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Sample records for crystallographic domains driven

  1. Multifunctionalities driven by ferroic domains

    SciTech Connect

    Yang, J. C.; Huang, Y. L.; Chu, Y. H.; He, Q.

    2014-08-14

    Considerable attention has been paid to ferroic systems in pursuit of advanced applications in past decades. Most recently, the emergence and development of multiferroics, which exhibit the coexistence of different ferroic natures, has offered a new route to create functionalities in the system. In this manuscript, we step from domain engineering to explore a roadmap for discovering intriguing phenomena and multifunctionalities driven by periodic domain patters. As-grown periodic domains, offering exotic order parameters, periodic local perturbations and the capability of tailoring local spin, charge, orbital and lattice degrees of freedom, are introduced as modeling templates for fundamental studies and novel applications. We discuss related significant findings on ferroic domain, nanoscopic domain walls, and conjunct heterostructures based on the well-organized domain patterns, and end with future prospects and challenges in the field.

  2. Crystallographically driven magnetic behaviour of arrays of monocrystalline Co nanowires.

    PubMed

    Ivanov, Yu P; Trabada, D G; Chuvilin, A; Kosel, J; Chubykalo-Fesenko, O; Vázquez, M

    2014-11-28

    Cobalt nanowires, 40 nm in diameter and several micrometers long, have been grown by controlled electrodeposition into ordered anodic alumina templates. The hcp crystal symmetry is tuned by a suitable choice of the electrolyte pH (between 3.5 and 6.0) during growth. Systematic high resolution transmission electron microscopy imaging and analysis of the electron diffraction patterns reveals a dependence of crystal orientation from electrolyte pH. The tailored modification of the crystalline signature results in the reorientation of the magnetocrystalline anisotropy and increasing experimental coercivity and squareness with decreasing polar angle of the 'c' growth axis. Micromagnetic modeling of the demagnetization process and its angular dependence is in agreement with the experiment and allows us to establish the change in the character of the magnetization reversal: from quasi-curling to vortex domain wall propagation modes when the crystal 'c' axis tilts more than 75° in respect to the nanowire axis.

  3. Crystallographic Insight into Collagen Recognition by Discoidin Domain Receptor 2

    PubMed Central

    Carafoli, Federico; Bihan, Dominique; Stathopoulos, Stavros; Konitsiotis, Antonios D.; Kvansakul, Marc; Farndale, Richard W.; Leitinger, Birgit; Hohenester, Erhard

    2009-01-01

    Summary The discoidin domain receptors, DDR1 and DDR2, are widely expressed receptor tyrosine kinases that are activated by triple-helical collagen. They control important aspects of cell behavior and are dysregulated in several human diseases. The major DDR2-binding site in collagens I–III is a GVMGFO motif (O is hydroxyproline) that also binds the matricellular protein SPARC. We have determined the crystal structure of the discoidin domain of human DDR2 bound to a triple-helical collagen peptide. The GVMGFO motifs of two collagen chains are recognized by an amphiphilic pocket delimited by a functionally critical tryptophan residue and a buried salt bridge. Collagen binding results in structural changes of DDR2 surface loops that may be linked to the process of receptor activation. A comparison of the GVMGFO-binding sites of DDR2 and SPARC reveals a striking case of convergent evolution in collagen recognition. PMID:20004161

  4. Crystallographic insight into collagen recognition by discoidin domain receptor 2.

    PubMed

    Carafoli, Federico; Bihan, Dominique; Stathopoulos, Stavros; Konitsiotis, Antonios D; Kvansakul, Marc; Farndale, Richard W; Leitinger, Birgit; Hohenester, Erhard

    2009-12-09

    The discoidin domain receptors, DDR1 and DDR2, are widely expressed receptor tyrosine kinases that are activated by triple-helical collagen. They control important aspects of cell behavior and are dysregulated in several human diseases. The major DDR2-binding site in collagens I-III is a GVMGFO motif (O is hydroxyproline) that also binds the matricellular protein SPARC. We have determined the crystal structure of the discoidin domain of human DDR2 bound to a triple-helical collagen peptide. The GVMGFO motifs of two collagen chains are recognized by an amphiphilic pocket delimited by a functionally critical tryptophan residue and a buried salt bridge. Collagen binding results in structural changes of DDR2 surface loops that may be linked to the process of receptor activation. A comparison of the GVMGFO-binding sites of DDR2 and SPARC reveals a striking case of convergent evolution in collagen recognition.

  5. Crystallographic Structure of Xanthorhodopsin, the Light-Driven Proton Pump With a Dual Chromophore

    SciTech Connect

    Luecke, H.; Schobert, B.; Stagno, J.; Imasheva, E.S.; Wang, J.M.; Balashov, S.P.; Lanyi, J.K.

    2009-05-19

    Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-{angstrom} resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK{sub a} of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as {approx}45%, and the 46{sup o} angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.

  6. Crystallographic and functional analyses of J-domain of JAC1 essential for chloroplast photorelocation movement in Arabidopsis thaliana.

    PubMed

    Takano, Akira; Suetsugu, Noriyuki; Wada, Masamitsu; Kohda, Daisuke

    2010-08-01

    An auxilin-like J-domain-containing protein, JAC1, is necessary for chloroplast movement in Arabidopsis thaliana, to capture photosynthetic light efficiently under weak light conditions. Here, we performed crystallographic and functional analyses of the J-domain of JAC1. The crystal structure of the J-domain is quite similar to that of bovine auxilin, and possesses a similar positively charged surface, which probably forms the interface with the Hsp70 chaperone. The mutation of the highly conserved HPD motif of the JAC1 J-domain abrogated the chloroplast photorelocation response. These results suggest that the requirement of JAC1 in chloroplast photorelocation movement is attributable to the J-domain's cochaperone activity.

  7. Purification, crystallization and preliminary crystallographic studies of the TLDc domain of oxidation resistance protein 2 from zebrafish

    PubMed Central

    Alsarraf, Husam M. A. B.; Laroche, Fabrice; Spaink, Herman; Thirup, Søren; Blaise, Mickael

    2011-01-01

    Cell metabolic processes are constantly producing reactive oxygen species (ROS), which have deleterious effects by triggering, for example, DNA damage. Numerous enzymes such as catalase, and small compounds such as vitamin C, provide protection against ROS. The TLDc domain of the human oxidation resistance protein has been shown to be able to protect DNA from oxidative stress; however, its mechanism of action is still not understood and no structural information is available on this domain. Structural information on the TLDc domain may therefore help in understanding exactly how it works. Here, the purification, crystallization and preliminary crystallographic studies of the TLDc domain from zebrafish are reported. Crystals belonging to the orthorhombic space group P21212 were obtained and diffracted to 0.97 Å resolution. Selenomethionine-substituted protein could also be crystallized; these crystals diffracted to 1.1 Å resolution and the structure could be solved by SAD/MAD methods. PMID:22102041

  8. Purification, crystallization and preliminary crystallographic analysis of the CBS-domain pair of cyclin M2 (CNNM2)

    PubMed Central

    Gómez-García, Inmaculada; Stuiver, Marchel; Ereño, June; Oyenarte, Iker; Corral-Rodríguez, María Angeles; Müller, Dominik; Martínez-Cruz, Luis Alfonso

    2012-01-01

    This work describes the purification and preliminary crystallographic analysis of the CBS-domain pair of the murine CNNM2 magnesium transporter (formerly known as ancient domain protein 2; ACDP2), which consists of a pair of cystathionine β-synthase (CBS) motifs and has 100% sequence identity to its human homologue. CNNM proteins represent the least-studied members of the eight different types of magnesium transporters identified to date in mammals. In humans, the CNNM family is encoded by four genes: CNNM1–4. CNNM1 acts as a cytosolic copper chaperone, whereas CNNM2 and CNNM4 have been associated with magnesium handling. Interestingly, mutations in the CNNM2 gene cause familial dominant hypomagnesaemia (MIM:607803), a rare human disorder characterized by renal and intestinal magnesium (Mg2+) wasting, which may lead to symptoms of Mg2+ depletion such as tetany, seizures and cardiac arrhythmias. This manuscript describes the preliminary crystallographic analysis of two different crystal habits of a truncated form of the protein containing its regulatory CBS-domain pair, which has been reported to host the pathological mutation T568I in humans. The crystals belonged to space groups P21212 and I222 (or I212121) and diffracted X-­rays to 2.0 and 3.6 Å resolution, respectively, using synchrotron radiation. PMID:23027747

  9. Antiferromagnetic Domain Wall Motion Driven by Spin-Orbit Torques.

    PubMed

    Shiino, Takayuki; Oh, Se-Hyeok; Haney, Paul M; Lee, Seo-Won; Go, Gyungchoon; Park, Byong-Guk; Lee, Kyung-Jin

    2016-08-19

    We theoretically investigate the dynamics of antiferromagnetic domain walls driven by spin-orbit torques in antiferromagnet-heavy-metal bilayers. We show that spin-orbit torques drive antiferromagnetic domain walls much faster than ferromagnetic domain walls. As the domain wall velocity approaches the maximum spin-wave group velocity, the domain wall undergoes Lorentz contraction and emits spin waves in the terahertz frequency range. The interplay between spin-orbit torques and the relativistic dynamics of antiferromagnetic domain walls leads to the efficient manipulation of antiferromagnetic spin textures and paves the way for the generation of high frequency signals from antiferromagnets.

  10. Antiferromagnetic domain wall motion driven by spin-orbit torques

    PubMed Central

    Shiino, Takayuki; Oh, Se-Hyeok; Haney, Paul M.; Lee, Seo-Won; Go, Gyungchoon; Park, Byong-Guk; Lee, Kyung-Jin

    2016-01-01

    We theoretically investigate dynamics of antiferromagnetic domain walls driven by spin-orbit torques in antiferromagnet/heavy metal bilayers. We show that spin-orbit torques drive antiferromagnetic domain walls much faster than ferromagnetic domain walls. As the domain wall velocity approaches the maximum spin-wave group velocity, the domain wall undergoes Lorentz contraction and emits spin-waves in the terahertz frequency range. The interplay between spin-orbit torques and the relativistic dynamics of antiferromagnetic domain walls leads to the efficient manipulation of antiferromagnetic spin textures and paves the way for the generation of high frequency signals from antiferromagnets. PMID:27588878

  11. Preliminary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization

    PubMed Central

    Chaves-Sanjuán, Antonio; Sánchez-Barrena, María José; González-Rubio, Juana María; Albert, Armando

    2014-01-01

    The Arabidopsis thaliana K+ transporter 1 (AKT1) participates in the maintenance of an adequate cell potassium (K+) concentration. The CBL-interacting protein kinase 23 (CIPK23) activates AKT1 for K+ uptake under low-K+ conditions. This process is mediated by the interaction between the cytosolic ankyrin-repeat (AR) domain of AKT1 and the kinase domain of CIPK23. However, the precise boundaries of the AR domain and the residues responsible for the interaction are still unknown. Here, the optimization procedure to obtain an AR domain construct suitable for crystallization and the preliminary crystallographic analysis of the obtained crystals are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 34.83, b = 65.89, c = 85.44 Å, and diffracted to 1.98 Å resolution. PMID:24699751

  12. Preliminary crystallographic analysis of the ankyrin-repeat domain of Arabidopsis thaliana AKT1: identification of the domain boundaries for protein crystallization.

    PubMed

    Chaves-Sanjuán, Antonio; Sánchez-Barrena, María José; González-Rubio, Juana María; Albert, Armando

    2014-04-01

    The Arabidopsis thaliana K(+) transporter 1 (AKT1) participates in the maintenance of an adequate cell potassium (K(+)) concentration. The CBL-interacting protein kinase 23 (CIPK23) activates AKT1 for K(+) uptake under low-K(+) conditions. This process is mediated by the interaction between the cytosolic ankyrin-repeat (AR) domain of AKT1 and the kinase domain of CIPK23. However, the precise boundaries of the AR domain and the residues responsible for the interaction are still unknown. Here, the optimization procedure to obtain an AR domain construct suitable for crystallization and the preliminary crystallographic analysis of the obtained crystals are reported. The crystals belonged to space group P21212, with unit-cell parameters a = 34.83, b = 65.89, c = 85.44 Å, and diffracted to 1.98 Å resolution.

  13. Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films

    DOE PAGES

    Han, Myung-Geun; Garlow, Joseph A.; Bugnet, Matthieu; ...

    2016-09-02

    Polar discontinuity at interfaces plays deterministic roles in charge transport, magnetism, and even superconductivity of functional oxides. To date, most polar discontinuity problems have been explored in hetero-interfaces between two dissimilar materials. Here, we show that charged domain walls (CDWs) in epitaxial thin films of ferroelectric PbZr0.2Ti0.8O3 are strongly coupled to polar interfaces through the formation of ½<101>{h0l} type crystallographic shear planes (CSPs). Using atomic resolution imaging and spectroscopy we illustrate that the CSPs consist of both conservative and nonconservative segments when coupled to the CDWs, where necessary compensating charges for stabilizing the CDWs are associated with vacancies at themore » CSPs. Lasly, the CDW/CSP coupling yields an atomically narrow domain walls, consisting of a single atomic layer of oxygen. This study shows that the CDW/CSP coupling is a fascinating venue to develop emergent material properties.« less

  14. Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films

    NASA Astrophysics Data System (ADS)

    Han, Myung-Geun; Garlow, Joseph A.; Bugnet, Matthieu; Divilov, Simon; Marshall, Matthew S. J.; Wu, Lijun; Dawber, Matthew; Fernandez-Serra, Marivi; Botton, Gianluigi A.; Cheong, Sang-Wook; Walker, Frederick J.; Ahn, Charles H.; Zhu, Yimei

    2016-09-01

    Polar discontinuity at interfaces plays deterministic roles in charge transport, magnetism, and even superconductivity of functional oxides. To date, most polar discontinuity problems have been explored in heterointerfaces between two dissimilar materials. Here, we show that charged domain walls (CDWs) in epitaxial thin films of ferroelectric PbZ r0.2T i0.8O3 are strongly coupled to polar interfaces through the formation of 1/2 <101 > {h 0 l } - type crystallographic shear planes (CSPs). Using atomic resolution imaging and spectroscopy we illustrate that the CSPs consist of both conservative and nonconservative segments when coupled to the CDWs where necessary compensating charges for stabilizing the CDWs are associated with vacancies at the CSPs. The CDW/CSP coupling yields an atomically narrow domain wall, consisting of a single atomic layer of oxygen. This study shows that the CDW/CSP coupling is a fascinating venue to develop emergent material properties.

  15. The application of domain-driven design in NMS

    NASA Astrophysics Data System (ADS)

    Zhang, Jinsong; Chen, Yan; Qin, Shengjun

    2011-12-01

    In the traditional design approach of data-model-driven, system analysis and design phases are often separated which makes the demand information can not be expressed explicitly. The method is also easy to lead developer to the process-oriented programming, making codes between the modules or between hierarchies disordered. So it is hard to meet requirement of system scalability. The paper proposes a software hiberarchy based on rich domain model according to domain-driven design named FHRDM, then the Webwork + Spring + Hibernate (WSH) framework is determined. Domain-driven design aims to construct a domain model which not only meets the demand of the field where the software exists but also meets the need of software development. In this way, problems in Navigational Maritime System (NMS) development like big system business volumes, difficulty of requirement elicitation, high development costs and long development cycle can be resolved successfully.

  16. Domain-driven morphogenesis of cellular membranes

    PubMed Central

    Shnyrova, Anna V.; Frolov, Vadim A.; Zimmerberg, Joshua

    2012-01-01

    SUMMARY Cellular shape is defined by its boundary: the membrane. Extremely dynamic at small scales, biological membranes retain identifiable stationary shape as large structures, such as organelles. The lipid bilayer serves as a matrix for this shape-defining membrane, linking membrane dynamics and structural stability. Here, we analyze the central role of proteo-lipid membrane domains in the coordination of membrane dynamics and in the self-organization of membrane shape. PMID:19906579

  17. Polarization control at spin-driven ferroelectric domain walls.

    PubMed

    Leo, Naëmi; Bergman, Anders; Cano, Andres; Poudel, Narayan; Lorenz, Bernd; Fiebig, Manfred; Meier, Dennis

    2015-04-14

    Unusual electronic states arise at ferroelectric domain walls due to the local symmetry reduction, strain gradients and electrostatics. This particularly applies to improper ferroelectrics, where the polarization is induced by a structural or magnetic order parameter. Because of the subordinate nature of the polarization, the rigid mechanical and electrostatic boundary conditions that constrain domain walls in proper ferroics are lifted. Here we show that spin-driven ferroelectricity promotes the emergence of charged domain walls. This provides new degrees of flexibility for controlling domain-wall charges in a deterministic and reversible process. We create and position a domain wall by an electric field in Mn0.95Co0.05WO4. With a magnetic field we then rotate the polarization and convert neutral into charged domain walls, while its magnetic properties peg the wall to its location. Using atomistic Landau-Lifshitz-Gilbert simulations we quantify the polarization changes across the two wall types and highlight their general occurrence.

  18. Cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the TIR domain from the Brucella melitensis TIR-domain-containing protein TcpB.

    PubMed

    Alaidarous, Mohammed; Ve, Thomas; Ullah, M Obayed; Valkov, Eugene; Mansell, Ashley; Schembri, Mark A; Sweet, Matthew J; Kobe, Bostjan

    2013-10-01

    In mammals, Toll-like receptors (TLRs) recognize conserved microbial molecular signatures and induce an early innate immune response in the host. TLR signalling is mediated by interactions between the cytosolic TIR (Toll/interleukin-1 receptor) domains of the receptor and the adaptor proteins. Increasingly, it is apparent that pathogens target this interaction via pathogen-expressed TIR-domain-containing proteins to modulate immune responses. A TIR-domain-containing protein TcpB has been reported in the pathogenic bacterium Brucella melitensis. Studies have shown that TcpB interferes with the TLR2 and TLR4 signalling pathways to inhibit TLR-mediated inflammatory responses. Such interference may involve TIR-TIR-domain interactions between bacterial and mammalian proteins, but there is a lack of information about these interactions at the molecular level. In this study, the cloning, expression, purification, crystallization and preliminary X-ray crystallographic analysis of the protein construct corresponding to the TIR domain of TcpB (residues 120-250) are reported. The crystals diffracted to 2.6 Å resolution, have the symmetry of the monoclinic space group P2₁ and are most likely to contain four molecules in the asymmetric unit. The structure should help in understanding the molecular basis of how TcpB affects the innate immunity of the host.

  19. Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of adhesion molecule CD44

    SciTech Connect

    Mori, Tomoyuki; Kitano, Ken; Terawaki, Shin-ichi; Maesaki, Ryoko; Hakoshima, Toshio

    2007-10-01

    The radixin FERM domain complexed with the CD44 cytoplasmic tail peptide has been crystallized. A diffraction data set from the complex was collected to 2.1 Å. CD44 is an important adhesion molecule that specifically binds hyaluronic acid and regulates cell–cell and cell–matrix interactions. Increasing evidence has indicated that CD44 is assembled in a regulated manner into the membrane–cytoskeletal junction, a process that is mediated by ERM (ezrin/radixin/moesin) proteins. Crystals of a complex between the radixin FERM domain and the C-terminal cytoplasmic region of CD44 have been obtained. The crystal of the radixin FERM domain bound to the CD44 cytoplasmic tail peptide belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.70, b = 66.18, c = 86.22 Å, and contain one complex in the crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.1 Å.

  20. Purification, crystallization and preliminary crystallographic characterization of the caspase-recruitment domain of human Nod1

    SciTech Connect

    Srimathi, Thiagarajan; Robbins, Sheila L.; Dubas, Rachel L.; Seo, Jang-Hoon; Park, Young Chul

    2007-01-01

    The caspase-recruitment domain of the cytosolic pathogen receptor Nod1 was crystallized. X-ray diffraction data were collected to 1.9 Å resolution. The caspase-recruitment domain (CARD) is known to play an important role in apoptosis and inflammation as an essential protein–protein interaction domain. The CARD of the cytosolic pathogen receptor Nod1 was overexpressed in Escherichia coli and purified by affinity chromatography and gel filtration. The purified CARD was crystallized at 277 K using the microseeding method. X-ray diffraction data were collected to 1.9 Å resolution. The crystals belong to space group P3{sub 1} or P3{sub 2}, with unit-cell parameters a = b = 79.1, c = 80.9 Å. Preliminary analysis indicates that there is one dimeric CARD molecule in the asymmetric unit.

  1. Overproduction, purification and preliminary crystallographic analysis of the carbohydrate-recognition domain of human langerin

    SciTech Connect

    Thépaut, Michel; Vivès, Corinne; Pompidor, Guillaume; Kahn, Richard; Fieschi, Franck

    2008-02-01

    Crystals of the carbohydrate-recognition domain of human langerin were obtained that diffracted synchrotron radiation to 1.5 Å resolution. Langerin, a lectin that is specific to Langerhans cells, interacts with glyco@@conjugates through its carbohydrate-recognition domain (CRD). This carbohydrate binding occurs by an avidity-based mechanism that is enabled by the neck domain responsible for trimerization. Langerin binds HIV through its CRD and thus plays a protective role against its propagation by the internalization of virions in Birbeck granules. Here, the overproduction, purification and crystallization of the langerin CRD is reported. Crystals obtained by the hanging-drop vapour-diffusion method allowed the collection of a complete data set to 1.5 Å resolution and belonged to the tetragonal space group P4{sub 2}, with unit-cell parameters a = b = 79.55, c = 90.14 Å.

  2. Combining Domain-driven Design and Mashups for Service Development

    NASA Astrophysics Data System (ADS)

    Iglesias, Carlos A.; Fernández-Villamor, José Ignacio; Del Pozo, David; Garulli, Luca; García, Boni

    This chapter presents the Romulus project approach to Service Development using Java-based web technologies. Romulus aims at improving productivity of service development by providing a tool-supported model to conceive Java-based web applications. This model follows a Domain Driven Design approach, which states that the primary focus of software projects should be the core domain and domain logic. Romulus proposes a tool-supported model, Roma Metaframework, that provides an abstraction layer on top of existing web frameworks and automates the application generation from the domain model. This metaframework follows an object centric approach, and complements Domain Driven Design by identifying the most common cross-cutting concerns (security, service, view, ...) of web applications. The metaframework uses annotations for enriching the domain model with these cross-cutting concerns, so-called aspects. In addition, the chapter presents the usage of mashup technology in the metaframework for service composition, using the web mashup editor MyCocktail. This approach is applied to a scenario of the Mobile Phone Service Portability case study for the development of a new service.

  3. Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films

    SciTech Connect

    Han, Myung-Geun; Garlow, Joseph A.; Bugnet, Matthieu; Divilov, Simon; Marshall, Matthew S. J.; Wu, Lijun; Dawber, Matthew; Fernandez-Serra, Marivi; Botton, Gianluigi A.; Cheong, Sang-Wook; Walker, Frederick J.; Ahn, Charles H.; Zhu, Yimei

    2016-09-02

    Polar discontinuity at interfaces plays deterministic roles in charge transport, magnetism, and even superconductivity of functional oxides. To date, most polar discontinuity problems have been explored in hetero-interfaces between two dissimilar materials. Here, we show that charged domain walls (CDWs) in epitaxial thin films of ferroelectric PbZr0.2Ti0.8O3 are strongly coupled to polar interfaces through the formation of ½<101>{h0l} type crystallographic shear planes (CSPs). Using atomic resolution imaging and spectroscopy we illustrate that the CSPs consist of both conservative and nonconservative segments when coupled to the CDWs, where necessary compensating charges for stabilizing the CDWs are associated with vacancies at the CSPs. Lasly, the CDW/CSP coupling yields an atomically narrow domain walls, consisting of a single atomic layer of oxygen. This study shows that the CDW/CSP coupling is a fascinating venue to develop emergent material properties.

  4. Coupling of bias-induced crystallographic shear planes with charged domain walls in ferroelectric oxide thin films

    SciTech Connect

    Han, Myung-Geun; Garlow, Joseph A.; Bugnet, Matthieu; Divilov, Simon; Marshall, Matthew S. J.; Wu, Lijun; Dawber, Matthew; Fernandez-Serra, Marivi; Botton, Gianluigi A.; Cheong, Sang-Wook; Walker, Frederick J.; Ahn, Charles H.; Zhu, Yimei

    2016-09-02

    Polar discontinuity at interfaces plays deterministic roles in charge transport, magnetism, and even superconductivity of functional oxides. To date, most polar discontinuity problems have been explored in hetero-interfaces between two dissimilar materials. Here, we show that charged domain walls (CDWs) in epitaxial thin films of ferroelectric PbZr0.2Ti0.8O3 are strongly coupled to polar interfaces through the formation of ½<101>{h0l} type crystallographic shear planes (CSPs). Using atomic resolution imaging and spectroscopy we illustrate that the CSPs consist of both conservative and nonconservative segments when coupled to the CDWs, where necessary compensating charges for stabilizing the CDWs are associated with vacancies at the CSPs. Lasly, the CDW/CSP coupling yields an atomically narrow domain walls, consisting of a single atomic layer of oxygen. This study shows that the CDW/CSP coupling is a fascinating venue to develop emergent material properties.

  5. Crystallization and preliminary X-ray crystallographic studies of the CARD domain of human CARMA1.

    PubMed

    Park, Jin Hee; Park, Hyun Ho

    2013-04-01

    The CARMA1 signalosome, which is composed of CARMA1 [caspase recruitment domain (CARD) containing MAGUK protein 1], BCL10 (B-cell lymphoma 10) and MALT1 (mucosa-associated lymphoid tissue lymphoma translocation protein 1), is a molecular-signalling complex that performs pivotal functions in T-cell receptor (TCR) and B-cell receptor (BCR) mediated NF-κB activation. In this study, the CARD domain of human CARMA1 (CARMA1 CARD), corresponding to amino acids 14-109, was overexpressed in Escherichia coli using an engineered C-terminal His tag. CARMA1 CARD was then purified to homogeneity and crystallized at 293 K. Finally, X-ray diffraction data were collected to a resolution of 3.2 Å from a crystal belonging to space group P2(1)2(1)2(1) with unit-cell parameters a = 45.73, b = 53.37, c = 91.89 Å.

  6. Crystallization and preliminary X-ray crystallographic studies of the axin DIX domain

    SciTech Connect

    Shibata, Naoki; Tomimoto, Yusuke; Hanamura, Toru; Yamamoto, Ryo; Ueda, Mai; Ueda, Yasufumi; Mizuno, Nobuhiro; Ogata, Hideaki; Komori, Hirofumi; Shomura, Yasuhito; Kataoka, Michihiko; Shimizu, Sakayu; Kondo, Jun; Yamamoto, Hideki; Kikuchi, Akira; Higuchi, Yoshiki

    2007-06-01

    The DIX domain of rat axin has been purified and crystallized. Crystals diffracted to 2.9 Å resolution using synchrotron radiation. Axin is a negative regulator of the canonical Wnt signalling pathway that mediates the phosphorylation of β-catenin by glycogen synthase kinase 3β. The DIX domain of rat axin, which is important for its homooligomerization and interactions with other regulators in the Wnt pathway, was purified and crystallized by the sitting-drop vapour-diffusion technique using polyethylene glycol 6000 and lithium sulfate as crystallization agents. Crystals belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 91.49, c = 84.92 Å. An X-ray diffraction data set has been collected to a nominal resolution of 2.9 Å.

  7. Crystallization and preliminary crystallographic study of a trypsin-resistant catalytic domain of human calcineurin

    PubMed Central

    Jin, Lei; Roehrl, Michael H. A.; Xiao, Li; He, Xiuyun; Li, Haibin; Ge, Linhu; Shi, Bingyi

    2012-01-01

    Calcineurin, a Ca2+/calmodulin-dependent serine/threonine protein phosphatase, plays a key role in a number of cellular pathways, including T-cell activation, and is an important molecular target of the immunosuppressive drugs cyclosporin A and FK506. To understand the structural basis underlying the activation of calcineurin by calmodulin, X-ray crystallography was employed to solve the three-dimensional structure of the free calcineurin catalytic domain (residues 20–347 of the A subunit). To accomplish this, a bacterially expressed glutathione S-­transferase (GST) fusion protein of the human calcineurin catalytic domain was first purified by GST-affinity chromatography. After limited digestion by trypsin, the catalytic domain (Cncat) was purified using anion-exchange and size-exclusion chromatography. Crystallization of Cncat was achieved by the hanging-drop vapour-diffusion method at pH 6.5 using PEG 6000 as precipitant. The diffraction results showed that the Cncat crystal belonged to the orthorhombic space group P21212, with unit-cell parameters a = 161.6, b = 87.4, c = 112.0 Å. There are four Cncat molecules in the asymmetric unit, with 49.5% solvent content. An X-ray diffraction data set was collected to 2.87 Å resolution and a clear molecular-replacement solution was obtained. The active site of Cncat is open to the solvent channels in the crystal packing. PMID:22691791

  8. Purification, Crystallization and Preliminary X-ray Crystallographic Studies of RAIDD Death-Domain (DD)

    SciTech Connect

    Jang, T.; Park, H

    2009-01-01

    Caspase-2 activation by formation of PIDDosome is critical for genotoxic stress induced apoptosis. PIDDosome is composed of three proteins, RAIDD, PIDD, and Caspase-2. RAIDD is an adaptor protein containing an N-terminal Caspase-Recruiting-Domain (CARD) and a C-terminal Death-Domain (DD). Its interactions with Caspase-2 and PIDD through CARD and DD respectively and formation of PIDDosome are important for the activation of Caspase-2. RAIDD DD cloned into pET26b vector was expressed in E. coli cells and purified by nickel affinity chromatography and gel filtration. Although it has been known that the most DDs are not soluble in physiological condition, RAIDD DD was soluble and interacts tightly with PIDD DD in physiological condition. The purified RAIDD DD alone has been crystallized. Crystals are trigonal and belong to space group P3121 (or its enantiomorph P3221) with unit-cell parameters a = 56.3, b = 56.3, c = 64.9 and ? = 120 degrees. The crystals were obtained at room temperature and diffracted to 2.0 A resolution.

  9. Crystallographic and Biochemical Analysis of the Ran-Binding Zinc Finger Domain

    SciTech Connect

    Partridge, James R.; Schwartz, Thomas U.; MIT

    2009-08-13

    The nuclear pore complex (NPC) resides in circular openings within the nuclear envelope and serves as the sole conduit to facilitate nucleocytoplasmic transport in eukaryotes. The asymmetric distribution of the small G protein Ran across the nuclear envelope regulates directionality of protein transport. Ran interacts with the NPC of metazoa via two asymmetrically localized components, Nup153 at the nuclear face and Nup358 at the cytoplasmic face. Both nucleoporins contain a stretch of distinct, Ran-binding zinc finger domains. Here, we present six crystal structures of Nup153-zinc fingers in complex with Ran and a 1.48 {angstrom} crystal structure of RanGDP. Crystal engineering allowed us to obtain well diffracting crystals so that all ZnF-Ran complex structures are refined to high resolution. Each of the four zinc finger modules of Nup153 binds one Ran molecule in apparently non-allosteric fashion. The affinity is measurably higher for RanGDP than for RanGTP and varies modestly between the individual zinc fingers. By microcalorimetric and mutational analysis, we determined that one specific hydrogen bond accounts for most of the differences in the binding affinity of individual zinc fingers. Genomic analysis reveals that only in animals do NPCs contain Ran-binding zinc fingers. We speculate that these organisms evolved a mechanism to maintain a high local concentration of Ran at the vicinity of the NPC, using this zinc finger domain as a sink.

  10. Experimental Study on Current-Driven Domain Wall Motion

    NASA Astrophysics Data System (ADS)

    Ono, T.; Yamaguchi, A.; Tanigawa, H.; Yano, K.; Kasai, S.

    2006-06-01

    Current-driven domain wall (DW) motion for a well-defined single DW in a micro-fabricated magnetic wire with submicron width was investigated by real-space observation with magnetic force microscopy. Magnetic force microscopy visualizes that a single DW introduced in a wire is displaced back and forth by positive and negative pulsed-current, respectively. Effect of the Joule heating, reduction of the threshold current density by shape control, and magnetic ratchet effect are also presented.

  11. Expression, purification and preliminary crystallographic analysis of the cryptic polo-box domain of Caenorhabditis elegans ZYG-1.

    PubMed

    Shimanovskaya, Ekaterina; Dong, Gang

    2014-10-01

    ZYG-1 is a polo-like kinase essential for centriole assembly in Caenorhabditis elegans. The targeting of ZYG-1 to nascent centrioles is via its central cryptic polo-box (CPB) domain. To shed light on the molecular basis of ZYG-1 recruitment, it is necessary to obtain structural knowledge of the ZYG-1 CPB. Here, the expression, purification and preliminary crystallographic analysis of the ZYG-1 CPB are reported. The protein was overexpressed in Escherichia coli strain BL21 (DE3), purified by multi-step chromatography and crystallized using the vapour-diffusion method. Crystals of the wild-type protein exhibited an order-disorder pathology, which was solved by reductive lysine methylation. A complete anomalous data set was collected to 2.54 Å resolution at the Se K edge (λ = 0.9792 Å). The crystal belonged to space group P2, with unit-cell parameters a = 53.3, b = 60.09, c = 87.51 Å, β = 93.31°. There were two molecules in the asymmetric unit.

  12. Domain wall motion driven by an oscillating magnetic field

    NASA Astrophysics Data System (ADS)

    Moon, Kyoung-Woong; Kim, Duck-Ho; Kim, Changsoo; Kim, Dae-Yun; Choe, Sug-Bong; Hwang, Chanyong

    2017-03-01

    The coherent unidirectional motion of magnetic domain walls (DWs) is a key technology used in memory and logic device applications, as demonstrated in magnetic strips by electric current flow as well as in films by oscillation of a tilted magnetic field. Here we introduce a coherent unidirectional motion of DWs in the strip, utilizing an oscillating field, which is described within a previous 1D model. The essential criterion for DW motion in this approach is the oscillating-field-induced modulation of the DW width, which has not been previously considered. This DW motion driven by width modulation sheds light on high frequency domain manipulation in spin devices. A comprehensive inspection of field angle dependence reveals that unidirectional DW motion in this model requires chiral DWs, followed by asymmetric deformation of the domain shape.

  13. Research on Domain-Driven Actionable Knowledge Discovery

    NASA Astrophysics Data System (ADS)

    Zhu, Zhengxiang; Gu, Jifa; Zhang, Lingling; Song, Wuqi; Gao, Rui

    Traditional data mining is a data-driven trial-and-error process, stop on general pattern discovered. However, in many cases the mined knowledge by this process could not meet the real-world business needs. Actually, in real-world business, knowledge must be actionable, that is to say, one can do something on it to profit. Actionable knowledge discovery is a complex task, due to it is strongly depend on domain knowledge, such as background knowledge expert experience, user interesting, environment context, business logic, even including law, regulation, habit, culture etc. The main challenge is moving data-driven into domain-driven data mining (DDDM), its goal is to discover actionable knowledge rather than general pattern. As a new generation data mining approach, main ideas of the DDDM are introduced. Two types of process models show the difference between loosely coupled and tightly coupled. Also the main characteristics, such as constraint-base, human-machine cooperated, loop-closed iterative refinement and meta-synthesis-base process management are proposed. System architecture will be introduced, as well as a paradigm will be introduced.

  14. Optical Frequency Domain Visualization of Electron Beam Driven Plasma Wakefields

    NASA Astrophysics Data System (ADS)

    Zgadzaj, Rafal; Downer, M. C.; Muggli, Patric; Yakimenko, Vitaly; Babzien, Marcus; Kusche, Karl; Fedurin, Mikhail

    2010-11-01

    Beam-driven plasma wakefield accelerators (PWFA), such as the ``plasma afterburner,'' are a promising approach for significantly increasing the particle energies of conventional accelerators. The study and optimization of PWFA would benefit from an experimental correlation between the parameters of the drive bunch, the accelerated bunch and the corresponding, accelerating plasma wave structure. However, the plasma wave structure has not yet been observed directly in PWFA. We will report our current work on noninvasive optical Frequency Domain Interferometric (FDI) and Holographic (FDH) visualization of beam-driven plasma waves. Both techniques employ two laser pulses (probe and reference) co-propagating with the particle drive-beam and its plasma wake. The reference pulse precedes the drive bunch, while the probe overlaps the plasma wave and maps its longitudinal and transverse structure. The experiment is being developed at the BNL/ATF Linac to visualize wakes generated by two and multi-bunch drive beams.

  15. The Peltier driven frequency domain approach in thermal analysis.

    PubMed

    De Marchi, Andrea; Giaretto, Valter

    2014-10-01

    The merits of Frequency Domain analysis as a tool for thermal system characterization are discussed, and the complex thermal impedance approach is illustrated. Pure AC thermal flux generation with negligible DC component is possible with a Peltier device, differently from other existing methods in which a significant DC component is intrinsically attached to the generated AC flux. Such technique is named here Peltier Driven Frequency Domain (PDFD). As a necessary prerequisite, a novel one-dimensional analytical model for an asymmetrically loaded Peltier device is developed, which is general enough to be useful in most practical situations as a design tool for measurement systems and as a key for the interpretation of experimental results. Impedance analysis is possible with Peltier devices by the inbuilt Seebeck effect differential thermometer, and is used in the paper for an experimental validation of the analytical model. Suggestions are then given for possible applications of PDFD, including the determination of thermal properties of materials.

  16. The Peltier driven frequency domain approach in thermal analysis

    NASA Astrophysics Data System (ADS)

    Marchi, Andrea De; Giaretto, Valter

    2014-10-01

    The merits of Frequency Domain analysis as a tool for thermal system characterization are discussed, and the complex thermal impedance approach is illustrated. Pure AC thermal flux generation with negligible DC component is possible with a Peltier device, differently from other existing methods in which a significant DC component is intrinsically attached to the generated AC flux. Such technique is named here Peltier Driven Frequency Domain (PDFD). As a necessary prerequisite, a novel one-dimensional analytical model for an asymmetrically loaded Peltier device is developed, which is general enough to be useful in most practical situations as a design tool for measurement systems and as a key for the interpretation of experimental results. Impedance analysis is possible with Peltier devices by the inbuilt Seebeck effect differential thermometer, and is used in the paper for an experimental validation of the analytical model. Suggestions are then given for possible applications of PDFD, including the determination of thermal properties of materials.

  17. Current-driven dynamics of chiral ferromagnetic domain walls.

    PubMed

    Emori, Satoru; Bauer, Uwe; Ahn, Sung-Min; Martinez, Eduardo; Beach, Geoffrey S D

    2013-07-01

    In most ferromagnets the magnetization rotates from one domain to the next with no preferred handedness. However, broken inversion symmetry can lift the chiral degeneracy, leading to topologically rich spin textures such as spin spirals and skyrmions through the Dzyaloshinskii-Moriya interaction (DMI). Here we show that in ultrathin metallic ferromagnets sandwiched between a heavy metal and an oxide, the DMI stabilizes chiral domain walls (DWs) whose spin texture enables extremely efficient current-driven motion. We show that spin torque from the spin Hall effect drives DWs in opposite directions in Pt/CoFe/MgO and Ta/CoFe/MgO, which can be explained only if the DWs assume a Néel configuration with left-handed chirality. We directly confirm the DW chirality and rigidity by examining current-driven DW dynamics with magnetic fields applied perpendicular and parallel to the spin spiral. This work resolves the origin of controversial experimental results and highlights a new path towards interfacial design of spintronic devices.

  18. Optical Frequency Domain Visualization of Electron Beam Driven Plasma Wakefields

    SciTech Connect

    Zgadzaj, Rafal; Downer, Michael C.; Muggli, Patric; Yakimenko, Vitaly; Kusche, Karl; Fedurin, Michhail; Babzien, Marcus

    2010-11-04

    Bunch driven plasma wakefield accelerators (PWFA), such as the 'plasma afterburner', are a promising emerging method for significantly increasing the energy output of conventional particle accelerators. The study and optimization of this method would benefit from an experimental correlation of the drive bunch parameters and the accelerated particle parameters with the corresponding plasma wave structure. However, the plasma wave structure has not been observed directly so far. We will report ongoing development of a noninvasive optical Frequency Domain Interferometric (FDI) and Holographic (FDH) diagnostics of bunch driven plasma wakes. Both FDI and FDH have been previously demonstrated in the case of laser driven wakes. These techniques employ two laser pulses co-propagating with the drive particle bunch and the trailing plasma wave. One pulse propagates ahead of the drive bunch and serves as a reference, while the second is overlapped with the plasma wave and probes its structure. The multi-shot FDI and single-shot FDH diagnostics permit direct noninvasive observation of longitudinal and transverse structure of the plasma wakes. The experiment is being developed at the 70 MeV Linac in the Accelerator Test Facility at Brookhaven National Laboratory to visualize wakes generated by two and multi-bunch drive beams.

  19. Optical Frequency Domain Visualization of Electron Beam Driven Plasma Wakefields

    NASA Astrophysics Data System (ADS)

    Zgadzaj, Rafal; Downer, Michael C.; Muggli, Patric; Yakimenko, Vitaly; Kusche, Karl; Fedurin, Michhail; Babzien, Marcus

    2010-11-01

    Bunch driven plasma wakefield accelerators (PWFA), such as the "plasma afterburner," are a promising emerging method for significantly increasing the energy output of conventional particle accelerators [1]. The study and optimization of this method would benefit from an experimental correlation of the drive bunch parameters and the accelerated particle parameters with the corresponding plasma wave structure. However, the plasma wave structure has not been observed directly so far. We will report ongoing development of a noninvasive optical Frequency Domain Interferometric (FDI) [2] and Holographic (FDH) [3] diagnostics of bunch driven plasma wakes. Both FDI and FDH have been previously demonstrated in the case of laser driven wakes. These techniques employ two laser pulses co-propagating with the drive particle bunch and the trailing plasma wave. One pulse propagates ahead of the drive bunch and serves as a reference, while the second is overlapped with the plasma wave and probes its structure. The multi-shot FDI and single-shot FDH diagnostics permit direct noninvasive observation of longitudinal and transverse structure of the plasma wakes. The experiment is being developed at the 70 MeV Linac in the Accelerator Test Facility at Brookhaven National Laboratory to visualize wakes generated by two [4] and multi-bunch [5] drive beams.

  20. Insights into an efficient light-driven hybrid P450 BM3 enzyme from crystallographic, spectroscopic and biochemical studies.

    PubMed

    Spradlin, Jessica; Lee, Diana; Mahadevan, Sruthi; Mahomed, Mavish; Tang, Lawrence; Lam, Quan; Colbert, Alexander; Shafaat, Oliver S; Goodin, David; Kloos, Marco; Kato, Mallory; Cheruzel, Lionel E

    2016-12-01

    In order to perform selective CH functionalization upon visible light irradiation, Ru(II)-diimine functionalized P450 heme enzymes have been developed. The sL407C-1 enzyme containing the Ru(bpy)2PhenA (bpy=2,2'-bipyridine and PhenA=5-acetamido-1,10-phenanthroline) photosensitizer (1) covalently attached to the non-native single cysteine L407C of the P450BM3 heme domain mutant, displays high photocatalytic activity in the selective CH bond hydroxylation of several substrates. A combination of X-ray crystallography, site-directed mutagenesis, transient absorption measurements and enzymatic assays was used to gain insights into its photocatalytic activity and electron transfer pathway. The crystal structure of the sL407C-1 enzyme was solved in the open and closed conformations revealing a through-space electron transfer pathway involving highly conserved, F393 and Q403, residues. Several mutations of these residues (F393A, F393W or Q403W) were introduced to probe their roles in the overall reaction. Transient absorption measurements confirm rapid electron transfer as heme reduction is observed in all four hybrid enzymes. Compared to the parent sL407C-1, photocatalytic activity was negligible in the dF393A-1 enzyme while 60% increase in activity with total turnover numbers of 420 and 90% product conversion was observed with the dQ403W-1 mutant. In the sL407C-1 enzyme, the photosensitizer is ideally located to rapidly deliver electrons, using the naturally occurring electron transfer pathway, to the heme center in order to activate molecular dioxygen and sustain photocatalytic activity. The results shed light on the design of efficient light-driven biocatalysts and the approach can be generalized to other members of the P450 superfamily. Copyright © 2016 Elsevier B.V. All rights reserved.

  1. 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.

  2. Crystallization and preliminary X-ray crystallographic analysis of the CARD domain of apoptosis repressor with CARD (ARC).

    PubMed

    Kim, Seong Hyun; Park, Hyun Ho

    2015-01-01

    Apoptosis repressor with caspase-recruiting domain (ARC) is an apoptosis repressor that inhibits both intrinsic and extrinsic apoptosis signalling. Human ARC contains an N-terminal caspase-recruiting domain (CARD domain) and a C-terminal proline- and glutamic acid-rich (P/E-rich) domain. The CARD domain in ARC is the domain that is directly involved in inhibition of the extrinsic pathway. In this study, the N-terminal CARD domain of ARC was overexpressed, purified and crystallized. X-ray diffraction data were collected to a resolution of 2.1 Å and the crystals were found to belong to space group P6(1) or P65, with unit-cell parameters a=98.28, b=98.28, c=51.86 Å, α=90, β=90, γ=120°.

  3. High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor-binding domain of botulinum neurotoxin serotype D

    SciTech Connect

    Zhang, Y.; Robinson, H.; Gao, X.; Qin, L.; Buchko, G. W.; Varnum, S. M.

    2010-12-01

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

  4. High-level Expression Purification Crystallization and Preliminary X-ray Crystallographic Studies of the Receptor Binding Domain of botulinum neurotoxin Serotype D

    SciTech Connect

    Y Zhang; X Gao; G Buchko; H Robinson; S Varnum

    2011-12-31

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and animals that are responsible for the deadly neuroparalytic disease botulism. Here, details of the expression and purification of the receptor-binding domain (HCR) of BoNT/D in Escherichia coli are presented. Using a codon-optimized cDNA, BoNT/D{_}HCR was expressed at a high level (150-200 mg per litre of culture) in the soluble fraction. Following a three-step purification protocol, very pure (>98%) BoNT/D{_}HCR was obtained. The recombinant BoNT/D{_}HCR was crystallized and the crystals diffracted to 1.65 {angstrom} resolution. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 60.8, b = 89.7, c = 93.9 {angstrom}. Preliminary crystallographic data analysis revealed the presence of one molecule in the asymmetric unit.

  5. Exceptionally High Piezoelectric Coefficient and Low Strain Hysteresis in Grain-Oriented (Ba, Ca)(Ti, Zr)O3 through Integrating Crystallographic Texture and Domain Engineering.

    PubMed

    Liu, Yingchun; Chang, Yunfei; Li, Fei; Yang, Bin; Sun, Yuan; Wu, Jie; Zhang, Shantao; Wang, Ruixue; Cao, Wenwu

    2017-09-06

    Both low strain hysteresis and high piezoelectric performance are required for practical applications in precisely controlled piezoelectric devices and systems. Unfortunately, enhanced piezoelectric properties were usually obtained with the presence of a large strain hysteresis in BaTiO3 (BT)-based piezoceramics. In this work, we propose to integrate crystallographic texturing and domain engineering strategies into BT-based ceramics to resolve this challenge. [001]c grain-oriented (Ba0.94Ca0.06)(Ti0.95Zr0.05)O3 (BCTZ) ceramics with a texture degree as high as 98.6% were synthesized by templated grain growth. A very high piezoelectric coefficient (d33) of 755 pC/N, and an extremely large piezoelectric strain coefficient (d33* = 2027 pm/V) along with an ultralow strain hysteresis (Hs) of 4.1% were simultaneously achieved in BT-based systems for the first time, which are among the best values ever reported on both lead-free and lead-based piezoceramics. The exceptionally high piezoelectric response is mainly from the reversible contribution, and can be ascribed to the piezoelectric anisotropy, the favorable domain configuration, and the formation of smaller sized domains in the BCTZ textured ceramics. This study paves a new pathway to develop lead-free piezoelectrics with both low strain hysteresis and high piezoelectric coefficient. More importantly, it represents a very exciting discovery with potential application of BT-based ceramics in high-precision piezoelectric actuators.

  6. Crystallographic Instrumentation

    NASA Astrophysics Data System (ADS)

    Aslanov, L. A.; Fetisov, G. V.; Howard, J. A. K.

    1998-07-01

    Innovations in crystallographic instrumentation and the rapid development of methods of diffraction measurement have led to a vast improvement in our ability to determine crystal and molecular structure. This up-to-date resource will allow the reader to harness the potential of X-ray diffraction instruments. Different sources of X-radiation used in crystallography are introduced, including synchrotron radiation, as well as a systematic review of detectors for X-rays and basic instruments for single crystal and powder diffractometry. The principles of the diffraction experiment are discussed and related to their practical application with a comparative description of different scan procedures. Diffraction data collection and processing are also reviewed and methods for error correction are described. This book will provide a useful guide for researchers and students starting in this area of science, as well as skilled crystallographers.

  7. Mechanically driven domain wall movement in magnetoelastic nanomagnets

    NASA Astrophysics Data System (ADS)

    Mathurin, Théo; Giordano, Stefano; Dusch, Yannick; Tiercelin, Nicolas; Pernod, Philippe; Preobrazhensky, Vladimir

    2016-07-01

    Magnetic domain walls are fundamental objects arising in ferromagnetic materials, largely investigated both through micromagnetic simulations and experiments. While current- and field-based techniques for inducing domain wall propagation have been widely studied for fundamental understanding and application-oriented purposes, the possibility to manipulate domain walls using mechanical stress in magnetoelastic materials has only recently drawn interest. Here, a complete analytical model describing stress-induced transverse domain wall movement in ferromagnetic nanostripe with variable cross-section is presented. This approach yields a nonlinear integro-differential equation describing the magnetization field. Its numerical implementation, based on the nonlinear relaxation method, demonstrates the possibility to precisely control the position of a domain wall through mechanical action.

  8. Purification, crystallization and preliminary crystallographic analysis of the globular domain of the human type V myosin Myo5a.

    PubMed

    Velvarska, Hana; Niessing, Dierk

    2013-11-01

    Type V myosins constitute the main cargo-transporting class of myosin motors in higher eukaryotes. They are mainly defined by their C-terminal globular domain, which is required for cargo binding as well as for motor auto-inhibition in the absence of cargo. To date, high-resolution structures only exist for globular domains from yeast. Since the majority of cellular cargoes in yeast are very different from the cargoes in higher eukaryotes, structural insights into the domain organization of globular domains from human type V myosins are important. The globular domain of human Myo5a was cloned, expressed and crystallized and data sets were collected. The crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 75.04, b = 86.70, c = 131.41 Å, α = β = γ = 90°, and diffracted with data-collection quality to 2.5 Å resolution.

  9. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the extracellular olfactomedin domain of gliomedin

    PubMed Central

    Han, Huijong; Kursula, Petri

    2014-01-01

    Gliomedin (GLDN) is one of the essential proteins in the development of the nodes of Ranvier in the vertebrate peripheral nervous system. An olfactomedin (OLF) domain is located at the GLDN extracellular C-terminus and is involved in the accumulation of neuronal plasma membrane voltage-gated sodium channels in the nodes by interacting with neurofascin and NrCAM. No structures of OLF domains have previously been reported. Here, the crystallization of the rat GLDN OLF domain, which was expressed in an insect-cell system, is reported. The crystal diffracted to 1.55 Å resolution and belonged to space group P21, with unit-cell parameters a = 37.5, b = 141.7, c = 46.0 Å, β = 110.6°, and had two molecules in the asymmetric unit. PMID:25372825

  10. Expression, purification, crystallization and preliminary X-ray crystallographic analysis of the extracellular olfactomedin domain of gliomedin.

    PubMed

    Han, Huijong; Kursula, Petri

    2014-11-01

    Gliomedin (GLDN) is one of the essential proteins in the development of the nodes of Ranvier in the vertebrate peripheral nervous system. An olfactomedin (OLF) domain is located at the GLDN extracellular C-terminus and is involved in the accumulation of neuronal plasma membrane voltage-gated sodium channels in the nodes by interacting with neurofascin and NrCAM. No structures of OLF domains have previously been reported. Here, the crystallization of the rat GLDN OLF domain, which was expressed in an insect-cell system, is reported. The crystal diffracted to 1.55 Å resolution and belonged to space group P2₁, with unit-cell parameters a=37.5, b=141.7, c=46.0 Å, β=110.6°, and had two molecules in the asymmetric unit.

  11. Purification, crystallization and preliminary X-ray crystallographic studies of the Mycobacterium tuberculosis DNA gyrase ATPase domain.

    PubMed

    Roué, Mélanie; Agrawal, Alka; Volker, Craig; Mossakowska, Danuta; Mayer, Claudine; Bax, Benjamin D

    2013-06-01

    Mycobacterium tuberculosis DNA gyrase, a nanomachine involved in the regulation of DNA topology, is the only type II topoisomerase present in this organism and hence is the sole target of fluoroquinolones in the treatment of tuberculosis. The ATPase domain provides the energy required for catalysis by ATP hydrolysis. Two constructs corresponding to this 43 kDa domain, Mtb-GyrB47(C1) and Mtb-GyrB47(C2), have been overproduced, purified and crystallized. Diffraction data were collected from three crystal forms. The crystals belonged to space groups P1 and P21 and diffracted to resolutions of 2.9 and 3.3 Å, respectively.

  12. Efficient stopping of current-driven domain wall using a local Rashba field

    NASA Astrophysics Data System (ADS)

    Tatara, Gen; Saarikoski, Henri; Mitsumata, Chiharu

    2016-10-01

    We show theoretically that a locally embedded Rashba interaction acts as a strong pinning center for current-driven domain walls and demonstrate efficient capturing and depinning of the wall using a weak Rashba interaction of the order of 0.01 eV Å. Our discovery is expected to be useful for highly reliable control of domain walls in racetrack memories.

  13. Crystallization and preliminary crystallographic characterization of the origin-binding domain of the bacteriophage λ O replication initiator

    SciTech Connect

    Struble, E. B.; Bianchet, M. A.; McMacken, R.

    2007-06-01

    Crystallization and preliminary diffraction data of the N-terminal 19–139 fragment of the origin-binding domain of bacteriophage λ O replication initiator are reported. The bacteriophage λ O protein binds to the λ replication origin (oriλ) and serves as the primary replication initiator for the viral genome. The binding energy derived from the binding of O to oriλ is thought to help drive DNA opening to facilitate initiation of DNA replication. Detailed understanding of this process is severely limited by the lack of high-resolution structures of O protein or of any lambdoid phage-encoded paralogs either with or without DNA. The production of crystals of the origin-binding domain of λ O that diffract to 2.5 Å is reported. Anomalous dispersion methods will be used to solve this structure.

  14. Preliminary X-ray crystallographic studies of the TIR domain of human Toll-like receptor 6.

    PubMed

    Jang, Tae-ho; Park, Hyun Ho

    2014-08-01

    Toll-like receptor (TLR) proteins have been identified and shown to play a role in the innate immune response. TLR6 associated with TLR2 can recognize diacylated lipoprotein. In this study, the human TLR6 TIR domain corresponding to amino acids 640-796 was overexpressed in Escherichia coli using engineered C-terminal His tags. The TLR6 TIR domain was then purified to homogeneity and crystallized at 20°C. Finally, X-ray diffraction data were collected to a resolution of 2.2 Å from a crystal belonging to space group C2, with unit-cell parameters a = 127.60, b = 44.20, c = 75.72 Å, β = 118.89°

  15. Cloning, expression, purification, crystallization and preliminary X-ray diffraction crystallographic study of human synaptotagmin 5 C2A domain.

    PubMed

    Qiu, Xiaoting; Huang, Kai; Liu, Yiwei; Zhang, Xiao; Gao, Yongxiang

    2011-11-01

    Synaptotagmin acts as the Ca(2+) sensor for neural and endocrine exocytosis. Synaptotagmin 5 has been demonstrated to play a key role in the acquisition of cathepsin D and the vesicular proton ATPase and in Ca(2+)-dependent insulin exocytosis. The C2 domains modulate the interaction of synaptotagmin with the phospholipid bilayer of the presynaptic terminus and effector proteins such as the SNARE complex. This study reports the cloning, expression in Escherichia coli, purification, crystallization and preliminary X-ray analysis of the C2A domain of human synaptotagmin 5 with an N-terminal His(6) tag. The crystals diffracted to 1.90 Å resolution and belonged to the hexagonal space group P6(5), with unit-cell parameters a = b = 93.97, c = 28.05 Å. A preliminary model of the protein structure has been built and refinement of the model is ongoing. © 2011 International Union of Crystallography. All rights reserved.

  16. Crystallization and preliminary crystallographic analysis of merohedrally twinned crystals of MJ0729, a CBS-domain protein from Methanococcus jannaschii

    PubMed Central

    Fernández-Millán, Pablo; Kortazar, Danel; Lucas, María; Martínez-Chantar, María Luz; Astigarraga, Egoitz; Fernández, José Andrés; Sabas, Olatz; Albert, Armando; Mato, Jose M.; Martínez-Cruz, Luis Alfonso

    2008-01-01

    CBS domains are small protein motifs, usually associated in tandem, that are implicated in binding to adenosyl groups. Several genetic diseases in humans have been associated with mutations in CBS sequences, which has made them very promising targets for rational drug design. Trigonal crystals of the CBS-domain protein MJ0729 from Methanococcus jannaschii were grown by the vapour-diffusion method at acidic pH. Preliminary analysis of nine X-ray diffraction data sets using Yeates statistics and Britton plots showed that slight variation in the pH as well as in the buffer used in the crystallization experiments led to crystals with different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning. PMID:18607087

  17. Current-driven periodic domain wall creation in ferromagnetic nanowires

    NASA Astrophysics Data System (ADS)

    Sitte, Matthias; Everschor-Sitte, Karin; Valet, Thierry; Rodrigues, Davi R.; Sinova, Jairo; Abanov, Ar.

    2016-08-01

    We predict the electrical generation and injection of domain walls into a ferromagnetic nanowire without the need of an assisting magnetic field. Our analytical and numerical results show that above a critical current jc domain walls are injected into the nanowire with a period T ˜(j-jc) -1 /2 . Importantly, domain walls can be produced periodically even in a simple exchange ferromagnet with uniaxial anisotropy, without requiring any standard "twisting" interaction such as Dzyaloshinskii-Moriya or dipole-dipole interactions. We show analytically that this process and the period exponents are universal and do not depend on the peculiarities of the microscopic Hamiltonian. Finally we give a specific proposal for an experimental realization.

  18. Fast Magnetic Domain-Wall Motion in a Ring-Shaped Nanowire Driven by a Voltage.

    PubMed

    Hu, Jia-Mian; Yang, Tiannan; Momeni, Kasra; Cheng, Xiaoxing; Chen, Lei; Lei, Shiming; Zhang, Shujun; Trolier-McKinstry, Susan; Gopalan, Venkatraman; Carman, Gregory P; Nan, Ce-Wen; Chen, Long-Qing

    2016-04-13

    Magnetic domain-wall motion driven by a voltage dissipates much less heat than by a current, but none of the existing reports have achieved speeds exceeding 100 m/s. Here phase-field and finite-element simulations were combined to study the dynamics of strain-mediated voltage-driven magnetic domain-wall motion in curved nanowires. Using a ring-shaped, rough-edged magnetic nanowire on top of a piezoelectric disk, we demonstrate a fast voltage-driven magnetic domain-wall motion with average velocity up to 550 m/s, which is comparable to current-driven wall velocity. An analytical theory is derived to describe the strain dependence of average magnetic domain-wall velocity. Moreover, one 180° domain-wall cycle around the ring dissipates an ultrasmall amount of heat, as small as 0.2 fJ, approximately 3 orders of magnitude smaller than those in current-driven cases. These findings suggest a new route toward developing high-speed, low-power-dissipation domain-wall spintronics.

  19. Nonstationary current-driven dynamics of vortex domain walls in films with in-plane anisotropy

    NASA Astrophysics Data System (ADS)

    Dubovik, M. N.; Filippov, B. N.; Korzunin, L. G.

    2017-02-01

    Micromagnetic simulation of a current-driven vortex domain wall motion in a film with in-plane anisotropy was carried out. The current density values j >jc were considered corresponding to the nonstationary motion, with the domain wall structure dynamic transformation occurred. A nonlinear dependence of the jc value on the film thickness was obtained. The nonstationary motion regime existence restricted the possibility to increase the domain wall velocity by increasing j and decreasing the damping parameter.

  20. AC driven magnetic domain quantification with 5 nm resolution

    NASA Astrophysics Data System (ADS)

    Li, Zhenghua; Li, Xiang; Dong, Dapeng; Liu, Dongping; Saito, H.; Ishio, S.

    2014-07-01

    As the magnetic storage density increases in commercial products, e.g. the hard disc drives, a full understanding of dynamic magnetism in nanometer resolution underpins the development of next-generation products. Magnetic force microscopy (MFM) is well suited to exploring ferromagnetic domain structures. However, atomic resolution cannot be achieved because data acquisition involves the sensing of long-range magnetostatic forces between tip and sample. Moreover, the dynamic magnetism cannot be characterized because MFM is only sensitive to the static magnetic fields. Here, we develop a side-band magnetic force microscopy (MFM) to locally observe the alternating magnetic fields in nanometer length scales at an operating distance of 1 nm. Variations in alternating magnetic fields and their relating time-variable magnetic domain reversals have been demonstrated by the side-band MFM. The magnetic domain wall motions, relating to the periodical rotation of sample magnetization, are quantified via micromagnetics. Based on the side-band MFM, the magnetic moment can be determined locally in a volume as small as 5 nanometers. The present technique can be applied to investigate the microscopic magnetic domain structures in a variety of magnetic materials, and allows a wide range of future applications, for example, in data storage and biomedicine.

  1. Detection of current-driven magnetic domains in [Co/Pd] nanowire by tunneling magnetoresistive sensor

    NASA Astrophysics Data System (ADS)

    Okuda, Mitsunobu; Miyamoto, Yasuyoshi; Miyashita, Eiichi; Saito, Nobuo; Hayashi, Naoto; Nakagawa, Shigeki

    2015-05-01

    Current-driven magnetic domain walls in magnetic nanowires have attracted a great deal of interest in terms of both physical studies and engineering applications. The anomalous Hall effect measurement is widely used for detecting the magnetization direction of current-driven magnetic domains in a magnetic nanowire. However, the problem with this measurement is that the detection point for current-driven domain wall motion is fixed at only the installed sensing wire across the specimen nanowire. A potential solution is the magnetic domain scope method, whereby the distribution of the magnetic flux leaking from the specimen can be analyzed directly by contact-scanning a tunneling magnetoresistive field sensor on a sample. In this study, we fabricated specimen nanowires consisting of [Co (0.3)/Pd (1.2)]21/Ta(3) films (units in nm) with perpendicular magnetic anisotropy on Si substrates. A tunneling magnetoresistive sensor was placed on the nanowire surface and a predetermined current pulse was applied. Real-time detection of the current-driven magnetic domain motion was successful in that the resistance of the tunneling magnetoresistive sensor was changed with the magnetization direction beneath the sensor. This demonstrates that magnetic domain detection using a tunneling magnetoresistive sensor is effective for the direct analysis of micro magnetic domain motion.

  2. Crystallization and preliminary crystallographic analysis of the transpeptidase domain of penicillin-binding protein 2B from Streptococcus pneumoniae

    SciTech Connect

    Yamada, Mototsugu Watanabe, Takashi; Baba, Nobuyoshi; Miyara, Takako; Saito, Jun; Takeuchi, Yasuo

    2008-04-01

    The selenomethionyl-substituted transpeptidase domain of penicillin-binding protein (PBP) 2B from S. pneumoniae was isolated from a limited proteolysis digest of the soluble form of recombinant PBP 2B and then crystallized. MAD data were collected to 2.4 Å resolution. Penicillin-binding protein (PBP) 2B from Streptococcus pneumoniae catalyzes the cross-linking of peptidoglycan precursors that occurs during bacterial cell-wall biosynthesis. A selenomethionyl (SeMet) substituted PBP 2B transpeptidase domain was isolated from a limited proteolysis digest of a soluble form of recombinant PBP 2B and then crystallized. The crystals belonged to space group P4{sub 3}2{sub 1}2, with unit-cell parameters a = b = 86.39, c = 143.27 Å. Diffraction data were collected to 2.4 Å resolution using the BL32B2 beamline at SPring-8. The asymmetric unit contains one protein molecule and 63.7% solvent.

  3. Crystallization and preliminary crystallographic characterization of the origin-binding domain of the bacteriophage λ O replication initiator

    PubMed Central

    Struble, E. B.; Gittis, A. G.; Bianchet, M. A.; McMacken, R.

    2007-01-01

    The bacteriophage λ O protein binds to the λ replication origin (oriλ) and serves as the primary replication initiator for the viral genome. The binding energy derived from the binding of O to oriλ is thought to help drive DNA opening to facilitate initiation of DNA replication. Detailed understanding of this process is severely limited by the lack of high-resolution structures of O protein or of any lambdoid phage-encoded paralogs either with or without DNA. The production of crystals of the origin-binding domain of λ O that diffract to 2.5 Å is reported. Anomalous dispersion methods will be used to solve this structure. PMID:17554183

  4. Crystallization and preliminary X-ray crystallographic analysis of the extracellular domain of LePRK2 from Lycopersicon esculentum.

    PubMed

    Xu, Anbi; Huang, Laiqiang

    2014-02-01

    The tomato (Lycopersicon esculentum) pollen-specific receptor kinase 2 (LePRK2) is a member of the large receptor-like kinase (RLK) family and is expressed specifically in mature pollen and pollen tubes in L. esculentum. Like other RLKs, LePRK2 contains a characteristic N-terminal leucine-rich repeat (LRR) extracellular domain, the primary function of which is in protein-protein interactions. The LePRK2 LRR is likely to bind candidate ligands from the external environment, leading to a signal transduction cascade required for successful pollination. LePRK2-LRR was purified using an insect-cell secretion expression system and was crystallized using the vapour-diffusion method. The crystals diffracted to a resolution of 2.50 Å and belonged to space group I4(1)22, with unit-cell parameters a = b = 93.94, c = 134.44 Å and one molecule per asymmetric unit.

  5. Rashba Torque Driven Domain Wall Motion in Magnetic Helices.

    PubMed

    Pylypovskyi, Oleksandr V; Sheka, Denis D; Kravchuk, Volodymyr P; Yershov, Kostiantyn V; Makarov, Denys; Gaididei, Yuri

    2016-03-24

    Manipulation of the domain wall propagation in magnetic wires is a key practical task for a number of devices including racetrack memory and magnetic logic. Recently, curvilinear effects emerged as an efficient mean to impact substantially the statics and dynamics of magnetic textures. Here, we demonstrate that the curvilinear form of the exchange interaction of a magnetic helix results in an effective anisotropy term and Dzyaloshinskii-Moriya interaction with a complete set of Lifshitz invariants for a one-dimensional system. In contrast to their planar counterparts, the geometrically induced modifications of the static magnetic texture of the domain walls in magnetic helices offer unconventional means to control the wall dynamics relying on spin-orbit Rashba torque. The chiral symmetry breaking due to the Dzyaloshinskii-Moriya interaction leads to the opposite directions of the domain wall motion in left- or right-handed helices. Furthermore, for the magnetic helices, the emergent effective anisotropy term and Dzyaloshinskii-Moriya interaction can be attributed to the clear geometrical parameters like curvature and torsion offering intuitive understanding of the complex curvilinear effects in magnetism.

  6. Rashba Torque Driven Domain Wall Motion in Magnetic Helices

    PubMed Central

    Pylypovskyi, Oleksandr V.; Sheka, Denis D.; Kravchuk, Volodymyr P.; Yershov, Kostiantyn V.; Makarov, Denys; Gaididei, Yuri

    2016-01-01

    Manipulation of the domain wall propagation in magnetic wires is a key practical task for a number of devices including racetrack memory and magnetic logic. Recently, curvilinear effects emerged as an efficient mean to impact substantially the statics and dynamics of magnetic textures. Here, we demonstrate that the curvilinear form of the exchange interaction of a magnetic helix results in an effective anisotropy term and Dzyaloshinskii–Moriya interaction with a complete set of Lifshitz invariants for a one-dimensional system. In contrast to their planar counterparts, the geometrically induced modifications of the static magnetic texture of the domain walls in magnetic helices offer unconventional means to control the wall dynamics relying on spin-orbit Rashba torque. The chiral symmetry breaking due to the Dzyaloshinskii–Moriya interaction leads to the opposite directions of the domain wall motion in left- or right-handed helices. Furthermore, for the magnetic helices, the emergent effective anisotropy term and Dzyaloshinskii–Moriya interaction can be attributed to the clear geometrical parameters like curvature and torsion offering intuitive understanding of the complex curvilinear effects in magnetism. PMID:27008975

  7. High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D

    SciTech Connect

    Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin; Buchko, Garry W.; Robinson, Howard; Varnum, Susan M.

    2010-12-01

    Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level with high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 Å resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 Å, b = 89.7 Å, c = 93.9 Å. Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.

  8. Crystallization and preliminary crystallographic analysis of an esterase with a novel domain from the hyperthermophile Thermotoga maritima

    SciTech Connect

    Sun, Lei; Levisson, Mark; Hendriks, Sjon; Akveld, Twan; Kengen, Servé W. M.; Dijkstra, Bauke W.; Oost, John van der

    2007-09-01

    A thermostable esterase (EstA) from Thermotoga maritima was cloned and purified. Crystals of EstA and its selenomethionine derivative were grown and diffract to beyond 2.6 Å resolution at 100 K using synchrotron radiation. A predicted esterase (EstA) with an unusual new domain from the hyperthermophilic bacterium Thermotoga maritima has been cloned and overexpressed in Escherichia coli. The purified protein was crystallized by the hanging-drop vapour-diffusion technique in the presence of lithium sulfate and polyethylene glycol 8000. Selenomethionine-substituted EstA crystals were obtained under the same conditions and three different-wavelength data sets were collected to 2.6 Å resolution. The crystal belongs to space group H32, with unit-cell parameters a = b = 130.2, c = 306.2 Å. There are two molecules in the asymmetric unit, with a V{sub M} of 2.9 Å{sup 3} Da{sup −1} and 58% solvent content.

  9. Crystallization and preliminary X-ray crystallographic analysis of the extracellular domain of LePRK2 from Lycopersicon esculentum

    PubMed Central

    Xu, Anbi; Huang, Laiqiang

    2014-01-01

    The tomato (Lycopersicon esculentum) pollen-specific receptor kinase 2 (LePRK2) is a member of the large receptor-like kinase (RLK) family and is expressed specifically in mature pollen and pollen tubes in L. esculentum. Like other RLKs, LePRK2 contains a characteristic N-terminal leucine-rich repeat (LRR) extracellular domain, the primary function of which is in protein–protein interactions. The LePRK2 LRR is likely to bind candidate ligands from the external environment, leading to a signal transduction cascade required for successful pollination. LePRK2-LRR was purified using an insect-cell secretion expression system and was crystallized using the vapour-diffusion method. The crystals diffracted to a resolution of 2.50 Å and belonged to space group I4122, with unit-cell parameters a = b = 93.94, c = 134.44 Å and one molecule per asymmetric unit. PMID:24637765

  10. UXDs-Driven Transferring Method from TRIZ Solution to Domain Solution

    NASA Astrophysics Data System (ADS)

    Ma, Lihui; Cao, Guozhong; Chang, Yunxia; Wei, Zihui; Ma, Kai

    The translation process from TRIZ solutions to domain solutions is an analogy-based process. TRIZ solutions, such as 40 inventive principles and the related cases, are medium-solutions for domain problems. Unexpected discoveries (UXDs) are the key factors to trigger designers to generate new ideas for domain solutions. The Algorithm of UXD resolving based on Means-Ends Analysis(MEA) is studied and an UXDs-driven transferring method from TRIZ solution to domain solution is formed. A case study shows the application of the process.

  11. Electric-field-driven dynamics of magnetic domain walls in magnetic nanowires patterned on ferroelectric domains

    NASA Astrophysics Data System (ADS)

    Van de Wiele, Ben; Leliaert, Jonathan; Franke, Kévin J. A.; van Dijken, Sebastiaan

    2016-03-01

    Strong coupling of magnetic domain walls onto straight ferroelastic boundaries of a ferroelectric layer enables full and reversible electric-field control of magnetic domain wall motion. In this paper, the dynamics of this new driving mechanism is analyzed using micromagnetic simulations. We show that transverse domain walls with a near-180° spin structure are stabilized in magnetic nanowires and that electric fields can move these walls with high velocities. Above a critical velocity, which depends on material parameters, nanowire geometry and the direction of domain wall motion, the magnetic domain walls depin abruptly from the ferroelastic boundaries. Depinning evolves either smoothly or via the emission and annihilation of a vortex or antivortex core (Walker breakdown). In both cases, the magnetic domain wall slows down after depinning in an oscillatory fashion and eventually comes to a halt. The simulations provide design rules for hybrid ferromagnetic-ferroelectric domain-wall-based devices and indicate that material disorder and structural imperfections only influence Walker-breakdown-like depinning at high domain wall velocities.

  12. Current-driven domain wall depinning from an anisotropy boundary in nanowires.

    PubMed

    Gerhardt, T; Drews, A; Meier, G

    2014-05-21

    The interaction of a current-driven domain wall with an anisotropy boundary in nanowires with perpendicular magnetic anisotropy is investigated. A local reduction of the anisotropy constant is used to create an artificial boundary where the domain wall gets pinned. Micromagnetic simulations and analytical calculations, based on a one-dimensional model, are employed to describe the interaction of the domain wall and the anisotropy boundary and to determine the depinning current densities. Two different pinning regimes-an intrinsic and an extrinsic-can be identified in dependence with the characteristic of the boundary. A very good agreement between simulated and analytically obtained data is achieved.

  13. Electric-field-driven domain wall dynamics in perpendicularly magnetized multilayers

    NASA Astrophysics Data System (ADS)

    López González, Diego; Shirahata, Yasuhiro; Van de Wiele, Ben; Franke, Kévin J. A.; Casiraghi, Arianna; Taniyama, Tomoyasu; van Dijken, Sebastiaan

    2017-03-01

    We report on reversible electric-field-driven magnetic domain wall motion in a Cu/Ni multilayer on a ferroelectric BaTiO3 substrate. In our heterostructure, strain-coupling to ferroelastic domains with in-plane and perpendicular polarization in the BaTiO3 substrate causes the formation of domains with perpendicular and in-plane magnetic anisotropy, respectively, in the Cu/Ni multilayer. Walls that separate magnetic domains are elastically pinned onto ferroelectric domain walls. Using magneto-optical Kerr effect microscopy, we demonstrate that out-of-plane electric field pulses across the BaTiO3 substrate move the magnetic and ferroelectric domain walls in unison. Our experiments indicate an exponential increase of domain wall velocity with electric field strength and opposite domain wall motion for positive and negative field pulses. The application of a magnetic field does not affect the velocity of magnetic domain walls, but independently tailors their internal spin structure, causing a change in domain wall dynamics at high velocities.

  14. Current-driven magnetic domain wall motion and its real-time detection

    NASA Astrophysics Data System (ADS)

    Kim, Kab-Jin; Yoshimura, Yoko; Ono, Teruo

    2017-08-01

    Current-controlled magnetic domain wall motion has opened the possibility of a novel type of shift register memory device, which has been optimistically predicted to replace existing magnetic memories. Owing to this promising prospect, intensive work has been carried out during the last few decades. In this article, we first review the progress in the study of current-induced magnetic domain wall motion. Underlying mechanisms behind the domain wall motion, which have been discovered during last few decades, as well as technological achievements are presented. We then present our recent experimental results on the real-time detection of current-driven multiple magnetic domain wall motion, which directly demonstrates the operation of a magnetic domain wall shift register.

  15. The macro domain as fusion tag for carrier-driven crystallization.

    PubMed

    Wild, Rebekka; Hothorn, Michael

    2017-02-01

    Obtaining well-ordered crystals remains a significant challenge in protein X-ray crystallography. Carrier-driven crystallization can facilitate crystal formation and structure solution of difficult target proteins. We obtained crystals of the small and highly flexible SPX domain from the yeast vacuolar transporter chaperone 4 (Vtc4) when fused to a C-terminal, non-cleavable macro tag derived from human histone macroH2A1.1. Initial crystals diffracted to 3.3 Å resolution. Reductive protein methylation of the fusion protein yielded a new crystal form diffracting to 2.1 Å. The structures were solved by molecular replacement, using isolated macro domain structures as search models. Our findings suggest that macro domain tags can be employed in recombinant protein expression in E. coli, and in carrier-driven crystallization.

  16. Current-Driven Motion of Magnetic Domain Wall with Many Bloch Lines

    NASA Astrophysics Data System (ADS)

    Iwasaki, Junichi; Nagaosa, Naoto

    2015-08-01

    The current-driven motion of a domain wall (DW) in a ferromagnet with many Bloch lines (BLs) via the spin transfer torque is studied theoretically. It is found that the motion of BLs changes the current-velocity (j-v) characteristic considerably. In particular, the critical current density for overcoming the pinning force is even lower than that of a skyrmion by the factor of the Gilbert damping coefficient α. This is in sharp contrast to the case of magnetic-field-driven motion, where the existence of BLs reduces the mobility of the DW.

  17. Current-driven vortex domain wall motion in wire-tube nanostructures

    SciTech Connect

    Espejo, A. P.; Vidal-Silva, N.; López-López, J. A.; Goerlitz, D.; Nielsch, K.; Escrig, J.

    2015-03-30

    We have investigated the current-driven domain wall motion in nanostructures comprised of a pair of nanotube and nanowire segments. Under certain values of external magnetic fields, it is possible to pin a vortex domain wall in the transition zone between the wire and tube segments. We explored the behavior of this domain wall under the action of an electron flow applied in the opposite direction to the magnetic field. Thus, for a fixed magnetic field, it is possible to release a domain wall pinned simply by increasing the intensity of the current density, or conversely, for a fixed current density, it is possible to release the domain wall simply decreasing the magnetic external field. When the domain wall remains pinned due to the competition between the current density and the magnetic external field, it exhibits a oscillation frequency close to 8 GHz. The amplitude of the oscillations increases with the current density and decreases over time. On the other hand, when the domain wall is released and propagated through the tube segment, this shows the standard separation between a steady and a precessional regime. The ability to pin and release a domain wall by varying the geometric parameters, the current density, or the magnetic field transforms these wire-tube nanostructures in an interesting alternative as an on/off switch nano-transistor.

  18. Current driven domain wall motion in rare-earth transition metal alloys with perpendicular magnetic anisotropy.

    PubMed

    Li, Songtian; Liu, Xiaoxi; Morisako, Akimistu

    2012-09-01

    The domain wall movement behaviors under current combining with magnetic field in perpendicularly magnetized TbFeCo wire were studied by a polar magneto-optical Kerr effect microscope. The velocity for domain wall creeping along electrons flowing direction was found to be apparently higher than that of domain wall creeping against electrons flowing, which is the signature of the spin transfer torque effect. By employing the modified field-driven creep motion law, a spin transfer efficiency of 2.7 Oe cm2/10(6) A was determined for TbFeCo wire by treating the spin transfer torque as an effective field adding to the external field. The high spin transfer efficiency suggests that perpendicularly magnetized system with sharp domain walls in TbFeCo film shows high superiorities for applications in spin transfer torque based devices compared with in-plane magnetized systems.

  19. Annealing effect on current-driven domain wall motion in Pt/[Co/Ni] wire

    NASA Astrophysics Data System (ADS)

    Furuta, Masaki; Liu, Yang; Sepehri-Amin, Hossein; Hono, Kazuhiro; Zhu, Jian-Gang Jimmy

    2017-09-01

    The annealing effect on the efficiency of current-driven domain wall motion governed by the spin Hall effect in perpendicularly magnetized Pt/[Co/Ni] wires is investigated experimentally. Important physical parameters, such as the Dzyaloshinskii-Moriya Interaction (DMI), spin Hall angle, and perpendicular anisotropy field strength, for the domain wall motion are all characterized at each annealing temperature. It is found that annealing of wires at temperatures over 120 °C causes significant reduction of the domain wall velocity. Energy dispersive X-ray spectroscopy analysis shows pronounced Co diffusion across the Pt/Co interface resulted from annealing at relatively high temperatures. The combined modeling study shows that the reduction of DMI caused by annealing is mostly responsible for the domain wall velocity reduction due to annealing.

  20. Universal Pinning Energy Barrier for Driven Domain Walls in Thin Ferromagnetic Films

    NASA Astrophysics Data System (ADS)

    Jeudy, V.; Mougin, A.; Bustingorry, S.; Savero Torres, W.; Gorchon, J.; Kolton, A. B.; Lemaître, A.; Jamet, J.-P.

    2016-07-01

    We report a comparative study of magnetic field driven domain wall motion in thin films made of different magnetic materials for a wide range of field and temperature. The full thermally activated creep motion, observed below the depinning threshold, is shown to be described by a unique universal energy barrier function. Our findings should be relevant for other systems whose dynamics can be modeled by elastic interfaces moving on disordered energy landscapes.

  1. Universal Pinning Energy Barrier for Driven Domain Walls in Thin Ferromagnetic Films.

    PubMed

    Jeudy, V; Mougin, A; Bustingorry, S; Savero Torres, W; Gorchon, J; Kolton, A B; Lemaître, A; Jamet, J-P

    2016-07-29

    We report a comparative study of magnetic field driven domain wall motion in thin films made of different magnetic materials for a wide range of field and temperature. The full thermally activated creep motion, observed below the depinning threshold, is shown to be described by a unique universal energy barrier function. Our findings should be relevant for other systems whose dynamics can be modeled by elastic interfaces moving on disordered energy landscapes.

  2. Terahertz Time-Domain Spectroscopy System Driven by a Monolithic Semiconductor Laser

    NASA Astrophysics Data System (ADS)

    Merghem, K.; Busch, S. F.; Lelarge, F.; Koch, M.; Ramdane, A.; Balzer, J. C.

    2017-08-01

    A fiber coupled terahertz time-domain spectroscopy (THz TDS) system which is driven by a pulsed monolithic semiconductor laser is presented. A bandwidth of over 0.6 THz with a signal to noise ratio (SNR) of 45 dB has been achieved at a wavelength of 1550 nm. This concept could pave the way towards ultra-compact and low-cost THz TDS systems.

  3. Asymmetric driven dynamics of Dzyaloshinskii domain walls in ultrathin ferromagnetic strips with perpendicular magnetic anisotropy

    NASA Astrophysics Data System (ADS)

    Sánchez-Tejerina, L.; Alejos, Ó.; Martínez, E.; Muñoz, J. M.

    2016-07-01

    The dynamics of domain walls in ultrathin ferromagnetic strips with perpendicular magnetic anisotropy is studied from both numerical and analytical micromagnetics. The influence of a moderate interfacial Dzyaloshinskii-Moriya interaction associated to a bi-layer strip arrangement has been considered, giving rise to the formation of Dzyaloshinskii domain walls. Such walls possess under equilibrium conditions an inner magnetization structure defined by a certain orientation angle that make them to be considered as intermediate configurations between Bloch and Néel walls. Two different dynamics are considered, a field-driven and a current-driven dynamics, in particular, the one promoted by the spin torque due to the spin-Hall effect. Results show an inherent asymmetry associated with the rotation of the domain wall magnetization orientation before reaching the stationary regime, characterized by a constant terminal speed. For a certain initial DW magnetization orientation at rest, the rotation determines whether the reorientation of the DW magnetization prior to reach stationary motion is smooth or abrupt. This asymmetry affects the DW motion, which can even reverse for a short period of time. Additionally, it is found that the terminal speed in the case of the current-driven dynamics may depend on either the initial DW magnetization orientation at rest or the sign of the longitudinally injected current.

  4. Secretion of the Intimin Passenger Domain Is Driven by Protein Folding*

    PubMed Central

    Leo, Jack C.; Oberhettinger, Philipp; Yoshimoto, Shogo; Udatha, D. B. R. K. Gupta; Morth, J. Preben; Schütz, Monika; Hori, Katsutoshi

    2016-01-01

    Intimin is an essential adhesin of attaching and effacing organisms such as entropathogenic Escherichia coli. It is also the prototype of type Ve secretion or inverse autotransport, where the extracellular C-terminal region or passenger is exported with the help of an N-terminal transmembrane β-barrel domain. We recently reported a stalled secretion intermediate of intimin, where the passenger is located in the periplasm but the β-barrel is already inserted into the membrane. Stalling of this mutant is due to the insertion of an epitope tag at the very N terminus of the passenger. Here, we examined how this insertion disrupts autotransport and found that it causes misfolding of the N-terminal immunoglobulin (Ig)-like domain D00. We could also stall the secretion by making an internal deletion in D00, and introducing the epitope tag into the second Ig-like domain, D0, also resulted in reduced passenger secretion. In contrast to many classical autotransporters, where a proximal folding core in the passenger is required for secretion, the D00 domain is dispensable, as the passenger of an intimin mutant lacking D00 entirely is efficiently exported. Furthermore, the D00 domain is slightly less stable than the D0 and D1 domains, unfolding at ∼200 piconewtons (pN) compared with ∼250 pN for D0 and D1 domains as measured by atomic force microscopy. Our results support a model where the secretion of the passenger is driven by sequential folding of the extracellular Ig-like domains, leading to vectorial transport of the passenger domain across the outer membrane in an N to C direction. PMID:27466361

  5. Field driven ferromagnetic phase evolution originating from the domain boundaries in antiferromagnetically coupled perpendicular anitsotropy films

    SciTech Connect

    Jones, Juanita; Hauet, Thomas; Gunther, Christian; Hovorka, Ondrej; Berger, Andreas; Im, Mi-Young; Fischer, Peter; Hellwig, Olav

    2008-05-01

    Strong perpendicular anisotropy systems consisting of Co/Pt multilayer stacks that are antiferromagnetically coupled via thin Ru or NiO layers have been used as model systems to study the competition between local interlayer exchange and long-range dipolar interactions [1,2]. Magnetic Force Microscopy (MFM) studies of such systems reveal complex magnetic configurations with a mix of antiferromagnetic (AF) and ferromagnetic (FM) phases. However, MFM allows detecting surface stray fields only and can interact strongly with the magnetic structure of the sample, thus altering the original domain configuration of interest [3,4]. In the current study they combine magnetometry and state-of-the-art soft X-ray transmission microscopy (MXTM) to investigate the external field driven FM phase evolution originating from the domain boundaries in such antiferromagnetically coupled perpendicular anisotropy films. MXTM allows directly imaging the perpendicular component of the magnetization in an external field at sub 100 nm spatial resolution without disturbing the magnetic state of the sample [5,6]. Here they compare the domain evolution for two similar [Co(4{angstrom})/Pt(7{angstrom})]x-1/{l_brace}Co(4{angstrom})/Ru(9{angstrom})/[Co(4{angstrom})/Pt(7{angstrom})]x-1{r_brace}16 samples with slightly different Co/Pt stack thickness, i.e. slightly different strength of internal dipolar fields. After demagnetization they obtain AF domains with either sharp AF domain walls for the thinner multilayer stacks or 'tiger-tail' domain walls (one dimensional FM phase) for the thicker stacks. When increasing the external field strength the sharp domain walls in the tinner stack sample transform into the one-dimensional FM phase, which then serves as nucleation site for further FM stripe domains that spread out into all directions to drive the system towards saturation. Energy calculations reveal the subtle difference between the two samples and help to understand the observed transition, when

  6. Activity-Centered Domain Characterization for Problem-Driven Scientific Visualization.

    PubMed

    Marai, G Elisabeta

    2017-08-29

    Although visualization design models exist in the literature in the form of higher-level methodological frameworks, these models do not present a clear methodological prescription for the domain characterization step. This work presents a framework and end-to-end model for requirements engineering in problem-driven visualization application design. The framework and model are based on the activity-centered design paradigm, which is an enhancement of human-centered design. The proposed activity-centered approach focuses on user tasks and activities, and allows an explicit link between the requirements engineering process with the abstraction stage-and its evaluation-of existing, higher-level visualization design models. In a departure from existing visualization design models, the resulting model: assigns value to a visualization based on user activities; ranks user tasks before the user data; partitions requirements in activity-related capabilities and nonfunctional characteristics and constraints; and explicitly incorporates the user workflows into the requirements process. A further merit of this model is its explicit integration of functional specifications, a concept this work adapts from the software engineering literature, into the visualization design nested model. A quantitative evaluation using two sets of interdisciplinary projects supports the merits of the activity-centered model. The result is a practical roadmap to the domain characterization step of visualization design for problem-driven data visualization. Following this domain characterization model can help remove a number of pitfalls that have been identified multiple times in the visualization design literature.

  7. Domain-size statistics in the time-dependent Ginzburg-Landau equation driven by a dichotomous Markov noise.

    PubMed

    Ouchi, Katsuya; Tsukamoto, Naofumi; Horita, Takehiko; Fujisaka, Hirokazu

    2007-10-01

    The domain dynamics of magnetization obeying the time-dependent Ginzburg-Landau equation driven by a dichotomous Markov noise is discussed. The system with various domain sizes in the early stage temporally evolves following an annihilation of neighboring domain walls, where each domain wall moves diffusively. Three statistics on the domain size, i.e., average domain size, the ensemble average of the domain size distribution function, and the spatial power spectrum of the magnetization, are evaluated to characterize the domain wall annihilation process. A phenomenological evolution equation for the domain-size distribution function is constructed by simplifying the annihilation process of the domain wall appropriately, and the underlying mechanism of those statistics is investigated.

  8. Field-driven Domain Wall Motion in Ferromagnetic Nanowires with Bulk Dzyaloshinskii-Moriya Interaction

    NASA Astrophysics Data System (ADS)

    Zhuo, Fengjun; Sun, Z. Z.

    2016-04-01

    Field-driven domain wall (DW) motion in ferromagnetic nanowires with easy- and hard-axis anisotropies was studied theoretically and numerically in the presence of the bulk Dzyaloshinskii-Moriya interaction (DMI) based on the Landau-Lifshitz-Gilbert equation. We propose a new trial function and offer an exact solution for DW motion along a uniaxial nanowire driven by an external magnetic field. A new strategy was suggested to speed up DW motion in a uniaxial magnetic nanowire with large DMI parameters. In the presence of hard-axis anisotropy, we find that the breakdown field and velocity of DW motion was strongly affected by the strength and sign of the DMI parameter under external fields. This work may be useful for future magnetic information storage devices based on DW motion.

  9. Field-driven Domain Wall Motion in Ferromagnetic Nanowires with Bulk Dzyaloshinskii-Moriya Interaction

    PubMed Central

    Zhuo, Fengjun; Sun, Z. Z.

    2016-01-01

    Field-driven domain wall (DW) motion in ferromagnetic nanowires with easy- and hard-axis anisotropies was studied theoretically and numerically in the presence of the bulk Dzyaloshinskii-Moriya interaction (DMI) based on the Landau-Lifshitz-Gilbert equation. We propose a new trial function and offer an exact solution for DW motion along a uniaxial nanowire driven by an external magnetic field. A new strategy was suggested to speed up DW motion in a uniaxial magnetic nanowire with large DMI parameters. In the presence of hard-axis anisotropy, we find that the breakdown field and velocity of DW motion was strongly affected by the strength and sign of the DMI parameter under external fields. This work may be useful for future magnetic information storage devices based on DW motion. PMID:27118064

  10. Field-driven Domain Wall Motion in Ferromagnetic Nanowires with Bulk Dzyaloshinskii-Moriya Interaction.

    PubMed

    Zhuo, Fengjun; Sun, Z Z

    2016-04-27

    Field-driven domain wall (DW) motion in ferromagnetic nanowires with easy- and hard-axis anisotropies was studied theoretically and numerically in the presence of the bulk Dzyaloshinskii-Moriya interaction (DMI) based on the Landau-Lifshitz-Gilbert equation. We propose a new trial function and offer an exact solution for DW motion along a uniaxial nanowire driven by an external magnetic field. A new strategy was suggested to speed up DW motion in a uniaxial magnetic nanowire with large DMI parameters. In the presence of hard-axis anisotropy, we find that the breakdown field and velocity of DW motion was strongly affected by the strength and sign of the DMI parameter under external fields. This work may be useful for future magnetic information storage devices based on DW motion.

  11. Domain-driven specification techniques simplify the analysis of requirements for the Kaon Factory central control system

    NASA Astrophysics Data System (ADS)

    Inwood, Clifford; Ludgate, G. A.; Dohan, D. A.; Osberg, E. A.; Koscielniak, S.

    1990-08-01

    Domain-driven modelling, outlined in this paper, has been successfully applied to the analysis, specification and design of the KAON Factory central control system (KF-CCS). This advanced object-oriented technique is especially suited to the development of complex systems. Early in the project, four very natural domains were identified which simplified the analysis of requirements.

  12. Piezoelectric control of the mobility of a domain wall driven by adiabatic and non-adiabatic torques.

    PubMed

    De Ranieri, E; Roy, P E; Fang, D; Vehsthedt, E K; Irvine, A C; Heiss, D; Casiraghi, A; Campion, R P; Gallagher, B L; Jungwirth, T; Wunderlich, J

    2013-09-01

    The rich internal degrees of freedom of magnetic domain walls make them an attractive complement to electron charge for exploring new concepts of storage, transport and processing of information. Here we use the tunable internal structure of a domain wall in a perpendicularly magnetized GaMnAsP/GaAs ferromagnetic semiconductor and demonstrate devices in which piezoelectrically controlled magnetic anisotropy yields up to 500% mobility variations for an electrical-current-driven domain wall. We observe current-induced domain wall motion over a wide range of current-pulse amplitudes and report a direct observation and the piezoelectric control of the Walker breakdown separating two regimes with different mobilities. Our work demonstrates that in spin-orbit-coupled ferromagnets with weak extrinsic domain wall pinning, the piezoelectric control allows one to experimentally assess the upper and lower boundaries of the characteristic ratio of adiabatic and non-adiabatic spin-transfer torques in the current-driven domain wall motion.

  13. Effect of Joule heating in current-driven domain wall motion

    NASA Astrophysics Data System (ADS)

    Yamaguchi, A.; Nasu, S.; Tanigawa, H.; Ono, T.; Miyake, K.; Mibu, K.; Shinjo, T.

    2005-01-01

    It was found that high current density needed for the current-driven domain wall motion results in the Joule heating of the sample. The sample temperature, when the current-driven domain wall motion occurred, was estimated by measuring the sample resistance during the application of a pulsed current. The sample temperature was 750 K for the threshold current density of 6.7×1011A/m2 in a 10-nm-thick Ni81Fe19 wire with a width of 240 nm on thermally oxidized silicon substrate. The temperature was raised to 830 K for the current density of 7.5×1011A/m2, which is very close to the Curie temperature of bulk Ni81Fe19. When the current density exceeded 7.5×1011A/m2, an appearance of a multidomain structure in the wire was observed by magnetic force microscopy, suggesting that the sample temperature exceeded the Curie temperature.

  14. Temperature-driven growth of antiferromagnetic domains in thin-film FeRh.

    PubMed

    Baldasseroni, C; Bordel, C; Antonakos, C; Scholl, A; Stone, K H; Kortright, J B; Hellman, F

    2015-07-01

    The evolution of the antiferromagnetic phase across the temperature-driven ferromagnetic (FM) to antiferromagnetic (AF) phase transition in epitaxial FeRh thin films was studied by x-ray magnetic linear and circular dichroism (XMLD and XMCD) and photoemission electron microscopy. By comparing XMLD and XMCD images recorded at the same temperature, the AF phase was identified, its structure directly imaged, and its evolution studied across the transition. A quantitative analysis of the correlation length of the images shows differences between the characteristic length scale of the two phases with the AF phase having a finer feature size. The asymmetry of the transition from FM to AF upon cooling and AF-FM upon heating is evidenced: upon cooling the formation of AF phase is dominated by nucleation at defects, with little subsequent growth, resulting in a small and non-random final AF domain structure, while upon heating, heterogeneous nucleation at different sites followed by significant domain size growth of the FM phase is observed, resulting in a non-reproducible final FM large domain structure.

  15. Current-driven domain wall motion enhanced by the microwave field

    SciTech Connect

    Wang, Xi-guang; Guo, Guang-hua Nie, Yao-zhuang; Wang, Dao-wei; Li, Zhi-xiong; Tang, Wei; Zeng, Zhong-ming

    2014-07-14

    The magnetic domain wall (DW) motion driven by a spin-polarized current opens a new concept for memory and logic devices. However, the critical current density required to overcome the intrinsic and/or extrinsic pinning of DW remains too large for practical applications. Here, we show, by using micromagnetic simulations and analytical approaches, that the application of a microwave field offers an effective solution to this problem. When a transverse microwave field is applied, the adiabatic spin-transfer torque (STT) alone can sustain a steady-state DW motion without the sign of Walker breakdown, meaning that the intrinsic pinning disappears. The extrinsic pinning can also be effectively reduced. Moreover, the DW velocity is increased greatly for the microwave-assisted DW motion. This provides a new way to manipulate the DW motion at low current densities.

  16. Ring-shaped Racetrack memory based on spin orbit torque driven chiral domain wall motions

    PubMed Central

    Zhang, Yue; Zhang, Xueying; Hu, Jingtong; Nan, Jiang; Zheng, Zhenyi; Zhang, Zhizhong; Zhang, Youguang; Vernier, Nicolas; Ravelosona, Dafine; Zhao, Weisheng

    2016-01-01

    Racetrack memory (RM) has sparked enormous interest thanks to its outstanding potential for low-power, high-density and high-speed data storage. However, since it requires bi-directional domain wall (DW) shifting process for outputting data, the mainstream stripe-shaped concept certainly suffers from the data overflow issue. This geometrical restriction leads to increasing complexity of peripheral circuits or programming as well as undesirable reliability issue. In this work, we propose and study ring-shaped RM, which is based on an alternative mechanism, spin orbit torque (SOT) driven chiral DW motions. Micromagnetic simulations have been carried out to validate its functionality and exhibit its performance advantages. The current flowing through the heavy metal instead of ferromagnetic layer realizes the “end to end” circulation of storage data, which remains all the data in the device even if they are shifted. It blazes a promising path for application of RM in practical memory and logic. PMID:27725741

  17. Ring-shaped Racetrack memory based on spin orbit torque driven chiral domain wall motions

    NASA Astrophysics Data System (ADS)

    Zhang, Yue; Zhang, Xueying; Hu, Jingtong; Nan, Jiang; Zheng, Zhenyi; Zhang, Zhizhong; Zhang, Youguang; Vernier, Nicolas; Ravelosona, Dafine; Zhao, Weisheng

    2016-10-01

    Racetrack memory (RM) has sparked enormous interest thanks to its outstanding potential for low-power, high-density and high-speed data storage. However, since it requires bi-directional domain wall (DW) shifting process for outputting data, the mainstream stripe-shaped concept certainly suffers from the data overflow issue. This geometrical restriction leads to increasing complexity of peripheral circuits or programming as well as undesirable reliability issue. In this work, we propose and study ring-shaped RM, which is based on an alternative mechanism, spin orbit torque (SOT) driven chiral DW motions. Micromagnetic simulations have been carried out to validate its functionality and exhibit its performance advantages. The current flowing through the heavy metal instead of ferromagnetic layer realizes the “end to end” circulation of storage data, which remains all the data in the device even if they are shifted. It blazes a promising path for application of RM in practical memory and logic.

  18. Stochastic Current-Driven Domain-Wall Motion Observed by X-Ray Microscopy

    NASA Astrophysics Data System (ADS)

    Meier, Guido

    2008-03-01

    Transmission x-ray microscopy can directly visualize the influence of a spin-polarized current on the magnetization of micro- and nanostructures. We investigate the stochastic motion of domain walls in curved wires [1] and the motion of vortices in squares [2]. To observe domain-wall motion pulses of nanosecond duration and high current density are send through permalloy wires and either move or deform the domain wall. The current pulses have nanosecond duration and a high current density of up to 1.0 10^12 A/m^2 and drive the wall either undisturbed, i.e. as a composite particle through the wire or causes structural changes of the magnetization. Repetitive pulse measurements reveal the stochastic nature of current induced domain-wall motion. From the experiments we estimate the ratio between the degree of nonadiabaticity and the Gilbert damping parameter indicating the importance of the nonadiabatic contribution to current driven domain-wall motion. To compare experimental results with theory the spin-torque transfer model of Zhang and Li [3] is implemented in the micromagnetic framework OOMMF [4]. The code is applied to determine the current-induced domain wall velocity using the material parameters of permalloy. The simulations support the interpretation of the experimental results. Sinusoidal high-density currents are applied to micrometer-sized permalloy squares containing ferromagnetic vortices. Spin-torque induced vortex gyration on the nanosecond timescale is observed. The phase of the gyration in structures with different chirality are compared to an analytical model and micromagnetic simulations, considering both alternating spin-polarized currents and the current's Oersted fields. This analysis reveals that spin-torque is the main source of motion. Supported by the DFG via SFB 668 and GK 1286 as well as by the U.S. DOE Contract No. DE-AC02-05-CH11231. References: [1] G. Meier, M. Bolte, R. Eiselt, U. Merkt, B. Krüger, D. Pfannkuche, D.-H. Kim, and P

  19. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement

    PubMed Central

    Borbulevych, Oleg; Martin, Roger I.; Tickle, Ian J.; Westerhoff, Lance M.

    2016-01-01

    Gaining an understanding of the protein–ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  20. XModeScore: a novel method for accurate protonation/tautomer-state determination using quantum-mechanically driven macromolecular X-ray crystallographic refinement.

    PubMed

    Borbulevych, Oleg; Martin, Roger I; Tickle, Ian J; Westerhoff, Lance M

    2016-04-01

    Gaining an understanding of the protein-ligand complex structure along with the proper protonation and explicit solvent effects can be important in obtaining meaningful results in structure-guided drug discovery and structure-based drug discovery. Unfortunately, protonation and tautomerism are difficult to establish with conventional methods because of difficulties in the experimental detection of H atoms owing to the well known limitations of X-ray crystallography. In the present work, it is demonstrated that semiempirical, quantum-mechanics-based macromolecular crystallographic refinement is sensitive to the choice of a protonation-state/tautomer form of ligands and residues, and can therefore be used to explore potential states. A novel scoring method, called XModeScore, is described which enumerates the possible protomeric/tautomeric modes, refines each mode against X-ray diffraction data with the semiempirical quantum-mechanics (PM6) Hamiltonian and scores each mode using a combination of energetic strain (or ligand strain) and rigorous statistical analysis of the difference electron-density distribution. It is shown that using XModeScore it is possible to consistently distinguish the correct bound protomeric/tautomeric modes based on routine X-ray data, even at lower resolutions of around 3 Å. These X-ray results are compared with the results obtained from much more expensive and laborious neutron diffraction studies for three different examples: tautomerism in the acetazolamide ligand of human carbonic anhydrase II (PDB entries 3hs4 and 4k0s), tautomerism in the 8HX ligand of urate oxidase (PDB entries 4n9s and 4n9m) and the protonation states of the catalytic aspartic acid found within the active site of an aspartic protease (PDB entry 2jjj). In each case, XModeScore applied to the X-ray diffraction data is able to determine the correct protonation state as defined by the neutron diffraction data. The impact of QM-based refinement versus conventional

  1. An Ontology Driven Information Architecture for Big Data and Diverse Domains

    NASA Astrophysics Data System (ADS)

    Hughes, John S.; Crichton, Dan; Hardman, Sean; Joyner, Ron; Ramirez, Paul

    2013-04-01

    The Planetary Data System's has just released the PDS4 system for first use. Its architecture is comprised of three principle parts, an ontology that captures knowledge from the planetary science domain, a federated registry/repository system for product identification, versioning, tracking, and storage, and a REST-based service layer for search, retrieval, and distribution. An ontology modeling tool is used to prescriptively capture product definitions that adhere to object-oriented principles and that are compliant with specific registry, archive, and data dictionary reference models. The resulting information model is product centric, allowing all information to be packaged into products and tracked in the registry. The flexibility required in a diverse domain is provided through the use of object-oriented extensions and a hierarchical governance scheme with common, discipline, and mission levels. Finally all PDS4 data standards are generated or derived from the information model. The federated registry provides identification, versioning, and tracking functionality across federated repositories and is configured for deployment using configuration files generated from the ontology. Finally a REST-based service layer provides for metadata harvest, product transformation, packaging, and search, and portal hosting. A model driven architecture allows the data and software engineering teams to develop in parallel with minimal team interaction. The resulting software remains relatively stable as the domain evolves. Finally the development of a single shared ontology promotes interoperability and data correlation and helps meet the expectations of modern scientists for science data discovery, access and use. This presentation will provide an overview of PDS4 focusing on the data standards, how they were developed, how they are now being used, and will present some of the lessons learned while developing in a diverse scientific community. Copyright 2013 California

  2. Structural Context of Disease-Associated Mutations and Putative Mechanism of Autoinhibition Revealed by X-Ray Crystallographic Analysis of the EZH2-SET Domain

    PubMed Central

    Antonysamy, Stephen; Condon, Bradley; Druzina, Zhanna; Bonanno, Jeffrey B.; Gheyi, Tarun; Zhang, Feiyu; MacEwan, Iain; Zhang, Aiping; Ashok, Sheela; Rodgers, Logan; Russell, Marijane; Gately Luz, John

    2013-01-01

    The enhancer-of-zeste homolog 2 (EZH2) gene product is an 87 kDa polycomb group (PcG) protein containing a C-terminal methyltransferase SET domain. EZH2, along with binding partners, i.e., EED and SUZ12, upon which it is dependent for activity forms the core of the polycomb repressive complex 2 (PRC2). PRC2 regulates gene silencing by catalyzing the methylation of histone H3 at lysine 27. Both overexpression and mutation of EZH2 are associated with the incidence and aggressiveness of various cancers. The novel crystal structure of the SET domain was determined in order to understand disease-associated EZH2 mutations and derive an explanation for its inactivity independent of complex formation. The 2.00 Å crystal structure reveals that, in its uncomplexed form, the EZH2 C-terminus folds back into the active site blocking engagement with substrate. Furthermore, the S-adenosyl-L-methionine (SAM) binding pocket observed in the crystal structure of homologous SET domains is notably absent. This suggests that a conformational change in the EZH2 SET domain, dependent upon complex formation, must take place for cofactor and substrate binding activities to be recapitulated. In addition, the data provide a structural context for clinically significant mutations found in the EZH2 SET domain. PMID:24367637

  3. Crystallization and preliminary X-ray crystallographic investigations on a betagamma-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens.

    PubMed

    Aravind, Penmatsa; Rajini, Bheemreddy; Sharma, Yogendra; Sankaranarayanan, Rajan

    2006-03-01

    AIM1g1 is a single betagamma-crystallin domain from the protein absent in melanoma 1 (AIM1), which appears to play a role in the suppression of melanomas. This domain is known to bind calcium and its structure would help in identifying calcium-coordinating sites in vertebrate crystallins, which have hitherto been believed to have lost this ability during evolution. Crystallization of this domain was performed by the hanging-drop vapour-diffusion method. Crystals diffracted to a maximum resolution of 1.86 A and were found to belong to space group P6(1) or P6(5), with unit-cell parameters a = b = 54.98, c = 59.73 A. Solvent-content analysis indicated the presence of one monomer per asymmetric unit.

  4. Preliminary X-ray crystallographic analysis of an engineered variant of human chimera-type galectin-3 with a shortened N-terminal domain.

    PubMed

    Flores-Ibarra, Andrea; Ruiz, Federico M; Vértesy, Sabine; André, Sabine; Gabius, Hans-Joachim; Romero, Antonio

    2015-02-01

    How lectins translate sugar-encoded information into cellular effects not only depends on glycan recognition. Other domains of the protein can contribute to the functional profile of a lectin. Human galectin-3 (Gal-3), an adhesion/growth-regulatory galectin, is composed of three different domains and is thus called a chimera-type protein. In addition to the carbohydrate-recognition domain, this lectin encompasses an N-terminal domain consisting of a peptide harbouring two phosphorylation sites and nine non-triple-helical collagen-like repeats. This region plays an as yet structurally undefined role in Gal-3 aggregation and ligand recognition. To date, crystallization of full-length Gal-3 has not been achieved. With the aim of providing structural insights into this modular organization, a Gal-3 variant was crystallized maintaining the terminal peptide and three of the nine collagen-like repeats. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 94.04, b = 97.96, c = 236.20 Å, and diffracted to a resolution of 3.3 Å.

  5. Preliminary X-ray crystallographic analysis of an engineered variant of human chimera-type galectin-3 with a shortened N-terminal domain

    PubMed Central

    Flores-Ibarra, Andrea; Ruiz, Federico M.; Vértesy, Sabine; André, Sabine; Gabius, Hans-Joachim; Romero, Antonio

    2015-01-01

    How lectins translate sugar-encoded information into cellular effects not only depends on glycan recognition. Other domains of the protein can contribute to the functional profile of a lectin. Human galectin-3 (Gal-3), an adhesion/growth-regulatory galectin, is composed of three different domains and is thus called a chimera-type protein. In addition to the carbohydrate-recognition domain, this lectin encompasses an N-terminal domain consisting of a peptide harbouring two phosphorylation sites and nine non-triple-helical collagen-like repeats. This region plays an as yet structurally undefined role in Gal-3 aggregation and ligand recognition. To date, crystallization of full-length Gal-3 has not been achieved. With the aim of providing structural insights into this modular organization, a Gal-3 variant was crystallized maintaining the terminal peptide and three of the nine collagen-like repeats. The crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 94.04, b = 97.96, c = 236.20 Å, and diffracted to a resolution of 3.3 Å. PMID:25664793

  6. Crystallization and preliminary X-ray crystallographic investigations on a βγ-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens

    SciTech Connect

    Aravind, Penmatsa; Rajini, Bheemreddy; Sharma, Yogendra; Sankaranarayanan, Rajan

    2006-03-01

    The crystallization and preliminary X-ray diffraction analysis of AIM1g1, a βγ-crystallin domain of absent in melanoma (AIM1) protein from H. sapiens, is reported. AIM1g1 is a single βγ-crystallin domain from the protein absent in melanoma 1 (AIM1), which appears to play a role in the suppression of melanomas. This domain is known to bind calcium and its structure would help in identifying calcium-coordinating sites in vertebrate crystallins, which have hitherto been believed to have lost this ability during evolution. Crystallization of this domain was performed by the hanging-drop vapour-diffusion method. Crystals diffracted to a maximum resolution of 1.86 Å and were found to belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 54.98, c = 59.73 Å. Solvent-content analysis indicated the presence of one monomer per asymmetric unit.

  7. Crystallographic Analysis of Murine Constitutive Androstane Receptor Ligand-Binding Domain Complexed with 5[alpha]-androst-16-en-3[alpha]-ol

    SciTech Connect

    Vincent, J.; Shan, L.; Fan, M.; Brunzelle, J.S.; Forman, B.M.; Fernandez, E.J.

    2010-03-08

    The constitutive androstane receptor (CAR) is a member of the nuclear receptor superfamily. In contrast to classical nuclear receptors, which possess small-molecule ligand-inducible activity, CAR exhibits constitutive transcriptional activity in the apparent absence of ligand. CAR is among the most important transcription factors; it coordinately regulates the expression of microsomal cytochrome P450 genes and other drug-metabolizing enzymes. The murine CAR ligand-binding domain (LBD) was coexpressed with the steroid receptor coactivator protein (SRC-1) receptor-interacting domain (RID) in Escherichia coli. The mCAR LBD subunit was purified away from SRC-1 by affinity, anion-exchange and size-exclusion chromatography, crystallized with androstenol and the structure of the complex determined by molecular replacement.

  8. Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E

    SciTech Connect

    J Zhang; P Sapienza; H Ke; A Chang; S Hengel; H Wang; G Phillips Jr.; A Lee

    2011-12-31

    PDZ (PSD95/Discs large/ZO-1) domains are ubiquitous protein interaction motifs found in scaffolding proteins involved in signal transduction. Despite the fact that many PDZ domains show a limited tendency to undergo structural change, the PDZ family has been associated with long-range communication and allostery. One of the PDZ domains studied most in terms of structure and biophysical properties is the second PDZ ('PDZ2') domain from protein tyrosine phosphatase 1E (PTP1E, also known as PTPL1). Previously, we showed through NMR relaxation studies that binding of the RA-GEF2 C-terminal peptide substrate results in long-range propagation of side-chain dynamic changes in human PDZ2 [Fuentes, E. J., et al. (2004) J. Mol. Biol. 335, 1105-1115]. Here, we present the first X-ray crystal structures of PDZ2 in the absence and presence of RA-GEF2 ligand, determined to resolutions of 1.65 and 1.3 {angstrom}, respectively. These structures deviate somewhat from previously determined NMR structures and indicate that very minor structural changes in PDZ2 accompany peptide binding. NMR residual dipolar couplings confirm the crystal structures to be accurate models of the time-averaged atomic coordinates of PDZ2. The impact on side-chain dynamics was further tested with a C-terminal peptide from APC, which showed results nearly identical to those of RA-GEF2. Thus, allosteric transmission in PDZ2 induced by peptide binding is conveyed purely and robustly by dynamics. {sup 15}N relaxation dispersion measurements did not detect appreciable populations of a kinetic structural intermediate. Collectively, for ligand binding to PDZ2, these data support a lock-and-key binding model from a structural perspective and an allosteric model from a dynamical perspective, which together suggest a complex energy landscape for functional transitions within the ensemble.

  9. Crystallization and preliminary X-ray crystallographic analysis of a conserved domain in plants and prokaryotes from Pyrococcus horikoshii OT3

    SciTech Connect

    Lin, Linyen; Nakano, Hiroaki; Uchiyama, Susumu; Fujimoto, Satoru; Matsunaga, Sachihiro; Nakamura, Shota; Kobayashi, Yuji; Ohkubo, Tadayasu; Fukui, Kiichi

    2005-04-01

    A plant- and prokaryote-conserved domain (PPC) has been crystallized. The crystal diffracted to 1.7 Å resolution and belonged to space group P6{sub 3}22. A plant- and prokaryote-conserved domain (PPC) has previously been found in AT-hook motif nuclear localized protein 1 (AHL1) localized in the nuclear matrix of Arabidopsis thaliana (AtAHL1). AtAHL1 has a DNA-binding function. Mutation analyses of AtAHL1 has previously revealed that the hydrophobic region of the PPC domain is essential for its nuclear localization. In this study, the PPC of the hyperthermophilic archaebacterium Pyrococcus horikoshii (PhPPC) was crystallized using the hanging-drop vapour-diffusion method. The crystals belonged to the hexagonal space group P6{sub 3}22, with unit-cell parameters a = b = 53.69, c = 159.2 Å. Data were obtained at 100 K, with diffraction being observed to a resolution of 1.7 Å. A complete data set from crystals of the SeMet-substituted protein was also obtained.

  10. Crystallographic characterization of mouse AIM2 HIN-200 domain bound to a 15 bp and an 18 bp double-stranded DNA.

    PubMed

    Sung, Min Woo; Watts, Tylan; Li, Pingwei

    2012-09-01

    AIM2 (absent in melanoma 2) is an innate immune receptor for cytosolic double-stranded DNA (dsDNA). The engagement of dsDNA by AIM2 activates the AIM2 inflammasome, resulting in the cleavage of pro-interleukin-1β by caspase-1. The DNA-binding HIN-200 domain of mouse AIM2 bound to a 15 bp dsDNA and to an 18 bp dsDNA was purified and crystallized. The AIM2 HIN-200 domain in complex with the 15 bp DNA crystallized in the cubic space group I23 or I2(1)3, with unit-cell parameter a = 235.60 Å. The complex of the AIM2 HIN-200 domain and the 18 bp DNA crystallized in a similar unit cell. Diffraction data for the two complexes were collected to about 4.0 Å resolution. Mutagenesis and DNA-binding studies suggest that mouse AIM2 uses a similar surface to human AIM2 to recognize DNA.

  11. Crystallization and preliminary crystallographic studies of the copper-binding domain of the amyloid precursor protein of Alzheimer’s disease

    SciTech Connect

    Kong, Geoffrey K.-W.; Galatis, Denise; Barnham, Kevin J.; Polekhina, Galina; Adams, Julian J.; Masters, Colin L.; Cappai, Roberto; Parker, Michael W.; McKinstry, William J.

    2005-01-01

    The binding of Cu{sup 2+} ions to the copper-binding domain of the amyloid precursor protein of Alzheimer’s disease reduces the production of the amyloid β peptide, which is centrally involved in Alzheimer’s disease. Structural studies of the copper-binding domain will provide a basis for structure-based drug design that might prove useful in treating this devastating disease. Alzheimer’s disease is thought to be triggered by production of the amyloid β (Aβ) peptide through proteolytic cleavage of the amyloid precursor protein (APP). The binding of Cu{sup 2+} to the copper-binding domain (CuBD) of APP reduces the production of Aβ in cell-culture and animal studies. It is expected that structural studies of the CuBD will lead to a better understanding of how copper binding causes Aβ depletion and will define a potential drug target. The crystallization of CuBD in two different forms suitable for structure determination is reported here.

  12. Crystallization and crystallographic analysis of the ligand-binding domain of the Pseudomonas putida chemoreceptor McpS in complex with malate and succinate

    PubMed Central

    Gavira, J. A.; Lacal, J.; Ramos, J. L.; García-Ruiz, J. M.; Krell, T.; Pineda-Molina, E.

    2012-01-01

    Methyl-accepting chemotaxis proteins (MCPs) are transmembrane proteins that sense changes in environmental signals, generating a chemotactic response and regulating other cellular processes. MCPs are composed of two main domains: a ligand-binding domain (LBD) and a cytosolic signalling domain (CSD). Here, the crystallization of the LBD of the chemoreceptor McpS (McpS-LBD) is reported. McpS-LBD is responsible for sensing most of the TCA-cycle intermediates in the soil bacterium Pseudomonas putida KT2440. McpS-LBD was expressed, purified and crystallized in complex with two of its natural ligands (malate and succinate). Crystals were obtained by both the counter-diffusion and the hanging-drop vapour-diffusion techniques after pre-incubation of McpS-LBD with the ligands. The crystals were isomorphous and belonged to space group C2, with two molecules per asymmetric unit. Diffraction data were collected at the ESRF synchrotron X-ray source to resolutions of 1.8 and 1.9 Å for the malate and succinate complexes, respectively. PMID:22505412

  13. Nicastrin functions to sterically hinder γ-secretase–substrate interactions driven by substrate transmembrane domain

    PubMed Central

    Bolduc, David M.; Montagna, Daniel R.; Gu, Yongli; Selkoe, Dennis J.; Wolfe, Michael S.

    2016-01-01

    γ-Secretase is an intramembrane-cleaving protease that processes many type-I integral membrane proteins within the lipid bilayer, an event preceded by shedding of most of the substrate’s ectodomain by α- or β-secretases. The mechanism by which γ-secretase selectively recognizes and recruits ectodomain-shed substrates for catalysis remains unclear. In contrast to previous reports that substrate is actively recruited for catalysis when its remaining short ectodomain interacts with the nicastrin component of γ-secretase, we find that substrate ectodomain is entirely dispensable for cleavage. Instead, γ-secretase–substrate binding is driven by an apparent tight-binding interaction derived from substrate transmembrane domain, a mechanism in stark contrast to rhomboid—another family of intramembrane-cleaving proteases. Disruption of the nicastrin fold allows for more efficient cleavage of substrates retaining longer ectodomains, indicating that nicastrin actively excludes larger substrates through steric hindrance, thus serving as a molecular gatekeeper for substrate binding and catalysis. PMID:26699478

  14. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of pseudo death-effector domain of HIPPI, a molecular partner of Huntingtin-interacting protein HIP-1

    SciTech Connect

    Banerjee, Manisha; Majumder, Pritha; Bhattacharyya, Nitai P.; Dattagupta, Jiban K.; Sen, Udayaditya

    2006-12-01

    A pseudo death-effector domain (pDED) of HIPPI, a partner of Huntingtin-interacting protein HIP1, has been cloned, overexpressed and crystallized. The crystals of pDED-HIPPI diffracted to 2.2 Å. The formation of a heterodimer between Huntingtin-interacting protein-1 (HIP-1) and its novel partner HIPPI (HIP-1 protein interactor) through their pseudo death-effector domains (pDEDs) is a key step that recruits caspase-8 and initiates apoptosis. This could be one of the pathways by which apoptosis is increased in Huntington’s disease (HD). A construct consisting of the pDED of HIPPI has been cloned and overexpressed as 6NH-tagged protein and purified by Ni–NTA affinity chromatography. Crystals of the pDED of HIPPI were grown in space group P4{sub 1}, with unit-cell parameters a = b = 77.42, c = 33.31 Å and a calculated Matthews coefficient of 1.88 Å{sup 3} Da{sup −1} (33% solvent content) with two molecules per asymmetric unit.

  15. Purification, crystallization and preliminary X-ray crystallographic analysis of the phosphatase domain (PA3346PD) of the response regulator PA3346 from Pseudomonas aeruginosa PAO1.

    PubMed

    Chen, Li Ying; Wu, Pei Hsun; Guan, Hong Hsiang; Fun, Hoong Kun; Chang, Hwan You; Chen, Chun Jung

    2015-04-01

    The phosphatase domain (PA3346PD) of the response regulator PA3346 modulates the downstream anti-anti-σ factor PA3347 to regulate swarming motility in Pseudomonas aeruginosa PAO1. PA3346PD, which comprises the protein phosphatase 2C domain (PP2C), is classified as a Ser/Thr phosphatase of the Mg(2+)- or Mn(2+)-dependent protein phosphatase (PPM) family. The recombinant PA3346PD, with molecular mass 26 kDa, was overexpressed in Escherichia coli, purified on an Ni(2+)-NTA agarose column and crystallized by the sitting-drop vapour-diffusion method. X-ray diffraction data were collected from PA3346PD crystals to a resolution of 2.58 Å and the crystals belonged to space group I4₁32 or I4₃32, with unit-cell parameter a = 157.61 Å. Preliminary analysis indicates the presence of a monomer of PA3346PD in the asymmetric unit with a solvent content of 58.4%.

  16. Crystallization and preliminary X-ray crystallographic study of the extracellular domain of the 4-1BB ligand, a member of the TNF family

    SciTech Connect

    Byun, Jung-Sue; Kim, Dong-Uk; Ahn, Byungchan; Kwon, Byoung Se; Cho, Hyun-Soo

    2006-01-01

    The extracellular domain of the 4-1BB ligand fused with glutathione-S-transferase was expressed in Escherichia coli (Origami) and purified by using affinity and ion-exchange column chromatographic methods. Crystals of the 4-1BB ligand were obtained at 290 K by the hanging-drop vapour-diffusion method. The 4-1BB ligand, a member of the tumour necrosis factor (TNF) family, is an important co-stimulatory molecule that plays a key role in the clonal expansion and survival of CD8+ T cells. Signalling through binding of the 4-1BB ligand and 4-1BB has been reported to enhance CD8+ T-cell expansion and protect activated CD8+ T cells from death. The 4-1BB ligand is an integral protein expressed on activated antigen-presenting cells. The extracellular domain of the 4-1BB ligand fused with glutathione-S-transferase was expressed in Escherichia coli (Origami) and purified by using affinity and ion-exchange column chromatographic methods. Crystals of the 4-1BB ligand were obtained at 290 K by the hanging-drop vapour-diffusion method. X-ray diffraction data were collected from these crystals to 2.8 Å resolution and the crystals belong to space group C2, with unit-cell parameters a = 114.6, b = 73.8, c = 118.50 Å, β = 115.5°.

  17. Crystallization and preliminary crystallographic analysis of the kinase-recruitment domain of the PP2C-type phosphatase RsbU.

    PubMed

    Dutta, Sujit; Lewis, Richard J

    2003-01-01

    The general stress response of Bacillus subtilis provides a protective resistance to a variety of pressures. The key molecule is a subunit of RNA polymerase, sigma(B), which confers promoter specificity and is regulated by two signalling modules. Each module comprises protein kinases and phosphatases and 'switch' protein substrates for the kinase and phosphatase. The phosphorylation state of the switch molecules indirectly controls the activity of sigma(B). The binding of the kinase RsbT to the phosphatase RsbU stimulates its enzymatic activity towards its substrate, phosphorylated RsbV. To understand how these enzymes interact, thus regulating transcription, crystallization of the kinase-recruitment domain of RsbU in a form suitable for high-resolution structure determination is reported.

  18. Cloning, purification, crystallization and X-ray crystallographic analysis of the periplasmic sensing domain of Pseudomonas fluorescens chemotactic transducer of amino acids type A (CtaA).

    PubMed

    Ud-Din, Abu Iftiaf Md Salah; Roujeinikova, Anna

    2016-09-05

    Chemotaxis towards nutrients plays a crucial role in root colonization by Pseudomonas fluorescens. The P. fluorescens chemotactic transducer of amino acids type A (CtaA) mediates movement towards amino acids present in root exudates. In this study, the periplasmic sensory domain of CtaA has been crystallized by the hanging-drop vapor diffusion method using ammonium sulfate as a precipitating agent. A complete data set was collected to 1.9 Å resolution using cryocooling conditions and synchrotron radiation. The crystals belong to space group I222 or I212121, with unit-cell parameters a = 67.2, b = 76.0, c = 113.3 Å. This is an important step towards elucidation of the structural basis of how CtaA recognizes its signal molecules and transduces the signal across the membrane.

  19. Preliminary Crystallographic Studies of the Regulatory Domain of Response Regulator YycF from an Essential Two-Component Signal Transduction System

    SciTech Connect

    Zhao, H.; Heroux, A; Sequeira, R; Tang, L

    2009-01-01

    YycGF is a crucial signal transduction system for the regulation of cell-wall metabolism in low-G+C Gram-positive bacteria, which include many important human pathogens. The response regulator YycF receives signals from its cognate histidine kinase YycG through a phosphotransfer reaction and elicits responses through regulation of gene expression. The N-terminal regulatory domain of YycF from Bacillus subtilis was overproduced and purified. The protein was crystallized and X-ray data were collected to 1.95 A resolution with a completeness of 97.7% and an overall Rmerge of 7.7%. The crystals belonged to space group P3121, with unit-cell parameters a = b = 59.50, c = 79.06 A.

  20. Preliminary crystallographic analysis of mouse Elf3 C-terminal DNA-binding domain in complex with type II TGF-[beta] receptor promoter DNA

    SciTech Connect

    Agarkar, Vinod B.; Babayeva, Nigar D.; Rizzino, Angie; Tahirov, Tahir H.

    2010-10-08

    Ets proteins are transcription factors that activate or repress the expression of genes that are involved in various biological processes, including cellular proliferation, differentiation, development, transformation and apoptosis. Like other Ets-family members, Elf3 functions as a sequence-specific DNA-binding transcriptional factor. A mouse Elf3 C-terminal fragment (amino-acid residues 269-371) containing the DNA-binding domain has been crystallized in complex with mouse type II TGF-{beta} receptor promoter (TR-II) DNA. The crystals belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 42.66, b = 52, c = 99.78 {angstrom}, and diffracted to a resolution of 2.2 {angstrom}.

  1. Crystallization and preliminary crystallographic studies of the complement 1qA globular domain from zebrafish, Dare-C1qAgD.

    PubMed

    Yuan, Hongyu; Chen, Rong; Liu, Yanjie; Tariq, Mansoor; Sun, Yaping; Xia, Chun

    2014-07-01

    Complement 1q (C1q) is the first component of the complement system which can initiate the classical complement pathway. In human, C1q is composed of 18 polypeptide chains: six C1qA chains, six C1qB chains and six C1qC chains. Each chain has a signal peptide and is comprised of a collagen-like region and a C-terminal C1q globular domain (C1qgD), which is organized as a heterotrimer. C1qgD can recognize antigen-antibody complexes containing IgG and IgM or can bind directly to the C-reactive protein. Although the classical complement pathway is found from fish to mammals, only the human C1qgD structure has been determined. Compared with that of mammals, fish C1q exhibits similar immune functions and genome arrangement. In order to illustrate the structure of C1qgD in fish, zebrafish (Danio rerio) C1qA globular domain (Dare-C1qAgD) was expressed, purified and crystallized. X-ray diffraction data were collected from a crystal to a resolution of 2.05 Å; the crystal belonged to the orthorhombic space group P2₁2₁2₁, with unit-cell parameters a=50.347, b=85.059, c=95.560 Å. It contained three molecules in the asymmetric unit. The Matthews coefficient value VM was 2.31 Å3 Da(-1), with a calculated solvent content of 46.7%. The data will help to give insight into the structural basis of C1qA in fish species.

  2. X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa

    SciTech Connect

    Li, Zhijie; Chakraborty, Sayan; Xu, Guozhou

    2016-10-26

    Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses inArabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein,Camelina sativalectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 Å resolution from a single crystal. The crystal belonged to space groupC222 orC2221, with unit-cell parametersa= 94.7,b= 191.5,c= 302.8 Å. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.

  3. 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…

  4. 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…

  5. Spin-wave-driven high-speed domain-wall motions in soft magnetic nanotubes

    SciTech Connect

    Yang, Jaehak; Yoo, Myoung-Woo; Kim, Sang-Koog

    2015-10-28

    We report on a micromagnetic simulation study of interactions between propagating spin waves and a head-to-head domain wall in geometrically confined magnetic nanotubes. We found that incident spin waves of specific frequencies can lead to sufficiently high-speed (on the order of a few hundreds of m/s or higher) domain-wall motions in the same direction as that of the incident spin-waves. The domain-wall motions and their speed vary remarkably with the frequency and the amplitude of the incident spin-waves. High-speed domain-wall motions originate from the transfer torque of spin waves' linear momentum to the domain wall, through the partial or complete reflection of the incident spin waves from the domain wall. This work provides a fundamental understanding of the interaction of the spin waves with a domain wall in the magnetic nanotubes as well as a route to all-magnetic control of domain-wall motions in the magnetic nanoelements.

  6. Sphingomyelinase-Induced Domain Shape Relaxation Driven by Out-of-Equilibrium Changes of Composition

    PubMed Central

    Fanani, Maria Laura; De Tullio, Luisina; Hartel, Steffen; Jara, Jorge; Maggio, Bruno

    2009-01-01

    Abstract Sphingomyelinase (SMase)-induced ceramide (Cer)-enriched domains in a lipid monolayer are shown to result from an out-of-equilibrium situation. This is induced by a change of composition caused by the enzymatic production of Cer in a sphingomyelin (SM) monolayer that leads to a fast SM/Cer demixing into a liquid-condensed (LC), Cer-enriched and a liquid-expanded, SM-enriched phases. The morphological evolution and kinetic dependence of Cer-enriched domains is studied under continuous observation by epifluorescence microscopy. Domain shape annealing is observed from branched to rounded shapes after SMase activity quenching by EDTA, with a decay halftime of ∼10 min. An out-of-equilibrium fast domain growth is not the determinant factor for domain morphology. Domain shape rearrangement in nearly equilibrium conditions result from the counteraction of intradomain dipolar repulsion and line tension, according to McConnell's shape transition theory. Phase separation causes a transient compositional overshoot within the LC phase that implies an increased out-of-equilibrium enrichment of Cer into the LC domains. As a consequence, higher intradomain repulsion leads to transient branched structures that relax to rounded shapes by lowering the proportion of Cer in the domain to equilibrium values. The fast action of SMase can be taken as a compositional perturbation that brings about important consequences for the surface organization. PMID:18849413

  7. Investigation of domain wall motion in RE-TM magnetic wire towards a current driven memory and logic

    NASA Astrophysics Data System (ADS)

    Awano, Hiroyuki

    2015-06-01

    Current driven magnetic domain wall (DW) motions of ferri-magnetic TbFeCo wires have been investigated. In the case of a Si substrate, the critical current density (Jc) of DW motion was successfully reduced to 3×106 A/cm2. Moreover, by using a polycarbonate (PC) substrate with a molding groove of 600 nm width, the Jc was decreased to 6×105 A/cm2. In order to fabricate a logic in memory, a current driven spin logics (AND, OR, NOT) have been proposed and successfully demonstrated under the condition of low Jc. These results indicate that TbFeCo nanowire is an excellent candidate for next generation power saving memory and logic.

  8. Domain wall motion driven by spin Hall effect—Tuning with in-plane magnetic anisotropy

    SciTech Connect

    Rushforth, A. W.

    2014-04-21

    This letter investigates the effects of in-plane magnetic anisotropy on the current induced motion of magnetic domain walls in systems with dominant perpendicular magnetic anisotropy, where accumulated spins from the spin Hall effect in an adjacent heavy metal layer are responsible for driving the domain wall motion. It is found that that the sign and magnitude of the domain wall velocity in the uniform flow regime can be tuned significantly by the in-plane magnetic anisotropy. These effects are sensitive to the ratio of the adiabatic and non-adiabatic spin transfer torque parameters and are robust in the presence of pinning and thermal fluctuations.

  9. Domain-wall theory and nonstationarity in driven flow with exclusion.

    PubMed

    Stinchcombe, R B; de Queiroz, S L A

    2016-07-01

    We study the dynamical evolution toward steady state of the stochastic nonequilibrium model known as the totally asymmetric simple exclusion process, in both uniform and nonuniform (staggered) one-dimensional systems with open boundaries. Domain-wall theory and numerical simulations are used and, where pertinent, their results are compared to existing mean-field predictions and exact solutions where available. For uniform chains we find that the inclusion of fluctuations inherent to the domain-wall formulation plays a crucial role in providing good agreement with simulations, which is severely lacking in the corresponding mean-field predictions. For alternating-bond chains the domain-wall predictions for the features of the phase diagram in the parameter space of injection and ejection rates turn out to be realized only in an incipient and quantitatively approximate way. Nevertheless, significant quantitative agreement can be found between several additional domain-wall theory predictions and numerics.

  10. Domain-wall theory and nonstationarity in driven flow with exclusion

    NASA Astrophysics Data System (ADS)

    Stinchcombe, R. B.; de Queiroz, S. L. A.

    2016-07-01

    We study the dynamical evolution toward steady state of the stochastic nonequilibrium model known as the totally asymmetric simple exclusion process, in both uniform and nonuniform (staggered) one-dimensional systems with open boundaries. Domain-wall theory and numerical simulations are used and, where pertinent, their results are compared to existing mean-field predictions and exact solutions where available. For uniform chains we find that the inclusion of fluctuations inherent to the domain-wall formulation plays a crucial role in providing good agreement with simulations, which is severely lacking in the corresponding mean-field predictions. For alternating-bond chains the domain-wall predictions for the features of the phase diagram in the parameter space of injection and ejection rates turn out to be realized only in an incipient and quantitatively approximate way. Nevertheless, significant quantitative agreement can be found between several additional domain-wall theory predictions and numerics.

  11. Proposal for a Domain Wall Nano-Oscillator driven by Non-uniform Spin Currents

    NASA Astrophysics Data System (ADS)

    Sharma, Sanchar; Muralidharan, Bhaskaran; Tulapurkar, Ashwin

    2015-09-01

    We propose a new mechanism and a related device concept for a robust, magnetic field tunable radio-frequency (rf) oscillator using the self oscillation of a magnetic domain wall subject to a uniform static magnetic field and a spatially non-uniform vertical dc spin current. The self oscillation of the domain wall is created as it translates periodically between two unstable positions, one being in the region where both the dc spin current and the magnetic field are present, and the other, being where only the magnetic field is present. The vertical dc spin current pushes it away from one unstable position while the magnetic field pushes it away from the other. We show that such oscillations are stable under noise and can exhibit a quality factor of over 1000. A domain wall under dynamic translation, not only being a source for rich physics, is also a promising candidate for advancements in nanoelectronics with the actively researched racetrack memory architecture, digital and analog switching paradigms as candidate examples. Devising a stable rf oscillator using a domain wall is hence another step towards the realization of an all domain wall logic scheme.

  12. Proposal for a Domain Wall Nano-Oscillator driven by Non-uniform Spin Currents

    PubMed Central

    Sharma, Sanchar; Muralidharan, Bhaskaran; Tulapurkar, Ashwin

    2015-01-01

    We propose a new mechanism and a related device concept for a robust, magnetic field tunable radio-frequency (rf) oscillator using the self oscillation of a magnetic domain wall subject to a uniform static magnetic field and a spatially non-uniform vertical dc spin current. The self oscillation of the domain wall is created as it translates periodically between two unstable positions, one being in the region where both the dc spin current and the magnetic field are present, and the other, being where only the magnetic field is present. The vertical dc spin current pushes it away from one unstable position while the magnetic field pushes it away from the other. We show that such oscillations are stable under noise and can exhibit a quality factor of over 1000. A domain wall under dynamic translation, not only being a source for rich physics, is also a promising candidate for advancements in nanoelectronics with the actively researched racetrack memory architecture, digital and analog switching paradigms as candidate examples. Devising a stable rf oscillator using a domain wall is hence another step towards the realization of an all domain wall logic scheme. PMID:26420544

  13. Semantics-driven modelling of user preferences for information retrieval in the biomedical domain.

    PubMed

    Gladun, Anatoly; Rogushina, Julia; Valencia-García, Rafael; Béjar, Rodrigo Martínez

    2013-03-01

    A large amount of biomedical and genomic data are currently available on the Internet. However, data are distributed into heterogeneous biological information sources, with little or even no organization. Semantic technologies provide a consistent and reliable basis with which to confront the challenges involved in the organization, manipulation and visualization of data and knowledge. One of the knowledge representation techniques used in semantic processing is the ontology, which is commonly defined as a formal and explicit specification of a shared conceptualization of a domain of interest. The work presented here introduces a set of interoperable algorithms that can use domain and ontological information to improve information-retrieval processes. This work presents an ontology-based information-retrieval system for the biomedical domain. This system, with which some experiments have been carried out that are described in this paper, is based on the use of domain ontologies for the creation and normalization of lightweight ontologies that represent user preferences in a determined domain in order to improve information-retrieval processes.

  14. An all-metallic logic gate based on current-driven domain wall motion.

    PubMed

    Xu, Peng; Xia, Ke; Gu, Changzhi; Tang, Ling; Yang, Haifang; Li, Junjie

    2008-02-01

    The walls of magnetic domains can become trapped in a ferromagnetic metallic point contact when the thickness of the film and the width of the contact are less than their critical values. The discovery that domain walls can be moved from such constrictions by a sufficiently large current has attracted considerable attention from researchers working on both fundamental research and potential applications. Here we show that Invar nanocontacts fabricated on silica substrates exhibit a sharp drop in resistance with increasing bias voltage at room temperature in the absence of an applied magnetic field. Moreover, when two nanocontacts are combined in an all-metallic comparison circuit, it is possible to perform logical NOT operations. The use of electrical currents rather than applied magnetic fields to control the domain walls also reduces energy consumption and the risk of crosstalk in devices.

  15. Electric field driven magnetic domain wall motion in ferromagnetic-ferroelectric heterostructures

    SciTech Connect

    Van de Wiele, Ben; Laurson, Lasse; Franke, Kévin J. A.; Dijken, Sebastiaan van

    2014-01-06

    We investigate magnetic domain wall (MDW) dynamics induced by applied electric fields in ferromagnetic-ferroelectric thin-film heterostructures. In contrast to conventional driving mechanisms where MDW motion is induced directly by magnetic fields or electric currents, MDW motion arises here as a result of strong pinning of MDWs onto ferroelectric domain walls (FDWs) via local strain coupling. By performing extensive micromagnetic simulations, we find several dynamical regimes, including instabilities such as spin wave emission and complex transformations of the MDW structure. In all cases, the time-averaged MDW velocity equals that of the FDW, indicating the absence of Walker breakdown.

  16. Geostrophic Turbulence in the Frequency-Wavenumber Domain: Eddy-Driven Low-Frequency Variability

    DTIC Science & Technology

    2014-01-01

    ALTODB.2.0.CO;2. Haidvogel, D. B., and I. M. Held, 1980: Homogeneous quasi - geostrophic turbulence driven by a uniform tempera- ture gradient. J...1978)008,0363:TROMEI.2.0.CO;2. Hua, B. L., andD. B. Haidvogel, 1986: Numerical simulations of the vertical structure of quasi - geostrophic turbulence. J...1978: Two-layer quasi - geostrophic turbulence in a simple special case. Geophys. Astrophys. Fluid Dyn., 10, 25– 52, doi:10.1080/03091927808242628

  17. Ultrahigh resolution endoscopic spectral domain optical coherence tomography with a tiny rotary probe driven by a hollow ultrasonic motor

    NASA Astrophysics Data System (ADS)

    Zhang, Ning; Chen, Tianyuan; Huo, Tiancheng; Wang, Chengming; Zheng, Jing-gao; Zhou, Tieying; Xue, Ping

    2013-03-01

    This paper proposes a novel rotary endoscopic probe for spectral-domain optical coherence tomography (SD-OCT). The probe with a large N.A. objective lens is driven by an ultra-small hollow rectangular ultrasonic motor for circular scanning. Compared to the conventional driven techniques, the hollow ultrasonic motor enables the fiber to pass through its inside. Therefore the fiber, the objective lens and the motor are all at the same side. This enables 360 degree unobstructed imaging without any shadow resulted from power wire as in the conventional motor-driven endoscopic OCT. Moreover, it shortens the length of the rigid tip and enhances the flexibility of the probe. Meanwhile, the ultrasonic motor is robust, simple, quiet and of high torque, very suitable for OCT endoscopic probe. The side length of the motor is 0.7 mm with 5mm in length. The outer diameter of the probe is 1.5mm. A significant improvement in the lateral resolution is demonstrated due to the novel design of the objective lens. A right-angle lens is utilized instead of the traditional right-angle prism as the last optics close to the sample, leading to a reduction of the working distance and an enlargement of the N.A. of the objective lens. It is demonstrated that the endoscopic SD-OCT system achieves an axial resolution of ~7μm, a lateral resolution of ~6μm and a SNR of ~96dB.

  18. Pedagogically-Driven Ontology Network for Conceptualizing the e-Learning Assessment Domain

    ERIC Educational Resources Information Center

    Romero, Lucila; North, Matthew; Gutiérrez, Milagros; Caliusco, Laura

    2015-01-01

    The use of ontologies as tools to guide the generation, organization and personalization of e-learning content, including e-assessment, has drawn attention of the researchers because ontologies can represent the knowledge of a given domain and researchers use the ontology to reason about it. Although the use of these semantic technologies tends to…

  19. AC driven magnetic domain quantification with 5 nm resolution

    PubMed Central

    Li, Zhenghua; Li, Xiang; Dong, Dapeng; Liu, Dongping; Saito, H.; Ishio, S.

    2014-01-01

    As the magnetic storage density increases in commercial products, e.g. the hard disc drives, a full understanding of dynamic magnetism in nanometer resolution underpins the development of next-generation products. Magnetic force microscopy (MFM) is well suited to exploring ferromagnetic domain structures. However, atomic resolution cannot be achieved because data acquisition involves the sensing of long-range magnetostatic forces between tip and sample. Moreover, the dynamic magnetism cannot be characterized because MFM is only sensitive to the static magnetic fields. Here, we develop a side-band magnetic force microscopy (MFM) to locally observe the alternating magnetic fields in nanometer length scales at an operating distance of 1 nm. Variations in alternating magnetic fields and their relating time-variable magnetic domain reversals have been demonstrated by the side-band MFM. The magnetic domain wall motions, relating to the periodical rotation of sample magnetization, are quantified via micromagnetics. Based on the side-band MFM, the magnetic moment can be determined locally in a volume as small as 5 nanometers. The present technique can be applied to investigate the microscopic magnetic domain structures in a variety of magnetic materials, and allows a wide range of future applications, for example, in data storage and biomedicine. PMID:25011670

  20. Geostrophic Turbulence in the Frequency-Wavenumber Domain: Eddy-Driven Low-Frequency Variability

    DTIC Science & Technology

    2014-08-01

    2453, doi:10.1175/1520-0442(1995)008,2440: ALTODB.2.0.CO;2. Haidvogel, D. B., and I. M. Held, 1980: Homogeneous quasi - geostrophic turbulence driven...structure of quasi - geostrophic turbulence. J. Atmos. Sci., 43, 2923–2936, doi:10.1175/1520-0469(1986)043,2923: NSOTVS.2.0.CO;2. Hurlburt, H. E., and J...doi:10.5670/oceanog.2002.40. Salmon, R., 1978: Two-layer quasi - geostrophic turbulence in a simple special case. Geophys. Astrophys. Fluid Dyn., 10, 25

  1. Indexing Flowers by Color Names Using Domain Knowledge-Driven Segmentation.

    DTIC Science & Technology

    1997-01-01

    We describe a solution to the problem of indexing image of flowers for searching a flower patents database by ers iii t color. We use a natural...segmentation algorithm with knowledge natnral driven feedback to isolate a flower region from the background. The color of the flower is defined by the...color names present in the flower region and their relative proportions. The database can be queried by example and by color names. We demonstrate the effectiveness of the strategy on a test database.

  2. Data-Driven Soft Decoding of Compressed Images in Dual Transform-Pixel Domain.

    PubMed

    Xianming Liu; Xiaolin Wu; Jiantao Zhou; Debin Zhao

    2016-04-01

    In the large body of research literature on image restoration, very few papers were concerned with compression-induced degradations, although in practice, the most common cause of image degradation is compression. This paper presents a novel approach to restoring JPEG-compressed images. The main innovation is in the approach of exploiting residual redundancies of JPEG code streams and sparsity properties of latent images. The restoration is a sparse coding process carried out jointly in the DCT and pixel domains. The prowess of the proposed approach is directly restoring DCT coefficients of the latent image to prevent the spreading of quantization errors into the pixel domain, and at the same time, using online machine-learned local spatial features to regulate the solution of the underlying inverse problem. Experimental results are encouraging and show the promise of the new approach in significantly improving the quality of DCT-coded images.

  3. Dynamic in situ visualization of voltage-driven magnetic domain evolution in multiferroic heterostructures.

    PubMed

    Gao, Ya; Hu, Jia-Mian; Wu, Liang; Nan, C W

    2015-12-23

    Voltage control of magnetism in multiferroic heterostructures provides a promising solution to the excessive heating in spintronic devices. Direct observation of voltage-modulated magnetic domain evolution dynamics is desirable for studying the mechanism of the voltage control of magnetism at mesoscale, but has remained challenging. Here we explored a characterization method for the dynamic in situ evolution of pure voltage modulated magnetic domains in the heterostructures by employing the scanning Kerr microscopy function in the magneto optic Kerr effect system. The local magnetization reorientation of a Ni/PMN-PT heterostructure were characterized under sweeping applied voltage on the PMN-PT single crystal, and the results show that the magnetization rotation angle in the local regions is much greater than that obtained from macroscopic magnetization hysteresis loops.

  4. Dynamic in situ visualization of voltage-driven magnetic domain evolution in multiferroic heterostructures

    NASA Astrophysics Data System (ADS)

    Gao, Ya; Hu, Jia-Mian; Wu, Liang; Nan, C. W.

    2015-12-01

    Voltage control of magnetism in multiferroic heterostructures provides a promising solution to the excessive heating in spintronic devices. Direct observation of voltage-modulated magnetic domain evolution dynamics is desirable for studying the mechanism of the voltage control of magnetism at mesoscale, but has remained challenging. Here we explored a characterization method for the dynamic in situ evolution of pure voltage modulated magnetic domains in the heterostructures by employing the scanning Kerr microscopy function in the magneto optic Kerr effect system. The local magnetization reorientation of a Ni/PMN-PT heterostructure were characterized under sweeping applied voltage on the PMN-PT single crystal, and the results show that the magnetization rotation angle in the local regions is much greater than that obtained from macroscopic magnetization hysteresis loops.

  5. ATP-Driven Remodeling of the Linker Domain in the Dynein Motor

    PubMed Central

    Roberts, Anthony J.; Malkova, Bara; Walker, Matt L.; Sakakibara, Hitoshi; Numata, Naoki; Kon, Takahide; Ohkura, Reiko; Edwards, Thomas A.; Knight, Peter J.; Sutoh, Kazuo; Oiwa, Kazuhiro; Burgess, Stan A.

    2012-01-01

    Summary Dynein ATPases are the largest known cytoskeletal motors and perform critical functions in cells: carrying cargo along microtubules in the cytoplasm and powering flagellar beating. Dyneins are members of the AAA+ superfamily of ring-shaped enzymes, but how they harness this architecture to produce movement is poorly understood. Here, we have used cryo-EM to determine 3D maps of native flagellar dynein-c and a cytoplasmic dynein motor domain in different nucleotide states. The structures show key sites of conformational change within the AAA+ ring and a large rearrangement of the “linker” domain, involving a hinge near its middle. Analysis of a mutant in which the linker “undocks” from the ring indicates that linker remodeling requires energy that is supplied by interactions with the AAA+ modules. Fitting the dynein-c structures into flagellar tomograms suggests how this mechanism could drive sliding between microtubules, and also has implications for cytoplasmic cargo transport. PMID:22863569

  6. Discrete domain wall positioning due to pinning in current driven motion along nanowires.

    PubMed

    Jiang, Xin; Thomas, Luc; Moriya, Rai; Parkin, Stuart S P

    2011-01-12

    Racetrack memory is a novel storage-class memory device in which a series of domain walls (DWs), representing zeros and ones, are shifted to and fro by current pulses along magnetic nanowires. Here we show, by precise measurements of the DW's position using spin-valve nanowires, that these positions take up discrete values. This results from DW relaxation after the end of the current pulse into local energy minima, likely derived from imperfections in the nanowire.

  7. The connectivity domain: Analyzing resting state fMRI data using feature-based data-driven and model-based methods.

    PubMed

    Iraji, Armin; Calhoun, Vince D; Wiseman, Natalie M; Davoodi-Bojd, Esmaeil; Avanaki, Mohammad R N; Haacke, E Mark; Kou, Zhifeng

    2016-07-01

    Spontaneous fluctuations of resting state functional MRI (rsfMRI) have been widely used to understand the macro-connectome of the human brain. However, these fluctuations are not synchronized among subjects, which leads to limitations and makes utilization of first-level model-based methods challenging. Considering this limitation of rsfMRI data in the time domain, we propose to transfer the spatiotemporal information of the rsfMRI data to another domain, the connectivity domain, in which each value represents the same effect across subjects. Using a set of seed networks and a connectivity index to calculate the functional connectivity for each seed network, we transform data into the connectivity domain by generating connectivity weights for each subject. Comparison of the two domains using a data-driven method suggests several advantages in analyzing data using data-driven methods in the connectivity domain over the time domain. We also demonstrate the feasibility of applying model-based methods in the connectivity domain, which offers a new pathway for the use of first-level model-based methods on rsfMRI data. The connectivity domain, furthermore, demonstrates a unique opportunity to perform first-level feature-based data-driven and model-based analyses. The connectivity domain can be constructed from any technique that identifies sets of features that are similar across subjects and can greatly help researchers in the study of macro-connectome brain function by enabling us to perform a wide range of model-based and data-driven approaches on rsfMRI data, decreasing susceptibility of analysis techniques to parameters that are not related to brain connectivity information, and evaluating both static and dynamic functional connectivity of the brain from a new perspective.

  8. Demand-Driven Clustering in Relational Domains for Predicting Adverse Drug Events.

    PubMed

    Davis, Jesse; Costa, Vítor Santos; Peissig, Peggy; Caldwell, Michael; Berg, Elizabeth; Page, David

    2012-01-01

    Learning from electronic medical records (EMR) is challenging due to their relational nature and the uncertain dependence between a patient's past and future health status. Statistical relational learning is a natural fit for analyzing EMRs but is less adept at handling their inherent latent structure, such as connections between related medications or diseases. One way to capture the latent structure is via a relational clustering of objects. We propose a novel approach that, instead of pre-clustering the objects, performs a demand-driven clustering during learning. We evaluate our algorithm on three real-world tasks where the goal is to use EMRs to predict whether a patient will have an adverse reaction to a medication. We find that our approach is more accurate than performing no clustering, pre-clustering, and using expert-constructed medical heterarchies.

  9. Demand-Driven Clustering in Relational Domains for Predicting Adverse Drug Events

    PubMed Central

    Davis, Jesse; Costa, Vítor Santos; Peissig, Peggy; Caldwell, Michael; Berg, Elizabeth; Page, David

    2013-01-01

    Learning from electronic medical records (EMR) is challenging due to their relational nature and the uncertain dependence between a patient's past and future health status. Statistical relational learning is a natural fit for analyzing EMRs but is less adept at handling their inherent latent structure, such as connections between related medications or diseases. One way to capture the latent structure is via a relational clustering of objects. We propose a novel approach that, instead of pre-clustering the objects, performs a demand-driven clustering during learning. We evaluate our algorithm on three real-world tasks where the goal is to use EMRs to predict whether a patient will have an adverse reaction to a medication. We find that our approach is more accurate than performing no clustering, pre-clustering, and using expert-constructed medical heterarchies. PMID:25285329

  10. Final Technical Report - Integrated Hydrogeophysical and Hydrogeologic Driven Parameter Upscaling for Dual-Domain Transport Modeling

    SciTech Connect

    Shafer, John M

    2012-11-05

    The three major components of this research were: 1. Application of minimally invasive, cost effective hydrogeophysical techniques (surface and borehole), to generate fine scale (~1m or less) 3D estimates of subsurface heterogeneity. Heterogeneity is defined as spatial variability in hydraulic conductivity and/or hydrolithologic zones. 2. Integration of the fine scale characterization of hydrogeologic parameters with the hydrogeologic facies to upscale the finer scale assessment of heterogeneity to field scale. 3. Determination of the relationship between dual-domain parameters and practical characterization data.

  11. Statics and field-driven dynamics of transverse domain walls in biaxial nanowires under uniform transverse magnetic fields

    NASA Astrophysics Data System (ADS)

    Lu, Jie

    2016-06-01

    In this work, we report analytical results on transverse domain wall (TDW) statics and field-driven dynamics in quasi-one-dimensional biaxial nanowires under arbitrary uniform transverse magnetic fields (TMFs) based on the Landau-Lifshitz-Gilbert equation. Without axial driving fields, the static TDW should be symmetric about its center while twisted in its azimuthal angle distribution. By decoupling polar and azimuthal degrees of freedom, an approximate solution is provided which reproduces these features to a great extent. When an axial driving field is applied, the dynamical behavior of a TDW is viewed as the response of its static profile to external excitations. By means of the asymptotic expansion method, the TDW velocity in the traveling-wave mode is obtained, which provides the extent and boundary of the "velocity-enhancement" effect of TMFs on TDWs in biaxial nanowires. Finally, numerical simulations are performed and strongly support our analytics.

  12. Ternary phase diagram of dipalmitoyl-PC/dilauroyl-PC/cholesterol: nanoscopic domain formation driven by cholesterol.

    PubMed Central

    Feigenson, G W; Buboltz, J T

    2001-01-01

    A ternary phase diagram is proposed for the hydrated lamellar lipid mixture dipalmitoylphosphatidylcholine/dilauroylphosphatidylcholine/cholesterol (DPPC/DLPC/cholesterol) at room temperature. The entire composition space has been thoroughly mapped by complementary experimental techniques, revealing interesting phase behavior that has not been previously described. Confocal fluorescence microscopy shows a regime of coexisting DPPC-rich ordered and DLPC-rich fluid lamellar phases, having an upper boundary at apparently constant cholesterol mole fraction chi(chol) approximately 0.16. Fluorescence resonance energy transfer experiments confirm the identification and extent of this two-phase regime and, furthermore, reveal a 1-phase regime between chi(chol) approximately 0.16 and 0.25, consisting of ordered and fluid nanoscopic domains. Dipyrene-PC excimer/monomer measurements confirm the new regime between chi(chol) approximately 0.16 and 0.25 and also show that rigidly ordered phases seem to disappear around chi(chol) approximately 0.25. This study should be considered as a step toward a more complete understanding of lateral heterogeneity within biomembranes. Cholesterol may play a role in domain separation on the nanometer scale. PMID:11371452

  13. Gel formation driven by tunable hydrophobic domain: design of acrylamide macromonomer with oligo hydrophobic segment.

    PubMed

    Nitta, Kyohei; Miyake, Junpei; Watanabe, Junji; Ikeda, Yoshiyuki

    2012-04-09

    Nowadays, biomaterials with amphiphilic properties are undergoing remarkable development. Here, we present one such development, in which we prepared amphiphilic graft copolymers, with a main chain composed of hydroxyethyl acrylamide (HEAA), to introduce hydrophilicity, and a side chain composed of poly(trimethylene carbonate) (PTMC) to introduce tunable hydrophobicity. These macromonomers were created with a novel molecular design, which introduced a ring-opening polymerization by the hydroxyl end group of HEAA in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene, and were analyzed by (1)H NMR and gel permeation chromatography. The amphiphilic graft copolymers were shown to form a hydrogel, the swelling ratio of which was greatly influenced by the number of trimethylene carbonate units. These copolymers also exhibited the Tyndall phenomenon in aqueous solution; they aggregated spontaneously due to hydrogen bonding and hydrophobic interactions, and a sodium 8-anilino-1-naphthalenesulfonate (ANS) fluorescence probe was introduced into the hydrophobic domain. The solution property of ANS in the polymer solution was analyzed by fluorescence measurement and (1)H NMR. The maximum fluorescence wavelength of ANS shifted to shorter wavelengths as the degree of polymerization of the hydrophobic PTMC, the composition of the macromonomer, and the concentration of the copolymer increased. The resulting copolymer formed a polymer micelle structure due to the tunable hydrophobic domain formation in selected solvents. Therefore, these amphiphilic graft copolymers containing a PTMC segment are excellent candidates for use as hydrophobic drug delivery carriers.

  14. Protective Effect of an Antibody against Specific Extracellular Domain of TLR2 on Agonists-Driven Inflammatory and Allergic Response

    PubMed Central

    Guo, Tianwu; Cai, Jun; Peng, Yanxia; Zhang, Lifang; Lan, Qiaofen; Chen, Yanwen; Liao, Huanjin; Xie, Tong; Wu, Ping; Pan, Qingjun

    2016-01-01

    Specific blocking strategies of TLR2-mediated inflammatory signaling and hypersensitivity reactions may offer novel therapeutic strategies to prevent a variety of diseases. In this study, we investigated the blocking effects of a new anti-TLR2 antibody anti-T20 against a 20 mer peptide T20 located in the extracellular specific domain of mouse TLR2. In addition, the effects of the anti-T20 in vitro, measuring the inhibition of the IL-6 and TNF-α production in response to PGN, LTA, and Pam3CSK4-stimulated RAW264.7 cells, were determined. In vivo, the effects of anti-T20 on a lethal anaphylaxis model using PGN-challenged OVA allergic mice, including the rectal temperature and mortality, and serum levels of TNF-α, IL-6, and LTC4 were assayed. The results showed that anti-T20 specifically bound to TLR2 and significantly inhibited PGN, LTA, and Pam3CSK4-driven TNF-α and IL-6 production by RAW264.7 cells. Also, anti-T20 protected OVA allergic mice from PGN-induced lethal anaphylaxis, and the serum levels of TNF-α, IL-6, and LTC4 of anti-T20 treated PGN-challenged OVA allergic mice were decreased as compared to isotype control of anti-T20 treated mice. In summary, this study produced a new antibody against the specific extracellular domain of TLR2 which has protective effect on TLR2 agonists-driven inflammatory and allergic response. PMID:27213155

  15. Magnetic domain-wall creep driven by field and current in Ta/CoFeB/MgO

    NASA Astrophysics Data System (ADS)

    DuttaGupta, S.; Fukami, S.; Kuerbanjiang, B.; Sato, H.; Matsukura, F.; Lazarov, V. K.; Ohno, H.

    2017-05-01

    Creep motion of magnetic domain wall (DW), thermally activated DW dynamics under subthreshold driving forces, is a paradigm to understand the interaction between driven interfaces and applied external forces. Previous investigation has shown that DW in a metallic system interacts differently with current and magnetic field, manifesting itself as different universality classes for the creep motion. In this article, we first review the experimental determination of the universality classes for current- and field-driven DW creeps in a Ta/CoFeB/MgO wire, and then elucidate the underlying factors governing the obtained results. We show that the nature of torque arising from current in association with DW configuration determines universality class for the current-induced creep in this system. We also discuss the correlation between the field-induced DW creep characteristics and structure observed by a transmission electron microscope. The observed results are expected to provide a deeper understanding for physics of DW motion in various magnetic materials.

  16. Phaser crystallographic software.

    PubMed

    McCoy, Airlie J; Grosse-Kunstleve, Ralf W; Adams, Paul D; Winn, Martyn D; Storoni, Laurent C; Read, Randy J

    2007-08-01

    Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F(+) and F(-), give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences DeltaF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community.

  17. Phaser crystallographic software

    PubMed Central

    McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Winn, Martyn D.; Storoni, Laurent C.; Read, Randy J.

    2007-01-01

    Phaser is a program for phasing macromolecular crystal structures by both molecular replacement and experimental phasing methods. The novel phasing algorithms implemented in Phaser have been developed using maximum likelihood and multivariate statistics. For molecular replacement, the new algorithms have proved to be significantly better than traditional methods in discriminating correct solutions from noise, and for single-wavelength anomalous dispersion experimental phasing, the new algorithms, which account for correlations between F + and F −, give better phases (lower mean phase error with respect to the phases given by the refined structure) than those that use mean F and anomalous differences ΔF. One of the design concepts of Phaser was that it be capable of a high degree of automation. To this end, Phaser (written in C++) can be called directly from Python, although it can also be called using traditional CCP4 keyword-style input. Phaser is a platform for future development of improved phasing methods and their release, including source code, to the crystallographic community. PMID:19461840

  18. Steady-state configurations of Dzyaloshinskii domain walls driven by field and current

    NASA Astrophysics Data System (ADS)

    Sánchez-Tejerina, L.; Alejos, O.; Martínez, E.

    2017-02-01

    The dynamics of Dzyaloshinskii domain walls (DDW) in ultrathin ferromagnetic strips with perpendicular magnetic anisotropy, for different values of both perpendicular field and longitudinal current excitation associated to the Spin-Hall effect, has been studied, taking into account different values of the interfacial Dzyaloshinskii-Moriya interaction (DMI). This study has been carried out with the help of the q-Φ one-dimensional model and micromagnetic simulations. We have found that Walker breakdown may be avoided by applying a certain threshold current, even though the inverse effect is also possible. We have also found that, for particular values of field and current, the magnetization within the DDW experiences an abrupt change of orientation, which provokes a change on the contribution of current to the terminal DDW velocity. This effect disappears for sufficiently strong DMI, as it is expected from the model.

  19. Theory of Current-Driven Domain Wall Motion: Spin Transfer versus Momentum Transfer

    NASA Astrophysics Data System (ADS)

    Tatara, Gen; Kohno, Hiroshi

    2004-02-01

    A self-contained theory of the domain wall dynamics in ferromagnets under finite electric current is presented. The current has two effects: one is momentum transfer, which is proportional to the charge current and wall resistivity (ρw); the other is spin transfer, proportional to spin current. For thick walls, as in metallic wires, the latter dominates and the threshold current for wall motion is determined by the hard-axis magnetic anisotropy, except for the case of very strong pinning. For thin walls, as in nanocontacts and magnetic semiconductors, the momentum-transfer effect dominates, and the threshold current is proportional to V0/ρw, V0 being the pinning potential.

  20. Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling.

    PubMed

    Cui, Haosheng; Mim, Carsten; Vázquez, Francisco X; Lyman, Edward; Unger, Vinzenz M; Voth, Gregory A

    2013-01-22

    Endophilin N-BAR (N-terminal helix and Bin/amphiphysin/Rvs) domain tubulates and vesiculates lipid membranes in vitro via its crescent-shaped dimer and four amphipathic helices that penetrate into membranes as wedges. Like F-BAR domains, endophilin N-BAR also forms a scaffold on membrane tubes. Unlike F-BARs, endophilin N-BARs have N-terminal H0 amphipathic helices that are proposed to interact with other N-BARs in oligomer lattices. Recent cryo-electron microscopy reconstructions shed light on the organization of the N-BAR lattice coats on a nanometer scale. However, because of the resolution of the reconstructions, the precise positioning of the amphipathic helices is still ambiguous. In this work, we applied a coarse-grained model to study various membrane remodeling scenarios induced by endophilin N-BARs. We found that H0 helices of N-BARs prefer to align in an antiparallel manner at two ends of the protein to form a stable lattice. The deletion of H0 helices causes disruption of the lattice. In addition, we analyzed the persistence lengths of the protein-coated tubes and found that the stiffness of endophilin N-BAR-coated tubules qualitatively agrees with previous experimental work studying N-BAR-coated tubules. Large-scale simulations on membrane liposomes revealed a systematic relation between H0 helix density and local membrane curvature fluctuations. The data also suggest that the H0 helix is required for BARs to form organized structures on the liposome, further illustrating its important function.

  1. Solvation driven conformational transitions in the second transmembrane domain of mycobacteriophage holin.

    PubMed

    Lella, Muralikrishna; Mahalakshmi, Radhakrishnan

    2017-01-01

    Holins are pore-forming membrane proteins synthesized by lytic phages. The second transmembrane domain (TM2) of Mycobacteriophage D29 holin presents an Ala- and Gly-rich sequence, with a currently unknown structure and function. In this study, we present the spectroscopic characterization of synthetic TM2 in various solvents, detergents, and lipids. We find that TM2 adopts α-helical conformation under conditions that promote intra-strand hydrogen bonding, such as organic solvents and detergent micelles. When we transfer the peptide to a well-hydrated environment, a polyproline II-like structure is obtained. Surprisingly, we find that the polyproline II-like conformation is retained in lipid vesicles. Based on our results, we present a putative role for TM2 in the process of pore formation by holin. © 2016 The Authors. Peptide Science Published by Wiley Periodicals, Inc. Biopolymers (Pept Sci) 108: 1-10, 2017. © 2016 The Authors. Peptide Science Published by Wiley Periodicals, Inc.

  2. Spin-Transfer-Torque Driven Domain Wall Motion in (Ga,Mn)(As,P)

    NASA Astrophysics Data System (ADS)

    Vehstedt, E. K.; Zarbo, L. P.; Vyborny, K.; de Ranieri, E.; Katzgraber, H. G.; Wunderlich, J.; Jungwirth, T.; Sinova, J.

    2012-02-01

    Precise control of domain wall (DW) motion in magnetic materials is a prerequisite for the realization of novel non-volatile and down-scalable logic/memory devices which promise to overcome the limitations of current technologies. While magnetic fields are the obvious choice for DW manipulation, in spin-orbit (SO) coupled materials, electric fields provide an additional means of control via current-induced spin torque. We extend the existing theoretical framework used to describe magnetization dynamics in uniform ferromagnets (FM) to dilute FM semiconductors. Analogous to the study of homogeneous systems, we compute the current-induced internal fields (CIF) corresponding to the spin torques and perform a quantitative analysis of the effect of CIFs on DW motion by solving the phenomenological Landau-Lifshitz-Gilbert equations. Microscopic calculations based on an accurate description of the SO coupling effects are used to estimate the observed anisotropies. Our theoretical efforts are complemented by experimental studies in the SO coupled FM (Ga,Mn)(As,P).

  3. Synthesis, structure-activity relationship and crystallographic studies of 3-substituted indolin-2-one RET inhibitors.

    PubMed

    Mologni, Luca; Rostagno, Roberta; Brussolo, Stefania; Knowles, Phillip P; Kjaer, Svend; Murray-Rust, Judith; Rosso, Enrico; Zambon, Alfonso; Scapozza, Leonardo; McDonald, Neil Q; Lucchini, Vittorio; Gambacorti-Passerini, Carlo

    2010-02-15

    The synthesis, structure-activity relationships (SAR) and structural data of a series of indolin-2-one inhibitors of RET tyrosine kinase are described. These compounds were designed to explore the available space around the indolinone scaffold within RET active site. Several substitutions at different positions were tested and biochemical data were used to draw a molecular model of steric and electrostatic interactions, which can be applied to design more potent and selective RET inhibitors. The crystal structures of RET kinase domain in complex with three inhibitors were solved. All three compounds bound in the ATP pocket and formed two hydrogen bonds with the kinase hinge region. Crystallographic analysis confirmed predictions from molecular modelling and helped refine SAR results. These data provide important information for the development of indolinone inhibitors for the treatment of RET-driven cancers. Copyright 2010 Elsevier Ltd. All rights reserved.

  4. Crystallographic topology and its applications

    SciTech Connect

    Johnson, C.K.; Burnett, M.N.; Dunbar, W.D.

    1996-10-01

    Geometric topology and structural crystallography concepts are combined to define a new area we call Structural Crystallographic Topology, which may be of interest to both crystallographers and mathematicians. In this paper, we represent crystallographic symmetry groups by orbifolds and crystal structures by Morse - functions. The Morse function uses mildly overlapping Gaussian thermal-motion probability density functions centered on atomic sites to form a critical net with peak, pass, pale, and pit critical points joined into a graph by density gradient-flow separatrices. Critical net crystal structure drawings can be made with the ORTEP-III graphics pro- An orbifold consists of an underlying topological space with an embedded singular set that represents the Wyckoff sites of the crystallographic group. An orbifold for a point group, plane group, or space group is derived by gluing together equivalent edges or faces of a crystallographic asymmetric unit. The critical-net-on-orbifold model incorporates the classical invariant lattice complexes of crystallography and allows concise quotient-space topological illustrations to be drawn without the repetition that is characteristic of normal crystal structure drawings.

  5. CIF (Crystallographic Information File): A Standard for Crystallographic Data Interchange

    PubMed Central

    Brown, I. D.

    1996-01-01

    The Crystallographic Information File (CIF) uses the self-defining STAR file structure. This requires the creation of a dictionary of data names and definitions. A basic dictionary of terms needed to describe the crystal structures of small molecules was approved in 1991 and is currently used for the submission of papers to Acta Crystallographica C. A number of extensions to this dictionary are in preparation. By storing the dictionary itself as a STAR file, the definitions and relationships in the CIF dictionary become computer interpretable. This offers many possibilities for the automatic handling of crystallographic information. PMID:27805170

  6. Reversible electrically-driven magnetic domain wall rotation in multiferroic heterostructures to manipulate suspended on-chip magnetic particles

    NASA Astrophysics Data System (ADS)

    Nowakowski, Mark; Sohn, Hyunmin; Liang, Cheng-Yen; Hockel, Joshua; Wetzlar, Kyle; Keller, Scott; McLellan, Brenda; Marcus, Matthew; Doran, Andrew; Young, Anthony; Kläui, Mathias; Carman, Gregory; Bokor, Jeffrey; Candler, Robert

    2015-03-01

    We experimentally demonstrate reversible electrically-driven, strain-mediated domain wall (DW) rotation in Ni rings fabricated on piezoelectric [Pb(Mg1/3Nb2/3) O3]0.66-[PbTiO3]0.34 (PMN-PT) substrates. An electric field applied across the PMN-PT substrate induces a strain in the Ni rings producing DW rotation around the ring toward the dominant PMN-PT strain axis by inverse magnetostriction. We observe DWs reversibly cycled between their initial and rotated state as a function of the applied electric field with x-ray magnetic circular dichroism photo-emission electron microscopy. The DW rotation is analytically predicted using a fully coupled micromagnetic/elastodyanmic multi-physics simulation to verify that the experimental behavior is caused by the electrically-generated strain in this multiferroic system. Finally, this DW rotation is used to capture and manipulate magnetic particles in a fluidic environment to demonstrate a proof-of-concept energy-efficient pathway for multiferroic-based lab-on-a-chip applications. Supported by TANMS (NSF 11-537), E3S, US Dept of Energy (DE-AC02-05CH11231), EU, and DFG.

  7. Electrically driven magnetic domain wall rotation in multiferroic heterostructures to manipulate suspended on-chip magnetic particles.

    PubMed

    Sohn, Hyunmin; Nowakowski, Mark E; Liang, Cheng-yen; Hockel, Joshua L; Wetzlar, Kyle; Keller, Scott; McLellan, Brenda M; Marcus, Matthew A; Doran, Andrew; Young, Anthony; Kläui, Mathias; Carman, Gregory P; Bokor, Jeffrey; Candler, Robert N

    2015-05-26

    In this work, we experimentally demonstrate deterministic electrically driven, strain-mediated domain wall (DW) rotation in ferromagnetic Ni rings fabricated on piezoelectric [Pb(Mg1/3Nb2/3)O3]0.66-[PbTiO3]0.34 (PMN-PT) substrates. While simultaneously imaging the Ni rings with X-ray magnetic circular dichroism photoemission electron microscopy, an electric field is applied across the PMN-PT substrate that induces strain in the ring structures, driving DW rotation around the ring toward the dominant PMN-PT strain axis by the inverse magnetostriction effect. The DW rotation we observe is analytically predicted using a fully coupled micromagnetic/elastodynamic multiphysics simulation, which verifies that the experimental behavior is caused by the electrically generated strain in this multiferroic system. Finally, this DW rotation is used to capture and manipulate micrometer-scale magnetic beads in a fluidic environment to demonstrate a proof-of-concept energy-efficient pathway for multiferroic-based lab-on-a-chip applications.

  8. Crystallographic Groups, Groupoids, and Orbifolds

    SciTech Connect

    Johnson, C.K.

    2000-09-11

    In this note, We first discuss the relationship among crystallographic lattice groups, space groups, and point groups by using a short exact sequence, then in footnotes indicate the classification of those groups. We then introduce screw and glide groupoids as an extension of point groups in a new exact sequence, and list the one-translational-dimension screw and glide groupoids, which require torus and truncated cylinder projection representations in addition to the spherical projection used for point groups. We then briefly discuss the two and three translational dimension groupoids associated with the remaining point groups. Examples of space groups and their groupoid based nomenclature, which is mainly the extended Hermana-Mauguin international crystallographic nomenclature system plus a specific type of coset decomposition, are then given. Next the crystallographic orbifolds are defined and some application problems associated with orbifolds discussed. Finally, the derivation of might be called orbifoldoids is suggested as future research.

  9. The tail domain of myosin M catalyses nucleotide exchange on Rac1 GTPases and can induce actin-driven surface protrusions.

    PubMed

    Geissler, H; Ullmann, R; Soldati, T

    2000-05-01

    Members of the myosin superfamily play crucial roles in cellular processes including management of the cortical cytoskeleton, organelle transport and signal transduction. GTPases of the Rho family act as key control elements in the reorganization of the actin cytoskeleton in response to growth factors, and other functions such as membrane trafficking, transcriptional regulation, growth control and development. Here, we describe a novel unconventional myosin from Dictyostelium discoideum, MyoM. Primary sequence analysis revealed that it has the appearance of a natural chimera between a myosin motor domain and a guanine nucleotide exchange factor (GEF) domain for Rho GTPases. The functionality of both domains was established. Binding of the motor domain to F-actin was ATP-dependent and potentially regulated by phosphorylation. The GEF domain displayed selective activity on Rac1-related GTPases. Overexpression, rather than absence of MyoM, affected the cell morphology and viability. Particularly in response to hypo-osmotic stress, cells overexpressing the MyoM tail domain extended massive actin-driven protrusions. The GEF was enriched at the tip of growing protuberances, probably through its pleckstrin homology domain. MyoM is the first unconventional myosin containing an active Rac-GEF domain, suggesting a role at the interface of Rac-mediated signal transduction and remodeling of the actin cytoskeleton.

  10. A thermophilic mini-chaperonin contains a conserved polypeptide-binding surface: combined crystallographic and NMR studies of the GroEL Apical Domain with implications for substrate interactions

    SciTech Connect

    Hua, Q. X. H.; Dementieva, I. S. D.; Walsh, M. A. W.; Hallenga, K. H.; Weiss, M. A. W.; Joachimiak, A. J.; Biosciences Division; Case Western Reserve Univ.; IRBM P. Angeletti; Purdue Univ.

    2001-02-23

    A homologue of the Escherichia coli GroEL apical domain was obtained from thermophilic eubacterium Thermus thermophilus. The domains share 70 % sequence identity (101 out of 145 residues). The thermal stability of the T. thermophilus apical domain (T{sub m}>100{sup o}C as evaluated by circular dichroism) is at least 35{sup o}C greater than that of the E. coli apical domain (T{sub m}=65{sup o}C). The crystal structure of a selenomethione-substituted apical domain from T. thermophilus was determined to a resolution of 1.78 {angstrom} using multiwavelength-anomalous-diffraction phasing. The structure is similar to that of the E. coli apical domain (root-mean-square deviation 0.45 {angstrom} based on main-chain atoms). The thermophilic structure contains seven additional salt bridges of which four contain charge-stabilized hydrogen bonds. Only one of the additional salt bridges would face the 'Anfinsen cage' in GroEL. High temperatures were exploited to map sites of interactions between the apical domain and molten globules. NMR footprints of apical domain-protein complexes were obtained at elevated temperature using {sup 15}N-{sup 1}H correlation spectra of {sup 15}N-labeled apical domain. Footprints employing two polypeptides unrelated in sequence or structure (an insulin monomer and the SRY high-mobility-group box, each partially unfolded at 50{sup o}C) are essentially the same and consistent with the peptide-binding surface previously defined in E. coli GroEL and its apical domain-peptide complexes. An additional part of this surface comprising a short N-terminal {alpha}-helix is observed. The extended footprint rationalizes mutagenesis studies of intact GroEL in which point mutations affecting substrate binding were found outside the 'classical' peptide-binding site. Our results demonstrate structural conservation of the apical domain among GroEL homologues and conservation of an extended non-polar surface recognizing diverse polypeptides.

  11. Crystallographic properties of fertilizer compounds

    SciTech Connect

    Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

    1991-02-01

    This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA's fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

  12. Triboluminescence dominated by crystallographic orientation

    NASA Astrophysics Data System (ADS)

    Wang, Kuifang; Ma, Liran; Xu, Xuefeng; Wen, Shizhu; Luo, Jianbin

    2016-05-01

    Triboluminescence (TL) is an optical phenomenon that has a long and varied history with broad applications, such as damage detection, X-ray source, and mass health monitoring sensor. So far, the properties and mechanisms of TL remain not completely understood. The TL properties emitted during the sliding contact between Al2O3 and SiO2 surfaces were studied along different crystallographic orientations. In this study, the TL intensity of Al2O3 was significantly enhanced as Al2O3 surface was along a particular crystallographic orientation, which is an unconventional phenomenon. TL enhancement of Al2O3 was not affected by air atmosphere and atomic stocking mode of Al2O3. The enhancement mechanism of Al2O3 may be influenced by the surface state of Al2O3. This work provides a new method to control the intensity of TL and novel ideas to elucidate the TL mechanism.

  13. Crystallographic properties of fertilizer compounds

    SciTech Connect

    Frazier, A.W.; Dillard, E.F.; Thrasher, R.D.; Waerstad, K.R.; Hunter, S.R.; Kohler, J.J.; Scheib, R.M.

    1991-02-01

    This bulletin is a compilation of crystallographic data collected at NFERC on 450 fertilizer-related compounds. In TVA`s fertilizer R and D program, petrographic examination, XRD, and infrared spectroscopy are combined with conventional chemical analysis methods in identifying the individual compounds that occur in fertilizer materials. This handbook brings together the results of these characterization studies and supplemental crystallographic data from the literature. It is in one-compound-per-page, loose-leaf format, ordered alphabetically by IUPAC name. Indexes provided include IUPAC name, formula, group, alternate formula, synonyms, x-ray data, optical data. Tables are given for solids, compounds in commercial MAP and DAP, and matrix materials in phosphate rock.

  14. Triboluminescence dominated by crystallographic orientation

    PubMed Central

    Wang, Kuifang; Ma, Liran; Xu, Xuefeng; Wen, Shizhu; Luo, Jianbin

    2016-01-01

    Triboluminescence (TL) is an optical phenomenon that has a long and varied history with broad applications, such as damage detection, X-ray source, and mass health monitoring sensor. So far, the properties and mechanisms of TL remain not completely understood. The TL properties emitted during the sliding contact between Al2O3 and SiO2 surfaces were studied along different crystallographic orientations. In this study, the TL intensity of Al2O3 was significantly enhanced as Al2O3 surface was along a particular crystallographic orientation, which is an unconventional phenomenon. TL enhancement of Al2O3 was not affected by air atmosphere and atomic stocking mode of Al2O3. The enhancement mechanism of Al2O3 may be influenced by the surface state of Al2O3. This work provides a new method to control the intensity of TL and novel ideas to elucidate the TL mechanism. PMID:27193511

  15. Evaporation-driven transport and precipitation of salt in porous-media: A multi-domain approach

    NASA Astrophysics Data System (ADS)

    Jambhekar, Vishal Arun; Schmid, Karen Sophie; Helmig, Rainer

    2014-05-01

    Introduction: Evaporative salinization a major concern worldwide is observed across many environmental, agricultural and engineering applications. In the context of agriculture, salinization caused due to excess irrigation and use of artificial fertilizers in last few decades deteriorated productive land to a large extent. Many scientists have conducted experimental and numerical studies related to evaporative salinization [1, 2]. However, to our knowledge most of the performed numerical studies neglect the influence of atmospheric processes and free-flow pours-media interaction, which could play a significant role for salinization in a natural system. With our model concept we attempt to study and analyze the influence of atmospheric processes on dissolved salt transport, evaporation dynamics and salt-precipitation. Evaporation is mainly driven by diffusion, related to the vapor pressure gradient across liquid-air interface and advection, related to the tangential wind velocity at the soil surface. Moreover, it is also affected by the complex interactions between the flow and transport processes in the atmosphere and the porous-medium. On the atmosphere side, it is influenced by wind velocity, air temperature, humidity, radiation etc. On the porous-medium side, it is strongly related to the advective and diffusive fluxes, heterogeneity in salinity distribution (causes osmosis) and salt precipitation (causes pore clogging). As discussed in [1] evaporation of saline solutions can be explained into three different stages. Model: Our model is capable to handle coupled single-phase-compositional free and three-phase-compositional porous-media flow and transport. It is based on a two-domain approach, where non-isothermal sub-models are used for free-flow and porous-media sub-domains [3]. The sub-models are coupled using interface conditions ensuring continuity of mass, momentum and energy. This facilitates to describe evaporation independent of any boundary condition at

  16. Crystallization and preliminary X-ray crystallographic study of the wild type and two mutants of the CP1 hydrolytic domain from Aquifex aeolicus leucyl-tRNA synthetase

    SciTech Connect

    Cura, Vincent; Olieric, Natacha; Guichard, Alexandre; Moras, Dino; Cavarelli, Jean

    2005-10-01

    The wild-type editing CP1 domain of A. aeolicus leucyl-tRNA synthetase and two mutant CP1 domains have been overexpressed, purified and crystallized. X-ray diffraction data have been collected to 1.8 Å, which has enabled determination of the structures by molecular replacement. The editing or hydrolytic CP1 domain of leucyl-tRNA synthetase (LeuRS) hydrolyses several misactivated amino acids. The CP1 domain of Aquifex aeolicus LeuRS was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 Å. Crystals diffract to beyond 1.8 Å resolution and contain two monomers in the asymmetric unit. Two CP1 mutants in which a conserved threonine residue essential for the fidelity of the hydrolytic pathway is mutated to alanine or glutamic acid have also been expressed and crystallized. Crystals of the two CP1 mutants are isomorphs of the wild type and diffract to beyond 1.9 Å resolution. All structures were solved by molecular-replacement techniques.

  17. A triad of lys12, lys41, arg78 spatial domain, a novel identified heparin binding site on tat protein, facilitates tat-driven cell adhesion.

    PubMed

    Ai, Jing; Xin, Xianliang; Zheng, Mingyue; Wang, Shuai; Peng, Shuying; Li, Jing; Wang, Limei; Jiang, Hualiang; Geng, Meiyu

    2008-01-01

    Tat protein, released by HIV-infected cells, has a battery of important biological effects leading to distinct AIDS-associated pathologies. Cell surface heparan sulfate protoglycans (HSPGs) have been accepted as endogenous Tat receptors, and the Tat basic domain has been identified as the heparin binding site. However, findings that deletion or substitution of the basic domain inhibits but does not completely eliminate Tat-heparin interactions suggest that the basic domain is not the sole Tat heparin binding site. In the current study, an approach integrating computational modeling, mutagenesis, biophysical and cell-based assays was used to elucidate a novel, high affinity heparin-binding site: a Lys12, Lys41, Arg78 (KKR) spatial domain. This domain was also found to facilitate Tat-driven β1 integrin activation, producing subsequent SLK cell adhesion in an HSPG-dependent manner, but was not involved in Tat internalization. The identification of this new heparin binding site may foster further insight into the nature of Tat-heparin interactions and subsequent biological functions, facilitating the rational design of new therapeutics against Tat-mediated pathological events.

  18. Crystallization and preliminary X-ray crystallographic study of the wild type and two mutants of the CP1 hydrolytic domain from Aquifex aeolicus leucyl-tRNA synthetase.

    PubMed

    Cura, Vincent; Olieric, Natacha; Guichard, Alexandre; Wang, En-Duo; Moras, Dino; Eriani, Gilbert; Cavarelli, Jean

    2005-10-01

    The editing or hydrolytic CP1 domain of leucyl-tRNA synthetase (LeuRS) hydrolyses several misactivated amino acids. The CP1 domain of Aquifex aeolicus LeuRS was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 A. Crystals diffract to beyond 1.8 A resolution and contain two monomers in the asymmetric unit. Two CP1 mutants in which a conserved threonine residue essential for the fidelity of the hydrolytic pathway is mutated to alanine or glutamic acid have also been expressed and crystallized. Crystals of the two CP1 mutants are isomorphs of the wild type and diffract to beyond 1.9 A resolution. All structures were solved by molecular-replacement techniques.

  19. Positive selection in the adhesion domain of Mus sperm Adam genes through gene duplications and function-driven gene complex formations.

    PubMed

    Grayson, Phil; Civetta, Alberto

    2013-09-30

    Sperm and testes-expressed Adam genes have been shown to undergo bouts of positive selection in mammals. Despite the pervasiveness of positive selection signals, it is unclear what has driven such selective bouts. The fact that only sperm surface Adam genes show signals of positive selection within their adhesion domain has led to speculation that selection might be driven by species-specific adaptations to fertilization or sperm competition. Alternatively, duplications and neofunctionalization of Adam sperm surface genes, particularly as it is now understood in rodents, might have contributed to an acceleration of evolutionary rates and possibly adaptive diversification. Here we sequenced and conducted tests of selection within the adhesion domain of sixteen known sperm-surface Adam genes among five species of the Mus genus. We find evidence of positive selection associated with all six Adam genes known to interact to form functional complexes on Mus sperm. A subset of these complex-forming sperm genes also displayed accelerated branch evolution with Adam5 evolving under positive selection. In contrast to our previous findings in primates, selective bouts within Mus sperm Adams showed no associations to proxies of sperm competition. Expanded phylogenetic analysis including sequence data from other placental mammals allowed us to uncover ancient and recent episodes of adaptive evolution. The prevailing signals of rapid divergence and positive selection detected within the adhesion domain of interacting sperm Adams is driven by duplications and potential neofunctionalizations that are in some cases ancient (Adams 2, 3 and 5) or more recent (Adams 1b, 4b and 6).

  20. Positive selection in the adhesion domain of Mus sperm Adam genes through gene duplications and function-driven gene complex formations

    PubMed Central

    2013-01-01

    Background Sperm and testes-expressed Adam genes have been shown to undergo bouts of positive selection in mammals. Despite the pervasiveness of positive selection signals, it is unclear what has driven such selective bouts. The fact that only sperm surface Adam genes show signals of positive selection within their adhesion domain has led to speculation that selection might be driven by species-specific adaptations to fertilization or sperm competition. Alternatively, duplications and neofunctionalization of Adam sperm surface genes, particularly as it is now understood in rodents, might have contributed to an acceleration of evolutionary rates and possibly adaptive diversification. Results Here we sequenced and conducted tests of selection within the adhesion domain of sixteen known sperm-surface Adam genes among five species of the Mus genus. We find evidence of positive selection associated with all six Adam genes known to interact to form functional complexes on Mus sperm. A subset of these complex-forming sperm genes also displayed accelerated branch evolution with Adam5 evolving under positive selection. In contrast to our previous findings in primates, selective bouts within Mus sperm Adams showed no associations to proxies of sperm competition. Expanded phylogenetic analysis including sequence data from other placental mammals allowed us to uncover ancient and recent episodes of adaptive evolution. Conclusions The prevailing signals of rapid divergence and positive selection detected within the adhesion domain of interacting sperm Adams is driven by duplications and potential neofunctionalizations that are in some cases ancient (Adams 2, 3 and 5) or more recent (Adams 1b, 4b and 6). PMID:24079728

  1. Pinning-dependent field-driven domain wall dynamics and thermal scaling in an ultrathin Pt/Co/Pt magnetic film.

    PubMed

    Gorchon, J; Bustingorry, S; Ferré, J; Jeudy, V; Kolton, A B; Giamarchi, T

    2014-07-11

    Magnetic-field-driven domain wall motion in an ultrathin Pt/Co(0.45  nm)/Pt ferromagnetic film with perpendicular anisotropy is studied over a wide temperature range. Three different pinning dependent dynamical regimes are clearly identified: the creep, the thermally assisted flux flow, and the depinning, as well as their corresponding crossovers. The wall elastic energy and microscopic parameters characterizing the pinning are determined. Both the extracted thermal rounding exponent at the depinning transition, ψ=0.15, and the Larkin length crossover exponent, ϕ=0.24, fit well with the numerical predictions.

  2. Field driven ferromagnetic phase nucleation and propagation from the domain boundaries in antiferromagnetically coupled perpendicular anisotropy films

    SciTech Connect

    Hauet, Thomas; Gunther, Christian M.; Hovorka, Ondrej; Berger, Andreas; Im, Mi-Young; Fischer, Peter; Hellwig, Olav

    2008-12-09

    We investigate the reversal process in antiferromagnetically coupled [Co/Pt]{sub X-1}/{l_brace}Co/Ru/[Co/Pt]{sub X-1}{r_brace}{sub 16} multilayer films by combining magnetometry and Magnetic soft X-ray Transmission Microscopy (MXTM). After out-of-plane demagnetization, a stable one dimensional ferromagnetic (FM) stripe domain phase (tiger-tail phase) for a thick stack sample (X=7 is obtained), while metastable sharp antiferromagnetic (AF) domain walls are observed in the remanent state for a thinner stack sample (X=6). When applying an external magnetic field the sharp domain walls of the thinner stack sample transform at a certain threshold field into the FM stripe domain wall phase. We present magnetic energy calculations that reveal the underlying energetics driving the overall reversal mechanisms.

  3. Asymmetrical quartz crystallographic fabrics formed during constrictional deformation

    NASA Astrophysics Data System (ADS)

    Sullivan, W. A.; Beane, R. J.

    2010-10-01

    Numerical simulations predict unique quartz crystallographic fabric patterns for plane strain, flattening, and constriction. Multiple studies support the predictions for plane strain and flattening. To test predictions for constriction, this paper analyzes five examples of quartz crystallographic fabrics from a 1-km-wide domain of L tectonites in the Pigeon Point high-strain zone, Klamath Mountains, California, U.S.A. These samples were deformed under greenschist- to amphibolite-facies conditions. Quartz c-axis fabrics are similar to the predicted double-girdle fabrics except that amphibolite-facies samples exhibit c-axis maxima and are distinctly asymmetrical about the elongation lineations. Activation of different slip systems combined with small deviations from pure constriction account for the c-axis maxima, and noncoaxial flow accounts for the fabric asymmetry. The simple-shear component is randomly oriented in geographic coordinates throughout the domain of L tectonites. These data confirm that numerical simulations predict the quartz c-axis fabric geometry developed during constriction for some deformation conditions, and they confirm the quartz a-axis patterns predicted for constriction for the first time. These data also demonstrate that the relationship between quartz crystallographic fabrics and strain geometry is not straightforward, and they indicate that a-axis fabrics may be more useful indicators of strain geometry variations.

  4. Counter machines and crystallographic structures.

    PubMed

    Jonoska, N; Krajcevski, M; McColm, G

    2016-03-01

    One way to depict a crystallographic structure is by a periodic (di)graph, i.e., a graph whose group of automorphisms has a translational subgroup of finite index acting freely on the structure. We establish a relationship between periodic graphs representing crystallographic structures and an infinite hierarchy of intersection languages ℒ d , d = 0, 1, 2, …, within the intersection classes of deterministic context-free languages. We introduce a class of counter machines that accept these languages, where the machines with d counters recognize the class ℒ d An intersection of d languages in ℒ1 defines ℒ d . We prove that there is a one-to-one correspondence between sets of walks starting and ending in the same unit of a d-dimensional periodic (di)graph and the class of languages in ℒ d . The proof uses the following result: given a digraph Δ and a group G, there is a unique digraph Γ such that G ≤ Aut Γ, G acts freely on the structure, and Γ/G ≅ Δ.

  5. Counter machines and crystallographic structures

    PubMed Central

    Krajcevski, M.; McColm, G.

    2016-01-01

    One way to depict a crystallographic structure is by a periodic (di)graph, i.e., a graph whose group of automorphisms has a translational subgroup of finite index acting freely on the structure. We establish a relationship between periodic graphs representing crystallographic structures and an infinite hierarchy of intersection languages 𝒟𝒞ℒd, d = 0, 1, 2, …, within the intersection classes of deterministic context-free languages. We introduce a class of counter machines that accept these languages, where the machines with d counters recognize the class 𝒟𝒞ℒd An intersection of d languages in 𝒟𝒞ℒ1 defines 𝒟𝒞ℒd. We prove that there is a one-to-one correspondence between sets of walks starting and ending in the same unit of a d-dimensional periodic (di)graph and the class of languages in 𝒟𝒞ℒd. The proof uses the following result: given a digraph Δ and a group G, there is a unique digraph Γ such that G ≤ Aut Γ, G acts freely on the structure, and Γ/G ≅ Δ. PMID:27616944

  6. Crystallization and preliminary X-ray crystallographic study of the wild type and two mutants of the CP1 hydrolytic domain from Aquifex aeolicus leucyl-tRNA synthetase

    PubMed Central

    Cura, Vincent; Olieric, Natacha; Guichard, Alexandre; Wang, En-Duo; Moras, Dino; Eriani, Gilbert; Cavarelli, Jean

    2005-01-01

    The editing or hydrolytic CP1 domain of leucyl-tRNA synthetase (LeuRS) hydrolyses several misactivated amino acids. The CP1 domain of Aquifex aeolicus LeuRS was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. Crystals belong to space group P212121, with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 Å. Crystals diffract to beyond 1.8 Å resolution and contain two monomers in the asymmetric unit. Two CP1 mutants in which a conserved threonine residue essential for the fidelity of the hydrolytic pathway is mutated to alanine or glutamic acid have also been expressed and crystallized. Crystals of the two CP1 mutants are isomorphs of the wild type and diffract to beyond 1.9 Å resolution. All structures were solved by molecular-replacement techniques. PMID:16511190

  7. Current-driven dynamics of Dzyaloshinskii domain walls in the presence of in-plane fields: Full micromagnetic and one-dimensional analysis

    NASA Astrophysics Data System (ADS)

    Martinez, Eduardo; Emori, Satoru; Perez, Noel; Torres, Luis; Beach, Geoffrey S. D.

    2014-06-01

    Current-induced domain wall motion along high perpendicular magnetocrystalline anisotropy multilayers is studied by means of full micromagnetic simulations and a one-dimensional model in the presence of in-plane fields. We consider domain wall motion driven by the spin Hall effect in the presence of the Dzyaloshinskii-Moriya interaction (DMI). In the case of relatively weak DMI, the wall propagates without significant tilting of the wall plane, and the full micromagnetic results are quantitatively reproduced by a simple rigid one-dimensional model. By contrast, significant wall-plane tilting is observed in the case of strong DMI, and a one-dimensional description including the wall tilting is required to qualitatively describe the micromagnetic results. However, in this strong-DMI case, the one-dimensional model exhibits significant quantitative discrepancies from the full micromagnetic results, in particular, when high longitudinal fields are applied in the direction of the internal domain wall magnetization. It is also shown that, even under thermal fluctuations and edge roughness, the domain wall develops a net tilting angle during its current-induced motion along samples with strong DMI.

  8. Current-driven dynamics of Dzyaloshinskii domain walls in the presence of in-plane fields: Full micromagnetic and one-dimensional analysis

    SciTech Connect

    Martinez, Eduardo Perez, Noel; Torres, Luis

    2014-06-07

    Current-induced domain wall motion along high perpendicular magnetocrystalline anisotropy multilayers is studied by means of full micromagnetic simulations and a one-dimensional model in the presence of in-plane fields. We consider domain wall motion driven by the spin Hall effect in the presence of the Dzyaloshinskii-Moriya interaction (DMI). In the case of relatively weak DMI, the wall propagates without significant tilting of the wall plane, and the full micromagnetic results are quantitatively reproduced by a simple rigid one-dimensional model. By contrast, significant wall-plane tilting is observed in the case of strong DMI, and a one-dimensional description including the wall tilting is required to qualitatively describe the micromagnetic results. However, in this strong-DMI case, the one-dimensional model exhibits significant quantitative discrepancies from the full micromagnetic results, in particular, when high longitudinal fields are applied in the direction of the internal domain wall magnetization. It is also shown that, even under thermal fluctuations and edge roughness, the domain wall develops a net tilting angle during its current-induced motion along samples with strong DMI.

  9. Crystallization and preliminary X-ray crystallographic analysis of the Escherichia coli outer membrane cobalamin transporter BtuB in complex with the carboxy-terminal domain of TonB

    SciTech Connect

    Shultis, David D.; Purdy, Michael D.; Banchs, Christian N.; Wiener, Michael C.

    2006-07-01

    Crystals of a complex of the E. coli proteins BtuB (outer membrane cobalamin transporter) and TonB (carboxy-terminal domain) diffracting to 2.1 Å resolution have been obtained. The energy-dependent uptake of organometallic compounds and other micronutrients across the outer membranes of Gram-negative bacteria is carried out by outer membrane active-transport proteins that utilize the proton-motive force of the inner membrane via coupling to the TonB protein. The Escherichia coli outer membrane cobalamin transporter BtuB and a carboxy-terminal domain of the TonB protein, residues 147–239 of the wild-type protein, were expressed and purified individually. A complex of BtuB and TonB{sup 147–239} was formed in the presence of the substrate cyanocobalamin (CN-Cbl; vitamin B{sub 12}) and calcium and was crystallized. BtuB was purified in the detergent LDAO (n-dodecyl-N,N-dimethylamine-N-oxide) and the complex was formed in a detergent mixture of LDAO and C{sub 8}E{sub 4} (tetraethylene glycol monooctylether). Crystals were obtained by sitting-drop vapor diffusion, with the reservoir containing 30%(v/v) polyethylene glycol (PEG 300) and 100 mM sodium acetate pH 5.2. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1} (unit-cell parameters a = 74.3, b = 82.4, c = 122.6 Å). The asymmetric unit consists of a single BtuB–TonB complex. Data sets have been collected to 2.1 Å resolution at a synchrotron beamline (APS SER-CAT 22-ID)

  10. Grade-two fluids on non-smooth domain driven by multiplicative noise: Existence, uniqueness and regularity

    NASA Astrophysics Data System (ADS)

    Razafimandimby, Paul André

    2017-09-01

    In this paper we present a systematic study of a stochastic PDE with multiplicative noise modeling the motion of viscous and inviscid grade-two fluids on a bounded domain O of R2. We aim to identify the minimal conditions on the boundary smoothness of the domain for the well-posedness and time regularity of the solution. In particular, we found out that the existence of a H1 (O) weak martingale solution holds for any bounded Lipschitz domain O. When O is a convex polygon the solution u lives in the Sobolev space W 2 , r (O) for some r > 2 and rot (u - αΔu) is continuous in L2 (O) with respect to the time variable. Moreover, pathwise uniqueness of solution holds. The existence result is new for the stochastic inviscid model and improves previous results for the viscous one. The time continuity result is new, even for the deterministic case when the domain O is a convex polygon.

  11. Fast switching and signature of efficient domain wall motion driven by spin-orbit torques in a perpendicular anisotropy magnetic insulator/Pt bilayer

    NASA Astrophysics Data System (ADS)

    Avci, Can Onur; Rosenberg, Ethan; Baumgartner, Manuel; Beran, Lukáš; Quindeau, Andy; Gambardella, Pietro; Ross, Caroline A.; Beach, Geoffrey S. D.

    2017-08-01

    We report fast and efficient current-induced switching of a perpendicular anisotropy magnetic insulator thulium iron garnet by using spin-orbit torques (SOT) from the Pt overlayer. We first show that, with quasi-DC (10 ms) current pulses, SOT-induced switching can be achieved with an external field as low as 2 Oe, making TmIG an outstanding candidate to realize efficient switching in heterostructures that produce moderate stray fields without requiring an external field. We then demonstrate deterministic switching with fast current pulses (≤20 ns) with an amplitude of ˜1012 A/m2, similar to all-metallic structures. We reveal that, in the presence of an initially nucleated domain, the critical switching current is reduced by up to a factor of five with respect to the fully saturated initial state, implying efficient current-driven domain wall motion in this system. Based on measurements with 2 ns-long pulses, we estimate the domain wall velocity of the order of ˜400 m/s per j = 1012 A/m2.

  12. Steady-state domain wall motion driven by adiabatic spin-transfer torque with assistance of microwave field

    SciTech Connect

    Wang, Xi-guang; Guo, Guang-hua Nie, Yao-zhuang; Xia, Qing-lin; Tang, Wei; Wang, D.; Zeng, Zhong-ming

    2013-12-23

    We have studied the current-induced displacement of a 180° Bloch wall by means of micromagnetic simulation and analytical approach. It is found that the adiabatic spin-transfer torque can sustain a steady-state domain wall (DW) motion in the direction opposite to that of the electron flow without Walker Breakdown when a transverse microwave field is applied. This kind of motion is very sensitive to the microwave frequency and can be resonantly enhanced by exciting the domain wall thickness oscillation mode. A one-dimensional analytical model was established to account for the microwave-assisted wall motion. These findings may be helpful for reducing the critical spin-polarized current density and designing DW-based spintronic devices.

  13. Ferroelectricity driven magnetism at domain walls in LaAlO3/PbTiO3 superlattices

    PubMed Central

    Zhou, P. X.; Dong, S.; Liu, H. M.; Ma, C. Y.; Yan, Z. B.; Zhong, C. G.; Liu, J. -M.

    2015-01-01

    Charge dipole moment and spin moment rarely coexist in single-phase bulk materials except in some multiferroics. Despite the progress in the past decade, for most multiferroics their magnetoelectric performance remains poor due to the intrinsic exclusion between charge dipole and spin moment. As an alternative approach, the oxide heterostructures may evade the intrinsic limits in bulk materials and provide more attractive potential to realize the magnetoelectric functions. Here we perform a first-principles study on LaAlO3/PbTiO3 superlattices. Although neither of the components is magnetic, magnetic moments emerge at the ferroelectric domain walls of PbTiO3 in these superlattices. Such a twist between ferroelectric domain and local magnetic moment, not only manifests an interesting type of multiferroicity, but also is possible useful to pursuit the electrical-control of magnetism in nanoscale heterostructures. PMID:26269322

  14. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain.

    PubMed

    Cruz-Gallardo, Isabel; Aroca, Ángeles; Gunzburg, Menachem J; Sivakumaran, Andrew; Yoon, Je-Hyun; Angulo, Jesús; Persson, Cecilia; Gorospe, Myriam; Karlsson, B Göran; Wilce, Jacqueline A; Díaz-Moreno, Irene

    2014-01-01

    T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein-nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5' TOPs (5' terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations.

  15. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain

    PubMed Central

    Cruz-Gallardo, Isabel; Aroca, Ángeles; Gunzburg, Menachem J; Sivakumaran, Andrew; Yoon, Je-Hyun; Angulo, Jesús; Persson, Cecilia; Gorospe, Myriam; Karlsson, B Göran; Wilce, Jacqueline A; Díaz-Moreno, Irene

    2014-01-01

    T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein–nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5′ TOPs (5′ terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations. PMID:24824036

  16. A knowledge-driven approach for crystallographic protein model completion

    PubMed Central

    Joosten, Krista; Cohen, Serge X.; Emsley, Paul; Mooij, Wijnand; Lamzin, Victor S.; Perrakis, Anastassis

    2008-01-01

    One of the most cumbersome and time-demanding tasks in completing a protein model is building short missing regions or ‘loops’. A method is presented that uses structural and electron-density information to build the most likely conformations of such loops. Using the distribution of angles and dihedral angles in pentapeptides as the driving parameters, a set of possible conformations for the Cα backbone of loops was generated. The most likely candidate is then selected in a hierarchical manner: new and stronger restraints are added while the loop is built. The weight of the electron-density correlation relative to geometrical considerations is gradually increased until the most likely loop is selected on map correlation alone. To conclude, the loop is refined against the electron density in real space. This is started by using structural information to trace a set of models for the Cα backbone of the loop. Only in later steps of the algorithm is the electron-density correlation used as a criterion to select the loop(s). Thus, this method is more robust in low-density regions than an approach using density as a primary criterion. The algorithm is implemented in a loop-building program, Loopy, which can be used either alone or as part of an automatic building cycle. Loopy can build loops of up to 14 residues in length within a couple of minutes. The average root-mean-square deviation of the Cα atoms in the loops built during validation was less than 0.4 Å. When implemented in the context of automated model building in ARP/wARP, Loopy can increase the completeness of the built models. PMID:18391408

  17. Internet Based Open Access Crystallographic Databases

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

    Two freely accessible crystallographic databases are discussed: the Crystallographic Open Database (COD, http://crystallography.net) which contains over 37,000 crystal structures, and the Nano-Crystallography Database (NCD, http://nanocrystallography.research.pdx.edu) which we recently started to support image-based nanocrystallography and (nano) materials science education. Both databases collect crystallographic relevant information in a standardized format; the Crystallographic Information File (CIF). CIF is the standard file format adopted by the International Union of Crystallography (http://iucr.org) for the archiving and distribution of crystallographic information. A subset of the COD, the Predicted Crystallographic Online Database, allows for 3D structural displays of structural polyhedra and wireframes of approximately 2,600 entries. Since electron microscopist are interested in simple, yet technologically important materials, the crystallographic information for those materials will be included in our database. At our NCD site, entries in the COD and the NCD can be visualized in three dimensions (3D) along with (2D) lattice fringe fingerprints plots. The latter supports the identification of unknown nanocrystal phases from high-resolution transmission electron microscopy (HRTEM) images. Morphological crystal information from the database ``Bestimmungstabellen f"ur Kristalle/ ???????????? ??????????,'' (A.K. Boldyrew and W.W. Doliwo-Dobrowolsky, Zentrales Wissenschaftlichers Institute der Geologie und Sch"urfung, Leningrad/ Moscow, 1937/1939) will also be included in the NCD to support image-based nanocrystallography in 3D.

  18. MHD mixed convection and entropy generation of nanofluid filled lid driven cavity under the influence of inclined magnetic fields imposed to its upper and lower diagonal triangular domains

    NASA Astrophysics Data System (ADS)

    Selimefendigil, Fatih; Öztop, Hakan F.; Chamkha, Ali J.

    2016-05-01

    In this study, mixed convection of CuO-water nanofluid filled lid driven cavity having its upper and lower triangular domains under the influence of inclined magnetic fields is numerically investigated. The top horizontal wall of the cavity is moving with constant speed of uw with +x direction while no-slip boundary conditions are imposed on the other walls of the cavity. The top wall of the cavity is maintained at constant cold temperature of Tc while the bottom wall is at hot temperature of Th and on the other walls of the cavity are assumed to be adiabatic. The governing equations are solved by using Galerkin weighted residual finite element formulation. Entropy generation is produced by using formulation and integrated with calculated velocities and temperatures. The numerical investigation is performed for a range of parameters: Richardson number (between 0.01 and 100), Hartmann number (between 0 and 50), inclination angle of magnetic field (between 0° and 90°) and solid volume fraction of the nanofluid (between 0 and 0.05). Different combinations of Hartmann numbers and inclination angles of the magnetic fields are imposed in the upper and lower triangular domains of the square cavity. It is observed that the local and averaged heat transfer deteriorates when the Richardson number, Hartmann number of the triangular domains increase. When the Hartmann number and magnetic angle of the upper triangle are increased, more deterioration of the averaged transfer is obtained when compared to lower triangular domain. Local and averaged heat transfer increase as the solid volume fraction of the nanoparticles increases and adding nanoparticles is more effective for the local enhancement of the heat transfer when the heat transfer rate is high and convection is not damped with lowering the Hartmann number. Second law analysis of the system for different combinations of flow parameters is also performed.

  19. Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation.

    PubMed

    Kronqvist, Nina; Otikovs, Martins; Chmyrov, Volodymyr; Chen, Gefei; Andersson, Marlene; Nordling, Kerstin; Landreh, Michael; Sarr, Médoune; Jörnvall, Hans; Wennmalm, Stefan; Widengren, Jerker; Meng, Qing; Rising, Anna; Otzen, Daniel; Knight, Stefan D; Jaudzems, Kristaps; Johansson, Jan

    2014-01-01

    The mechanisms controlling the conversion of spider silk proteins into insoluble fibres, which happens in a fraction of a second and in a defined region of the silk glands, are still unresolved. The N-terminal domain changes conformation and forms a homodimer when pH is lowered from 7 to 6; however, the molecular details still remain to be determined. Here we investigate site-directed mutants of the N-terminal domain from Euprosthenops australis major ampullate spidroin 1 and find that the charged residues D40, R60 and K65 mediate intersubunit electrostatic interactions. Protonation of E79 and E119 is required for structural conversions of the subunits into a dimer conformation, and subsequent protonation of E84 around pH 5.7 leads to the formation of a fully stable dimer. These residues are highly conserved, indicating that the now proposed three-step mechanism prevents premature aggregation of spidroins and enables fast formation of spider silk fibres in general.

  20. Calcium-Driven Folding of RTX Domain β-Rolls Ratchets Translocation of RTX Proteins through Type I Secretion Ducts.

    PubMed

    Bumba, Ladislav; Masin, Jiri; Macek, Pavel; Wald, Tomas; Motlova, Lucia; Bibova, Ilona; Klimova, Nela; Bednarova, Lucie; Veverka, Vaclav; Kachala, Michael; Svergun, Dmitri I; Barinka, Cyril; Sebo, Peter

    2016-04-07

    Calcium-binding RTX proteins are equipped with C-terminal secretion signals and translocate from the Ca(2+)-depleted cytosol of Gram-negative bacteria directly into the Ca(2+)-rich external milieu, passing through the "channel-tunnel" ducts of type I secretion systems (T1SSs). Using Bordetella pertussis adenylate cyclase toxin, we solved the structure of an essential C-terminal assembly that caps the RTX domains of RTX family leukotoxins. This is shown to scaffold directional Ca(2+)-dependent folding of the carboxy-proximal RTX repeat blocks into β-rolls. The resulting intramolecular Brownian ratchets then prevent backsliding of translocating RTX proteins in the T1SS conduits and thereby accelerate excretion of very large RTX leukotoxins from bacterial cells by a vectorial "push-ratchet" mechanism. Successive Ca(2+)-dependent and cosecretional acquisition of a functional RTX toxin structure in the course of T1SS-mediated translocation, through RTX domain folding from the C-terminal cap toward the N terminus, sets a paradigm that opens for design of virulence inhibitors of major pathogens. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. The New NRL Crystallographic Database

    NASA Astrophysics Data System (ADS)

    Mehl, Michael; Curtarolo, Stefano; Hicks, David; Toher, Cormac; Levy, Ohad; Hart, Gus

    For many years the Naval Research Laboratory maintained an online graphical database of crystal structures for a wide variety of materials. This database has now been redesigned, updated and integrated with the AFLOW framework for high throughput computational materials discovery (http://materials.duke.edu/aflow.html). For each structure we provide an image showing the atomic positions; the primitive vectors of the lattice and the basis vectors of every atom in the unit cell; the space group and Wyckoff positions; Pearson symbols; common names; and Strukturbericht designations, where available. References for each structure are provided, as well as a Crystallographic Information File (CIF). The database currently includes almost 300 entries and will be continuously updated and expanded. It enables easy search of the various structures based on their underlying symmetries, either by Bravais lattice, Pearson symbol, Strukturbericht designation or commonly used prototypes. The talk will describe the features of the database, and highlight its utility for high throughput computational materials design. Work at NRL is funded by a Contract with the Duke University Department of Mechanical Engineering.

  2. Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite.

    PubMed

    Xu, Xuan; Wollenberger, Ulla; Qian, Jing; Lettau, Katrin; Jung, Christiane; Liu, Songqin

    2013-12-01

    Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanoparticles and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (ket) of 154.8 ± 0.1s(-1) at the scan rate of 5 Vs(-1). Moreover, the substrate N(ω)-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at +0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III

    PubMed Central

    Bezerra, Gustavo A.; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramić, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

    2012-01-01

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft (“entropy reservoir”) as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies. PMID:22493238

  4. Temperature estimation in a ferromagnetic Fe-Ni nanowire involving a current-driven domain wall motion.

    PubMed

    Yamaguchi, A; Hirohata, A; Ono, T; Miyajima, H

    2012-01-18

    We observed a magnetic domain wall (DW) motion induced by the spin-polarized pulsed current in a nanoscale Fe(19)Ni(81) wire using a magnetic force microscope. High current density, which is of the order of 10(11) A m(-2), was required for the DW motion. A simple method to estimate the temperature of the wire was developed by comparing the wire resistance measured during the DW motion with the temperature dependence of the wire resistance. Using this method, we found the temperature of the wire was proportional to the square of the current density and became just beneath at the threshold Curie temperature. Our experimental data qualitatively support this analytical model that the temperature is proportional to the resistivity, thickness, width of the wire and the square of the current density, and also inversely proportional to the thermal conductivity.

  5. Tim50’s presequence receptor domain is essential for signal driven transport across the TIM23 complex

    PubMed Central

    Schulz, Christian; Lytovchenko, Oleksandr; Melin, Jonathan; Chacinska, Agnieszka; Guiard, Bernard; Neumann, Piotr; Ficner, Ralf; Schmidt, Bernhard

    2011-01-01

    N-terminal targeting signals (presequences) direct proteins across the TOM complex in the outer mitochondrial membrane and the TIM23 complex in the inner mitochondrial membrane. Presequences provide directionality to the transport process and regulate the transport machineries during translocation. However, surprisingly little is known about how presequence receptors interact with the signals and what role these interactions play during preprotein transport. Here, we identify signal-binding sites of presequence receptors through photo-affinity labeling. Using engineered presequence probes, photo cross-linking sites on mitochondrial proteins were mapped mass spectrometrically, thereby defining a presequence-binding domain of Tim50, a core subunit of the TIM23 complex that is essential for mitochondrial protein import. Our results establish Tim50 as the primary presequence receptor at the inner membrane and show that targeting signals and Tim50 regulate the Tim23 channel in an antagonistic manner. PMID:22065641

  6. Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III.

    PubMed

    Bezerra, Gustavo A; Dobrovetsky, Elena; Viertlmayr, Roland; Dong, Aiping; Binter, Alexandra; Abramic, Marija; Macheroux, Peter; Dhe-Paganon, Sirano; Gruber, Karl

    2012-04-24

    Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.

  7. ReVeaLD: a user-driven domain-specific interactive search platform for biomedical research.

    PubMed

    Kamdar, Maulik R; Zeginis, Dimitris; Hasnain, Ali; Decker, Stefan; Deus, Helena F

    2014-02-01

    Bioinformatics research relies heavily on the ability to discover and correlate data from various sources. The specialization of life sciences over the past decade, coupled with an increasing number of biomedical datasets available through standardized interfaces, has created opportunities towards new methods in biomedical discovery. Despite the popularity of semantic web technologies in tackling the integrative bioinformatics challenge, there are many obstacles towards its usage by non-technical research audiences. In particular, the ability to fully exploit integrated information needs using improved interactive methods intuitive to the biomedical experts. In this report we present ReVeaLD (a Real-time Visual Explorer and Aggregator of Linked Data), a user-centered visual analytics platform devised to increase intuitive interaction with data from distributed sources. ReVeaLD facilitates query formulation using a domain-specific language (DSL) identified by biomedical experts and mapped to a self-updated catalogue of elements from external sources. ReVeaLD was implemented in a cancer research setting; queries included retrieving data from in silico experiments, protein modeling and gene expression. ReVeaLD was developed using Scalable Vector Graphics and JavaScript and a demo with explanatory video is available at http://www.srvgal78.deri.ie:8080/explorer. A set of user-defined graphic rules controls the display of information through media-rich user interfaces. Evaluation of ReVeaLD was carried out as a game: biomedical researchers were asked to assemble a set of 5 challenge questions and time and interactions with the platform were recorded. Preliminary results indicate that complex queries could be formulated under less than two minutes by unskilled researchers. The results also indicate that supporting the identification of the elements of a DSL significantly increased intuitiveness of the platform and usability of semantic web technologies by domain users

  8. Flow in complex domains simulated by Dissipative Particle Dynamics driven by geometry-specific body-forces

    NASA Astrophysics Data System (ADS)

    Yazdani, Alireza; Deng, Mingge; Caswell, Bruce; Karniadakis, George Em

    2016-01-01

    We demonstrate how the quality of simulations by Dissipative Particle Dynamics (DPD) of flows in complex geometries is greatly enhanced when driven by body forces suitably tailored to the geometry. In practice, the body force fields are most conveniently chosen to be the pressure gradient of the corresponding Navier-Stokes (N-S) flow. In the first of three examples, the driving-force required to yield a stagnation-point flow is derived from the pressure field of the potential flow for a lattice of counter-rotating line vortices. Such a lattice contains periodic squares bounded by streamlines with four vortices within them. Hence, the DPD simulation can be performed with periodic boundary conditions to demonstrate the value of a non-uniform driving-force without the need to model real boundaries. The second example is an irregular geometry consisting of a 2D rectangular cavity on one side of an otherwise uniform channel. The Navier-Stokes pressure field for the same geometry is obtained numerically, and its interpolated gradient is then employed as the driving-force for the DPD simulation. Finally, we present a third example, where the proposed method is applied to a complex 3D geometry of an asymmetric constriction. It is shown that in each case the DPD simulations closely reproduce the Navier-Stokes solutions. Convergence rates are found to be much superior to alternative methods; in addition, the range of convergence with respect to Reynolds number and Mach number is greatly extended.

  9. Defining the Crystallographic Fingerprint of Extraterrestrial Treasures

    NASA Astrophysics Data System (ADS)

    Forman, L. V.; Bland, P. A.; Timms, N. E.; Daly, L.; Benedix, G. K.; Trimby, P. W.

    2016-08-01

    An approach to determine the crystallographic fingerprint of chondritic matrix grains, which is complimentary to the geochemical signature commonly identified to constrain some aspects of the petrogenesis of a sample.

  10. Kinetically driven refolding of the hyperstable EBNA1 origin DNA-binding dimeric beta-barrel domain into amyloid-like spherical oligomers.

    PubMed

    Freire, Eleonora; Oddo, Cristian; Frappier, Lori; de Prat-Gay, Gonzalo

    2008-02-01

    The Epstein-Barr nuclear antigen 1 (EBNA1) is essential for DNA replication and episome segregation of the viral genome, and participates in other gene regulatory processes of the Epstein-Barr virus in benign and malignant diseases related to this virus. Despite the participation of other regions of the protein in evading immune response, its DNA binding, dimeric beta-barrel domain (residues 452-641) is necessary and sufficient for the main functions. This domain has an unusual topology only shared by another viral origin binding protein (OBP), the E2 DNA binding domain of papillomaviruses. Both the amino acid and DNA target sequences are completely different for these two proteins, indicating a link between fold conservation and function. In this work we investigated the folding and stability of the DNA binding domain of EBNA1 OBP and found it is extremely resistant to chemical, temperature, and pH denaturation. The thiocyanate salt of guanidine is required for obtaining a complete transition to a monomeric unfolded state. The unfolding reaction is extremely slow and shows a marked uncoupling between tertiary and secondary structure, indicating the presence of intermediate species. The Gdm.SCN unfolded protein refolds to fully soluble and spherical oligomeric species of 1.2 MDa molecular weight, with identical fluorescence centre of spectral mass but different intensity and different secondary structure. The refolded spherical oligomers are substantially less stable than the native recombinant dimer. In keeping with the substantial structural rearrangement in the oligomers, the spherical oligomers do not bind DNA, indicating that the DNA binding site is either disrupted or participates in the oligomerization interface. The puzzling extreme stability of a dimeric DNA binding domain from a protein from a human infecting virus in addition to a remarkable kinetically driven folding where all molecules do not return to the most stable original species suggests a co

  11. Effect of metallic walls on dynamos generated by laminar boundary-driven flow in a spherical domain.

    PubMed

    Guervilly, Céline; Wood, Toby S; Brummell, Nicholas H

    2013-11-01

    We present a numerical study of dynamo action in a conducting fluid encased in a metallic spherical shell. Motions in the fluid are driven by differential rotation of the outer metallic shell, which we refer to as "the wall." The two hemispheres of the wall are held in counter-rotation, producing a steady, axisymmetric interior flow consisting of differential rotation and a two-cell meridional circulation with radial inflow in the equatorial plane. From previous studies, this type of flow is known to maintain a stationary equatorial dipole by dynamo action if the magnetic Reynolds number is larger than about 300 and if the outer boundary is electrically insulating. We vary independently the thickness, electrical conductivity, and magnetic permeability of the wall to determine their effect on the dynamo action. The main results are the following: (a) Increasing the conductivity of the wall hinders the dynamo by allowing eddy currents within the wall, which are induced by the relative motion of the equatorial dipole field and the wall. This processes can be viewed as a skin effect or, equivalently, as the tearing apart of the dipole by the differential rotation of the wall, to which the field lines are anchored by high conductivity. (b) Increasing the magnetic permeability of the wall favors dynamo action by constraining the magnetic field lines in the fluid to be normal to the wall, thereby decoupling the fluid from any induction in the wall. (c) Decreasing the wall thickness limits the amplitude of the eddy currents, and is therefore favorable for dynamo action, provided that the wall is thinner than the skin depth. We explicitly demonstrate these effects of the wall properties on the dynamo field by deriving an effective boundary condition in the limit of vanishing wall thickness.

  12. Adaptive Immunity against Leishmania Nucleoside Hydrolase Maps Its C-Terminal Domain as the Target of the CD4+ T Cell–Driven Protective Response

    PubMed Central

    Nico, Dirlei; Claser, Carla; Borja-Cabrera, Gulnara P.; Travassos, Luiz R.; Palatnik, Marcos; da Silva Soares, Irene; Rodrigues, Mauricio Martins; Palatnik-de-Sousa, Clarisa B.

    2010-01-01

    Nucleoside hydrolases (NHs) show homology among parasite protozoa, fungi and bacteria. They are vital protagonists in the establishment of early infection and, therefore, are excellent candidates for the pathogen recognition by adaptive immune responses. Immune protection against NHs would prevent disease at the early infection of several pathogens. We have identified the domain of the NH of L. donovani (NH36) responsible for its immunogenicity and protective efficacy against murine visceral leishmaniasis (VL). Using recombinant generated peptides covering the whole NH36 sequence and saponin we demonstrate that protection against L. chagasi is related to its C-terminal domain (amino-acids 199–314) and is mediated mainly by a CD4+ T cell driven response with a lower contribution of CD8+ T cells. Immunization with this peptide exceeds in 36.73±12.33% the protective response induced by the cognate NH36 protein. Increases in IgM, IgG2a, IgG1 and IgG2b antibodies, CD4+ T cell proportions, IFN-γ secretion, ratios of IFN-γ/IL-10 producing CD4+ and CD8+ T cells and percents of antibody binding inhibition by synthetic predicted epitopes were detected in F3 vaccinated mice. The increases in DTH and in ratios of TNFα/IL-10 CD4+ producing cells were however the strong correlates of protection which was confirmed by in vivo depletion with monoclonal antibodies, algorithm predicted CD4 and CD8 epitopes and a pronounced decrease in parasite load (90.5–88.23%; p = 0.011) that was long-lasting. No decrease in parasite load was detected after vaccination with the N-domain of NH36, in spite of the induction of IFN-γ/IL-10 expression by CD4+ T cells after challenge. Both peptides reduced the size of footpad lesions, but only the C-domain reduced the parasite load of mice challenged with L. amazonensis. The identification of the target of the immune response to NH36 represents a basis for the rationale development of a bivalent vaccine against leishmaniasis and for

  13. The effect of Dzyaloshinskii-Moriya interaction on field-driven domain wall dynamics analysed by a semi-analytical approach

    NASA Astrophysics Data System (ADS)

    Vandermeulen, J.; Nasseri, S. A.; Van de Wiele, B.; Durin, G.; Van Waeyenberge, B.; Dupré, L.

    2016-11-01

    Fast domain wall (DW) propagation through perpendicularly magnetized nanostrips with a Dzyaloshinskii-Moriya interaction (DMI) offers promising opportunities for the development of magnetic memory and logic devices. However, as the DW speed increases, the DW magnetization is also progressively affected which ultimately leads to an unstable DW and a drop in the velocity, i.e. the Walker breakdown. In this paper, we introduce a semi-analytical approach to describe and quantify changes to the internal degrees of freedom of the DW. By spatially averaging the Landau-Lifshitz-Gilbert equation, we derive equations of motion and identify seven DW variables in addition to the DW position. This contrasts analytical models where such variables are introduced in an ansatz for the DW shape. We apply this to a field driven DW motion and we study the effect of DMI in detail. Our method helps characterize the opposing and reinforcing effects of the different interactions involved, contributing to our understanding of the Walker breakdown.

  14. Field-driven domain wall motion under a bias current in the creep and flow regimes in Pt/[CoSiB/Pt]N nanowires.

    PubMed

    Choi, Y H; Yoshimura, Y; Kim, K-J; Lee, K; Kim, T W; Ono, T; You, C-Y; Jung, M H

    2016-03-31

    The dynamics of magnetic domain wall (DW) in perpendicular magnetic anisotropy Pt/[CoSiB/Pt]N nanowires was studied by measuring the DW velocity under a magnetic field (H) and an electric current (J) in two extreme regimes of DW creep and flow. Two important findings are addressed. One is that the field-driven DW velocity increases with increasing N in the flow regime, whereas the trend is inverted in the creep regime. The other is that the sign of spin current-induced effective field is gradually reversed with increasing N in both DW creep and flow regimes. To reveal the underlying mechanism of new findings, we performed further experiment and micromagnetic simulation, from which we found that the observed phenomena can be explained by the combined effect of the DW anisotropy, Dzyaloshinskii-Moriya interaction, spin-Hall effect, and spin-transfer torques. Our results shed light on the mechanism of DW dynamics in novel amorphous PMA nanowires, so that this work may open a path to utilize the amorphous PMA in emerging DW-based spintronic devices.

  15. Field-driven domain wall motion under a bias current in the creep and flow regimes in Pt/[CoSiB/Pt]N nanowires

    PubMed Central

    Choi, Y. H.; Yoshimura, Y.; Kim, K.-J.; Lee, K.; Kim, T. W.; Ono, T.; You, C.-Y.; Jung, M. H.

    2016-01-01

    The dynamics of magnetic domain wall (DW) in perpendicular magnetic anisotropy Pt/[CoSiB/Pt]N nanowires was studied by measuring the DW velocity under a magnetic field (H) and an electric current (J) in two extreme regimes of DW creep and flow. Two important findings are addressed. One is that the field-driven DW velocity increases with increasing N in the flow regime, whereas the trend is inverted in the creep regime. The other is that the sign of spin current-induced effective field is gradually reversed with increasing N in both DW creep and flow regimes. To reveal the underlying mechanism of new findings, we performed further experiment and micromagnetic simulation, from which we found that the observed phenomena can be explained by the combined effect of the DW anisotropy, Dzyaloshinskii-Moriya interaction, spin-Hall effect, and spin-transfer torques. Our results shed light on the mechanism of DW dynamics in novel amorphous PMA nanowires, so that this work may open a path to utilize the amorphous PMA in emerging DW-based spintronic devices. PMID:27030379

  16. Avertin®, but Not Volatile Anesthetics Addressing the Two-Pore Domain K+ Channel, TASK-1, Slows Down Cilia-Driven Particle Transport in the Mouse Trachea

    PubMed Central

    Murtaza, Ghulam; Mermer, Petra; Pfeil, Uwe; Kummer, Wolfgang

    2016-01-01

    Rationale Volatile anesthetics inhibit mucociliary clearance in the airways. The two-pore domain K+ channel, TASK-1, represents one of their molecular targets in that they increase its open probability. Here, we determine whether particle transport speed (PTS) at the mucosal surface of the mouse trachea, an important factor of the cilia-driven mechanism in mucociliary clearance, is regulated by TASK-1. Methodology/Results RT-PCR analysis revealed expression of TASK-1 mRNA in the manually dissected and laser-assisted microdissected tracheal epithelium of the mouse. Effects of anesthetics (isoflurane and Avertin®) and TASK-1 inhibitors (anandamide and A293) on ciliary activity were investigated by assessment of PTS at the mucosal surface of the explanted and opened murine trachea. Neither TASK-1 inhibitors nor isoflurane had any impact on basal and ATP-stimulated PTS. Avertin® reduced basal PTS, and ATP-stimulated PTS decreased in its presence in wild-type (WT) mice. Avertin®-induced decrease in basal PTS persisted in WT mice in the presence of TASK-1 inhibitors, and in two different strains of TASK-1 knockout mice. Conclusions/Significance Our findings indicate that TASK-1 is expressed by the tracheal epithelium but is not critically involved in the regulation of tracheal PTS in mice. Avertin® reduces PTS independent of TASK-1. PMID:27930725

  17. Mutations in NOTCH1 PEST-domain orchestrate CCL19-driven homing of Chronic Lymphocytic Leukemia cells by modulating the tumor suppressor gene DUSP22.

    PubMed

    Arruga, F; Gizdic, B; Bologna, C; Cignetto, S; Buonincontri, R; Serra, S; Vaisitti, T; Gizzi, K; Vitale, N; Garaffo, G; Mereu, E; Diop, F; Neri, F; Incarnato, D; Coscia, M; Allan, J; Piva, R; Oliviero, S; Furman, R R; Rossi, D; Gaidano, G; Deaglio, S

    2016-12-26

    Even if NOTCH1 is commonly mutated in Chronic Lymphocytic Leukemia (CLL), its functional impact in the disease remains unclear. Using CRISPR/Cas9-generated Mec-1 cell line models, we show that NOTCH1 regulates growth and homing of CLL cells by dictating expression levels of the tumor suppressor gene DUSP22. Specifically, NOTCH1 affects the methylation of DUSP22 promoter by modulating a nuclear complex, which tunes the activity of DNA methyltransferase 3A (DNMT3A). These effects are enhanced by PEST-domain mutations, which stabilize the molecule and prolong signaling. CLL patients with a NOTCH1-mutated clone showed low levels of DUSP22 and active chemotaxis to CCL19. Lastly, in xenograft models, NOTCH1-mutated cells displayed a unique homing behavior, localizing preferentially to the spleen and brain. These findings connect NOTCH1, DUSP22, and CCL19-driven chemotaxis within a single functional network, suggesting that modulation of the homing process may provide a relevant contribution to the unfavorable prognosis associated with NOTCH1 mutations in CLL.Leukemia accepted article preview online, 26 December 2016. doi:10.1038/leu.2016.383.

  18. Metrics for comparison of crystallographic maps

    SciTech Connect

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; Terwilliger, Thomas C.; Adams, Paul D.

    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, such as regions of high density, are of interest.

  19. Confessions of an icosahedral virus crystallographer.

    PubMed

    Johnson, John E

    2013-02-01

    This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses.

  20. Confessions of an icosahedral virus crystallographer

    PubMed Central

    Johnson, John E.

    2013-01-01

    This is a personal history of my structural studies of icosahedral viruses that evolved from crystallographic studies, to hybrid methods with electron cryo-microscopy and image reconstruction (cryoEM) and then developed further by incorporating a variety of physical methods to augment the high resolution crystallographic studies. It is not meant to be comprehensive, even for my own work, but hopefully provides some perspective on the growth of our understanding of these remarkable biologic assemblies. The goal is to provide a historical perspective for those new to the field and to emphasize the limitations of any one method, even those that provide atomic resolution information about viruses. PMID:23291268

  1. Metrics for comparison of crystallographic maps

    PubMed Central

    Urzhumtsev, Alexandre; Afonine, Pavel V.; Lunin, Vladimir Y.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-01-01

    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, such as regions of high density, are of interest. PMID:25286844

  2. 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…

  3. Crystallographic orientation inhomogeneity and crystal splitting in biogenic calcite

    PubMed Central

    Checa, Antonio G.; Bonarski, Jan T.; Willinger, Marc G.; Faryna, Marek; Berent, Katarzyna; Kania, Bogusz; González-Segura, Alicia; Pina, Carlos M.; Pospiech, Jan; Morawiec, Adam

    2013-01-01

    The calcitic prismatic units forming the outer shell of the bivalve Pinctada margaritifera have been analysed using scanning electron microscopy–electron back-scatter diffraction, transmission electron microscopy and atomic force microscopy. In the initial stages of growth, the individual prismatic units are single crystals. Their crystalline orientation is not consistent but rather changes gradually during growth. The gradients in crystallographic orientation occur mainly in a direction parallel to the long axis of the prism, i.e. perpendicular to the shell surface and do not show preferential tilting along any of the calcite lattice axes. At a certain growth stage, gradients begin to spread and diverge, implying that the prismatic units split into several crystalline domains. In this way, a branched crystal, in which the ends of the branches are independent crystalline domains, is formed. At the nanometre scale, the material is composed of slightly misoriented domains, which are separated by planes approximately perpendicular to the c-axis. Orientational gradients and splitting processes are described in biocrystals for the first time and are undoubtedly related to the high content of intracrystalline organic molecules, although the way in which these act to induce the observed crystalline patterns is a matter of future research. PMID:23804442

  4. Preliminary crystallographic characterization of an RNA helicase from Kunjin virus

    SciTech Connect

    Mastrangelo, Eloise; Bollati, Michela; Milani, Mario; Brisbarre, Nadège; Lamballerie, Xavier de; Coutard, Bruno; Canard, Bruno; Khromykh, Alexander; Bolognesi, Martino

    2006-09-01

    The C-terminal 440 amino acids of the NS3 protein from Kunjin virus (Flaviviridae) code for a helicase. The protein has been overexpressed and crystallized. Characterization of the isolated monoclinic crystal form and diffraction data (at 3.0 Å resolution) are presented, together with a preliminary molecular-replacement solution. Kunjin virus is a member of the Flavivirus genus and is an Australian variant of West Nile virus. The C-terminal domain of the Kunjin virus NS3 protein displays helicase activity. The protein is thought to separate daughter and template RNA strands, assisting the initiation of replication by unwinding RNA secondary structure in the 3′ nontranslated region. Expression, purification and preliminary crystallographic characterization of the NS3 helicase domain are reported. It is shown that Kunjin virus helicase may adopt a dimeric assembly in absence of nucleic acids, oligomerization being a means to provide the helicases with multiple nucleic acid-binding capability, facilitating translocation along the RNA strands. Kunjin virus NS3 helicase domain is an attractive model for studying the molecular mechanisms of flavivirus replication, while simultaneously providing a new basis for the rational development of anti-flaviviral compounds.

  5. 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

  6. A preliminary neutron crystallographic study of thaumatin.

    PubMed

    Teixeira, Susana C M; Blakeley, Matthew P; Leal, Ricardo M F; Mitchell, Edward P; Forsyth, V Trevor

    2008-05-01

    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 A on the LADI-III diffractometer at the Institut Laue Langevin (ILL). 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.

  7. A preliminary neutron crystallographic study of thaumatin

    PubMed Central

    Teixeira, Susana C. M.; Blakeley, Matthew P.; Leal, Ricardo M. F.; Mitchell, Edward P.; Forsyth, V. Trevor

    2008-01-01

    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). 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. PMID:18453706

  8. 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

  9. Quantum crystallographic charge density of urea

    SciTech Connect

    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 data 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.

  10. A preliminary neutron crystallographic study of thaumatin

    SciTech Connect

    Teixeira, Susana C. M.; Blakeley, Matthew P.; Leal, Ricardo M. F.; Mitchell, Edward P.; Forsyth, V. Trevor

    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). 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.

  11. Quantum crystallographic charge density of urea.

    PubMed

    Wall, Michael E

    2016-07-01

    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 data 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. 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.

  12. Crystallographic texture determinations from inverse susceptibility measurements

    NASA Astrophysics Data System (ADS)

    Lewis, L. H.; Welch, D. O.

    1997-04-01

    Determination of the quantitative relationship between crystallographic texture and magnetic properties in advanced permanent magnets may be hampered by complex microstructures, which complicate methods that rely on diffraction, or by interparticulate interactions, which adversely affect methods based on magnetic remanence measurements. To this end, new techniques in the determination of texture of bulk permanent magnets are being explored to overcome these inherent experimental difficulties. The analysis of inverse paramagnetic susceptibility measurements constitutes a new method to investigate crystallographic texture. Such measurements also provide Curie temperature data, which are sensitive to chemical changes that may have occurred in the magnetic phase during processing. The mathematical formalism underlying the analysis of inverse susceptibility measurements is outlined, and is used to evaluate magnetic measurements taken from a series of Nd2Fe14B magnets that have been processed by different means, and thus contain different degrees of texture. While this method does provide qualitative information concerning the relative crystallographic alignment of magnet samples, it needs calibration to obtain an explicit value for a texture order parameter.

  13. Crystallographic studies of the Anthrax lethal toxin. Annual report

    SciTech Connect

    Frederick, C.A.

    1996-07-01

    The lethal form of Anthrax results from the inhalation of anthrax spores. Death is primarily due to the effects of the lethal toxin (Protective Antigen (PA) + Lethal Factor) from the causative agent, Bacillus anthracis. All the Anthrax vaccines currently in use or under development contain or produce PA, the major antigenic component of anthrax toxin, and there is a clear need for an improved vaccine for human use. In the previous report we described the first atomic resolution structure of PA, revealing that the molecule is composed largely of beta-sheets organized into four domains. This information can be used in the design. of recombinant PA vaccines. In this report we describe additional features of the full-length PA molecule derived from further crystallographic refinement and careful examination of the structure. We compare two crystal forms of PA grown at different pH values and discuss the functional implications. A complete definition of the function of each domain must await the crystal structure of the PA63 heptamer. We have grown crystals of the heptamer under both detergent and detergent-free conditions, and made substantial progress towards the crystal structure. The mechanism of anthrax intoxication in the light of our results is reviewed.

  14. Crystallographic Texture in Ceramics and Metals.

    PubMed

    Vaudin, M D

    2001-01-01

    Preferred crystallographic orientation, or texture, occurs almost universally, both in natural and man-made systems. Many components and devices in electronic and magnetic systems are fabricated from materials that have crystallographic texture. With the rapidly increasing use of thin film technology, where sharp axisymmetric crystallographic texture normal to the film plane is frequently observed, the occurrence and impact of texture are rising. Thin film applications in which the texture of the material plays a key role in determining properties and performance are broad: complex oxides in random access memory devices, ZnO thin film resonators for cell phone applications, metallic alloys in magnetic recording media, and Al and Cu interconnects in integrated circuits are but a few examples. Texture is established during the synthesis or post-synthesis heat treatment of a material and thus has a strong dependence upon processing history. Accurate measurement of texture is not simple and a variety of tools and approaches are being actively employed in texture studies. X-ray, neutron and electron diffraction based techniques are practiced around the world at varying levels of complexity with regard to equipment and analysis methods. Despite the well-documented existence of these varied approaches, many reported texture measurements on electronic materials are based solely on the relative intensities of conventional θ-2θ x-ray diffraction peaks, which typically yield inaccurate results. NIST has developed quantitative texture measurement techniques that employ equipment commonly available in most industrial and academic settings. A number of examples of texture measurement in ceramic and metal systems will be presented, taken from the historical development and application of these techniques at NIST over the past 7 years.

  15. Domain-wall velocities of up to 750 m s-1 driven by exchange-coupling torque in synthetic antiferromagnets

    NASA Astrophysics Data System (ADS)

    Yang, See-Hun; Ryu, Kwang-Su; Parkin, Stuart

    2015-03-01

    The operation of racetrack memories is based on the motion of domain walls in atomically thin, perpendicularly magnetized nanowires, which are interfaced with adjacent metal layers with high spin-orbit coupling. Such domain walls have a chiral Néel structure and can be moved efficiently by electrical currents. High-capacity racetrack memory requires closely packed domain walls, but their density is limited by dipolar coupling from their fringing magnetic fields. These fields can be eliminated using a synthetic antiferromagnetic structure composed of two magnetic sub-layers, exchange-coupled via an ultrathin antiferromagnetic-coupling spacer layer. Here, we show that nanosecond-long current pulses can move domain walls in synthetic antiferromagnetic racetracks that have almost zero net magnetization. The domain walls can be moved even more efficiently and at much higher speeds (up to ˜750 m s-1) compared with similar racetracks in which the sub-layers are coupled ferromagnetically. This is due to a stabilization of the Néel domain wall structure, and an exchange coupling torque that is directly proportional to the strength of the antiferromagnetic exchange coupling between the two sub-layers. Moreover, the dependence of the wall velocity on the magnetic field applied along the nanowire is distinct from that of the single-layer racetrack due to the exchange coupling torque. The high domain wall velocities in racetracks that have no net magnetization allow for densely packed yet highly efficient domain-wall-based spintronics.

  16. Crystallographic orientations of olivine inclusions in diamonds

    NASA Astrophysics Data System (ADS)

    Milani, S.; Nestola, F.; Angel, R. J.; Nimis, P.; Harris, J. W.

    2016-11-01

    In this work we report for the first time the crystallographic orientations of olivine inclusions trapped in diamonds from the Kaapvaal craton (South Africa) determined by single-crystal X-ray diffraction, and analyze them together with all available data in the literature. The overall data set indicates no preferred orientation of the olivine inclusions with respect to their diamond hosts. However, diamonds containing multiple olivine inclusions sometimes show clusters of olivines with the same orientation in the same diamond host. We conclude that such clusters can only be interpreted as the remnants of single olivine crystals pre-dating the growth of the host diamonds.

  17. Crystallographic Studies of the Anthrax Lethal Toxin.

    DTIC Science & Technology

    1997-01-01

    Singh, K. R. Klimpel, C. P. Quinn, Y. K. Chaudhary, J. Biol. Chem. 266, 15493-97 (1991). The carboxyl- terminal end of protective antigen is required for...AD CONTRACT NUMBER DAMD17-94-C-4047 TITLE: Crystallographic Studies of the Anthrax Lethal Toxin PRINCIPAL INVESTIGATOR: Christin A. Frederick, Ph.D...FUNDING NUMBERS Anthrax Lethal Toxin DAMDI7-94-C-4047 6. AUTHOR(S) Christin A. Frederick, Ph.D. 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) 8

  18. Orbits of crystallographic embedding of non-crystallographic groups and applications to virology.

    PubMed

    Twarock, Reidun; Valiunas, Motiejus; Zappa, Emilio

    2015-11-01

    The architecture of infinite structures with non-crystallographic symmetries can be modelled via aperiodic tilings, but a systematic construction method for finite structures with non-crystallographic symmetry at different radial levels is still lacking. This paper presents a group theoretical method for the construction of finite nested point sets with non-crystallographic symmetry. Akin to the construction of quasicrystals, a non-crystallographic group G is embedded into the point group P of a higher-dimensional lattice and the chains of all G-containing subgroups are constructed. The orbits of lattice points under such subgroups are determined, and it is shown that their projection into a lower-dimensional G-invariant subspace consists of nested point sets with G-symmetry at each radial level. The number of different radial levels is bounded by the index of G in the subgroup of P. In the case of icosahedral symmetry, all subgroup chains are determined explicitly and it is illustrated that these point sets in projection provide blueprints that approximate the organization of simple viral capsids, encoding information on the structural organization of capsid proteins and the genomic material collectively, based on two case studies. Contrary to the affine extensions previously introduced, these orbits endow virus architecture with an underlying finite group structure, which lends itself better to the modelling of dynamic properties than its infinite-dimensional counterpart.

  19. Expression, purification and preliminary crystallographic characterization of FlhF from Bacillus subtilis

    SciTech Connect

    Bange, Gert; Petzold, Georg; Wild, Klemens; Sinning, Irmgard

    2007-05-01

    Preliminary crystallographic data are reported for the third SRP GTPase FlhF from Bacillus subtilis. The Gram-positive bacterium Bacillus subtilis contains three proteins belonging to the signal recognition particle (SRP) type GTPase family. The well characterized signal sequence-binding protein SRP54 and the SRP receptor protein FtsY are universally conserved components of the SRP system of protein transport. The third member, FlhF, has been implicated in the placement and assembly of polar flagella. This article describes the overexpression and preliminary X-ray crystallographic analysis of an FlhF fragment that corresponds to the well characterized GTPase domains in SRP54 and FtsY. Three crystal forms are reported with either GDP or GMPPNP and diffract to a resolution of about 3 Å.

  20. Chiral symmetry breaking dictated by electric-field-driven shape transitions of nucleating conglomerate domains in a bent-core liquid crystal

    NASA Astrophysics Data System (ADS)

    Deepa, G. B.; Pratibha, R.

    2014-04-01

    Generating and controlling chiral symmetry breaking and enantiomeric excess is not only interesting from a fundamental perspective but can also lead to novel functional materials. In this work, we show how the dark conglomerate (DC) liquid crystalline phase characterized by macroscopic chiral domains offers such a possibility if formed under an electric field. In addition the chiral domains are electro-optically switchable. The chiral segregation in the DC phase can be tuned by using dc or ac fields at different frequencies. Consequently, the enantioselectivity, dielectric parameters and switching polarization in the DC phase become tunable. Another interesting aspect is that the nucleating conglomerate domains formed under ac fields exhibit frequency dependent shape transitions which have a striking resemblance to domain shape changes observed in two-dimensional monolayers. This can therefore be used as a model experimental system to get a physical insight into the effects of chiral and electrostatic interactions, under external fields, on domain growth and interface structures. The domain shape transitions can also be used to investigate the role of growth morphology in coarsening and scaling hypotheses. From a technological point of view this opens up the possibility of obtaining chiral thin films with preferential sense of chirality which can be useful in chiroptical and nonlinear optical applications.

  1. Architecture of the Nitric-oxide Synthase Holoenzyme Reveals Large Conformational Changes and a Calmodulin-driven Release of the FMN Domain*♦

    PubMed Central

    Yokom, Adam L.; Morishima, Yoshihiro; Lau, Miranda; Su, Min; Glukhova, Alisa; Osawa, Yoichi; Southworth, Daniel R.

    2014-01-01

    Nitric-oxide synthase (NOS) is required in mammals to generate NO for regulating blood pressure, synaptic response, and immune defense. NOS is a large homodimer with well characterized reductase and oxygenase domains that coordinate a multistep, interdomain electron transfer mechanism to oxidize l-arginine and generate NO. Ca2+-calmodulin (CaM) binds between the reductase and oxygenase domains to activate NO synthesis. Although NOS has long been proposed to adopt distinct conformations that alternate between interflavin and FMN-heme electron transfer steps, structures of the holoenzyme have remained elusive and the CaM-bound arrangement is unknown. Here we have applied single particle electron microscopy (EM) methods to characterize the full-length of the neuronal isoform (nNOS) complex and determine the structural mechanism of CaM activation. We have identified that nNOS adopts an ensemble of open and closed conformational states and that CaM binding induces a dramatic rearrangement of the reductase domain. Our three-dimensional reconstruction of the intact nNOS-CaM complex reveals a closed conformation and a cross-monomer arrangement with the FMN domain rotated away from the NADPH-FAD center, toward the oxygenase dimer. This work captures, for the first time, the reductase-oxygenase structural arrangement and the CaM-dependent release of the FMN domain that coordinates to drive electron transfer across the domains during catalysis. PMID:24737326

  2. Antiferromagnetic domains in epitaxial thin films

    NASA Astrophysics Data System (ADS)

    Scholl, Andreas

    2002-03-01

    Interface and surface effects play a central role in modern magnet structures. Magnetic exchange coupling and bias, spin injection across the boundary between magnetic and non-magnetic layers, and the surface and interface anisotropy in multilayers are examples for interface phenomena that are utilized in magneto-electronics. In particular, the microscopic origin of exchange bias at ferromagnet/antiferromagnet interfaces is still an unsolved problem despite of intense research, driven by the important application of exchange bias in hard disk read-heads and magnetic RAM. Knowledge of the microscopic magnetic structure in antiferromagnetic thin films and surfaces is of crucial importance for a better understanding of the exchange bias effect. Microscopic experiments on magnetically coupled ferromagnet/antiferromagnet layers using X-ray Photoemission Electron Microscopy (X-PEEM) now provide a new insight into the microscopic processes at this important interface. Using a combination of x-ray magnetic dichroism (XMD) contrast and microscopic electron yield detection we have resolved the magnetic domain structure in LaFeO3 and NiO thin films and crystals. The antiferromagnetic domain structure is linked to the crystallographic structure of the material and vanishes approaching the magnetic ordering temperature. Ferromagnetic films grown on the antiferromagnetic substrate show a corresponding ferromagnetic domain structure, an uniaxial exchange anistropy and a local bias which increases with decreasing domain size, suggesting a statistical origin of the bias effect. The role of uncompensated interface spins will also be discussed. We will present first experiments on magnetic interlayer coupling across metallic antiferromagnets, which suggest a similar origin of bias in full-metallic exchange bias system. A. Scholl et al., Science 287, 1014 (2000), F. Nolting et al., Nature 405, 767 (2000), H. Ohldag et al., Phys. Rev. Lett. 86, 2878 (2001)

  3. A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure.

    PubMed

    Jeong, Jay I; Lattman, Eaton E; Chirikjian, Gregory S

    2006-04-01

    This paper presents a methodology to obtain candidate conformations of multidomain proteins for use in molecular replacement. For each separate domain, the orientational relationship between the template and the target structure is obtained using standard molecular replacement. The orientational relationships of the domains are then used to calculate the relative rotation between the domains in the target conformation by using pose-estimation techniques from the field of robotics and computer vision. With the angle of relative rotation between the domains as a cost function, iterative normal-mode analysis is used to drive the template structure to a candidate conformation that matches the X-ray crystallographic data obtained for the target conformation. The selection of the correct intra-protein domain orientations from among the many spurious maxima in the rotation function (including orientations obtained from domains in symmetry mates rather than within the same copy of the protein) presents a challenge. This problem is resolved by checking R factors of each domain, measuring the absolute value of relative rotation between domains, and evaluating the cost value after each candidate conformation is driven to convergence with iterative NMA. As a validation, the proposed method is applied to three test proteins: ribose-binding protein, lactoferrin and calcium ATPase. In each test case, the orientation and translation of the final candidate conformation in the unit cell are generated correctly from the suggested procedure. The results show that the proposed method can yield viable candidate conformations for use in molecular replacement and can reveal the structural details and pose of the target conformation in the crystallographic unit cell.

  4. Current-driven domain wall motion due to volume spin transfer torque in Co/Ni multilayer systems on Au underlayer

    NASA Astrophysics Data System (ADS)

    Ryu, Kwang-Su; Yang, See-Hun; Thomas, Luc; Parkin, Stuart

    2016-09-01

    We have studied the current-induced domain wall (CIDW) dynamics in perpendicularly magnetized Co/Ni multilayers deposited on Au underlayer, where the conventional spin transfer torque governs the domain wall dynamics, by the Kerr microscope. It is found that the DW angle tilting following Oersted field profile plays an important role in domain wall (DW) motion at high current density J by decreasing DW velocity with the increasing J, while distorting its DW morphology. Also we find that the DW pinning becomes pronounced as the anisotropy decreases by increasing number of Co/Ni repeats. Most remarkably, the DW tilting angle changes its sign by inserting ultrathin Pt layer between Au and Co layer, which suggests that the Dzyaloshinskii-Moriya interaction and spin Hall effect induces opposite effect in DW tilting. Our findings can be of use for application of CIDW to spintronics with perpendicularly magnetized systems.

  5. Teaching Biochemists and Pharmacologists How to Use Crystallographic Data.

    ERIC Educational Resources Information Center

    Duax, William L.

    1988-01-01

    Describes a one-semester course designed to teach first year graduate students how to extract, interpret, evaluate, and use the information provided by an X-ray crystallographic crystal structure determination. Presents a course outline and discusses the treatment of crystal composition, crystallographic parameters, molecular geometry and…

  6. 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

  7. Crystallographic education in the 21st century.

    PubMed

    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

    2015-12-01

    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.

  8. Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographers

    PubMed Central

    Klinger, Miloslav; Jäger, Aleš

    2015-01-01

    Three tools for an automated analysis of electron diffraction pattern and crystallographic visualization are presented. Firstly, diffractGUI determines the zone axis from selected area diffraction, convergent beam diffraction or nanodiffraction patterns and allows for indexing of individual reflections. Secondly, ringGUI identifies crystallographic planes corresponding to the depicted rings in the ring diffraction pattern and can select the sample material from a list of candidates. Both diffractGUI and ringGUI employ methods of computer vision for a fast, robust and accurate analysis. Thirdly, cellViewer is an intuitive visualization tool which is also helpful for crystallographic calculations or educational purposes. diffractGUI and cellViewer can be used together during a transmission electron microscopy session to determine the sample holder tilts required to reach a desired zone axis. All the tools offer a graphical user interface. The toolbox is distributed as a standalone application, so it can be installed on the microscope computer and launched directly from DigitalMicrograph (Gatan Inc.). PMID:26664349

  9. Proliferation and Morphogenesis of the Endoplasmic Reticulum Driven by the Membrane Domain of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase in Plant Cells1[OPEN

    PubMed Central

    Ferrero, Sergi; Grados-Torrez, Ricardo Enrique; Antolín-Llovera, Meritxell; López-Iglesias, Carmen; Cortadellas, Nuria; Ferrer, Joan Carles

    2015-01-01

    The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) has a key regulatory role in the mevalonate pathway for isoprenoid biosynthesis and is composed of an endoplasmic reticulum (ER)-anchoring membrane domain with low sequence similarity among eukaryotic kingdoms and a conserved cytosolic catalytic domain. Organized smooth endoplasmic reticulum (OSER) structures are common formations of hypertrophied tightly packed ER membranes devoted to specific biosynthetic and secretory functions, the biogenesis of which remains largely unexplored. We show that the membrane domain of plant HMGR suffices to trigger ER proliferation and OSER biogenesis. The proliferating membranes become highly enriched in HMGR protein, but they do not accumulate sterols, indicating a morphogenetic rather than a metabolic role for HMGR. The N-terminal MDVRRRPP motif present in most plant HMGR isoforms is not required for retention in the ER, which was previously proposed, but functions as an ER morphogenic signal. Plant OSER structures are morphologically similar to those of animal cells, emerge from tripartite ER junctions, and mainly build up beside the nuclear envelope, indicating conserved OSER biogenesis in high eukaryotes. Factors other than the OSER-inducing HMGR construct mediate the tight apposition of the proliferating membranes, implying separate ER proliferation and membrane association steps. Overexpression of the membrane domain of Arabidopsis (Arabidopsis thaliana) HMGR leads to ER hypertrophy in every tested cell type and plant species, whereas the knockout of the HMG1 gene from Arabidopsis, encoding its major HMGR isoform, causes ER aggregation at the nuclear envelope. Our results show that the membrane domain of HMGR contributes to ER morphogenesis in plant cells. PMID:26015445

  10. Proliferation and Morphogenesis of the Endoplasmic Reticulum Driven by the Membrane Domain of 3-Hydroxy-3-Methylglutaryl Coenzyme A Reductase in Plant Cells.

    PubMed

    Ferrero, Sergi; Grados-Torrez, Ricardo Enrique; Leivar, Pablo; Antolín-Llovera, Meritxell; López-Iglesias, Carmen; Cortadellas, Nuria; Ferrer, Joan Carles; Campos, Narciso

    2015-07-01

    The enzyme 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) has a key regulatory role in the mevalonate pathway for isoprenoid biosynthesis and is composed of an endoplasmic reticulum (ER)-anchoring membrane domain with low sequence similarity among eukaryotic kingdoms and a conserved cytosolic catalytic domain. Organized smooth endoplasmic reticulum (OSER) structures are common formations of hypertrophied tightly packed ER membranes devoted to specific biosynthetic and secretory functions, the biogenesis of which remains largely unexplored. We show that the membrane domain of plant HMGR suffices to trigger ER proliferation and OSER biogenesis. The proliferating membranes become highly enriched in HMGR protein, but they do not accumulate sterols, indicating a morphogenetic rather than a metabolic role for HMGR. The N-terminal MDVRRRPP motif present in most plant HMGR isoforms is not required for retention in the ER, which was previously proposed, but functions as an ER morphogenic signal. Plant OSER structures are morphologically similar to those of animal cells, emerge from tripartite ER junctions, and mainly build up beside the nuclear envelope, indicating conserved OSER biogenesis in high eukaryotes. Factors other than the OSER-inducing HMGR construct mediate the tight apposition of the proliferating membranes, implying separate ER proliferation and membrane association steps. Overexpression of the membrane domain of Arabidopsis (Arabidopsis thaliana) HMGR leads to ER hypertrophy in every tested cell type and plant species, whereas the knockout of the HMG1 gene from Arabidopsis, encoding its major HMGR isoform, causes ER aggregation at the nuclear envelope. Our results show that the membrane domain of HMGR contributes to ER morphogenesis in plant cells. © 2015 American Society of Plant Biologists. All Rights Reserved.

  11. Validation of crystallographic models containing TLS or other descriptions of anisotropy

    PubMed Central

    Zucker, Frank; Champ, P. Christoph; Merritt, Ethan A.

    2010-01-01

    The use of TLS (translation/libration/screw) models to describe anisotropic displacement of atoms within a protein crystal structure has become increasingly common. These models may be used purely as an improved methodology for crystallographic refinement or as the basis for analyzing inter-domain and other large-scale motions implied by the crystal structure. In either case it is desirable to validate that the crystallographic model, including the TLS description of anisotropy, conforms to our best understanding of protein structures and their modes of flexibility. A set of validation tests has been implemented that can be integrated into ongoing crystallographic refinement or run afterwards to evaluate a previously refined structure. In either case validation can serve to increase confidence that the model is correct, to highlight aspects of the model that may be improved or to strengthen the evidence supporting specific modes of flexibility inferred from the refined TLS model. Automated validation checks have been added to the PARVATI and TLSMD web servers and incorporated into the CCP4i user interface. PMID:20693688

  12. Successively thresholded domain boundary roughening driven by pinning centers and missing bonds: Hard-spin mean-field theory applied to d =3 Ising magnets

    NASA Astrophysics Data System (ADS)

    Ćaǧlar, Tolga; Berker, A. Nihat

    2015-12-01

    Hard-spin mean-field theory has recently been applied to Ising magnets, correctly yielding the absence and presence of an interface roughening transition respectively in d =2 and d =3 dimensions and producing the ordering-roughening phase diagram for isotropic and anisotropic systems. The approach has now been extended to the effects of quenched random pinning centers and missing bonds on the interface of isotropic and anisotropic Ising models in d =3 . We find that these frozen impurities cause domain boundary roughening that exhibits consecutive thresholding transitions as a function of interaction anisotropy. For both missing-bond and pinning-center impurities, for moderately large values of the anisotropy, the systems saturate to the "solid-on-solid" limit, exhibiting a single universal curve for the domain boundary width as a function of impurity concentration.

  13. Successively Thresholded Domain Boundary Roughening Driven by Pinning Centers and Missing Bonds: Hard-Spin Mean-Field Theory Applied to d =3 Ising Magnets

    NASA Astrophysics Data System (ADS)

    Caglar, Tolga; Berker, A. Nihat

    Hard-spin mean-field theory has recently been applied to Ising magnets, correctly yielding the absence and presence of an interface roughening transition respectively in d = 2 and d = 3 dimensions and producing the ordering-roughening phase diagram for isotropic and anisotropic systems. The approach has now been extended to the effects of quenched random pinning centers and missing bonds on the interface of isotropic and anisotropic Ising models in d = 3. We find that these frozen impurities cause domain boundary roughening that exhibits consecutive thresholding transitions as a function of interaction anisotropy. For both missing-bond and pinning-center impurities, for moderately large values of the anisotropy, the systems saturate to the ''solid-on-solid'' limit, exhibiting a single universal curve for the domain boundary width as a function of impurity concentration.

  14. Successively thresholded domain boundary roughening driven by pinning centers and missing bonds: Hard-spin mean-field theory applied to d=3 Ising magnets.

    PubMed

    Çağlar, Tolga; Berker, A Nihat

    2015-12-01

    Hard-spin mean-field theory has recently been applied to Ising magnets, correctly yielding the absence and presence of an interface roughening transition respectively in d=2 and d=3 dimensions and producing the ordering-roughening phase diagram for isotropic and anisotropic systems. The approach has now been extended to the effects of quenched random pinning centers and missing bonds on the interface of isotropic and anisotropic Ising models in d=3. We find that these frozen impurities cause domain boundary roughening that exhibits consecutive thresholding transitions as a function of interaction anisotropy. For both missing-bond and pinning-center impurities, for moderately large values of the anisotropy, the systems saturate to the "solid-on-solid" limit, exhibiting a single universal curve for the domain boundary width as a function of impurity concentration.

  15. CRYSTMET -- The NRCC Metals Crystallographic Data File

    SciTech Connect

    Wood, G.H.; Rodgers, J.R.; Gough, S.R.; Villars, P.

    1996-05-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60,000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool.

  16. Improved Crystallographic Structures using Extensive Combinatorial Refinement

    PubMed Central

    Nwachukwu, Jerome C.; Southern, Mark R.; Kiefer, James R.; Afonine, Pavel V.; Adams, Paul D.; Terwilliger, Thomas C.; Nettles, Kendall W.

    2013-01-01

    Summary Identifying errors and alternate conformers, and modeling multiple main-chain conformers in poorly ordered regions are overarching problems in crystallographic structure determination that have limited automation efforts and structure quality. Here, we show that implementation of a full factorial designed set of standard refinement approaches, which we call ExCoR (Extensive Combinatorial Refinement), significantly improves structural models compared to the traditional linear tree approach, in which individual algorithms are tested linearly, and only incorporated if the model improves. ExCoR markedly improved maps and models, and reveals building errors and alternate conformations that were masked by traditional refinement approaches. Surprisingly, an individual algorithm that renders a model worse in isolation could still be necessary to produce the best overall model, suggesting that model distortion allows escape from local minima of optimization target function, here shown to be a hallmark limitation of the traditional approach. ExCoR thus provides a simple approach to improving structure determination. PMID:24076406

  17. Cross-talk between the octarepeat domain and the fifth binding site of prion protein driven by the interaction of copper(II) with the N-terminus.

    PubMed

    Di Natale, Giuseppe; Turi, Ildikó; Pappalardo, Giuseppe; Sóvágó, Imre; Rizzarelli, Enrico

    2015-03-02

    Prion diseases are a group of neurodegenerative diseases based on the conformational conversion of the normal form of the prion protein (PrP(C)) to the disease-related scrapie isoform (PrP(Sc)). Copper(II) coordination to PrP(C) has attracted considerable interest for almost 20 years, mainly due to the possibility that such an interaction would be an important event for the physiological function of PrP(C). In this work, we report the copper(II) coordination features of the peptide fragment Ac(PEG11)3PrP(60-114) [Ac = acetyl] as a model for the whole N-terminus of the PrP(C) metal-binding domain. We studied the complexation properties of the peptide by means of potentiometric, UV/Vis, circular dichroism and electrospray ionisation mass spectrometry techniques. The results revealed that the preferred histidyl binding sites largely depend on the pH and copper(II)/peptide ratio. Formation of macrochelate species occurs up to a 2:1 metal/peptide ratio in the physiological pH range and simultaneously involves the histidyl residues present both inside and outside the octarepeat domain. However, at increased copper(II)/peptide ratios amide-bound species form, especially within the octarepeat domain. On the contrary, at basic pH the amide-bound species predominate at any copper/peptide ratio and are formed preferably with the binding sites of His96 and His111, which is similar to the metal-binding-affinity order observed in our previous studies.

  18. Detection of the TCDD Binding-Fingerprint within the Ah Receptor Ligand Binding Domain by Structurally Driven Mutagenesis and Functional Analysis†

    PubMed Central

    Pandini, Alessandro; Soshilov, Anatoly A.; Song, Yujuan; Zhao, Jing; Bonati, Laura; Denison, Michael S.

    2010-01-01

    The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix–loop–helix Per-Arnt-Sim (PAS)-containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Our previous three-dimensional homology model of the mouse AhR (mAhR) PAS B ligand binding domain allowed identification of the binding site and its experimental validation. We have extended this analysis by conducting comparative structural modeling studies of the ligand binding domains of six additional high-affinity mammalian AhRs. These results, coupled with site-directed mutagenesis and AhR functional analysis, have allowed detection of the “TCDD binding-fingerprint” of conserved residues within the ligand binding cavity necessary for high-affinity TCDD binding and TCDD-dependent AhR transformation DNA binding. The essential role of selected residues was further evaluated using molecular docking simulations of TCDD with both wild-type and mutant mAhRs. Taken together, our results dramatically improve our understanding of the molecular determinants of TCDD binding and provide a basis for future studies directed toward rationalizing the observed species differences in AhR sensitivity to TCDD and understanding the mechanistic basis for the dramatic diversity in AhR ligand structure. PMID:19456125

  19. Crystallographic Description for Nanoparticle Asemblies - Application to Cadmium Selenide Clusters

    DTIC Science & Technology

    2001-01-01

    Application to Cadmium Selenide Clusters DISTRIBUTION: Approved for public release, distribution unlimited This paper is part of the following report...Proc. Vol. 635 © 2001 Materials Research Society Crystallographic Description for Nanoparticle Asemblies - Application to Cadmium Selenide Clusters. A

  20. Correlation between crystallographic orientation and surface faceting in UO2

    NASA Astrophysics Data System (ADS)

    Miao, Yinbin; Mo, Kun; Yao, Tiankai; Lian, Jie; Fortner, Jeffrey; Jamison, Laura; Xu, Ruqing; Yacout, Abdellatif M.

    2016-09-01

    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 dominate 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.

  1. Correlation between Crystallographic Orientation and Surface Faceting in UO2

    SciTech Connect

    Miao, Yinbin; Mo, Kun; Yao, Tiankai; Lian, Jie; Fortner, Jeffrey; Jamison, Laura; Xu, Ruqing; Yacout, Abdellatif M.

    2016-09-01

    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 dominate 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.

  2. Thioredoxin as a fusion tag for carrier-driven crystallization.

    PubMed

    Corsini, Lorenzo; Hothorn, Michael; Scheffzek, Klaus; Sattler, Michael; Stier, Gunter

    2008-12-01

    Structural investigations are frequently hindered by difficulties in obtaining diffracting crystals of the target protein. Here, we report the crystallization and structure solution of the U2AF homology motif (UHM) domain of splicing factor Puf60 fused to Escherichia coli thioredoxin A. Both modules make extensive crystallographic contacts, contributing to a well-defined crystal lattice with clear electron density for both the thioredoxin and the Puf60-UHM module. We compare two short linker sequences between the two fusion domains, GSAM and GSPPM, for which only the GSAM-linked fusion protein yielded diffracting crystals. While specific interdomain contacts are not observed for both fusion proteins, NMR relaxation data in solution indicate reduced interdomain mobility between the Trx and Puf60-UHM modules. The GSPPM-linked fusion protein is significantly more flexible, albeit both linker sequences have the same number of degrees of torsional freedom. Our analysis provides a rationale for the crystallization of the GSAM-linked fusion protein and indicates that in this case, a four-residue linker between thioredoxin A and the fused target may represent the maximal length for crystallization purposes. Our data provide an experimental basis for the rational design of linker sequences in carrier-driven crystallization and identify thioredoxin A as a powerful fusion partner that can aid crystallization of difficult targets.

  3. High-throughput RNAi screen in Ewing sarcoma cells identifies leucine rich repeats and WD repeat domain containing 1 (LRWD1) as a regulator of EWS-FLI1 driven cell viability.

    PubMed

    He, Tao; Surdez, Didier; Rantala, Juha K; Haapa-Paananen, Saija; Ban, Jozef; Kauer, Maximilian; Tomazou, Eleni; Fey, Vidal; Alonso, Javier; Kovar, Heinrich; Delattre, Olivier; Iljin, Kristiina

    2017-01-05

    A translocation leading to the formation of an oncogenic EWS-ETS fusion protein defines Ewing sarcoma. The most frequent gene fusion, present in 85 percent of Ewing sarcomas, is EWS-FLI1. Here, a high-throughput RNA interference screen was performed to identify genes whose function is critical for EWS-FLI1 driven cell viability. In total, 6781 genes were targeted by siRNA molecules and the screen was performed both in presence and absence of doxycycline-inducible expression of the EWS-FLI1 shRNA in A673/TR/shEF Ewing sarcoma cells. The Leucine rich repeats and WD repeat Domain containing 1 (LRWD1) targeting siRNA pool was the strongest hit reducing cell viability only in EWS-FLI1 expressing Ewing sarcoma cells. LRWD1 had been previously described as a testis specific gene with only limited information on its function. Analysis of LRWD1 mRNA levels in patient samples indicated that high expression associated with poor overall survival in Ewing sarcoma. Gene ontology analysis of LRWD1 co-expressed genes in Ewing tumors revealed association with DNA replication and analysis of differentially expressed genes in LRWD1 depleted Ewing sarcoma cells indicated a role in connective tissue development and cellular morphogenesis. Moreover, EWS-FLI1 repressed genes with repressive H3K27me3 chromatin marks were highly enriched among LRWD1 target genes in A673/TR/shEF Ewing sarcoma cells, suggesting that LRWD1 contributes to EWS-FLI1 driven transcriptional regulation. Taken together, we have identified LRWD1 as a novel regulator of EWS-FLI1 driven cell viability in A673/TR/shEF Ewing sarcoma cells, shown association between high LRWD1 mRNA expression and aggressive disease and identified processes by which LRWD1 may promote oncogenesis in Ewing sarcoma.

  4. Improved low-resolution crystallographic refinement with Phenix and Rosetta.

    PubMed

    DiMaio, Frank; Echols, Nathaniel; Headd, Jeffrey J; Terwilliger, Thomas C; Adams, Paul D; Baker, David

    2013-11-01

    Refinement of macromolecular structures against low-resolution crystallographic data is limited by the ability of current methods to converge on a structure with realistic geometry. We developed a low-resolution crystallographic refinement method that combines the Rosetta sampling methodology and energy function with reciprocal-space X-ray refinement in Phenix. On a set of difficult low-resolution cases, the method yielded improved model geometry and lower free R factors than alternate refinement methods.

  5. 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.

  6. ``Crystallographic'' holes: new insights for a beneficial structural feature for photocatalytic applications

    NASA Astrophysics Data System (ADS)

    Vajda, Krisztina; Kása, Zsolt; Dombi, András; Németh, Zoltán; Kovács, Gábor; Danciu, Virginia; Radu, Teodora; Ghica, Corneliu; Baia, Lucian; Hernádi, Klára; Pap, Zsolt

    2015-03-01

    One of the most fundamental aspects of the heterogeneous catalysis field is the manipulation of the catalysts' activity. In photocatalysis this is carried out by maximizing the right crystal plane of a semiconductor oxide. Until now, most of the papers have achieved this by a combination of different oxides, with noble metals and sometimes with carbon nanomaterials. In this work MWCNTs (multiwalled carbon nanotubes) were applied as ``crystallization promoters'' in a very simple, safe, one-step hydrothermal method. By this method TiO2 nano/micro crystals with exposed {001} facets were obtained in the first step. The next episode in the crystal manipulation ``saga'' was the modification of the (001) crystallographic plane's structure by creating ordered/own faceted ``crystallographic holes''. These elements are capable of further enhancing the obtained activity of titania microcrystals to a higher extent, as shown by the UV driven photocatalytic phenol degradation experiments. The appearance of the holes was ``provoked'' by simple calcination and their presence and influence were demonstrated by XPS and HRTEM.One of the most fundamental aspects of the heterogeneous catalysis field is the manipulation of the catalysts' activity. In photocatalysis this is carried out by maximizing the right crystal plane of a semiconductor oxide. Until now, most of the papers have achieved this by a combination of different oxides, with noble metals and sometimes with carbon nanomaterials. In this work MWCNTs (multiwalled carbon nanotubes) were applied as ``crystallization promoters'' in a very simple, safe, one-step hydrothermal method. By this method TiO2 nano/micro crystals with exposed {001} facets were obtained in the first step. The next episode in the crystal manipulation ``saga'' was the modification of the (001) crystallographic plane's structure by creating ordered/own faceted ``crystallographic holes''. These elements are capable of further enhancing the obtained activity of

  7. Intermonomer hydrogen bonds enhance GxxxG-driven dimerization of the BNIP3 transmembrane domain: roles for sequence context in helix-helix association in membranes

    PubMed Central

    Lawrie, Charles M.; Sulistijo, Endah S.; MacKenzie, Kevin R.

    2009-01-01

    We determined the sequence dependence of human BNIP3 transmembrane domain dimerization using the biological assay TOXCAT. Mutants in which intermonomer hydrogen bonds between Ser 172 and His 173 are abolished show moderate interaction, indicating that side chain hydrogen bonds contribute to dimer stability but are not essential to dimerization. Mutants in which a GxxxG motif composed of Gly 180 and Gly 184 has been abolished show little or no interaction, demonstrating the critical nature of the GxxxG motif to BNIP3 dimerization. These findings show that side chain hydrogen bonds can enhance the intrinsic dimerization of a GxxxG motif and that sequence context can control how hydrogen bonds influence helix-helix interactions in membranes. The dimer interface mapped by TOXCAT mutagenesis agrees closely with the interfaces observed in the NMR structure and inferred from mutational analysis of dimerization on SDS-PAGE, showing that the native dimer structure is retained in detergents. We show that TOXCAT and SDS-PAGE give complementary and consistent information about BNIP3 TMD dimerization: TOXCAT is insensitive to mutations that have modest effects on self-association in detergents but readily discriminates among mutations that completely disrupt detergent-resistant dimerization. The close agreement between conclusions reached from TOXCAT and SDS-PAGE data for BNIP3 suggests that accurate estimates of the relative effects of mutations on native state protein-protein interactions can be obtained even when the detergent environment is strongly disruptive. PMID:20026130

  8. "helix Nebula - the Science Cloud", a European Science Driven Cross-Domain Initiative Implemented in via AN Active Ppp Set-Up

    NASA Astrophysics Data System (ADS)

    Lengert, W.; Mondon, E.; Bégin, M. E.; Ferrer, M.; Vallois, F.; DelaMar, J.

    2015-12-01

    Helix Nebula, a European science cross-domain initiative building on an active PPP, is aiming to implement the concept of an open science commons[1] while using a cloud hybrid model[2] as the proposed implementation solution. This approach allows leveraging and merging of complementary data intensive Earth Science disciplines (e.g. instrumentation[3] and modeling), without introducing significant changes in the contributors' operational set-up. Considering the seamless integration with life-science (e.g. EMBL), scientific exploitation of meteorological, climate, and Earth Observation data and models open an enormous potential for new big data science. The work of Helix Nebula has shown that is it feasible to interoperate publicly funded infrastructures, such as EGI [5] and GEANT [6], with commercial cloud services. Such hybrid systems are in the interest of the existing users of publicly funded infrastructures and funding agencies because they will provide "freedom and choice" over the type of computing resources to be consumed and the manner in which they can be obtained. But to offer such freedom and choice across a spectrum of suppliers, various issues such as intellectual property, legal responsibility, service quality agreements and related issues need to be addressed. Finding solutions to these issues is one of the goals of the Helix Nebula initiative. [1] http://www.egi.eu/news-and-media/publications/OpenScienceCommons_v3.pdf [2] http://www.helix-nebula.eu/events/towards-the-european-open-science-cloud [3] e.g. https://sentinel.esa.int/web/sentinel/sentinel-data-access [5] http://www.egi.eu/ [6] http://www.geant.net/

  9. Crystallographic orientation and concentric layers in spicules of calcareous sponges.

    PubMed

    Rossi, André Linhares; Ribeiro, Bárbara; Lemos, Moara; Werckmann, Jacques; Borojevic, Radovan; Fromont, Jane; Klautau, Michelle; Farina, Marcos

    2016-11-01

    In this work, the crystallography of calcareous sponges (Porifera) spicules and the organization pattern of the concentric layers present in their inner structure were investigated in 10 species of the subclass Calcaronea and three species of the subclass Calcinea. Polished spicules had specific concentric patterns that varied depending on the plane in which the spicules were sectioned. A 3D model of the concentric layers was created to interpret these patterns and the biomineralization process of the triactine spicules. The morphology of the spicules was compared with the crystallographic orientation of the calcite crystals by analyzing the Kikuchi diffraction patterns using a scanning electron microscope. Triactine spicules from the subclass Calcinea had actines (rays) elongated in the 〈210〉 direction, which is perpendicular to the c-axis. The scale spicules of the hypercalcified species Murrayona phanolepis presented the c-axis perpendicular to the plane of the scale, which is in accordance with the crystallography of all other Calcinea. The triactine spicules of the calcaronean species had approximately the same crystallographic orientation with the unpaired actine elongated in the ∼[211] direction. Only one Calcaronea species, whose triactine was regular, had a different orientation. Three different crystallographic orientations were found in diactines. Spicules with different morphologies, dimensions and positions in the sponge body had similar crystallographic directions suggesting that the crystallographic orientation of spicules in calcareous sponges is conserved through evolution.

  10. Crystallographic effects during micromachining — A finite-element model

    NASA Astrophysics Data System (ADS)

    Song, Shin-Hyung; Choi, Woo Chun

    2015-07-01

    Mechanical micromachining is a powerful and effective way for manufacturing small sized machine parts. Even though the micromachining process is similar to the traditional machining, the material behavior during the process is much different. In particular, many researchers report that the basic mechanics of the work material is affected by microstructures and their crystallographic orientations. For example, crystallographic orientations of the work material have significant influence on force response, chip formation and surface finish. In order to thoroughly understand the effect of crystallographic orientations on the micromachining process, finite-element model (FEM) simulating orthogonal cutting process of single crystallographic material was presented. For modeling the work material, rate sensitive single crystal plasticity of face-centered cubic (FCC) crystal was implemented. For the chip formation during the simulation, element deletion technique was used. The simulation model is developed using ABAQUS/explicit with user material subroutine via user material subroutine (VUMAT). Simulations showed that variation of the specific cutting energy at different crystallographic orientations of work material shows significant anisotropy. The developed FEM model can be a useful prediction tool of micromachining of crystalline materials.

  11. Crystallographic transformation of limestone during calcination under CO2.

    PubMed

    Valverde, Jose Manuel; Medina, Santiago

    2015-09-14

    The calcination reaction of limestone (CaCO3) to yield lime (CaO) is at the heart of many industrial applications as well as natural processes. In the recently emerged calcium-looping technology, CO2 capture is accomplished by the carbonation of CaO in a gas-solid reactor (carbonator). CaO is derived by the calcination of limestone in a calciner reactor under necessarily high CO2 partial pressure and high temperature. In situ X-ray diffraction (XRD) has been employed in this work to gain further insight into the crystallographic transformation that takes place during the calcination of limestone under CO2, at partial pressures (P) close to the equilibrium pressure (Peq) and at high temperature. Calcination under these conditions becomes extremely slow. The in situ XRD analysis presented here suggests the presence of an intermediate metastable CaO* phase stemming from the parent CaCO3 structure. According to the reaction mechanism proposed elsewhere, the exothermicity of the CaO* → CaO transformation and high values of P/Peq inhibit the nucleation of CaO at high temperatures. The wt% of CaO* remains at a relatively high level during slow calcination. Two diverse stages have been identified in the evolution of CaO crystallite size, L. Initially, L increases with CaCO3 conversion, following a logarithmic law. Slow calcination allows the crystallite size to grow up from a few nanometers at nucleation up to around 100 nm near the end of conversion. Otherwise, quick calcination at relatively lower CO2 concentrations limits CaO crystallite growth. Once calcination reaches an advanced state, the presence of CaO* drops to zero and the rate of increase of the CaO crystallite size is significantly hindered. Arguably, the first stage in CaO crystallite growth is driven by aggregation of the metastable CaO* nanocrystals, due to surface attractive forces, whereas the second one is consistent with sintering of the aggregated CaO crystals, and persists with time after full

  12. Bi-crystallographic lattice structure directs grain boundary motion under shear stress

    NASA Astrophysics Data System (ADS)

    Wan, Liang; Han, Weizhong; Chen, Kai

    2015-08-01

    Shear stress driven grain boundary (GB) migration was found to be a ubiquitous phenomenon in small grained polycrystalline materials. Here we show that the GB displacement shift complete (DSC) dislocation mechanism for GB shear coupled migration is still functioning even if the geometry orientation of the GBs deviates a few degrees from the appropriate coincidence site lattice (CSL) GBs. It means that any large angle GB can have a considerable chance to be such a “CSL-related GB” for which the shear coupled GB migration motion can happen by the GB DSC dislocation mechanism. We conclude that the CSL-DSC bi-crystallographic lattice structure in GB is the main reason that GB can migrate under shear stress.

  13. Ge/SrTiO{sub 3}(001): Correlation between interface chemistry and crystallographic orientation

    SciTech Connect

    Gobaut, B.; Penuelas, J.; Grenet, G.; Ferrah, D.; Benamrouche, A.; Chettaoui, A.; Robach, Y.; Botella, C.; Saint-Girons, G.; El Kazzi, M.; Silly, M. G.; Sirotti, F.

    2012-11-01

    In this work, the desorption of a submonolayer deposit of Ge on SrTiO{sub 3}(001) is studied by reflection high energy electron diffraction. The results are compared to those of a previous experiment done using soft x-ray photoelectron spectroscopy. Combining these techniques allows for correlating interface chemistry and crystal orientation, and for bringing clarifying elements concerning the competition between (111) and (001) crystal orientation typical for the semiconductor/perovskite epitaxial systems. Despite poor interface matching, (111)-oriented islands are stabilized at the expense of (001)-oriented islands due to the relatively low energy of their free facets. Such 'surface energy driven' crystallographic orientation of the deposit is enhanced by the low adhesion energy characteristic of the Ge/SrTiO{sub 3} system.

  14. Crystallographic Topology 2: Overview and Work in Progress

    SciTech Connect

    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.

  15. An aluminophosphate molecular sieve with 36 crystallographically distinct tetrahedral sites.

    PubMed

    Lee, Jun Kyu; Turrina, Alessandro; Zhu, Liangkui; Seo, Seungwan; Zhang, Daliang; Cox, Paul A; Wright, Paul A; Qiu, Shilun; Hong, Suk Bong

    2014-07-14

    The structure of the new medium-pore aluminophosphate molecular sieve PST-6 is determined by the combined use of rotation electron diffraction tomography, synchrotron X-ray powder diffraction, and computer modeling. PST-6 was prepared by calcination of another new aluminophosphate material with an unknown structure synthesized using diethylamine as a structure-directing agent, which is thought to contain bridging hydroxy groups. PST-6 has 36 crystallographically distinct tetrahedral sites in the asymmetric unit and is thus crystallographically the most complex zeolitic structure ever solved. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    SciTech Connect

    Jang, S. A.; Lee, H. J.; Oh, Y. J.; Thompson, C. V.; Ross, C. A.

    2015-12-01

    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.

  17. Crystallographic Relationships of Silicate-hosted Magnetite Inclusions Determined with Electron Backscatter Pattern Indexing (EBSP)

    NASA Astrophysics Data System (ADS)

    Feinberg, J. M.; Wenk, H.; Renne, P. R.; Scott, G. R.

    2002-12-01

    Crystallographically controlled laths of magnetite exsolved in silicates such as clinopyroxene and plagioclase are common features in gabbros and mafic granulite facies rocks. As the inclusions cool below the Curie temperature of magnetite (580°C) they record a component of the direction and intensity of the Earth's ambient magnetic field. The extreme anisotropy of the inclusions' aspect ratio allows them to retain an unusually stable magnetization, as exemplified by their single-domain behavior. In order to transform these magnetite inclusions into a useful paleomagnetic tool it is necessary to clearly describe the epitaxial relationship between the magnetite and its host silicate phases. In the past the crystallographic orientation of magnetite inclusions and their host silicates were determined using single-crystal X-ray diffraction or diffraction patterns obtained with a transmission electron microscope. Although both of these techniques are ultimately successful, they are time consuming and cumbersome. The Electron Backscatter Diffraction Pattern (EBSP) technique is an alternative approach that uses diffraction patterns of Kikuchi bands generated in a scanning electron microscope. The geometric relationships between intersecting Kikuchi bands can be used to determine the orientation of a crystal. Generally the EBSP technique is used to determine preferred orientation patterns in aggregates. However, in this application we use it to investigate local crystallographic relationships. First, inclusions in a thin section are visualized on a backscattered electron image and verified chemically with an EDX signal. Then EBSPs are produced for both the host silicate and the magnetite inclusions and the orientation relationship is ascertained. The EBSP technique's straightforward sample preparation and rapid measurement time, combined with the broad accessibility of scanning electron microscopes allow scientists to more efficiently determine crystallographic

  18. X-ray Crystallographic Computations Using a Programmable Calculator.

    ERIC Educational Resources Information Center

    Attard, Alfred E.; Lee, Henry C.

    1979-01-01

    Describes six crystallographic programs which have been developed to illustrate the range of usefulness of programmable calculators in providing computational assistance in chemical analysis. These programs are suitable for the analysis of x-ray diffraction data in the laboratory by students. (HM)

  19. X-ray Crystallographic Computations Using a Programmable Calculator.

    ERIC Educational Resources Information Center

    Attard, Alfred E.; Lee, Henry C.

    1979-01-01

    Describes six crystallographic programs which have been developed to illustrate the range of usefulness of programmable calculators in providing computational assistance in chemical analysis. These programs are suitable for the analysis of x-ray diffraction data in the laboratory by students. (HM)

  20. Gas-driven microturbine

    SciTech Connect

    Sniegowski, J.J.; Rodgers, M.S.; McWhorter, P.J.; Aeschliman, D.P.; Miller, W.M.

    1996-06-27

    This paper describes an invention which relates to microtechnology and the fabrication process for developing microelectrical systems. It describes a means for fabricating a gas-driven microturbine capable of providing autonomous propulsion in which the rapidly moving gases are directed through a micromachined turbine to power devices by direct linkage or turbo-electric generators components in a domain ranging from tenths of micrometers to thousands of micrometers.

  1. 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

  2. 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.

  3. 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

  4. 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

  5. Expression, purification, crystallization and preliminary crystallographic analysis of human Rad GTPase

    SciTech Connect

    Yanuar, Arry; Sakurai, Shigeru; Kitano, Ken; Hakoshima, Toshio

    2005-11-01

    Human Rad has been crystallized. A diffraction data set was collected to a resolution of 1.8 Å. Human Rad is a new member of the Ras GTPase superfamily and is overexpressed in human skeletal muscle of individuals with type II diabetes. The GTPase core domain was overexpressed in Escherichia coli and purified for crystallization. Crystals were obtained at 293 K by vapour diffusion using a crystallization robot. The crystals were found to belong to space group P2{sub 1}, with unit-cell parameters a = 52.2, b = 58.6, c = 53.4 Å, β = 97.9°, and contained two Rad molecules in the crystallographic asymmetric unit. A diffraction data set was collected to a resolution of 1.8 Å using synchrotron radiation at SPring-8.

  6. 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

  7. 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 PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. 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. Lastly, the results demonstrate a method by which the effects of radiation on crystallographic structuremore » may be investigated.« less

  8. Crystallographic Transitions in Perovskite Crystals Observed with Raman Spectroscopy

    NASA Astrophysics Data System (ADS)

    Castillo-Andaeta, F.; Mura-Mardones, J.; Cabrera, G. B.; Cabrera, A. L.; Altamirano-Busschots, L. A.

    2001-03-01

    We have studied the interaction of carbon dioxide with the surface of ferroelectric oxides such as barium titanate and potassium niobate. The surface chemistry of KNbO3 towards CO2 changes when the oxide particles become smaller than 100 microns. We have used Micro-Raman spectroscopy to determine if the structure of the grains change depending on their size and temperature. We have been able of observing crystallographic transition in small grains of the Perovskite with Raman spectroscopy. Small grains of 50 microns BaTiO3 undergo a transition at 133 degree C and small grains of 50 microns KNbO3 undergo a transition around 224 and 408 degrees C. A correlation between CO2 desorption and crystallographic changes can be observed. References: [1] A. L. Cabrera, F. Vargas and R. Zarate J. Phys. Chem. Sol. 55 (1994) 1303. [2] A. L. Cabrera, F. Vargas and J. J. Albers, Surf. Sci. 336 (1995) 280.

  9. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    SciTech Connect

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    2014-11-15

    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{sub 0.5}Ti{sub 0.5}O{sub 3} after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 10{sup 15} neutrons/cm{sup 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 the effects of radiation on crystallographic structure may be investigated.

  10. Crystallographic data processing for free-electron laser sources

    SciTech Connect

    White, Thomas A. Barty, Anton; Stellato, Francesco; Holton, James M.; Kirian, Richard A.; Zatsepin, Nadia A.; Chapman, Henry N.

    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 that 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.

  11. Crystallographic changes in lead zirconate titanate due to neutron irradiation

    SciTech Connect

    Henriques, Alexandra; Graham, Joseph T.; Landsberger, Sheldon; Ihlefeld, Jon F.; Brennecka, Geoff L.; Brown, Donald W.; Forrester, Jennifer S.; Jones, Jacob L.

    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 PbZr0.5Ti0.5O3 after exposure to a 1 MeV equivalent neutron fluence of 1.7 × 1015 neutrons/cm2. 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 the effects of radiation on crystallographic structure may be investigated.

  12. 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.

  13. An alternative to the crystallographic reconstruction of austenite in steels

    SciTech Connect

    Bernier, Nicolas; Bracke, Lieven; Malet, Loïc; Godet, Stéphane

    2014-03-01

    An alternative crystallographic austenite reconstruction programme written in Matlab is developed by combining the best features of the existing models: the orientation relationship refinement, the local pixel-by-pixel analysis and the nuclei identification and spreading strategy. This programme can be directly applied to experimental electron backscatter diffraction mappings. Its applicability is demonstrated on both quenching and partitioning and as-quenched lath-martensite steels. - Highlights: • An alternative crystallographic austenite reconstruction program is developed. • The method combines a local analysis and a nuclei identification/spreading strategy. • The validity of the calculated orientation relationship is verified on a Q and P steel. • The accuracy of the reconstructed microtexture is investigated on a martensite steel.

  14. Crystallographic texture of light tinplate coatings made in various electrolytes

    NASA Astrophysics Data System (ADS)

    Gburík, R.; Černík, M.; Leggat, R.; Vranec, P.

    2015-04-01

    Two electrolytic tinplating processes are currently used in Europe: PSA (based on phenolsulfonic acid) and MSA (based on methanesulfonic acid). The Halogen Process is used in other parts of the world. The electrolyte composition and process parameters affect the electrodeposit and ultimately the tinplate appearance and performance. In order to better understand the impact of electrolyte composition on the crystallographic texture of tin coating tinplate, light tin coatings on single reduced, continuously annealed (CA) tinplate produced in three electrolytes: Halogen, PSA and MSA were analyzed. The crystallographic texture of thin tin coating (<2.8gm-2) was analyzed by X-ray Diffraction and Electron Backscatter Diffraction. The effect of reflow (melting of the tin followed by rapid solidification) and ironing during drawn and wall ironed (DWI) can forming on the tin crystallography were evaluated. Both texture analysis by XRD and EBSD confirmed that all un-melted tin coatings, made in three different electrolytes, contain texture fibers. The effect of steel sheet crystallographic texture was investigated by comparing the tin crystallographic orientation on continuously annealed steel substrate (with α and γ fiber texture) versus batch annealed (BA) steel with a strong γ fiber texture. The main electrolytic parameters, current density and line speed, did not affect the texture formation of tin coating produced in MSA-based electrolyte within the commercial ranges. Un-melted tin coatings produced in the MSA-based electrolyte showed sharper texture than those produced in PSA and Halogen electrolytes. The FeSn2 alloy structure was not observed in un-melted tin coatings; however, it was detected after ironing in the DWI process.

  15. Biochemical and Crystallographic Analysis of Substrate Binding and Conformational Changes in Acetyl-CoA Synthetase

    SciTech Connect

    Reger,A.; Carney, J.; Gulick, A.

    2007-01-01

    The adenylate-forming enzymes, including acyl-CoA synthetases, the adenylation domains of non-ribosomal peptide synthetases (NRPS), and firefly luciferase, perform two half-reactions in a ping-pong mechanism. We have proposed a domain alternation mechanism for these enzymes whereby, upon completion of the initial adenylation reaction, the C-terminal domain of these enzymes undergoes a 140{sup o} rotation to perform the second thioester-forming half-reaction. Structural and kinetic data of mutant enzymes support this hypothesis. We present here mutations to Salmonella enterica acetyl-CoA synthetase (Acs) and test the ability of the enzymes to catalyze the complete reaction and the adenylation half-reaction. Substitution of Lys609 with alanine results in an enzyme that is unable to catalyze the adenylate reaction, while the Gly524 to leucine substitution is unable to catalyze the complete reaction yet catalyzes the adenylation half-reaction with activity comparable to the wild-type enzyme. The positions of these two residues, which are located on the mobile C-terminal domain, strongly support the domain alternation hypothesis. We also present steady-state kinetic data of putative substrate-binding residues and demonstrate that no single residue plays a dominant role in dictating CoA binding. We have also created two mutations in the active site to alter the acyl substrate specificity. Finally, the crystallographic structures of wild-type Acs and mutants R194A, R584A, R584E, K609A, and V386A are presented to support the biochemical analysis.

  16. Crystallographically uniform arrays of ordered (In)GaN nanocolumns

    SciTech Connect

    Gačević, Ž. Bengoechea-Encabo, A.; Albert, S.; Calleja, E.

    2015-01-21

    In this work, through a comparative study of self-assembled (SA) and selective area grown (SAG) (In)GaN nanocolumn (NC) ensembles, we first give a detailed insight into improved crystallographic uniformity (homogeneity of crystallographic tilts and twists) of the latter ones. The study, performed making use of: reflective high energy electron diffraction, X-ray diffraction and scanning electron microscopy, reveals that unlike their SA counterparts, the ensembles of SAG NCs show single epitaxial relationship to both sapphire(0001) and Si(111) underlying substrates. In the second part of the article, making use of X-ray diffraction, we directly show that the selective area growth leads to improved compositional uniformity of InGaN NC ensembles. This further leads to improved spectral purity of their luminescence, as confirmed by comparative macro-photoluminescence measurements performed on SA and SAG InGaN NC ensembles. An improved crystallographic uniformity of NC ensembles facilitates their integration into optoelectronic devices, whereas their improved compositional uniformity allows for their employment in single-color optoelectronic applications.

  17. Crystallographic influences on pressure solution in a Quartzose Sandstone

    SciTech Connect

    Hicks, B.D.; Houseknecht, D.W.; Applin, K.R.

    1985-02-01

    The solubility of quartz differs with crystallographic direction. A universal stage was used to measure the orientations of the optic axes and contact planes of 160 pairs of quartz grains in the Bromide Formation (Simpson Group) of Oklahoma. These quartz grains exhibit long, sutured, and concave-convex contacts. Results indicate that the geometry of a pressolved contact is independent of the crystallographic orientation of opposing grains. However, given a concave-convex contact, the optic axis of the concave grain tends to lie at a higher angle to the contact plane than the optic axis of the convex grain. The authors conclude that the extent and type of pressure-solution contacts in quartzose sandstones are not significantly influenced by crystallographic orientation. Other factors, such as grain size and clay content, are probably more important in controlling the pressure-solution features. Geometric etch pits, which form at the point of emergence of crystal defects, were produced by hydrothermally etching quartz crystals, quartz sand, and quartzose sandstones. The abundance, nature, and distribution pattern of crystal defects inherited from source rocks might be more important factors in affecting pressure solution of quartz grains than differences in quartz solubilities arising solely from variations in Si-O bond strengths. The extent of etch-pit formation on quartz cement may also serve as a qualitative indicator of the dissolved silica saturation in pore fluids.

  18. Atoms.inp Archive: Crystallographic Data from GSECARS

    DOE Data Explorer

    Newville, Matthew

    The Atoms.inp Archive is a collection of crystallographic data for use in XAFS analysis. The crystallographic data is stored as atoms.inp files, which contain all the information necessary to describe the crystal, and can be used by the program ATOMS to generate feff.inp files. These files can then be used by the FEFF program [See http://leonardo.phys.washington.edu/feff/] to calculate a theoretical XAFS spectrum for the crystal. This archive exists because it can take a considerable amount of time to locate a suitable reference for a model structure to use for making theoretical XAFS standards. Even then, references sometimes give non-standard or incomplete crystallographic notation that ATOMS has difficulty interpreting. All of this means that getting a reliable atoms.inp file can take quite a bit of effort. It is hoped that this collection of well-documented and well-tested atoms.inp files will eliminate much of the work in creating theoretical XAFS standards from FEFF. [Taken from http://cars9.uchicago.edu/~newville/adb/]. The collection currently has more than 200 crystal structures, 2748 data files, and it continues to expand. The collection is related to the UWXAFS Project [http://depts.washington.edu/uwxafs/] and to the work of the Consortium for Advanced Radiation Sources (CARS). After searching the Archive, a user may also choose to run the web version of ATOMS software.

  19. MAGNETIC DOMAINS AND TWINNING IN ALPHA-IRON.

    DTIC Science & Technology

    Alpha - iron is another instance of mimetic twinning in which an edifice formed by a group of twinned tetragonal crystals presents an appearance of...cubic symmetry. This confirms earlier suggestions that magnetic domains are crystallographic twins. Crystals of alpha - iron were grown in thin strips of

  20. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited.

    PubMed

    Šink, Roman; Kotnik, Miha; Zega, Anamarija; Barreteau, Hélène; Gobec, Stanislav; Blanot, Didier; Dessen, Andréa; Contreras-Martel, Carlos

    2016-01-01

    The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway.

  1. Crystallographic Study of Peptidoglycan Biosynthesis Enzyme MurD: Domain Movement Revisited

    PubMed Central

    Zega, Anamarija; Barreteau, Hélène; Gobec, Stanislav; Blanot, Didier; Dessen, Andréa; Contreras-Martel, Carlos

    2016-01-01

    The biosynthetic pathway of peptidoglycan, an essential component of bacterial cell wall, is a well-recognized target for antibiotic development. Peptidoglycan precursors are synthesized in the bacterial cytosol by various enzymes including the ATP-hydrolyzing Mur ligases, which catalyze the stepwise addition of amino acids to a UDP-MurNAc precursor to yield UDP-MurNAc-pentapeptide. MurD catalyzes the addition of D-glutamic acid to UDP-MurNAc-L-Ala in the presence of ATP; structural and biochemical studies have suggested the binding of the substrates with an ordered kinetic mechanism in which ligand binding inevitably closes the active site. In this work, we challenge this assumption by reporting the crystal structures of intermediate forms of MurD either in the absence of ligands or in the presence of small molecules. A detailed analysis provides insight into the events that lead to the closure of MurD and reveals that minor structural modifications contribute to major overall conformation alterations. These novel insights will be instrumental in the development of new potential antibiotics designed to target the peptidoglycan biosynthetic pathway. PMID:27031227

  2. Sparsity driven ultrasound imaginga)

    PubMed Central

    Tuysuzoglu, Ahmet; Kracht, Jonathan M.; Cleveland, Robin O.; C¸etin, Müjdat; Karl, W. Clem

    2012-01-01

    An image formation framework for ultrasound imaging from synthetic transducer arrays based on sparsity-driven regularization functionals using single-frequency Fourier domain data is proposed. The framework involves the use of a physics-based forward model of the ultrasound observation process, the formulation of image formation as the solution of an associated optimization problem, and the solution of that problem through efficient numerical algorithms. The sparsity-driven, model-based approach estimates a complex-valued reflectivity field and preserves physical features in the scene while suppressing spurious artifacts. It also provides robust reconstructions in the case of sparse and reduced observation apertures. The effectiveness of the proposed imaging strategy is demonstrated using experimental data. PMID:22352501

  3. The use of Fourier reverse transforms in crystallographic phase refinement

    SciTech Connect

    Ringrose, Sharon

    1997-10-08

    Often a crystallographer obtains an electron density map which shows only part of the structure. In such cases, the phasing of the trial model is poor enough that the electron density map may show peaks in some of the atomic positions, but other atomic positions are not visible. There may also be extraneous peaks present which are not due to atomic positions. A method for determination of crystal structures that have resisted solution through normal crystallographic methods has been developed. PHASER is a series of FORTRAN programs which aids in the structure solution of poorly phased electron density maps by refining the crystallographic phases. It facilitates the refinement of such poorly phased electron density maps for difficult structures which might otherwise not be solvable. The trial model, which serves as the starting point for the phase refinement, may be acquired by several routes such as direct methods or Patterson methods. Modifications are made to the reverse transform process based on several assumptions. First, the starting electron density map is modified based on the fact that physically the electron density map must be non-negative at all points. In practice a small positive cutoff is used. A reverse Fourier transform is computed based on the modified electron density map. Secondly, the authors assume that a better electron density map will result by using the observed magnitudes of the structure factors combined with the phases calculated in the reverse transform. After convergence has been reached, more atomic positions and less extraneous peaks are observed in the refined electron density map. The starting model need not be very large to achieve success with PHASER; successful phase refinement has been achieved with a starting model that consists of only 5% of the total scattering power of the full molecule. The second part of the thesis discusses three crystal structure determinations.

  4. Uncertainty in retained austenite measurements applied to individual crystallographic orientations

    NASA Astrophysics Data System (ADS)

    Creuziger, A.; Gnäupel-Herold, T.

    2015-04-01

    A technique to measure the phase volume fraction of an individual orientation and the uncertainty in the measurement is demonstrated in this paper. The technique of complete pole figure averaging using neutron diffraction was used to assess the phase fraction of retained austenite in transformation induced plasticity (TRIP) steels and quantify the uncertainty in the phase fraction. In parallel, an ensemble of orientation distribution functions was calculated to assess crystallographic volume fractions of particular orientations and the uncertainty of these volume fractions using Monte Carlo techniques. These methods were combined to measure the retained austenite phase volume fraction of an individual orientation.

  5. Substructures of the (252) ferrous martensite and their crystallographic significance

    SciTech Connect

    Wang Shidao |; Hei Zukun

    1999-04-23

    Many ferrous martensites have been found to possess a macroscopically invariant habit plane close to (252){sub f} and to exhibit complex and variable substructures that cannot be not only satisfactorily explained but also fully characterized so far. The present work attempts to examine the mechanism of occurrence of the complex substructures and their correlation to other crystallographic properties, esp. to the shape strain, on the basis of a new theory. The theory describes the atomic movements in the lattice change represented with the Bain distortion in the past.

  6. X-ray Crystallographic and Steady State Fluorescence Characterization of the Protein Dynamics of Yeast Polyadenylate Polymerase.

    SciTech Connect

    Balbo,P.; Toth, J.; Bohm, A.

    2007-01-01

    Polyadenylate polymerase (PAP) catalyzes the synthesis of poly(A) tails on the 3'-end of pre-mRNA. PAP is composed of three domains: an N-terminal nucleotide-binding domain (homologous to the palm domain of DNA and RNA polymerases), a middle domain (containing other conserved, catalytically important residues), and a unique C-terminal domain (involved in protein-protein interactions required for 3'-end formation). Previous X-ray crystallographic studies have shown that the domains are arranged in a V-shape such that they form a central cleft with the active site located at the base of the cleft at the interface between the N-terminal and middle domains. In the previous studies, the nucleotides were bound directly to the N-terminal domain and exhibited a conspicuous lack of adenine-specific interactions that would constitute nucleotide recognition. Furthermore, it was postulated that base-specific contacts with residues in the middle domain could occur either as a result of a change in the conformation of the nucleotide or domain movement. To address these issues and to better characterize the structural basis of substrate recognition and catalysis, we report two new crystal structures of yeast PAP. A comparison of these structures reveals that the N-terminal and C-terminal domains of PAP move independently as rigid bodies along two well defined axes of rotation. Modeling of the nucleotide into the most closed state allows us to deduce specific nucleotide interactions involving residues in the middle domain (K215, Y224 and N226) that are proposed to be involved in substrate binding and specificity. To further investigate the nature of PAP domain flexibility, 2-aminopurine labeled molecular probes were employed in steady state fluorescence and acrylamide quenching experiments. The results suggest that the closed domain conformation is stabilized upon recognition of the correct substrate, MgATP, in an enzyme-substrate ternary complex. The implications of these results

  7. Evolution of ferroelectric domain structures embedded inside polychrystalline BaTiO3 during heating

    SciTech Connect

    Varlioglu, Mesut; Ustundag, Ersan; Tamura, Nobumichi; Jones, Jacob L.

    2010-01-01

    The evolution of ferroelectric domains inside a single grain of a polycrystalline BaTiO{sub 3} ceramic was investigated under quasistatic heating by using polychromatic scanning x-ray microdiffraction. Four domain orientations were observed, three of which exhibited a classic of {approx}90{sup o} ferroelastic relationship. The fourth domain orientation was found to be crystallographically related with one of the other orientations by a rotation of either 180.47{sup o} or 0.47{sup o}. While heating the polycrystalline BaTiO{sub 3} from room temperature to above the Curie temperature (125 C), all four ferroelectric domain orientations rotated toward a paraelectric cubic orientation which was found to be at an intermediate orientation relative to the four domain orientations. The crystallographic relationships of the domains with respect to paraelectric phase were explained using a domain structure model by Nepochatenko.

  8. Structure of NS1A effector domain from the influenza A/Udorn/72 virus

    SciTech Connect

    Xia, Shuangluo; Monzingo, Arthur F.; Robertus, Jon D.

    2009-01-01

    The structure of the effector domain of the influenza protein NS1, a validated antiviral drug target, has been solved in two space groups. The nonstructural protein NS1A from influenza virus is a multifunctional virulence factor and a potent inhibitor of host immunity. It has two functional domains: an N-terminal 73-amino-acid RNA-binding domain and a C-terminal effector domain. Here, the crystallographic structure of the NS1A effector domain of influenza A/Udorn/72 virus is presented. Structure comparison with the NS1 effector domain from mouse-adapted influenza A/Puerto Rico/8/34 (PR8) virus strain reveals a similar monomer conformation but a different dimer interface. Further analysis and evaluation shows that the dimer interface observed in the structure of the PR8 NS1 effector domain is likely to be a crystallographic packing effect. A hypothetical model of the intact NS1 dimer is presented.

  9. 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

  10. Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.

    PubMed

    Murakami, Midori; Kouyama, Tsutomu

    2015-01-01

    Upon absorption of light, the retinal chromophore in rhodopsin isomerizes from the 11-cis to the trans configuration, initiating a photoreaction cycle. The primary photoreaction state, bathorhodopsin (BATHO), relaxes thermally through lumirhodopsin (LUMI) into a photoactive state, metarhodopsin (META), which stimulates the conjugated G-protein. Previous crystallographic studies of squid and bovine rhodopsins have shown that the structural change in the primary photoreaction of squid rhodopsin is considerably different from that observed in bovine rhodopsin. It would be expected that there is a fundamental difference in the subsequent thermal relaxation process between vertebrate and invertebrate rhodopsins. In this work, we performed crystallographic analyses of the LUMI state of squid rhodopsin using the P62 crystal. When the crystal was illuminated at 100 K with blue light, a half fraction of the protein was converted into BATHO. This reaction state relaxed into LUMI when the illuminated crystal was warmed in the dark to 170 K. It was found that, whereas trans retinal is largely twisted in BATHO, it takes on a more planar configuration in LUMI. This relaxation of retinal is accompanied by reorientation of the Schiff base NH bond, the hydrogen-bonding partner of which is switched to Asn185 in LUMI. Unlike bovine rhodopsin, the BATHO-to-LUMI transition in squid rhodopsin was accompanied by no significant change in the position/orientation of the beta-ionone ring of retinal.

  11. Incorporating crystallographic orientation in the development of resonant ultrasound spectroscopy

    NASA Astrophysics Data System (ADS)

    Adebisi, R. A.; Sathish, S.; Shade, P. A.

    2017-02-01

    Resonant ultrasound spectroscopy (RUS) measures the mechanical resonance of solids and uses the resonance frequencies to extract a complete set of elastic constants of the solid material. One of the advantages of the RUS method is its applicability to small single crystals. In the past two decades, the RUS technique has gained more acceptance as a nondestructive method to measure elastic properties. The inherent assumptions in the conventional RUS algorithm include free boundary condition on the specimen faces and the faces of the specimens are normal/parallel to the principal crystallographic axes. This assumption is fulfilled through a time consuming procedure that typically involves multiple iterations of sample cutting and inspection using an x-ray Laue method. Such an intensive method is not suitable for many samples in engineering applications. To estimate the elastic constants of such samples, a modified RUS algorithm has been developed to incorporate the sample crystallographic orientation expressed in terms of Euler angles. This modified RUS algorithm has been applied to estimate the elastic constants of cubic and hexagonal crystal structure samples with known orientation. The obtained values are comparable to literature values. With the incorporation of crystal orientation into the RUS algorithm, the elastic constants of samples with random crystal orientation were obtained.

  12. Crystallographic preferred orientations and deformation mechanisms in mantle shear zones

    NASA Astrophysics Data System (ADS)

    Drury, Martyn; Pennock, Gill; Palasse, Laurie; Ave Lallemant, Hans; Vissers, Reinoud

    2013-04-01

    In this contribution we will review our research on deformation mechanisms and olivine crystallographic preferred orientation (CPO) development in naturally deformed peridotites from mantle shear zones. In naturally deformed exhumed upper mantle rocks a strong olivine crystallographic preferred orientation (CPO) is generally developed in coarse grained rocks. Fine grained peridotites (grain size less than 15 microns) tend to have random to weak olivine CPO and this weak CPO is usually interpreted in terms of dominant grain size sensitive deformation mechanisms. Recently examples have been found of modest CPO development in pyroxene rich olivine rocks with ultra-fine grain size and microstructures consistent with dominant grain boundary sliding and diffusion creep. Several mechanisms can explain CPO development and preservation during grain size sensitive creep, indicating that the magnitude of seismic anisotropy in mantle shear zones may not be simply related to deformation mechanisms. The studies on mantle rocks indicate that grain size sensitive creep is often important in exhumed mantle shear zones, although, in many cases deformation involves a combination of dislocation creep and grain size sensitive mechanisms. We will discuss the significance of observations made on exhumed mantle rocks to shear zones in the lithosphere and asthenosphere.

  13. International summer school on macromolecular crystallographic computing. Final report

    SciTech Connect

    1998-08-01

    The School was the seventh in a series of International Union of Crystallography (IUCr) Crystallographic Symposia. The format of the School was formal lectures in the morning, tutorials in the afternoon, and software demonstrations and more lectures in the evening. The full program which left both the organizers and attendees exhausted, reflects the current state of excitement in the field of macromolecular structure determination using the technique of X-ray crystallography. The new and improved technologies and techniques described in these Proceedings are contributing to that growth and at the same time, as pointed out in the paper given by Sussman, creating challenges for the Protein Data Bank (PDB). As the School progressed, the authors were struck by the similarities to events which took place in small molecule crystallography beginning some 20 to 25 years ago. Growth then was fueled by the advent of new algorithms, affordable computer hardware, and good software. So it is today for macromolecular crystallography, but with the added bonus of the Internet which is changing how scientist conduct their research. Flack presented this view as part of his on-going contribution to how crystallographers use the Internet. After presentations discussing structures en masse they returned to the more traditional mode of presentation which parallels the determination of a single macromolecular structure: data collection -- phasing -- model building and visualization -- refinement.

  14. 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.

  15. Crystallographic Orientation Control in PZT Thin Films for Microelectromechanical Applications

    NASA Astrophysics Data System (ADS)

    Maack, Bryan; Gibbons, Brady; Mason, Ashley

    2011-10-01

    Pb(Zr1-xTix)O3 (PZT) is widely used in ferroelectric and piezoelectric applications both in bulk and thin film form. As the piezoelectric response is strongly anisotropic, it is highly desirable to control the crystallographic orientation in order to maximize the displacement (for actuation) or charge generated (for sensing). Control of crystallographic texture in PZT thin films has been shown to be dependent on a variety of processing conditions including deposition method, substrate choice, chemical doping, etc. This work is focused on systematically exploring how processing conditions and substrate choice affect orientation in chemical solution derived PZT films. It was found that sputtered Pt/TiOx/SiO2/Si substrates provided a significantly improved template over evaporated Pt/Ti/SiO2/Si substrates. Additionally, alternative adhesion layers to Ti and TiOx resulted in improved chemical homogeneity within the PZT itself, which should lead to enhanced piezoelectric properties. Ongoing work to demonstrate improved piezoelectric properties will be presented.

  16. 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.

    2017-07-01

    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.

  17. Crystallographic investigation of grain selection during initial solidification

    NASA Astrophysics Data System (ADS)

    Esaka, H.; Kataoka, Y.; Shinozuka, K.

    2016-03-01

    Normally, macroscopic solidified structure consists of chill, columnar and equiaxed zones. In a chill zone, many fine grains nucleate on the mold surface and grow their own preferred growth direction. Only a few of them continue to grow because of grain selection. In order to understand the grain selection process, crystallographic investigation has been carried out in the zone of initial solidification in this study. 10 g of Al-6 wt%Si alloy was melted at 850 °C and poured on the thick copper plate. Longitudinal cross section of the solidified shell was observed by a SEM and analyzed by EBSD. The result of EBSD mapping reveals that crystallographic orientation was random in the range of initial solidification. Further, some grains are elongated along their <100> direction. Columnar grains, whose growth directions are almost parallel to the heat flow direction, develop via grain selection. Here, a dendrite whose growth direction is close to the heat flow direction overgrows the other dendrite whose growth direction is far from the heat flow direction. However, sometimes we observed that dendrite, whose zenith angle is large, overgrew the other dendrite. It can be deduced that the time of nucleation on the mold surface is not constant.

  18. Diffusion-equation method for crystallographic figure of merits.

    PubMed

    Markvardsen, Anders J; David, William I F

    2010-09-01

    Global optimization methods play a significant role in crystallography, particularly in structure solution from powder diffraction data. This paper presents the mathematical foundations for a diffusion-equation-based optimization method. The diffusion equation is best known for describing how heat propagates in matter. However, it has also attracted considerable attention as the basis for global optimization of a multimodal function [Piela et al. (1989). J. Phys. Chem. 93, 3339-3346]. The method relies heavily on available analytical solutions for the diffusion equation. Here it is shown that such solutions can be obtained for two important crystallographic figure-of-merit (FOM) functions that fully account for space-group symmetry and allow the diffusion-equation solution to vary depending on whether atomic coordinates are fixed or not. The resulting expression is computationally efficient, taking the same order of floating-point operations to evaluate as the starting FOM function measured in terms of the number of atoms in the asymmetric unit. This opens the possibility of implementing diffusion-equation methods for crystallographic global optimization algorithms such as structure determination from powder diffraction data.

  19. 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.

  20. Structure of a shark IgNAR antibody variable domain and modeling of an early-developmental isotype.

    PubMed

    Streltsov, Victor A; Carmichael, Jennifer A; Nuttall, Stewart D

    2005-11-01

    The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded dimers of two protein chains, each containing one variable and five constant domains. Three types of IgNAR variable domains have been discovered, with Type 3 appearing early in shark development and being overtaken by the antigen-driven affinity-matured Type 1 and 2 response. Here, we have determined the first structure of a naturally occurring Type 2 IgNAR variable domain, and identified the disulphide bond that links and stabilizes the CDR1 and CDR3 loops. This disulphide bridge locks the CDR3 loop in an "upright" conformation in contrast to other shark antibody structures, where a more lateral configuration is observed. Further, we sought to model the Type 3 isotype based on the crystallographic structure reported here. This modeling indicates (1) that internal Type 3-specific residues combine to pack into a compact immunoglobulin core that supports the CDR loop regions, and (2) that despite apparent low-sequence variability, there is sufficient plasticity in the CDR3 loop to form a conformationally diverse antigen-binding surface.

  1. Structure of a shark IgNAR antibody variable domain and modeling of an early-developmental isotype

    PubMed Central

    Streltsov, Victor A.; Carmichael, Jennifer A.; Nuttall, Stewart D.

    2005-01-01

    The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded dimers of two protein chains, each containing one variable and five constant domains. Three types of IgNAR variable domains have been discovered, with Type 3 appearing early in shark development and being overtaken by the antigen-driven affinity-matured Type 1 and 2 response. Here, we have determined the first structure of a naturally occurring Type 2 IgNAR variable domain, and identified the disulphide bond that links and stabilizes the CDR1 and CDR3 loops. This disulphide bridge locks the CDR3 loop in an “upright” conformation in contrast to other shark antibody structures, where a more lateral configuration is observed. Further, we sought to model the Type 3 isotype based on the crystallographic structure reported here. This modeling indicates (1) that internal Type 3-specific residues combine to pack into a compact immunoglobulin core that supports the CDR loop regions, and (2) that despite apparent low-sequence variability, there is sufficient plasticity in the CDR3 loop to form a conformationally diverse antigen-binding surface. PMID:16199666

  2. High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages.

    PubMed

    Baek, Seung Bin; Moon, Dohyun; Graf, Robert; Cho, Woo Jong; Park, Sung Woo; Yoon, Tae-Ung; Cho, Seung Joo; Hwang, In-Chul; Bae, Youn-Sang; Spiess, Hans W; Lee, Hee Cheon; Kim, Kwang S

    2015-11-17

    Crystallographic observation of adsorbed gas molecules is a highly difficult task due to their rapid motion. Here, we report the in situ single-crystal and synchrotron powder X-ray observations of reversible CO2 sorption processes in an apparently nonporous organic crystal under varying pressures at high temperatures. The host material is formed by hydrogen bond network between 1,3,5-tris-(4-carboxyphenyl)benzene (H3BTB) and N,N-dimethylformamide (DMF) and by π-π stacking between the H3BTB moieties. The material can be viewed as a well-ordered array of cages, which are tight packed with each other so that the cages are inaccessible from outside. Thus, the host is practically nonporous. Despite the absence of permanent pathways connecting the empty cages, they are permeable to CO2 at high temperatures due to thermally activated molecular gating, and the weakly confined CO2 molecules in the cages allow direct detection by in situ single-crystal X-ray diffraction at 323 K. Variable-temperature in situ synchrotron powder X-ray diffraction studies also show that the CO2 sorption is reversible and driven by temperature increase. Solid-state magic angle spinning NMR defines the interactions of CO2 with the organic framework and dynamic motion of CO2 in cages. The reversible sorption is attributed to the dynamic motion of the DMF molecules combined with the axial motions/angular fluctuations of CO2 (a series of transient opening/closing of compartments enabling CO2 molecule passage), as revealed from NMR and simulations. This temperature-driven transient molecular gating can store gaseous molecules in ordered arrays toward unique collective properties and release them for ready use.

  3. High-temperature in situ crystallographic observation of reversible gas sorption in impermeable organic cages

    PubMed Central

    Baek, Seung Bin; Moon, Dohyun; Graf, Robert; Cho, Woo Jong; Park, Sung Woo; Yoon, Tae-Ung; Cho, Seung Joo; Hwang, In-Chul; Bae, Youn-Sang; Spiess, Hans W.; Lee, Hee Cheon; Kim, Kwang S.

    2015-01-01

    Crystallographic observation of adsorbed gas molecules is a highly difficult task due to their rapid motion. Here, we report the in situ single-crystal and synchrotron powder X-ray observations of reversible CO2 sorption processes in an apparently nonporous organic crystal under varying pressures at high temperatures. The host material is formed by hydrogen bond network between 1,3,5-tris-(4-carboxyphenyl)benzene (H3BTB) and N,N-dimethylformamide (DMF) and by π–π stacking between the H3BTB moieties. The material can be viewed as a well-ordered array of cages, which are tight packed with each other so that the cages are inaccessible from outside. Thus, the host is practically nonporous. Despite the absence of permanent pathways connecting the empty cages, they are permeable to CO2 at high temperatures due to thermally activated molecular gating, and the weakly confined CO2 molecules in the cages allow direct detection by in situ single-crystal X-ray diffraction at 323 K. Variable-temperature in situ synchrotron powder X-ray diffraction studies also show that the CO2 sorption is reversible and driven by temperature increase. Solid-state magic angle spinning NMR defines the interactions of CO2 with the organic framework and dynamic motion of CO2 in cages. The reversible sorption is attributed to the dynamic motion of the DMF molecules combined with the axial motions/angular fluctuations of CO2 (a series of transient opening/closing of compartments enabling CO2 molecule passage), as revealed from NMR and simulations. This temperature-driven transient molecular gating can store gaseous molecules in ordered arrays toward unique collective properties and release them for ready use. PMID:26578758

  4. Internal structure of basalt flows: insights from magnetic and crystallographic fabrics of the La Palisse volcanics, French Massif Central

    NASA Astrophysics Data System (ADS)

    Boiron, T.; Bascou, J.; Camps, P.; Ferré, E. C.; Maurice, C.; Guy, B.; Gerbe, M.-C.; Launeau, P.

    2013-05-01

    We present a new interpretation of anisotropy of magnetic susceptibility (AMS) fabrics in basaltic lava flows based on the detailed study of magnetic mineralogy and silicate crystallographic fabric of a Quaternary lava flow from the French Massif Central (La Palisse). We consider the model of AMS fabric imbrication between magnetic foliation and flow surface, as initially proposed for dykes. At the two sampling sites, the concordance between the flow direction deduced from the AMS foliation and that deduced from field observations indicates that the imbrication model could apply to the lava flows. However, the flow senses inferred from AMS are systematically opposed between the two sampling sites suggesting permutations between K1 and K3 AMS axes, a configuration referred to as inverse fabric. Electron backscatter diffraction (EBSD) measurements show strong lattice-preferred orientations (LPO) for plagioclase, especially the (010) plagioclase plane, which tends to be parallel to the flow. Clinopyroxene LPO remains less marked than plagioclase LPO, whereas titanomagnetite does not display a significant LPO. Comparison between magnetic and crystallographic fabrics suggests that the AMS fabric of the lava flow results from the distribution of titanomagnetite grains, which is in turn controlled by the fabric of the silicate framework. Magnetic hysteresis parameters and anisotropy of remanent magnetization (ARM) measurements exclude a significant contribution from single-domain grains, often called upon to explain inverse magnetic fabrics. The origin of the observed inverse magnetic fabric may relate to the dip of the palaeosurface, which is the only remarkable difference between the two sampling sites. AMS appears as a good tool to determine the direction of basaltic lava flows and coupling with local crystallographic fabric data provides a valuable control of relationships between magnetic fabrics and flow and thus contributes to better constrain the AMS signature of

  5. Metamodel-Driven Evolution with Grammar Inference

    NASA Astrophysics Data System (ADS)

    Bryant, Barrett R.; Liu, Qichao; Mernik, Marjan

    2010-10-01

    Domain-specific modeling (DSM) has become one of the most popular techniques for incorporating model-driven engineering (MDE) into software engineering. In DSM, domain experts define metamodels to describe the essential problems in a domain. A model conforms to a schema definition represented by a metamodel in a similar manner to a programming language conforms to a grammar. Metamodel-driven evolution is when a metamodel undergoes evolutions to incorporate new concerns in the domain. However, this results in losing the ability to use existing model instances. Grammar inference is the problem of inferring a grammar from sample strings which the grammar should generate. This paper describes our work in solving the problem of metamodel-driven evolution with grammar inference, by inferring the metamodel from model instances.

  6. 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.

  7. Crystallographic shear mechanisms in Rh one-dimensional oxides

    NASA Astrophysics Data System (ADS)

    Hernando, María; Boulahya, Khalid; Parras, Marina; González-Calbet, José M.

    2005-02-01

    Electron diffraction and high resolution electron microscopy have been used to characterize two new one-dimensional superstructures in the A sbnd Rh sbnd O system (A = Ca, Sr) related to the 2H-ABO 3-type. They are formed by the intergrowth of n A 3A'BO 6 blocks, showing the Sr 4RhO 6-type, with A 12A' 2B 8O 30 blocks, constituted by two A 3O 9 and two A 3A'O 6 layers alternating in the stacking sequence 1:1, leading to the A 27A' 7B 13O 60 ( n=5) and A 30A' 8B 14O 66 ( n=6) compositions. A crystallographic shear mechanism is proposed to describe the structural relationship between Sr 4RhO 6 (A 3A'BO 6-type) and the new superstructures.

  8. 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

  9. Rapid visualization of hydrogen positions in protein neutron crystallographic structures.

    PubMed

    Munshi, Parthapratim; Chung, Shang-Lin; Blakeley, Matthew P; Weiss, Kevin L; Myles, Dean A A; Meilleur, Flora

    2012-01-01

    Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.

  10. Automated identification of crystallographic ligands using sparse-density representations

    PubMed Central

    Carolan, C. G.; Lamzin, V. S.

    2014-01-01

    A novel procedure for the automatic identification of ligands in macromolecular crystallographic electron-density maps is introduced. It is based on the sparse parameterization of density clusters and the matching of the pseudo-atomic grids thus created to conformationally variant ligands using mathematical descriptors of molecular shape, size and topology. In large-scale tests on experimental data derived from the Protein Data Bank, the procedure could quickly identify the deposited ligand within the top-ranked compounds from a database of candidates. This indicates the suitability of the method for the identification of binding entities in fragment-based drug screening and in model completion in macromolecular structure determination. PMID:25004962

  11. Crystallographic analysis of a series of inorganic compounds

    NASA Astrophysics Data System (ADS)

    Borisov, S. V.; Magarill, S. A.; Pervukhina, N. V.

    2015-04-01

    The method of crystallographic analysis relies on the mechanical-wave concept that treats the crystalline state as the result of ordering of atomic positions by families of parallel equidistant planes. Using this method, a large set of fluoride, oxide and sulfide structures was analyzed. The pseudo-translational ordering of various atomic groups (including the presence of cation and anion sublattices) in the structures of various classes of inorganic compounds was established. The crucial role of local ordering of heavy cations (coherent assembly) in the structures comprising large cluster fragments (Keggin polyanions, polyoxoniobates, etc.) is discussed. The role of symmetry and the regular distribution of heavy atoms in the formation of stable crystal structures, which is to be taken into account in the targeted design, is considered. The universality of configurations of atomic positions in the structures of various classes of inorganic compounds resulting from the ordering mechanism organized by mechanical (elastic) forces is demonstrated. The bibliography includes 158 references.

  12. Crystallographic and spectroscopic study on a known orally active progestin.

    PubMed

    Ferraboschi, Patrizia; Ciuffreda, Pierangela; Ciceri, Samuele; Grisenti, Paride; Castellano, Carlo; Meneghetti, Fiorella

    2015-12-01

    6,17α-Dimethyl-4,6-pregnadiene-3,20-dione (medrogestone, 2) is for a long time known steroid endowed with progestational activity. In order to study its crystallographic and NMR spectroscopic properties with the aim to fill the literature gap, we prepared medrogestone following a traditional procedure. A careful NMR study allowed the complete assignment of the (1)H and (13)C NMR signals not only of medrogestone but also of its synthetic intermediates. The structural and stereochemical characterizations of medrogestone together with its precursor 17α-methyl-3-ethoxy-pregna-3,5-dien-20-one were described by means of X-ray analysis, allowing a deepened conformational investigation.

  13. Crystallographic preferred orientation (CPO) of gypsum measured by electron backscatter diffraction (EBSD).

    PubMed

    Hildyard, R C; Prior, D J; Mariani, E; Faulkner, D R

    2009-12-01

    An investigation by electron backscatter diffraction on gypsum shows that this technique can be used to study the microstructures and crystallographic preferred orientation of gypsum. Presented here are the methods, verification tests and data obtained from a naturally deformed sample of gypsum-rich rock. The electron backscatter diffraction data show the sample has a strong crystallographic preferred orientation.

  14. 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.

  15. Oriented crystallographic textures of olivine in quenched silicate melt spherules

    NASA Astrophysics Data System (ADS)

    Isobe, H.

    2015-12-01

    Olivine is one of the most common minerals in the planetary materials including solid Earth and chondritic meteorites. Olivine crystals show characteristic textures in chondrules and micrometeorites (MMs) depending on heating and cooling histories, especially in extraordinary quick cooling rates. We have constructed a fine particle free fall apparatus in a high temperature furnace and carried out crystallization experiments of fine particles with quick heating and quenching (Isobe and Gondo, 2013). The falling particles in the furnace can reach 1400 degrees C within 2 seconds, keep above 1400 degrees C more than 1 second, and are quenched within 1 second. Run products from olivine particles show various textures depending on proportions of three kinds of starting materials in the particles. Fayalite particles melt completely and form barred olivine-like spherules with low pyramid structures on the surface. Dendritic olivine crystals with regulated crystallographic orientation are developed in melted particles. Surface texture of melted particles may be affected by the dendritic olivine crystals grown in the spherules. Oriented dendrites of magnetite also occur between olivine crystals. The texture of oriented dendrite of olivine with tiny magnetite is quite similar to natural cosmic spherules (CSs). In the completely melted spherules, barred olivine-like structures can be seen. Due to extraordinary high cooling rate up to 2×10^6 degrees C/hour and degrees of supercooling, olivine bars show chained structure of H-shaped or hourglass shaped units which are distinctive characteristics for quick growth of olivine in quenching. In spite of quite short period of crystal growth processes, chained olivine aligns parallel bars in the almost entire spherule. Nucleation of barred olivine crystals may be initiated at surface of spherules. Starting points of olivine growth can be seen as peaks on surface of the spherules. The crystallographic textures of olivine develop

  16. Preliminary crystallographic analysis of the bacteriophage P22 portal protein.

    PubMed

    Cingolani, Gino; Moore, Sean D; Prevelige, Peter E; Johnson, John E

    2002-07-01

    Portal proteins are components of large oligomeric dsDNA pumps connecting the icosahedral capsid of tailed bacteriophages to the tail. Prior to the tail attachment, dsDNA is actively pumped through a central cavity formed by the subunits. We have studied the portal protein of bacteriophage P22, which is the largest connector characterized among the tailed bacteriophages. The molecular weight of the monomer is 82.7 kDa, and it spontaneously assembles into an oligomeric structure of approximately 1.0 MDa. Here we present a preliminary biochemical and crystallographic characterization of this large macromolecular complex. The main difficulties related to the crystallization of P22 portal protein lay in the intrinsic dynamic nature of the portal oligomer. Recombinant connectors assembled from portal monomers expressed in Escherichia coli form rings of different stoichiometry in solution, which cannot be separated on the basis of their size. To overcome this intrinsic heterogeneity we devised a biochemical purification that separates different ring populations on the basis of their charge. Small ordered crystals were grown from drops containing a high concentration of the kosmotropic agent tert-butanol and used for data collection. A preliminary crystallographic analysis to 7.0-A resolution revealed that the P22 portal protein crystallized in space group I4 with unit cell dimensions a=b=409.4A, c=260.4A. This unit cell contains a total of eight connectors. Analysis of the noncrystallographic symmetry by the self-rotation function unambiguously confirmed that bacteriophage P22 portal protein is a dodecamer with a periodicity of 30 degrees. The cryo-EM reconstruction of the dodecahedral bacteriophage T3 portal protein will be used as a model to initiate phase extension and structure determination.

  17. 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, Pro

  18. Purification, crystallization and preliminary crystallographic analysis of human cystathionine β-synthase

    PubMed Central

    Oyenarte, Iker; Majtan, Tomas; Ereño, June; Corral-Rodríguez, María Angeles; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

    2012-01-01

    Human cystathionine β-synthase (CBS) is a pyridoxal-5′-phosphate-dependent hemeprotein, whose catalytic activity is regulated by S-adenosylmethionine. CBS catalyzes the β-replacement reaction of homocysteine (Hcy) with serine to yield cystathionine. CBS is a key regulator of plasma levels of the thrombogenic Hcy and deficiency in CBS is the single most common cause of homocystinuria, an inherited metabolic disorder of sulfur amino acids. The properties of CBS enzymes, such as domain organization, oligomerization degree or regulatory mechanisms, are not conserved across the eukaryotes. The current body of knowledge is insufficient to understand these differences and their impact on CBS function and physiology. To overcome this deficiency, we have addressed the crystallization and preliminary crystallographic analysis of a protein construct (hCBS516–525) that contains the full-length CBS from Homo sapiens (hCBS) and just lacks amino-acid residues 516–525, which are located in a disordered loop. The human enzyme yielded crystals belonging to space group I222, with unit-cell parameters a = 124.98, b = 136.33, c = 169.83 Å and diffracting X-rays to a resolution of 3.0 Å. The crystal structure appears to contain two molecules in the asymmetric unit which presumably correspond to a dimeric form of the enzyme. PMID:23143240

  19. Crystallographic Complexes of Surfactant Protein A and Carbohydrates Reveal Ligand-induced Conformational Change*

    PubMed Central

    Shang, Feifei; Rynkiewicz, Michael J.; McCormack, Francis X.; Wu, Huixing; Cafarella, Tanya M.; Head, James F.; Seaton, Barbara A.

    2011-01-01

    Surfactant protein A (SP-A), a C-type lectin, plays an important role in innate lung host defense against inhaled pathogens. Crystallographic SP-A·ligand complexes have not been reported to date, limiting available molecular information about SP-A interactions with microbial surface components. This study describes crystal structures of calcium-dependent complexes of the C-terminal neck and carbohydrate recognition domain of SP-A with d-mannose, d-α-methylmannose, and glycerol, which represent subdomains of glycans on pathogen surfaces. Comparison of these complexes with the unliganded SP-A neck and carbohydrate recognition domain revealed an unexpected ligand-associated conformational change in the loop region surrounding the lectin site, one not previously reported for the lectin homologs SP-D and mannan-binding lectin. The net result of the conformational change is that the SP-A lectin site and the surrounding loop region become more compact. The Glu-202 side chain of unliganded SP-A extends out into the solvent and away from the calcium ion; however, in the complexes, the Glu-202 side chain translocates 12.8 Å to bind the calcium. The availability of Glu-202, together with positional changes involving water molecules, creates a more favorable hydrogen bonding environment for carbohydrate ligands. The Lys-203 side chain reorients as well, extending outward into the solvent in the complexes, thereby opening up a small cation-friendly cavity occupied by a sodium ion. Binding of this cation brings the large loop, which forms one wall of the lectin site, and the adjacent small loop closer together. The ability to undergo conformational changes may help SP-A adapt to different ligand classes, including microbial glycolipids and surfactant lipids. PMID:21047777

  20. Equilibrium shape of graphene domains on Ni(111)

    NASA Astrophysics Data System (ADS)

    Li, Meifang; Hannon, James B.; Tromp, Rudoff M.; Sun, Jiebing; Li, Junwen; Shenoy, Vivek B.; Chason, Eric

    2013-07-01

    We have determined the equilibrium shape of graphene domains grown on Ni(111) via carbon segregation at 925∘C. In situ, spatially resolved electron diffraction measurements were used to determine the crystallographic orientation of the edges of the graphene domains. In contrast to recent theoretical predictions of a nearly circular shape, we show that graphene domains, which nucleate with random shapes, all evolve toward a triangular equilibrium shape with “zigzag” edges. Only one of the two possible zigzag edge orientations is observed.

  1. Domain wall orientation and domain shape in KTiOPO4 crystals

    NASA Astrophysics Data System (ADS)

    Shur, V. Ya.; Vaskina, E. M.; Pelegova, E. V.; Chuvakova, M. A.; Akhmatkhanov, A. R.; Kizko, O. V.; Ivanov, M.; Kholkin, A. L.

    2016-09-01

    Domain shape evolution and domain wall motion have been studied in KTiOPO4 (KTP) ferroelectric single crystals using complementary experimental methods. The in situ visualization of domain kinetics has allowed revealing: (1) qualitative change of the domain shape, (2) dependence of the domain wall velocity on its orientation, (3) jump-like domain wall motion caused by domain merging, (4) effect of domain shape stability. The model of domain wall motion driven by generation of elementary steps (kink-pair nucleation) and subsequent kink motion is presented. The decrease in the relative velocity of the approaching parallel domain walls is attributed to electrostatic interaction. The effect of polarization reversal induced by chemical etching is observed. The obtained results are important for the development of domain engineering in the crystals of KTP family.

  2. Effect of Zr on the crystallographic texture of precipitation-hardened Sm(Co,Fe,Cu,Zr)7 ribbons

    NASA Astrophysics Data System (ADS)

    Rong, Chuan-bing; Zhang, Hong-wei; He, Shu-li; Chen, Ren-jie; Shen, Bao-gen

    2005-03-01

    Sm(CobalFe0.1Cu0.1Zrw)7 (w=0.01-0.09) ribbons have been prepared by conventional melt spinning followed by precipitation hardening. The Zr addition can suppress the nucleation of solidification and increase the velocity of grain growth. This leads to the increase of texture degree of the ribbons with increasing Zr content. The crystallographic texture is still preserved in ribbons after the precipitation hardening. The remanence ratio of the heat-treated ribbons increases from 0.7 for w=0.01 to 0.9 for w=0.08. An energy product of about 10 MGOe has been obtained in the ribbon with w=0.03. The angular dependence of coercivity suggests that the magnetization reversal of the precipitation-hardened ribbons is controlled by both domain-wall pinning and nucleation mechanism.

  3. Forsteritic olivine: effect of crystallographic direction on dissolution kinetics

    NASA Astrophysics Data System (ADS)

    Awad, Aida; Koster van Groos, A. F.; Guggenheim, Stephen

    2000-05-01

    Directional dissolution along the three crystallographic axes of gem-quality olivine (Fo 91), San Carlos, Arizona was studied at pH 1 and pH 2 at 23, 50, 70, and 90°C and 1 atm. The rate constant of dissolution for olivine at pH 1 and 70°C down the a-, b-, and c-axis (based on space group Pbnm) is 2.7 × 10 -4, 5.6 × 10 -3, and 8.1 × 10 -4 mm/h, respectively. At pH 2 and 70°C the dissolution rates are 1.3 × 10 -4, 2.1 × 10 -3, and 4.3 × 10 -4 mm/h, respectively. At 50°C and 90°C, these rates are ˜0.2 and 5 times the rates at 70°C. The much higher dissolution rate in the direction of the b-axis is attributed to preferential protonation of the oxygen atoms around the M(1) site, which would result in a higher dissolution rate of the SiO 2-M(1) network. The activation energy of dissolution E adis in the direction down the a-, b-, and c-axis is 114.5 ± 23 kJ/mol, 69.9 ± 8 kJ/mol, and 72.9 ± 15 kJ/mol, respectively. Because of differences in the directional E adis, dissolution in the direction down the a-axis will become dominant at temperatures above ˜140°C. The bulk E adis, based on the dissolution rate along the crystallographic axes, is 71.5 ± 12 kJ/mol at the temperature range of the study. Because of the larger E adis perpendicular to the a-axis, bulk E adis must increase with temperature. The results indicate that the weathering rate of olivine is more temperature dependent than was considered previously.

  4. 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

  5. Domain wall orientation in magnetic nanowires.

    PubMed

    Vedmedenko, E Y; Kubetzka, A; von Bergmann, K; Pietzsch, O; Bode, M; Kirschner, J; Oepen, H P; Wiesendanger, R

    2004-02-20

    Scanning tunneling microscopy reveals that domain walls in ultrathin Fe nanowires are oriented along a certain crystallographic direction, regardless of the orientation of the wires. Monte Carlo simulations on a discrete lattice are in accordance with the experiment if the film relaxation is taken into account. We demonstrate that the wall orientation is determined by the atomic lattice and the resulting strength of an effective exchange interaction. The magnetic anisotropy and the magnetostatic energy play a minor role for the wall orientation in that system.

  6. Transport domain unlocking sets the uptake rate of an aspartate transporter

    PubMed Central

    Akyuz, Nurunisa; Georgieva, Elka R.; Zhou, Zhou; Stolzenberg, Sebastian; Cuendet, Michel A.; Khelashvili, George; Altman, Roger B.; Terry, Daniel S.; Freed, Jack H.; Weinstein, Harel; Boudker, Olga; Blanchard, Scott C.

    2015-01-01

    Glutamate transporters terminate neurotransmission by clearing synaptically released glutamate from the extracellular space, allowing repeated rounds of signaling and preventing glutamate-mediated excitotoxicity. Crystallographic studies on an archaeal homologue, GltPh, showed that distinct transport domains translocate substrates into the cytoplasm by moving across the membrane within a central trimerization scaffold. Here, we report direct observations of these 'elevator-like' transport domain motions in the context of reconstituted proteoliposomes and physiological ion gradients using single-molecule fluorescence resonance energy transfer (smFRET) imaging. We show that GltPh bearing two “humanizing” mutations exhibits markedly increased transport domain dynamics, which parallels an increased rate of substrate transport, thereby establishing a direct temporal relationship between transport domain motions and substrate uptake. Crystallographic and computational investigations reveal that these mutations favor structurally “unlocked” states with increased solvent occupancy at the interface between the transport domain and the trimeric scaffold. PMID:25652997

  7. Origin of anomalous magnetite properties in crystallographic matched heterostructures: Fe3O4(111)/MgAl2O4(111).

    PubMed

    Gilks, D; Lari, L; Naughton, J; Cespedes, O; Cai, Z; Gerber, A; Thompson, S M; Ziemer, K; Lazarov, V K

    2013-12-04

    Magnetite films grown on crystallographically matched substrates such as MgAl2O4 are not expected to show anomalous properties such as negative magnetoresistance and high saturation fields. By atomic resolution imaging using scanning transmission electron microscopy we show direct evidence of anti-phase domain boundaries (APB) present in these heterostructures. Experimentally identified 1/4<101> shifts determine the atomic structure of the observed APBs. The dominant non-bulk superexchange interactions are between 180° octahedral-Fe/O/octahedral-Fe sites which provide strong antiferromagnetic coupling across the defect interface resulting in non-bulk magnetic and magnetotransport properties.

  8. Expression, purification and primary crystallographic study of human androgen receptor in complex with DNA and coactivator motifs

    SciTech Connect

    Zhou, X. Edward; Suino-Powell, Kelly; Ludidi, Phumzile L.; McDonnell, Donald P.; Xu, H. Eric

    2012-10-24

    The androgen receptor (AR) is a DNA-binding and hormone-activated transcription factor that plays critical roles in the development and progression of prostate cancer. The transcriptional function of AR is modulated by intermolecular interactions with DNA elements and coactivator proteins, as well as intramolecular interactions between AR domains; thus, the structural information from the full-length AR or a multi-domain fragment is essential for understanding the molecular basis of AR functions. Here we report the expression and purification of full-length AR protein and of a fragment containing its DNA-binding and ligand-binding domains connected by the hinge region in the presence of its natural ligand, dihydrotestosterone. Crystals of ligand-bound full-length AR and of the AR fragment in complex with DNA elements and coactivator motifs have been obtained and diffracted to low resolutions. These results help establish a foundation for pursuing further crystallographic studies of an AR/DNA complex.

  9. Domain decomposition algorithms and computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    Some of the new domain decomposition algorithms are applied to two model problems in computational fluid dynamics: the two-dimensional convection-diffusion problem and the incompressible driven cavity flow problem. First, a brief introduction to the various approaches of domain decomposition is given, and a survey of domain decomposition preconditioners for the operator on the interface separating the subdomains is then presented. For the convection-diffusion problem, the effect of the convection term and its discretization on the performance of some of the preconditioners is discussed. For the driven cavity problem, the effectiveness of a class of boundary probe preconditioners is examined.

  10. Domain decomposition algorithms and computational fluid dynamics

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    Some of the new domain decomposition algorithms are applied to two model problems in computational fluid dynamics: the two-dimensional convection-diffusion problem and the incompressible driven cavity flow problem. First, a brief introduction to the various approaches of domain decomposition is given, and a survey of domain decomposition preconditioners for the operator on the interface separating the subdomains is then presented. For the convection-diffusion problem, the effect of the convection term and its discretization on the performance of some of the preconditioners is discussed. For the driven cavity problem, the effectiveness of a class of boundary probe preconditioners is examined.

  11. Correlating Atom Probe Crystallographic Measurements with Transmission Kikuchi Diffraction Data.

    PubMed

    Breen, Andrew J; Babinsky, Katharina; Day, Alec C; Eder, K; Oakman, Connor J; Trimby, Patrick W; Primig, Sophie; Cairney, Julie M; Ringer, Simon P

    2017-03-14

    Correlative microscopy approaches offer synergistic solutions to many research problems. One such combination, that has been studied in limited detail, is the use of atom probe tomography (APT) and transmission Kikuchi diffraction (TKD) on the same tip specimen. By combining these two powerful microscopy techniques, the microstructure of important engineering alloys can be studied in greater detail. For the first time, the accuracy of crystallographic measurements made using APT will be independently verified using TKD. Experimental data from two atom probe tips, one a nanocrystalline Al-0.5Ag alloy specimen collected on a straight flight-path atom probe and the other a high purity Mo specimen collected on a reflectron-fitted instrument, will be compared. We find that the average minimum misorientation angle, calculated from calibrated atom probe reconstructions with two different pole combinations, deviate 0.7° and 1.4°, respectively, from the TKD results. The type of atom probe and experimental conditions appear to have some impact on this accuracy and the reconstruction and measurement procedures are likely to contribute further to degradation in angular resolution. The challenges and implications of this correlative approach will also be discussed.

  12. Nanocrystalline materials: recent advances in crystallographic characterization techniques.

    PubMed

    Ringe, Emilie

    2014-11-01

    Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask 'how are nanoshapes created?', 'how does the shape relate to the atomic packing and crystallography of the material?', 'how can we control and characterize the external shape and crystal structure of such small nanocrystals?'. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed.

  13. CRYSTMET-The NRCC Metals Crystallographic Data File.

    PubMed

    Wood, Gordon H; Rodgers, John R; Gough, S Roger; Villars, Pierre

    1996-01-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool.

  14. Cassia grandis Linn. f. seed galactomannan: structural and crystallographical studies.

    PubMed

    Joshi, Harsha; Kapoor, Virendra P

    2003-09-01

    Cassia grandis is a small or medium sized tree, found in abundance throughout India. The seeds contain about 50% endosperm gum and possess the characteristics of becoming a potential source of seed gum. The purified polysaccharide has been characterized as a pure galactomannan having a mannose-galactose ratio of 3.15; molecular weight (Mw) 80,200; polydispersity (Mw/Mn), 1.35 and intrinsic viscosity [eta], 848 mL/g. Methylation, periodate oxidation, Smith degradation and 13C NMR studies confirm that the polysaccharide has the basic structure of legume galactomannans consisting of a beta-(1-->4)-linked main mannan backbone to which galactose units are attached at O-6. The orthorhombic lattice constants of the hydrated gum are as follows: a=9.00, b=24.81, c=10.30 A. The crystallographic data establish that the probable space group symmetry of the unit cell is P2(1)2(1)2. The results are in contradiction to earlier reports (Indian J. Chem. 16B (1978) 966; J. Indian Chem. Soc. 55 (1978) 1216) in which a non-galactomannan polysaccharide structure has been assigned having a main chain of (1-->4)-linked galactose and mannose units in the molar ratio 6:3, where 50% of the galactose units branched with two galactose and one mannose through 1-->3 linkage.

  15. Crystallographic texture analysis of archaeological metals: interpretation of manufacturing techniques

    NASA Astrophysics Data System (ADS)

    Artioli, G.

    2007-12-01

    Neutron probes and high energy X-rays are sources of primary importance for the non-invasive characterization of materials related to cultural heritage. Their employment in the characterization of archaeological metal objects, combined with the recent instrumental and computational developments in the field of crystallographic texture analysis (CTA) from diffraction data proves to be a powerful tool for the interpretation of ancient metal working techniques. Diffraction based CTA, when performed using penetrating probes and adequate detector coverage of reciprocal space, for example using large detector arrays and/or ToF mode, allows simultaneous identification and quantification of crystalline phases, besides the microstructural and textural characterization of the object, and it can be effectively used as a totally non-invasive tool for metallographic analysis. Furthermore, the chemical composition of the object may also be obtained by the simultaneous detection of prompt gamma rays induced by neutron activation, or by the fluorescence signal from high energy X-rays, in order to obtain a large amount of complementary information in a single experiment. The specific application of neutron CTA to the characterization of the manufacturing processes of prehistoric copper axes is discussed in detail.

  16. Crystallographic Orientation of Cuttlebone Shield Determined by Electron Backscatter Diffraction

    NASA Astrophysics Data System (ADS)

    Cusack, Maggie; Chung, Peter

    2014-01-01

    In common with many cephalopod mollusks, cuttlefish produce an internal biomineral buoyancy device. This cuttlebone is analogous to a surf board in shape and structure, providing rigidity and a means of controlling buoyancy. The cuttlebone is composed of calcium carbonate in the form of aragonite and comprises an upper dorsal shield and a lower lamellar matrix. The lamellar matrix comprises layers of chambers with highly corrugated walls. The dorsal shield comprises bundles of aragonite needles stacked on top of each other. Electron backscatter diffraction analyses of the dorsal shield reveal that the c-axis of aragonite is parallel with the long axis of the needles in the bundles such that any spread in crystallographic orientation is consistent with the spread in orientation of the fibers as they radiate to form the overall structure of the dorsal shield. This arrangement of c-axis coincident with the long axis of the biomineral structure is similar to the arrangement in corals and in contrast to the situation in the molluskan aragonite nacre of brachiopod calcite where the c-axis is perpendicular to the aragonite tablet or calcite fiber, respectively.

  17. Nanocrystalline materials: recent advances in crystallographic characterization techniques

    PubMed Central

    Ringe, Emilie

    2014-01-01

    Most properties of nanocrystalline materials are shape-dependent, providing their exquisite tunability in optical, mechanical, electronic and catalytic properties. An example of the former is localized surface plasmon resonance (LSPR), the coherent oscillation of conduction electrons in metals that can be excited by the electric field of light; this resonance frequency is highly dependent on both the size and shape of a nanocrystal. An example of the latter is the marked difference in catalytic activity observed for different Pd nanoparticles. Such examples highlight the importance of particle shape in nanocrystalline materials and their practical applications. However, one may ask ‘how are nanoshapes created?’, ‘how does the shape relate to the atomic packing and crystallography of the material?’, ‘how can we control and characterize the external shape and crystal structure of such small nanocrystals?’. This feature article aims to give the reader an overview of important techniques, concepts and recent advances related to these questions. Nucleation, growth and how seed crystallography influences the final synthesis product are discussed, followed by shape prediction models based on seed crystallography and thermodynamic or kinetic parameters. The crystallographic implications of epitaxy and orientation in multilayered, core-shell nanoparticles are overviewed, and, finally, the development and implications of novel, spatially resolved analysis tools are discussed. PMID:25485133

  18. Crystallization and preliminary crystallographic analysis of recombinant human galectin-1

    PubMed Central

    Scott, Stacy A.; Scott, Ken; Blanchard, Helen

    2007-01-01

    Galectin-1 is considered to be a regulator protein as it is ubiquitously expressed throughout the adult body and is responsible for a broad range of cellular regulatory functions. Interest in galectin-1 from a drug-design perspective is founded on evidence of its overexpression by many cancers and its immunomodulatory properties. The development of galectin-1-specific inhibitors is a rational approach to the fight against cancer because although galectin-1 induces a plethora of effects, null mice appear normal. X-ray crystallographic structure determination will aid the structure-based design of galectin-1 inhibitors. Here, the crystallization and preliminary diffraction analysis of human galectin-1 crystals generated under six different conditions is reported. X-ray diffraction data enabled the assignment of unit-cell parameters for crystals grown under two conditions, one belongs to a tetragonal crystal system and the other was determined as monoclinic P21, representing two new crystal forms of human galectin-1. PMID:18007053

  19. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

    DOE PAGES

    Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; ...

    2016-08-31

    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows.PHENIX–AFITTrefinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentiallymore » difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows.PHENIX–AFITTrefinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combiningAFITTand thePHENIXsoftware suite on a data set of 189 protein–ligand PDB structures are presented. Refinements usingPHENIX–AFITTsignificantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. Finally, for the data presented,PHENIX–AFITTrefinements result in more chemically accurate models for small-molecule ligands.« less

  20. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX

    PubMed Central

    Janowski, Pawel A.; Moriarty, Nigel W.; Kelley, Brian P.; Case, David A.; York, Darrin M.; Adams, Paul D.; Warren, Gregory L.

    2016-01-01

    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX–AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX–AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein–ligand PDB structures are presented. Refinements using PHENIX–AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX–AFITT refinements result in more chemically accurate models for small-molecule ligands. PMID:27599738

  1. Mantle dynamics inferred from the crystallographic preferred orientation of bridgmanite

    NASA Astrophysics Data System (ADS)

    Tsujino, Noriyoshi; Nishihara, Yu; Yamazaki, Daisuke; Seto, Yusuke; Higo, Yuji; Takahashi, Eiichi

    2016-11-01

    Seismic shear wave anisotropy is observed in Earth’s uppermost lower mantle around several subducted slabs. The anisotropy caused by the deformation-induced crystallographic preferred orientation (CPO) of bridgmanite (perovskite-structured (Mg,Fe)SiO3) is the most plausible explanation for these seismic observations. However, the rheological properties of bridgmanite are largely unknown. Uniaxial deformation experiments have been carried out to determine the deformation texture of bridgmanite, but the dominant slip system (the slip direction and plane) has not been determined. Here we report the CPO pattern and dominant slip system of bridgmanite under conditions that correspond to the uppermost lower mantle (25 gigapascals and 1,873 kelvin) obtained through simple shear deformation experiments using the Kawai-type deformation-DIA apparatus. The fabrics obtained are characterized by [100] perpendicular to the shear plane and [001] parallel to the shear direction, implying that the dominant slip system of bridgmanite is [001](100). The observed seismic shear- wave anisotropies near several subducted slabs (Tonga-Kermadec, Kurile, Peru and Java) can be explained in terms of the CPO of bridgmanite as induced by mantle flow parallel to the direction of subduction.

  2. Improved ligand geometries in crystallographic refinement using AFITT in PHENIX.

    PubMed

    Janowski, Pawel A; Moriarty, Nigel W; Kelley, Brian P; Case, David A; York, Darrin M; Adams, Paul D; Warren, Gregory L

    2016-09-01

    Modern crystal structure refinement programs rely on geometry restraints to overcome the challenge of a low data-to-parameter ratio. While the classical Engh and Huber restraints work well for standard amino-acid residues, the chemical complexity of small-molecule ligands presents a particular challenge. Most current approaches either limit ligand restraints to those that can be readily described in the Crystallographic Information File (CIF) format, thus sacrificing chemical flexibility and energetic accuracy, or they employ protocols that substantially lengthen the refinement time, potentially hindering rapid automated refinement workflows. PHENIX-AFITT refinement uses a full molecular-mechanics force field for user-selected small-molecule ligands during refinement, eliminating the potentially difficult problem of finding or generating high-quality geometry restraints. It is fully integrated with a standard refinement protocol and requires practically no additional steps from the user, making it ideal for high-throughput workflows. PHENIX-AFITT refinements also handle multiple ligands in a single model, alternate conformations and covalently bound ligands. Here, the results of combining AFITT and the PHENIX software suite on a data set of 189 protein-ligand PDB structures are presented. Refinements using PHENIX-AFITT significantly reduce ligand conformational energy and lead to improved geometries without detriment to the fit to the experimental data. For the data presented, PHENIX-AFITT refinements result in more chemically accurate models for small-molecule ligands.

  3. Towards automated crystallographic structure refinement with phenix.refine

    PubMed Central

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel; Headd, Jeffrey J.; Moriarty, Nigel W.; Mustyakimov, Marat; Terwilliger, Thomas C.; Urzhumtsev, Alexandre; Zwart, Peter H.; Adams, Paul D.

    2012-01-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods. PMID:22505256

  4. Towards automated crystallographic structure refinement with phenix.refine.

    PubMed

    Afonine, Pavel V; Grosse-Kunstleve, Ralf W; Echols, Nathaniel; Headd, Jeffrey J; Moriarty, Nigel W; Mustyakimov, Marat; Terwilliger, Thomas C; Urzhumtsev, Alexandre; Zwart, Peter H; Adams, Paul D

    2012-04-01

    phenix.refine is a program within the PHENIX package that supports crystallographic structure refinement against experimental data with a wide range of upper resolution limits using a large repertoire of model parameterizations. It has several automation features and is also highly flexible. Several hundred parameters enable extensive customizations for complex use cases. Multiple user-defined refinement strategies can be applied to specific parts of the model in a single refinement run. An intuitive graphical user interface is available to guide novice users and to assist advanced users in managing refinement projects. X-ray or neutron diffraction data can be used separately or jointly in refinement. phenix.refine is tightly integrated into the PHENIX suite, where it serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.

  5. CRYSTMET—The NRCC Metals Crystallographic Data File

    PubMed Central

    Wood, Gordon H.; Rodgers, John R.; Gough, S. Roger; Villars, Pierre

    1996-01-01

    CRYSTMET is a computer-readable database of critically evaluated crystallographic data for metals (including alloys, intermetallics and minerals) accompanied by pertinent chemical, physical and bibliographic information. It currently contains about 60 000 entries and covers the literature exhaustively from 1913. Scientific editing of the abstracted entries, consisting of numerous automated and manual checks, is done to ensure consistency with related, previously published studies, to assign structure types where necessary and to help guarantee the accuracy of the data and related information. Analyses of the entries and their distribution across key journals as a function of time show interesting trends in the complexity of the compounds studied as well as in the elements they contain. Two applications of CRYSTMET are the identification of unknowns and the prediction of properties of materials. CRYSTMET is available either online or via license of a private copy from the Canadian Scientific Numeric Database Service (CAN/SND). The indexed online search and analysis system is easy and economical to use yet fast and powerful. Development of a new system is under way combining the capabilities of ORACLE with the flexibility of a modern interface based on the Netscape browsing tool. PMID:27805157

  6. 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.

  7. Crystallization and preliminary crystallographic analysis of recombinant human galectin-1

    SciTech Connect

    Scott, Stacy A.; Scott, Ken; Blanchard, Helen

    2007-11-01

    Human galectin-1 has been cloned, expressed in E. coli, purified and crystallized in the presence of both lactose (ligand) and β-mercaptoethanol under six different conditions. The X-ray diffraction data obtained have enabled the assignment of unit-cell parameters for two novel crystal forms of human galectin-1. Galectin-1 is considered to be a regulator protein as it is ubiquitously expressed throughout the adult body and is responsible for a broad range of cellular regulatory functions. Interest in galectin-1 from a drug-design perspective is founded on evidence of its overexpression by many cancers and its immunomodulatory properties. The development of galectin-1-specific inhibitors is a rational approach to the fight against cancer because although galectin-1 induces a plethora of effects, null mice appear normal. X-ray crystallographic structure determination will aid the structure-based design of galectin-1 inhibitors. Here, the crystallization and preliminary diffraction analysis of human galectin-1 crystals generated under six different conditions is reported. X-ray diffraction data enabled the assignment of unit-cell parameters for crystals grown under two conditions, one belongs to a tetragonal crystal system and the other was determined as monoclinic P2{sub 1}, representing two new crystal forms of human galectin-1.

  8. Crystallographic orientation variation of isothermal pearlite under high magnetic field

    SciTech Connect

    Meng, Lan Zhou, Xiaoling Chen, Jianhao

    2015-07-15

    Crystallographic orientation (CO) variation of magnetic-induced pearlite (MIP) during its microstructure evolution in 19.8 T was investigated by electron back-scatter diffraction (EBSD). It is closely related to the isothermal temperatures (ITs) and the applied magnetic time (MT) during the process of MIP formation. The <100> easy magnetization direction in MIP colonies is strengthened with the MT within the certain transformed fraction of MIP (f{sub MIP}) at the relatively lower IT (983 K) above the eutectoid temperature but below the magnetically shifted upward eutectoid temperature, while this special CO tends to be weakened at a relatively higher IT (995 K). For the same MT, the higher the IT, the relatively larger is the proportion in <100> orientation for MIP colonies at the early growth stage. These results have demonstrated that the change of <100> orientation of MIP is closely related to the growth rate of pearlite ferrite (PF), and strengthened mainly at early transformation stage. When f{sub MIP} reaches some value, the growth rate of MIP at other COs, such as <110>, even at the hard magnetization direction, turns to present speed-up. - Highlights: • HMF can induce pearlite with different fractions above the eutectoid temperature. • CO is closely related to isothermal temperatures and applied magnetic time. • <100> direction is related to the growth rate of PF, and strengthened at early stage. • When f{sub MIP} reaches some value, the growth rate at other COs turns to present speed-up.

  9. Dynamically-driven enhancement of the catalytic machinery of the SARS 3C-like protease by the S284-T285-I286/A mutations on the extra domain.

    PubMed

    Lim, Liangzhong; Shi, Jiahai; Mu, Yuguang; Song, Jianxing

    2014-01-01

    Previously we revealed that the extra domain of SARS 3CLpro mediated the catalysis via different mechanisms. While the R298A mutation completely abolished the dimerization, thus resulting in the inactive catalytic machinery, N214A inactivated the enzyme by altering its dynamics without significantly perturbing its structure. Here we studied another mutant with S284-T285-I286 replaced by Ala (STI/A) with a 3.6-fold activity increase and slightly enhanced dimerization. We determined its crystal structure, which still adopts the dimeric structure almost identical to that of the wild-type (WT), except for slightly tighter packing between two extra-domains. We then conducted 100-ns molecular dynamics (MD) simulations for both STI/A and WT, the longest reported so far for 3CLpro. In the simulations, two STI/A extra domains become further tightly packed, leading to a significant volume reduction of the nano-channel formed by residues from both catalytic and extra domains. The enhanced packing appears to slightly increase the dynamic stability of the N-finger and the first helix residues, which subsequently triggers the redistribution of dynamics over residues directly contacting them. This ultimately enhances the dynamical stability of the residues constituting the catalytic dyad and substrate-binding pockets. Further correlation analysis reveals that a global network of the correlated motions exists in the protease, whose components include all residues identified so far to be critical for the dimerization and catalysis. Most strikingly, the N214A mutation globally decouples this network while the STI/A mutation alters the correlation pattern. Together with previous results, the present study establishes that besides the classic structural allostery, the dynamic allostery also operates in the SARS 3CLpro, which is surprisingly able to relay the perturbations on the extra domain onto the catalytic machinery to manifest opposite catalytic effects. Our results thus imply a

  10. Domain- and symmetry-transition origins of reduced nanosecond piezoelectricity in ferroelectric/dielectric superlattices

    SciTech Connect

    Chen, Pice; Jo, Ji Young; Lee, Ho Nyung; Dufresne, Eric M.; Nakhmanson, Serge; Evans, Paul G.

    2012-01-01

    Complex-oxide superlattices (SLs) with atomic-scale periodicity have dynamical properties that are distinct from thin films of uniform composition. The origins of these properties are closely related to the dynamics of polarization domains and to field-driven changes in the symmetries resulting from interfacial coupling between different components. These dynamics are apparent at timescales from a few nanoseconds to several milliseconds in experiments probing the piezoelectricity of a ferroelectric/dielectric BaTiO{sub 3}(BTO)/CaTiO{sub 3} (CTO) SL using time-resolved x-ray microdiffraction. At the 100 ns timescale, the piezoelectric distortion is approximately ten times smaller than in the millisecond regime. This reduced piezoelectricity at short timescales is not observed in previously studied PbTiO{sub 3}/SrTiO{sub 3} SLs or compositionally uniform ferroelectrics such as tetragonal compositions of Pb(Zr,Ti)O{sub 3}. The unusual behavior of the BTO/CTO SL can be linked to the switching of a nanodomain state into a uniform polarization state or to a field-induced crystallographic symmetry transition. A comparison of the results with the characteristic timescales of these two dynamical phenomena in other complex oxides with different compositions suggests that the phase transition is a more likely possibility.

  11. CRYSTALLOGRAPHICALLY ANISOTROPIC SHAPE OF FORSTERITE: NEW PROBE FOR EVALUATING DUST FORMATION HISTORY FROM INFRARED SPECTROSCOPY

    SciTech Connect

    Takigawa, Aki; Tachibana, Shogo

    2012-05-10

    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 {mu}m. 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 {mu}m and 15-20 {mu}m. 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 ({approx}25%) of forsterite dust may have experienced high-temperature evaporation (>1600 K).

  12. Crystallographic control on the substructure of nacre tablets.

    PubMed

    Checa, Antonio G; Mutvei, Harry; Osuna-Mascaró, Antonio J; Bonarski, Jan T; Faryna, Marek; Berent, Katarzyna; Pina, Carlos M; Rousseau, Marthe; Macías-Sánchez, Elena

    2013-09-01

    Nacre tablets of mollusks develop two kinds of features when either the calcium carbonate or the organic portions are removed: (1) parallel lineations (vermiculations) formed by elongated carbonate rods, and (2) hourglass patterns, which appear in high relief when etched or in low relief if bleached. In untreated tablets, SEM and AFM data show that vermiculations correspond to aligned and fused aragonite nanogloblules, which are partly surrounded by thin organic pellicles. EBSD mapping of the surfaces of tablets indicates that the vermiculations are invariably parallel to the crystallographic a-axis of aragonite and that the triangles are aligned with the b-axis and correspond to the advance of the {010} faces during the growth of the tablet. According to our interpretation, the vermiculations appear because organic molecules during growth are expelled from the a-axis, where the Ca-CO3 bonds are the shortest. In this way, the subunits forming nacre merge uninterruptedly, forming chains parallel to the a-axis, whereas the organic molecules are expelled to the sides of these chains. Hourglass patterns would be produced by preferential adsorption of organic molecules along the {010}, as compared to the {100} faces. A model is presented for the nanostructure of nacre tablets. SEM and EBSD data also show the existence within the tablets of nanocrystalline units, which are twinned on {110} with the rest of the tablet. Our study shows that the growth dynamics of nacre tablets (and bioaragonite in general) results from the interaction at two different and mutually related levels: tablets and nanogranules. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Calculation of Crystallographic Texture of BCC Steels During Cold Rolling

    NASA Astrophysics Data System (ADS)

    Das, Arpan

    2017-05-01

    BCC alloys commonly tend to develop strong fibre textures and often represent as isointensity diagrams in φ 1 sections or by fibre diagrams. Alpha fibre in bcc steels is generally characterised by <110> crystallographic axis parallel to the rolling direction. The objective of present research is to correlate carbon content, carbide dispersion, rolling reduction, Euler angles (ϕ) (when φ 1 = 0° and φ 2 = 45° along alpha fibre) and the resulting alpha fibre texture orientation intensity. In the present research, Bayesian neural computation has been employed to correlate these and compare with the existing feed-forward neural network model comprehensively. Excellent match to the measured texture data within the bounding box of texture training data set has been already predicted through the feed-forward neural network model by other researchers. Feed-forward neural network prediction outside the bounds of training texture data showed deviations from the expected values. Currently, Bayesian computation has been similarly applied to confirm that the predictions are reasonable in the context of basic metallurgical principles, and matched better outside the bounds of training texture data set than the reported feed-forward neural network. Bayesian computation puts error bars on predicted values and allows significance of each individual parameters to be estimated. Additionally, it is also possible by Bayesian computation to estimate the isolated influence of particular variable such as carbon concentration, which exactly cannot in practice be varied independently. This shows the ability of the Bayesian neural network to examine the new phenomenon in situations where the data cannot be accessed through experiments.

  14. Variations in Reactivity on Different Crystallographic Orientations of Cerium Oxide

    SciTech Connect

    Mullins, David R; Albrecht, Peter M; Calaza, Florencia C

    2013-01-01

    Cerium oxide is a principal component in many heterogeneous catalytic processes. One of its key characteristics is the ability to provide or remove oxygen in chemical reactions. The different crystallographic faces of ceria present significantly different surface structures and compositions that may alter the catalytic reactivity. The structure and composition determine the number of coordination vacancies surrounding surface atoms, the availability of adsorption sites, the spacing between adsorption sites and the ability to remove O from the surface. To investigate the role of surface orientation on reactivity, CeO2 films were grown with two different orientations. CeO2(100) films were grown ex situ by pulsed laser deposition on Nb-doped SrTiO3(100). CeO2(111) films were grown in situ by thermal deposition of Ce metal onto Ru(0001) in an oxygen atmosphere. The chemical reactivity was characterized by the adsorption and decomposition of various molecules such as alcohols, aldehydes and organic acids. In general the CeO2(100) surface was found to be more active, i.e. molecules adsorbed more readily and reacted to form new products, especially on a fully oxidized substrate. However the CeO2(100) surface was less selective with a greater propensity to produce CO, CO2 and water as products. The differences in chemical reactivity are discussed in light of possible structural terminations of the two surfaces. Recently nanocubes and nano-octahedra have been synthesized that display CeO2(100) and CeO2(111) faces, respectively. These nanoparticles enable us to correlate reactions on high surface area model catalysts at atmospheric pressure with model single crystal films in a UHV environment.

  15. Shape and crystallographic orientation of nanodiamonds for quantum sensing.

    PubMed

    Ong, S Y; Chipaux, M; Nagl, A; Schirhagl, R

    2017-01-23

    Nanodiamonds with dimensions down to a few tens of nanometers containing nitrogen-vacancy (NV) color centers have revealed their potential as powerful and versatile quantum sensors with a unique combination of spatial resolution and sensitivity. The NV centers allow transducing physical properties, such as strain, temperature, and electric or magnetic field, to an optical transition that can be detected in the single photon range. For example, this makes it possible to sense a single electron spin or a few nuclear spins by detecting their magnetic resonance. The location and orientation of these defects with respect to the diamond surface play a crucial role in interpreting the data and predicting their sensitivities. Despite its relevance, the geometry of these nanodiamonds has never been thoroughly investigated. Without accurate data, spherical models have been applied to interpret or predict results in the past. With the use of High Resolution Transmission Electron Microscopy (HR-TEM), Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM), we investigated nanodiamonds with an average hydrodynamic diameter of 25 nm (the most common type for quantum sensing) and found a flake-like geometry, with 23.2 nm and 4.5 nm being the average lateral and vertical dimensions. We have also found evidence for a preferred crystallographic orientation of the main facet in the (110) direction. Furthermore, we discuss the consequences of this difference in geometry on diamond-based applications. Shape not only influences the creation efficiency of nitrogen-vacancy centers and their quantum coherence properties (and thus sensing performance), but also the optical properties of the nanodiamonds, their interaction with living cells, and their surface chemistry.

  16. Chemical and crystallographic events in the caries process.

    PubMed

    LeGeros, R Z

    1990-02-01

    The chemical and crystallographic events associated with the caries process can be described based on the results from the following studies: (a) effects of carbonate, magnesium, fluoride, and strontium on the physico-chemical properties--lattice parameters, crystallinity (crystal size and strain); dissolution properties of synthetic apatites; (b) factors influencing the in vitro formation and transformation of DCPD, OCP, AP (Ca-deficient apatites), FAP, beta-TCMP (Mg-substituted), and CaF2; and (c) studies on properties (crystallinity, composition, chemical, and thermal stabilities) of enamel, dentin, and bone. The dissolution of CO3-rich/Mg-rich/F-poor dental apatite crystals and re-precipitation of CO3-poor/Mg-poor/F-rich apatite in the presence of F- ions in solution contribute to a more acid-resistant surface layer of the caries lesion. Fluoride promotes the formation of less Ca-deficient and more stable apatite crystals. The presence of Ca, P, and F in solution inhibits dissolution of apatite more than does the presence of F alone. Low levels of F in solution promote the formation of (F, OH)-apatite, even under very acid conditions; an increase in F levels causes the formation of CaF2 at the expense of DCPD or apatite, especially in acid conditions. F in apatite and/or in solution suppresses extensive dissolution of dental apatite and enhances the formation of (F, OH)-apatite crystals which are more resistant against acid-dissolution than are F-free apatite crystals.

  17. The Influence of Domain Knowledge on Strategy Use during Simulation-Based Inquiry Learning

    ERIC Educational Resources Information Center

    Lazonder, Ard W.; Wilhelm, Pascal; Hagemans, Mieke G.

    2008-01-01

    This study investigated how students' knowledge of a particular domain influences the type of investigative strategy they utilize in an inquiry learning task within that domain. Students with high domain knowledge were assumed to employ a theory-driven strategy, whereas less knowledgeable students were expected to start off in a data-driven mode…

  18. The Skap-hom dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch.

    PubMed

    Swanson, Kenneth D; Tang, Yong; Ceccarelli, Derek F; Poy, Florence; Sliwa, Jan P; Neel, Benjamin G; Eck, Michael J

    2008-11-21

    PH domains, by binding to phosphoinositides, often serve as membrane-targeting modules. Using crystallographic, biochemical, and cell biological approaches, we have uncovered a mechanism that the integrin-signaling adaptor Skap-hom uses to mediate cytoskeletal interactions. Skap-hom is a homodimer containing an N-terminal four-helix bundle dimerization domain, against which its two PH domains pack in a conformation incompatible with phosphoinositide binding. The isolated PH domains bind PI[3,4,5]P(3), and mutations targeting the dimerization domain or the PH domain's PI[3,4,5]P(3)-binding pocket prevent Skap-hom localization to ruffles. Targeting is retained when the PH domain is deleted or by combined mutation of the PI[3,4,5]P(3)-binding pocket and the PH/dimerization domain interface. Thus, the dimerization and PH domain form a PI[3,4,5]P(3)-responsive molecular switch that controls Skap-hom function.

  19. Surface structure, crystallographic and ice-nucleating properties of cellulose

    NASA Astrophysics Data System (ADS)

    Hiranuma, Naruki; Möhler, Ottmar; Kiselev, Alexei; Saathoff, Harald; Weidler, Peter; Shutthanandan, Shuttha; Kulkarni, Gourihar; Jantsch, Evelyn; Koop, Thomas

    2015-04-01

    Increasing evidence of the high diversity and efficient freezing ability of biological ice-nucleating particles is driving a reevaluation of their impact upon climate. Despite their potential importance, little is known about their atmospheric abundance and ice nucleation efficiency, especially non-proteinaceous ones, in comparison to non-biological materials (e.g., mineral dust). Recently, microcrystalline cellulose (MCC; non-proteinaceous plant structural polymer) has been identified as a potential biological ice-nucleating particle. However, it is still uncertain if the ice-nucleating activity is specific to the MCC structure or generally relevant to all cellulose materials, such that the results of MCC can be representatively scaled up to the total cellulose content in the atmosphere to address its role in clouds and the climate system. Here we use the helium ion microscopy (HIM) imaging and the X-ray diffraction (XRD) technique to characterize the nanoscale surface structure and crystalline properties of the two different types of cellulose (MCC and fibrous cellulose extracted from natural wood pulp) as model proxies for atmospheric cellulose particles and to assess their potential accessibility for water molecules. To complement these structural characterizations, we also present the results of immersion freezing experiments using the cold stage-based droplet freezing BINARY (Bielefeld Ice Nucleation ARaY) technique. The HIM results suggest that both cellulose types have a complex porous morphology with capillary spaces between the nanoscale fibrils over the microfiber surface. These surface structures may make cellulose accessible to water. The XRD results suggest that the structural properties of both cellulose materials are in agreement (i.e., P21 space group; a=7.96 Å, b=8.35 Å, c=10.28 Å) and comparable to the crystallographic properties of general monoclinic cellulose (i.e., Cellulose Iβ). The results obtained from the BINARY measurements suggest

  20. Zircon Lu-Hf isotopes and granite geochemistry of the Murchison Domain of the Yilgarn Craton: Evidence for reworking of Eoarchean crust during Meso-Neoarchean plume-driven magmatism

    NASA Astrophysics Data System (ADS)

    Ivanic, Timothy J.; Van Kranendonk, Martin J.; Kirkland, Christopher L.; Wyche, Stephen; Wingate, Michael T. D.; Belousova, Elena A.

    2012-09-01

    New in situ Lu-Hf data on zircons from GSWA geochronology samples has provided a unique isotopic dataset with a high temporal resolution for the Murchison Domain of the Yilgarn Craton in Western Australia. These data identify extended periods of juvenile mantle input (positive ɛHf values) into the crust firstly at c. 2980 Ma and then from c. 2820 Ma to c. 2640 Ma with significant pulses of crustal recycling at c. 2750 Ma and c. 2620 Ma (highly negative ɛHf values). Geochemical data from well-characterised granitic suites of the Murchison Domain provide additional constraints on the crustal evolution of the area and indicate a prolonged period of crustal melting and remelting at progressively shallower depths from c. 2750 to c. 2600 Ma. At c. 2760-2753 Ma, widespread calc-alkaline, intermediate to silicic volcanic rocks of the Polelle Group were erupted, accompanied by intrusion of felsic to intermediate melts derived from a variety of crustal sources that likely formed by partial mixing with basaltic melts. The intrusive rocks include a wide geochemical array of rocks in the Cullculli and Eelya suites that were sourced over a wide range of crustal depths. At this time a major departure to negative ɛHf values (<-5) occurred, indicating sampling of c. 3.80 Ga model aged source rocks as well as continued juvenile input. Post-volcanic granitic rocks emplaced between c. 2710 and c. 2600 Ma show geochemical evidence for progressive fractionation through time and derivation from an evolving crustal source. We interpret the driving force for this protracted history of mantle and crustal melting to be two mantle plumes at 2.81 and 2.72 Ga. These data document the process of cratonization through progressive melt depletion of the lower crust, progressively fractionating and shallower melts, culminating with a final phase of crustal recycling (ɛHf < - 5) and the cessation of juvenile input at c. 2630-2600 Ma during intrusion of the Bald Rock Supersuite, resulting in

  1. Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.

    PubMed

    Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang

    2015-04-01

    Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

  2. Ontology-Driven Information Integration

    NASA Technical Reports Server (NTRS)

    Tissot, Florence; Menzel, Chris

    2005-01-01

    Ontology-driven information integration (ODII) is a method of computerized, automated sharing of information among specialists who have expertise in different domains and who are members of subdivisions of a large, complex enterprise (e.g., an engineering project, a government agency, or a business). In ODII, one uses rigorous mathematical techniques to develop computational models of engineering and/or business information and processes. These models are then used to develop software tools that support the reliable processing and exchange of information among the subdivisions of this enterprise or between this enterprise and other enterprises.

  3. Educational Accountability: A Qualitatively Driven Mixed-Methods Approach

    ERIC Educational Resources Information Center

    Hall, Jori N.; Ryan, Katherine E.

    2011-01-01

    This article discusses the importance of mixed-methods research, in particular the value of qualitatively driven mixed-methods research for quantitatively driven domains like educational accountability. The article demonstrates the merits of qualitative thinking by describing a mixed-methods study that focuses on a middle school's system of…

  4. Educational Accountability: A Qualitatively Driven Mixed-Methods Approach

    ERIC Educational Resources Information Center

    Hall, Jori N.; Ryan, Katherine E.

    2011-01-01

    This article discusses the importance of mixed-methods research, in particular the value of qualitatively driven mixed-methods research for quantitatively driven domains like educational accountability. The article demonstrates the merits of qualitative thinking by describing a mixed-methods study that focuses on a middle school's system of…

  5. Life sciences domain analysis model.

    PubMed

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H; Klemm, Juli D

    2012-01-01

    Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science.

  6. Crystallographic Preferred Orientation of Amphibole Experimentally Deformed in Simple Shear

    NASA Astrophysics Data System (ADS)

    Ko, B.; Jung, H.

    2013-12-01

    Seismic anisotropy of the intermediate to lower crust can be attributed to the crystallographic preferred orientation (CPO) of deformed amphibole because of its high anisotropy and abundance in the deep crust. However, the lack of in-depth studies on simple-shear experiments of amphibole has obstructed the view of the CPO of amphibole to explain the intricate flow patterns in the crust. Therefore, we conducted simple-shear deformation experiments of amphibolite at the pressure of 1 GPa and at the temperatures of 500 - 700°C. Starting material is a fine-grained natural amphibolite which consists of hornblende (70 %), anorthite (30 %), and minor ilmenite and titanite (~2 %). Sample was deformed to large shear strain with a strain rate of 10-5 to 10-4 s-1 by using a modified griggs apparatus installed at Seoul National University (SNU). Microstructure of the deformed amphibolite was observed by scanning electron microscope, and the CPO of hornblende was analyzed by electron backscatter diffraction (EBSD) technique with Channel 5 software. Deformed amphibolites showed strong grain-size reduction by fracturing with strain localization, suggesting that the dominant deformation mechanism was cataclastic flow accompanied by mechanical rotation of grains. We found three types of CPOs of hornblende: type-I, type-II, and type-III. All fabric types showed (100) plane aligning nearly parallel to the shear plane. Type-I fabric represented that [001] axes are aligned subparallel to the shear direction. Type-II fabric represented that (010) poles are aligned subparallel to the shear direction. Type-III fabric represented that (010) poles and [001] axes form a girdle nearly parallel to the shear plane. Type-I fabric was produced at low temperatures (500 - 550°C), but type-II and type-III fabrics were developed at higher temperatures (600 - 700°C) in a dry and wet condition, respectively. Seismic velocities and anisotropies corresponding to each CPO type were calculated. The P

  7. Magnetic anisotropy induced by crystallographic orientation and morphological alignment in directionally-solidified eutectic Mn-Sb alloy

    NASA Astrophysics Data System (ADS)

    Lou, Chang-Sheng; Liu, Tie; Dong, Meng; Wu, Chun; Shao, Jian-Guo; Wang, Qiang

    2017-02-01

    The influences of the crystallographic orientation and morphological alignment upon the magnetic anisotropic behavior of polycrystalline materials were investigated. Microstructures obtained in eutectic Mn-Sb alloys via directional solidification simultaneously displayed crystallographic orientation and morphological alignment. Both the crystallographic orientation and the morphological alignment were able to induce magnetic anisotropy in the alloys, wherein the influence of the crystallographic orientation and the morphological alignment upon the magnetic anisotropic behavior of the alloys strongly depended upon their directions and exhibited either mutual promotion or competition. These findings may provide useful guidance for the fabrication design of functional magnetic materials.

  8. Advanced Crystallographic Data Collection Protocols for Experimental Phasing.

    PubMed

    Finke, Aaron D; Panepucci, Ezequiel; Vonrhein, Clemens; Wang, Meitian; Bricogne, Gérard; Oliéric, Vincent

    2016-01-01

    Experimental phasing by single- or multi-wavelength anomalous dispersion (SAD or MAD) has become the most popular method of de novo macromolecular structure determination. Continuous advances at third-generation synchrotron sources have enabled the deployment of rapid data collection protocols that are capable of recording SAD or MAD data sets. However, procedural simplifications driven by the pursuit of high throughput have led to a loss of sophistication in data collection strategies, adversely affecting measurement accuracy from the viewpoint of anomalous phasing. In this chapter, we detail optimized strategies for collecting high-quality data for experimental phasing, with particular emphasis on minimizing errors from radiation damage as well as from the instrument. This chapter also emphasizes data processing for "on-the-fly" decision-making during data collection, a critical process when data quality depends directly on information gathered while at the synchrotron.

  9. CBS domains: structure, function, and pathology in human proteins.

    PubMed

    Ignoul, Sofie; Eggermont, Jan

    2005-12-01

    The cystathionine-beta-synthase (CBS) domain is an evolutionarily conserved protein domain that is present in the proteome of archaebacteria, prokaryotes, and eukaryotes. CBS domains usually come in tandem repeats and are found in cytosolic and membrane proteins performing different functions (metabolic enzymes, kinases, and channels). Crystallographic studies of bacterial CBS domains have shown that two CBS domains form an intramolecular dimeric structure (CBS pair). Several human hereditary diseases (homocystinuria, retinitis pigmentosa, hypertrophic cardiomyopathy, myotonia congenital, etc.) can be caused by mutations in CBS domains of, respectively, cystathionine-beta-synthase, inosine 5'-monophosphate dehydrogenase, AMP kinase, and chloride channels. Despite their clinical relevance, it remains to be established what the precise function of CBS domains is and how they affect the structural and/or functional properties of an enzyme, kinase, or channel. Depending on the protein in which they occur, CBS domains have been proposed to affect multimerization and sorting of proteins, channel gating, and ligand binding. However, recent experiments revealing that CBS domains can bind adenosine-containing ligands such ATP, AMP, or S-adenosylmethionine have led to the hypothesis that CBS domains function as sensors of intracellular metabolites.

  10. Lipid membrane domains in the brain.

    PubMed

    Aureli, Massimo; Grassi, Sara; Prioni, Simona; Sonnino, Sandro; Prinetti, Alessandro

    2015-08-01

    The brain is characterized by the presence of cell types with very different functional specialization, but with the common trait of a very high complexity of structures originated by their plasma membranes. Brain cells bear evident membrane polarization with the creation of different morphological and functional subcompartments, whose formation, stabilization and function require a very high level of lateral order within the membrane. In other words, the membrane specialization of brain cells implies the presence of distinct membrane domains. The brain is the organ with the highest enrichment in lipids like cholesterol, glycosphingolipids, and the most recently discovered brain membrane lipid, phosphatidylglucoside, whose collective behavior strongly favors segregation within the membrane leading to the formation of lipid-driven membrane domains. Lipid-driven membrane domains function as dynamic platforms for signal transduction, protein processing, and membrane turnover. Essential events involved in the development and in the maintenance of the functional integrity of the brain depend on the organization of lipid-driven membrane domains, and alterations in lipid homeostasis, leading to deranged lipid-driven membrane organization, are common in several major brain diseases. In this review, we summarize the forces behind the formation of lipid membrane domains and their biological roles in different brain cells. This article is part of a Special Issue entitled Brain Lipids.

  11. Crystallographic texture engineering through novel melt strategies via electron beam melting: Inconel 718

    SciTech Connect

    Dehoff, Ryan R.; Kirka, Michael M.; List, III, Frederick Alyious; Unocic, Kinga A.; Sames, William J.

    2014-01-01

    Preliminary research has demonstrated the ability to utilise novel scan strategies in the electron beam melting (EBM) process to establish control of crystallographic texture within Inconel 718 deposits. Conventional EBM scan strategies and process parameters yield coarse columnar grains aligned parallel to the build direction. Through varying process parameters such as beam power, beam velocity, beam focus and scan strategy, the behaviour of the electron beam can be manipulated from a line source to a point source. The net effect of these variations is that the resulting crystallographic texture is controlled in a manner to produce either epitaxial deposits or fully equiaxed deposits. Furthermore, this research demonstrates the ability to change the crystallographic texture on the macroscale indicating that EBM technology can be used to create complex geometric components with both site-specific microstructures and material properties.

  12. 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.

  13. Influence of Defects and Crystallographic Orientation on Mechanical Behavior of Nanocrystalline Aluminium

    NASA Astrophysics Data System (ADS)

    Cai, Jun; Deng, Qiong; An, Min-Rong; Song, Hai-Yang; Su, Meng-Jia

    2016-10-01

    Simulation of molecular dynamics using Embedded Atom Method (EAM) potentials is performed to investigate the mechanical properties of single crystal Al along various crystallographic orientations under tensile loading. The specimens are provided with one or two embedded circular voids to analyze the damage evolution by void growth and coalescence. The simulation result shows that the Young's modulus, yielding stress and ultimate stress decrease with the emergence of the voids. Besides, the simulations show that the single-crystal Al in different crystallographic orientations behaves differently in elongation deformations. The single-crystal Al with <100> crystallographic orientations has greater ductility than other orientated specimens. The incipient plastic deformation and the stress-strain curves are presented and discussed for further understanding of the mechanical properties of single-crystal Al. Supported by the National Science Foundation of China under Grant No. 11572259

  14. Crystallographic Features of The Martensitic Transformation in PbTiO3 Compound

    NASA Astrophysics Data System (ADS)

    Navruz, N.

    2010-01-01

    Martensitic transformations are displacive in nature and occur in the solid state in a wide variety of metallic and non metallic materials. Although the occurrence of martensitic transformations in inorganic and ceramic compounds has been well recognized for many years, it is only in the last decade that they have achieved prominence. An important group of materials in which martensitic transformations play a significant role in determining microstructure and thus properties are the perovskite-type oxides such as PbTiO3. In this study, emphasis is given to the crystallography of the paraelectric cubic to ferroelectric tetragonal phase transformation in PbTiO3 compound. A detailed crystallographic analysis is performed in Lead Titanate (PbTiO3) and the crystallographic parameters are calculated. The predictions of the crystallographic analysis are compared with the experimental results available.

  15. Crystallographic texture engineering through novel melt strategies via electron beam melting: Inconel 718

    DOE PAGES

    Dehoff, Ryan R.; Kirka, Michael M.; List, III, Frederick Alyious; ...

    2014-01-01

    Preliminary research has demonstrated the ability to utilise novel scan strategies in the electron beam melting (EBM) process to establish control of crystallographic texture within Inconel 718 deposits. Conventional EBM scan strategies and process parameters yield coarse columnar grains aligned parallel to the build direction. Through varying process parameters such as beam power, beam velocity, beam focus and scan strategy, the behaviour of the electron beam can be manipulated from a line source to a point source. The net effect of these variations is that the resulting crystallographic texture is controlled in a manner to produce either epitaxial deposits ormore » fully equiaxed deposits. Furthermore, this research demonstrates the ability to change the crystallographic texture on the macroscale indicating that EBM technology can be used to create complex geometric components with both site-specific microstructures and material properties.« less

  16. Advanced yield strength of interconnector ribbon for photovoltaic module using crystallographic texture control

    NASA Astrophysics Data System (ADS)

    Kang, Byungjun; Park, Nochang; Tark, Sung Ju; Oh, Won Wook; Park, Sungeun; Kim, Young Do; Lee, Hae-Seok; Kim, Donghwan

    2014-03-01

    This paper reports a study on reducing the yield strength of Cu ribbon wire used for Si solar cell interconnections in solar panels. Low yield strength Cu core should be used as the interconnector ribbon to minimize the fracture of Si solar cells during the tabbing process. We lowered the yield strength of Cu ribbon by controlling the crystallographic texture without increasing the annealing time and temperature. The crystallographic texture was controlled by lubrication in a cold rolling process. The crystallographic texture was observed by scanning electron microscopy with electron back scattered diffraction. A tensile test was performed for the comparison of the mechanical properties of Cu with and without lubrication. The average yield strength was 91.2 MPa with lubrication whereas the yield strength was 99.6 MPa without lubrication. The lower value of the lubricated samples seemed to be caused by the higher cube texture intensity than that of the samples without lubrication.

  17. Crystallographic Texture Evolution of a Zinc Sheet Subjected to Different Strain Paths

    NASA Astrophysics Data System (ADS)

    Schlosser, Fernando; Schwindt, Claudio; Fuster, Valeria; Tommasi, Andrea; Signorelli, Javier Walter

    2017-06-01

    The use of zinc sheets has largely increased in the last years, fundamentally because of new tendencies in architecture and, at the same time, due to its excellent properties, as corrosion resistance under aggressive climatic conditions, malleability, recyclability, and surface finishing aspect. In the present work, the X-ray diffraction technique is used to characterize the crystallographic texture evolution of a strongly anisotropic Zn20 zinc sheet (Zn-Cu-Ti) subjected to uniaxial tension, plane strain, and equibiaxial tension, for specimens cut at 0, 45, and 90 deg with respect to the rolling direction. The crystallographic texture evolution is evaluated by means of pole figures, orientation distribution function, and Kearns factors. For all tested strain paths, deformation produces a decrease in the intensity of the crystallographic textures, due to a dispersion of the orientations of the different axes around the initial maxima.

  18. Experimental and Theoretical Investigation of Crystallographic Orientation Dependence of Nanoscratching of Single Crystalline Copper

    PubMed Central

    Geng, Yanquan; Zhang, Junjie; Yan, Yongda; Yu, Bowen; Geng, Lin; Sun, Tao

    2015-01-01

    In the present work, we perform experiments and molecular dynamics simulations to elucidate the underlying deformation mechanisms of single crystalline copper under the load-controlled multi-passes nanoscratching using a triangular pyramidal probe. The correlation of microscopic deformation behavior of the material with macroscopically-observed machining results is revealed. Moreover, the influence of crystallographic orientation on the nanoscratching of single crystalline copper is examined. Our simulation results indicate that the plastic deformation of single crystalline Cu under the nanoscratching is exclusively governed by dislocation mechanisms. However, there is no glissile dislocation structure formed due to the probe oscillation under the load-controlled mode. Both experiments and MD simulations demonstrate that the machined surface morphologies in terms of groove depth and surface pile-up exhibit strong crystallographic orientation dependence, because of different geometries of activated slip planes cutting with free surfaces and strain hardening abilities associated with different crystallographic orientations. PMID:26147506

  19. Determination of crystallographic orientation of lead-free piezoelectric (K,Na)NbO{sub 3} epitaxial thin films grown on SrTiO{sub 3} (100) surfaces

    SciTech Connect

    Yu, Qi; Zhu, Fang-Yuan; Cheng, Li-Qian; Wang, Ke; Li, Jing-Feng

    2014-03-10

    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.

  20. Indirect control of antiferromagnetic domain walls with spin current.

    PubMed

    Wieser, R; Vedmedenko, E Y; Wiesendanger, R

    2011-02-11

    The indirect controlled displacement of an antiferromagnetic domain wall by a spin current is studied by Landau-Lifshitz-Gilbert spin dynamics. The antiferromagnetic domain wall can be shifted both by a spin-polarized tunnel current of a scanning tunneling microscope or by a current driven ferromagnetic domain wall in an exchange coupled antiferromagnetic-ferromagnetic layer system. The indirect control of antiferromagnetic domain walls opens up a new and promising direction for future spin device applications based on antiferromagnetic materials.

  1. Automatic domain decomposition of proteins by a Gaussian Network Model.

    PubMed

    Kundu, Sibsankar; Sorensen, Dan C; Phillips, George N

    2004-12-01

    Proteins are often comprised of domains of apparently independent folding units. These domains can be defined in various ways, but one useful definition divides the protein into substructures that seem to move more or less independently. The same methods that allow fairly accurate calculation of motion can be used to help classify these substructures. We show how the Gaussian Network Model (GNM), commonly used for determining motion, can also be adapted to automatically classify domains in proteins. Parallels between this physical network model and graph theory implementation are apparent. The method is applied to a nonredundant set of 55 proteins, and the results are compared to the visual assignments by crystallographers. Apart from decomposing proteins into structural domains, the algorithm can generally be applied to any large macromolecular system to decompose it into motionally decoupled sub-systems. Copyright 2004 Wiley-Liss, Inc.

  2. The effect of silicon crystallographic orientation on the formation of silicon nanoclusters during anodic electrochemical etching

    SciTech Connect

    Timokhov, D. F. Timokhov, F. P.

    2009-01-15

    Possible ways for increasing the photoluminescence quantum yield of porous silicon layers have been investigated. The effect of the anodization parameters on the photoluminescence properties for porous silicon layers formed on silicon substrates with different crystallographic orientations was studied. The average diameters for silicon nanoclusters are calculated from the photoluminescence spectra of porous silicon. The influence of the substrate crystallographic orientation on the photoluminescence quantum yield of porous silicon is revealed. A model explaining the effect of the substrate orientation on the photoluminescence properties for the porous silicon layers formed by anode electrochemical etching is proposed.

  3. The Ultrasonic Measurement of Crystallographic Orientation for Imaging Anisotropic Components with 2d Arrays

    NASA Astrophysics Data System (ADS)

    Lane, C. J. L.; Dunhill, A. K.; Drinkwater, B. W.; Wilcox, P. D.

    2011-06-01

    Single crystal components are used widely in the gas-turbine industry. However, these components are elastically anisotropic which causes difficulties when performing NDE inspections with ultrasound. Recently an ultrasonic algorithm for a 2D array has been corrected to perform the reliable volumetric inspection of single crystals. For the algorithm to be implemented the crystallographic orientation of the components must be known. This paper, therefore, develops and reviews crystallographic orientation methods using 2D ultrasonic arrays. The methods under examination are based on the anisotropic propagation of surface and bulk waves and an image-based orientation method is also considered.

  4. Crystallographic point groups of five-dimensional space. 1. Their elements and their subgroups.

    PubMed

    Veysseyre, R; Veysseyre, H

    2002-09-01

    The purpose of this work is to introduce a method with a view to obtaining the crystallographic point groups of five-dimensional space, i.e. the subgroups of the holohedries of these space crystal families. This paper is specifically devoted to numerical analysis, whereas the following ones deal with some applications to crystallography. These results have been obtained through a collaboration between two teams: H. Veysseyre (Institut Supérieur des Matériaux) for the numerical analysis, R. Veysseyre, D. Weigel and Th. Phan (Ecole Centrale Paris) for the crystallographic part.

  5. Hematite and Goethite (U-Th)/He/Ne ages interpretation using crystallographic data and diffusion parameters

    NASA Astrophysics Data System (ADS)

    Gautheron, Cécile; Balout, Hilal; Roques, Jérôme; Allard, Thierry; Morin, Guillaume; Tassan-Got, Laurent

    2016-04-01

    At the Earth's surface, hematite and goethite are common minerals occurring in soils and sediments, including ores. The understanding of the corresponding alteration and weathering processes relies on our ability to perform the dating of formation of these minerals. Two relevant and recent dating methods have been developed, which are related to (U-Th)/He and (U-Th)/Ne geochronometers. They are based on accumulation of 4He and 21Ne associated with the alpha decay of U and Th. Both methods are of particular interest because of possible He and Ne retention over geological ages at surface temperature. However, because of different atomic radius between He and Ne, retention behavior of these two species can be quite different. Moreover, the dating procedure is particularly challenging because of the small crystals size and frequent polycrystalline structure of hematite and goethite. As a matter of fact, some uncertainty exists about He and Ne diffusion parameters, due to the nanometric to micrometric crystal size of natural iron oxide mineral. Accordingly, the determination of (U-Th)/He and (U-Th)/Ne ages requires the understanding of He and Ne production and retention (which may be partial) in iron oxide crystals. In this study, we theoretically investigate and discuss for the first time the age evolution for pure goethite and hematite crystals with different thermal histories, including reheating to simulate burial. The aim is to quantify the He and/or Ne loss by ejection and diffusion for crystals of different morphology and polycrystalline structures. This will allow one to provide some correction factor for the age. For this purpose, we used new He and Ne diffusion coefficients obtained by multi-scale theoretical approach using Density Functional Theory (DFT) (Balout et al., submitted, a,b), associated with 3D production and diffusion code (Gautheron and Tassan-Got, 2010). The impact of Multi Diffusion Domains simulating polycrystalline structure has been

  6. Crystallographic preferred orientation and deformation of deep Earth minerals

    NASA Astrophysics Data System (ADS)

    Kaercher, Pamela Michelle

    This thesis aims to provide further insight into crystallographic preferred orientation (CPO) and deformation mechanisms active at high pressure. Preferred orientation of iron-rich magnesiowustite (Mg,Fe)O, a major mantle mineral phase, stishovite (SiO2), the high pressure polymorph of quartz that is likely present in the lower crust and mantle, and in NaMgF3 + NaCl, an analog system to lower mantle minerals MgSiO3 + MgO, have been examined with synchrotron X-ray diffraction while at high pressure in either a diamond anvil cell or a multianvil press. Magnesiowustite, (Mg0.08Fe0.88)O, and wustite, Fe0.94O, were compressed up to 37 GPa at ambient temperature in diamond anvil cells (DAC) at the Advanced Light Source (ALS). X-ray diffraction patterns were taken in situ in radial geometry in order to study the evolution of CPO through the cubic-to-rhombohedral phase transition. Under uniaxial stress in the DAC, cubic texture developed (i.e. {100} c planes aligned perpendicular to the compression direction). Variant selection of preferred orientation was observed immediately following the transition to the rhombohedral phase. Upon decompression in the DAC, FeO reverted back to cubic symmetry and the cubic texture reappeared, demonstrating that the transition is reversible and has texture memory. The crystal structure of the high pressure SiO2 polymorph stishovite has been studied in detail, but little is known about texture development during deformation, which provides information for understanding subduction of quartz-bearing crustal rocks into the mantle. Radial DAC experiments were done at the ALS and the Advanced Photon Source (APS) while collecting X-ray diffraction patterns in radial geometry to examine in situ development of CPO. Starting pressure in the sample chamber was still in the quartz stability field, and compression of quartz produced a weak texture, likely due to Dauphine twinning. Following compression of quartz into the stishovite stability field

  7. Implications for Collagen Binding from the Crystallographic Structure of Fibronectin 6FnI1–2FnII7FnI

    PubMed Central

    Erat, Michèle C.; Schwarz-Linek, Ulrich; Pickford, Andrew R.; Farndale, Richard W.; Campbell, Iain D.; Vakonakis, Ioannis

    2010-01-01

    Collagen and fibronectin (FN) are two abundant and essential components of the vertebrate extracellular matrix; they interact directly with cellular receptors and affect cell adhesion and migration. Past studies identified a FN fragment comprising six modules, 6FnI1–2FnII7–9FnI, and termed the gelatin binding domain (GBD) as responsible for collagen interaction. Recently, we showed that the GBD binds tightly to a specific site within type I collagen and determined the structure of domains 8–9FnI in complex with a peptide from that site. Here, we present the crystallographic structure of domains 6FnI1–2FnII7FnI, which form a compact, globular unit through interdomain interactions. Analysis of NMR titrations with single-stranded collagen peptides reveals a dominant collagen interaction surface on domains 2FnII and 7FnI; a similar surface appears involved in interactions with triple-helical peptides. Models of the complete GBD, based on the new structure and the 8–9FnI·collagen complex show a continuous putative collagen binding surface. We explore the implications of this model using long collagen peptides and discuss our findings in the context of FN interactions with collagen fibrils. PMID:20739283

  8. Crystallographic structure and substrate-binding interactions of the molybdate-binding protein of the phytopathogen Xanthomonas axonopodis pv. citri.

    PubMed

    Balan, Andrea; Santacruz-Pérez, Carolina; Moutran, Alexandre; Ferreira, Luís Carlos Souza; Neshich, Goran; Gonçalves Barbosa, João Alexandre Ribeiro

    2008-02-01

    In Xanthomonas axonopodis pv. citri (Xac or X. citri), the modA gene codes for a periplasmic protein (ModA) that is capable of binding molybdate and tungstate as part of the ABC-type transporter required for the uptake of micronutrients. In this study, we report the crystallographic structure of the Xac ModA protein with bound molybdate. The Xac ModA structure is similar to orthologs with known three-dimensional structures and consists of two nearly symmetrical domains separated by a hinge region where the oxyanion-binding site lies. Phylogenetic analysis of different ModA orthologs based on sequence alignments revealed three groups of molybdate-binding proteins: bacterial phytopathogens, enterobacteria and soil bacteria. Even though the ModA orthologs are segregated into different groups, the ligand-binding hydrogen bonds are mostly conserved, except for Archaeglobus fulgidus ModA. A detailed discussion of hydrophobic interactions in the active site is presented and two new residues, Ala38 and Ser151, are shown to be part of the ligand-binding pocket.

  9. Purification, crystallization and preliminary crystallographic analysis of the catalytic core of cystathionine β-synthase from Saccharomyces cerevisiae

    PubMed Central

    Ereño-Orbea, June; Majtan, Tomas; Oyenarte, Iker; Kraus, Jan P.; Martínez-Cruz, Luis Alfonso

    2014-01-01

    Cystathionine β-synthase (CBS; EC 4.2.1.22) catalyzes the condensation of homocysteine and serine to form cystathionine, with the release of water. In humans, deficiency in CBS activity is the most common cause of hyperhomocysteinaemia and homocystinuria. More than 160 pathogenic mutations in the human CBS gene have been described to date. Here, the purification and preliminary crystallographic analysis of the catalytic core of CBS from Saccharomyces cerevisiae (ScCBS) is described which, in contrast to other eukaryotic CBSs, lacks the N-terminal haem-binding domain and is considered to be a useful model for investigation of the pyridoxal-5′-phosphate-mediated reactions of human CBS (hCBS). The purified protein yielded two different crystal forms belonging to space groups P41212 and P212121, with unit-cell parameters a = b = 72.390, c = 386.794 Å and a = 58.156, b = 89.988, c = 121.687 Å, respectively. Diffraction data were collected to 2.7 and 3.1 Å resolution, respectively, using synchrotron radiation. Preliminary analysis of the X-ray data suggests the presence of ScCBS homodimers in both types of crystals. PMID:24598918

  10. Domain relaxation in Langmuir films

    NASA Astrophysics Data System (ADS)

    Alexander, James C.; Bernoff, Andrew J.; Mann, Elizabeth K.; Mann, J. Adin; Wintersmith, Jacob R.; Zou, Lu

    We report on theoretical studies of molecularly thin Langmuir films on the surface of a quiescent subfluid and qualitatively compare the results to both new and previous experiments. The film covers the entire fluid surface, but domains of different phases are observed. In the absence of external forcing, the compact domains tend to relax to circles, driven by a line tension at the phase boundaries. When stretched (by a transient applied stagnation-point flow or by stirring), a compact domain elongates, creating a bola consisting of two roughly circular reservoirs connected by a thin tether. This shape will then relax slowly to the minimum-energy configuration of a circular domain. The tether is never observed to rupture, even when it is more than a hundred times as long as it is wide. We model these experiments by taking previous descriptions of the full hydrodynamics, identifying the dominant effects via dimensional analysis, and reducing the system to a more tractable form. The result is a free boundary problem for an inviscid Langmuir film whose motion is driven by the line tension of the domain and damped by the viscosity of the subfluid. Using this model we derive relaxation rates for perturbations of a uniform strip and a circular patch. We also derive a boundary integral formulation which allows an efficient numerical solution of the problem. Numerically this model replicates the formation of a bola and the subsequent relaxation observed in the experiments. Finally, we suggest physical properties of the system (such as line tension) that can be deduced by comparison of the theory and numerical simulations to the experiment. Two movies are available with the online version of the paper.

  11. Control of crystallographic orientation in diamond synthesis through laser resonant vibrational excitation of precursor molecules

    PubMed Central

    Xie, Zhi Qiang; Bai, Jaeil; Zhou, Yun Shen; Gao, Yi; Park, Jongbok; Guillemet, Thomas; Jiang, Lan; Zeng, Xiao Cheng; Lu, Yong Feng

    2014-01-01

    Crystallographic orientations determine the optical, electrical, mechanical, and thermal properties of crystals. Control of crystallographic orientations has been studied by changing the growth parameters, including temperature, pressure, proportion of precursors, and surface conditions. However, molecular dynamic mechanisms underlying these controls remain largely unknown. Here we achieved control of crystallographic orientations in diamond growth through a joint experimental and theoretical study of laser resonant vibrational excitation of precursor molecules (ethylene). Resonant vibrational excitation of the ethylene molecules using a wavelength-tunable CO2 laser steers the chemical reactions and promotes proportion of intermediate oxide species, which results in preferential growth of {100}-oriented diamond films and diamond single crystals in open air. Quantum molecular dynamic simulations and calculations of chemisorption energies of radicals detected from our mass-spectroscopy experiment provide an in-depth understanding of molecular reaction mechanisms in the steering of chemical reactions and control of crystallographic orientations. This finding opens up a new avenue for controlled chemical vapor deposition of crystals through resonant vibrational excitations to steer surface chemistry. PMID:24694918

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

    SciTech Connect

    McLean, Larry R.; Zhang, Ying; Degnen, William; Peppard, Jane; Cabel, Dasha; Zou, Chao; Tsay, Joseph T.; Subramaniam, Arun; Vaz, Roy J.; Li, Yi

    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.

  13. Crystallographic structural organization of human rhinovirus serotype 16, 14, 3, 2 and 1A

    NASA Astrophysics Data System (ADS)

    Janner, A.

    2006-07-01

    The capsid of the icosahedral virion is encapsulated between two polyhedra scaled according to the golden mean, each being composed of an icosahedron and a dodecahedron. Structural units of the coat proteins are enclosed into forms whose projections along the icosahedral symmetry axes obey the crystallographic law of rational indices.

  14. 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

  15. Crystallization and preliminary X-ray crystallographic studies of human cyclophilin J

    SciTech Connect

    Hu, Hao; Huang, Chao-Qun; Liu, He-Li; Han, Yi; Yu, Long; Bi, Ru-Chang

    2005-02-01

    Human cyclophilin J is a member of the cyclophilin family and recent studies have indicated that it plays a role in the formation of liver cancers as a regulation factor or messenger. The preparation, crystallization and preliminary X-ray crystallographic studies of human cyclophilin J are reported.

  16. Contribution to crystallographic slip assessment by means of topographic measurements achieved with atomic force microscopy

    SciTech Connect

    Kahloun, C.; Badji, R.; Bacroix, B.; Bouabdallah, M.

    2010-09-15

    In this paper, atomic force microscopy (AFM) is used to quantitatively characterize the plastic glide occurring during tensile deformation of a duplex 2205 stainless steel sample. We demonstrate that an appropriate treatment of the topographic image issued from AFM measurements allows precise and quantitative information about the characteristics of plastic deformation and especially the amount of crystallographic slip.

  17. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error

    PubMed Central

    Read, Randy J.; McCoy, Airlie J.

    2016-01-01

    The crystallographic diffraction experiment measures Bragg intensities; crystallo­graphic electron-density maps and other crystallographic calculations in phasing require structure-factor amplitudes. If data were measured with no errors, the structure-factor amplitudes would be trivially proportional to the square roots of the intensities. When the experimental errors are large, and especially when random errors yield negative net intensities, the conversion of intensities and their error estimates into amplitudes and associated error estimates becomes nontrivial. Although this problem has been addressed intermittently in the history of crystallographic phasing, current approaches to accounting for experimental errors in macromolecular crystallography have numerous significant defects. These have been addressed with the formulation of LLGI, a log-likelihood-gain function in terms of the Bragg intensities and their associated experimental error estimates. LLGI has the correct asymptotic behaviour for data with large experimental error, appropriately downweighting these reflections without introducing bias. LLGI abrogates the need for the conversion of intensity data to amplitudes, which is usually performed with the French and Wilson method [French & Wilson (1978 ▸), Acta Cryst. A35, 517–525], wherever likelihood target functions are required. It has general applicability for a wide variety of algorithms in macromolecular crystallography, including scaling, characterizing anisotropy and translational noncrystallographic symmetry, detecting outliers, experimental phasing, molecular replacement and refinement. Because it is impossible to reliably recover the original intensity data from amplitudes, it is suggested that crystallographers should always deposit the intensity data in the Protein Data Bank. PMID:26960124

  18. Crystallization and preliminary X-ray crystallographic analysis of the catalytic domain of membrane type 1 matrix metalloproteinase

    PubMed Central

    Ogata, Hideaki; Decaneto, Elena; Grossman, Moran; Havenith, Martina; Sagi, Irit; Lubitz, Wolfgang; Knipp, Markus

    2014-01-01

    Membrane type 1 matrix metalloproteinase (MT1-MMP) belongs to the large family of zinc-dependent endopeptidases termed MMPs that are located in the extracellular matrix. MT1-MMP was crystallized at 277 K using the vapour-diffusion method with PEG as a precipitating agent. Data sets for MT1-MMP were collected to 2.24 Å resolution at 100 K. The crystals belonged to space group P43212, with unit-cell parameters a = 62.99, c = 122.60 Å. The crystal contained one molecule per asymmetric unit, with a Matthews coefficient (V M) of 2.90 Å3 Da−1; the solvent content is estimated to be 57.6%. PMID:24637763

  19. Crystallographic study of FABP5 as an intracellular endocannabinoid transporter

    SciTech Connect

    Sanson, Benoît; Wang, Tao; Sun, Jing; Wang, Liqun; Kaczocha, Martin; Ojima, Iwao; Deutsch, Dale; Li, Huilin

    2014-02-01

    FABP5 was recently found to intracellularly transport endocannabinoid signaling lipids. The structures of FABP5 complexed with two endocannabinoids and an inhibitor were solved. Human FABP5 was found to dimerize via a domain-swapping mechanism. This work will help in the development of inhibitors to raise endocannabinoid levels. In addition to binding intracellular fatty acids, fatty-acid-binding proteins (FABPs) have recently been reported to also transport the endocannabinoids anandamide (AEA) and 2-arachidonoylglycerol (2-AG), arachidonic acid derivatives that function as neurotransmitters and mediate a diverse set of physiological and psychological processes. To understand how the endocannabinoids bind to FABPs, the crystal structures of FABP5 in complex with AEA, 2-AG and the inhibitor BMS-309403 were determined. These ligands are shown to interact primarily with the substrate-binding pocket via hydrophobic interactions as well as a common hydrogen bond to the Tyr131 residue. This work advances our understanding of FABP5–endocannabinoid interactions and may be useful for future efforts in the development of small-molecule inhibitors to raise endocannabinoid levels.

  20. Analysis of the different slip systems activated by tension in a {alpha}/{beta} titanium alloy in relation with local crystallographic orientation

    SciTech Connect

    Bridier, F.; Villechaise, P. . E-mail: p.villechaise@lmpm.ensma.fr; Mendez, J.

    2005-02-01

    The gliding modes of a duplex Ti-6Al-4V titanium alloy were investigated through in situ (scanning electron microscopy) tensile tests. A method based on electron back-scattering diffraction (EBSD) measurements was used to identify activated slip systems. The approach applied to a large number of grains allowed a statistical analysis of the nature (basal, prismatic, pyramidal) and distribution of the slip systems according to the crystallographic texture. A discussion concerning the pertinence of Schmid's law to explain the occurrence and succession of slip events is then proposed. The domain in favor of each type of slip system is finally presented by using inverse pole figures mapped with Schmid's factor iso-curves.

  1. Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.

    PubMed

    Dong, Danghong; Ihara, Tokuo; Motoshima, Hiroyuki; Watanabe, Keiichi

    2005-03-01

    The psychrophilic alkaline serine protease Apa1 secreted by the Antarctic psychrotroph Pseudoalteromonas sp. strain AS-11 consists of a subtilisin-like region (293 residues) and an additional insert region (148 residues) that does not show a sequence homology to any proteins in the RCSB Protein Data Bank. Apa1 inhibited with phenylmethanesulfonyl fluoride has been crystallized and X-ray diffraction data have been collected to 1.78 A resolution. The crystals belong to space group C2, with unit-cell parameters a = 122.94, b = 138.48, c = 64.77 A, alpha = gamma = 90, beta = 97.5 degrees. A molecular-replacement solution has been found using the structure of the mesophilic counterpart subtilisin DY with 38% sequence identity to the catalytic domain of Apa1 as a search model. This is the first crystallographic study of a cold-adapted subtilisin-like protease.

  2. Automotion of domain walls for spintronic interconnects

    SciTech Connect

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-07

    We simulate “automotion,” the transport of a magnetic domain wall under the influence of demagnetization and magnetic anisotropy, in nanoscale spintronic interconnects. In contrast to spin transfer driven magnetic domain wall motion, the proposed interconnects operate without longitudinal charge current transfer, with only a transient current pulse at domain wall creation and have favorable scaling down to the 20 nm dimension. Cases of both in-plane and out-of-plane magnetization are considered. Analytical dependence of the velocity of domain walls on the angle of magnetization are compared with full micromagnetic simulations. Deceleration, attenuation and disappearance, and reflection of domain walls are demonstrated through simulation. Dependences of the magnetization angle on the current pulse parameters are studied. The energy and delay analysis suggests that automotion is an attractive option for spintronic logic interconnects.

  3. Crystal structures of wild-type Trichoderma reesei Cel7A catalytic domain in open and closed states.

    PubMed

    Bodenheimer, Annette M; Meilleur, Flora

    2016-12-01

    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.

  4. Domain wall order and motion in Mn3O4

    NASA Astrophysics Data System (ADS)

    Thaler, Alexander; Zakjevskii, Alexander; Nguyen, Brian; Gim, Yewon; Aczel, Adam; Debeer-Schmitt, Lisa; Cooper, S. Lance; MacDougall, Gregory

    Mn3O4 is an orbitally ordered, magnetically frustrated spinel with strong spin-lattice coupling, which exhibits a series of low temperature magnetic and structural transitions. Transverse field μSR has shown that ordered and disordered volumes coexist within this material, while MFM measurements have further shown that the magnetic domain walls themselves order in specific crystallographic directions, with a typical length scale of 100's of nm. In order to directly study these phenomena, we have performed small angle neutron scattering (SANS) measurements at both zero and applied magnetic field. We will present the results of these measurements and discuss what they show as far as the formation of domains, as well as the motion of the domain walls. We will also discuss the effects of internal disorder on the behavior of the material. This work was sponsored by the National Science Foundation, under Grant Number DMR-1455264.

  5. Life sciences domain analysis model

    PubMed Central

    Freimuth, Robert R; Freund, Elaine T; Schick, Lisa; Sharma, Mukesh K; Stafford, Grace A; Suzek, Baris E; Hernandez, Joyce; Hipp, Jason; Kelley, Jenny M; Rokicki, Konrad; Pan, Sue; Buckler, Andrew; Stokes, Todd H; Fernandez, Anna; Fore, Ian; Buetow, Kenneth H

    2012-01-01

    Objective Meaningful exchange of information is a fundamental challenge in collaborative biomedical research. To help address this, the authors developed the Life Sciences Domain Analysis Model (LS DAM), an information model that provides a framework for communication among domain experts and technical teams developing information systems to support biomedical research. The LS DAM is harmonized with the Biomedical Research Integrated Domain Group (BRIDG) model of protocol-driven clinical research. Together, these models can facilitate data exchange for translational research. Materials and methods The content of the LS DAM was driven by analysis of life sciences and translational research scenarios and the concepts in the model are derived from existing information models, reference models and data exchange formats. The model is represented in the Unified Modeling Language and uses ISO 21090 data types. Results The LS DAM v2.2.1 is comprised of 130 classes and covers several core areas including Experiment, Molecular Biology, Molecular Databases and Specimen. Nearly half of these classes originate from the BRIDG model, emphasizing the semantic harmonization between these models. Validation of the LS DAM against independently derived information models, research scenarios and reference databases supports its general applicability to represent life sciences research. Discussion The LS DAM provides unambiguous definitions for concepts required to describe life sciences research. The processes established to achieve consensus among domain experts will be applied in future iterations and may be broadly applicable to other standardization efforts. Conclusions The LS DAM provides common semantics for life sciences research. Through harmonization with BRIDG, it promotes interoperability in translational science. PMID:22744959

  6. Crystallographic Texture and Orientation Variants in Al2O3-Y3Al5O12 Directionally Solidified Eutectic Crystals

    NASA Technical Reports Server (NTRS)

    Frazer, Colleen S.; Dickey, Elizabeth C.; Sayir, Ali; Farmer, Serene (Technical Monitor)

    2001-01-01

    Eutectic rods of Al2O3 and Y3Al5O12 were grown by a laser-heated float zone method, and their microstructure and crystallographic texture were studied by scanning electron microscopy, electron backscattered diffraction and x-ray diffraction. The composites were found to be highly textured with two twin-related crystallographic orientation relationships between the phases. Electron backscattered diffraction was employed to determine the spatial distribution of the orientational variants within the samples and to define the crystallographic orientation of various microstructural features.

  7. 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.

  8. Crystallographic dependence of CO activation on cobalt catalysts: HCP versus FCC.

    PubMed

    Liu, Jin-Xun; Su, Hai-Yan; Sun, Da-Peng; Zhang, Bing-Yan; Li, Wei-Xue

    2013-11-06

    Identifying the structure sensitivity of catalysts in reactions, such as Fischer-Tropsch synthesis from CO and H2 over cobalt catalysts, is an important yet challenging issue in heterogeneous catalysis. Based on a first-principles kinetic study, we find for the first time that CO activation on hexagonal close-packed (HCP) Co not only has much higher intrinsic activity than that of face centered-cubic (FCC) Co but also prefers a different reaction route, i.e., direct dissociation with HCP Co but H-assisted dissociation on the FCC Co. The origin is identified from the formation of various denser yet favorable active sites on HCP Co not available for FCC Co, due to their distinct crystallographic structure and morphology. The great dependence of the activity on the crystallographic structure and morphology of the catalysts revealed here may open a new avenue for better, stable catalysts with maximum mass-specific reactivity.

  9. Growth and crystallographic feature-dependent characterization of spinel zinc ferrite thin films by RF sputtering.

    PubMed

    Liang, Yuan-Chang; Hsia, Hao-Yuan

    2013-12-19

    ZnFe2O4 (ZFO) thin films exhibiting varying crystallographic features ((222)-epitaxially, (400)-epitaxially, and randomly oriented films) were grown on various substrates by radio-frequency magnetron sputtering. The type of substrate used profoundly affected the surface topography of the resulting ZFO films. The surface of the ZFO (222) epilayer was dense and exhibited small rectangular surface grains; however, the ZFO (400) epilayer exhibited small grooves. The surface of the randomly oriented ZFO thin film exhibited distinct three-dimensional island-like grains that demonstrated considerable surface roughness. Magnetization-temperature curves revealed that the ZFO thin films exhibited a spin-glass transition temperature of approximately 40 K. The crystallographic orientation of the ZFO thin films strongly affected magnetic anisotropy. The ZFO (222) epitaxy exhibited the strongest magnetic anisotropy, whereas the randomly oriented ZFO thin film exhibited no clear magnetic anisotropy.

  10. 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.

  11. Application of electron backscatter diffraction for crystallographic characterization of tin whiskers.

    PubMed

    Michael, Joseph R; McKenzie, Bonnie B; Susan, Donald F

    2012-08-01

    Understanding the growth of whiskers or high aspect ratio features on substrates can be aided when the crystallography of the feature is known. This study has evaluated three methods that utilize electron backscatter diffraction (EBSD) for the determination of the crystallographic growth direction of an individual whisker. EBSD has traditionally been a technique applied to planar, polished samples, and thus the use of EBSD for out-of-surface features is somewhat more difficult and requires additional steps. One of the methods requires the whiskers to be removed from the substrate resulting in the loss of valuable physical growth relationships between the whisker and the substrate. The other two techniques do not suffer this disadvantage and provide the physical growth information as well as the crystallographic growth directions. The final choice of method depends on the information required. The accuracy and the advantages and disadvantages of each method are discussed.

  12. 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.

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

    SciTech Connect

    Quesada, Odayme; Gurda, Brittney; Govindasamy, Lakshmanan; McKenna, Robert; Kohlbrenner, Erik; Aslanidi, George; Zolotukhin, Sergei; Muzyczka, Nicholas; Agbandje-McKenna, Mavis

    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 a 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.

  14. 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

  15. Novel Kac-Moody-type affine extensions of non-crystallographic Coxeter groups

    NASA Astrophysics Data System (ADS)

    Dechant, Pierre-Philippe; Bœhm, Céline; Twarock, Reidun

    2012-07-01

    Motivated by recent results in mathematical virology, we present novel asymmetric {Z}[\\tau ]-integer-valued affine extensions of the non-crystallographic Coxeter groups H2, H3 and H4 derived in a Kac-Moody-type formalism. In particular, we show that the affine reflection planes which extend the Coxeter group H3 generate (twist) translations along two-, three- and five-fold axes of icosahedral symmetry, and we classify these translations in terms of the Fibonacci recursion relation applied to different start values. We thus provide an explanation of previous results concerning affine extensions of icosahedral symmetry in a Coxeter group context, and extend this analysis to the case of the non-crystallographic Coxeter groups H2 and H4. These results will enable new applications of group theory in physics (quasicrystals), biology (viruses) and chemistry (fullerenes).

  16. Crystallographic anisotropy of the resistivity size effect in single crystal tungsten nanowires.

    PubMed

    Choi, Dooho; Moneck, Matthew; Liu, Xuan; Oh, Soong Ju; Kagan, Cherie R; Coffey, Kevin R; Barmak, Katayun

    2013-01-01

    This work demonstrates an anisotropic increase in resistivity with decreasing width in single crystal tungsten (W) nanowires having a height of 21 nm. Nanowire-widths were in the range of 15-451 nm, with the anisotropy observed for widths below 50 nm. The longitudinal directions of the nanowires coincided with the <100>, <110> and <111> orientations of the body centered cubic phase of W. The resistivity increase was observed to be minimized for the <111>-oriented single crystal nanowires, exhibiting a factor of two lower increase in resistivity at a width of ~15 nm, relative to the thin film resistivity (i.e., an infinitely wide wire). The observed anisotropy is attributed to crystallographic anisotropy of the Fermi velocity and the resultant anisotropy of the electron mean free path in W, and underscores the critical role of crystallographic orientation in nanoscale metallic conduction.

  17. INTRINSIC FINE-SCALE STRUCTURE IN COMPLEX MATERIALS: BEYOND GLOBAL CRYSTALLOGRAPHIC ANALYSIS

    SciTech Connect

    A. MIGLIORI; ET AL

    2000-12-01

    Many important classes of materials owe their interesting properties to structures and patterns produced by local atomic deviations from ideal crystallographic positions. The pattern scale may vary from a few atomic spacings to many microns. In a macroscopic sample these deviations may still average to an ideal lattice while retaining the intrinsic fine-scale structures, or a phase transition may create a pattern of variants of a new crystallographic structure. We have carried out experiments on the formation of fine-scale structures in a range of materials, particularly those produced by phase transitions. We have used Resonant Ultrasound Spectroscopy for elastic properties and dissipation, neutron pair-distribution function, and electronic transport measurements to characterize samples. We have carried out extensive dynamical modeling based on Ginzberg-Landau formalisms to simulate the development and appearance of the structures. Our results highlight the importance of long-range strain fields and the intrinsic unstable equilibrium features of the materials studied.

  18. 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.

  19. Model-building strategies for low-resolution X-ray crystallographic data.

    PubMed

    Karmali, Anjum M; Blundell, Tom L; Furnham, Nicholas

    2009-02-01

    The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 A is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  20. Crystallographic anisotropy of the resistivity size effect in single crystal tungsten nanowires

    PubMed Central

    Choi, Dooho; Moneck, Matthew; Liu, Xuan; Oh, Soong Ju; Kagan, Cherie R.; Coffey, Kevin R.; Barmak, Katayun

    2013-01-01

    This work demonstrates an anisotropic increase in resistivity with decreasing width in single crystal tungsten (W) nanowires having a height of 21 nm. Nanowire-widths were in the range of 15–451 nm, with the anisotropy observed for widths below 50 nm. The longitudinal directions of the nanowires coincided with the <100>, <110> and <111> orientations of the body centered cubic phase of W. The resistivity increase was observed to be minimized for the <111>-oriented single crystal nanowires, exhibiting a factor of two lower increase in resistivity at a width of ~15 nm, relative to the thin film resistivity (i.e., an infinitely wide wire). The observed anisotropy is attributed to crystallographic anisotropy of the Fermi velocity and the resultant anisotropy of the electron mean free path in W, and underscores the critical role of crystallographic orientation in nanoscale metallic conduction. PMID:24005230

  1. 3D mapping of crystallographic phase distribution using energy-selective neutron tomography.

    PubMed

    Woracek, Robin; Penumadu, Dayakar; Kardjilov, Nikolay; Hilger, Andre; Boin, Mirko; Banhart, John; Manke, Ingo

    2014-06-25

    Nondestructive 3D mapping of crystallographic phases is introduced providing distribution of phase fractions within the bulk (centimeter range) of samples with micrometer-scale resolution. The novel neutron tomography based technique overcomes critical limitations of existing techniques and offers a wide range of potential applications. It is demonstrated for steel samples exhibiting phase transformation after being subjected to tensile and torsional deformation. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    SciTech Connect

    Ahmed, M.M.Z.; Wynne, B.P.; Rainforth, W.M.; Threadgill, P.L.

    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. 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.

  3. Crystallization and preliminary crystallographic analysis of acetophenone reductase from Geotrichum candidum NBRC 4597

    PubMed Central

    Sugiyama, Yosuke; Senda, Miki; Senda, Toshiya; Matsuda, Tomoko

    2015-01-01

    Acetophenone reductase (APRD) from Geotrichum candidium NBRC 4597 was crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as a precipitant. The crystal belonged to space group P6522, with unit-cell parameters a = b = 104.5, c = 273.7 Å, and diffracted to 2.6 Å resolution. Phasing using the single-wavelength anomalous diffraction method was successful. Model building and crystallographic refinement are in progress. PMID:25760708

  4. Keep it together: restraints in crystallographic refinement of macromolecule–ligand complexes

    PubMed Central

    Steiner, Roberto A.; Tucker, Julie A.

    2017-01-01

    A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future. PMID:28177305

  5. Keep it together: restraints in crystallographic refinement of macromolecule-ligand complexes.

    PubMed

    Steiner, Roberto A; Tucker, Julie A

    2017-02-01

    A short introduction is provided to the concept of restraints in macromolecular crystallographic refinement. A typical ligand restraint-generation process is then described, covering types of input, the methodology and the mechanics behind the software in general terms, how this has evolved over recent years and what to look for in the output. Finally, the currently available restraint-generation software is compared, concluding with some thoughts for the future.

  6. 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

  7. Definition of the domain boundaries is critical to the expression of the nucleotide-binding domains of P-glycoprotein.

    PubMed

    Kerr, Ian D; Berridge, Georgina; Linton, Kenneth J; Higgins, Christopher F; Callaghan, Richard

    2003-11-01

    Heterologous expression of domains of eukaryotic proteins is frequently associated with formation of inclusion bodies, consisting of aggregated mis-folded protein. This phenomenon has proved a significant barrier to the characterization of domains of eukaryotic ATP binding cassette (ABC) transporters. We hypothesized that the solubility of heterologously expressed nucleotide binding domains (NBDs) of ABC transporters is dependent on the definition of the domain boundaries. In this paper we have defined a core NBD, and tested the effect of extensions to and deletions of this core domain on protein expression. Of 10 NBDs constructed, only one was expressed as a soluble protein in Escherichia coli, with expression of the remaining NBDs being associated with inclusion body formation. The soluble NBD protein we have obtained corresponds to residues 386-632 of P-glycoprotein and represents an optimally defined domain. The NBD has been isolated and purified to 95% homogeneity by a two-step purification protocol, involving affinity chromatography and gel filtration. Although showing no detectable ATP hydrolysis, the protein retains specific ATP binding and has a secondary structure compatible with X-ray crystallographic data on bacterial NBDs. We have interpreted our results in terms of homology models, which suggest that the N-terminal NBD of P-glycoprotein can be produced as a stable, correctly folded, isolate domain with judicious design of the expression construct.

  8. Crystallization and preliminary crystallographic analysis of San Miguel sea lion virus: an animal calicivirus.

    PubMed

    Chen, Rong; Neill, John D; Prasad, B V Venkataram

    2003-02-01

    The Caliciviridae is a family of nonenveloped, icosahedral, positive-sense single-stranded RNA viruses. This family of viruses consists of both animal and human pathogens. Adapting human caliciviruses to cell culture has not been successful, whereas some animal caliciviruses, including San Miguel sea lion virus, have been successfully propagated in vitro. Here we report the crystallization of San Miguel sea lion virus serotype 4 (SMSV4) and the preliminary X-ray crystallographic analysis of the crystals. SMSV4 have been crystallized using the hanging-drop method. These crystals diffracted to approximately 3A resolution using a synchrotron radiation source. A single crystal under cryo-conditions yielded a complete set of diffraction data. Data processing of the diffraction patterns showed that SMSV crystals belong to I23 space group with cell dimensions a=b=c=457 A. The crystallographic asymmetric unit includes five icosahedral asymmetric units, each consisting of three capsid protein subunits. In the space group I23, given the icosahedral symmetry and the size of the virus particle, the location of the particle is constrained to be at the point where the crystallographic 2- and 3-fold axes intersect. The orientation of the virus particle in the unit cell was ascertained by self-rotation function calculations.

  9. High-resolution neutron crystallographic studies of the hydration of the coenzyme cob(II)alamin

    SciTech Connect

    Jogl, Gerwald; Wang, Xiaoping; Mason, Sax A.; Kovalevsky, Andrey; Mustyakimov, Marat; Fisher, Zöe; Hoffman, Christina; Kratky, Christoph; Langan, Paul

    2011-06-01

    High-resolution crystallographic studies of the hydration of the coenzyme cob(II)alamin have provided hydrogen-bond parameters of unprecedented accuracy for a biomacromolecule. The hydration of the coenzyme cob(II)alamin has been studied using high-resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of 0.92 Å on the original D19 diffractometer with a prototype 4° × 64° detector at the high-flux reactor neutron source run by the Institute Laue–Langevin. The resulting structure provides hydrogen-bonding parameters for the hydration of biomacromolecules to unprecedented accuracy. These experimental parameters will be used to define more accurate force fields for biomacromolecular structure refinement. The presence of a hydrophobic bowl motif surrounded by flexible side chains with terminal functional groups may be significant for the efficient scavenging of ligands. The feasibility of extending the resolution of this structure to ultrahigh resolution was investigated by collecting time-of-flight neutron crystallographic data during commissioning of the TOPAZ diffractometer with a prototype array of 14 modular 2° × 21° detectors at the Spallation Neutron Source run by Oak Ridge National Laboratory.

  10. IChemPIC: A Random Forest Classifier of Biological and Crystallographic Protein-Protein Interfaces.

    PubMed

    Da Silva, Franck; Desaphy, Jérémy; Bret, Guillaume; Rognan, Didier

    2015-09-28

    Protein-protein interactions are becoming a major focus of academic and pharmaceutical research to identify low molecular weight compounds able to modulate oligomeric signaling complexes. As the number of protein complexes of known three-dimensional structure is constantly increasing, there is a need to discard biologically irrelevant interfaces and prioritize those of high value for potential druggability assessment. A Random Forest model has been trained on a set of 300 protein-protein interfaces using 45 molecular interaction descriptors as input. It is able to predict the nature of external test interfaces (crystallographic vs biological) with accuracy at least equal to that of the best state-of-the-art methods. However, our method presents unique advantages in the early prioritization of potentially ligandable protein-protein interfaces: (i) it is equally robust in predicting either crystallographic or biological contacts and (ii) it can be applied to a wide array of oligomeric complexes ranging from small-sized biological interfaces to large crystallographic contacts.

  11. Model-building strategies for low-resolution X-ray crystallographic data

    SciTech Connect

    Karmali, Anjum M.; Blundell, Tom L.; Furnham, Nicholas

    2009-02-01

    Interpretation of low-resolution X-ray crystallographic data can prove to be a difficult task. The challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The interpretation of low-resolution X-ray crystallographic data proves to be challenging even for the most experienced crystallographer. Ambiguity in the electron-density map makes main-chain tracing and side-chain assignment difficult. However, the number of structures solved at resolutions poorer than 3.5 Å is growing rapidly and the structures are often of high biological interest and importance. Here, the challenges faced in electron-density interpretation, the strategies that have been employed to overcome them and developments to automate the process are reviewed. The methods employed in model generation from electron microscopy, which share many of the same challenges in providing high-confidence models of macromolecular structures and assemblies, are also considered.

  12. Critical role of charged residues in helix 7 of the ligand binding domain in Hepatocyte Nuclear Factor 4α dimerisation and transcriptional activity

    PubMed Central

    Eeckhoute, Jérôme; Oxombre, Bénédicte; Formstecher, Pierre; Lefebvre, Philippe; Laine, Bernard

    2003-01-01

    Hepatocyte Nuclear Factor 4α (HNF4α, NR2A1) is central to hepatocyte and pancreatic β-cell functions. Along with retinoid X receptor α (RXRα), HNF4α belongs to the nuclear receptor subfamily 2 (NR2), characterised by a conserved arginyl residue and a glutamate residue insert in helix 7 (H7) of the ligand binding domain (LBD). Crystallographic studies indicate that R348 and E352 residues in RXRα H7 are involved in charge-driven interactions that improve dimerisation. Consistent with these findings, we showed that removing the charge of the corresponding residues in HNF4α H7, R258 and E262, impaired dimerisation in solution. Moreover, our results provide a new concept according to which helices of the HNF4α LBD dimerisation interface contribute differently to dimerisation required for DNA binding; unlike H9 and H10, H7 is not involved in DNA binding. Substitutions of E262 decreased the repression of HNF4α transcriptional activity by a dominant-negative HNF4α mutant, highlighting the importance of this residue for dimerisation in the cell context. The E262 insert is crucial for HNF4α function since its deletion abolished HNF4α transcriptional activity and coactivator recruitment. The glutamate residue insert and the conserved arginyl residue in H7 most probably represent a signature of the NR2 subfamily of nuclear receptors. PMID:14602925

  13. Critical role of charged residues in helix 7 of the ligand binding domain in Hepatocyte Nuclear Factor 4alpha dimerisation and transcriptional activity.

    PubMed

    Eeckhoute, Jérôme; Oxombre, Bénédicte; Formstecher, Pierre; Lefebvre, Philippe; Laine, Bernard

    2003-11-15

    Hepatocyte Nuclear Factor 4alpha (HNF4alpha, NR2A1) is central to hepatocyte and pancreatic beta-cell functions. Along with retinoid X receptor alpha (RXRalpha), HNF4alpha belongs to the nuclear receptor subfamily 2 (NR2), characterised by a conserved arginyl residue and a glutamate residue insert in helix 7 (H7) of the ligand binding domain (LBD). Crystallographic studies indicate that R348 and E352 residues in RXRalpha H7 are involved in charge-driven interactions that improve dimerisation. Consistent with these findings, we showed that removing the charge of the corresponding residues in HNF4alpha H7, R258 and E262, impaired dimerisation in solution. Moreover, our results provide a new concept according to which helices of the HNF4alpha LBD dimerisation interface contribute differently to dimerisation required for DNA binding; unlike H9 and H10, H7 is not involved in DNA binding. Substitutions of E262 decreased the repression of HNF4alpha transcriptional activity by a dominant-negative HNF4alpha mutant, highlighting the importance of this residue for dimerisation in the cell context. The E262 insert is crucial for HNF4alpha function since its deletion abolished HNF4alpha transcriptional activity and coactivator recruitment. The glutamate residue insert and the conserved arginyl residue in H7 most probably represent a signature of the NR2 subfamily of nuclear receptors.

  14. Laser-Driven Fusion.

    ERIC Educational Resources Information Center

    Gibson, A. F.

    1980-01-01

    Discusses the present status and future prospects of laser-driven fusion. Current research (which is classified under three main headings: laser-matter interaction processes, compression, and laser development) is also presented. (HM)

  15. Laser-Driven Fusion.

    ERIC Educational Resources Information Center

    Gibson, A. F.

    1980-01-01

    Discusses the present status and future prospects of laser-driven fusion. Current research (which is classified under three main headings: laser-matter interaction processes, compression, and laser development) is also presented. (HM)

  16. De novo design of synthetic prion domains.

    PubMed

    Toombs, James A; Petri, Michelina; Paul, Kacy R; Kan, Grace Y; Ben-Hur, Asa; Ross, Eric D

    2012-04-24

    Prions are important disease agents and epigenetic regulatory elements. Prion formation involves the structural conversion of proteins from a soluble form into an insoluble amyloid form. In many cases, this structural conversion is driven by a glutamine/asparagine (Q/N)-rich prion-forming domain. However, our understanding of the sequence requirements for prion formation and propagation by Q/N-rich domains has been insufficient for accurate prion propensity prediction or prion domain design. By focusing exclusively on amino acid composition, we have developed a prion aggregation prediction algorithm (PAPA), specifically designed to predict prion propensity of Q/N-rich proteins. Here, we show not only that this algorithm is far more effective than traditional amyloid prediction algorithms at predicting prion propensity of Q/N-rich proteins, but remarkably, also that PAPA is capable of rationally designing protein domains that function as prions in vivo.

  17. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the variable lymphocyte receptor 2913 ectodomain fused with internalin B

    PubMed Central

    Lee, Ji Yeon; Kim, Hyoun Sook; Baek, In Wha; Back, Jang Mi; Han, Mi Ra; Kong, Sun-Young; Kim, Ji Hyeon; Kirchdoerfer, Robert N.; Kim, Jae-Ouk; Cooper, Max D.; Wilson, Ian A.; Kim, Hyun-Jung; Han, Byung Woo

    2013-01-01

    In jawless vertebrates, variable lymphocyte receptors (VLRs) play a crucial role in the recognition of antigens as part of the adaptive immune system. Leucine-rich repeat (LRR) modules and the highly variable insert (HVI) of VLRs contribute to the specificity and diversity of antigen recognition. VLR2913, the antigen of which is not known, contains the same HVI amino-acid sequence as that of VLR RBC36, which recognizes the H-trisaccharide from human blood type O erythrocytes. Since the HVI sequence is rarely identical among all known VLRs, identification of the antigen for VLR2913 and the main contributing factors for antigen recognition based on a comparison of VLR2913 and VLR RBC36 has been attempted. To initiate and facilitate this structural approach, the ectodomain of VLR2913 was fused with the N-terminal domain of internalin B (InlB-VLR2913-ECD). Three amino-acid residues on the concave surface of the LRR modules of InlB-VLR2913-ECD were mutated, considering important residues for hydrogen bonds in the recognition of H-trisaccharide by VLR RBC36. InlB-VLR2913-ECD was overexpressed in Escherichia coli and was crystallized at 295 K using the sitting-drop vapour-diffusion method. X-ray diffraction data were collected to 2.04 Å resolution and could be indexed in the tetragonal space group P41212 (or P43212), with unit-cell parameters a = 91.12, b = 91.12, c = 62.87 Å. Assuming that one monomer molecule was present in the crystallographic asymmetric unit, the calculated Matthews coefficient (V M) was 2.75 Å3 Da−1 and the solvent content was 55.2%. Structural determination of InlB-VLR2913-ECD by molecular replacement is in progress. PMID:23295483

  18. Understanding the Public Domain.

    ERIC Educational Resources Information Center

    Russell, Carrie

    2003-01-01

    This overview of the public domain covers: defining the public domain; figuring out if a work is protected by copyright; being sure a work is in the public domain; asserting the copyright protection and term; the Creative Commons initiative; building the Information Commons; when permission is needed for using a public domain work; and special…

  19. Domain Relaxation in Langmuir Films

    NASA Astrophysics Data System (ADS)

    Bernoff, Andrew J.; Alexander, James C.; Mann, Elizabeth K.; Mann, J. Adin; Zou, Lu; Wintersmith, Jacob R.

    2007-11-01

    We report on an experimental, theoretical and computational study of a molecularly thin polymer Langmuir layer domain on the surface of a subfluid. When stretched (by a transient stagnation flow), the Langmuir layer takes the form of a bola consisting of two roughly circular reservoirs connected by a thin tether. This shape relaxes to the circular minimum energy configuration. The tether is never observed to rupture, even when it is more than a hundred times as long as it is thin. We model these experiments as a free boundary problem where motion is driven by the line tension of the domain and damped by the viscosity of the subfluid. We process the digital images of the experiment to extract the domain shape, use one of these shapes as an initial condition for the numerical solution of a boundary-integral model of the underlying hydrodynamics, and compare the subsequent images of the experiment to the numerical simulation. The numerical evolutions verify that our hydrodynamical model can reproduce the observed dynamics. They also allow us to deduce the magnitude of the line tension in the system, often to within 1%.

  20. Group-theoretical description of domain and phase boundaries in crystalline solids

    NASA Astrophysics Data System (ADS)

    Zieliński, Piotr

    1990-06-01

    The theory is reviewed of domains and domain boundaries arising in phase transitions accompanied by symmetry breaking. Conclusions concerning the number, the crystallographic type and the spatial orientation of coherent interfaces between crystals of the same structure (domain boundaries) and between different structures of the same material (interphase boundaries) are presented in terms of the space group theory and of the Landau theory of phase transitions. The application of the two-dimensional space groups and the diperiodic groups in three dimensions to the discussed objects is described. The conditions for the coexistence of domains and phases without macroscopic stress are given. An example of the group-theoretical analysis of domain structure is given for a real material: NaO 2.

  1. Novel domain wall dynamics in synthetic antiferromagnets

    NASA Astrophysics Data System (ADS)

    Yang, See-Hun; Parkin, Stuart

    2017-08-01

    In this article, we review fascinating new mechanisms on recently observed remarkable current driven domain wall motion in nanowires formed from perpendicularly magnetized synthetic antiferromagnets interfaced with heavy metallic layers, sources of spin-orbit torques. All the associated torques such as volumetric adiabatic and non-adiabatic spin-transfer-torque, spin-orbit torques, shape anisotropy field torques, Dzyaloshinkii-Moriya interaction torques and most importantly a new powerful torque, exchange coupling torque, will be discussed based on an analytical model that provides an intuitive description of domain wall dynamics in synthetic ferromagnets as well as synthetic antiferromagnets. In addition, the current driven DW motion in the presence of in-plane fields will be investigated, thus deepening our knowledge about the role of the exchange coupling torque, which will be of potential use for application to various novel spintronic devices.

  2. PARP-1 activation requires local unfolding of an autoinhibitory domain

    PubMed Central

    Dawicki-McKenna, Jennine M.; Langelier, Marie-France; DeNizio, Jamie E.; Riccio, Amanda A.; Cao, Connie D.; Karch, Kelly R.; McCauley, Michael; Steffen, Jamin D.; Black, Ben E.; Pascal, John M.

    2015-01-01

    SUMMARY Poly(ADP-ribose) polymerase-1 (PARP-1) creates the posttranslational modification PAR from substrate NAD+ to regulate multiple cellular processes. DNA breaks sharply elevate PARP-1 catalytic activity to mount a cell survival repair response, whereas persistent PARP-1 hyperactivation during severe genotoxic stress is associated with cell death. The mechanism for tight control of the robust catalytic potential of PARP-1 remains unclear. By monitoring PARP-1 dynamics using hydrogen/deuterium exchange-mass spectrometry (HXMS), we unexpectedly find that a specific portion of the helical subdomain (HD) of the catalytic domain rapidly unfolds when PARP-1 encounters a DNA break. Together with biochemical and crystallographic analysis of HD deletion mutants, we show that the HD is an autoinhibitory domain that blocks productive NAD+ binding. Our molecular model explains how PARP-1 DNA damage detection leads to local unfolding of the HD that relieves autoinhibition, and has important implications for the design of PARP inhibitors. PMID:26626480

  3. Magnetic domains and surface effects in hollow maghemite nanoparticles

    SciTech Connect

    Cabot, Andreu; Alivisatos, A. Paul; Puntes, Victor; Balcells, Lluis; Iglesias, Oscar; Labarta, Amilcar

    2008-09-30

    In the present work, we investigate the magnetic properties of ferrimagnetic and non-interacting maghemite hollow nanoparticles obtained by the Kirkendall effect. From the experimental characterization of their magnetic behavior, we find that polycrystalline hollow maghemite nanoparticles exhibit low blocked-to-superparamagnetic transition temperatures, small magnetic moments, significant coercivities and irreversibility fields, and no magnetic saturation on external magnetic fields up to 5 T. These results are interpreted in terms of the microstructural parameters characterizing the maghemite shells by means of atomistic Monte Carlo simulations of an individual spherical shell. The model comprises strongly interacting crystallographic domains arranged in a spherical shell with random orientations and anisotropy axis. The Monte Carlo simulation allows discernment between the influence of the polycrystalline structure and its hollow geometry, while revealing the magnetic domain arranggement in the different temperataure regimes.

  4. The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling

    PubMed Central

    Naschberger, Andreas; Fürnrohr, Barbara G.; Lenac Rovis, Tihana; Malic, Suzana; Scheffzek, Klaus; Dieplinger, Hans; Rupp, Bernhard

    2016-01-01

    The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1–6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested. PMID:27917827

  5. The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservative versus enthusiastic modelling.

    PubMed

    Naschberger, Andreas; Fürnrohr, Barbara G; Lenac Rovis, Tihana; Malic, Suzana; Scheffzek, Klaus; Dieplinger, Hans; Rupp, Bernhard

    2016-12-01

    The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1-6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable VL and VH domains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.

  6. The formation of a covalent complex between a dipeptide ligand and the src SH2 domain.

    PubMed

    Alligood, K J; Charifson, P S; Crosby, R; Consler, T G; Feldman, P L; Gampe, R T; Gilmer, T M; Jordan, S R; Milstead, M W; Mohr, C; Peel, M R; Rocque, W; Rodriguez, M; Rusnak, D W; Shewchuk, L M; Sternbach, D D

    1998-05-19

    The X-ray crystal structure of the src SH2 domain revealed the presence of a thiol residue (Cys 188) located proximal to the phosphotyrosine portion of a dipeptide ligand. An aldehyde bearing ligand (1) was designed to position an electrophilic carbonyl group in the vicinity of the thiol. X-ray crystallographic and NMR examination of the complex formed between (1) and the src SH2 domain revealed a hemithioacetal formed by addition of the thiol to the aldehyde group with an additional stabilizing hydrogen bond between the acetal hydroxyl and a backbone carbonyl.

  7. Structural Basis for Ubiquitin Recognition by the Human ESCRT-II EAP45 GLUE Domain

    SciTech Connect

    Alam,S.; Langelier, C.; Whitby, F.; Koirala, S.; Robinson, H.; Hill, C.; Sundquist, W.

    2006-01-01

    ESCRT-IESCRT-IIGLUEEAP45VPS36The ESCRT-I and ESCRT-II complexes help sort ubiquitinated proteins into vesicles that accumulate within multivesicular bodies (MVBs). Crystallographic and biochemical analyses reveal that the GLUE domain of the human ESCRT-II EAP45 (also called VPS36) subunit is a split pleckstrin-homology domain that binds ubiquitin along one edge of the {beta}-sandwich. The structure suggests how human ESCRT-II can couple recognition of ubiquitinated cargoes and endosomal phospholipids during MVB protein sorting.

  8. Domain-Independent Heuristics for Goal Formulation

    DTIC Science & Technology

    2013-05-01

    While this increases autonomy, it employs a domain- dependent reward function; indirectly, LGDA’s goal selection strategy is guided by a human. MADBot...autonomy for responding to unexpected events in strategy simulations. To appear in Computational Intelligence. Molineaux, M., Klenk, M., & Aha, D.W...2010a). Goal-driven autonomy in a Navy strategy simulation. In Proceedings of the Twenty-Fourth AAAI Conference on Artificial Intelligence. Atlanta

  9. Indexing Flower Patent Images using Domain Knowledge

    DTIC Science & Technology

    1998-01-01

    approach is illustrated by using it to provide a solution to the problem of indexing images of flowers for searching a flower patents database by color...The flower region is isolated from the background by using an automatic iterative segmentation algorithm with domain knowledge driven feedback. The...color of the flower is defined by the color names present in the flower region and their relative proportions. The database can be queried by example

  10. Domains in multiband superconductors

    NASA Astrophysics Data System (ADS)

    Tanaka, Y.; Yanagisawa, T.; Crisan, A.; Shirage, P. M.; Iyo, A.; Tokiwa, K.; Nishio, T.; Sundaresan, A.; Terada, N.

    2011-11-01

    Multiband superconductors can have several types of domains that are inhibited in conventional single-band superconductors. These domains are phase domains and chiral domains and their domain wall are an interband phase difference soliton. In a superconductor with an odd number of electronic bands (five or more) and with positive interband Josephson interactions, we find other types of domains with different interband phase differences. We call these domains configuration domains because pseudo-order parameters for each band are dispersed in the complex plain and several configurations, which have several local minima. Fractional vortices serve as hubs for phase difference solitons (configuration domain walls). The divergence of the number of configurations with local minima would pose a serious problem for the stability of superconductivity.

  11. Chiral spin torque at magnetic domain walls.

    PubMed

    Ryu, Kwang-Su; Thomas, Luc; Yang, See-Hun; Parkin, Stuart

    2013-07-01

    Spin-polarized currents provide a powerful means of manipulating the magnetization of nanodevices, and give rise to spin transfer torques that can drive magnetic domain walls along nanowires. In ultrathin magnetic wires, domain walls are found to move in the opposite direction to that expected from bulk spin transfer torques, and also at much higher speeds. Here we show that this is due to two intertwined phenomena, both derived from spin-orbit interactions. By measuring the influence of magnetic fields on current-driven domain-wall motion in perpendicularly magnetized Co/Ni/Co trilayers, we find an internal effective magnetic field acting on each domain wall, the direction of which alternates between successive domain walls. This chiral effective field arises from a Dzyaloshinskii-Moriya interaction at the Co/Pt interfaces and, in concert with spin Hall currents, drives the domain walls in lock-step along the nanowire. Elucidating the mechanism for the manipulation of domain walls in ultrathin magnetic films will enable the development of new families of spintronic devices.

  12. Application of combined EBSD and 3D-SEM technique on crystallographic facet analysis of steel at low temperature.

    PubMed

    Mohseni, P; Solberg, J K; Karlsen, M; Akselsen, O M; Ostby, E

    2013-07-01

    Electron backscatter diffraction has been increasingly used to identify the crystallographic planes and orientation of cleavage facets with respect to the rolling direction in fracture surfaces. The crystallographic indices of cleavage planes can be determined either directly from the fracture surface or indirectly from metallographic sections perpendicular to the plane of the fracture surface. A combination of electron backscatter diffraction and 3D scanning electron microscopy imaging technique has been modified to determine crystallographic facet orientations. The main purpose of this work has been to identify the macroscopic crystallographic orientations of cleavage facets in the fracture surfaces of weld heat affected zones in a well-known steel fractured at low temperatures. The material used for the work was an American Petroleum Institute (API) X80 grade steel developed for applications at low temperatures, and typical heat affected zone microstructures were obtained by carrying out weld thermal simulation. The fracture toughness was measured at different temperatures (0°C, -30°C, -60°C and -90°C) by using Crack Tip Opening Displacement testing. Fracture surfaces and changes in microstructure were analyzed by scanning electron microscopy and light microscopy. Crystallographic orientations were identified by electron backscatter diffraction, indirectly from a polished section perpendicular to the major fracture surface of the samples. Computer assisted 3D imaging was used to measure the angles between the cleavage facets and the adjacent polished surface, and then these angles were combined with electron backscatter diffraction measurements to determine the macroscopic crystallographic planes of the facets. The crystallographic indices of the macroscopic cleavage facet planes were identified to be {100}, {110}, {211} and {310} at all temperatures. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

  13. Structural model of the cytosolic domain of the plant ethylene receptor 1 (ETR1).

    PubMed

    Mayerhofer, Hubert; Panneerselvam, Saravanan; Kaljunen, Heidi; Tuukkanen, Anne; Mertens, Haydyn D T; Mueller-Dieckmann, Jochen

    2015-01-30

    Ethylene initiates important aspects of plant growth and development through disulfide-linked receptor dimers located in the endoplasmic reticulum. The receptors feature a small transmembrane, ethylene binding domain followed by a large cytosolic domain, which serves as a scaffold for the assembly of large molecular weight complexes of different ethylene receptors and other cellular participants of the ethylene signaling pathway. Here we report the crystallographic structures of the ethylene receptor 1 (ETR1) catalytic ATP-binding and the ethylene response sensor 1 dimerization histidine phosphotransfer (DHp) domains and the solution structure of the entire cytosolic domain of ETR1, all from Arabidopsis thaliana. The isolated dimeric ethylene response sensor 1 DHp domain is asymmetric, the result of different helical bending angles close to the conserved His residue. The structures of the catalytic ATP-binding, DHp, and receiver domains of ethylene receptors and of a homologous, but dissimilar, GAF domain were refined against experimental small angle x-ray scattering data, leading to a structural model of the entire cytosolic domain of the ethylene receptor 1. The model illustrates that the cytosolic domain is shaped like a dumbbell and that the receiver domain is flexible and assumes a position different from those observed in prokaryotic histidine kinases. Furthermore the cytosolic domain of ETR1 plays a key role, interacting with all other receptors and several participants of the ethylene signaling pathway. Our model, therefore, provides the first step toward a detailed understanding of the molecular mechanics of this important signal transduction process in plants.

  14. Soliton-dependent plasmon reflection at bilayer graphene domain walls.

    PubMed

    Jiang, Lili; Shi, Zhiwen; Zeng, Bo; Wang, Sheng; Kang, Ji-Hun; Joshi, Trinity; Jin, Chenhao; Ju, Long; Kim, Jonghwan; Lyu, Tairu; Shen, Yuen-Ron; Crommie, Michael; Gao, Hong-Jun; Wang, Feng

    2016-08-01

    Layer-stacking domain walls in bilayer graphene are emerging as a fascinating one-dimensional system that features stacking solitons structurally and quantum valley Hall boundary states electronically. The interactions between electrons in the 2D graphene domains and the one-dimensional domain-wall solitons can lead to further new quantum phenomena. Domain-wall solitons of varied local structures exist along different crystallographic orientations, which can exhibit distinct electrical, mechanical and optical properties. Here we report soliton-dependent 2D graphene plasmon reflection at different 1D domain-wall solitons in bilayer graphene using near-field infrared nanoscopy. We observe various domain-wall structures in mechanically exfoliated graphene bilayers, including network-forming triangular lattices, individual straight or bent lines, and even closed circles. The near-field infrared contrast of domain-wall solitons arises from plasmon reflection at domain walls, and exhibits markedly different behaviours at the tensile- and shear-type domain-wall solitons. In addition, the plasmon reflection at domain walls exhibits a peculiar dependence on electrostatic gating. Our study demonstrates the unusual and tunable coupling between 2D graphene plasmons and domain-wall solitons.

  15. Dynamic dependence to domain wall propagation through artificial spin ice

    NASA Astrophysics Data System (ADS)

    Burn, D. M.; Chadha, M.; Branford, W. R.

    2017-03-01

    Domain wall propagation dynamics has been studied in nanostructured artificial kagome spin-ice structures. A stripline circuit has been used to provide localized pulsed magnetic fields within the artificial spin-ice (ASI) structure. This provides control of the system through electrically assisted domain wall nucleation events. Synchronization of the pulsed fields with additional global magnetic fields and the use of a focused magneto-optical Kerr effect magnetometer allows our experiments to probe the domain wall transit through an extended ASI structure. We find that the propagation distance depends on the driving field revealing field-driven properties of domain walls below their intrinsic nucleation field.

  16. 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.

  17. Periodically driven holographic superconductor

    NASA Astrophysics Data System (ADS)

    Li, Wei-Jia; Tian, Yu; Zhang, Hongbao

    2013-07-01

    As a first step towards our holographic investigation of the far-from-equilibrium physics of periodically driven systems at strong coupling, we explore the real time dynamics of holographic superconductor driven by a monochromatically alternating electric field with various frequencies. As a result, our holographic superconductor is driven to the final oscillating state, where the condensate is suppressed and the oscillation frequency is controlled by twice of the driving frequency. In particular, in the large frequency limit, the three distinct channels towards the final steady state are found, namely under damped to superconducting phase, over damped to superconducting and normal phase, which can be captured essentially by the low lying spectrum of quasi-normal modes in the time averaged approximation, reminiscent of the effective field theory perspective.

  18. Nanointerstice-driven microflow.

    PubMed

    Chung, Seok; Yun, Hoyoung; Kamm, Roger D

    2009-03-01

    To generate flow in microchannels, various actuation schemes such as electrokinetic, pressure-driven, and capillary-driven flow have been suggested. Capillary-driven flow is widely used in plastic disposable diagnostic platforms due to its simplicity and because it requires no external power. However, plastics such as poly(methyl methacrylate) (PMMA), generally used in microfluidics, are hydrophobic, which inhibits capillary force generation and requires surface enhancement that deteriorates with age. It is shown that the microchannels made of PMMA lose their acquired hydrophilicity by oxygen plasma treatment in long-term storage and tend to generate slow capillary flow exhibiting large variability. To promote consistency and drive flow in the microchannel, nanointerstices (NI) are introduced at the side wall of the microchannel, which results in capillary flow that is less dependent on surface characteristics. The results show that NI flow generation can be a useful alternative technique to create long-term predictable flow in commercialized products with microchannels.

  19. Regularities of crystallographic texture formation in cladding tubes from Zr-based alloys during their production

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

    This paper summarizes researches of the authors, which are directed on the development of the methodological basis of X-ray studies in the materials science of zirconium and on the systematization of new experimental results obtained using developed methods. The paper describes regularities of the formation of the crystallographic texture and the substructure inhomogeneity of cladding tubes from zirconium alloys at various stages of their manufacturing, i.e. during hot and cold deformation, recrystallization, phase transformations and interactions of the above processes.

  20. Crystallographic dependence of photocatalytic activity of WO3 thin films prepared by molecular beam epitaxy.

    PubMed

    Li, Guoqiang; Varga, Tamas; Yan, Pengfei; Wang, Zhiguo; Wang, Chongmin; Chambers, Scott A; Du, Yingge

    2015-06-21

    We investigated the impact of crystallographic orientation on the photocatalytic activity of single crystalline WO3 thin films prepared by molecular beam epitaxy on the photodegradation of rhodamine B (RhB). A clear effect is observed, with (111) being the most reactive surface, followed by (110) and (001). Photoreactivity is directly correlated with the surface free energy determined by density functional theory calculations. The RhB photodegradation mechanism is found to involve hydroxyl radicals in solution formed from photo-generated holes and differs from previous studies performed on nanoparticles and composites.

  1. 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

  2. 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.

  3. Phonon softening and crystallographic orientation of strained graphene studied by Raman spectroscopy

    PubMed Central

    Huang, Mingyuan; Yan, Hugen; Chen, Changyao; Song, Daohua; Heinz, Tony F.; Hone, James

    2009-01-01

    We present a systematic study of the Raman spectra of optical phonons in graphene monolayers under tunable uniaxial tensile stress. Both the G and 2D bands exhibit significant red shifts. The G band splits into 2 distinct subbands (G+, G−) because of the strain-induced symmetry breaking. Raman scattering from the G+ and G− bands shows a distinctive polarization dependence that reflects the angle between the axis of the stress and the underlying graphene crystal axes. Polarized Raman spectroscopy therefore constitutes a purely optical method for the determination of the crystallographic orientation of graphene. PMID:19380746

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

    PubMed

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

    2016-08-23

    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.

  5. Crystallographic, luminescence and photoconductive characteristics of chemically tailored ZnO nanorods

    SciTech Connect

    Bayan, Sayan Chakraborty, Purushottam

    2014-04-24

    The optoelectronic properties of zinc oxide (ZnO) nanorods synthesized using two different chemical methods have been explored in the light of microstructural features. The presence/absence of band edge emission in the luminescence spectra of the nanorods is found to be governed by the crystallographic properties. Moreover, we observed a pronounced effect of variation in crystallite size on the UV photoconductivity of the nanorods. Understanding the influence of microstructural aspects on the optical and electronic properties of the nanostructures may help in the fabrication of prototype, miniaturized optoelectronic devices.

  6. Morphological and crystallographic evolution of bainite transformation in Fe-0.15C binary alloy.

    PubMed

    Zhang, Di; Terasaki, Hidenori; Komizo, Yuichi

    2010-01-01

    In this article, an in situ observation method, combining laser scanning confocal microscopy and electron backscattering diffraction, was used to investigate the morphological and crystallographic evolution of bainite transformation in a Fe-0.15C binary alloy. The nucleation at a grain boundary and inclusions, sympathetic nucleation, and impingement event of bainitic ferrite were directly shown in real time. The variant evolution during bainite transformation and misorientation between bainitic ferrites were clarified. Strong variant selection was observed during sympathetic nucleation. (c) 2009 Wiley-Liss, Inc.

  7. Blocks and residual stresses in sapphire rods of different crystallographic orientations grown by the Stepanov method

    SciTech Connect

    Krymov, V. M. Nosov, Yu. G.; Bakholdin, S. I.; Maslov, V. N.; Shul’pina, I. L.

    2015-05-15

    The formation of blocks in shaped sapphire rods of two crystallographic orientations has been investigated. It is shown that, when growth occurs in the direction of the optical c axis, blocks are formed with a higher probability than in the case of growth in the a direction. A model of formation of blocks in rods of different orientations is proposed. The distribution of residual stresses over sapphire rod cross sections is measured by conoscopy. It is found that stresses increase from the middle of a rod to its periphery and reach 20 MPa.

  8. Crystal structures of wild-type Trichoderma reesei Cel7A catalytic domain in open and closed states

    SciTech Connect

    Bodenheimer, Annette M.; Meilleur, Flora

    2016-11-07

    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.

  9. Screw dislocation driven growth of nanomaterials.

    PubMed

    Meng, Fei; Morin, Stephen A; Forticaux, Audrey; Jin, Song

    2013-07-16

    Nanoscience and nanotechnology impact our lives in many ways, from electronic and photonic devices to biosensors. They also hold the promise of tackling the renewable energy challenges facing us. However, one limiting scientific challenge is the effective and efficient bottom-up synthesis of nanomaterials. We can approach this core challenge in nanoscience and nanotechnology from two perspectives: (a) how to controllably grow high-quality nanomaterials with desired dimensions, morphologies, and material compositions and (b) how to produce them in a large quantity at reasonable cost. Because many chemical and physical properties of nanomaterials are size- and shape-dependent, rational syntheses of nanomaterials to achieve desirable dimensionalities and morphologies are essential to exploit their utilities. In this Account, we show that the dislocation-driven growth mechanism, where screw dislocation defects provide self-perpetuating growth steps to enable the anisotropic growth of various nanomaterials at low supersaturation, can be a powerful and versatile synthetic method for a wide variety of nanomaterials. Despite significant progress in the last two decades, nanomaterial synthesis has often remained an "art", and except for a few well-studied model systems, the growth mechanisms of many anisotropic nanostructures remain poorly understood. We strive to go beyond the empirical science ("cook-and-look") and adopt a fundamental and mechanistic perspective to the anisotropic growth of nanomaterials by first understanding the kinetics of the crystal growth process. Since most functional nanomaterials are in single-crystal form, insights from the classical crystal growth theories are crucial. We pay attention to how screw dislocations impact the growth kinetics along different crystallographic directions and how the strain energy of defected crystals influences their equilibrium shapes. Furthermore, such inquiries are supported by detailed structural investigation to

  10. The driven spinning top

    NASA Astrophysics Data System (ADS)

    Grosu, Ioan; Featonby, David

    2016-05-01

    This driven top is quite a novelty and can, with some trials, be made using the principles outlined here. This new top has many applications in developing both understanding and skills and these are detailed in the article. Depending on reader’s available time and motivation they may feel an urge to make one themselves, or simply invest a few pounds in the one that has been designed, tested and manufactured to a high standard. Either way the unique design of the driven top can provide several hours of interesting experimentation. Our aim here is simply to inform and inspire readers to further investigation and experimentation.

  11. Identification of inversion domains in KTiOPO{sub 4}via resonant X-ray diffraction

    SciTech Connect

    Fabrizi, Federica; Thomas, Pamela A.; Nisbet, Gareth; Collins, Stephen P.

    2015-05-14

    The identification and high-resolution mapping of the absolute crystallographic structure in multi-domain ferroelectric KTiOPO{sub 4} is achieved through a novel synchrotron X-ray diffraction method. On a single Bragg reflection, the intensity ratio in resonant diffraction below and above the Ti absorption K edge demonstrates a domain contrast up to a factor of ∼270, thus implementing a non-contact, non-destructive imaging technique with micrometre spatial resolution, applicable to samples of arbitrarily large dimensions. A novel method is presented for the identification of the absolute crystallographic structure in multi-domain polar materials such as ferroelectric KTiOPO{sub 4}. Resonant (or ‘anomalous’) X-ray diffraction spectra collected across the absorption K edge of Ti (4.966 keV) on a single Bragg reflection demonstrate a huge intensity ratio above and below the edge, providing a polar domain contrast of ∼270. This allows one to map the spatial domain distribution in a periodically inverted sample, with a resolution of ∼1 µm achieved with a microfocused beam. This non-contact, non-destructive technique is well suited for samples of large dimensions (in contrast with traditional resonant X-ray methods based on diffraction from Friedel pairs), and its potential is particularly relevant in the context of physical phenomena connected with an absence of inversion symmetry, which require characterization of the underlying absolute atomic structure (such as in the case of magnetoelectric coupling and multiferroics)

  12. Electrically Driven Prosthetic Elbow.

    DTIC Science & Technology

    The invention relates to an improved electrically driven prosthetic elbow wherein the elbow is capable of being rigidly locked into place in any...desired position, and upon driving the arm to the fully extended position, the elbow is automatically unlocked.

  13. The Driven Spinning Top

    ERIC Educational Resources Information Center

    Grosu, Ioan; Featonby, David

    2016-01-01

    This driven top is quite a novelty and can, with some trials, be made using the principles outlined here. This new top has many applications in developing both understanding and skills and these are detailed in the article. Depending on reader's available time and motivation they may feel an urge to make one themselves, or simply invest a few…

  14. Argument-Driven Inquiry

    ERIC Educational Resources Information Center

    Sampson, Victor; Grooms, Jonathon; Walker, Joi

    2009-01-01

    Argument-Driven Inquiry (ADI) is an instructional model that enables science teachers to transform a traditional laboratory activity into a short integrated instructional unit. To illustrate how the ADI instructional model works, this article describes an ADI lesson developed for a 10th-grade chemistry class. This example lesson was designed to…

  15. The Driven Spinning Top

    ERIC Educational Resources Information Center

    Grosu, Ioan; Featonby, David

    2016-01-01

    This driven top is quite a novelty and can, with some trials, be made using the principles outlined here. This new top has many applications in developing both understanding and skills and these are detailed in the article. Depending on reader's available time and motivation they may feel an urge to make one themselves, or simply invest a few…

  16. Argument-Driven Inquiry

    ERIC Educational Resources Information Center

    Sampson, Victor; Grooms, Jonathon; Walker, Joi

    2009-01-01

    Argument-Driven Inquiry (ADI) is an instructional model that enables science teachers to transform a traditional laboratory activity into a short integrated instructional unit. To illustrate how the ADI instructional model works, this article describes an ADI lesson developed for a 10th-grade chemistry class. This example lesson was designed to…

  17. Internationalized Domain Names.

    ERIC Educational Resources Information Center

    Wielansky, Marc D.

    2002-01-01

    Reports on an investigation of what may appear at first to be an arcane topic--the internationalization of domain names on the Internet. Concludes that expanding domain names internationally poses challenges to the inherent open structure of the Internet; to its ease of use for those accustomed to Latin-alphabet-only domain names; and to corporate…

  18. Preliminary X-ray crystallographic analysis of α-carbonic anhydrase from Thiomicrospira crunogena XCL-2.

    PubMed

    Díaz Torres, Natalia; González, Guillermo; Biswas, Shyamasri; Scott, Kathleen M; McKenna, Robert

    2012-09-01

    Thiomicrospira crunogena XCL-2 is a novel sulfur-oxidizing chemolithoautotroph that plays a significant role in the sustainability of deep-sea hydrothermal vent communities. This recently discovered gammaproteobacterium encodes and expresses four carbonic anhydrases (CAs) from three evolutionarily and structurally distinct CA families: an α-CA, two β-CAs and a γ-CA. In order to characterize and elucidate the physiological roles of these CAs, X-ray crystallographic structural studies have been initiated on the α-CA. The α-CA crystallized in space group C2. The crystals diffracted to a maximum resolution of 2.6 Å, with unit-cell parameters a = 127.1, b = 102.2, c = 105.0 Å, β = 127.3°, and a calculated Matthews coefficient of 2.04 Å(3) Da(-1) with four identical protein molecules in the crystallographic asymmetric unit. A preliminary solution was determined by molecular replacement with the PHENIX AutoMR wizard, which had an initial TFZ score of 17.9. Refinement of the structure is currently in progress.

  19. Conformation-changing aggregation in hydroxyacetone: a combined low-temperature FTIR, jet, and crystallographic study.

    PubMed

    Sharma, Archna; Reva, Igor; Fausto, Rui; Hesse, Susanne; Xue, Zhifeng; Suhm, Martin A; Nayak, Susanta K; Sathishkumar, Ranganthan; Pal, Rumpa; Row, Tayur N Guru

    2011-12-21

    Aggregation in hydroxyacetone (HA) is studied using low-temperature FTIR, supersonic jet expansion, and X-ray crystallographic (in situ cryocrystallization) techniques. Along with quantum chemical methods (MP2 and DFT), the experiments unravel the conformational preferences of HA upon aggregation to dimers and oligomers. The O-H···O═C intramolecular hydrogen bond present in the gas-phase monomer partially opens upon aggregation in supersonic expansions, giving rise to intermolecular cooperatively enhanced O-H···O-H hydrogen bonds in competition with isolated O-H···O═C hydrogen bonds. On the other hand, low-temperature IR studies on the neat solid and X-ray crystallographic data reveal that HA undergoes profound conformational changes upon crystallization, with the HOCC dihedral angle changing from ~0° in the gas phase to ~180° in the crystalline phase, hence giving rise to a completely new conformation. These conclusions are supported by theoretical calculations performed on the geometry derived from the crystalline phase. © 2011 American Chemical Society

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

    SciTech Connect

    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 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.