031873 and 1031874. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4sc03985h Click here for additional data file. Click here for additional data file.

PubMed Central

Lin, Rui-Biao; Li, Tai-Yang; Zhou, Hao-Long; He, Chun-Ting; Chen, Xiao-Ming

2015-01-01

Adsorption heat transformation is one of the most energy-efficient technologies, which relies much on the type and performance of the adsorbent–adsorbate pair. Here, we report adsorption behaviors of a typical fluorocarbon R22 (CHClF2) in a new series of isoreticular porous coordination polymers [Zn4O(bpz)2(ldc)], in which the typical Zn4O clusters are connected by hydrophobic 3,3′,5,5′-tetramethyl-4,4′-bipyrazolate (bpz2–) and different linear dicarboxylates (ldc2–) to form non-interpenetrated pcu networks with variable pore sizes, shapes, and volumes. Fluorocarbon sorption measurements of these materials revealed high R22 uptakes of 0.73–0.97 g g–1 (0.62–0.65 g cm–3) at 298 K and 1 bar and working capacities of 0.41–0.72 g g–1 (0.35–0.47 g cm–3) between 273 and 313 K at about 0.13, 0.11 and 0.52 bar, respectively, as well as very large diffusion coefficients of 5.1–7.3 × 10–7 cm2 s–1. Noteworthily, the R22 sorption performance can be dramatically improved by subtle modification of the pore size and shape, demonstrating porous coordination polymer–fluorocarbon as a promising adsorbent–adsorbate pair for heat transformation applications. PMID:29308161

Molecular Syntheses of Extended Materials

NASA Astrophysics Data System (ADS)

Paley, Daniel W.

Bottom-up molecular synthesis is a route to chemically and crystallographically uniform polymers and solid-state materials. Through the use of molecular precursors, we gain atomic-level control of functionality and fine-tuning of the collective properties of materials. This dissertation presents two studies that demonstrate this approach. Ring-opening alkyne metathesis polymerization is a possible approach to monodisperse conjugated polymers, but its applications have been limited by difficult syntheses and high air sensitivity of known organometallic ROAMP initiators. We designed a dimeric, air-stable molybdenum alkylidyne with a tris(phenolate) supporting ligand. The precatalyst is activated by addition of methanol and polymerizes cyclooctynes with excellent chemical selectivity and functional group tolerance. The Nuckolls and Roy groups have introduced a new family of solid-state compounds synthesized from cobalt chalcogenide clusters Co6Q 8(PR3)6 and fullerenes. The first examples of these materials crystallized in superatom lattices with the symmetry of simple inorganic solids CdI2 (P-3m1) and NaCl (Fm-3m). This dissertation reveals that further members of the family feature extraordinary diversity of structure, including a pseudo-trigonal array of fulleride dimers in [Co 6Te8(PEt3)6]2[C140 ][C70]2 and a heterolayered van der Waals cocrystal [Co6Se8(PEt2phen)6][C 60]5. In addition to these unusual crystal structures, this dissertation presents a method for assigning redox states from crystallographic data in Co6Q8 clusters. Finally, a detailed guide to the collection and solution of single-crystal X-ray data is presented. The guide is intended for independent study by new crystallographers.

Application of Single Crystal Failure Criteria: Theory and Turbine Blade Case Study

NASA Technical Reports Server (NTRS)

Sayyah, Tarek; Swanson, Gregory R.; Schonberg, W. P.

1999-01-01

The orientation of the single crystal material within a structural component is known to affect the strength and life of the part. The first stage blade of the High Pressure Fuel Turbopump (HPFTP)/ Alternative Turbopump Development (ATD), of the Space Shuttle Main Engine (SSME) was used to study the effects of secondary axis'orientation angles on the failure rate of the blade. A new failure criterion was developed based on normal and shear strains on the primary crystallographic planes. The criterion was verified using low cycle fatigue (LCF) specimen data and a finite element model of the test specimens. The criterion was then used to study ATD/HPFTP first stage blade failure events. A detailed ANSYS finite element model of the blade was used to calculate the failure parameter for the different crystallographic orientations. A total of 297 cases were run to cover a wide range of acceptable orientations within the blade. Those orientations are related to the base crystallographic coordinate system that was created in the ANSYS finite element model. Contour plots of the criterion as a function of orientation for the blade tip and attachment were obtained. Results of the analysis revealed a 40% increase in the failure parameter due to changing of the primary and secondary axes of material orientations. A comparison between failure criterion predictions and actual engine test data was then conducted. The engine test data comes from two ATD/HPFTP builds (units F3- 4B and F6-5D), which were ground tested on the SSME at the Stennis Space Center in Mississippi. Both units experienced cracking of the airfoil tips in multiple blades, but only a few cracks grew all the way across the wall of the hollow core airfoil.

Observation of a re-entrant phase transition in the molecular complex tris(μ 2-3,5-diisopropyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) under high pressure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodall, Christopher H.; Christensen, Jeppe; Skelton, Jonathan M.

We report a molecular crystal that exhibits four successive phase transitions under hydro­static pressure, driven by aurophilic interactions, with the ground-state structure re-emerging at high pressure. The effect of pressure on two polytypes of tris(μ 2-3,5-diiso­propyl-1,2,4-triazolato-κ 2 N 1: N 2)trigold(I) (denoted Form-I and Form-II) has been analysed using luminescence spectroscopy, single-crystal X-ray diffraction and first-principles computation. A unique phase behaviour was observed in Form-I, with a complex sequence of phase transitions between 1 and 3.5 GPa. The ambient C2/c mother cell transforms to a P2 1/n phase above 1 GPa, followed by a P2 1/a phase above 2 GPamore » and a large-volume C2/c supercell at 2.70 GPa, with the previously observed P2 1/n phase then reappearing at higher pressure. The observation of crystallographically identical low- and high-pressure P2 1/n phases makes this a rare example of a re-entrant phase transformation. The phase behaviour has been characterized using detailed crystallographic theory and modelling, and rationalized in terms of molecular structural distortions. The dramatic changes in conformation are correlated with shifts of the luminescence maxima, from a band maximum at 14040 cm –1 at 2.40 GPa, decreasing steeply to 13550 cm –1 at 3 GPa. A similar study of Form-II displays more conventional crystallographic behaviour, indicating that the complex behaviour observed in Form-I is likely to be a direct consequence of the differences in crystal packing between the two polytypes.« less

Interfacial band alignment and structural properties of nanoscale TiO2 thin films for integration with epitaxial crystallographic oriented germanium

NASA Astrophysics Data System (ADS)

Jain, N.; Zhu, Y.; Maurya, D.; Varghese, R.; Priya, S.; Hudait, M. K.

2014-01-01

We have investigated the structural and band alignment properties of nanoscale titanium dioxide (TiO2) thin films deposited on epitaxial crystallographic oriented Ge layers grown on (100), (110), and (111)A GaAs substrates by molecular beam epitaxy. The TiO2 thin films deposited at low temperature by physical vapor deposition were found to be amorphous in nature, and high-resolution transmission electron microscopy confirmed a sharp heterointerface between the TiO2 thin film and the epitaxially grown Ge with no traceable interfacial layer. A comprehensive assessment on the effect of substrate orientation on the band alignment at the TiO2/Ge heterointerface is presented by utilizing x-ray photoelectron spectroscopy and spectroscopic ellipsometry. A band-gap of 3.33 ± 0.02 eV was determined for the amorphous TiO2 thin film from the Tauc plot. Irrespective of the crystallographic orientation of the epitaxial Ge layer, a sufficient valence band-offset of greater than 2 eV was obtained at the TiO2/Ge heterointerface while the corresponding conduction band-offsets for the aforementioned TiO2/Ge system were found to be smaller than 1 eV. A comparative assessment on the effect of Ge substrate orientation revealed a valence band-offset relation of ΔEV(100) > ΔEV(111) > ΔEV(110) and a conduction band-offset relation of ΔEC(110) > ΔEC(111) > ΔEC(100). These band-offset parameters are of critical importance and will provide key insight for the design and performance analysis of TiO2 for potential high-κ dielectric integration and for future metal-insulator-semiconductor contact applications with next generation of Ge based metal-oxide field-effect transistors.

Crystallographic structure and superconductive properties of Nb-Ti films with an artificially layered structure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sato, N.

1990-06-15

Artificially layered niobium-titanium (Nb-Ti) films with various thickness ratios (3/1--1/3) and periodicities (2--100 A) are made in an argon or in a mixed argon/nitrogen atmosphere by a dc magnetron sputtering method. Films with small periodicities (less than 30 A) have an artificial superlattice structure (ASL) with crystallographic coherence between constituent layers, where Nb and Ti grow epitaxially on the closest planes. The crystallographic structures of films are bcc with the (110) plane parallel to the film for films with the same or a thicker Nb layer than a Ti layer, and hcp with the (001) plane parallel to the filmmore » for films with a thinner Nb layer than a Ti layer. Films with large periodicities have an artificial superstructure (ASS) with only periodic stacking of constituent layers. Films deposited in the Ar/N atmosphere also have the artificially layered structures of ASL or ASS. The artificially layered structure is thermally stable at temperatures up to 500 {degree}C. The superconducting properties of the films depend strongly on the periodicity and thickness ratio of Nb and Ti layers. The dependence of the transition temperature on the periodicity and thickness ratio is qualitatively explained by a proximity effect with a three-region model. Films with periodicities less than 20 A, composed of the same or a thicker Nb layer than a Ti layer, show high transition temperatures (above 9.3 K). The highest {ital T}{sub {ital c}} of about 13.6 K is obtained in the film composed of monatomic layers of constituents deposited in an Ar atmosphere including 30 vol % N.« less

Computational study of textured ferroelectric polycrystals: Dielectric and piezoelectric properties of template-matrix composites

NASA Astrophysics Data System (ADS)

Zhou, Jie E.; Yan, Yongke; Priya, Shashank; Wang, Yu U.

2017-01-01

Quantitative relationships between processing, microstructure, and properties in textured ferroelectric polycrystals and the underlying responsible mechanisms are investigated by phase field modeling and computer simulation. This study focuses on three important aspects of textured ferroelectric ceramics: (i) grain microstructure evolution during templated grain growth processing, (ii) crystallographic texture development as a function of volume fraction and seed size of the templates, and (iii) dielectric and piezoelectric properties of the obtained template-matrix composites of textured polycrystals. Findings on the third aspect are presented here, while an accompanying paper of this work reports findings on the first two aspects. In this paper, the competing effects of crystallographic texture and template seed volume fraction on the dielectric and piezoelectric properties of ferroelectric polycrystals are investigated. The phase field model of ferroelectric composites consisting of template seeds embedded in matrix grains is developed to simulate domain evolution, polarization-electric field (P-E), and strain-electric field (ɛ-E) hysteresis loops. The coercive field, remnant polarization, dielectric permittivity, piezoelectric coefficient, and dissipation factor are studied as a function of grain texture and template seed volume fraction. It is found that, while crystallographic texture significantly improves the polycrystal properties towards those of single crystals, a higher volume fraction of template seeds tends to decrease the electromechanical properties, thus canceling the advantage of ferroelectric polycrystals textured by templated grain growth processing. This competing detrimental effect is shown to arise from the composite effect, where the template phase possesses material properties inferior to the matrix phase, causing mechanical clamping and charge accumulation at inter-phase interfaces between matrix and template inclusions. The computational results are compared with complementary experiments, where good agreement is obtained.

Review of aragonite and calcite crystal morphogenesis in thermal spring systems

NASA Astrophysics Data System (ADS)

Jones, Brian

2017-06-01

Aragonite and calcite crystals are the fundamental building blocks of calcareous thermal spring deposits. The diverse array of crystal morphologies found in these deposits, which includes monocrystals, mesocrystals, skeletal crystals, dendrites, and spherulites, are commonly precipitated under far-from-equilibrium conditions. Such crystals form through both abiotic and biotic processes. Many crystals develop through non-classical crystal growth models that involve the arrangement of nanocrystals in a precisely controlled crystallographic register. Calcite crystal morphogenesis has commonly been linked to a ;driving force;, which is a conceptual measure of the distance of the growth conditions from equilibrium conditions. Essentially, this scheme indicates that increasing levels of supersaturation and various other parameters that produce a progressive change from monocrystals and mesocrystals to skeletal crystals to crystallographic and non-crystallographic dendrites, to dumbbells, to spherulites. Despite the vast amount of information available from laboratory experiments and natural spring systems, the precise factors that control the driving force are open to debate. The fact that calcite crystal morphogenesis is still poorly understood is largely a reflection of the complexity of the factors that influence aragonite and calcite precipitation. Available information indicates that variations in calcite crystal morphogenesis can be attributed to physical and chemical parameters of the parent water, the presence of impurities, the addition of organic or inorganic additives to the water, the rate of crystal growth, and/or the presence of microbes and their associated biofilms. The problems in trying to relate crystal morphogenesis to specific environmental parameters arise because it is generally impossible to disentangle the controlling factor(s) from the vast array of potential parameters that may act alone or in unison with each other.

Long-term stability of Cu surface nanotips

NASA Astrophysics Data System (ADS)

Jansson, V.; Baibuz, E.; Djurabekova, F.

2016-07-01

Sharp nanoscale tips on the metal surfaces of electrodes enhance locally applied electric fields. Strongly enhanced electric fields trigger electron field emission and atom evaporation from the apexes of nanotips. Together, these processes may explain electric discharges in the form of small local arcs observed near metal surfaces in the presence of electric fields, even in ultra-high vacuum conditions. In the present work, we investigate the stability of nanoscale tips by means of computer simulations of surface diffusion processes on copper, the main material used in high-voltage electronics. We study the stability and lifetime of thin copper (Cu) surface nanotips at different temperatures in terms of diffusion processes. For this purpose we have developed a surface kinetic Monte Carlo (KMC) model where the jump processes are described by tabulated precalculated energy barriers. We show that tall surface features with high aspect ratios can be fairly stable at room temperature. However, the stability was found to depend strongly on the temperature: 13 nm nanotips with the major axes in the < 110> crystallographic directions were found to flatten down to half of the original height in less than 100 ns at temperatures close to the melting point, whereas no significant change in the height of these nanotips was observed after 10 {{μ }}{{s}} at room temperature. Moreover, the nanotips built up along the < 110> crystallographic directions were found to be significantly more stable than those oriented in the < 100> or < 111> crystallographic directions. The proposed KMC model has been found to be well-suited for simulating atomic surface processes and was validated against molecular dynamics simulation results via the comparison of the flattening times obtained by both methods. We also note that the KMC simulations were two orders of magnitude computationally faster than the corresponding molecular dynamics calculations.

Bacterial expression of the phosphodiester-binding site of the cation-independent mannose 6-phosphate receptor for crystallographic and NMR studies

PubMed Central

Olson, Linda J.; Jensen, Davin R.; Volkman, Brian F.; Kim, Jung-Ja P.; Peterson, Francis C.; Gundry, Rebekah L.; Dahms, Nancy M.

2015-01-01

The cation-independent mannose 6-phosphate receptor (CI-MPR) is a multifunctional protein that interacts with diverse ligands and plays central roles in autophagy, development, and tumor suppression. By delivering newly synthesized phosphomannosyl-containing acid hydrolases from the Golgi to endosomal compartments, CI-MPR is an essential component in the generation of lysosomes that are critical for the maintenance of cellular homeostasis. The ability of CI-MPR to interact with ~60 different acid hydrolases is facilitated by its large extracellular region, with four out of its 15 domains binding phosphomannosyl residues. Although the glycan specificity of CI-MPR has been elucidated, the molecular basis of carbohydrate binding has not been determined for two out of these four carbohydrate recognition domains (CRD). Here we report expression of CI-MPR’s CRD located in domain 5 that preferentially binds phosphodiester-containing glycans. Domain 5 of CI-MPR was expressed in Escherichia coli BL21 (DE3) cells as a fusion protein containing an N-terminal histidine tag and the small ubiquitin-like modifier (SUMO) protein. The His6-SUMO-CRD construct was recovered from inclusion bodies, refolded in buffer to facilitate disulfide bond formation, and subjected to Ni-NTA affinity chromatography and size exclusion chromatography. Surface plasmon resonance analyses demonstrated that the purified protein was active and bound phosphorylated glycans. Characterization by NMR spectroscopy revealed high quality 1H–15N HSQC spectra. Additionally, crystallization conditions were identified and a crystallographic data set of the CRD was collected to 1.8 Å resolution. Together, these studies demonstrate the feasibility of producing CI-MPR’s CRD suitable for three-dimensional structure determination by NMR spectroscopic and X-ray crystallographic approaches. PMID:25863146

Development of Microstructure and Crystallographic Texture in a Double-Sided Friction Stir Welded Microalloyed Steel

NASA Astrophysics Data System (ADS)

Rahimi, S.; Wynne, B. P.; Baker, T. N.

2017-01-01

The evolution of microstructure and crystallographic texture has been investigated in double-sided friction stir welded microalloyed steel, using electron backscatter diffraction (EBSD). The microstructure analyses show that the center of stirred zone reached a temperature between Ac1 and Ac3 during FSW, resulting in a dual-phase austenitic/ ferritic microstructure. The temperatures in the thermo-mechanically affected zone and the overlapped area between the first and second weld pass did not exceed the Ac1. The shear generated by the rotation probe occurs in austenitic/ferritic phase field where the austenite portion of the microstructure is transformed to a bainitic ferrite, on cooling. Analysis of crystallographic textures with regard to shear flow lines generated by the probe tool shows the dominance of simple shear components across the whole weld. The austenite texture at Ac1 - Ac3 is dominated by the B { {1bar{1}2} }< 110rangle and bar{B} { {bar{1}1bar{2}} }< bar{1}bar{1}0rangle simple shear texture components, where the bainite phase textures formed on cooling were inherited from the shear textures of the austenite phase with relatively strong variant selection. The ferrite portion of the stirred zone and the ferrites in the thermo-mechanically affected zones and the overlapped area underwent shear deformation with textures dominated by the D1 { {bar{1}bar{1}2} }< 111rangle and D2 { {11bar{2}} }< 111rangle simple shear texture components. The formation of ultrafine equiaxed ferrite with submicron grain size has been observed in the overlapped area between the first and second weld pass. This is due to continuous dynamic strain-induced recrystallization as a result of simultaneous severe shear deformation and drastic undercooling.

On the formation and functions of high and very high magnesium calcites in the continuously growing teeth of the echinoderm Lytechinus variegatus: development of crystallinity and protein involvement.

PubMed

Veis, Arthur; Stock, Stuart R; Alvares, Keith; Lux, Elizabeth

2011-01-01

Sea urchin teeth grow continuously and develop a complex mineralized structure consisting of spatially separate but crystallographically aligned first stage calcitic elements of high Mg content (5-15 mol% mineral). These become cemented together by epitaxially oriented second stage very high Mg calcite (30-40 mol% mineral). In the tooth plumula, ingressing preodontoblasts create layered cellular syncytia. Mineral deposits develop within membrane-bound compartments between cellular syncytial layers. We seek to understand how this complex tooth architecture is developed, how individual crystalline calcitic elements become crystallographically aligned, and how their Mg composition is regulated. Synchrotron microbeam X-ray scattering was performed on live, freshly dissected teeth. We observed that the initial diffracting crystals lie within independent syncytial spaces in the plumula. These diffraction patterns match those of mature tooth calcite. Thus, the spatially separate crystallites grow with the same crystallographic orientation seen in the mature tooth. Mineral-related proteins from regions with differing Mg contents were isolated, sequenced, and characterized. A tooth cDNA library was constructed, and selected matrix-related proteins were cloned. Antibodies were prepared and used for immunolocaliztion. Matrix-related proteins are acidic, phosphorylated, and associated with the syncytial membranes. Time-of-flight secondary ion mass spectroscopy of various crystal elements shows unique amino acid, Mg, and Ca ion distributions. High and very high Mg calcites differ in Asp content. Matrix-related proteins are phosphorylated. Very high Mg calcite is associated with Asp-rich protein, and it is restricted to the second stage mineral. Thus, the composition at each part of the tooth is related to architecture and function. Copyright © 2011 S. Karger AG, Basel.

Transuranic Hybrid Materials: Crystallographic and Computational Metrics of Supramolecular Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Surbella, Robert G.; Ducati, Lucas C.; Pellegrini, Kristi L.

A family of twelve supramolecular [AnO2Cl4]2- (An = U, Np, Pu) containing compounds assembled via hydrogen and halogen bonds donated by substituted 4-X-pyridinium cations (X = H, Cl, Br, I) is reported. These materials were prepared from a room-temperature synthesis wherein crystallization of unhydrolyzed and valence pure [An(VI)O2Cl4]2- (An = U, Np, Pu) tectons are the norm. We present a hierarchy of assembly criteria based on crystallographic observations, and subsequently quantify the strengths of the non-covalent interactions using Kohn-Sham density functional calculations. We provide, for the first time, a detailed description of the electrostatic potentials (ESPs) of the actinyl tetrahalidemore » dianions and reconcile crystallographically observed structural motifs and non-covalent interaction (NCI) acceptor-donor pairings. Our findings indicate that the average electrostatic potential across the halogen ligands (the acceptors) changes by only ~2 kJ mol-1 across the AnO22+ series, indicating the magnitude of the potential is independent of the metal center. The role of the cation is therefore critical in directing structural motifs and dictating the resulting hydrogen and halogen bond strengths, the former being stronger due to the positive charge centralized on the pyridyl nitrogen N-H+. Subsequent analyses using the Quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) approaches support this conclusion and highlight the structure directing role of the cations. Whereas one can infer that the 2 Columbic attraction is the driver for assembly, the contribution of the non-covalent interaction is to direct the molecular-level arrangement (or disposition) of the tectons.« less

Subsurface Stress Fields in FCC Single Crystal Anisotropic Contacts

NASA Technical Reports Server (NTRS)

Arakere, Nagaraj K.; Knudsen, Erik; Swanson, Gregory R.; Duke, Gregory; Ham-Battista, Gilda

2004-01-01

Single crystal superalloy turbine blades used in high pressure turbomachinery are subject to conditions of high temperature, triaxial steady and alternating stresses, fretting stresses in the blade attachment and damper contact locations, and exposure to high-pressure hydrogen. The blades are also subjected to extreme variations in temperature during start-up and shutdown transients. The most prevalent high cycle fatigue (HCF) failure modes observed in these blades during operation include crystallographic crack initiation/propagation on octahedral planes, and non-crystallographic initiation with crystallographic growth. Numerous cases of crack initiation and crack propagation at the blade leading edge tip, blade attachment regions, and damper contact locations have been documented. Understanding crack initiation/propagation under mixed-mode loading conditions is critical for establishing a systematic procedure for evaluating HCF life of single crystal turbine blades. This paper presents analytical and numerical techniques for evaluating two and three dimensional subsurface stress fields in anisotropic contacts. The subsurface stress results are required for evaluating contact fatigue life at damper contacts and dovetail attachment regions in single crystal nickel-base superalloy turbine blades. An analytical procedure is presented for evaluating the subsurface stresses in the elastic half-space, based on the adaptation of a stress function method outlined by Lekhnitskii. Numerical results are presented for cylindrical and spherical anisotropic contacts, using finite element analysis (FEA). Effects of crystal orientation on stress response and fatigue life are examined. Obtaining accurate subsurface stress results for anisotropic single crystal contact problems require extremely refined three-dimensional (3-D) finite element grids, especially in the edge of contact region. Obtaining resolved shear stresses (RSS) on the principal slip planes also involves considerable post-processing work. For these reasons it is very advantageous to develop analytical solution schemes for subsurface stresses, whenever possible.

Tri-p-tolyl­phosphine

PubMed Central

Wang, Hao; Wang, Yi-Bin; Liu, Bo-Nian; Tang, Shi-Gui; Wei, Ping

2008-01-01

In the title compound C21H21P, the P atom is situated on a crystallographic threefold rotatory-inversion axis, resulting in threefold rotation symmetry of the title compound. The dihedral angles between the symmetry-related benzene rings are 87.40 (18)°. PMID:21201763

Capturing the Complexity of Additively Manufactured Microstructures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Livescu, Veronica; Bronkhorst, Curt Allan; Vander Wiel, Scott Alan

2016-05-12

The underlying mechanisms and kinetics controlling damage nucleation and growth as a function of material microstructure and loading paths are discussed. These experiments indicate that structural features such as grain boundaries, grain size distribution, grain morphology crystallographic texture are all factors that influence mechanical behavior.

Expression, purification and preliminary crystallographic analysis of Mycobacterium tuberculosis CysQ, a phosphatase involved in sulfur metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Erickson, Anna I.; Sarsam, Reta D.; Fisher, Andrew J., E-mail: ajfisher@ucdavis.edu

The cysQ gene from Mycobacterium tuberculosis was cloned and the expressed protein, a 3′-phosphoadenosine-5′’-phosphatase, was purified and crystallized. X-ray diffraction data were collected to 1.7 Å resolution.

Mechanical alignment of particles for use in fabricating superconducting and permanent magnetic materials

DOEpatents

Nellis, William J.; Maple, M. Brian

1992-01-01

A method for mechanically aligning oriented superconducting or permanently magnetic materials for further processing into constructs. This pretreatment optimizes the final crystallographic orientation and, thus, properties in these constructs. Such materials as superconducting fibers, needles and platelets are utilized.

Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes

PubMed Central

2017-01-01

The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together. PMID:28691111

Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Montange, R.; Mondragon, E; van Tyne, D

2010-01-01

The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-{angstrom} X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-{angstrom} improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity ofmore » SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.« less

Cryo-quenched Fe-Ni-Cr alloy single crystals: A new decorative steel

DOE PAGES

Boatner, Lynn A.; Kolopus, James A.; Lavrik, Nicolay V.; ...

2016-08-31

In this paper, a decorative steel is described that is formed by a process that is unlike that of the fabrication methods utilized in making the original Damascus steels over 2000 years ago. The decorative aspect of the steel arises from a three-dimensional surface pattern that results from cryogenically quenching polished austenitic alloy single crystals into the martensitic phase that is present below 190 K. No forging operations are involved – the mechanism is entirely based on the metallurgical phase properties of the ternary alloy. The symmetry of the decorative pattern is determined and controlled by the crystallographic orientation andmore » symmetry of the 70%Fe,15%Ni,15%Cr alloy single crystals. Finally, in addition to using “cuts” made along principal crystallographic surface directions, an effectively infinite number of other random-orientation “cuts” can be utilized to produce decorative patterns where each pattern is unique after the austenitic-to-martensitic phase transformation.« less

Local atomic and magnetic structure of dilute magnetic semiconductor ( Ba , K ) ( Zn , Mn ) 2 As 2

DOE PAGES

Frandsen, Benjamin A.; Gong, Zizhou; Terban, Maxwell W.; ...

2016-09-06

We studied the atomic and magnetic structure of the dilute ferromagnetic semiconductor system (Ba,K)(Zn,Mn) 2As 2 through atomic and magnetic pair distribution function analysis of temperature-dependent x-ray and neutron total scattering data. Furthermore, we detected a change in curvature of the temperature-dependent unit cell volume of the average tetragonal crystallographic structure at a temperature coinciding with the onset of ferromagnetic order. We also observed the existence of a well-defined local orthorhombic structure on a short length scale of ≲5Å, resulting in a rather asymmetrical local environment of the Mn and As ions. Finally, the magnetic PDF revealed ferromagnetic alignment ofmore » Mn spins along the crystallographic c axis, with robust nearest-neighbor ferromagnetic correlations that exist even above the ferromagnetic ordering temperature. Finally, we discuss these results in the context of other experiments and theoretical studies on this system.« less

Expression, purification, crystallization and preliminary X-ray crystallographic analysis of a resuscitation-promoting factor from Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ruggiero, Alessia; Tizzano, Barbara; Geerlof, Arie

2007-10-01

The first crystallization of a resuscitation-promoting factor has been performed. Multiwavelength anomalous dispersion experiments have been carried out to obtain experimental phases using data at 2.9 Å resolution from a selenomethionine derivative. The resuscitation-promoting factor RpfB, the most complex of the five resuscitation-promoting factors produced by M. tuberculosis, is devoted to bacterial reactivation from the dormant state. RpfB consists of 362 residues predicted to form five domains. An RpfB fragment containing the protein catalytic domain and a G5 domain has been successfully crystallized using vapour-diffusion methods. This is the first crystallographic study of a resuscitation-promoting factor. Crystals of this proteinmore » belong to space group I422, with unit-cell parameters a = 97.63, b = 97.63, c = 114.87 Å. Diffraction data have also been collected from a selenomethionine derivative at 2.9 Å resolution. Model building using the phases derived from the multiwavelength anomalous dispersion experiment is in progress.« less

Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

PubMed Central

Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

2016-01-01

Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields. PMID:27156575

Improved Crystal Quality By Detached Solidification in Microgravity

NASA Technical Reports Server (NTRS)

Regel, Liya L.; Wilcox, William R.; Wang, Yaz-Hen; Wang, Jian-Bin

2003-01-01

Many microgravity directional solidification experiments yielded ingots with portions that grew without contacting the ampoule wall, leading to greatly improved crystallographic perfection. Our long term goals have been: (1) To develop a complete understanding of all of the phenomena of detached solidification.; (2) To make it possible to achieve detached solidification reproducibly; (3) To increase crystallographic perfection through detached solidification. We have three major achievements to report here: (1) We obtained a new material balance solution for the Moving Meniscus Model of detached solidification. This solution greatly clarifies the physics as well as the roles of the parameters in the system; (2) We achieved detached solidification of InSb growing on earth in BN-coated ampoules; (3) We performed an extensive series of experiments on freezing water that showed how to form multiple gas bubbles or tubes on the ampoule wall. However, these did not propagate around the wall and lead to fully detached solidification unless the ampoule wall was extremely rough and non-wetted.

Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5

DOE Office of Scientific and Technical Information (OSTI.GOV)

DiMattia,M.; Govindasamy, L.; Levy, H.

2005-01-01

Adeno-associated virus serotype 5 (AAV5) is under development for gene-therapy applications for the treatment of cystic fibrosis. To elucidate the structural features of AAV5 that control its enhanced transduction of the apical surface of airway epithelia compared with other AAV serotypes, X-ray crystallographic studies of the viral capsid have been initiated. The production, purification, crystallization and preliminary crystallographic analysis of empty AAV5 viral capsids are reported. The crystals diffract X-rays to beyond 3.2 Angstroms resolution using synchrotron radiation and belong to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 264.7, b = 447.9, c =more » 629.7 Angstroms. There is one complete T = 1 viral capsid per asymmetric unit. The orientation and position of the viral capsid in the asymmetric unit have been determined by rotation and translation functions, respectively, and the AAV5 structure determination is in progress.« less

Optical characterization of a low solubility organic compound.

PubMed

Huber, H E

1981-10-01

The X, Y, and Z principal vibration directions along with the principal refractive indexes, optic angle, optical sign, birefringence, optical orientation, and crystal system for the low solubility compound 5-(tetradecyloxy)-2-furancarboxylic acid were determined with a polarizing microscope and spindle stage. The X and Z principal vibration directions are not coincident with the a and c crystallographic axes; however, the Y direction is considered to be coincident with the b axis. Therefore, the crystal is assigned to the monoclinic crystal system. The bladed/lath-shaped crystals rest on one of the two large orthopinacoid (100) faces and present the microscopist with a single plane of optical symmetry. A beta refractive index of 1.555 is observed with the crystal axis of elongation parallel to the polarizer, and a gamma of 1.600-1.660 is observed in the contiguous extinction position. Determination of the optic angle principal vibration directions, and principal refractive indexes was facilitated by mounting the crystals on a spindle stage for rotation about the b crystallographic axis (optic normal).

Orientation relationship between the T structure and the icosahedral quasicrystal in the Zn-Mg-Al alloy system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakayama, Kei, E-mail: k.n@aoni.waseda.jp; Watanabe, Junya; Koyama, Yasumasa, E-mail: ykoyama@waseda.jp

2016-08-26

To understand the crystallographic relation between the Bergman-type icosahedral quasicrystal and its approximant-T structure, we have investigated the crystallographic features of prepared Zn-Mg-Al alloy samples, mainly by transmission electron microscopy. It was found that there existed three kinds of regions: that is, C14-Laves, approximant-T, and icosahedral-quasicrystal regions, in Zn-Mg-Al alloy samples with the composition of Zn-36at.%Mg-9at.%Al. Among these regions, in particular, we tried to determine an orientation relationship between neighboring icosahedral-quasicrystal and approximant-T regions. Based on the determined relationship, for instance, four threefold rotatory-inversion axes in the T structure were found to be parallel to four of ten threefold rotatory-inversionmore » axes in the icosahedral quasicrystal. It was thus understood that the atomic arrangements of the Bergman-type icosahedral quasicrystal and its approximant-T structure are likely to resemble each other.« less

Crystallographic observation of nonenzymatic RNA primer extension.

PubMed

Zhang, Wen; Walton, Travis; Li, Li; Szostak, Jack W

2018-05-31

The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. © 2018, Zhang et al.