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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. Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain.

    PubMed

    Cámara-Artigas, Ana

    2016-07-15

    Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation. PMID:26924596

  3. Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore

    PubMed Central

    Luecke, Hartmut; Schobert, Brigitte; Stagno, Jason; Imasheva, Eleonora S.; Wang, Jennifer M.; Balashov, Sergei P.; Lanyi, Janos K.

    2008-01-01

    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-Å 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 pKa 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 ≈45%, and the 46° 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. PMID:18922772

  4. Current driven asymmetric domain wall propagation

    NASA Astrophysics Data System (ADS)

    Garg, Chirag; Pushp, Aakash; Phung, Timothy; Yang, See-Hun; Hughes, Brian P.; Rettner, Charles; Parkin, Stuart S. P.

    In ultrathin magnetic heterostructures, the presence of spin-orbit coupling gives rise to chiral Neel walls which are stabilized by the Dzyaloshinskii-Moriya Interaction (DMI), and also to a highly efficient chiral spin torque mechanism. In straight nanowires, the current-driven propagation of alternating Néel DWs without the presence of an in-plane field is equivalent, leading to the lock-step motion of several DWs in a nanowire. Here, we show that by engineering the structure in which the domain walls propagate, which in our case is in the shape of a Y-shaped junction, the DW propagation process becomes selective to the polarity of the DWs even in the absence of any externally applied magnetic fields. We remarkably find that after splitting at the Y-shaped junction, the DW velocity in one branch remains largely unaffected compared to its initial velocity whereas simultaneously the DW velocity in the other branch decreases by as much as 10-90%. We show that this large change in the DW velocity in a particular branch depends on the relative angle between the local magnetization of the DW and the spin current emanating from the underlying heavy-metal layer in these nanowires.

  5. 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. PMID:27588878

  6. Dynamics of domain wall driven by spin-transfer torque

    SciTech Connect

    Chureemart, P.; Evans, R. F. L.; Chantrell, R. W.

    2011-05-01

    Spin-torque switching of magnetic devices offers new technological possibilities for data storage and integrated circuits. We have investigated domain-wall motion in a ferromagnetic thin film driven by a spin-polarized current using an atomistic spin model with a modified Landau-Lifshitz-Gilbert equation including the effect of the spin-transfer torque. The presence of the spin-transfer torque is shown to create an out-of-plane domain wall, in contrast to the external-field-driven case where an in-plane wall is found. We have investigated the effect of the spin torque on domain-wall displacement, domain-wall velocity, and domain-wall width, as well as the equilibration time in the presence of the spin-transfer torque. We have shown that the minimum spin-current density, regarded as the critical value for domain-wall motion, decreases with increasing temperature.

  7. 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.

  8. 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

  9. 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

  10. Polarization control at spin-driven ferroelectric domain walls

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    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.

  11. 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.

  12. Purification, crystallization and preliminary crystallographic analysis of the CBS-domain protein MJ1004 from Methanocaldococcus jannaschii

    PubMed Central

    Oyenarte, Iker; Lucas, María; Gómez García, Inmaculada; Martínez-Cruz, Luis Alfonso

    2011-01-01

    The purification and preliminary crystallographic analysis of the archaeal CBS-domain protein MJ1004 from Methanocaldococcus jannaschii are described. The native protein was overexpressed, purified and crystallized in the monoclinic space group P21, with unit-cell parameters a = 54.4, b = 53.8, c = 82.6 Å, β = 106.1°. The crystals diffracted X-rays to 2.7 Å resolution using synchrotron radiation. Matthews-volume calculations suggested the presence of two molecules in the asymmetric unit that are likely to correspond to a dimeric species, which is also observed in solution. PMID:21393835

  13. Purification, crystallization and preliminary X-ray crystallographic analysis of the CIDE-N domain of Fsp27.

    PubMed

    Wang, Xiaodan; Zhang, Bo; Xu, Duo; Gao, Jinlan; Wang, Linfang; Wang, Zhi; Shan, Yaming; Yu, Xianghui

    2012-12-01

    Fsp27, a member of the CIDE protein family which is selectively expressed in adipocytes, has emerged as a novel regulator for unilocular lipid droplet (LD) formation, lipid metabolism, differentiation of adipocytes and insulin sensitivity. An LD is a subcellular compartment that is used by adipocytes for the efficient storage of fats. The CIDE-N domain of Fsp27 functions as a recruitment platform that induces the correct configuration of the Fsp27 CIDE-C domain to facilitate LD fusion. This study reports the high-yield expression of the mouse Fsp27 CIDE-N domain in Escherichia coli; a two-step purification protocol with high efficiency was established and crystallographic analysis was performed. The purity of the recombinant Fsp27 was >95% as assessed by SDS-PAGE. Crystals were obtained at 291 K using 28% polyethylene glycol 4000 as a precipitant. Diffraction data were collected to 1.92 Å resolution and the crystal belonged to space group P6(5), with unit-cell parameters a=b=63.3, c=37.4 Å, α=β=90, γ=120°. The components of the crystal were identified by ion-trap LC/MS/MS spectrometric analysis. The structure has been solved by molecular replacement and refinement is in progress. PMID:23192040

  14. 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.

  15. Crystallographic characterization of the DIX domain of the Wnt signalling positive regulator Ccd1

    PubMed Central

    Terawaki, Shin-ichi; Yano, Koumei; Katsutani, Takuya; Shiomi, Kensuke; Keino-Masu, Kazuko; Masu, Masayuki; Shomura, Yasuhito; Komori, Hirofumi; Shibata, Naoki; Higuchi, Yoshiki

    2011-01-01

    Coiled-coil DIX1 (Ccd1) is a positive regulator that activates the canonical Wnt signalling pathway by inhibiting the degradation of the key signal transducer β-­catenin. The C-terminal DIX domain of Ccd1 plays an important role in the regulation of signal transduction through homo-oligomerization and protein complex formation with other DIX domain-containing proteins, i.e. axin and dishevelled proteins. Here, the expression, purification, crystallization and X-ray data collection of the Ccd1 DIX domain are reported. The crystals of the Ccd1 DIX domain belonged to space group P212121, with unit-cell parameters a = 72.9, b = 75.7, c = 125.6 Å. An X-ray diffraction data set was collected at 3.0 Å resolution. PMID:21795788

  16. Crystallization and preliminary crystallographic analysis of human LR11 Vps10p domain.

    PubMed

    Nakata, Zenzaburo; Nagae, Masamichi; Yasui, Norihisa; Bujo, Hideaki; Nogi, Terukazu; Takagi, Junichi

    2011-01-01

    Low-density lipoprotein receptor (LDLR) relative with 11 binding repeats (LR11; also known as sorLA) is genetically associated with late-onset Alzheimer's disease and is thought to be involved in neurodegenerative processes. LR11 contains a vacuolar protein-sorting 10 protein (Vps10p) domain. As this domain has been implicated in protein-protein interaction in other receptors, its structure and function are of great biological interest. Human LR11 Vps10p domain was expressed in mammalian cells and the purified protein was crystallized using the hanging-drop vapour-diffusion method. Enzymatic deglycosylation of the sample was critical to obtaining diffraction-quality crystals. Deglycosylated LR11 Vps10p-domain crystals belonged to the hexagonal space group P6(1)22. A diffraction data set was collected to 2.4 Å resolution and a clear molecular-replacement solution was obtained. PMID:21206043

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

    PubMed

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

    2015-01-01

    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. PMID:25868608

  18. 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.

  19. 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.

  20. 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.

  1. Overexpression, purification and preliminary crystallographic analysis of human M-ficolin fibrinogen-like domain

    SciTech Connect

    Tanio, Michikazu; Kondo, Shin; Sugio, Shigetoshi; Kohno, Toshiyuki

    2006-07-01

    Human M-ficolin fibrinogen-like domain has been overexpressed in P. pastoris, purified and crystallized. Diffraction data have been collected to 1.9 Å. Ficolins, which are comprised of a collagen-like domain and a fibrinogen-like domain, are a kind of pattern-recognition molecule for pathogens in the innate immunity system. To investigate the molecular mechanism of the discrimination between self and non-self by ficolins, human M-ficolin fibrinogen-like domain (FD1), which contains the ligand-binding site, was overexpressed in Pichia pastoris, purified and crystallized using the vapour-diffusion method at 293 K. The crystals belong to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 55.16, b = 117.45, c = 55.19 Å, β = 99.88°, and contain three molecules per asymmetric unit. An X-ray data set was collected to 1.9 Å resolution using synchrotron radiation at beamline BL24XU at the SPring-8 facility in Japan.

  2. 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.

  3. 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.

  4. Novel current driven domain wall dynamics in synthetic antiferromagnets

    NASA Astrophysics Data System (ADS)

    Yang, See-Hun

    It was reported that the domain walls in nanowires can be moved efficiently by electrical currents by a new type of torque, chiral spin torque (CST), the combination of spin Hall effect and Dzyaloshinskii-Moriya interaction. Recently we domonstrated that ns-long current pulses can move domain walls at extraordinarily high speeds (up to ~750 m s -1) in synthetic antiferromagnetic (SAF) nanowires that have almost zero net magnetization, which is much more efficient compared with similar nanowires in which the sub-layers are coupled ferromagnetically (SF). This high speed is found to be due to a new type of powerful torque, exchange coupling torque (ECT) that is directly proportional to the strength of the antiferromagnetic exchange coupling between the two sub-layers, showing that the ECT is effective only in SAF not in SF. Moreover, it is found that the dependence of the wall velocity on the magnetic field applied along the nanowire is non-monotonic. Most recently we predict an Walker-breakdown-like domain wall precession in SAF nanowires in the presence of in-plane field based on the model we develop, and this extraordinary precession has been observed. In this talk I will discuss this in details by showing a unique characteristics of SAF sublayers' DW boost-and-drag mechanism along with CST and ECT. Novel current driven domain wall dynamics in synthetic antiferromagnets.

  5. 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.

  6. 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.

  7. Frequency-Domain Interferometry of Electron Bunch Driven Wakefields

    NASA Astrophysics Data System (ADS)

    Zgadzaj, Rafal; Downer, M. C.; Yi, Austin; Shvets, Gennady; Fang, Yun; Muggli, Patric; Yakimenko, Vitaly; Babzien, Marcus; Fedurin, Mikhail; Kusche, Karl

    2012-10-01

    Beam-driven plasma wakefield accelerators (PWFA), such as the ``plasma afterburner'' can potentially greatly increase the particle energies of conventional accelerators . Various schemes using single and multiple bunches of electrons, positrons and protons have been investigated. Appropriately delayed witness bunches have been the usual method to probe the fields of such wakes, and indirectly, the corresponding plasma wake structures. However, the wake structure has not been observed directly in the PWFA. We will report our progress in the development of direct, optical interferometric methods of measuring the plasma density modulation in electron beam driven wakefields. Frequency Domain Holography (FDH), employing two chirped laser pulses (probe and reference) co-propagating with the particle drive-beam and its plasma wake, permits single shot observation of an extended section of the wakefield behind a drive bunch. The chirped, temporally stretched, probe samples several periods of the wake, while the undisturbed reference pulse propagates ahead of the electron drive bunch. The technique is being developed in the Accelerator Test Facility at the Brookhaven National Laboratory as a probe for two and multibunch driven plasmawakefield experiments

  8. 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.

  9. 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.

  10. Expression, purification, crystallization and crystallographic analysis of the N-terminal domain of translocated intimin receptor.

    PubMed

    Huang, Bing Yang; Gu, Jiang; Zhang, Yan Fang; Zhou, Jun Jun; Song, Xiao Yong; Lin, Yi; Li, Xin Min; Li, Lu

    2016-01-01

    Translocated intimin receptor (Tir) is an Escherichia coli-encoded protein that is transported into the host cell through a sophisticated bacterial type III secretion system (T3SS). Tir anchors the infected cell membrane twice using both its N- and C-termini from inside the host cytoplasm for signalling. It plays a key role in enterohemorrhagic Escherichia coli (EHEC) infection, attaching and effacing (A/E) lesions and intracellular signal transduction. Here, the overexpression, purification and crystallization of its N-terminal intracellular domain are reported. The crystal belonged to the orthorhombic space group I4122, with unit-cell parameters a = b = 59.79, c = 183.11 Å. The asymmetric unit contained one molecule, with a solvent content of 51% and a VM of 2.55 Å(3) Da(-1). PMID:26750484

  11. Crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from Mycobacterium tuberculosis

    SciTech Connect

    Goyal, Aneesh; Yousuf, Malikmohamed; Rajakumara, Eerappa; Arora, Pooja; Gokhale, Rajesh S.; Sankaranarayanan, Rajan

    2006-04-01

    The crystallization and preliminary X-ray crystallographic studies of the N-terminal domain of FadD28, a fatty-acyl AMP ligase from M. tuberculosis, are reported. FadD28 from Mycobacterium tuberculosis belongs to the fatty-acyl AMP ligase (FAAL) family of proteins. It is essential for the biosynthesis of a virulent phthiocerol dimycocerosate (PDIM) lipid that is only found in the cell wall of pathogenic mycobacteria. The N-terminal domain, comprising of the first 460 residues, was crystallized by the hanging-drop vapour-diffusion method at 295 K. The crystals belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 50.97, b = 60.74, c = 136.54 Å. The crystal structure of the N-terminal domain of FadD28 at 2.35 Å resolution has been solved using the MAD method.

  12. Optical Spin-Transfer-Torque-Driven Domain-Wall Motion in a Ferromagnetic Semiconductor

    NASA Astrophysics Data System (ADS)

    Ramsay, A. J.; Roy, P. E.; Haigh, J. A.; Otxoa, R. M.; Irvine, A. C.; Janda, T.; Campion, R. P.; Gallagher, B. L.; Wunderlich, J.

    2015-02-01

    We demonstrate optical manipulation of the position of a domain wall in a dilute magnetic semiconductor, GaMnAsP. Two main contributions are identified. First, photocarrier spin exerts a spin-transfer torque on the magnetization via the exchange interaction. The direction of the domain-wall motion can be controlled using the helicity of the laser. Second, the domain wall is attracted to the hot spot generated by the focused laser. Unlike magnetic-field-driven domain-wall depinning, these mechanisms directly drive domain-wall motion, providing an optical tweezerlike ability to position and locally probe domain walls.

  13. 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.

  14. 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. PMID:22107601

  15. 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. PMID:27002341

  16. AC driven magnetic domain quantification with 5 nm resolution.

    PubMed

    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

  17. 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.

  18. 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.

  19. Rashba Torque Driven Domain Wall Motion in Magnetic Helices

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  20. 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

    2016-01-01

    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

  1. 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

  2. Domain wall motion driven by adiabatic spin transfer torque through excitation of nonlinear dynamics

    NASA Astrophysics Data System (ADS)

    Wang, D.; Dong, Yulan; Yan, Zhou; Wang, Xi-guang; He, Jun; Guo, Guang-hua

    2016-05-01

    Domain wall dynamics under the joint action of a linearly polarized microwave magnetic field and spin transfer torque was analysed in terms of the domain wall collective coordinates. It was found that a microwave-assisted steady domain wall motion driven by adiabatic spin transfer torque can be adequately described by three domain wall collective coordinates. Analytical expression for the domain wall velocity showed that there are two contributions to the steady domain wall motion. One is derived from the nonlinear oscillation of domain wall width excited by the microwave field, and the other is from the heterodyne process between the width oscillation and the microwave field. The former always propels a domain wall to move in the positive direction, which is defined as the direction of the applied current. The latter contribution to the domain wall velocity can be positive or negative, depending on the polarization of the microwave field. The final domain wall velocity is determined by the competition between those two contributions, which indicates that by simply changing the polarization of the microwave field, the direction of the domain wall motion can be reversed. Our analysis demonstrated that the characteristics of domain wall motion can be tuned by selective excitation of nonlinear domain wall dynamics.

  3. 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.

  4. Current driven dynamics of magnetic domain walls in permalloy nanowires

    NASA Astrophysics Data System (ADS)

    Hayashi, Masamitsu

    The significant advances in micro-fabrication techniques opened the door to access interesting properties in solid state physics. With regard to magnetic materials, geometrical confinement of magnetic structures alters the defining parameters that govern magnetism. For example, development of single domain nano-pillars made from magnetic multilayers led to the discovery of electrical current controlled magnetization switching, which revealed the existence of spin transfer torque. Magnetic domain walls (DWs) are boundaries in magnetic materials that divide regions with distinct magnetization directions. DWs play an important role in the magnetization reversal processes of both bulk and thin film magnetic materials. The motion of DW is conventionally controlled by magnetic fields. Recently, it has been proposed that spin polarized current passed across the DW can also control the motion of DWs. Current in most magnetic materials is spin-polarized, due to spin-dependent scattering of the electrons, and thus can deliver spin angular momentum to the DW, providing a "spin transfer" torque on the DW which leads to DW motion. In addition, owing to the development of micro-fabrication techniques, geometrical confinement of magnetic materials enables creation and manipulation of a "single" DW in magnetic nanostructures. New paradigms for DW-based devices are made possible by the direct manipulation of DWs using spin polarized electrical current via spin transfer torque. This dissertation covers research on current induced DW motion in magnetic nanowires. Fascinating effects arising from the interplay between DWs with spin polarized current will be revealed.

  5. Comparison of Current and Field Driven Domain Wall Motion in Beaded Permalloy Nanowires

    NASA Astrophysics Data System (ADS)

    Lage, Enno; Dutta, Sumit; Ross, Caroline A.

    2015-03-01

    Domain wall based devices are promising candidates for non-volatile memory devices with no static power consumption. A common approach is the use of (field assisted) current driven domain wall motion in magnetic nanowires. In such systems local variations in linewidth act as obstacles for propagating domain walls. In this study we compare simulated field driven and current driven domain wall motion in permalloy nanowires with anti-notches. The simulations were obtained using the Object Oriented MicroMagnetics Framework (OOMMF). The wires with a constant thickness of 8 nm exhibit linewidths ranging from 40 nm to 300 nm. Circular shaped anti-notches extend the linewidth locally by 10% to 30% and raise information about the domain wall propagation in such beaded nanowires. The results are interpreted in terms of the observed propagation behavior and summarized in maps indicating ranges of different ability to overcome the pinning caused by anti-notches of different sizes. Furthermore, regimes of favored domain wall type (transverse walls or vortex walls) and complex propagation effects like walker breakdown behavior or dynamic change between domain wall structures are identified The authors thank the German Academic Exchange Service (DAAD) for funding.

  6. 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.

  7. Expression, purification and preliminary crystallographic studies of the C-terminal SH3 domain of human Tks4.

    PubMed

    Huang, Yuxin; Qian, Huolian; Wang, Xiaoying; Cheng, Zhong; Ren, Jixia; Zhao, Weichen; Xie, Yong

    2014-03-01

    The Src homology 3 (SH3) domain is a small, noncatalytic domain with a conserved sequence of about 60 amino-acid residues that interacts with proline-rich peptides to form a protein complex. In this study, the C-terminal SH3 domain of human Tks4 (residues 853-911) was expressed, purified and crystallized. X-ray diffraction data were collected to 2.3 Å resolution. The crystal belonged to the trigonal space group P3121 (or P3221), with unit-cell parameters a = b = 83.87, c = 108.44 Å, α = β = 90, γ = 120°. Calculating the self-rotation and the native Patterson function did not lead to the detection of any noncrystallographic translational symmetry. Six, seven or eight protein molecules are likely to be present in the asymmetric unit, resulting in a Matthews coefficient and approximate solvent content of 2.71 Å(3) Da(-1) and 55%, 2.32 Å(3) Da(-1) and 47%, and 2.03 Å(3) Da(-1) and 39%, respectively. To solve the crystal structure of the C-terminal SH3 domain of human Tks4, the isomorphous replacement method is presently being utilized. PMID:24598923

  8. Preparation, purification, crystallization and preliminary crystallographic analysis of dual-domain β-propeller phytase from Bacillus sp. HJB17.

    PubMed

    Lu, Fang; Guo, Gangxin; Li, Qianqian; Feng, Duo; Liu, Yong; Huang, Huoqing; Yang, Peilong; Gao, Wei; Yao, Bin

    2014-12-01

    β-Propeller phytases (BPPs) are abundant in nature. Recently, dual-domain BPPs have been found in which the typical BPP domain is responsible for phytate hydrolysis. The dual-domain BPP (PhyH) from Bacillus sp. HJB17 was obtained with an incomplete N-terminal BPP domain (PhyH-DI; residues 41-318) and a typical BPP domain (PhyH-DII; residues 319-644) at the C-terminus. PhyH-DI was found to act synergistically (with a 1.2-2.5-fold increase in phosphate release) with PhyH-DII, other BPPs (PhyP and 168PhyA) and a histidine acid phosphatase. The structure of PhyH was therefore studied with the aim of explaining these functions. PhyH with the secreted signal peptide of the first 40 amino acids deleted (PhyHT) was cloned and expressed in Escherichia coli. Purified and active PhyHT protein was obtained by refolding from the precipitant. PhyHT was crystallized using the vapour-diffusion method. The crystal grew in a condition consisting of 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl pH 9.5, 25%(w/v) polyethylene glycol 4000 using 1 mg ml(-1) protein solution at 289 K. A complete data set was collected from a crystal to 2.85 Å resolution using synchrotron radiation at 100 K. The crystal belonged to space group P1211, with unit-cell parameters a = 46.82, b = 140.19, c = 81.94 Å, α = 90.00, β = 92.00, γ = 90.00°. The asymmetric unit was estimated to contain one molecule of PhyHT. PMID:25484224

  9. 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.

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

    SciTech Connect

    Fernández-Millán, Pablo; Kortazar, Danel; Lucas, María; Martínez-Chantar, María Luz; Astigarraga, Egoitz; Fernández, José Andrés; Albert, Armando; Martínez-Cruz, Luis Alfonso

    2008-07-01

    Trigonal crystals of MJ0729 showing different degrees of merohedral twinning that may vary from perfect hemihedral twinning to perfect tetartohedral twinning were obtained upon slight variation of the pH. 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.

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

    PubMed Central

    Jang, Tae-ho; Park, Hyun Ho

    2014-01-01

    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° PMID:25084380

  12. 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

  13. Purification, crystallization and preliminary crystallographic analysis of the catalytic domain of the extracellular cellulase CBHI from Trichoderma harzianum

    PubMed Central

    Colussi, Francieli; Textor, Larissa C.; Serpa, Viviane; Maeda, Roberto Nobuyuki; Pereira, Nei; Polikarpov, Igor

    2010-01-01

    The filamentous fungus Trichoderma harzianum has a considerable cellulolytic activity that is mediated by a complex of enzymes which are essential for the hydrolysis of microcrystalline cellulose. These enzymes were produced by the induction of T. harzianum with microcrystalline cellulose (Avicel) under submerged fermentation in a bioreactor. The catalytic core domain (CCD) of cellobiohydrolase I (CBHI) was purified from the extracellular extracts and submitted to robotic crystallization. Diffraction-quality CBHI CCD crystals were grown and an X-ray diffraction data set was collected under cryogenic conditions using a synchrotron-radiation source. PMID:20823521

  14. 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.

  15. Crystallization and preliminary X-ray crystallographic analysis of the PH-GRAM domain of human MTMR4

    PubMed Central

    Lee, Jee Un; Son, Ji Young; Yoo, Ki-Young; Shin, Woori; Im, Dong-Won; Kim, Seung Jun; Ryu, Seong Eon; Heo, Yong-Seok

    2014-01-01

    Phosphoinositide lipid molecules play critical roles in intracellular signalling pathways and are regulated by phospholipases, lipid kinases and phosphatases. In particular, phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate are related to endosomal trafficking events through the recruitment of effector proteins and are involved in the degradation step of autophagy. Myotubularin-related proteins (MTMRs) are a large family of phosphatases that catalyze the dephosphorylation of phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate at the D3 position, thereby regulating cellular phosphoinositide levels. In this study, the PH-GRAM domain of human MTMR4 was cloned, overexpressed in Escherichia coli, purified and crystallized by the vapour-diffusion method. The crystals diffracted to 3.20 Å resolution at a synchrotron beamline and belonged to either space group P61 or P65, with unit-cell parameters a = b = 109.10, c = 238.97 Å. PMID:25195910

  16. The periplasmic sensing domain of Vibrio fischeri chemoreceptor protein A (VfcA): cloning, purification and crystallographic analysis.

    PubMed

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

    2016-05-01

    Flagella-mediated motility and chemotaxis towards nutrients are important characteristics of Vibrio fischeri that play a crucial role in the development of its symbiotic relationship with its Hawaiian squid host Euprymna scolopes. The V. fischeri chemoreceptor A (VfcA) mediates chemotaxis toward amino acids. The periplasmic sensory domain of VfcA has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 3350 as a precipitating agent. The crystals belonged to space group P1, with unit-cell parameters a = 39.9, b = 57.0, c = 117.0 Å, α = 88.9, β = 80.5, γ = 89.7°. A complete X-ray diffraction data set has been collected to 1.8 Å resolution using cryocooling conditions and synchrotron radiation. PMID:27139830

  17. Structural features of interfacial tyrosine residue in ROBO1 fibronectin domain-antibody complex: Crystallographic, thermodynamic, and molecular dynamic analyses

    PubMed Central

    Nakayama, Taisuke; Mizohata, Eiichi; Yamashita, Takefumi; Nagatoishi, Satoru; Nakakido, Makoto; Iwanari, Hiroko; Mochizuki, Yasuhiro; Kado, Yuji; Yokota, Yuki; Satoh, Reiko; Tsumoto, Kouhei; Fujitani, Hideaki; Kodama, Tatsuhiko; Hamakubo, Takao; Inoue, Tsuyoshi

    2015-01-01

    ROBO1, fibronectin Type-III domain (Fn)-containing protein, is a novel immunotherapeutic target for hepatocellular carcinoma in humans. The crystal structure of the antigen-binding fragment (Fab) of B2212A, the monoclonal antibody against the third Fn domain (Fn3) of ROBO1, was determined in pursuit of antibody drug for hepatocellular carcinoma. This effort was conducted in the presence or absence of the antigen, with the chemical features being investigated by determining the affinity of the antibody using molecular dynamics (MD) and thermodynamics. The structural comparison of B2212A Fab between the complex and the free form revealed that the interfacial TyrL50 (superscripts L, H, and F stand for the residues in the light chain, heavy chain, and Fn3, respectively) played important roles in Fn3 recognition. That is, the aromatic ring of TyrL50 pivoted toward PheF68, forming a CH/π interaction and a new hydrogen bond with the carbonyl O atom of PheF68. MD simulations predicted that the TyrL50-PheF68 interaction almost entirely dominated Fab-Fn3 binding, and Ala-substitution of TyrL50 led to a reduced binding of the resultant complex. On the contrary, isothermal titration calorimetry experiments underscored that Ala-substitution of TyrL50 caused an increase of the binding enthalpy between B2212A and Fn3, but importantly, it induced an increase of the binding entropy, resulting in a suppression of loss in the Gibbs free energy in total. These results suggest that mutation analysis considering the binding entropy as well as the binding enthalpy will aid in the development of novel antibody drugs for hepatocellular carcinoma. PMID:25492858

  18. Preliminary crystallographic studies of a Schistosoma mansoni antigen (Sm21.7) dynein light-chain (DLC) domain

    PubMed Central

    Costa, M. A. F.; Rodrigues, F. T. G.; Chagas, B. C. A.; Rezende, C. M. F.; Goes, A. M.; Nagem, R. A. P.

    2014-01-01

    Schistosomiasis is an inflammatory chronic disease that represents a major health problem in tropical and subtropical countries. The drug of choice for treatment, praziquantel, is effective in killing adult worms but fails to kill immature forms and prevent reinfection. One prominent antigen candidate for an anti-schistosomiasis vaccine is the protein Sm21.7 (184 amino-acid residues) from Schistosoma mansoni, a tegumental protein capable of reducing the worm burden in a murine immunization model. In the present work, the Sm21.7 gene was cloned and expressed in Escherichia coli and the full-length protein was purified to homogeneity. Crystals of recombinant Sm21.7 suitable for X-ray diffraction were obtained using PEG monomethyl ether 2000 as a precipitant. X-ray diffraction images of a native crystal (at 2.05 Å resolution) and a quick-cryosoaked NaI derivative (at 1.95 Å resolution) were collected on the W01B-MX2 beamline at the Laboratório Nacional de Luz Síncrotron (LNLS, Brazilian Synchrotron Light Laboratory/MCT). Both crystals belonged to the hexagonal space group P6122, with similar unit-cell parameters a = b = 108.5, c = 55.8 Å. SIRAS-derived phases were used to generate the first electron-density map, from which a partial three-dimensional model of Sm21.7 (from Gln89 to Asn184) was automatically constructed. Anaysis of dissolved crystals by SDS–PAGE confirmed that the protein was cleaved in the crystallization drop and only the Sm21.7 C-terminal domain was crystallized. The structure of the Sm21.7 C-terminal domain will help in the localization of the epitopes responsible for its protective immune responses, constituting important progress in the development of an anti-schistosomiasis vaccine. PMID:24915098

  19. 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.

  20. TEM investigation of non-crystallographic displacements near antiphase domain boundaries in D0{sub 3} ordered Fe{sub 3}Al

    SciTech Connect

    Liu, W.; Nembach, E.; Gemperle, A.; Gemperlova, J.; Paidar, V.

    1998-11-02

    Antiphase domain boundaries (APBs) have been studied by means of transmission electron microscopy in a D0{sub 3} long-range ordered Fe{sub 3}Al single crystal. Two types of APB contrasts have been observed. The normal {pi}-type APB contrast was imaged with superlattice reflections. This type of contrast is caused by the basic displacement R{sub 0} = 1/4{l_angle}111{r_angle} or 1/2{l_angle}111{r_angle} across the APB. On the other hand, the anomalous {alpha}-type APB contrast was imaged with fundamental reflections. The latter contrast was weak, asymmetric in dark field and discontinuous along a close APB loop. It has been demonstrated that the anomalous {alpha}-type contrast is caused by a small non-crystallographic displacement r of atoms near the APBs. Detailed examination of the anomalous APB contrast indicated that the fault vector r depends on the basic displacement R{sub 0} as well as on the APB orientation. The main component of r was found to be perpendicular to the APBs with R{sub 0} = 1/4{l_angle}111{r_angle}. The addition displacement is discussed in terms of the mechanical and chemical relaxations of the APBs and with reference to the anomalous plastic behavior of Fe{sub 3}Al.

  1. Crystallization and preliminary X-ray crystallographic studies of the oligomeric death-domain complex between PIDD and RAIDD

    SciTech Connect

    Park, Hyun Ho; Wu, Hao

    2007-03-01

    The PIDD DD–RAIDD DD complex has been crystallized. The crystals are hexagonal and belong to space group P6{sub 5}, with unit-cell parameters a = b = 138.4, c = 207.6 Å. The crystals were obtained at room temperature; a native crystal diffracted to 3.2 Å resolution and a Hg-derivatized crystal to 4.0 Å resolution. Three large macromolecular complexes known as the death-inducing signaling complex (DISC), the apoptosome and the PIDDosome mediate caspase activation in apoptosis signaling pathways. The PIDDosome, which activates caspase-2, is composed of three protein components: PIDD, RAIDD and caspase-2. Within the PIDDosome, the interaction between PIDD and RAIDD is mediated by a homotypic interaction between their death domains (DDs). PIDD DD and RAIDD DD were overexpressed in Escherichia coli with engineered C-terminal His tags. The proteins were purified and mixed to allow complex formation. Gel-filtration and multi-angle light scattering (MALS) analyses showed that the complex is around 150 kDa in solution. The purified PIDD DD–RAIDD DD complex was crystallized at 293 K. X-ray diffraction data were collected to resolutions of 3.2 and 4.0 Å from a native and a Hg-derivative crystal, respectively. The crystals belong to space group P6{sub 5}, with unit-cell parameters a = b = 138.4, c = 207.6 Å.

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    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.

  3. 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.

  4. Temperature-driven nucleation of ferromagnetic domains in FeRh thin films

    NASA Astrophysics Data System (ADS)

    Baldasseroni, C.; Bordel, C.; Gray, A. X.; Kaiser, A. M.; Kronast, F.; Herrero-Albillos, J.; Schneider, C. M.; Fadley, C. S.; Hellman, F.

    2012-06-01

    The evolution of ferromagnetic (FM) domains across the temperature-driven antiferromagnetic (AF) to FM phase transition in uncapped and capped epitaxial FeRh thin films was studied by x-ray magnetic circular dichroism and photoemission electron microscopy. The coexistence of the AF and FM phases was evidenced across the broad transition and the different stages of nucleation, growth, and coalescence were directly imaged. The FM phase nucleates into single domain islands and the width of the transition of an individual nucleus is sharper than that of the transition in a macroscopic average.

  5. 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. PMID:27517790

  6. 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.

  7. Speed of field-driven domain walls in nanowires with large transverse magnetic anisotropy

    NASA Astrophysics Data System (ADS)

    Depassier, M. C.

    2015-07-01

    Recent analytical and numerical work on field-driven domain wall propagation in nanowires and thin films has shown that for large transverse anisotropy and sufficiently large applied fields the Walker profile becomes unstable before the breakdown field, giving way to a domain wall whose speed increases at a slower rate with the applied field. We perform an asymptotic expansion of the Landau-Lifshitz-Gilbert equation for large transverse magnetic anisotropy and show that the asymptotic dynamics reproduces this behavior. The appearance of a different regime in the asymptotic dynamics is due to a transition from a pushed to a pulled front of a reaction diffusion equation in which the speed of the domain wall increases with the square root of the applied field

  8. Externally driven transmission and collisions of domain walls in ferromagnetic wires

    SciTech Connect

    Janutka, Andrzej

    2011-05-15

    Analytical multidomain solutions to the dynamical (Landau-Lifshitz-Gilbert) equation of a one-dimensional ferromagnet including an external magnetic field and spin-polarized electric current are found using the Hirota bilinearization method. A standard approach to solve the Landau-Lifshitz equation (without the Gilbert term) is modified in order to treat the dissipative dynamics. I establish the relations between the spin interaction parameters (the constants of exchange, anisotropy, dissipation, external-field intensity, and electric-current intensity) and the domain-wall parameters (width and velocity) and compare them to the results of the Walker approximation and micromagnetic simulations. The domain-wall motion driven by a longitudinal external field is analyzed with especial relevance to the field-induced collision of two domain walls. I determine the result of such a collision (which is found to be an elastic one) on the domain-wall parameters below and above the Walker breakdown (in weak- and strong-field regimes). Single-domain-wall dynamics in the presence of an external transverse field is studied with relevance to the challenge of increasing the domain-wall velocity below the breakdown.

  9. Externally driven transmission and collisions of domain walls in ferromagnetic wires.

    PubMed

    Janutka, Andrzej

    2011-05-01

    Analytical multidomain solutions to the dynamical (Landau-Lifshitz-Gilbert) equation of a one-dimensional ferromagnet including an external magnetic field and spin-polarized electric current are found using the Hirota bilinearization method. A standard approach to solve the Landau-Lifshitz equation (without the Gilbert term) is modified in order to treat the dissipative dynamics. I establish the relations between the spin interaction parameters (the constants of exchange, anisotropy, dissipation, external-field intensity, and electric-current intensity) and the domain-wall parameters (width and velocity) and compare them to the results of the Walker approximation and micromagnetic simulations. The domain-wall motion driven by a longitudinal external field is analyzed with especial relevance to the field-induced collision of two domain walls. I determine the result of such a collision (which is found to be an elastic one) on the domain-wall parameters below and above the Walker breakdown (in weak- and strong-field regimes). Single-domain-wall dynamics in the presence of an external transverse field is studied with relevance to the challenge of increasing the domain-wall velocity below the breakdown. PMID:21728682

  10. 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

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

    PubMed

    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

  12. Field-driven domain wall motion in ferromagnetic nanowires with Dzyaloshinskii-Moriya interaction

    NASA Astrophysics Data System (ADS)

    Fengjun, Zhuo; Zhouzhou, Sun

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

  13. 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.

  14. 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

  15. Sustained chiral magnetic domain wall motion driven by spin-orbit torques under the tilted current

    NASA Astrophysics Data System (ADS)

    He, Peng-Bin; Yan, Han; Cai, Meng-Qiu; Li, Zai-Dong

    2016-06-01

    We theoretically investigate the steady magnetic domain wall driven by spin-orbit torques in the heavy-metal/magnet bilayers with perpendicular anisotropy. Based on collective coordinates method and stability analysis, we analyze the effects of tilted current and Dzyaloshinskii-Moriya interaction on the wall. We find that the wall acquires a sustained motion in the high-current regime by deviating the current from the wall track. Also, a persistent motion can be supported by the competition between spin-orbit torques and Dzyaloshinskii-Moriya interaction in transforming wall type. In the low-current regime, there exist a switching of wall chirality and a reversal of wall motion.

  16. Thermodynamic theory for thermally driven domain wall motion in magnetic nanostructures

    NASA Astrophysics Data System (ADS)

    Wang, Xiang Rong

    2015-03-01

    It is well-established now that a thermal gradient can be used to manipulate spins in a magnetic texture like skyrmions and domain walls (DWs). A thermal gradient can interact with spins through different channels. For example, a thermal gradient can affect spins through the thermoelectric effects by which spin polarized electric current is generated in a ferromagnetic metal. In turn, the thermally generated electric current can interact with magnetic texture via spin-transfer torque (STT). A thermal gradient can also generate magnons or spin waves that interact with magnetic textures. This effect should be important in a ferromagnetic insulator. Spin waves (or magnons) interact with magnetic domain walls (DWs) in a complicated way that a DW can propagate either along or against magnon flow, similar to its electron counterpart. Probably differ from its electron counterpart where one may attribute the ``wrong'' DW propagation direction to the Dzyaloshinskii-Moriya interaction and various types of torques due to spin-orbit interactions, it will be very difficult to understand why a DW can move along the magnon flow if the angular momentum transfer is the only mechanism behind the magnon driven DW motion. It will also be difficulty to explain why ``wrong'' DW propagation direction has not been observed in thermally driven DW motion in both simulations and experiments. Thus, there must be other interaction(s) between spin waves and magnetic textures. In terms of thermal gradient driven DW propagation along a nanowire, a DW always propagates to the hot region of a magnetic insulator wire. We theoretically illustrate why it is surely so from thermodynamic viewpoint. It is shown that DW entropy is always larger than that of a domain. Equivalently, the free energy difference of a DW and a domain decreases as the temperature increases. The larger DW entropy is related to the increase of magnon density of states at low energy originated from the gapless bound spin waves in

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

    NASA Astrophysics Data System (ADS)

    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.

  18. High efficiency motility of bacteria-driven liposome with raft domain binding method.

    PubMed

    Kojima, Masaru; Zhang, Zhenhai; Nakajima, Masahiro; Fukuda, Toshio

    2012-12-01

    From the viewpoint of energy efficiency and size reduction, many people have proposed the use of microbes as actuators. Some bacteria can swim in an aqueous environment. Therefore, flagellated chemotactic bacteria have been utilized as actuators for the propulsion of micro-objects by randomly attaching several bacteria to their surface. A liposome is a well-known component used for drug delivery that can contain biologically active compounds. In the present study, we used an antibody and biotin-streptavidin binding technique to combine bacteria and liposomes and create bacteria-driven liposomes. Furthermore, a novel raft domain binding technique was developed and used to limit the attachment of bacteria to small areas of the liposome surface. The effect of the number and configuration of the attached bacteria on propulsion speed was then studied experimentally. The motility of the raft domain liposome with bacteria was higher than that of the normal liposome with bacteria. This method could be used to create bacteria-driven liposomes with highly efficient motility and could lead to the development of microrobots as drug delivery systems. PMID:23053448

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

    NASA Astrophysics Data System (ADS)

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

    2015-06-01

    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.

  20. 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. PMID:26043719

  1. 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.

  2. Influence of nonlocal damping on the field-driven domain wall motion

    NASA Astrophysics Data System (ADS)

    Yuan, H. Y.; Yuan, Zhe; Xia, Ke; Wang, X. R.

    2016-08-01

    We derive a general expression of nonlocal damping in noncollinear magnetization due to the nonuniform spin current pumped by precessional magnetization and incorporate it into a generalized Thiele equation to study its effects on the dynamics of the transverse and vortex domain walls (DWs) in ferromagnetic nanowires. We demonstrate that the transverse component of nonlocal damping slows down the field-driven DW propagation and increases the Walker breakdown field, whereas it is neglected in many previous works in literature. The experimentally measured DW mobility variation with the damping tuned by doping with heavy rare-earth elements that had discrepancy from micromagnetic simulation is now well understood with the nonlocal damping. Our results suggest that the nonlocal damping should be properly included as a prerequisite for quantitative studies of current-induced torques in noncollinear magnetization.

  3. Fourier-domain study of drift turbulence driven sheared flow in a laboratory plasma

    SciTech Connect

    Xu, M.; Tynan, G. R.; Holland, C.; Muller, S. H.; Yan, Z.; Yu, J. H.

    2010-03-15

    Frequency-resolved nonlinear internal and kinetic energy transfer rates have been measured in the Controlled Shear Decorrelation Experiment (CSDX) linear plasma device using a recently developed technique [Xu et al., Phys. Plasmas 16, 042312 (2009)]. The results clearly show a net kinetic energy transfer into the zonal flow frequency region, consistent with previous time-domain observations of turbulence-driven shear flows [Tynan et al., Plasma Phys. Controlled Fusion 48, S51 (2006)]. The experimentally measured dispersion relation has been used to map the frequency-resolved energy transfer rates into the wave number domain, which shows that the shear flow drive comes from midrange (k{sub t}hetarho{sub S}>0.3) drift fluctuations, and the strongest flow drive comes from k{sub t}hetarho{sub S}approx =1 fluctuations. Linear growth rates have been inferred from a linearized Hasegawa-Wakatani model [Hasegawa et al., Phys. Fluids 22, 2122 (1979)], which indicates that the m=0 mode is linearly stable and the m=1-10 modes (corresponding to k{sub t}hetarho{sub S}>0.3) are linearly unstable for the n=1 and n=2 radial eigenmodes. This is consistent with our energy transfer measurements.

  4. 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

  5. Visualization and measurement of capillary-driven blood flow using spectral domain optical coherence tomography

    PubMed Central

    Cito, Salvatore; Ahn, Yeh-Chan; Pallares, Jordi; Duarte, Rodrigo Martinez; Chen, Zhongping; Madou, Marc; Katakis, Ioanis

    2013-01-01

    Capillary-driven flow (CD-flow) in microchannels plays an important role in many microfluidic devices. These devices, the most popular being those based in lateral flow, are becoming increasingly used in health care and diagnostic applications. CD-flow can passively pump biological fluids as blood, serum or plasma, in microchannels and it can enhance the wall mass transfer by exploiting the convective effects of the flow behind the meniscus. The flow behind the meniscus has not been experimentally identified up to now because of the lack of high-resolution, non-invasive, cross-sectional imaging means. In this study, spectral-domain Doppler optical coherence tomography is used to visualize and measure the flow behind the meniscus in CD-flows of water and blood. Microchannels of polydimethylsiloxane and glass with different cross-sections are considered. The predictions of the flow behind the meniscus of numerical simulations using the power-law model for non-Newtonian fluids are in reasonable agreement with the measurements using blood as working fluid. The extension of the Lucas–Washburn equation to non-Newtonian power-law fluids predicts well the velocity of the meniscus of the experiments using blood. PMID:23795150

  6. Bistability and domain formation in driven-dissipative photon cavity arrays

    NASA Astrophysics Data System (ADS)

    Foss-Feig, Michael; Wilson, Ryan; Gorshkov, Alexey

    2016-05-01

    Atomic, molecular, and optical systems afford exciting opportunities to engineer simple, driven-dissipative quantum systems. Even when these systems reach a steady state, they generally remain far from thermal equilibrium, creating many difficulties in describing them theoretically. We confront some of these difficulties in a simple context by studying coupled arrays of non-linear optical cavities. In the limit of strong photon-photon interactions, and making a mean-field approximation, this system exhibits collective bistability between bright and dark states, in close analogy to single-mode quantum optical systems studied decades ago. While this mean-field picture hints at the existence of a first-order phase transition in the true steady state, we are unaware of any general arguments for whether, and if so in what spatial dimensions, such a transition actually exists; the answer depends upon the detailed dynamics of domains in the presence of both quantum and dissipative fluctuations. We study the effects of such fluctuations at various levels of approximation, and develop some simple qualitative pictures of what is going on in the true quantum steady state.

  7. 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. PMID:23749266

  8. Purification, crystallization and preliminary X-ray crystallographic analysis of the C-terminal cytoplasmic domain of FlhB from Salmonella typhimurium

    PubMed Central

    Meshcheryakov, Vladimir A.; Samatey, Fadel A.

    2011-01-01

    FlhB is a key protein in the regulation of protein export by the bacterial flagellar secretion system. It is composed of two domains: an N-terminal transmembrane domain and a C-terminal cytoplasmic domain (FlhBc). FlhBc from Salmonella typhimurium has been successfully crystallized using the vapour-diffusion method. The crystals diffracted to 2.45 Å resolution and belonged to space group P42212, with unit-cell parameters a = b = 49.06, c = 142.94 Å. A selenomethionine-containing variant of FlhBc has also been crystallized in the same space group and was used for initial phase calculation by the multiwavelength anomalous dispersion (MAD) method. PMID:21795800

  9. 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

  10. 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

  11. 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.

  12. Crystallization and preliminary crystallographic analysis of the C-terminal domain of MamM, a magnetosome-associated protein from Magnetospirillum gryphiswaldense MSR-1

    PubMed Central

    Zeytuni, Natalie; Offer, Tal; Davidov, Geula; Zarivach, Raz

    2012-01-01

    MamM is a unique magnetosome-associated protein that shares substantial homology with cation diffusion facilitator (CDF) proteins, a group of heavy-metal-ion efflux transporters that participate in metal-ion homeostasis in all domains of life. Magnetotactic bacteria utilize CDF proteins in iron-oxide biomineralization and in magnetosome formation. Here, the crystallization and preliminary X-ray analysis of recombinant Magnetospirillum gryphiswaldense MamM is reported. The C-terminal domain of MamM was crystallized in the orthorhombic space group C2221, with unit-cell parameters a = 37.1, b = 94.0, c = 53.3 Å. X-ray diffraction data were collected to a resolution of 2.0 Å. PMID:22869124

  13. Cloning, expression, refolding, purification and preliminary crystallographic analysis of the sensory domain of the Campylobacter chemoreceptor for aspartate A (CcaA).

    PubMed

    Machuca, Mayra A; Liu, Yu C; Roujeinikova, Anna

    2015-01-01

    In Campylobacter jejuni, chemotaxis and motility have been identified as important virulence factors that are required for host colonization and invasion. Chemotactic recognition of extracellular signals is mediated by the periplasmic sensory domains of its transducer-like proteins (Tlps). In this study, the sensory domain of the C. jejuni chemoreceptor for aspartate A (CcaA) has been expressed in Escherichia coli and purified from inclusion bodies. The urea-denatured protein was refolded and then crystallized by the hanging-drop vapour-diffusion method using PEG 3350 as a precipitating agent. A complete data set has been collected to 1.4 Å resolution using cryocooling conditions and synchrotron radiation. The crystals belonged to space group P1, with unit-cell parameters a=39.3, b=43.3, c=50.9 Å, α=92.5, β=111.4, γ=114.7°. PMID:25615981

  14. 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.

  15. Cloning, expression, purification and preliminary crystallographic analysis of the RNase HI domain of the Mycobacterium tuberculosis protein Rv2228c as a maltose-binding protein fusion

    PubMed Central

    Watkins, Harriet A.; Baker, Edward N.

    2008-01-01

    The predicted ribonuclease (RNase) HI domain of the open reading frame Rv2228c from Mycobacterium tuberculosis has been cloned as a hexahistidine fusion and a maltose-binding protein (MBP) fusion. Expression was only observed for the MBP-fusion protein, which was purified using amylose affinity chromatography and gel filtration. The RNase HI domain could be cleaved from the MBP-fusion protein by factor Xa digestion, but was very unstable. In contrast, the fusion protein was stable, could be obtained in high yield and gave crystals which diffracted to 2.25 Å resolution. The crystals belong to space group P21 and have unit-cell parameters a = 73.63, b = 101.38, c = 76.09 Å, β = 109.0°. Two fusion-protein molecules of 57 417 Da were present in each asymmetric unit. PMID:18678948

  16. 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.

  17. 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.

  18. 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.

  19. Expression, purification, crystallization and preliminary crystallographic analysis of a stand-alone RAM domain with hydrolytic activity from the hyperthermophile Pyrococcus furiosus

    SciTech Connect

    Agapay, Ramelito C.; Savvides, Savvas N.; Van Driessche, Gonzalez; Devreese, Bart; Van Beeumen, Jozef; Jongejan, Jaap A. Hagen, Wilfred R.

    2005-10-01

    A P. furiosus stand-alone RAM domain with hydrolytic activity has been cloned and expressed in E. coli. The purified protein was crystallized alone and with EPNP and PMSF, producing crystals that yield diffraction data to resolutions of 2.8, 2.2 and 2.8 Å, respectively. The RAM domain is one of several ligand-binding modules present in prokaryotes that are presumed to regulate the transcription of specific genes. To date, no hydrolytic activity has been reported for such modules. Curiously, a stand-alone RAM domain in Pyrococcus furiosus was isolated during a screen for hydrolytic activity against chromogenic esters. The gene encoding this protein was cloned and expressed in Escherichia coli and crystallized after a single purification step. X-ray diffraction data from the crystals were obtained to a resolution of 2.8 Å using a conventional X-ray source. The cocrystallization of the recombinant protein with 1,2-epoxy-3-(4-nitrophenoxy)propane (EPNP) and phenylmethylsulfonyl fluoride (PMSF) produced crystals that yielded data to 2.2 and 2.8 Å, respectively, using synchrotron radiation. Both the untreated and EPNP-treated crystals crystallize isomorphously in space group C2 and contain three dimers in the asymmetric unit. The PMSF-treated crystals also belong to this space group and have almost identical packing density, but show dramatically different unit-cell parameters.

  20. 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°.

  1. 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.

  2. 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.

  3. 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}.

  4. Direct Imaging of Thermally Driven Domain Wall Motion in Magnetic Insulators

    NASA Astrophysics Data System (ADS)

    Jiang, Wanjun; Upadhyaya, Pramey; Fan, Yabin; Zhao, Jing; Wang, Minsheng; Chang, Li-Te; Lang, Murong; Wong, Kin L.; Lewis, Mark; Lin, Yen-Ting; Tang, Jianshi; Cherepov, Sergiy; Zhou, Xuezhi; Tserkovnyak, Yaroslav; Schwartz, Robert N.; Wang, Kang L.

    2013-04-01

    Thermally induced domain wall motion in a magnetic insulator was observed using spatiotemporally resolved polar magneto-optical Kerr effect microscopy. The following results were found: (i) the domain wall moves towards hot regime; (ii) a threshold temperature gradient (5K/mm), i.e., a minimal temperature gradient required to induce domain wall motion; (iii) a finite domain wall velocity outside of the region with a temperature gradient, slowly decreasing as a function of distance, which is interpreted to result from the penetration of a magnonic current into the constant temperature region; and (iv) a linear dependence of the average domain wall velocity on temperature gradient, beyond a threshold thermal bias. Our observations can be qualitatively explained using a magnonic spin transfer torque mechanism, which suggests the utility of magnonic spin transfer torque for controlling magnetization dynamics.

  5. 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.

  6. Curvature and torsion effects in spin-current driven domain wall motion

    NASA Astrophysics Data System (ADS)

    Yershov, Kostiantyn V.; Kravchuk, Volodymyr P.; Sheka, Denis D.; Gaididei, Yuri

    2016-03-01

    The domain wall motion along a helix-shaped nanowire is studied for the case of spin-current driving via the Zhang-Li mechanism. The analysis is based on the collective variable approach. Two effects are ascertained: (i) the curvature results in the appearance of the Walker limit for a uniaxial wire, and (ii) the torsion results in effective shift of the nonadiabatic spin torque parameter β . The latter effect changes considerably the domain wall velocity and can result in negative domain wall mobility. This effect can be also used for an experimental determination of the nonadiabatic parameter β and damping coefficient α .

  7. 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.

  8. Time-resolved observation of fast domain-walls driven by vertical spin currents in short tracks

    NASA Astrophysics Data System (ADS)

    Sampaio, Joao; Lequeux, Steven; Metaxas, Peter J.; Chanthbouala, Andre; Matsumoto, Rie; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Maehara, Hiroki; Tsunekawa, Koji; Cros, Vincent; Grollier, Julie

    2013-12-01

    We present time-resolved measurements of the displacement of magnetic domain-walls (DWs) driven by vertical spin-polarized currents in track-shaped magnetic tunnel junctions. In these structures, we observe very high DW velocities (600 m/s) at current densities below 107 A/cm2. We show that the efficient spin-transfer torque combined with a short propagation distance allows avoiding the Walker breakdown process and achieving deterministic, reversible, and fast (≈1 ns) DW-mediated switching of magnetic tunnel junction elements, which is of great interest for the implementation of fast DW-based spintronic devices.

  9. Time-resolved observation of fast domain-walls driven by vertical spin currents in short tracks

    SciTech Connect

    Sampaio, Joao; Lequeux, Steven; Chanthbouala, Andre; Cros, Vincent; Grollier, Julie; Matsumoto, Rie; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Maehara, Hiroki; Tsunekawa, Koji

    2013-12-09

    We present time-resolved measurements of the displacement of magnetic domain-walls (DWs) driven by vertical spin-polarized currents in track-shaped magnetic tunnel junctions. In these structures, we observe very high DW velocities (600 m/s) at current densities below 10{sup 7} A/cm{sup 2}. We show that the efficient spin-transfer torque combined with a short propagation distance allows avoiding the Walker breakdown process and achieving deterministic, reversible, and fast (≈1 ns) DW-mediated switching of magnetic tunnel junction elements, which is of great interest for the implementation of fast DW-based spintronic devices.

  10. Externally driven collisions of domain walls in bistable systems near criticality

    SciTech Connect

    Janutka, Andrzej

    2011-05-15

    Multidomain solutions to the time-dependent Ginzburg-Landau equation in the presence of an external field are analyzed using the Hirota bilinearization method. Domain-wall collisions are studied in detail considering different regimes of the critical parameter. I show the dynamics of the Ising and Bloch domain walls of the Ginzburg-Landau equation in the bistable regime to be similar to that of the Landau-Lifshitz domain walls. Domain-wall reflections lead to the appearance of bubble and pattern structures. Above the Bloch-Ising transition point, spatial structures are determined by the collisions of fronts propagating into an unstable state. Mutual annihilation of such fronts is described.

  11. 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.

  12. 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. PMID:27575075

  13. Importance of a flexible hinge near the motor domain in kinesin-driven motility.

    PubMed Central

    Grummt, M; Woehlke, G; Henningsen, U; Fuchs, S; Schleicher, M; Schliwa, M

    1998-01-01

    Conventional kinesin is a molecular motor consisting of an N-terminal catalytic motor domain, an extended stalk and a small globular C-terminus. Whereas the structure and function of the catalytic motor domain has been investigated, little is known about the function of domains outside the globular head. A short coiled-coil region adjacent to the motor domain, termed the neck, is known to be important for dimerization and may be required for kinesin processivity. We now provide evidence that a helix-disrupting hinge region (hinge 1) that separates the neck from the first extended coiled-coil of the stalk plays an essential role in basic motor activity. A fast fungal kinesin from Syncephalastrum racemosum was used for these studies. Deletion, substitution by a coiled-coil and truncation of the hinge 1 region all reduce motor speed and uncouple ATP turnover from gliding velocity. Insertion of hinge 1 regions from two conventional kinesins, Nkin and DmKHC, fully restores motor activity, whereas insertion of putative flexible linkers of other proteins does not, suggesting that hinge 1 regions of conventional kinesins can functionally replace each other. We suggest that this region is essential for kinesin movement in its promotion of chemo-mechanical coupling of the two heads and therefore the functional motor domain should be redefined to include not only the catalytic head but also the adjacent neck and hinge 1 domains. PMID:9755154

  14. 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

  15. 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.

  16. 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. PMID:18654469

  17. Field-driven sense elements for chirality-dependent domain wall detection and storage

    SciTech Connect

    Bowden, S. R.; Unguris, J.

    2013-12-14

    A method for locally sensing and storing data of transverse domain wall chirality in planar nanowire logic and memory systems is presented. Patterned elements, in close proximity to the nanowires, respond to the asymmetry in the stray field from the domain wall to produce a chirality-dependent response. When a bias field is applied, a stray field-assisted reversal of the element magnetization results in a reversed remanent state, measurable by scanning electron microscopy with polarization analysis (SEMPA). The elements are designed as triangles with tips pointing toward the nanowire, allowing the shape anisotropy to be dominated by the base but having a portion with lower volume and lower energy barrier closest to the domain wall. Micromagnetic modeling assists in the design of the nanowire-triangle systems and experiments using SEMPA confirm the importance of aspect ratio and spacing given a constant bias field magnitude.

  18. 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.

  19. 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.

  20. 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

  1. 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…

  2. Crystallization and preliminary X-ray crystallographic analysis of the complex between the N-D1 domain of VCP from Homo sapiens and the N domain of OTU1 from Saccharomyces cerevisiae

    PubMed Central

    Kim, Su Jin; Kim, Eunice EunKyeong

    2014-01-01

    VCP (valosin-containing protein; also known as p97) plays important roles in many biological processes including the ERAD (endoplasmic reticulum-associated degradation) pathway and its function is governed by binding partners. OTU1 (ovarian tumour domain-containing protein 1) is a recently discovered deubiquitinating enzyme that interacts directly with VCP in the ERAD pathway. In order to understand the interactions between the two proteins, the N-D1 domain of VCP and the UBXL domain of OTU1 were cloned, overexpressed, purified and crystallized. The crystals of the complex diffracted to 3.25 Å resolution and belonged to space group P21, with unit-cell parameters a = 165.45, b = 176.73, c = 165.59 Å, β = 120.095°. There are two molecules of the complex in the asymmetric unit with a Matthews coefficient of 2.62 Å3 Da−1 and a solvent content of 53%. PMID:25084388

  3. 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.

  4. 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. PMID:26613293

  5. 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…

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

    PubMed Central

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

    2016-01-01

    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. PMID:27079528

  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. PMID:27079528

  8. Formation of semi-dilute adhesion domains driven by weak elasticity-mediated interactions.

    PubMed

    Dharan, Nadiv; Farago, Oded

    2016-08-21

    Cell-cell adhesion is established by specific binding of receptor and ligand proteins anchored in the cell membranes. The adhesion bonds attract each other and often aggregate into large clusters that are central to many biological processes. One possible origin of attractive interactions between adhesion bonds is the elastic response of the membranes to their deformation by the bonds. Here, we analyze these elasticity-mediated interactions using a novel mean-field approach. Our analysis of systems at different densities of bonds, ϕ, reveals that the phase diagram, i.e., the binodal and spinodal lines, exhibit a nearly universal behavior when the temperature T is plotted against the scaled density x = ϕξ(2), where ξ is the linear size of the membrane's region affected by the presence of a single isolated bond. The critical point (ϕc , Tc) is located at very low densities, and slightly below Tc we identify phase coexistence between two low-density phases. Dense adhesion domains are observed only when the height by which the bonds deform the membranes, h0, is much larger than their thermal roughness, Δ, which occurs at very low temperatures T≪Tc. We, thus, conclude that the elasticity-mediated interactions are weak and cannot be regarded as responsible for the formation of dense adhesion domains. The weakness of the elasticity-mediated effect and its relevance to dilute systems only can be attributed to the fact that the membrane's elastic energy saturates in the semi-dilute regime, when the typical spacing between the bonds r≳ξ, i.e., for x≲ 1. Therefore, at higher densities, only the mixing entropy of the bonds (which always favors uniform distributions) is thermodynamically relevant. We discuss the implications of our results for the question of immunological synapse formation, and demonstrate that the elasticity-mediated interactions may be involved in the aggregation of these semi-dilute membrane domains. PMID:27426284

  9. 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.

  10. Chirped pulse reflectivity and frequency domain interferometry in laser driven shock experiments.

    PubMed

    Benuzzi-Mounaix, A; Koenig, M; Boudenne, J M; Hall, T A; Batani, D; Scianitti, F; Masini, A; Di Santo, D

    1999-09-01

    We show the simultaneous applicability of the frequency domain interferometry and the chirped pulse reflectometry techniques to measure shock parameters. The experiment has been realized with the laser at the Laboratoire pour l'Utilisation des Lasers Intenses (LULI) with a 550-ps pulse duration and an intensity on target approximately 5 x 10(13) W/cm(2) to produce a shock in a layered aluminum-fused silica target. A second low energy, partially compressed chirped probe beam was used to irradiate the target rear side and the reflected light has been analyzed with a spectrometer, achieving a temporal resolution of the order of 1 ps. PMID:11970183

  11. Chirped pulse reflectivity and frequency domain interferometry in laser driven shock experiments

    NASA Astrophysics Data System (ADS)

    Benuzzi-Mounaix, A.; Koenig, M.; Boudenne, J. M.; Hall, T. A.; Batani, D.; Scianitti, F.; Masini, A.; di Santo, D.

    1999-09-01

    We show the simultaneous applicability of the frequency domain interferometry and the chirped pulse reflectometry techniques to measure shock parameters. The experiment has been realized with the laser at the Laboratoire pour l'Utilisation des Lasers Intenses (LULI) with a 550-ps pulse duration and an intensity on target ~5×1013 W/cm2 to produce a shock in a layered aluminum-fused silica target. A second low energy, partially compressed chirped probe beam was used to irradiate the target rear side and the reflected light has been analyzed with a spectrometer, achieving a temporal resolution of the order of 1 ps.

  12. 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

  13. 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.

  14. Gating of the CFTR Cl- channel by ATP-driven nucleotide-binding domain dimerisation.

    PubMed

    Hwang, Tzyh-Chang; Sheppard, David N

    2009-05-15

    The cystic fibrosis transmembrane conductance regulator (CFTR) plays a fundamental role in fluid and electrolyte transport across epithelial tissues. Based on its structure, function and regulation, CFTR is an ATP-binding cassette (ABC) transporter. These transporters are assembled from two membrane-spanning domains (MSDs) and two nucleotide-binding domains (NBDs). In the vast majority of ABC transporters, the NBDs form a common engine that utilises the energy of ATP hydrolysis to pump a wide spectrum of substrates through diverse transmembrane pathways formed by the MSDs. By contrast, in CFTR the MSDs form a pathway for passive anion flow that is gated by cycles of ATP binding and hydrolysis by the NBDs. Here, we consider how the interaction of ATP with two ATP-binding sites, formed by the NBDs, powers conformational changes in CFTR structure to gate the channel pore. We explore how conserved sequences from both NBDs form ATP-binding sites at the interface of an NBD dimer and highlight the distinct roles that each binding site plays during the gating cycle. Knowledge of how ATP gates the CFTR Cl- channel is critical for understanding CFTR's physiological role, its malfunction in disease and the mechanism of action of small molecules that modulate CFTR channel gating. PMID:19332488

  15. Gating of the CFTR Cl− channel by ATP-driven nucleotide-binding domain dimerisation

    PubMed Central

    Hwang, Tzyh-Chang; Sheppard, David N

    2009-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) plays a fundamental role in fluid and electrolyte transport across epithelial tissues. Based on its structure, function and regulation, CFTR is an ATP-binding cassette (ABC) transporter. These transporters are assembled from two membrane-spanning domains (MSDs) and two nucleotide-binding domains (NBDs). In the vast majority of ABC transporters, the NBDs form a common engine that utilises the energy of ATP hydrolysis to pump a wide spectrum of substrates through diverse transmembrane pathways formed by the MSDs. By contrast, in CFTR the MSDs form a pathway for passive anion flow that is gated by cycles of ATP binding and hydrolysis by the NBDs. Here, we consider how the interaction of ATP with two ATP-binding sites, formed by the NBDs, powers conformational changes in CFTR structure to gate the channel pore. We explore how conserved sequences from both NBDs form ATP-binding sites at the interface of an NBD dimer and highlight the distinct roles that each binding site plays during the gating cycle. Knowledge of how ATP gates the CFTR Cl− channel is critical for understanding CFTR's physiological role, its malfunction in disease and the mechanism of action of small molecules that modulate CFTR channel gating. PMID:19332488

  16. 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

  17. Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling

    PubMed Central

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

    2013-01-01

    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. PMID:23442862

  18. 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. PMID:25906195

  19. 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.

  20. 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

  1. Crystallization and preliminary X-ray crystallographic studies of an oligomeric species of a refolded C39 peptidase-like domain of the Escherichia coli ABC transporter haemolysin B

    PubMed Central

    Schwarz, Christian K. W.; Tschapek, Britta; Jumpertz, Thorsten; Jenewein, Stefan; Lecher, Justin; Willbold, Dieter; Panjikar, Santosh; Holland, I. Barry; Smits, Sander H. J.; Schmitt, Lutz

    2011-01-01

    The ABC transporter haemolysin B (HlyB) from Escherichia coli is part of a type I secretion system that translocates a 110 kDa toxin in one step across both membranes of this Gram-negative bacterium in an ATP-dependent manner. Sequence analysis indicates that HlyB contains a C39 peptidase-like domain at its N-terminus. C39 domains are thiol-dependent peptidases that cleave their substrates after a GG motif. Interestingly, the catalytically invariant cysteine is replaced by a tyrosine in the C39-like domain of HlyB. Here, the overexpression, purification and crystallization of the isolated C39-like domain are described as a first step towards obtaining structural insights into this domain and eventually answering the question concerning the function of a degenerated C39 domain in the ABC transporter HlyB. PMID:21543878

  2. 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.

  3. Dynamic coupling-decoupling crossover in the current-driven vortex-state in Tl[sub 2]Ba[sub 2]CaCu[sub 2]O[sub 8]studied using terahertz time-domain spectroscopy

    SciTech Connect

    Thorsmølle, V. K.; Averitt, R. D.; Aranson, I. S.; Maley, M. P.; Bulaevskiĭ, L. N.; Taylor, Antoinette J.,

    2004-01-01

    Employing terahertz time-domain spectroscopy in transmission, they have measured the Josephson plasma resonance in Tl{sub 2}Ba{sub 2}CaCu{sub 2}O{sub 8} high-T{sub c} thin films, and studied the current-driven coupling-decoupling crossover in the driven vortex lattice.

  4. 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.

  5. Domain-wall motion in ferromagnetic nanowires driven by arbitrary time-dependent fields: an exact result.

    PubMed

    Goussev, Arseni; Robbins, J M; Slastikov, Valeriy

    2010-04-01

    We address the dynamics of magnetic domain walls in ferromagnetic nanowires under the influence of external time-dependent magnetic fields. We report a new exact spatiotemporal solution of the Landau-Lifshitz-Gilbert equation for the case of soft ferromagnetic wires and nanostructures with uniaxial anisotropy. The solution holds for applied fields with arbitrary strength and time dependence. We further extend this solution to applied fields slowly varying in space and to multiple domain walls. PMID:20481956

  6. 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.

  7. Enhancement of spin Hall effect induced torques for current-driven magnetic domain wall motion: Inner interface effect

    NASA Astrophysics Data System (ADS)

    Bang, Do; Yu, Jiawei; Qiu, Xuepeng; Wang, Yi; Awano, Hiroyuki; Manchon, Aurelien; Yang, Hyunsoo

    2016-05-01

    We investigate the current-induced domain wall motion in perpendicular magnetized Tb/Co wires with structure inversion asymmetry and different layered structures. We find that the critical current density to drive domain wall motion strongly depends on the layered structure. The lowest critical current density ˜15 MA /c m2 and the highest slope of domain wall velocity curve are obtained for the wire having thin Co sublayers and more inner Tb/Co interfaces, while the largest critical current density ˜26 MA /c m2 required to drive domain walls is observed in the Tb-Co alloy magnetic wire. It is found that the Co/Tb interface contributes negligibly to Dzyaloshinskii-Moriya interaction, while the effective spin-orbit torque strongly depends on the number of Tb/Co inner interfaces (n ). An enhancement of the antidamping torques by extrinsic spin Hall effect due to Tb rare-earth impurity-induced skew scattering is suggested to explain the high efficiency of current-induced domain wall motion.

  8. Size-Dependent Multi- to Single Domain Transition of UV Laser-Driven Ferromagnetic Co Nanoparticles Under External Magnetic Field.

    PubMed

    Lee, Jun Seok; Lee, Ja Bin; Yang, Jung Yup; Hong, Jin Pyo

    2015-06-01

    The magnetic domain of cobalt (Co) nanoparticles (NPs) was studied as a function of particle size. Various single crystalline and uniform Co NPs were prepared using a novel UV laser irradiation technique on ultra thin Co films under an external applied magnetic field. Structural and magnetic characteristics were analyzed with transmission electron microscopy and superconducting quantum interference devices. The experimental observations indicate that during Co NP growth, externally applied magnetic fields and size-dependent NP surface effects strongly facilitate multi-to-single domain transition at a critical diameter of about 10 nm, an extremely small NP size that is suitable for higher density storage applications. PMID:26369084

  9. Crystallographic and Spectroscopic Symmetry Notations.

    ERIC Educational Resources Information Center

    Sharma, B. D.

    1982-01-01

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

  10. Detection of a static eccentricity fault in a closed loop driven induction motor by using the angular domain order tracking analysis method

    NASA Astrophysics Data System (ADS)

    Akar, Mehmet

    2013-01-01

    In this study, a new method was presented for the detection of a static eccentricity fault in a closed loop operating induction motor driven by inverter. Contrary to the motors supplied by the line, if the speed and load, and therefore the amplitude and frequency, of the current constantly change then this also causes a continuous change in the location of fault harmonics in the frequency spectrum. Angular Domain Order Tracking analysis (AD-OT) is one of the most frequently used fault diagnosis methods in the monitoring of rotating machines and the analysis of dynamic vibration signals. In the presented experimental study, motor phase current and rotor speed were monitored at various speeds and load levels with a healthy and static eccentricity fault in the closed loop driven induction motor with vector control. The AD-OT method was applied to the motor current and the results were compared with the traditional FFT and Fourier Transform based Order Tracking (FT-OT) methods. The experimental results demonstrate that AD-OT method is more efficient than the FFT and FT-OT methods for fault diagnosis, especially while the motor is operating run-up and run-down. Also the AD-OT does not incur any additional cost for the user because in inverter driven systems, current and speed sensor coexist in the system. The main innovative parts of this study are that AD-OT method was implemented on the motor current signal for the first time.

  11. High speed domain wall motion in MgO-based magnetic tunnel junctions driven by perpendicular current injection

    NASA Astrophysics Data System (ADS)

    Metaxas, P. J.; Chanthbouala, A.; Matsumoto, R.; Cros, V.; Anane, A.; Grollier, J.; Fert, A.; Zvezdin, K. A.; Fukushima, A.; Yuasa, S.

    2012-02-01

    The ability to efficiently drive fast domain wall (DW) motion will pave the way for revolutionary new electronic devices ranging from DW-MRAMs to spintronic memristors. The majority of domain wall devices use a lateral, current-in-plane configuration in which critical current densities for domain wall motion remain quite high, typically being on the order of 100 MA/cm^2 with velocities generally limited to about 100 m/s. In this contribution we show that critical current densities can be decreased by up to two orders of magnitude using the current-perpendicular-to-plane geometry. Indeed, we demonstrate that a DW can be propagated back and forth along the free layer of a MgO-based magnetic tunnel junction (MTJ) in the absence of an external magnetic field using current densities that are on the order of 5 MA/cm^2. More notably however, we obtain high domain wall velocities for these low current densities: the MTJ's large resistance variations allow us to carry out time-resolved measurements of the wall motion from which we evidence DW velocities exceeding 500m/s.

  12. 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.

  13. 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.

  14. 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

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

    PubMed

    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

  16. 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. PMID:24824036

  17. 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

  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. 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

  20. 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.

  1. 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.

  2. Triboluminescence dominated by crystallographic orientation.

    PubMed

    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

  3. 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.

  4. 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

    2016-04-01

    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. PMID:27058787

  5. 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

  6. 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)

  7. 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.

  8. Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B.

    PubMed

    Rønningen, Torunn; Shah, Akshay; Oldenburg, Anja R; Vekterud, Kristin; Delbarre, Erwan; Moskaug, Jan Øivind; Collas, Philippe

    2015-12-01

    Dynamic interactions of nuclear lamins with chromatin through lamin-associated domains (LADs) contribute to spatial arrangement of the genome. Here, we provide evidence for prepatterning of differentiation-driven formation of lamin A/C LADs by domains of histone H2B modified on serine 112 by the nutrient sensor O-linked N-acetylglucosamine (H2BS112GlcNAc), which we term GADs. We demonstrate a two-step process of lamin A/C LAD formation during in vitro adipogenesis, involving spreading of lamin A/C-chromatin interactions in the transition from progenitor cell proliferation to cell-cycle arrest, and genome-scale redistribution of these interactions through a process of LAD exchange within hours of adipogenic induction. Lamin A/C LADs are found both in active and repressive chromatin contexts that can be influenced by cell differentiation status. De novo formation of adipogenic lamin A/C LADs occurs nonrandomly on GADs, which consist of megabase-size intergenic and repressive chromatin domains. Accordingly, whereas predifferentiation lamin A/C LADs are gene-rich, post-differentiation LADs harbor repressive features reminiscent of lamin B1 LADs. Release of lamin A/C from genes directly involved in glycolysis concurs with their transcriptional up-regulation after adipogenic induction, and with downstream elevations in H2BS112GlcNAc levels and O-GlcNAc cycling. Our results unveil an epigenetic prepatterning of adipogenic LADs by GADs, suggesting a coupling of developmentally regulated lamin A/C-genome interactions to a metabolically sensitive chromatin modification. PMID:26359231

  9. GTPase domain driven dimerization of SEPT7 is dispensable for the critical role of septins in fibroblast cytokinesis

    PubMed Central

    Abbey, Megha; Hakim, Cosima; Anand, Roopsee; Lafera, Juri; Schambach, Axel; Kispert, Andreas; Taft, Manuel H.; Kaever, Volkhard; Kotlyarov, Alexey; Gaestel, Matthias; Menon, Manoj B.

    2016-01-01

    Septin 7 (SEPT7) has been described to be essential for successful completion of cytokinesis in mouse fibroblasts, and Sept7-deficiency in fibroblasts constitutively results in multinucleated cells which stop proliferation. Using Sept7flox/floxfibroblasts we generated a cellular system, where the cytokinetic defects of Cre-mediated deletion of the Sept7 gene can be rescued by ectopically expressed doxycycline-inducible wild type SEPT7. Using this system, we analyzed the ability of SEPT7-mutants with alterations in their GTPase domain-dependent dimerization to prevent multinucleation and rescue proliferation. Although biochemical analysis of the mutants demonstrates differences in homo- and/or hetero-polymerization, in GTP-binding and/or GTPase activities, all analyzed mutants were able to rescue the cytokinesis phenotype of Sept7flox/floxfibroblasts associated with Cre-mediated deletion of endogenous Sept7. These findings indicate that the ability of septins to assemble into well-defined SEPT7-dimerization dependent native filaments is dispensable for cytokinesis in fibroblasts and opens the way to search for other mechanisms of the involvement of SEPT7 in cytokinesis. PMID:26818767

  10. 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

  11. 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

  12. 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

    2016-01-01

    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

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

    NASA Astrophysics Data System (ADS)

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

    2016-03-01

    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.

  14. Crystallographic Control in Ilmenite Reduction

    NASA Astrophysics Data System (ADS)

    de Vries, M. L.; Grey, I. E.; Fitz Gerald, J. D.

    2007-04-01

    Scanning electron microscopy and transmission electron microscopy techniques were used to characterize the products from hydrogen reduction of polygranular synthetic ilmenite discs at temperatures in the range 823 to 1173 K and pressures in the range 1 to 13 atm. Reduction commences at grain boundaries and cracks and advances progressively to grain interiors. Within individual grains, the morphology of the reduction products was found to be crystallographically controlled. Near parallel bands of metallic iron (Fe m ) form within each grain, aligned with the basal plane of ilmenite (il) (0001) il . The separation between bands is of the order of 1 μm and is relatively constant with change of pressure and temperature. In the interband region, conversion of ilmenite to rutile occurs preferentially parallel to \\{ 11ifmmodeexpandafterbarelseexpandafter\\=fi{2}0\\} _{{il}} ilmenite planes, generating platelets of rutile that grow normal to the Fe m bands. The intergrain duplex morphology of the reduction products closely resembles cellular precipitation in alloys. At reduction temperatures above ˜1000 K, the interband region comprises dense, nonporous oriented intergrowths of rutile platelets and residual ilmenite, whereas below ˜900 K, the interband region contains a fine, filamentary network of pores. In the intermediate temperature regime, a change from dense to porous interband region occurs with increasing pressure. The observations have been interpreted in terms of the relative rates of interfacial chemical reaction and solid-state diffusion, with the latter having a controlling influence at lower temperatures or higher pressures.

  15. 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.

  16. 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.

  17. 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

  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. 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…

  20. 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.

  1. 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

  2. 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.

  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. PMID:16552141

  4. 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

  5. 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. PMID:26015445

  6. Metrics for comparison of crystallographic maps

    DOE PAGESBeta

    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,more » such as regions of high density, are of interest.« less

  7. Predicting domain-domain interactions using a parsimony approach

    PubMed Central

    Guimarães, Katia S; Jothi, Raja; Zotenko, Elena; Przytycka, Teresa M

    2006-01-01

    We propose a novel approach to predict domain-domain interactions from a protein-protein interaction network. In our method we apply a parsimony-driven explanation of the network, where the domain interactions are inferred using linear programming optimization, and false positives in the protein network are handled by a probabilistic construction. This method outperforms previous approaches by a considerable margin. The results indicate that the parsimony principle provides a correct approach for detecting domain-domain contacts. PMID:17094802

  8. 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. PMID:27437111

  9. Quantum crystallographic charge density of urea

    DOE PAGESBeta

    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 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

  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 Central

    Wall, Michael E.

    2016-01-01

    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. PMID:27437111

  12. 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. PMID:26764656

  13. Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignments.

    PubMed

    Ortiz, A R; Kolinski, A; Skolnick, J

    1998-02-15

    Using a recently developed protein folding algorithm, a prediction of the tertiary structure of the KIX domain of the CREB binding protein is described. The method incorporates predicted secondary and tertiary restraints derived from multiple sequence alignments in a reduced protein model whose conformational space is explored by Monte Carlo dynamics. Secondary structure restraints are provided by the PHD secondary structure prediction algorithm that was modified for the presence of predicted U-turns, i.e., regions where the chain reverses global direction. Tertiary restraints are obtained via a two-step process: First, seed side-chain contacts are identified from a correlated mutation analysis, and then, a threading-based algorithm expands the number of these seed contacts. Blind predictions indicate that the KIX domain is a putative three-helix bundle, although the chirality of the bundle could not be uniquely determined. The expected root-mean-square deviation for the correct chirality of the KIX domain is between 5.0 and 6.2 A. This is to be compared with the estimate of 12.9 A that would be expected by a random prediction, using the model of F. Cohen and M. Sternberg (J. Mol. Biol. 138:321-333, 1980). PMID:9517544

  14. 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.

  15. Bilbao Crystallographic Server. II. Representations of crystallographic point groups and space groups.

    PubMed

    Aroyo, Mois I; Kirov, Asen; Capillas, Cesar; Perez-Mato, J M; Wondratschek, Hans

    2006-03-01

    The Bilbao Crystallographic Server is a web site with crystallographic programs and databases freely available on-line (http://www.cryst.ehu.es). The server gives access to general information related to crystallographic symmetry groups (generators, general and special positions, maximal subgroups, Brillouin zones etc.). Apart from the simple tools for retrieving the stored data, there are programs for the analysis of group-subgroup relations between space groups (subgroups and supergroups, Wyckoff-position splitting schemes etc.). There are also software packages studying specific problems of solid-state physics, structural chemistry and crystallography. This article reports on the programs treating representations of point and space groups. There are tools for the construction of irreducible representations, for the study of the correlations between representations of group-subgroup pairs of space groups and for the decompositions of Kronecker products of representations. PMID:16489249

  16. Anionic Phospholipid Interactions of the Prion Protein N Terminus Are Minimally Perturbing and Not Driven Solely by the Octapeptide Repeat Domain*

    PubMed Central

    Boland, Martin P.; Hatty, Claire R.; Separovic, Frances; Hill, Andrew F.; Tew, Deborah J.; Barnham, Kevin J.; Haigh, Cathryn L.; James, Michael; Masters, Colin L.; Collins, Steven J.

    2010-01-01

    Although the N terminus of the prion protein (PrPC) has been shown to directly associate with lipid membranes, the precise determinants, biophysical basis, and functional implications of such binding, particularly in relation to endogenously occurring fragments, are unresolved. To better understand these issues, we studied a range of synthetic peptides: specifically those equating to the N1 (residues 23–110) and N2 (23–89) fragments derived from constitutive processing of PrPC and including those representing arbitrarily defined component domains of the N terminus of mouse prion protein. Utilizing more physiologically relevant large unilamellar vesicles, fluorescence studies at synaptosomal pH (7.4) showed absent binding of all peptides to lipids containing the zwitterionic headgroup phosphatidylcholine and mixtures containing the anionic headgroups phosphatidylglycerol or phosphatidylserine. At pH 5, typical of early endosomes, quartz crystal microbalance with dissipation showed the highest affinity binding occurred with N1 and N2, selective for anionic lipid species. Of particular note, the absence of binding by individual peptides representing component domains underscored the importance of the combination of the octapeptide repeat and the N-terminal polybasic regions for effective membrane interaction. In addition, using quartz crystal microbalance with dissipation and solid-state NMR, we characterized for the first time that both N1 and N2 deeply insert into the lipid bilayer with minimal disruption. Potential functional implications related to cellular stress responses are discussed. PMID:20679345

  17. 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

  18. 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. PMID:27500066

  19. Crystallographic Texture in Ceramics and Metals

    PubMed Central

    Vaudin, Mark 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.

  20. 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.

  1. 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. PMID:26522406

  2. "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/

  3. 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…

  4. Preliminary neutron crystallographic study of human transthyretin

    PubMed Central

    Haupt, Melina; Blakeley, Matthew P.; Teixeira, Susana C. M.; Mason, Sax A.; Mitchell, Edward P.; Cooper, Jonathan B.; Forsyth, V. Trevor

    2011-01-01

    Preliminary studies of perdeuterated crystals of human transthyretin (TTR) have been carried out using the LADI-III and D19 diffractometers at the Institut Laue–Langevin in Grenoble. The results demonstrate the feasibility of a full crystallographic analysis to a resolution of 2.0 Å using Laue diffraction and also illustrate the potential of using monochromatic instruments such as D19 for higher resolution studies where larger crystals having smaller unit cells are available. This study will yield important information on hydrogen bonding, amino-acid protonation states and hydration in the protein. Such information will be of general interest for an understanding of the factors that stabilize/destabilize TTR and for the design of ligands that may be used to counter TTR amyloid fibrillogenesis. PMID:22102249

  5. XTAL system of crystallographic programs: programmer's manual

    SciTech Connect

    Hall, S.R.; Stewart, J.M.; Norden, A.P.; Munn, R.J.; Freer, S.T.

    1980-02-01

    This document establishes the basis for collaborative writing of transportable computer programs for x-ray crystallography. The concepts and general-purpose utility subroutines described here can be readily adapted to other scientific calculations. The complete system of crystallographic programs and subroutines is called XTAL and replaces the XRAY (6,7,8) system of programs. The coding language for the XTAL system is RATMAC (5). The XTAL system of programs contains routines for controlling execution of application programs. In this sense it forms a suboperating system that presents the same computational environment to the user and programmer irrespective of the operating system in use at a particular installation. These control routines replace all FORTRAN I/O code, supply character reading and writing, supply binary file reading and writing, serve as a support library for applications programs, and provide for interprogram communication.

  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. 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

  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. Crystallographic model quality at a glance

    PubMed Central

    Urzhumtseva, Ludmila; Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

    2009-01-01

    A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ‘ideal values’ is shown graphically as a point on a ‘ruler’. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ‘red zones’ indicate parameters which lie outside typical values. PMID:19237753

  10. Crystallographic model quality at a glance.

    PubMed

    Urzhumtseva, Ludmila; Afonine, Pavel V; Adams, Paul D; Urzhumtsev, Alexandre

    2009-03-01

    A crystallographic macromolecular model is typically characterized by a list of quality criteria, such as R factors, deviations from ideal stereochemistry and average B factors, which are usually provided as tables in publications or in structural databases. In order to facilitate a quick model-quality evaluation, a graphical representation is proposed. Each key parameter such as R factor or bond-length deviation from ;ideal values' is shown graphically as a point on a ;ruler'. These rulers are plotted as a set of lines with the same origin, forming a hub and spokes. Different parts of the rulers are coloured differently to reflect the frequency (red for a low frequency, blue for a high frequency) with which the corresponding values are observed in a reference set of structures determined previously. The points for a given model marked on these lines are connected to form a polygon. A polygon that is strongly compressed or dilated along some axes reveals unusually low or high values of the corresponding characteristics. Polygon vertices in ;red zones' indicate parameters which lie outside typical values. PMID:19237753

  11. Crystallization of PTP Domains.

    PubMed

    Levy, Colin; Adams, James; Tabernero, Lydia

    2016-01-01

    Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed. PMID:27514806

  12. ``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

  13. 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.

  14. Correlated crystallographic etching of graphene and nanoribbon formation

    NASA Astrophysics Data System (ADS)

    Johnson, Stephen; Hunley, D. Patrick; Stieha, Joseph; Sundararajan, Abhishek; Kar, Arunita; Johnson, A. T. Charlie; Strachan, Douglas

    2011-03-01

    Catalytic etching is a promising method for constructing crystallographically defined graphene structures such as nanoribbons. Catalytic etching experiments are performed and shown to contain significant correlation yielding crystallographic graphene nanoribbons. This correlation is investigated as a function of etching conditions and compared to simulations with possible sources discussed. Supported in part by NSF Award No. DMR-0805136, the Kentucky NSF EPSCoR program, the University of Kentucky Center for Advanced Materials, and the University of Kentucky Center for Nanoscale Science and Engineering.

  15. Biological control of crystallographic architecture: hierarchy and co-alignment parameters.

    PubMed

    Maier, B J; Griesshaber, E; Alexa, P; Ziegler, A; Ubhi, H S; Schmahl, W W

    2014-09-01

    Mytilus edulis prismatic calcite and nacre layers exhibit a crystallographic structural hierarchy which differs substantially from the morphological hierarchy. This makes these biomaterials fundamentally different from classical crystalline materials. Morphological building units are defined by their surrounding organic matrix membranes, e.g. calcite fibers or nacre tablets. The crystallographic building units are defined by crystallographic co-orientation. Electron backscatter diffraction quantitatively shows how crystallographic co-orientation propagates across matrix membranes to form highly co-oriented low-mosaic composite-crystal grains, i.e. calcite fiber bundles with an internal mosaic spread of 0.5° full width at half maximum (FWHM) or nacre towergrains with an internal mosaic spread of 2° FWHM. These low-mosaic composite crystals form much larger composite-crystal supergrains, which exhibit a high mosaicity due to misorientations of their constituting calcite fiber bundles or nacre towergrains. For the aragonite layer these supergrains nucleate in one of three aragonite {110} twin orientations; as a consequence the nacre layer exhibits a twin-domain structure, i.e. the boundaries of adjacent supergrains exhibit a high probability for misorientations around the aragonite c-axis with an angle near 63.8°. Within the supergrains, the constituting towergrains exhibit a high probability for misorientations around the aragonite a-axis with a geometric mean misorientation angle of 10.6°. The calcite layer is composed of a single composite-crystal supergrain on at least the submillimeter length scale. Mutual misorientations of adjacent fiber bundles within the calcite supergrain are mainly around the calcite c-axis with a geometric mean misorientation angle of 9.4°. The c-axis is not parallel to the long axis of the fibers but rather to the (107) plane normal. The frequency distribution for the occurrence of misorientation angles within supergrains reflects

  16. 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.

  17. Some algebraic properties of crystallographic sublattices.

    PubMed

    Rutherford, John S

    2006-03-01

    In this article, a number of the results relevant to the concept of sublattices of a basic crystallographic lattice are reviewed, emphasizing particularly previously unpublished work on the algebraic aspects. A three-dimensional geometric lattice L can be considered as an infinite Abelian group under addition. A sublattice S of L, which is also three-dimensional, is a subgroup of L such that the finite quotient group, G approximately equals L/S, is an Abelian group of order the index of S in L. The sublattice itself in its standard form is represented by an upper triangular matrix. The index of the sublattice is given by the determinant of this matrix. It is first noted that a sublattice described by an arbitrary basis set in L may be converted to this standard form. Next the sublattice is expressed as the intersection of a set of sublattices of individual index a power of a distinct prime, i.e. S(n = p(a)(1)p(b)(2)...) = S(1)(p(a)(1)[cap]S(2)(p(b)(2)...[cap]... = [bigcap](i)S(i)(p(alpha(i)), where p(1), p(2) etc. are prime numbers and n = Pi(i)p(alpha)(i) is the Euclidean factorization of n. This decomposition is important because it corresponds to the Sylow decomposition of the corresponding quotient group G approximately equals (i)[sign: see text] A(p)(i). It is also useful to be able to carry out two commutative binary operations on sublattices of L; these are to find their common sublattice of lowest index in L, which is their intersection S(cap) = S(a)(m)[cap]S(b)(n) and their common superlattice of highest index in L, given by S(< >) = , where < > indicates the span of the sublattices. PMID:16489245

  18. Butene oxidation by molybdenum crystallographic shear compounds

    SciTech Connect

    McCormick, R.L.

    1984-06-01

    The reduced molybdenum oxides Mo/sub 4/O/sub 11/-orh, Mo/sub 4/O/sub 11/-mon, Mo/sub 8/O/sub 23/, and Mo/sub 18/O/sub 52/ were synthesized. These compounds, as well as MoO/sub 3/, were characterized by x-ray diffraction, x-ray photoelectron spectroscopy, Raman and FT-IR spectroscopies, and BET surface area measurements. The oxides were then studied in a pulsed reactor at 500/sup 0/C in the selective oxidation of butene and butadiene. The data suggested a process in which the surface site must become more oxidized in parallel with the oxidation of the adsorbed hydrocarbon. Evidence supporting this idea included the high selectivity to maleic anhydride observed over a completely oxidized surface and differences in the reactivity of butene and butadiende. In particular, oxygen insertion into butadiene to form furan occurred in the absence of gas phase O/sub 2/ over the reduced phases, while oxygen insertion into butene required the presence of molecular oxygen. Maleic anhydride formation required the presence of molecular oxygen except in the case of butadiene oxidation over MoO/sub 3/. The long range ordering of defects, known as crystallographic shear, was not shown to have any influence on the initial interaction of reactant and solid. However, the unusual coordination geometries and surface structures that are thought to be caused by the presence of shear planes may be related to the differences in catalytic selectivity observed for these oxides.

  19. "Crystallographic" holes: new insights for a beneficial structural feature for photocatalytic applications.

    PubMed

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

    2015-03-19

    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. PMID:25757557

  20. 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

  1. 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.

  2. 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.

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

    PubMed Central

    Wan, Liang; Han, Weizhong; Chen, Kai

    2015-01-01

    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. PMID:26304553

  4. 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.

  5. 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.

  6. Fission gas bubble percolation on crystallographically consistent grain boundary networks

    NASA Astrophysics Data System (ADS)

    Sabogal-Suárez, Daniel; David Alzate-Cardona, Juan; Restrepo-Parra, Elisabeth

    2016-07-01

    Fission gas release in nuclear fuels can be modeled in the framework of percolation theory, where each grain boundary is classified as open or closed to the release of the fission gas. In the present work, two-dimensional grain boundary networks were assembled both at random and in a crystallographically consistent manner resembling a general textured microstructure. In the crystallographically consistent networks, grain boundaries were classified according to its misorientation. The percolation behavior of the grain boundary networks was evaluated as a function of radial cracks and radial thermal gradients in the fuel pellet. Percolation thresholds tend to shift to the left with increasing length and number of cracks, especially in the presence of thermal gradients. In general, the topology and percolation behavior of the crystallographically consistent networks differs from those of the random network.

  7. Domain Engineering

    NASA Astrophysics Data System (ADS)

    Bjørner, Dines

    Before software can be designed we must know its requirements. Before requirements can be expressed we must understand the domain. So it follows, from our dogma, that we must first establish precise descriptions of domains; then, from such descriptions, “derive” at least domain and interface requirements; and from those and machine requirements design the software, or, more generally, the computing systems.

  8. Data-Driven Objectness.

    PubMed

    Hongwen Kang; Hebert, Martial; Efros, Alexei A; Kanade, Takeo

    2015-01-01

    We propose a data-driven approach to estimate the likelihood that an image segment corresponds to a scene object (its "objectness") by comparing it to a large collection of example object regions. We demonstrate that when the application domain is known, for example, in our case activity of daily living (ADL), we can capture the regularity of the domain specific objects using millions of exemplar object regions. Our approach to estimating the objectness of an image region proceeds in two steps: 1) finding the exemplar regions that are the most similar to the input image segment; 2) calculating the objectness of the image segment by combining segment properties, mutual consistency across the nearest exemplar regions, and the prior probability of each exemplar region. In previous work, parametric objectness models were built from a small number of manually annotated objects regions, instead, our data-driven approach uses 5 million object regions along with their metadata information. Results on multiple data sets demonstrates our data-driven approach compared to the existing model based techniques. We also show the application of our approach in improving the performance of object discovery algorithms. PMID:26353218

  9. 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.

  10. Crystallographic variant selection in {alpha}-{beta} brass

    SciTech Connect

    Stanford, N.; Bate, P.S. . E-mail: pete.bate@man.ac.uk

    2005-02-01

    The transformation texture of {alpha}/{beta} brass with a diffusional Widmanstaetten {alpha} growth morphology has been investigated. Electron micrographs and electron backscattered diffraction was used to determine that the orientation relationship between the {beta} phase and the {alpha} associated with nucleation at {beta} grain boundaries was 44.3 deg <1 1 6>. Crystallographic variant selection was observed across those prior {beta}/{beta} grain boundaries, but this has little effect on the transformation texture due to the crystal symmetry. The effect of the crystallographic variant selection on texture is further weakened by nucleation of diffusional transformed {alpha} in the grain interior.

  11. Temperature driven nano-domain evolution in lead-free Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics

    NASA Astrophysics Data System (ADS)

    Lu, Shengbo; Xu, Zhengkui; Su, Shi; Zuo, Ruzhong

    2014-07-01

    Hierarchical micro- and nanoscale domain structures in Pb-free Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics were investigated by transmission electron microscopy. In situ heating and cooling studies of domain structure evolution reveal an irreversible domain transformation from a wedge-shaped rhombohedral nanodomain structure to a lamellar tetragonal domain structure, which could be associated with strong piezoelectricity in Ba(Zr0.2Ti0.8)O3-50(Ba0.7Ca0.3)TiO3 piezoceramics.

  12. Expression, crystallization and preliminary crystallographic data analysis of filamin A repeats 14–16

    SciTech Connect

    Aguda, Adeleke Halilu; Sakwe, Amos Malle; Rask, Lars; Robinson, Robert Charles

    2007-04-01

    The crystallization and crystallographic data analysis of filamin repeats 14–16 are reported. Human filamin A is a 280 kDa protein involved in actin-filament cross-linking. It is structurally divided into an actin-binding headpiece (ABD) and a rod domain containing 24 immunoglobulin-like (Ig) repeats. A fragment of human filamin A (Ig repeats 14–16) was cloned and expressed in Escherichia coli and the purified protein was crystallized in 1.6 M ammonium sulfate, 2% PEG 1000 and 100 mM HEPES pH 7.5. The crystals diffracted to 1.95 Å and belong to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 50.63, b = 52.10, c = 98.46 Å, α = β = γ = 90°.

  13. 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.

  14. 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)

  15. Characterization of Crystallographic Properties and Defects VIA X-ray Microdiffraction in GaN (0001) Layers

    SciTech Connect

    Barabash, Rozaliya; Barabash, Oleg M; Ice, Gene E; Roder, C.; Figge, S.; Einfeldt, S.; Hommel, D.; Katona, T. M.; Speck, J. S.; DenBaars, S. P.; Davis, R. F.

    2006-01-01

    Intrinsic stresses due to lattice mismatch, high densities of threading dislocations, and extrinsic stresses resulting from the mismatch in the coefficients of thermal expansion, are present in almost all III-Nitride heterostructures. Stress relaxation in the GaN layers occurs in conventional, cantilever (CE) and in pendeo-epitaxial (PE) films via the formation of additional misfit dislocations, domain boundaries, elastic strain and wing tilt. Polychromatic X-ray microdiffraction, high resolution monochromatic X-ray diffraction and SEM analysis have been used to determine the crystallographic properties, misfit dislocations distribution and crystallographic tilts in uncoalesced GaN layers grown by PE and CE. The crystallographic tilt between the GaN(0001) and Si(111) planes was detected in the CE grown samples on Si(111). In contrast there was no tilt between GaN(0001) and SiC(0001) planes in PE grown samples. The wings are tilted upward for both the PE and CE grown uncoalesced GaN layers.

  16. Characterization of crystallographic properties and defects via X-ray microdiffraction in GaN (0001) layers

    NASA Astrophysics Data System (ADS)

    Barabash, R. I.; Barabash, O. M.; Ice, G. E.; Roder, C.; Figge, S.; Einfeldt, S.; Hommel, D.; Katona, T. M.; Speck, J. S.; Denbaars, S. P.; Davis, R. F.

    2006-01-01

    Intrinsic stresses due to lattice mismatch, high densities of threading dislocations, and extrinsic stresses resulting from the mismatch in the coefficients of thermal expansion, are present in almost all III-Nitride heterostructures. Stress relaxation in the GaN layers occurs in conventional, cantilever (CE) and in pendeo-epitaxial (PE) films via the formation of additional misfit dislocations, domain boundaries, elastic strain and wing tilt. Polychromatic X-ray microdiffraction, high resolution monochromatic X-ray diffraction and SEM analysis have been used to determine the crystallographic properties, misfit dislocations distribution and crystallographic tilts in uncoalesced GaN layers grown by PE and CE. The crystallographic tilt between the GaN(0001) and Si(111) planes was detected in the CE grown samples on Si(111). In contrast there was no tilt between GaN(0001) and SiC(0001) planes in PE grown samples. The wings are tilted upward for both the PE and CE grown uncoalesced GaN layers.

  17. Periodic magnetic domains in single-crystalline cobalt filament arrays

    NASA Astrophysics Data System (ADS)

    Chen, Fei; Wang, Fan; Jia, Fei; Li, Jingning; Liu, Kai; Huang, Sunxiang; Luan, Zhongzhi; Wu, Di; Chen, Yanbin; Zhu, Jianmin; Peng, Ru-Wen; Wang, Mu

    2016-02-01

    Magnetic structures with controlled domain wall pattern may be applied as potential building blocks for three-dimensional magnetic memory and logic devices. Using a unique electrochemical self-assembly method, we achieve regular single-crystalline cobalt filament arrays with specific geometric profile and crystallographic orientation, and the magnetic domain configuration can be conveniently tailored. We report the transition of periodic antiparallel magnetic domains to compressed vortex magnetic domains depending on the ratio of height to width of the wires. A "phase diagram" is obtained to describe the dependence of the type of magnetic domain and the geometrical profiles of the wires. Magnetoresistance of the filaments demonstrates that the contribution of a series of 180∘ domain walls is over 0.15 % of the zero-field resistance ρ (H =0 ) . These self-assembled magnetic nanofilaments, with controlled periodic domain patterns, offer an interesting platform to explore domain-wall-based memory and logic devices.

  18. 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.

  19. 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

  20. Expression, purification, crystallization and preliminary crystallographic analysis of human myotubularin-related protein 3

    PubMed Central

    Son, Ji Young; Lee, Jee Un; Yoo, Ki-Young; Shin, Woori; Im, Dong-Won; Kim, Seung Jun; Ryu, Seong Eon; Heo, Yong-Seok

    2014-01-01

    Myotubularin-related proteins are a large family of phosphatases that have the catalytic activity of dephosphorylating the phospholipid molecules phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. Each of the 14 family members contains a phosphatase catalytic domain, which is inactive in six family members owing to amino-acid changes in a key motif for the activity. All of the members also bear PH-GRAM domains, which have low homologies between them and have roles that are not yet clear. Here, the cloning, expression, purification and crystallization of human myotubularin-related protein 3 encompassing the PH-GRAM and the phosphatase catalytic domain are reported. Preliminary X-ray crystallographic analysis shows that the crystals diffracted to 3.30 Å resolution at a synchrotron X-ray source. The crystals belonged to space group C2, with unit-cell parameters a = 323.3, b = 263.3, c = 149.4 Å, β = 109.7°. PMID:25195900

  1. Coarse-grained modeling of the structural states and transition underlying the powerstroke of dynein motor domain.

    PubMed

    Zheng, Wenjun

    2012-04-21

    This study aims to model a minimal dynein motor domain capable of motor function, which consists of the linker domain, six AAA+ modules (AAA1-AAA6), coiled coil stalk, and C-terminus domain. To this end, we have used the newly solved X-ray structures of dynein motor domain to perform a coarse-grained modeling of dynein's post- and pre-powerstroke conformation and the conformational transition between them. First, we have used normal mode analysis to identify a single normal mode that captures the coupled motions of AAA1-AAA2 closing and linker domain rotation, which enables the ATP-driven recovery stroke of dynein. Second, based on the post-powerstroke conformation solved crystallographically, we have modeled dynein's pre-powerstroke conformation by computationally inducing AAA1-AAA2 closing and sliding of coiled coil stalk, and the resulting model features a linker domain near the pre-powerstroke position and a slightly tilted stalk. Third, we have modeled the conformational transition from pre- to post-powerstroke conformation, which predicts a clear sequence of structural events that couple microtubule binding, powerstroke and product release, and supports a signaling path from stalk to AAA1 via AAA3 and AAA4. Finally, we have found that a closed AAA3-AAA4 interface (compatible with nucleotide binding) is essential to the mechano-chemical coupling in dynein. Our modeling not only offers unprecedented structural insights to the motor function of dynein as described by past single-molecule, fluorescence resonance energy transfer, and electron microscopy studies, but also provides new predictions for future experiments to test. PMID:22519354

  2. 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.

  3. 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

  4. 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. PMID:27031227

  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. A crystallographic perspective on sharing data and knowledge.

    PubMed

    Bruno, Ian J; Groom, Colin R

    2014-10-01

    The crystallographic community is in many ways an exemplar of the benefits and practices of sharing data. Since the inception of the technique, virtually every published crystal structure has been made available to others. This has been achieved through the establishment of several specialist data centres, including the Cambridge Crystallographic Data Centre, which produces the Cambridge Structural Database. Containing curated structures of small organic molecules, some containing a metal, the database has been produced for almost 50 years. This has required the development of complex informatics tools and an environment allowing expert human curation. As importantly, a financial model has evolved which has, to date, ensured the sustainability of the resource. However, the opportunities afforded by technological changes and changing attitudes to sharing data make it an opportune moment to review current practices. PMID:25091065

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

    DOE PAGESBeta

    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 maymore » be investigated.« less

  8. 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.

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

    DOE PAGESBeta

    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. Lastly, the results demonstrate a method by which the effects of radiation on crystallographic structuremore » may be investigated.« less

  10. 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. Lastly, the results demonstrate a method by which the effects of radiation on crystallographic structure may be investigated.

  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.

    2014-11-15

    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.

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

    SciTech Connect

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

    2014-07-01

    A novel procedure for identifying ligands in macromolecular crystallographic electron-density maps is introduced. Density clusters in such maps can be rapidly attributed to one of 82 different ligands in an automated manner. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Crystallographic variant selection of martensite during fatigue deformation

    NASA Astrophysics Data System (ADS)

    Das, Arpan

    2015-03-01

    Metastable austenitic stainless steels are prone to form deformation-induced martensite under the influence of externally applied stress. Crystallographic variant selection during martensitic transformation of metastable austenite has been investigated thoroughly with respect to the interaction between the applied uniaxial cyclic stress and the resulting accumulated plastic strain during cyclic plastic deformation. The orientation of all the Kurdjomov-Sachs (K-S) variants has been evaluated extensively and compared with the measured orientation of martensite with their corresponding interaction energies by applying the elegant transformation texture model recently developed by Kundu and Bhadeshia. Encouraging correlation between model prediction and experimental data generation for martensite pole figures at many deformed austenite grains has been observed. It has been found that both the applied uniaxial cyclic stress and the accumulated plastic strain are having strong influence on crystallographic variant selection during cyclic plastic deformation. Patel and Cohen's classical theory can be utilized to predict the crystallographic variant selection, if it is correctly used along with the phenomenological theory of martensite crystallography.

  17. 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.

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

    NASA Astrophysics Data System (ADS)

    Gačević, Ž.; Bengoechea-Encabo, A.; Albert, S.; Torres-Pardo, A.; González-Calbet, J. M.; Calleja, E.

    2015-01-01

    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.

  19. 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.

  20. 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

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

    SciTech Connect

    Ringrose, S.

    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.

  2. Determination of crystallographic orientation of lead-free piezoelectric (K,Na)NbO3 epitaxial thin films grown on SrTiO3 (100) surfaces

    NASA Astrophysics Data System (ADS)

    Yu, Qi; Zhu, Fang-Yuan; Cheng, Li-Qian; Wang, Ke; Li, Jing-Feng

    2014-03-01

    Crystallographic structure of sol-gel-processed lead-free (K,Na)NbO3 (KNN) epitaxial films on [100]-cut SrTiO3 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 SrTiO3 (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.

  3. Polyhedra with noncrystallographic symmetry as the orbits of crystallographic point symmetry groups

    NASA Astrophysics Data System (ADS)

    Ovsetsina, T. I.; Chuprunov, E. V.

    2015-11-01

    Polyhedra with noncrystallographic symmetry are analyzed as the orbits of crystallographic point symmetry groups on a set of smooth or structured ("hatched") planes. Polyhedra with symmetrically equivalent faces, obtained using crystallographic point groups but having noncrystallographic symmetry, and polyhedra, the symmetry group T of which is crystallographic but can be implemented only on the assumption of a noncrystallographic character of the internal structure of polyhedron, are studied. The results of the analysis for all 32 point symmetry groups are listed in table.

  4. 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. PMID:26578758

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Microstructures and crystallographic preferred orientations evolution in upper mantle rocks submitted to HT-HP extension tests

    NASA Astrophysics Data System (ADS)

    Ben-Ismail, W.; Tommasi, A.; Rutter, E.; Holloway, R.

    2003-04-01

    We analyse the changes in microstructure and the development of lattice preferred orientation (LPO) in upper mantle rocks deformed in extension. Extension experiments have been chosen because although the bulk extensional strain was under 50%, the non-linearity of the flow was sufficient to provoke the formation of a neck, in the center of which strain attained up to 1000%. These extension tests been performed using a gas medium, internally heated apparatus at 1200 deg C, 300 MPa confining pressure at an unloading rate of 0.015 mm/minutes corresponding to a strain rate of 10 5 S-1. The development of LPO as a function of strain has been studied in a natural harzburgite from the Oman ophiolite and two dunites from the Balmuccia massif in the Alps. The Oman harburgite is a fine-grained mylonite (500 to 10 micron) with a foliation marked by alignment of spinels and by a weak shape fabric of small olivine and enstatite porphyroclasts and a weak crystallographic preferred orientation. The extension tests resulted in the development of a new foliation marked by elongated olivine and spinel grains as well as in a significant grain size reduction by dynamic recrystallisation (mainly by bulging). This microstructure suggests that the deformation is accommodated by mainly by dislocation creep and, in the fine-grained, highly-recrystallised domains, also by grain boundary sliding. EBSD measurements made in a thin section parallel to the extension direction allow the investigation of the evolution of the crystallographic fabric as a function of finite strain. The dunites from the Balmuccia massif display a annealed microstructure characterized by polygonal grains of olivine (1 to 6 mm) displaying no internal deformation features. Although similar in microstructure one sample displays a strong [100](010) olivine LPO while the other is almost isotropic. For this sample, extension experiments have been performed in four different directions in respect to the original

  11. Parallel Computing of Multi-scale Finite Element Sheet Forming Analyses Based on Crystallographic Homogenization Method

    SciTech Connect

    Kuramae, Hiroyuki; Okada, Kenji; Uetsuji, Yasutomo; Nakamachi, Eiji; Tam, Nguyen Ngoc; Nakamura, Yasunori

    2005-08-05

    Since the multi-scale finite element analysis (FEA) requires large computation time, development of the parallel computing technique for the multi-scale analysis is inevitable. A parallel elastic/crystalline viscoplastic FEA code based on a crystallographic homogenization method has been developed using PC cluster. The homogenization scheme is introduced to compute macro-continuum plastic deformations and material properties by considering a polycrystal texture. Since the dynamic explicit method is applied to this method, the analysis using micro crystal structures computes the homogenized stresses in parallel based on domain partitioning of macro-continuum without solving simultaneous linear equations. The micro-structure is defined by the Scanning Electron Microscope (SEM) and the Electron Back Scan Diffraction (EBSD) measurement based crystal orientations. In order to improve parallel performance of elastoplasticity analysis, which dynamically and partially increases computational costs during the analysis, a dynamic workload balancing technique is introduced to the parallel analysis. The technique, which is an automatic task distribution method, is realized by adaptation of subdomain size for macro-continuum to maintain the computational load balancing among cluster nodes. The analysis code is applied to estimate the polycrystalline sheet metal formability.

  12. Graphene on Crystallographically Oriented mm-size grains of Polycrystalline Cu Foil

    NASA Astrophysics Data System (ADS)

    Arseven, Merve; Eren Kalay, Y.; Ozdas, Engin

    2012-02-01

    Graphene is a promising candidate for novel technological applications due to its unique band structure and electronic properties. CVD methods on polycrystalline Cu foils has been attracted a great attention for providing not only a cost effective way but also large scale growth of mono-few layer graphene [1]. Controlling the homogenity of graphene layers and its scale is one of the most important step for its quality to achieve its unique properties. Our research is focused on investigating the graphene island shapes and their qualities which are strongly depend on Cu texture orientation. Optimizing the surface by tuning the CVD parameters is indispensable to get oriented, defectless and large scale single crystal like grain structure. The effect of the crystallographic textures of Cu surface on the growth quality and the shape of graphene domains were analyzed by SEM and Raman Spectroscopy, and its key role on grain size distribution were investigated by EBSD and optical microscope. [1] Li X. et al. Science 324, 1312, 2009.

  13. 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

  14. Purification, crystallization and preliminary X-ray crystallographic analysis of TssL from Vibrio cholerae

    PubMed Central

    Jeong, Jae-Hee; Chang, Jeong Ho; Kim, Yeon-Gil

    2014-01-01

    The type VI secretion system (T6SS) is a macromolecular complex that is conserved in Gram-negative bacteria. The T6SS secretes effector proteins into recipient cells in a contact-dependent manner in order to accomplish cooperative and competitive interactions with the cells. Although the composition and mechanism of the T6SS have been intensively investigated across many Gram-negative bacteria, to date structural information on T6SS components from the important pathogen Vibrio cholerae has been rare. Here, the cloning, purification, crystallization and preliminary X-ray crystallographic analysis of the cytoplasmic domain of TssL, an inner membrane protein of the T6SS, from V. cholerae are reported. Diffraction data were collected to 1.5 Å resolution using synchrotron radiation. The crystal belonged to the hexagonal space group P61, with unit-cell parameters a = 78.4, b = 78.4, c = 49.5 Å. The successful structural characterization of TssL from V. cholerae will contribute to understanding the role of the membrane-associated subunits of the T6SS in more detail. PMID:25195905

  15. Soliton-dependent plasmon reflection at bilayer graphene domain walls

    NASA Astrophysics Data System (ADS)

    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.

  16. Synthesis and Crystallographic Analysis of 5-Se-Thymidine DNAs

    SciTech Connect

    Hassan, A.; Sheng, J; Jiang, J; Zhanbg, W; Huang, Z

    2009-01-01

    We investigated the possibility of the interaction of 5-CH3 of thymidine and its 5?-phosphate backbone (C-H O-PO3 interaction) in DNA via the insertion of the atomic probe (a selenium atom) into the exo-5-position of thymidine (5-Se-T). 5-Se-T was synthesized for the first time, via Mn(OAc)3 assisted electrophilic addition of CH3SeSeCH3 to 3?,5?-di-O-benzoyl-2?-deoxyuridine. The 5-Se-T phosphoramidite was subsequently synthesized and incorporated into DNA in over 99% coupling yield. Biophysical and structural investigations of the 5-Se-T DNAs revealed that the Se-modified and nonmodified DNAs are virtually identical. In addition, the crystallographic analysis of a 5-Se-T DNA strongly suggests a hydrogen-bond formation between the 5-CH3 and 5?-phosphate groups (CH3 PO4- interaction).

  17. 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

  18. Crystallographic data processing for free-electron laser sources.

    PubMed

    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 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. PMID:23793149

  19. Crystallographic variant selection in Ti-6Al-4V

    SciTech Connect

    Stanford, N.; Bate, P.S. . E-mail: pete.bate@man.ac.uk

    2004-10-04

    Transformation textures in the two-phase alloy Ti-6Al-4V have been studied. Samples were heated into the fully {beta} phase condition and then slow cooled to allow diffusional transformation to {alpha}. This produced a microstructure of grain boundary {alpha} encircling colonies of Widmanstaetten {alpha}. Electron backscattered diffraction (EBSD) texture measurements showed that the {alpha} texture was markedly sharper than that calculated on a basis of equal variant probability, indicating that significant variant selection was occurring during diffusional transformation. Investigation of the {alpha} variants produced across prior {beta} grain boundaries has shown that the selection of variants during transformation is highly dependant on the crystallography of those boundaries. The effect of this crystallographic variant selection on the transformation texture has been modelled.

  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. 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

    2013-12-01

    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. PMID:24177186

  2. 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.

  3. Thermal stability of ferroelectric domain gratings in Rb-doped KTP

    NASA Astrophysics Data System (ADS)

    Lindgren, Gustav; Peña, Alexandra; Zukauskas, Andrius; Liljestrand, Charlotte; Ménaert, Bertrand; Boulanger, Benoît.; Canalias, Carlota

    2015-08-01

    We study the thermal stability of domain walls in periodically poled Rb-doped KTP crystals. Domain-wall motion is observed after annealing the crystals above 550 °C. This motion is highly anisotropic along the a- and b- crystallographic axes. Along the b-axis domain wall motion is in the order of tens of micrometers. In the a-direction, it results in either three orders of magnitude smaller domain wall displacement or in domain merging, depending on the initial domain configuration. We show that the thermal stability of the domain gratings depends on their periodicity, resulting in complete backswitching for sub-micrometer domains annealed at 730 °C.

  4. 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.

  5. 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

  6. 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. PMID:22505256

  7. Crystallographic Studies of Chemically Modified Nucleic Acids: A Backward Glance

    PubMed Central

    Egli, Martin; Pallan, Pradeep S.

    2010-01-01

    Chemically modified nucleic acids (CNAs) are widely explored as antisense oligonucleotide or small interfering RNA (siRNA) candidates for therapeutic applications. CNAs are also of interest in diagnostics, high-throughput genomics and target validation, nanotechnology and as model systems in investigations directed at a better understanding of the etiology of nucleic acid structure as well as the physical-chemical and pairing properties of DNA and RNA and for probing protein-nucleic acid interactions. In this article we review research conducted by our laboratory over the past two decades with a focus on crystal structure analyses of CNAs and artificial pairing systems. We highlight key insights into issues ranging from conformational distortions as a consequence of modification to the modulation of pairing strength and RNA affinity by stereoelectronic effects and hydration. Although crystal structures have only been determined for a subset of the large number of modifications that were synthesized and analyzed in the oligonucleotide context to date, they have yielded guiding principles for the design of new analogs with tailormade properties, including pairing specificity, nuclease resistance and cellular uptake. And, perhaps less obviously, crystallographic studies of CNAs and synthetic pairing systems have shed light on fundamental aspects of DNA and RNA structure and function that would not have been disclosed by investigations solely focused on the natural nucleic acids. PMID:20087997

  8. 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

  9. 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. PMID:27599738

  10. Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study.

    PubMed

    Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

    2015-08-01

    The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

  11. 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

  12. 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.

  13. 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.

  14. Integration of Nanotubes, Etch Tracks, and Nanoribbons in Crystallographic Alignment

    NASA Astrophysics Data System (ADS)

    Boland, Mathias J.; Hunley, D. Patrick; Sundrarajan, Abhishek; Nasseri, Mohsen; Strachan, Douglas R.

    2015-03-01

    Three nanomaterial components, carbon nanotubes (CNTs), few-layer graphene (FLG), and etch tracks exposing insulating SiO2 regions, are integrated to form crystallographically-aligned nanoscale systems. These integrated systems consist of CNTs grown across nanogap etch tracks and nanoribbons formed within the FLG films as a result of chemical vapor deposition (CVD) processing. Each nanoscale component is aligned along the underlying graphene lattice, resulting in their orientations being locked into precise values, with CNTs maintaining alignment even after crossing etch tracks. The growth of aligned CNTs across nanogap etch tracks and nanoribbons suggests that integrated formations can be achieved by growing CNTs directly over nanogap etch tracks and nanoribbons. This is supported by calculations of the vibrational energy of CNTs indicating that they should be capable of maintaining atomic registry with an underlying graphene lattice as they grow across a typical etch track, in agreement with our experimental results. Thus, this work is relevant to the integration of semiconducting, conducting, and insulating nano-materials all together into precise nano-electronic systems.

  15. Crystallographic structure of ubiquitin in complex with cadmium ions

    PubMed Central

    2009-01-01

    Background Ubiquitination plays a critical role in regulating many cellular processes, from DNA repair and gene transcription to cell cycle and apoptosis. It is catalyzed by a specific enzymatic cascade ultimately leading to the conjugation of ubiquitin to lysine residues of the target protein that can be the ubiquitin molecule itself and to the formation of poly-ubiquitin chains. Findings We present the crystal structure at 3.0 Å resolution of bovine ubiquitin crystallized in presence of cadmium ions. Two molecules of ubiquitin are present in the asymmetric unit. Interestingly this non-covalent dimeric arrangement brings Lys-6 and Lys-63 of each crystallographically-independent monomer in close contact with the C-terminal ends of the other monomer. Residues Leu-8, Ile-44 and Val-70 that form a hydrophobic patch at the surface of the Ub monomer are trapped at the dimer interface. Conclusions The structural basis for signalling by poly-Ub chains relies on a visualization of conformations of alternatively linked poly-Ub chains. This arrangement of ubiquitin could illustrate how linkages involving Lys-6 or Lys-63 of ubiquitin are produced in the cell. It also details how ubiquitin molecules can specifically chelate cadmium ions. PMID:20003470

  16. Effects of crystallographic orientation on plastic deformation and SCC initiation of zirconium alloys

    NASA Astrophysics Data System (ADS)

    Kubo, T.; Wakashima, Y.; Amano, K.; Nagai, M.

    1985-05-01

    In order to investigate the effects of crystallographic orientation on deformation and crack initiation in iodine-induced SCC of zirconium alloys, uniaxial tensile tests of zirconium and Zircaloy-2 plates were conducted in an iodine atmosphere. The crystallographic orientation of individual grains was determined by an etch-pit technique prior to testing. After testing, the etch-pit technique showed that prismatic slip was predominant in the plastic deformation and that cleavage cracks extended along basal planes. The plastic deformation of individual grains was significantly influenced by their crystallographic orientations, which varied from one grain to another. Accordingly, inhomogeneous plastic deformation occurred between grains. The crack initiation took place preferentially at grain boundaries where differences of crystallographic orientations were large between adjacent grains. This indicated that crack initiations was caused by stress concentration due to strain incompatibility at those grain boundaries.

  17. The first synthesis and X-ray crystallographic analysis of an oxygen-bridged planarized triphenylborane.

    PubMed

    Kitamoto, Yuichi; Suzuki, Takatsugu; Miyata, Yasuo; Kita, Hiroshi; Funaki, Kenji; Oi, Shuichi

    2016-06-01

    An oxygen-bridged planarized triphenylborane has been successfully synthesized. X-ray crystallographic analysis revealed that the molecule has a complete planarized structure and the shortest C-B bonds among the triarylboranes synthesized to date. PMID:27161278

  18. Crystallographic study of fatigue cracking in Ni{sub 3}Al(CrB) single crystal

    SciTech Connect

    Zhang, G.P.; Wang, Z.G.; Li, G.Y.; Wu, S.D.

    1997-03-01

    The effect of crystallographic orientation on the fatigue-crack initiation and propagation in Ni{sub 3}Al(CrB) single crystal was studied using a compact-tension specimen. Stage I crystallographic cracking and cleavage fracture were observed. Crystallographic cracking can occur on two or more {l_brace}111{r_brace} slip planes simultaneously. It was shown that the threshold stress intensity for crack initiation from the notch root exhibits a dependence on crystallographic orientation. In addition, an effect of orientation on microcracking behavior was also shown. The number of {l_brace}111{r_brace} planes intersecting with each other determines the different microscopic features on the cleavage fracture surface.

  19. 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.

  20. Automotion of domain walls for spintronic interconnects

    NASA Astrophysics Data System (ADS)

    Nikonov, Dmitri E.; Manipatruni, Sasikanth; Young, Ian A.

    2014-06-01

    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.

  1. Purification, crystallization and preliminary crystallographic analysis of the CBS pair of the human metal transporter CNNM4

    PubMed Central

    Gómez García, Inmaculada; Oyenarte, Iker; Martínez-Cruz, Luis Alfonso

    2011-01-01

    This work describes the purification and preliminary crystallographic analysis of the CBS-pair regulatory domain of the human ancient domain protein 4 (ACDP4), also known as CNNM4. ACDP proteins represent the least-studied members of the eight different types of magnesium transporters that have been identified in mammals to date. In humans the ACDP family includes four members: CNNM1–4. CNNM1 acts as a cytosolic copper chaperone and has been associated with urofacial syndrome, whereas CNNM2 and CNNM4 have been identified as magnesium transporters. Interestingly, mutations in the CNNM4 gene have clinical consequences that are limited to retinal function and biomineralization and are considered to be the cause of Jalili syndrome, which consists of autosomal recessive cone-rod dystrophy and amelogenesis imperfecta. The truncated protein was overexpressed, purified and crystallized in the orthorhombic space group C222. The crystals diffracted X-rays to 3.6 Å resolution using synchrotron radiation. Matthews volume calculations suggested the presence of two molecules in the asymmetric unit, which were likely to correspond to a CBS module of the CBS pair of CNNM4. PMID:21393841

  2. Flexibility in the insulin receptor ectodomain enables docking of insulin in crystallographic conformation observed in a hormone-bound microreceptor.

    PubMed

    Vashisth, Harish

    2014-01-01

    Insulin binding to the insulin receptor (IR) is the first key step in initiating downstream signaling cascades for glucose homeostasis in higher organisms. The molecular details of insulin recognition by IR are not yet completely understood, but a picture of hormone/receptor interactions at one of the epitopes (Site 1) is beginning to emerge from recent structural evidence. However, insulin-bound structures of truncated IR suggest that crystallographic conformation of insulin cannot be accommodated in the full IR ectodomain due to steric overlap of insulin with the first two type III fibronectin domains (F1 and F2), which are contributed to the insulin binding-pocket by the second subunit in the IR homodimer. A conformational change in the F1-F2 pair has thus been suggested. In this work, we present an all-atom structural model of complex of insulin and the IR ectodomain, where no structural overlap of insulin with the receptor domains (F1 and F2) is observed. This structural model was arrived at by flexibly fitting parts of our earlier insulin/IR all-atom model into the simulated density maps of crystallized constructs combined with conformational sampling from apo-IR solution conformations. Importantly, our experimentally-consistent model helps rationalize yet unresolved Site. PMID:25309993

  3. Magnetic and crystallographic structures in UTX intermetallic compounds

    SciTech Connect

    Robinson, R.A.; Lawson, A.C.; Sechovsky, V.; Havela, L.; Kergadallan, Y.; Nakotte, H.; de Boer, F.R.

    1993-08-01

    Uranium, along with other actinides and lanthanides, forms a large group of ternary intermetallic compounds of stoichiometry UTX (T = transition metal, X = p-electron metal). These compounds are formed in several structure types and the occurrence and stability of particular structures with respect to the transition metal content suggests reasonable systematics. The authors have also investigated the magnetic structures of selected UTX compounds and it is revealing to relate the crystallographic and magnetic structures, because of the relationship between the magnetic symmetry and that of the U-atom environment produced by the 5f-ligand hybridization, and the consequent anisotropic exchange. Those of ZrNiAl structure type are collinear, with moments along the hexagonal c-axis. In the orthorhombic NiSiTi structure type, the moments are confined to the b- c plane (perpendicular to the uranium chains) and the structures are often incommensurate. In the hexagonal CaIn{sub 2} (or GaGeLi) structure type, the magnetic structures form in an orthorhombic cell, and at least in the disordered centric group, again the moments lie perpendicular to the nearest-neighbor uranium spacing. This work presents a phenomenology of trends in UTX ternary compounds. It is shown that there is an apparent strong hybridization parallel to nearest neighbor U-U directions, with ferromagnetic coupling in the same directions. There may be a systematic relationship between the hybridization anisotropy and the magnetic anisotropy, in which the quantization axes are the same and the moments point along directions of relatively weak hybridization.

  4. Energetic, crystallographic and diffusion characteristics of hydrogen isotopes in iron

    NASA Astrophysics Data System (ADS)

    Sivak, A. B.; Sivak, P. A.; Romanov, V. A.; Chernov, V. M.

    2015-06-01

    Energetic, crystallographic and diffusion characteristics of various interstitial configurations of H atoms and their complexes with self-point defects (SIA - self-interstitial atom, V - vacancy) in bcc iron have been calculated by molecular statics and molecular dynamics using Fe-H interatomic interaction potential developed by Ramasubramaniam et al. (2009) and modified by the authors of the present work and Fe-Fe matrix potential M07 developed by Malerba et al. (2010). The most energetically favorable configuration of an interstitial H atom is tetrahedral configuration. The energy barrier for H atom migration is 0.04 eV. The highest binding energy of all the considered complexes "vacancy - H atom" and "SIA - H atom" is 0.54 and 0.15 eV, respectively. The binding energy of H atom with edge dislocations in slip systems <1 1 1>{1 1 0}, <1 1 1>{1 1 2}, <1 0 0>{1 0 0}, <1 0 0>{1 1 0} is 0.32, 0.30, 0.45, 0.54 eV, respectively. The binding energy of H atom in VHn complexes (n = 1 … 15) decreases from 0.54 to 0.35 eV with increasing of n from 1 to 6. At n > 6, it decreases to ∼0.1 eV. The temperature dependences of hydrogen isotopes (P, D, T) diffusivities have been calculated for the temperature range 70-1800 K. Arrhenius-type dependencies describe the calculated data at temperatures T < 100 K. At T > 250 K, the temperature dependencies of the diffusivities DP, DD, DT have a parabolic form. The diffusivities of H isotopes are within 10% at room temperature. The isotope effect becomes stronger at higher temperatures, e.g., ratios DP/DD and DP/DT at 1800 K equal 1.23 and 1.40, respectively.

  5. 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.

  6. 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

  7. Structure of the yeast Bre1 RING domain

    PubMed Central

    Kumar, Pankaj; Wolberger, Cynthia

    2015-01-01

    Monoubiquitination of histone H2B at Lys123 in yeast plays a critical role in regulating transcription, mRNA export, DNA replication and the DNA damage response. The RING E3 ligase, Bre1, catalyzes monoubiquitination of H2B in concert with the E2 ubiquitin conjugating enzyme, Rad6. The crystal structure of a C-terminal fragment of Bre1 shows that the catalytic RING domain is preceded by an N-terminal helix that mediates coiled-coil interactions with a crystallographically related monomer. Homology modeling suggests that the human homologue of Bre1, RNF20/RNF40, heterodimerizes through similar coiled coil interactions. PMID:25864391

  8. 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.

  9. Domain wall manipulation with a magnetic tip.

    PubMed

    Stapelfeldt, T; Wieser, R; Vedmedenko, E Y; Wiesendanger, R

    2011-07-01

    A theoretical concept of local manipulation of magnetic domain walls is introduced. In the proposed procedure, a domain wall is driven by a spin-polarized current induced by a magnetic tip, as used in a scanning tunneling microscope, placed above a magnetic nanostripe and then moved along its long axis with a current flowing through the vacuum barrier. The angular momentum from the spin-polarized current exerts a torque on the magnetic moments underneath the tip and leads to a displacement of the domain wall. Particularly, the manipulation of a ferromagnetic 180° transverse domain wall has been studied by means of Landau-Lifshitz-Gilbert dynamics and Monte Carlo simulations. Different relative orientations of the tip and the sample magnetization have been considered. PMID:21797636

  10. A log-likelihood-gain intensity target for crystallographic phasing that accounts for experimental error.

    PubMed

    Read, Randy J; McCoy, Airlie J

    2016-03-01

    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

  11. X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.

    PubMed

    Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

    2016-06-01

    Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. PMID:27129243

  12. New molecular engineering approaches for crystallographic studies of large RNAs.

    PubMed

    Zhang, Jinwei; Ferré-D'Amaré, Adrian R

    2014-06-01

    Crystallization of RNAs with complex three-dimensional architectures remains a formidable experimental challenge. We review a number of successful heuristics involving engineering of the target RNAs to facilitate crystal contact formation, such as those that enabled the crystallization and structure determination of the cognate tRNA complexes of RNase P holoenzyme and the Stem I domain of the T-box riboswitch. Recently, RNA-targeted antibody Fab fragments and Kink-turn binding proteins have joined the ranks of successful chaperones for RNA crystallization. Lastly, we review the use of structured RNAs to facilitate crystallization of RNA-binding proteins and other RNAs. PMID:24607443

  13. Preliminary crystallographic studies of BRCA1 BRCT-ABRAXAS complex.

    PubMed

    Badgujar, Dilip C; Sawant, Ulka; Yadav, Lumbini; Hosur, M V; Varma, Ashok K

    2013-12-01

    The BRCA1 holoenzyme complex plays an important role in DNA damage repair. ABRAXAS is a newly discovered component of this complex and its C-terminal region directly binds to the BRCA1 BRCT domain. Single crystals of the BRCA1 BRCT-ABRAXAS complex grown by co-crystallization belonged to space group P4(1)2(1)2, with unit-cell parameters a = b = 187.18, c = 85.31 Å. Diffraction data were collected on the BM-14 beamline at the ESRF. Molecular-replacement calculations using Phaser led to three molecules in the asymmetric unit and a high solvent content of 76%. PMID:24316840

  14. 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. PMID:26227043

  15. 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

  16. Cloning, expression, purification, crystallization and preliminary crystallographic analysis of the C-terminal domain of Par-4 (PAWR)

    PubMed Central

    Tiruttani Subhramanyam, Udaya Kumar; Kubicek, Jan; Eidhoff, Ulf B.; Labahn, Joerg

    2014-01-01

    Prostate apoptosis response-4 protein is an intrinsically disordered pro-apoptotic protein with tumour suppressor function. Par-4 is known for its selective induction of apoptosis in cancer cells only and its ability to interact with various apoptotic proteins via its C-terminus. Par-4, with its unique function and various interacting partners, has gained importance as a potential target for cancer therapy. The C-terminus of the rat homologue of Par-4 was crystallized and a 3.7 Å resolution X-ray diffraction data set was collected. Preliminary data analysis shows the space group to be P41212. The unit-cell parameters are a = b = 115.351, c = 123.663 Å, α = β = γ = 90°. PMID:25195896

  17. Crystallographic texture engineering through novel melt strategies via electron beam melting: Inconel 718

    DOE PAGESBeta

    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 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

  18. 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.

  19. Experimental and Theoretical Investigation of Crystallographic Orientation Dependence of Nanoscratching of Single Crystalline Copper.

    PubMed

    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

  20. 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.

  1. 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

  2. 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

  3. Measurement of thermal diffusivity, elastic anisotropy and crystallographic orientation by interferometric photothermal microscopy

    NASA Astrophysics Data System (ADS)

    Jumel, Julien; Rochais, Denis

    2007-07-01

    This paper describes the use of interferometric photothermal microscopy for measuring the thermal diffusivity, crystallographic orientation and elastic anisotropy of a microscopic homogeneous volume of matter. This purely optical technique makes use of an intensity-modulated and focused laser beam to periodically heat the surface of the sample tested. An interferometer is used to detect the thermal expansion. After describing the experimental setup, we explain the inversion scheme allowing the determination of the local thermal diffusivity from the periodic sample surface displacement map, as well as the crystallographic orientation and elastic anisotropy in the case of cubic materials. These parameters are measured with a spatial resolution of a few cubic micrometres.

  4. 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.

  5. Elasto-Plastic Behavior of High RRR Niobium: Effects of Crystallographic Texture, Microstructure and Hydrogen Concentration

    SciTech Connect

    G.R. Myneni; S.R. Agnew

    2002-11-01

    Conventional assessments of the mechanical properties of polycrystalline high RRR niobium via tensile testing have revealed unusually low apparent Young's moduli and yield strength in annealed samples. These observations motivated the current investigation of a variety of possible contributors: crystallographic texture, grain size, and impurity concentration. It is shown that the crystallographic textures of a single lot of niobium are essentially unchanged by post-recrystallization anneals at temperatures up to 800 C. Ultrasonic measurements reveal that the elastic response is not degraded by annealing. Rather, the material's extremely low yield point gives the impression of a low elastic modulus during tensile testing.

  6. 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

  7. 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. PMID:21405493

  8. 3D domain swapping in a chimeric c-Src SH3 domain takes place through two hinge loops.

    PubMed

    Cámara-Artigas, Ana; Martínez-Rodríguez, Sergio; Ortiz-Salmerón, Emilia; Martín-García, José M

    2014-04-01

    In the Src Homology 3 domain (SH3) the RT and n-Src loops form a pocket that accounts for the specificity and affinity in binding of proline rich motifs (PRMs), while the distal and diverging turns play a key role in the folding of the protein. We have solved the structure of a chimeric mutant c-Src-SH3 domain where specific residues at the RT- and n-Src-loops have been replaced by those present in the corresponding Abl-SH3 domain. Crystals of the chimeric protein show a single molecule in the asymmetric unit, which appears in an unfolded-like structure that upon generation of the symmetry related molecules reveals the presence of a domain swapped dimer where both, RT- and n-Src loops, act as hinge loops. In contrast, the fold of the diverging type II β-turn and the distal loop are well conserved. Our results are the first evidence for the presence of a structured diverging type II β-turn in an unfolded-like intermediate of the c-Src-SH3 domain, which can be stabilized by interactions from the β-strands of the same polypeptide chain or from a neighboring one. Futhermore, this crystallographic structure opens a unique opportunity to study the effect of the amino acid sequence of the hinge loops on the 3D domain swapping process of c-Src-SH3. PMID:24556574

  9. 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

  10. Model Driven Engineering

    NASA Astrophysics Data System (ADS)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    A relevant initiative from the software engineering community called Model Driven Engineering (MDE) is being developed in parallel with the Semantic Web (Mellor et al. 2003a). The MDE approach to software development suggests that one should first develop a model of the system under study, which is then transformed into the real thing (i.e., an executable software entity). The most important research initiative in this area is the Model Driven Architecture (MDA), which is Model Driven Architecture being developed under the umbrella of the Object Management Group (OMG). This chapter describes the basic concepts of this software engineering effort.

  11. 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.

  12. 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. PMID:27240109

  13. Avalanches in tip-driven interfaces in random media

    NASA Astrophysics Data System (ADS)

    Aragón, L. E.; Kolton, A. B.; Le Doussal, P.; Wiese, K. J.; Jagla, E. A.

    2016-01-01

    We analyse by numerical simulations and scaling arguments the avalanche statistics of 1-dimensional elastic interfaces in random media driven at a single point. Both global and local avalanche sizes are power-law distributed, with universal exponents given by the depinning roughness exponent ζ and the interface dimension d, and distinct from their values in the uniformly driven case. A crossover appears between uniformly driven behaviour for small avalanches, and point-driven behaviour for large avalanches. The scale of the crossover is controlled by the ratio between the stiffness of the pulling spring and the elasticity of the interface; it is visible both in the global and local avalanche-size distributions, as in the average spatial avalanche shape. Our results are relevant to model experiments involving locally driven elastic manifolds at low temperatures, such as magnetic domain walls or vortex lines in superconductors.

  14. 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.

  15. 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

  16. 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

  17. 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)

  18. 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.

  19. Conduction at domain walls in oxide multiferroics

    SciTech Connect

    Seidel, Jan; Martin, Lane W; He, Q; Zhan, Q; Rother, A; Hawkridge, M. E.; Maksymovych, Petro; Yu, Pu; Gajek, Martin; Balke, Nina; Kalinin, Sergei V; Gemming, S; Catalan, G; Scott, J F; Spalding, Nicola A; Orenstein, J; Ramesh, R.

    2009-01-01

    Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO{sub 3}. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

  20. Transport domain unlocking sets the uptake rate of an aspartate transporter.

    PubMed

    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

    2015-02-01

    Glutamate transporters terminate neurotransmission by clearing synaptically released glutamate from the extracellular space, allowing repeated rounds of signalling and preventing glutamate-mediated excitotoxicity. Crystallographic studies of a glutamate transporter homologue from the archaeon Pyrococcus horikoshii, 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 mutations introduced to impart characteristics of the human transporter exhibits markedly increased transport domain dynamics, which parallels an increased rate of substrate transport, thereby establishing a direct temporal relationship between transport domain motion and substrate uptake. Crystallographic and computational investigations corroborated these findings by revealing that the 'humanizing' mutations favour structurally 'unlocked' intermediate states in the transport cycle exhibiting increased solvent occupancy at the interface between the transport domain and the trimeric scaffold. PMID:25652997

  1. 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)

  2. Domains and Naive Theories

    PubMed Central

    Gelman, Susan A.; Noles, Nicholaus S.

    2013-01-01

    Human cognition entails domain-specific cognitive processes that influence memory, attention, categorization, problem-solving, reasoning, and knowledge organization. This review examines domain-specific causal theories, which are of particular interest for permitting an examination of how knowledge structures change over time. We first describe the properties of commonsense theories, and how commonsense theories differ from scientific theories, illustrating with children’s classification of biological and non-biological kinds. We next consider the implications of domain-specificity for broader issues regarding cognitive development and conceptual change. We then examine the extent to which domain-specific theories interact, and how people reconcile competing causal frameworks. Future directions for research include examining how different content domains interact, the nature of theory change, the role of context (including culture, language, and social interaction) in inducing different frameworks, and the neural bases for domain-specific reasoning. PMID:24187603

  3. 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.

  4. Learning and Domain Adaptation

    NASA Astrophysics Data System (ADS)

    Mansour, Yishay

    Domain adaptation is a fundamental learning problem where one wishes to use labeled data from one or several source domains to learn a hypothesis performing well on a different, yet related, domain for which no labeled data is available. This generalization across domains is a very significant challenge for many machine learning applications and arises in a variety of natural settings, including NLP tasks (document classification, sentiment analysis, etc.), speech recognition (speakers and noise or environment adaptation) and face recognition (different lighting conditions, different population composition).

  5. The insulin and IGF1 receptor kinase domains are functional dimers in the activated state

    NASA Astrophysics Data System (ADS)

    Cabail, M. Zulema; Li, Shiqing; Lemmon, Eric; Bowen, Mark E.; Hubbard, Stevan R.; Miller, W. Todd

    2015-03-01

    The insulin receptor (IR) and insulin-like growth factor-1 receptor (IGF1R) are highly related receptor tyrosine kinases with a disulfide-linked homodimeric architecture. Ligand binding to the receptor ectodomain triggers tyrosine autophosphorylation of the cytoplasmic domains, which stimulates catalytic activity and creates recruitment sites for downstream signalling proteins. Whether the two phosphorylated tyrosine kinase domains within the receptor dimer function independently or cooperatively to phosphorylate protein substrates is not known. Here we provide crystallographic, biophysical and biochemical evidence demonstrating that the phosphorylated kinase domains of IR and IGF1R form a specific dimeric arrangement involving an exchange of the juxtamembrane region proximal to the kinase domain. In this dimer, the active position of α-helix C in the kinase N lobe is stabilized, which promotes downstream substrate phosphorylation. These studies afford a novel strategy for the design of small-molecule IR agonists as potential therapeutic agents for type 2 diabetes.

  6. Structures of and Interactions Between Domains of Trigger Factor from Thermotoga maritima

    SciTech Connect

    Martinez-Hackert,E.; Hendrickson, W.

    2007-01-01

    Trigger factor (TF) is a eubacterial chaperone that associates with ribosomes at the peptide-exit tunnel and also occurs in excess free in the cytosol. TF is a three-domain protein that appears to exist in a dynamic equilibrium of oligomerization states and interdomain conformations. X-ray crystallography and chemical cross-linking were used to study the roles of the N- and C-terminal domains of Thermotoga maritima TF in TF oligomerization and chaperone activity. The structural conservation of both the N- and C-terminal TF domains was unambiguously established. The biochemical and crystallographic data reveal a tendency for these domains to partake in diverse and apparently nonspecific protein-protein interactions. It is found that the T. maritima and Escherichia coli TF surfaces lack evident exposed hydrophobic patches. Taken together, these data suggest that TF chaperones could interact with nascent proteins via hydrophilic surfaces.

  7. Surface Diffusion Directed Growth of Anisotropic Graphene Domains on Different Copper Lattices

    PubMed Central

    Jung, Da Hee; Kang, Cheong; Nam, Ji Eun; Jeong, Heekyung; Lee, Jin Seok

    2016-01-01

    Anisotropic graphene domains are of significant interest since the electronic properties of pristine graphene strongly depend on its size, shape, and edge structures. In this work, considering that the growth of graphene domains is governable by the dynamics of the graphene-substrate interface during growth, we investigated the shape and defects of graphene domains grown on copper lattices with different indices by chemical vapor deposition of methane at either low pressure or atmospheric pressure. Computational modeling identified that the crystallographic orientation of copper strongly influences the shape of the graphene at low pressure, yet does not play a critical role at atmospheric pressure. Moreover, the defects that have been previously observed in the center of four-lobed graphene domains grown under low pressure conditions were demonstrated for the first time to be caused by a lattice mismatch between graphene and the copper substrate. PMID:26883174

  8. Driven Markovian Quantum Criticality.

    PubMed

    Marino, Jamir; Diehl, Sebastian

    2016-02-19

    We identify a new universality class in one-dimensional driven open quantum systems with a dark state. Salient features are the persistence of both the microscopic nonequilibrium conditions as well as the quantum coherence of dynamics close to criticality. This provides a nonequilibrium analogue of quantum criticality, and is sharply distinct from more generic driven systems, where both effective thermalization as well as asymptotic decoherence ensue, paralleling classical dynamical criticality. We quantify universality by computing the full set of independent critical exponents within a functional renormalization group approach. PMID:26943517

  9. 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.

  10. Transport in driven plasmas

    SciTech Connect

    Fisch, N.J.

    1985-03-01

    A plasma in contact with an external source of power, especially a source that interacts specifically with high-velocity electrons, exhibits transport properties, such as conductivity, different from those of an isolated plasma near thermal equilibrium. This is true even when the bulk of the particles in the driven plasma are near thermal equilibrium. To describe the driven plasma we derive an adjoint equation to the inhomogeneous, linearized, dynamic Boltzmann equation. The Green's functions for a variety of plasma responses can then be generated. It is possible to modify the Chapman-Enskog expansion in order to incorporate the response functions derived here.

  11. Phase Transition in strongly-correlated VO2: Time-domainAssignment of Cause and Effect

    SciTech Connect

    Cavalleri, A.; Dekorsy, Th.; Chong, H.H.; Kieffer, J.C.; Schoenlein, R.W.

    2004-07-22

    We establish time-domain hierarchy between structural andelectronic effects in the strongly correlated system VO2. Theinsulator-to-metal transition is driven directly by structural changerather than by electron-electron correlations.

  12. Rsp5 WW domains interact directly with the carboxyl-terminal domain of RNA polymerase II.

    PubMed

    Chang, A; Cheang, S; Espanel, X; Sudol, M

    2000-07-01

    RSP5 is an essential gene in Saccharomyces cerevisiae and was recently shown to form a physical and functional complex with RNA polymerase II (RNA pol II). The amino-terminal half of Rsp5 consists of four domains: a C2 domain, which binds membrane phospholipids; and three WW domains, which are protein interaction modules that bind proline-rich ligands. The carboxyl-terminal half of Rsp5 contains a HECT (homologous to E6-AP carboxyl terminus) domain that catalytically ligates ubiquitin to proteins and functionally classifies Rsp5 as an E3 ubiquitin-protein ligase. The C2 and WW domains are presumed to act as membrane localization and substrate recognition modules, respectively. We report that the second (and possibly third) Rsp5 WW domain mediates binding to the carboxyl-terminal domain (CTD) of the RNA pol II large subunit. The CTD comprises a heptamer (YSPTSPS) repeated 26 times and a PXY core that is critical for interaction with a specific group of WW domains. An analysis of synthetic peptides revealed a minimal CTD sequence that is sufficient to bind to the second Rsp5 WW domain (Rsp5 WW2) in vitro and in yeast two-hybrid assays. Furthermore, we found that specific "imperfect" CTD repeats can form a complex with Rsp5 WW2. In addition, we have shown that phosphorylation of this minimal CTD sequence on serine, threonine and tyrosine residues acts as a negative regulator of the Rsp5 WW2-CTD interaction. In view of the recent data pertaining to phosphorylation-driven interactions between the RNA pol II CTD and the WW domain of Ess1/Pin1, we suggest that CTD dephosphorylation may be a prerequisite for targeted RNA pol II degradation. PMID:10781604

  13. Acanthamoeba polyphaga mimivirus NDK: preliminary crystallographic analysis of the first viral nucleoside diphosphate kinase

    PubMed Central

    Jeudy, Sandra; Coutard, Bruno; Lebrun, Régine; Abergel, Chantal

    2005-01-01

    The complete sequence of the largest known double-stranded DNA virus, Acanthamoeba polyphaga mimivirus, has recently been determined [Raoult et al. (2004 ▶), Science, 306, 1344–1350] and revealed numerous genes not expected to be found in a virus. A comprehensive structural and functional study of these gene products was initiated [Abergel et al. (2005 ▶), Acta Cryst. F61, 212–215] both to better understand their role in the virus physiology and to obtain some clues to the origin of DNA viruses. Here, the preliminary crystallographic analysis of the viral nucleoside diphosphate kinase protein is reported. The crystal belongs to the cubic space group P213, with unit-cell parameter 99.425 Å. The self-rotation function confirms that there are two monomers per asymmetric unit related by a twofold non-crystallographic axis and that the unit cell thus contains four biological entities. PMID:16511098

  14. 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).

  15. 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.

  16. Finding non-crystallographic symmetry in density maps of macromolecular structures.

    PubMed

    Terwilliger, Thomas C

    2013-09-01

    The internal symmetry of a macromolecule is both an important aspect of its function and a useful feature in obtaining a structure by X-ray crystallography and other techniques. A method is presented for finding internal symmetry and other non-crystallographic symmetry in a structure based on patterns of density in a density map for that structure. Regions in map that are similar are identified by cutting out a sphere of density from a region that has high local variation and using an FFT-based correlation search to find other regions that match. The relationships among correlated regions are then refined to maximize their correlations and are found to accurately represent non-crystallographic symmetry in the map. PMID:23881095

  17. 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

    2013-11-01

    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. PMID:24147726

  18. Growth and crystallographic feature-dependent characterization of spinel zinc ferrite thin films by RF sputtering

    PubMed Central

    2013-01-01

    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. PMID:24354428

  19. 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.

  20. Crystallographic Analysis of Nucleation at Hardness Indentations in High-Purity Aluminum

    NASA Astrophysics Data System (ADS)

    Xu, Chaoling; Zhang, Yubin; Lin, Fengxiang; Wu, Guilin; Liu, Qing; Juul Jensen, Dorte

    2016-08-01

    Nucleation at Vickers hardness indentations has been studied in high-purity aluminum cold-rolled 12 pct. Electron channeling contrast was used to measure the size of the indentations and to detect nuclei, while electron backscattering diffraction was used to determine crystallographic orientations. It is found that indentations are preferential nucleation sites. The crystallographic orientations of the deformed grains affect the hardness and the nucleation potentials at the indentations. Higher hardness gives increased nucleation probabilities. Orientation relationships between nuclei developed at different indentations within one original grain are analyzed and it is found that the orientation distribution of the nuclei is far from random. It is suggested that it relates to the orientations present near the indentation tips which in turn depend on the orientation of the selected grain in which they form. Finally, possible nucleation mechanisms are briefly discussed.

  1. 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.

  2. 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. PMID:19588518

  3. Crystallographically oriented Zn nanocrystals formed in ZnO by Mn{sup +}-implantation

    SciTech Connect

    Li, Y. J.; Zhang, B.; Lu, W.; Wang, Y.; Zou, J.

    2008-09-29

    The nanostructural characteristics of ZnO implanted with Mn{sup +} to doses ranging from 1x10{sup 15} to 1x10{sup 17} cm{sup -2} are systematically studied for both as-implanted and postannealed cases. The detailed structural characterizations confirmed that the Mn{sup +} implantation and postannealing result in (1) the formation of crystallographically orientated Zn nanocrystals in the ZnO matrix and (2) Mn atoms occupy the Zn sites in ZnO.

  4. Segregation anisotropy of Sn on different crystallographic orientation surfaces of coarse-grained Zircaloy-4

    NASA Astrophysics Data System (ADS)

    Xie, Shijing; Zhou, Bangxin; Chen, Chuanming; Wang, Boyang; Jiang, Dong

    2016-02-01

    X-ray photoelectron spectroscopy (XPS) technique was utilized to study the correlation between the tendency of Sn surface segregation and the crystallographic orientation of grain surface in coarse-grained (0.2-0.8 mm in diameter) Zircaloy-4 specimen. The results indicated that the intensity of Sn surface segregation was in an order of (0001) < (1 bar 2 1 bar 0) ≈ (01 1 bar 0) , and it was in agreement with the prediction from bond-breaking theory.

  5. Aurophilicity under pressure: a combined crystallographic and in situ spectroscopic study.

    PubMed

    O'Connor, Alice E; Mirzadeh, Nedaossadat; Bhargava, Suresh K; Easun, Timothy L; Schröder, Martin; Blake, Alexander J

    2016-05-21

    High pressure crystallographic studies on [1,4-C6H4{PPh2(AuCl)}2] (1) reveal the largest pressure-induced contraction of an aurophilic interaction observed for any Au(i) complex; Hirshfeld surface analysis and Raman spectroscopy reveal the presence of several types of intermolecular interaction, which play an important role in the behaviour of 1 as a function of pressure. PMID:27009745

  6. Plasma sheath driven targets

    NASA Astrophysics Data System (ADS)

    Brownell, J. H.; Freeman, B. L.

    1980-02-01

    Plasma focus driven target implosions are simulated using hydrodynamic-burn codes. Support is given to the idea that the use of a target in a plasma focus should allow 'impedance matching' between the fuel and gun, permitting larger fusion yields from a focus-target geometry than the scaling laws for a conventional plasma focus would predict.

  7. Data Driven Teachers

    ERIC Educational Resources Information Center

    Tech & Learning, 2009

    2009-01-01

    Data-driven decision-making (DDDM) is a system of teaching and management practices that gets better information about students into the hands of classroom teachers. This article discusses the five major elements: (1) good baseline data; (2) measurable instructional goals; (3) frequent formative assessment; (4) professional learning communities;…

  8. 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…

  9. 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…

  10. Causal Learning Across Domains

    ERIC Educational Resources Information Center

    Schulz, Laura E.; Gopnik, Alison

    2004-01-01

    Five studies investigated (a) children's ability to use the dependent and independent probabilities of events to make causal inferences and (b) the interaction between such inferences and domain-specific knowledge. In Experiment 1, preschoolers used patterns of dependence and independence to make accurate causal inferences in the domains of…

  11. Modeling Protein Domain Function

    ERIC Educational Resources Information Center

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  12. Domain wall filters

    SciTech Connect

    Baer, Oliver; Narayanan, Rajamani; Neuberger, Herbert; Witzel, Oliver

    2007-03-15

    We propose using the extra dimension separating the domain walls carrying lattice quarks of opposite handedness to gradually filter out the ultraviolet fluctuations of the gauge fields that are felt by the fermionic excitations living in the bulk. This generalization of the homogeneous domain wall construction has some theoretical features that seem nontrivial.

  13. Anisotropies of the cosmic background radiation by domain wall networks

    SciTech Connect

    Nambu, Yasusada; Ishihara, Hideki; Gouda, Naoteru; Sugiyama, Naoshi )

    1991-06-01

    This paper discusses cosmological effects by domain wall formation associated with a late time phase transition after decoupling. Assuming the existence of rigid domain wall networks, a simple one-dimensional model is constructed and the quadrupole anisotropy of the cosmic background radiation (CBR) is calculated. Contrary to expectation, the gravitational potential of a domain wall itself does not disturb the isotropy of CBR. Estimating the quadrupole anisotropy of CBR induced by the wall-driven growth of matter density perturbations, a 100/h Mpc periodic wall structure is found to be consistent with the observed upper bound. 12 refs.

  14. Crystallographic preferred orientation of akimotoite and seismic anisotropy of Tonga slab.

    PubMed

    Shiraishi, Rei; Ohtani, Eiji; Kanagawa, Kyuichi; Shimojuku, Akira; Zhao, Dapeng

    2008-10-01

    The mineral akimotoite, ilmenite-structured MgSiO(3), exists at the bottom of the Earth's mantle transition zone and within the uppermost lower mantle, especially under low-temperature conditions. Akimotoite is thought to be a major constituent of the harzburgite layer of subducting slabs, and the most anisotropic mineral in the mantle transition zone. It has been predicted that if akimotoite crystals are preferentially oriented by plastic deformation, a cold subducted slab would be extremely anisotropic. However, there have been no studies of crystallographic preferred orientations and very few reports of plastic deformation experiments for MgSiO(3) ilmenite. Here we present plastic deformation experiments on polycrystalline akimotoite, which were conducted at confining pressures of 20-22 GPa and temperatures of 1,000-1,300 degrees C. We found a change in crystallographic preferred orientation pattern of akimotoite with temperature, where the c-axis maximum parallel to the compression direction develops at high temperature, whereas the c axes are preferentially oriented parallel to the shear direction or perpendicular to the compression direction at lower temperature. The previously reported difference in compressional-wave seismic anisotropy between the northern and southern segments of the Tonga slab at depths of the mantle transition zone can conceivably be attributed to the difference in the crystallographic preferred orientation pattern of akimotoite at varying temperature within the slab. PMID:18833278

  15. 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.

  16. 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.

  17. Field-driven magnetization dynamics of nanoparticles and nanowires

    NASA Astrophysics Data System (ADS)

    Lu, Jie

    This thesis is about micromagnetism in confined magnetic microstructures. The field-driven magnetization dynamics of nanoparticles and nanowires is systematically discussed following a clear thread of thought: from "macrospin" to "microspin". At the same time, four topics are raised and investigated. First, inspired by the traditional ferromagnetic resonance technique, two strategies for measuring the Gilbert damping coefficient using the magnetic circular dichroism effect are presented and discussed. The investigation is performed within a framework of the linear response of the macrospin in 2-D magnetic films to external time-dependent fields. The object of the study then turns to Stoner particles, which are single-domain magnetic nanoparticles, that are quasi 0-D systems and still assumed to be macrospins. The field-driven magnetization reversal in multi-axial Stoner particles is investigated and the corresponding Eular equations are presented. The Eular equations provide a unified framework for research of this kind. After that, the macrospin assumption itself is examined. The study of when and how it fails results in the famous "nucleation problem" in micromagnetism, thus the discussion then moves into the microspin category. The nucleation problem of single-domain cuboid permalloy nanowires, which are quasi 1-D systems, is investigated and a magnetization reversal mode named "domain formation and domain wall propagation" is revealed. Field-driven magnetic domain wall propagation is an excellent example of microspin behavior, and has been a hot issue in recent spintronic research. The effects of transverse magnetic anisotropies on field-driven transverse wall propagation in narrow magnetic nanowires are systematically investigated. These results should not only deepen the understanding of the domain wall dynamics in magnetic nanowires, but also offer inspiration for further developments of ultrafast nano-devices with higher integration levels.

  18. Field-driven dynamics of nematic microcapillaries.

    PubMed

    Khayyatzadeh, Pouya; Fu, Fred; Abukhdeir, Nasser Mohieddin

    2015-12-01

    Polymer-dispersed liquid-crystal (PDLC) composites long have been a focus of study for their unique electro-optical properties which have resulted in various applications such as switchable (transparent or translucent) windows. These composites are manufactured using desirable "bottom-up" techniques, such as phase separation of a liquid-crystal-polymer mixture, which enable production of PDLC films at very large scales. LC domains within PDLCs are typically spheroidal, as opposed to rectangular for an LCD panel, and thus exhibit substantially different behavior in the presence of an external field. The fundamental difference between spheroidal and rectangular nematic domains is that the former results in the presence of nanoscale orientational defects in LC order while the latter does not. Progress in the development and optimization of PDLC electro-optical properties has progressed at a relatively slow pace due to this increased complexity. In this work, continuum simulations are performed in order to capture the complex formation and electric field-driven switching dynamics of approximations of PDLC domains. Using a simplified elliptic cylinder (microcapillary) geometry as an approximation of spheroidal PDLC domains, the effects of geometry (aspect ratio), surface anchoring, and external field strength are studied through the use of the Landau-de Gennes model of the nematic LC phase. PMID:26764713

  19. Intersubunit binding domains within tyrosine hydroxylase and tryptophan hydroxylase.

    PubMed

    Yohrling, G J; Jiang, G C; Mockus, S M; Vrana, K E

    2000-08-01

    Tryptophan hydroxylase (TPH), the rate-limiting enzyme in the biosynthesis of the neurotransmitter serotonin (5-HT) belongs to the aromatic amino acid hydroxylase superfamily, which includes phenylalanine hydroxylase (PAH) and tyrosine hydroxylase (TH). The crystal structures for both PAH and TH have been reported, but a crystallographic model of TPH remains elusive. For this reason, we have utilized the information presented in the TH crystal structure in combination with primary sequence alignments to design point mutations in potential structural domains of the TPH protein. Mutation of a TH salt bridge (K170E) was sufficient to alter enzyme macromolecular assembly. We found that the disruption of the cognate intersubunit dimerization salt bridge (K111-E223) in TPH, however, did not affect the macromolecular assembly of TPH. Enzyme peaks representing only tetramers were observed with size exclusion chromatography. By contrast, a single-point mutation within the tetramerization domain of TPH (L435A) was sufficient to disrupt the normal homotetrameric assembly of TPH. These studies indicate that, although the proposed salt bridge dimerization interface of TH is conserved in TPH, this hypothetical TPH intersubunit binding domain, K111-E223, is not required for the proper macromolecular assembly of the protein. However, leucine 435 within the tetramerization domain is necessary for the proper macromolecular assembly of TPH. PMID:10900078

  20. Temperature driven nano-domain evolution in lead-free Ba(Zr{sub 0.2}Ti{sub 0.8})O{sub 3}-50(Ba{sub 0.7}Ca{sub 0.3})TiO{sub 3} piezoceramics

    SciTech Connect

    Lu, Shengbo Xu, Zhengkui; Su, Shi; Zuo, Ruzhong

    2014-07-21

    Hierarchical micro- and nanoscale domain structures in Pb-free Ba(Zr{sub 0.2}Ti{sub 0.8})O{sub 3}-50(Ba{sub 0.7}Ca{sub 0.3})TiO{sub 3} piezoceramics were investigated by transmission electron microscopy. In situ heating and cooling studies of domain structure evolution reveal an irreversible domain transformation from a wedge-shaped rhombohedral nanodomain structure to a lamellar tetragonal domain structure, which could be associated with strong piezoelectricity in Ba(Zr{sub 0.2}Ti{sub 0.8})O{sub 3}-50(Ba{sub 0.7}Ca{sub 0.3})TiO{sub 3} piezoceramics.

  1. Similar quartz crystallographic textures in rocks of continental earth's crust (by neutron diffraction data): I. Quartz textures in monomineral rocks

    NASA Astrophysics Data System (ADS)

    Nikitin, A. N.; Ivankina, T. I.; Ullemeyer, K.; Vasin, R. N.

    2008-09-01

    Quartz crystallographic textures in different rocks have been investigated by neutron diffraction. Various types of crystallographic textures of quartz-bearing mineral associations in monomineral and multiphase rocks from a representative collection of samples have been revealed and classified. Experimental investigations have been performed on special neutron texture diffractometers designed at the Frank Laboratory of Neutron Physics and mounted in the seventh channel of the IBR-2 reactor at the Joint Institute for Nuclear Research (Dubna).

  2. Similar quartz crystallographic textures in rocks of continental earth's crust (by neutron diffraction data): I. Quartz textures in monomineral rocks

    SciTech Connect

    Nikitin, A. N. Ivankina, T. I.; Ullemeyer, K.; Vasin, R. N.

    2008-09-15

    Quartz crystallographic textures in different rocks have been investigated by neutron diffraction. Various types of crystallographic textures of quartz-bearing mineral associations in monomineral and multiphase rocks from a representative collection of samples have been revealed and classified. Experimental investigations have been performed on special neutron texture diffractometers designed at the Frank Laboratory of Neutron Physics and mounted in the seventh channel of the IBR-2 reactor at the Joint Institute for Nuclear Research (Dubna).

  3. Domain decomposition algorithms and computation fluid dynamics

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.

    1988-01-01

    In the past several years, domain decomposition was a very popular topic, partly motivated by the potential of parallelization. While a large body of theory and algorithms were developed for model elliptic problems, they are only recently starting to be tested on realistic applications. The application of some of these methods to two model problems in computational fluid dynamics are investigated. Some examples are two dimensional convection-diffusion problems and the incompressible driven cavity flow problem. The construction and analysis of efficient preconditioners for the interface operator to be used in the iterative solution of the interface solution is described. For the convection-diffusion problems, 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 discussed.

  4. Magnetoelectric domain control in multiferroic TbMnO3

    NASA Astrophysics Data System (ADS)

    Matsubara, Masakazu; Manz, Sebastian; Mochizuki, Masahito; Kubacka, Teresa; Iyama, Ayato; Aliouane, Nadir; Kimura, Tsuyoshi; Johnson, Steven L.; Meier, Dennis; Fiebig, Manfred

    2015-06-01

    The manipulation of domains by external fields in ferroic materials is of major interest for applications. In multiferroics with strongly coupled magnetic and electric order, however, the magnetoelectric coupling on the level of the domains is largely unexplored. We investigated the field-induced domain dynamics of TbMnO3 in the multiferroic ground state and across a first-order spin-flop transition. In spite of the discontinuous nature of this transition, the reorientation of the order parameters is deterministic and preserves the multiferroic domain pattern. Landau-Lifshitz-Gilbert simulations reveal that this behavior is intrinsic. Such magnetoelectric correlations in spin-driven ferroelectrics may lead to domain wall-based nanoelectronics devices.

  5. Multiferroics. Magnetoelectric domain control in multiferroic TbMnO₃.

    PubMed

    Matsubara, Masakazu; Manz, Sebastian; Mochizuki, Masahito; Kubacka, Teresa; Iyama, Ayato; Aliouane, Nadir; Kimura, Tsuyoshi; Johnson, Steven L; Meier, Dennis; Fiebig, Manfred

    2015-06-01

    The manipulation of domains by external fields in ferroic materials is of major interest for applications. In multiferroics with strongly coupled magnetic and electric order, however, the magnetoelectric coupling on the level of the domains is largely unexplored. We investigated the field-induced domain dynamics of TbMnO3 in the multiferroic ground state and across a first-order spin-flop transition. In spite of the discontinuous nature of this transition, the reorientation of the order parameters is deterministic and preserves the multiferroic domain pattern. Landau-Lifshitz-Gilbert simulations reveal that this behavior is intrinsic. Such magnetoelectric correlations in spin-driven ferroelectrics may lead to domain wall-based nanoelectronics devices. PMID:26045431

  6. Optical Frequency Domain Imaging

    NASA Astrophysics Data System (ADS)

    Bouma, Brett E.; Tearney, Guillermo J.; Vakoc, Benjamin; Yun, Seok Hyun

    In this chapter, we discuss a frequency-domain approach, optical frequency-domain imaging (OFDI), which is based on optical frequency-domain reflectometry and uses a wavelength-swept laser and standard single-element photodetectors. The chapter begins with an overview of the fundamental aspects of the technology, including the detected signal, sensitivity, depth range, and resolution, and then goes on to discuss specific component technologies including the light source, interferometer and acquisition electronics, and image processing. The final section of the chapter provides a brief glimpse at some of the biomedical applications that most directly take advantage of the improved speed and sensitivity of OFDI.

  7. Electrically driven optical antennas

    NASA Astrophysics Data System (ADS)

    Kern, Johannes; Kullock, René; Prangsma, Jord; Emmerling, Monika; Kamp, Martin; Hecht, Bert

    2015-09-01

    Unlike radiowave antennas, so far optical nanoantennas cannot be fed by electrical generators. Instead, they are driven by light or indirectly via excited discrete states in active materials in their vicinity. Here we demonstrate the direct electrical driving of an in-plane optical antenna by the broadband quantum-shot noise of electrons tunnelling across its feed gap. The spectrum of the emitted photons is determined by the antenna geometry and can be tuned via the applied voltage. Moreover, the direction and polarization of the light emission are controlled by the antenna resonance, which also improves the external quantum efficiency by up to two orders of magnitude. The one-material planar design offers facile integration of electrical and optical circuits and thus represents a new paradigm for interfacing electrons and photons at the nanometre scale, for example for on-chip wireless communication and highly configurable electrically driven subwavelength photon sources.

  8. Laser driven radiography

    SciTech Connect

    Perry, M.D.; Sefcik, J.; Cowan, T.

    1997-12-20

    Intense laser (> 1021 W/cm{sup 3}) driven hard x-ray sources offer a new alternative to conventional electron accelerator Bremsstrahlung sources. These laser driven sources offer considerable simplicity in design and potential cost advantage for multiple axis views. High spatial and temporal resolution is achievable as a result of the very small source size (<100 um) and short-duration of the laser pulse. We have begun a series of experiments with the Petawatt laser at LLNL to determine the photon flux achievable with these sources and assess their potential for Stewardship applications. Additionally, we are developing a conceptual design and cost estimate of a multi-pulse, multi-axis (up to five) radiographic facility utilizing the Contained Firing Facility at site 300 and existing laser hardware.

  9. Test-driven programming

    NASA Astrophysics Data System (ADS)

    Georgiev, Bozhidar; Georgieva, Adriana

    2013-12-01

    In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

  10. Adiabatically driven Brownian pumps.

    PubMed

    Rozenbaum, Viktor M; Makhnovskii, Yurii A; Shapochkina, Irina V; Sheu, Sheh-Yi; Yang, Dah-Yen; Lin, Sheng Hsien

    2013-07-01

    We investigate a Brownian pump which, being powered by a flashing ratchet mechanism, produces net particle transport through a membrane. The extension of the Parrondo's approach developed for reversible Brownian motors [Parrondo, Phys. Rev. E 57, 7297 (1998)] to adiabatically driven pumps is given. We demonstrate that the pumping mechanism becomes especially efficient when the time variation of the potential occurs adiabatically fast or adiabatically slow, in perfect analogy with adiabatically driven Brownian motors which exhibit high efficiency [Rozenbaum et al., Phys. Rev. E 85, 041116 (2012)]. At the same time, the efficiency of the pumping mechanism is shown to be less than that of Brownian motors due to fluctuations of the number of particles in the membrane. PMID:23944411

  11. Trace anomaly driven inflation

    NASA Astrophysics Data System (ADS)

    Hawking, S. W.; Hertog, T.; Reall, H. S.

    2001-04-01

    This paper investigates Starobinsky's model of inflation driven by the trace anomaly of conformally coupled matter fields. This model does not suffer from the problem of contrived initial conditions that occurs in most models of inflation driven by a scalar field. The universe can be nucleated semiclassically by a cosmological instanton that is much larger than the Planck scale provided there are sufficiently many matter fields. There are two cosmological instantons: the four sphere and a new ``double bubble'' solution. This paper considers a universe nucleated by the four sphere. The AdS/CFT correspondence is used to calculate the correlation function for scalar and tensor metric perturbations during the ensuing de Sitter phase. The analytic structure of the scalar and tensor propagators is discussed in detail. Observational constraints on the model are discussed. Quantum loops of matter fields are shown to strongly suppress short scale metric perturbations, which implies that short distance modifications of gravity would probably not be observable in the cosmic microwave background. This is probably true for any model of inflation provided there are sufficiently many matter fields. This point is illustrated by a comparison of anomaly driven inflation in four dimensions and in a Randall-Sundrum brane-world model.

  12. Driven superconducting quantum circuits

    NASA Astrophysics Data System (ADS)

    Nakamura, Yasunobu

    2014-03-01

    Driven nonlinear quantum systems show rich phenomena in various fields of physics. Among them, superconducting quantum circuits have very attractive features such as well-controlled quantum states with design flexibility, strong nonlinearity of Josephson junctions, strong coupling to electromagnetic driving fields, little internal dissipation, and tailored coupling to the electromagnetic environment. We have investigated properties and functionalities of driven superconducting quantum circuits. A transmon qubit coupled to a transmission line shows nearly perfect spatial mode matching between the incident and scattered microwave field in the 1D mode. Dressed states under a driving field are studied there and also in a semi-infinite 1D mode terminated by a resonator containing a flux qubit. An effective Λ-type three-level system is realized under an appropriate driving condition. It allows ``impedance-matched'' perfect absorption of incident probe photons and down conversion into another frequency mode. Finally, the weak signal from the qubit is read out using a Josephson parametric amplifier/oscillator which is another nonlinear circuit driven by a strong pump field. This work was partly supported by the Funding Program for World-Leading Innovative R&D on Science and Technology (FIRST), Project for Developing Innovation Systems of MEXT, MEXT KAKENHI ``Quantum Cybernetics,'' and the NICT Commissioned Research.

  13. Water-driven micromotors.

    PubMed

    Gao, Wei; Pei, Allen; Wang, Joseph

    2012-09-25

    We demonstrate the first example of a water-driven bubble-propelled micromotor that eliminates the requirement for the common hydrogen peroxide fuel. The new water-driven Janus micromotor is composed of a partially coated Al-Ga binary alloy microsphere prepared via microcontact mixing of aluminum microparticles and liquid gallium. The ejection of hydrogen bubbles from the exposed Al-Ga alloy hemisphere side, upon its contact with water, provides a powerful directional propulsion thrust. Such spontaneous generation of hydrogen bubbles reflects the rapid reaction between the aluminum alloy and water. The resulting water-driven spherical motors can move at remarkable speeds of 3 mm s(-1) (i.e., 150 body length s(-1)), while exerting large forces exceeding 500 pN. Factors influencing the efficiency of the aluminum-water reaction and the resulting propulsion behavior and motor lifetime, including the ionic strength and environmental pH, are investigated. The resulting water-propelled Al-Ga/Ti motors move efficiently in different biological media (e.g., human serum) and hold considerable promise for diverse biomedical or industrial applications. PMID:22891973

  14. LHC RF System Time-Domain Simulation

    SciTech Connect

    Mastorides, T.; Rivetta, C.; /SLAC

    2010-09-14

    Non-linear time-domain simulations have been developed for the Positron-Electron Project (PEP-II) and the Large Hadron Collider (LHC). These simulations capture the dynamic behavior of the RF station-beam interaction and are structured to reproduce the technical characteristics of the system (noise contributions, non-linear elements, and more). As such, they provide useful results and insight for the development and design of future LLRF feedback systems. They are also a valuable tool for the study of diverse longitudinal beam dynamics effects such as coupled-bunch impedance driven instabilities and single bunch longitudinal emittance growth. Results from these studies and related measurements from PEP-II and LHC have been presented in multiple places. This report presents an example of the time-domain simulation implementation for the LHC.

  15. Visualizing Knowledge Domains.

    ERIC Educational Resources Information Center

    Borner, Katy; Chen, Chaomei; Boyack, Kevin W.

    2003-01-01

    Reviews visualization techniques for scientific disciplines and information retrieval and classification. Highlights include historical background of scientometrics, bibliometrics, and citation analysis; map generation; process flow of visualizing knowledge domains; measures and similarity calculations; vector space model; factor analysis;…

  16. Oscillons and domain walls

    SciTech Connect

    Hindmarsh, Mark; Salmi, Petja

    2008-05-15

    Oscillons, extremely long-lived localized oscillations of a scalar field, are shown to be produced by evolving domain wall networks in {phi}{sup 4} theory in two spatial dimensions. We study the oscillons in frequency space using the classical spectral function at zero momentum, and obtain that the velocity distribution is suppressed as {gamma}{sup -2} at large Lorentz factor {gamma}, with oscillons produced up to at least {gamma}{approx}10. This leads us to speculate that oscillons are produced at cusps, regions of the domain wall travelling near the speed of light. In order to gain some insight onto the dilute oscillon 'gas' produced by the domain walls, we prepare a denser gas by filling the simulation volume with oscillons boosted in random directions. We finish the study by revisiting collisions between oscillons and between an oscillon and a domain wall, showing that in the latter case they can pass straight through with minimal distortion.

  17. Tandem BRCT Domains

    PubMed Central

    Mesquita, Rafael D.; Woods, Nicholas T.; Seabra-Junior, Eloy S.; Monteiro, Alvaro N.A.

    2010-01-01

    The cell’s ability to sense and respond to specific stimuli is a complex system derived from precisely regulated protein-protein interactions. Some of these protein-protein interactions are mediated by the recognition of linear peptide motifs by protein modular domains. BRCT (BRCA1 C-terminal) domains and their linear motif counterparts, which contain phosphoserines, are one such pair-wise interaction system that seems to have evolved to serve as a surveillance system to monitor threats to the cell’s genetic integrity. Evidence indicates that BRCT domains found in tandem can cooperate to provide sequence-specific binding of phosphorylated peptides as is the case for the breast and ovarian cancer susceptibility gene BRCA1 and the PAX transcription factor–interacting protein PAXIP1. Particular interest has been paid to tandem BRCT domains as “readers” of signaling events in the form of phosphorylated serine moieties induced by the activation of DNA damage response kinases ATM, ATR, and DNA-PK. However, given the diversity of tandem BRCT-containing proteins, questions remain as to the origin and evolution of this domain. Here, we discuss emerging views of the origin and evolving roles of tandem BRCT domain repeats in the DNA damage response. PMID:21533002

  18. Structure of the yeast Bre1 RING domain.

    PubMed

    Kumar, Pankaj; Wolberger, Cynthia

    2015-06-01

    Monoubiquitination of histone H2B at Lys123 in yeast plays a critical role in regulating transcription, mRNA export, DNA replication, and the DNA damage response. The RING E3 ligase, Bre1, catalyzes monoubiquitination of H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The crystal structure of a C-terminal fragment of Bre1 shows that the catalytic RING domain is preceded by an N-terminal helix that mediates coiled-coil interactions with a crystallographically related monomer. Homology modeling suggests that the human homologue of Bre1, RNF20/RNF40, heterodimerizes through similar coiled-coil interactions. PMID:25864391

  19. Dynamic phases, pinning, and pattern formation for driven dislocation assemblies

    SciTech Connect

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-23

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Lastly, our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems.

  20. Dynamic phases, pinning, and pattern formation for driven dislocation assemblies

    DOE PAGESBeta

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-23

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Lastly, our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation andmore » dynamics in these systems.« less

  1. Dynamic Phases, Pinning, and Pattern Formation for Driven Dislocation Assemblies

    PubMed Central

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-01

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems. PMID:25613839

  2. Dynamic Phases, Pinning, and Pattern Formation for Driven Dislocation Assemblies

    NASA Astrophysics Data System (ADS)

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-01

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems.

  3. 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. PMID:23692572

  4. Domains in Ferroelectric Nanostructures

    NASA Astrophysics Data System (ADS)

    Gregg, Marty

    2010-03-01

    Ferroelectric materials have great potential in influencing the future of small scale electronics. At a basic level, this is because ferroelectric surfaces are charged, and so interact strongly with charge-carrying metals and semiconductors - the building blocks for all electronic systems. Since the electrical polarity of the ferroelectric can be reversed, surfaces can both attract and repel charges in nearby materials, and can thereby exert complete control over both charge distribution and movement. It should be no surprise, therefore, that microelectronics industries have already looked very seriously at harnessing ferroelectric materials in a variety of applications, from solid state memory chips (FeRAMs) to field effect transistors (FeFETs). In all such applications, switching the direction of the polarity of the ferroelectric is a key aspect of functional behavior. The mechanism for switching involves the field-induced nucleation and growth of domains. Domain coarsening, through domain wall propagation, eventually causes the entire ferroelectric to switch its polar direction. It is thus the existence and behavior of domains that determine the switching response, and ultimately the performance of the ferroelectric device. A major issue, associated with the integration of ferroelectrics into microelectronic devices, has been that the fundamental properties associated with ferroelectrics, when in bulk form, appear to change quite dramatically and unpredictably when at the nanoscale: new modes of behaviour, and different functional characteristics from those seen in bulk appear. For domains, in particular, the proximity of surfaces and boundaries have a dramatic effect: surface tension and depolarizing fields both serve to increase the equilibrium density of domains, such that minor changes in scale or morphology can have major ramifications for domain redistribution. Given the importance of domains in dictating the overall switching characteristics of a device

  5. Development of Dynamic Explicit Crystallographic Homogenization Finite Element Analysis Code to Assess Sheet Metal Formability

    NASA Astrophysics Data System (ADS)

    Nakamura, Yasunori; Tam, Nguyen Ngoc; Ohata, Tomiso; Morita, Kiminori; Nakamachi, Eiji

    2004-06-01

    The crystallographic texture evolution induced by plastic deformation in the sheet metal forming process has a great influence on its formability. In the present study, a dynamic explicit finite element (FE) analysis code is newly developed by introducing a crystallographic homogenization method to estimate the polycrystalline sheet metal formability, such as the extreme thinning and "earing." This code can predict the plastic deformation induced texture evolution at the micro scale and the plastic anisotropy at the macro scale, simultaneously. This multi-scale analysis can couple the microscopic crystal plasticity inhomogeneous deformation with the macroscopic continuum deformation. In this homogenization process, the stress at the macro scale is defined by the volume average of those of the corresponding microscopic crystal aggregations in satisfying the equation of motion and compatibility condition in the micro scale "unit cell," where the periodicity of deformation is satisfied. This homogenization algorithm is implemented in the conventional dynamic explicit finite element code by employing the updated Lagrangian formulation and the rate type elastic/viscoplastic constitutive equation. At first, it has been confirmed through a texture evolution analyses in cases of typical deformation modes that Taylor's "constant strain homogenization algorithm" yields extreme concentration toward the preferred crystal orientations compared with our homogenization one. Second, we study the plastic anisotropy effects on "earing" in the hemispherical cup deep drawing process of pure ferrite phase sheet metal. By the comparison of analytical results with those of Taylor's assumption, conclusions are drawn that the present newly developed dynamic explicit crystallographic homogenization FEM shows more reasonable prediction of plastic deformation induced texture evolution and plastic anisotropy at the macro scale.

  6. Identifying the multiplicity of crystallographically equivalent variants generated by iterative phase transformations in Ti.

    PubMed

    Grammatikopoulos, Panagiotis; Pond, Robert Charles

    2016-02-01

    This work describes phase transformations in Ti from a purely crystallographic perspective. Iterative heating and cooling above and below 1155 K induce phase transitions between a low-temperature h.c.p. (hexagonal close packed) (6/m mm) and a high-temperature b.c.c. (body centred cubic) (m3m) structure. The crystallography of the two phases has been found to be related by the Burgers Orientation Relationship (Burgers OR). The transitions are accompanied by changes in texture, as an ever-increasing number of crystallographically equivalent variants occur with every cycle. Identifying their multiplicity is important to relate the textures before and after the transformation, in order to predict the resultant one and refine its microstructure. The four-dimensional Frank space was utilized to describe both h.c.p. and b.c.c. structures within the same orthogonal framework, and thus allow for their easy numerical manipulation through matrix algebra. Crystallographic group decomposition showed that the common symmetry maintained in both groups was that of group 2/m; therefore, the symmetry operations that generated the variants were of groups 3m and 23 for cubic and hexagonal generations, respectively. The number of all potential variants was determined for the first three variant generations, and degeneracy was indeed detected, reducing the number of variants from 72 to 57 and from 432 to 180 for the second and third generations, respectively. Degeneracy was attributed on some special alignments of symmetry operators, as a result of the Burgers OR connecting the relative orientation of the two structures. PMID:26830797

  7. Large exchange-dominated domain wall velocities in antiferromagnetically coupled nanowires

    NASA Astrophysics Data System (ADS)

    Kuteifan, Majd; Lubarda, M. V.; Fu, S.; Chang, R.; Escobar, M. A.; Mangin, S.; Fullerton, E. E.; Lomakin, V.

    2016-04-01

    Magnetic nanowires supporting field- and current-driven domain wall motion are envisioned for methods of information storage and processing. A major obstacle for their practical use is the domain-wall velocity, which is traditionally limited for low fields and currents due to the Walker breakdown occurring when the driving component reaches a critical threshold value. We show through numerical and analytical modeling that the Walker breakdown limit can be extended or completely eliminated in antiferromagnetically coupled magnetic nanowires. These coupled nanowires allow for large domain-wall velocities driven by field and/or current as compared to conventional nanowires.

  8. 19F Nuclear Magnetic Resonance and Crystallographic Studies of 5-Fluorotryptophan-Labeled Anthrax Protective Antigen and Effects of the Receptor on Stability

    PubMed Central

    2015-01-01

    The anthrax protective antigen (PA) is an 83 kDa protein that is one of three protein components of the anthrax toxin, an AB toxin secreted by Bacillus anthracis. PA is capable of undergoing several structural changes, including oligomerization to either a heptameric or octameric structure called the prepore, and at acidic pH a major conformational change to form a membrane-spanning pore. To follow these structural changes at a residue-specific level, we have conducted initial studies in which we have biosynthetically incorporated 5-fluorotryptophan (5-FTrp) into PA, and we have studied the influence of 5-FTrp labeling on the structural stability of PA and on binding to the host receptor capillary morphogenesis protein 2 (CMG2) using 19F nuclear magnetic resonance (NMR). There are seven tryptophans in PA, but of the four domains in PA, only two contain tryptophans: domain 1 (Trp65, -90, -136, -206, and -226) and domain 2 (Trp346 and -477). Trp346 is of particular interest because of its proximity to the CMG2 binding interface, and because it forms part of the membrane-spanning pore. We show that the 19F resonance of Trp346 is sensitive to changes in pH, consistent with crystallographic studies, and that receptor binding significantly stabilizes Trp346 to both pH and temperature. In addition, we provide evidence that suggests that resonances from tryptophans distant from the binding interface are also stabilized by the receptor. Our studies highlight the positive impact of receptor binding on protein stability and the use of 19F NMR in gaining insight into structural changes in a high-molecular weight protein. PMID:24387629

  9. 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.

  10. 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

    2016-01-01

    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

  11. 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

  12. 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.

  13. 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.

  14. Structure of Tl18Pb2Ti7S25 as a masterpiece of crystallographic symmetry

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

    A crystallographic analysis of the cubic structure of Tl18Pb2Ti7S25 has established the arrangement of all cations and anions according to the law of the 27-fold (with respect to volume) structure type of PbS(NaCl) with strictly fixed anionic vacancies. The nonintersecting axes of symmetry of four directions organizing the structure distribute cations differing in sizes, charges, and amounts over general and particular sites of the sp. gr. Pa3 to form a high-symmetry design in the simple atomic matrix.

  15. System Driven Workarounds

    NASA Technical Reports Server (NTRS)

    Connell, Linda; Wichner, David; Jakey, Abegael Marie

    2013-01-01

    The Aviation Safety Reporting System (ASRS) in a partnership between the National Aeronautics and Space Administration (NASA), the Federal Aviation Administration (FAA), participating carriers, and labor organizations. It is designed to improve the National Airspace System by collecting and studying reports detailing unsafe conditions and events in the aviation industry. Employees are able to report safety issues or concerns with confidentiality and without fear of discipline. Safety reports highlighting system driven workarounds for the aviation community highlight the human workaround for the complex aviation system.

  16. HAMP Domain Conformers That Propagate Opposite Signals in Bacterial Chemoreceptors

    PubMed Central

    Airola, Michael V.; Sukomon, Nattakan; Samanta, Dipanjan; Borbat, Peter P.; Freed, Jack H.; Watts, Kylie J.; Crane, Brian R.

    2013-01-01

    HAMP domains are signal relay modules in >26,000 receptors of bacteria, eukaryotes, and archaea that mediate processes involved in chemotaxis, pathogenesis, and biofilm formation. We identify two HAMP conformations distinguished by a four- to two-helix packing transition at the C-termini that send opposing signals in bacterial chemoreceptors. Crystal structures of signal-locked mutants establish the observed structure-to-function relationships. Pulsed dipolar electron spin resonance spectroscopy of spin-labeled soluble receptors active in cells verify that the crystallographically defined HAMP conformers are maintained in the receptors and influence the structure and activity of downstream domains accordingly. Mutation of HR2, a key residue for setting the HAMP conformation and generating an inhibitory signal, shifts HAMP structure and receptor output to an activating state. Another HR2 variant displays an inverted response with respect to ligand and demonstrates the fine energetic balance between “on” and “off” conformers. A DExG motif found in membrane proximal HAMP domains is shown to be critical for responses to extracellular ligand. Our findings directly correlate in vivo signaling with HAMP structure, stability, and dynamics to establish a comprehensive model for HAMP-mediated signal relay that consolidates existing views on how conformational signals propagate in receptors. Moreover, we have developed a rational means to manipulate HAMP structure and function that may prove useful in the engineering of bacterial taxis responses. PMID:23424282

  17. Axion domain wall baryogenesis

    SciTech Connect

    Daido, Ryuji; Kitajima, Naoya; Takahashi, Fuminobu

    2015-07-28

    We propose a new scenario of baryogenesis, in which annihilation of axion domain walls generates a sizable baryon asymmetry. Successful baryogenesis is possible for a wide range of the axion mass and decay constant, m≃10{sup 8}–10{sup 13} GeV and f≃10{sup 13}–10{sup 16} GeV. Baryonic isocurvature perturbations are significantly suppressed in our model, in contrast to various spontaneous baryogenesis scenarios in the slow-roll regime. In particular, the axion domain wall baryogenesis is consistent with high-scale inflation which generates a large tensor-to-scalar ratio within the reach of future CMB B-mode experiments. We also discuss the gravitational waves produced by the domain wall annihilation and its implications for the future gravitational wave experiments.

  18. THERMALLY DRIVEN ATMOSPHERIC ESCAPE

    SciTech Connect

    Johnson, Robert E.

    2010-06-20

    Accurately determining the escape rate from a planet's atmosphere is critical for determining its evolution. A large amount of Cassini data is now available for Titan's upper atmosphere and a wealth of data is expected within the next decade on escape from Pluto, Mars, and extra-solar planets. Escape can be driven by upward thermal conduction of energy deposited well below the exobase, as well as by nonthermal processes produced by energy deposited in the exobase region. Recent applications of a model for escape driven by upward thermal conduction, called the slow hydrodynamic escape model, have resulted in surprisingly large loss rates for the atmosphere of Titan, Saturn's largest moon. Based on a molecular kinetic simulation of the exobase region, these rates appear to be orders of magnitude too large. Therefore, the slow hydrodynamic model is evaluated here. It is shown that such a model cannot give a reliable description of the atmospheric temperature profile unless it is coupled to a molecular kinetic description of the exobase region. Therefore, the present escape rates for Titan and Pluto must be re-evaluated using the atmospheric model described here.

  19. Heat driven pulse pump

    NASA Technical Reports Server (NTRS)

    Benner, Steve M (Inventor); Martins, Mario S. (Inventor)

    2000-01-01

    A heat driven pulse pump includes a chamber having an inlet port, an outlet port, two check valves, a wick, and a heater. The chamber may include a plurality of grooves inside wall of the chamber. When heated within the chamber, a liquid to be pumped vaporizes and creates pressure head that expels the liquid through the outlet port. As liquid separating means, the wick, disposed within the chamber, is to allow, when saturated with the liquid, the passage of only liquid being forced by the pressure head in the chamber, preventing the vapor from exiting from the chamber through the outlet port. A plurality of grooves along the inside surface wall of the chamber can sustain the liquid, which is amount enough to produce vapor for the pressure head in the chamber. With only two simple moving parts, two check valves, the heat driven pulse pump can effectively function over the long lifetimes without maintenance or replacement. For continuous flow of the liquid to be pumped a plurality of pumps may be connected in parallel.

  20. TBC-Domain GAPs for Rab GTPases Accelerate GTP Hydrolysis by a Dual-Finger Mechanism

    SciTech Connect

    Pan,X.; Eathiraj, S.; Lambright, D.

    2006-01-01

    Rab GTPases regulate membrane trafficking by cycling between inactive (GDP-bound) and active (GTP-bound) conformations. The duration of the active state is limited by GTPase-activating proteins (GAPs), which accelerate the slow intrinsic rate of GTP hydrolysis. Proteins containing TBC (Tre-2, Bub2 and Cdc16) domains are broadly conserved in eukaryotic organisms and function as GAPs for Rab GTPases as well as GTPases that control cytokinesis. An exposed arginine residue is a critical determinant of GAP activity in vitro and in vivo. It has been expected that the catalytic mechanism of TBC domains would parallel that of Ras and Rho family GAPs. Here we report crystallographic, mutational and functional analyses of complexes between Rab GTPases and the TBC domain of Gyp1p. In the crystal structure of a TBC-domain-Rab-GTPase-aluminium fluoride complex, which approximates the transition-state intermediate for GTP hydrolysis, the TBC domain supplies two catalytic residues in trans, an arginine finger analogous to Ras/Rho family GAPs and a glutamine finger that substitutes for the glutamine in the DxxGQ motif of the GTPase. The glutamine from the Rab GTPase does not stabilize the transition state as expected but instead interacts with the TBC domain. Strong conservation of both catalytic fingers indicates that most TBC-domain GAPs may accelerate GTP hydrolysis by a similar dual-finger mechanism.

  1. The Crystal Structure of the Heparin-Binding Reelin-N Domain of F-Spondin

    SciTech Connect

    Tan, Kemin; Duquette, Mark; Liu, Jin-huan; Lawler, Jack; Wang, Jia-huai

    2008-09-23

    The extracellular matrix protein F-spondin mediates axon guidance during neuronal development. Its N-terminal domain, termed the reelin-N domain, is conserved in F-spondins, reelins, and other extracellular matrix proteins. In this study, a recombinant human reelin-N domain has been expressed, purified, and shown to bind heparin. The crystal structure of the reelin-N domain resolved to 2.0 {angstrom} reveals a variant immunoglobulin-like fold and potential heparin-binding sites. Substantial conformational variations even in secondary structure are observed between the two chemically identical reelin-N domains in one crystallographic asymmetric unit. The variations may result from extensive, highly specific interactions across the interface of the two reelin-N domains. The calculated values of buried surface area and the interface's shape complementarity are consistent with the formation of a weak dimer. The homophilic asymmetric dimer can potentially offer advantages in binding to ligands such as glycosaminoglycans, which may, in turn, bridge the two reelin-N domains and stabilize the dimer.

  2. Domain structure and reorientation in CoF e2O4

    NASA Astrophysics Data System (ADS)

    Abes, M.; Koops, C. T.; Hrkac, S. B.; McCord, J.; Urs, N. O.; Wolff, N.; Kienle, L.; Ren, W. J.; Bouchenoire, L.; Murphy, B. M.; Magnussen, O. M.

    2016-05-01

    The microscopic processes underlying magnetostriction in ferrites were studied for the case of CoF e2O4 single crystals by high-resolution in situ x-ray diffraction and complementary magnetic microscopy techniques. The data support the reports of Yang and Ren [Phys. Rev. B 77, 014407 (2008), 10.1103/PhysRevB.77.014407] that magnetostriction in these materials originates from the switching of crystallographic domains, similar to ferroelastic or ferroelectric domain switching, and reveals the presence of two coexisting tetragonal spinel structures, corresponding to domains of high and of low strain. The latter alternate in the crystal, separated by 90° domain boundaries, and can be explained by the effect of internal stress emerging during the transition into the ferrimagnetic phase. During magnetization of the sample two structural transitions are observed: a conversion of the transversal into axial domains at 1.95 kOe and a growth of the high-strain domains at the cost of the low-strain axial domains at 2.8 kOe. These microscopic changes are in good agreement with the macroscopic magnetization and magnetostriction behavior of CoF e2O4 .

  3. Magnetic domain-wall dynamics in wide permalloy strips

    NASA Astrophysics Data System (ADS)

    Estévez, Virginia; Laurson, Lasse

    2016-02-01

    Domain walls in soft permalloy strips may exhibit various equilibrium micromagnetic structures depending on the width and thickness of the strip, ranging from the well-known transverse and vortex walls in narrow and thin strips to double and triple vortex walls recently reported in wider strips [V. Estévez and L. Laurson, Phys. Rev. B 91, 054407 (2015), 10.1103/PhysRevB.91.054407]. Here, we analyze the field driven dynamics of such domain walls in permalloy strips of widths from 240 nm up to 6 μ m , using the known equilibrium domain wall structures as initial configurations. Our micromagnetic simulations show that the domain wall dynamics in wide strips is very complex, and depends strongly on the geometry of the system, as well as on the magnitude of the driving field. We discuss in detail the rich variety of the dynamical behaviors found, including dynamic transitions between different domain wall structures, periodic dynamics of a vortex core close to the strip edge, transitions towards simpler domain wall structures of the multi-vortex domain walls controlled by vortex polarity, and the fact that for some combinations of the strip geometry and the driving field the system cannot support a compact domain wall.

  4. Influence of crystallographic orientation and anisotropy on Kapitza conductance via classical molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Duda, J. C.; Kimmer, C. J.; Soffa, W. A.; Zhou, X. W.; Jones, R. E.; Hopkins, P. E.

    2012-11-01

    We investigate the influence of crystallographic orientation and anisotropy on local phonon density of states, phonon transmissivity, and Kapitza conductance at interfaces between Lennard-Jones solids via classical molecular dynamics simulations. In agreement with prior works, we find that the Kapitza conductance at an interface between two face-centered cubic materials is independent of crystallographic orientation. On the other hand, at an interface between a face-centered cubic material and a tetragonal material, the Kapitza conductance is strongly dependent on the relative orientation of the tetragonal material, albeit this dependence is subject to the overlap in vibrational spectra of the cubic and tetragonal materials. Furthermore, we show that interactions between acoustic phonons in the cubic material and optical phonons in the tetragonal material can lead to the interface exhibiting greater "thermal anisotropy" as compared to that of the constituent materials. Finally, it is noted that the relative match or mismatch between the Debye temperatures of two materials comprising an interface does not serve an accurate gauge of the efficiency of interfacial thermal transport when those materials have different crystal structures.

  5. Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors

    PubMed Central

    Johnston, Jennifer M.; Filizola, Marta

    2014-01-01

    The recent mu-opioid receptor (MOPr) and kappa-opioid receptor (KOPr) crystal structures have inspired hypotheses of physiologically relevant dimerization contacts, specifically: a closely packed interface involving transmembrane (TM) helices TM5 and TM6, and a less compact interface, involving TM1, TM2, and helix 8 (H8). While the former was only found in MOPr crystals, similar arrangements of the latter were identified for both KOPr and MOPr. The relevance of these interfaces outside of a crystal lattice is called into question by the possibility that they might be influenced by the specific crystallization conditions. In this study, we have employed umbrella sampling molecular dynamics simulations of coarse-grained representations of the interacting MOPr or KOPr crystallographic structures, in the absence of the T4 lysozyme, and in an explicit lipid-water environment, to determine the strength of receptor dimerization at the different crystallographic interfaces. We note that the shape of the interface plays a dominant role in the strength of the interaction, and the pattern of contacting residues defines the shape of the potential of mean force. This information can be used to guide experiments aimed at exploring the role of dimerization in opioid receptor function. PMID:24651466

  6. Identification of Material Properties of PZT Single Crystals through Crystallographic Homogenization Method

    NASA Astrophysics Data System (ADS)

    Uetsuji, Yasutomo; Tanaka, Satoshi; Tsuchiya, Kazuyoshi; Ueda, Sei; Nakamachi, Eiji

    Single crystals of lead zirconium titanate (PZT) are difficult to fabricate. Thus, not all material properties of PZT have been fully characterized. In this paper, the mechanical and electrical properties of a PZT single crystal, which can be assumed to be identical to those of a crystal grain in a polycrystal, have been computed from those of a polycrystalline PZT ceramic by the steepest decent method and multiscale finite element modeling based on crystallographic homogenization method. Crystallographic homogenization enables us to predict macroscopic properties of ceramics taking into account the inhomogeneous microstructure of an aggregate of crystal grains. The crystal morphology of the PZT ceramic was measured by the SEM·EBSD technique, and the result was used in the microscopic finite element model. Then, the mechanical and electrical properties of the crystal grain were derived by the steepest decent method so that its macroscopic properties would correspond to the measured properties of the PZT ceramic. The proposed computational method was applied to barium titanate (BT) and validated by comparison of the computed material properties with known properties of the BT single crystal. Finally, the computed material properties, such as the elastic compliance, and the dielectric and piezoelectric constants, were presented for the PZT single crystal.

  7. Integration of first-principles methods and crystallographic database searches for new ferroelectrics: Strategies and explorations

    SciTech Connect

    Bennett, Joseph W.; Rabe, Karin M.

    2012-11-15

    In this concept paper, the development of strategies for the integration of first-principles methods with crystallographic database mining for the discovery and design of novel ferroelectric materials is discussed, drawing on the results and experience derived from exploratory investigations on three different systems: (1) the double perovskite Sr(Sb{sub 1/2}Mn{sub 1/2})O{sub 3} as a candidate semiconducting ferroelectric; (2) polar derivatives of schafarzikite MSb{sub 2}O{sub 4}; and (3) ferroelectric semiconductors with formula M{sub 2}P{sub 2}(S,Se){sub 6}. A variety of avenues for further research and investigation are suggested, including automated structure type classification, low-symmetry improper ferroelectrics, and high-throughput first-principles searches for additional representatives of structural families with desirable functional properties. - Graphical abstract: Integration of first-principles methods with crystallographic database mining, for the discovery and design of novel ferroelectric materials, could potentially lead to new classes of multifunctional materials. Highlights: Black-Right-Pointing-Pointer Integration of first-principles methods and database mining. Black-Right-Pointing-Pointer Minor structural families with desirable functional properties. Black-Right-Pointing-Pointer Survey of polar entries in the Inorganic Crystal Structural Database.

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

    NASA Astrophysics Data System (ADS)

    Mojekwu, Nneoma

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

  9. Enhancing nanoscale SEM image segmentation and reconstruction with crystallographic orientation data and machine learning

    SciTech Connect

    Converse, Matthew I. Fullwood, David T.

    2013-09-15

    Current methods of image segmentation and reconstructions from scanning electron micrographs can be inadequate for resolving nanoscale gaps in composite materials (1–20 nm). Such information is critical to both accurate material characterizations and models of piezoresistive response. The current work proposes the use of crystallographic orientation data and machine learning for enhancing this process. It is first shown how a machine learning algorithm can be used to predict the connectivity of nanoscale grains in a Nickel nanostrand/epoxy composite. This results in 71.9% accuracy for a 2D algorithm and 62.4% accuracy in 3D. Finally, it is demonstrated how these algorithms can be used to predict the location of gaps between distinct nanostrands — gaps which would otherwise not be detected with the sole use of a scanning electron microscope. - Highlights: • A method is proposed for enhancing the segmentation/reconstruction of SEM images. • 3D crystallographic orientation data from a nickel nanocomposite is collected. • A machine learning algorithm is used to detect trends in adjacent grains. • This algorithm is then applied to predict likely regions of nanoscale gaps. • These gaps would otherwise be unresolved with the sole use of an SEM.

  10. Synthesis of crystallographically oriented olivine aggregates using colloidal processing in a strong magnetic field

    NASA Astrophysics Data System (ADS)

    Koizumi, Sanae; Suzuki, Tohru S.; Sakka, Yoshio; Yabe, Kosuke; Hiraga, Takehiko

    2016-07-01

    This study develops a fabrication technique to obtain Fe-free and Fe-bearing (Fe:Mg = 1:9) olivine aggregates not only with high density and fine grain size but with crystallographic preferred orientation (CPO). A magnetic field (≤12 T) is applied to synthetic, fine-grained (~120 nm), olivine particles dispersed in solvent. The alignment of certain crystallographic axes of the particles with respect to a magnetic direction is anticipated due to magnetic anisotropy of olivine. The dispersed particles are gradually consolidated on a porous alumina mold covered with a solid-liquid separation filter during drainage of the solvent. The resultant aligned consolidated aggregate is then isostatically pressed and vacuum sintered. We find that (1) preparation of fully reacted olivine particles, with less propensity to coalesce; (2) preparation of a suspension with highly dispersed particles; and (3) application of a certain strength of the magnetic field are essential to obtain well-sintered and well-aligned aggregates. High density (i.e., <1 vol% porosity) and fine grain size (~1 μm) Fe-free and Fe-bearing olivine aggregates were successfully synthesized with uniaxially aligned a- and c-axes, respectively. Attempts to uniaxially align the magnetization hard axis and to triaxially align Fe-bearing olivine by rotating the suspension in the magnetic field succeeded in obtaining weakly developed CPO aggregates.

  11. Effect of tungsten crystallographic orientation on He-ion-induced surface morphology changes

    SciTech Connect

    Parish, Chad M; Hijazi, Hussein Dib; Meyer III, Harry M; Meyer, Fred W

    2014-01-01

    In order to study the early stages of nanofuzz growth in fusion-plasma-facing tungsten, mirror-polished high-purity tungsten was exposed to 80 eV helium at 1130 C to a fluence of 4 1024 He/m2. The previously smooth surface shows morphology changes, and grains form one of four qualitatively different morphologies: smooth, wavy, pyramidal, or terraced/wide waves. Combining high-resolution scanning electron microscopy (SEM) observations to determine the morphology of each grain with quantitative measurement of the grain's orientation via electron backscatter diffraction (EBSD) in SEM shows that the normal-direction crystallographic orientation of the underlying grain controls the growth morphology. Specifically, near-<001> || normal direction (ND) grains formed pyramids, near-<114> to <112> || ND grains formed wavy and stepped structures, and near-<103> || ND grains remained smooth. Comparisons to control specimens indicate no changes to underlying bulk crystallographic texture, and the effects are attributed to surface energy anisotropy, although, surprisingly, the expected {101} low-energy planes were not the most stable. Future developments to control tungsten texture via thermomechanical processing, ideally obtaining a sharp near- <103> || ND processing texture, may delay the formation of nanofuzz.

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

    PubMed Central

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

    2008-01-01

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

  13. Crystallographic structure of Ni-Co coating on the affinity adsorption of histidine-tagged protein.

    PubMed

    Chang, Yaw-Jen; Chen, Sheng-Zheng; Ho, Ching-Yuan

    2015-04-01

    The principle of immobilized metal affinity chromatography (IMAC) has been recently implemented for protein microarrays for the study of protein abundance and function. Ni-Co film fabricated by electrodeposition is a novel microarray surface in an alloy type for immobilizing histidine-tagged proteins based on IMAC. In this paper, the effects of crystallographic structures and surface properties of Ni-Co coatings, with and without the annealing process, on the immobilization of histidine-tagged proteins were systematically investigated. The experimental results reveal that the stronger hcp texture, due to a higher Co content, results in better affinity adsorption for histidine-tagged biotin. Nevertheless, the allotropic phase transformation from hcp to fcc, due to the annealing process, leads to the decrease of affinity adsorption. The wettability property and the surface roughness of Ni-Co coating are, however, not important factors. Obviously, the crystallographic structure of Ni-Co coating is the dominant factor for the specific affinity adsorption of histidine-tagged protein. PMID:25731093

  14. High resolution neutron crystallographic studies of the hydration of coenzyme cob(II)alamin

    SciTech Connect

    Jogl, Gerwald; Wang, Xiaoping; Mason, Sax; Kovalevsky, Andrey; Mustyakimov, Marat; Fisher, Zoe; Hoffmann, Christina; Kratky, Christoph; Langan, Paul

    2011-01-01

    The hydration of coenzyme cob(II)alamin has been studied using high resolution monochromatic neutron crystallographic data collected at room temperature to a resolution of surrounded by flexible side chains with terminal functional groups may be significant for 0.92 on the original diffractometer D19 with a prototype 4o x 64o detector at the high-flux reactor neutron source run by the Institute Laue Langevin. The resulting structure provides H 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 efficient scavenging of ligands. The feasibility of extending the resolution of this structure to ultra high resolution was investigated by collecting time-of-flight neutron crystallographic data on diffractometer TOPAZ with a prototype array of 14 modular 21o x 21o detectors at the Spallation Neutron Source run by Oak Ridge National Laboratory.

  15. Crystallographic study of grain refinement in low and medium carbon steels

    NASA Astrophysics Data System (ADS)

    Li, Ming; Li, Jianmin; Qiu, Dong; Zheng, Qing; Wang, Geoff; Zhang, Ming-Xing

    2016-05-01

    In order to clarify and articulate the long-standing problems associated with the role of various compounds in grain refinement of as-cast steels, a comprehensive crystallographic study on grain refiners in a number of low carbon steels has been conducted using the edge-to-edge matching (E2EM) model, which has been successfully applied to explain and predict effective grain refiners in light metals. Five commonly investigated compounds, namely NbO, CeS, TiN, Ce2O3 and TiC, in steels were examined. According to the extent of crystallographic matching, the predicted grain refining potency of these five grain refiners is ranked in the order of NbO > CeS > TiN > Ce2O3 > TiC, which is consistent with previously reported experimental results. Four different orientation relationships between δ-ferrite and these grain refiners were predicted. One of them has been verified by previously published experimental data. The similarity and the advantages of the E2EM model over conventional Bramfitt's model were also discussed.

  16. Erbium-ion implantation into various crystallographic cuts of Al2O3

    NASA Astrophysics Data System (ADS)

    Nekvindova, P.; Mackova, A.; Malinsky, P.; Cajzl, J.; Svecova, B.; Oswald, J.; Wilhelm, R. A.

    2015-12-01

    This paper reports on the importance of crystallographic cuts with a different orientation on the luminescent properties and structural changes of Al2O3 implanted with Er+ ions at 190 keV and with a fluence of 1.0 × 1016 cm-2. Post-implantation annealing at 1000 °C in oxygen atmosphere was also done. The chemical compositions and erbium concentration-depth profiles of implanted layers were studied by Rutherford Backscattering Spectrometry (RBS) and compared to SRIM simulations. The same value of the maximum erbium concentration (up to 2 at.%) was observed at a depth of about 40 nm for all crystallographic cuts. The structural properties of the prepared layers were characterised by RBS/channelling. The relative amount of disordered atoms of 70-80% was observed in the prepared implanted layers and discussed for various cuts. It has been found that erbium is positioned randomly in the Al2O3 crystalline matrix, and no preferential positions appeared even after the annealing procedure. Erbium luminescence properties were measured in the wavelength range of 1440-1650 nm for all samples. As-implanted Al2O3 samples had a significant luminescence band at 1530 nm. The best luminescence was repeatedly observed in the <0 0 0 1> cut of Al2O3. The annealing procedure significantly improved the luminescent properties.

  17. Distinguishing crystallographic misorientations of lanthanum zirconate epilayers on nickel substrates by electron backscatter diffraction.

    PubMed

    Ji, Yuan; Wang, Li; Zhang, Yinqi; Wei, Bin; Wang, Jianhong; Cheng, Yanling; Suo, Hongli

    2011-04-01

    Electron backscatter diffraction (EBSD) was used for distinguishing crystallographic orientations and local lattice misfits of a La(2)Zr(2)O(7) (LZO) buffer layer epitaxially grown on a cube textured Ni-5.%W (Ni-W) substrate for a YBCO superconductor film. Orientation data were obtained from the LZO epilayer using low energy primary electrons (5keV) and from the Ni-W substrate by increasing the voltage to 15keV. In-plane and out-of-plane orientations of the LZO epilayer were revealed with respect to its Ni-W substrate. A strong {100} 〈011〉 rotated-cube texture in the LZO epilayer was formed on the {100} 〈001〉 cube-textured Ni-W substrates. LZO and Ni in-plane crystallographic axes are related by an expected 45° rotation. The step-misorientations and the local misfit strains between the LZO epilayer and the substrate were also analyzed. PMID:21396525

  18. Structural Model of the Cytosolic Domain of the Plant Ethylene Receptor 1 (ETR1)

    PubMed Central

    Mayerhofer, Hubert; Panneerselvam, Saravanan; Kaljunen, Heidi; Tuukkanen, Anne; Mertens, Haydyn D. T.; Mueller-Dieckmann, Jochen

    2015-01-01

    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. PMID:25451923

  19. Crystallographically controlled crystal-plastic deformation of zircon in shear zones

    NASA Astrophysics Data System (ADS)

    Kovaleva, Elizaveta; Klötzli, Urs

    2014-05-01

    Plastically-deformed zircons from various types of strained natural metamorphic rocks have been investigated in-situ by electron backscatter diffraction analysis (EBSD), allowing crystallographic orientation mapping at high spatial resolution. Plastic deformation often forms under the control of grain-internal heterogeneities. At the crystal structure scale deformation is controlled by the physical anisotropy of the lattice. Three most common slip systems in zircon are [100]{010}, [010]{001} and [001]{010} (Leroux et. al., 1999; Reddy et. al., 2007). They are genetically connected with the main zircon crystallographic directions: [001] (c-axis), [100] and [010] (a and b axes). Atomic models show weak planes normal to these directions that preferably evolve to glide planes in the deforming crystal. The visualization of seismic (elastic) properties of zircon with the MATLAB toolbox MTEX shows a similar pattern. The slowest S-wave velocities are observed in directions parallel to [100], [010] and [001] crystallographic directions. The highest Young's modulus values lie in the same directions. In natural zircon grains, the common slip systems are preferably activated when zircon is hosted by rheologically comparatively weaker phases or a fine-grained matrix. In these cases zircon behaves as a rigid clast. During progressive deformation high deviatoric stresses together with high strain rates concentrate at crystal tips, as shown by numerical modeling. Softer host phases allow more degrees of freedom for zircon to be deformed according to its crystallographic and internal properties. These conclusions are supported by the misorientation axes density distribution maps, derived with MTEX. Deformed zircon hosted by a relatively soft phase (mostly biotite) develops a crystallographic preferred orientation (CPO), which has not been documented for zircon before. At the same time deformation of zircon hosted by a rheologically stronger matrix causes the activation of less

  20. Time-domain imaging

    NASA Technical Reports Server (NTRS)

    Tolliver, C. L.

    1989-01-01

    The quest for the highest resolution microwave imaging and principle of time-domain imaging has been the primary motivation for recent developments in time-domain techniques. With the present technology, fast time varying signals can now be measured and recorded both in magnitude and in-phase. It has also enhanced our ability to extract relevant details concerning the scattering object. In the past, the interface of object geometry or shape for scattered signals has received substantial attention in radar technology. Various scattering theories were proposed to develop analytical solutions to this problem. Furthermore, the random inversion, frequency swept holography, and the synthetic radar imaging, have two things in common: (1) the physical optic far-field approximation, and (2) the utilization of channels as an extra physical dimension, were also advanced. Despite the inherent vectorial nature of electromagnetic waves, these scalar treatments have brought forth some promising results in practice with notable examples in subsurface and structure sounding. The development of time-domain techniques are studied through the theoretical aspects as well as experimental verification. The use of time-domain imaging for space robotic vision applications has been suggested.

  1. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, O.; Shpiegl, I.; Goldstein, M.; Doi, R.

    1998-11-17

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

  2. Cellulose binding domain proteins

    DOEpatents

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  3. Nanoscale imaging of grain orientations and ferroelectric domains in (Bi1-xLax)4Ti3O12 films for ferroelectric memories

    NASA Astrophysics Data System (ADS)

    Yang, B.; Park, N. J.; Seo, B. I.; Oh, Y. H.; Kim, S. J.; Hong, S. K.; Lee, S. S.; Park, Y. J.

    2005-08-01

    We report results of nanoscopic investigation of grain crystallographic orientations and ferroelectric domains by electron backscatter diffraction (EBSD) technique and piezoresponse force microscope (PFM), respectively, in (Bi1-xLax)4Ti3O12 (BLT) films for ferroelectric semiconductor memories. It is demonstrated that the EBSD technique is useful in characterizing nanoscale grain crystallographic orientations of BLT films. Comparison studies of grain orientations by EBSD technique and switching properties of ferroelectric domains by PFM show that c-axis parallel to normal oriented grains with almost linear dielectric properties have platelike morphology. However, a- or b-axis oriented grains with superior ferroelectric properties have ellipsoidal morphology with a size of less than 0.2μm in long axis. Consequently, the suppression of the platelike structures through process controls is important for the realization of high-density BLT-based memories.

  4. Qplus AFM driven nanostencil.

    PubMed

    Grévin, B; Fakir, M; Hayton, J; Brun, M; Demadrille, R; Faure-Vincent, J

    2011-06-01

    We describe the development of a novel setup, in which large stencils with suspended silicon nitride membranes are combined with atomic force microscopy (AFM) regulation by using tuning forks. This system offers the possibility to perform separate AFM and nanostencil operations, as well as combined modes when using stencil chips with integrated tips. The flexibility and performances are demonstrated through a series of examples, including wide AFM scans in closed loop mode, probe positioning repeatability of a few tens of nanometer, simultaneous evaporation of large (several hundred of micron square) and nanoscopic metals and fullerene patterns in static, multistep, and dynamic modes. This approach paves the way for further developments, as it fully combines the advantages of conventional stenciling with the ones of an AFM driven shadow mask. PMID:21721701

  5. Muscle-driven nanogenerators

    DOEpatents

    Wang, Zhong L.; Yang, Rusen

    2011-03-01

    In a method of generating electricity, a plurality of living cells are grown on an array of piezoelectric nanowires so that the cells engage the piezoelectric nanowires. Induced static potentials are extracted from at least one of the piezoelectric nanowires when at least one of the cells deforms the at least one of the piezoelectric nanowires. A cell-driven electrical generator that includes a substrate and a plurality of spaced-apart piezoelectric nanowires disposed on the substrate. A plurality of spaced-apart conductive electrodes interact with the plurality of piezoelectric nanowires. A biological buffer layer that is configured to promote growth of cells is disposed on the substrate so that cells placed on the substrate will grow and engage the piezoelectric nanowires.

  6. Soliton driven angiogenesis

    PubMed Central

    Bonilla, L. L.; Carretero, M.; Terragni, F.; Birnir, B.

    2016-01-01

    Angiogenesis is a multiscale process by which blood vessels grow from existing ones and carry oxygen to distant organs. Angiogenesis is essential for normal organ growth and wounded tissue repair but it may also be induced by tumours to amplify their own growth. Mathematical and computational models contribute to understanding angiogenesis and developing anti-angiogenic drugs, but most work only involves numerical simulations and analysis has lagged. A recent stochastic model of tumour-induced angiogenesis including blood vessel branching, elongation, and anastomosis captures some of its intrinsic multiscale structures, yet allows one to extract a deterministic integropartial differential description of the vessel tip density. Here we find that the latter advances chemotactically towards the tumour driven by a soliton (similar to the famous Korteweg-de Vries soliton) whose shape and velocity change slowly. Analysing these collective coordinates paves the way for controlling angiogenesis through the soliton, the engine that drives this process. PMID:27503562

  7. Steady Capillary Driven Flow

    NASA Technical Reports Server (NTRS)

    Weislogel, Mark M.

    1996-01-01

    A steady capillary driven flow is developed for a liquid index in a circular tube which is partially coated with a surface modifier to produce a discontinuous wetting condition from one side of the tube to the other. The bulk flow is novel in that it is truly steady, and controlled solely by the physics associated with dynamic wetting. The influence of gravity on the flow is minimized through the use of small diameter tubes approximately O(1 mm) tested horizontally in a laboratory and larger tubes approximately O(10 mm) tested in the low gravity environment of a drop tower. Average steady velocities are predicted and compared against a large experimental data set which includes the effects of tube dimensions and fluid properties. The sensitivity of the velocity to surface cleanliness is dramatic and the advantages of experimentation in a microgravity environment are discussed.

  8. Consistent model driven architecture

    NASA Astrophysics Data System (ADS)

    Niepostyn, Stanisław J.

    2015-09-01

    The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.

  9. Multilane driven diffusive systems

    NASA Astrophysics Data System (ADS)

    Curatolo, A. I.; Evans, M. R.; Kafri, Y.; Tailleur, J.

    2016-03-01

    We consider networks made of parallel lanes along which particles hop according to driven diffusive dynamics. The particles also hop transversely from lane to lane, hence indirectly coupling their longitudinal dynamics. We present a general method for constructing the phase diagram of these systems which reveals that in many cases their physics reduce to that of single-lane systems. The reduction to an effective single-lane description legitimizes, for instance, the use of a single TASEP to model the hopping of molecular motors along the many tracks of a single microtubule. Then, we show how, in quasi-2D settings, new phenomena emerge due to the presence of non-zero transverse currents, leading, for instance, to strong ‘shear localization’ along the network.

  10. Soliton driven angiogenesis

    NASA Astrophysics Data System (ADS)

    Bonilla, L. L.; Carretero, M.; Terragni, F.; Birnir, B.

    2016-08-01

    Angiogenesis is a multiscale process by which blood vessels grow from existing ones and carry oxygen to distant organs. Angiogenesis is essential for normal organ growth and wounded tissue repair but it may also be induced by tumours to amplify their own growth. Mathematical and computational models contribute to understanding angiogenesis and developing anti-angiogenic drugs, but most work only involves numerical simulations and analysis has lagged. A recent stochastic model of tumour-induced angiogenesis including blood vessel branching, elongation, and anastomosis captures some of its intrinsic multiscale structures, yet allows one to extract a deterministic integropartial differential description of the vessel tip density. Here we find that the latter advances chemotactically towards the tumour driven by a soliton (similar to the famous Korteweg-de Vries soliton) whose shape and velocity change slowly. Analysing these collective coordinates paves the way for controlling angiogenesis through the soliton, the engine that drives this process.

  11. Soliton driven angiogenesis.

    PubMed

    Bonilla, L L; Carretero, M; Terragni, F; Birnir, B

    2016-01-01

    Angiogenesis is a multiscale process by which blood vessels grow from existing ones and carry oxygen to distant organs. Angiogenesis is essential for normal organ growth and wounded tissue repair but it may also be induced by tumours to amplify their own growth. Mathematical and computational models contribute to understanding angiogenesis and developing anti-angiogenic drugs, but most work only involves numerical simulations and analysis has lagged. A recent stochastic model of tumour-induced angiogenesis including blood vessel branching, elongation, and anastomosis captures some of its intrinsic multiscale structures, yet allows one to extract a deterministic integropartial differential description of the vessel tip density. Here we find that the latter advances chemotactically towards the tumour driven by a soliton (similar to the famous Korteweg-de Vries soliton) whose shape and velocity change slowly. Analysing these collective coordinates paves the way for controlling angiogenesis through the soliton, the engine that drives this process. PMID:27503562

  12. 4He behavior in calcite filling viewed by (U-Th)/He dating, 4He diffusion and crystallographic studies

    NASA Astrophysics Data System (ADS)

    Cros, Alexandre; Gautheron, Cécile; Pagel, Maurice; Berthet, Patrick; Tassan-Got, Laurent; Douville, Eric; Pinna-Jamme, Rosella; Sarda, Philippe

    2014-01-01

    Fault-filling calcite crystals sampled from the Eocene/Oligocene Gondrecourt graben, Paris Basin, Eastern France, have been studied in order to test the potentiality of calcite (U-Th)/He dating, based on recognized He retention behavior in crystal lattice at surface temperature (Copeland et al., 2007). The samples have been selected because of their relatively old Eocene to Oligocene precipitation age and cold thermal history (<40 °C since precipitation). They were sorted into three main tectonic and morphological groups in order of precipitation, including (1) micro-fracture calcites, (2) breccia and associated geodic calcites, and (3) vein and associated geodic calcites. (U-Th)/He dating of 63 calcite fragments yields ages dispersed from 0.2 ± 0.02 to 35.8 ± 2.7 Ma, as well as two older dates of 117 ± 10 and 205 ± 28 Ma (1σ). These He ages correlate with grain chemistry, such as Sr, ΣREE concentrations or (La/Yb)N ratios, likely reflecting parent fluid evolution. Only the oldest He ages, which correspond to the most recently precipitated crystals, have preserved the total 4He budget since precipitation. To better understand both the age dispersion and why calcites precipitated earlier show younger ages, 4He diffusion experiments have been conducted on 10 Gondrecourt calcite fragments from 3 samples with He ages of ∼0.2-6 Ma. Additionally, a crystallographic investigation by X-ray diffraction (XRD) performed on similar samples reveals that crystal structure evolves with increasing temperature, beginning with micro-cracks and cleavage opening. These XRD results shed light on the (U-Th)/He data, indicating that, in fault-filling calcite, He retention is controlled by multiple diffusion domains (MDD) with various sizes, and therefore, evolves through time with strong consequences on (U-Th)/He age. We thus interpret the Gondrecourt calcite (U-Th)/He age scatter as a consequence of the production of defects due to successive calcite crystallization phases

  13. Fluid-driven metamorphism

    NASA Astrophysics Data System (ADS)

    Jamtveit, B.; Ulven, O. I.; Malthe-Sorenssen, A.

    2014-12-01

    Metamorphic processes in the Earth crust are almost invariably associated with fluid migration. Many lines of evidence suggest that fluid migration is intimately coupled both to the metamorphic reactions, and to associated deformation processes. Petrologic arguments suggest that all granulite facies and most amphibolite facies rocks are essentially dry (no free fluid phase) at normal geothermal gradients outside periods of heating-produced fluid generation. In addition, except at high pressure - low temperature condition, fluid-consuming reactions leads to an increase in solid volume and a potential clogging of any initial pore space. Hence, fluid migration in medium and high-grade metamorphic rocks is in general associated with some porosity producing process. Porosity generation may occur by either chemical or mechanical processes. In systems with high fluid fluxes, porosity may be produced by dissolution and transport of mass out of the system. Such fluxes can normally only be sustained over short length scales and limited time scales. In systems where the infiltrating fluid is far from equilibrium with the rock matrix, mechanical porosity generation can arise from local stresses generated by the volume change of volatilization reactions. Furthermore, it has become increasingly clear that crustal rocks may be under significant tectonic stress, even far from plate tectonic boundaries. In situations where the rocks are close to critically stressed, any stress perturbations caused by reaction driven changes in solid volume or fluid pressure gradients may lead to dilatant deformation and porosity production on a scale much larger than the characteristic length scales of the reacting rock units. Field observations, experimental studies and modeling results will be presented that focus on reaction driven porosity generation in systems subject to variable initial differential stresses.

  14. Expansion and relaxation of magnetic mirror domains in a Pt/Co/Pt/Co/Pt multilayer with antiferromagnetic interlayer coupling

    NASA Astrophysics Data System (ADS)

    Metaxas, P. J.; Stamps, R. L.; Jamet, J.-P.; Ferré, J.; Baltz, V.; Rodmacq, B.

    2012-01-01

    We detail measurements of field-driven expansion and zero-field relaxation of magnetic mirror domains in antiferromagnetically coupled perpendicularly magnetized ultrathin Co layers. The zero-field stability of aligned ('mirror') domains in such systems results from non-homogeneous dipolar stray fields which exist in the vicinity of the domain walls. During field-driven domain expansion, we evidence a separation of the domain walls which form the mirror domain boundary. However, the walls realign, thereby reforming a mirror domain, if their final separation is below a critical distance at the end of the field pulse. This critical distance marks the point at which the effective net interaction between the walls changes from attractive to repulsive.

  15. Expansion and relaxation of magnetic mirror domains in a Pt/Co/Pt/Co/Pt multilayer with antiferromagnetic interlayer coupling.

    PubMed

    Metaxas, P J; Stamps, R L; Jamet, J-P; Ferré, J; Baltz, V; Rodmacq, B

    2012-01-18

    We detail measurements of field-driven expansion and zero-field relaxation of magnetic mirror domains in antiferromagnetically coupled perpendicularly magnetized ultrathin Co layers. The zero-field stability of aligned ('mirror') domains in such systems results from non-homogeneous dipolar stray fields which exist in the vicinity of the domain walls. During field-driven domain expansion, we evidence a separation of the domain walls which form the mirror domain boundary. However, the walls realign, thereby reforming a mirror domain, if their final separation is below a critical distance at the end of the field pulse. This critical distance marks the point at which the effective net interaction between the walls changes from attractive to repulsive. PMID:22173339

  16. Mechanically Shaped Two-Dimensional Covalent Organic Frameworks Reveal Crystallographic Alignment and Fast Li-Ion Conductivity.

    PubMed

    Vazquez-Molina, Demetrius A; Mohammad-Pour, Gavin S; Lee, Chain; Logan, Matthew W; Duan, Xiangfeng; Harper, James K; Uribe-Romo, Fernando J

    2016-08-10

    Covalent organic frameworks (COFs) usually crystallize as insoluble powders, and their processing for suitable devices is thought to be limited. We demonstrate that COFs can be mechanically pressed into shaped objects having anisotropic ordering with preferred orientation between hk0 and 00l crystallographic planes. Five COFs with different functionality and symmetry exhibited similar crystallographic behavior and remarkable stability, indicating the generality of this processing. Pellets prepared from bulk COF powders impregnated with LiClO4 displayed room temperature conductivity up to 0.26 mS cm(-1) and high electrochemical stability. This outcome portends use of COFs as solid-state electrolytes in batteries. PMID:27414065

  17. Dynamics of antiferromagnets driven by spin current

    NASA Astrophysics Data System (ADS)

    Cheng, Ran; Niu, Qian

    2014-02-01

    When a spin-polarized current flows through a ferromagnetic (FM) metal, angular momentum is transferred to the background magnetization via spin-transfer torques. In antiferromagnetic (AFM) materials, however, the corresponding problem is unsolved. We derive microscopically the dynamics of an AFM system driven by spin current generated by an attached FM polarizer, and find that the spin current exerts a driving force on the local staggered order parameter. The mechanism does not rely on the conservation of spin angular momentum, nor does it depend on the induced FM moments on top the AFM background. Two examples are studied: (i) A domain wall is accelerated to a terminal velocity by purely adiabatic effect where the Walker's breakdown is avoided. (ii) Spin injection modifies the AFM resonance frequency, and spin current injection triggers spin wave instability of local moments above a threshold.

  18. OMOGENIA: A Semantically Driven Collaborative Environment

    NASA Astrophysics Data System (ADS)

    Liapis, Aggelos

    Ontology creation can be thought of as a social procedure. Indeed the concepts involved in general need to be elicited from communities of domain experts and end-users by teams of knowledge engineers. Many problems in ontology creation appear to resemble certain problems in software design, particularly with respect to the setup of collaborative systems. For instance, the resolution of conceptual conflicts between formalized ontologies is a major engineering problem as ontologies move into widespread use on the semantic web. Such conflict resolution often requires human collaboration and cannot be achieved by automated methods with the exception of simple cases. In this chapter we discuss research in the field of computer-supported cooperative work (CSCW) that focuses on classification and which throws light on ontology building. Furthermore, we present a semantically driven collaborative environment called OMOGENIA as a natural way to display and examine the structure of an evolving ontology in a collaborative setting.

  19. High domain wall velocities via spin transfer torque using vertical current injection

    PubMed Central

    Metaxas, Peter J.; Sampaio, Joao; Chanthbouala, André; Matsumoto, Rie; Anane, Abdelmadjid; Fert, Albert; Zvezdin, Konstantin A.; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Maehara, Hiroki; Tsunekawa, Koji; Cros, Vincent; Grollier, Julie

    2013-01-01

    Domain walls, nanoscale transition regions separating oppositely oriented ferromagnetic domains, have significant promise for use in spintronic devices for data storage and memristive applications. The state of these devices is related to the wall position and thus rapid operation will require a controllable onset of domain wall motion and high speed wall displacement. These processes are traditionally driven by spin transfer torque due to lateral injection of spin polarized current through a ferromagnetic nanostrip. However, this geometry is often hampered by low maximum wall velocities and/or a need for prohibitively high current densities. Here, using time-resolved magnetotransport measurements, we show that vertical injection of spin currents through a magnetic tunnel junction can drive domain walls over hundreds of nanometers at ~500 m/s using current densities on the order of 6 MA/cm2. Moreover, these measurements provide information about the stochastic and deterministic aspects of current driven domain wall mediated switching. PMID:23670402

  20. High domain wall velocities via spin transfer torque using vertical current injection.

    PubMed

    Metaxas, Peter J; Sampaio, Joao; Chanthbouala, André; Matsumoto, Rie; Anane, Abdelmadjid; Fert, Albert; Zvezdin, Konstantin A; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Maehara, Hiroki; Tsunekawa, Koji; Cros, Vincent; Grollier, Julie

    2013-01-01

    Domain walls, nanoscale transition regions separating oppositely oriented ferromagnetic domains, have significant promise for use in spintronic devices for data storage and memristive applications. The state of these devices is related to the wall position and thus rapid operation will require a controllable onset of domain wall motion and high speed wall displacement. These processes are traditionally driven by spin transfer torque due to lateral injection of spin polarized current through a ferromagnetic nanostrip. However, this geometry is often hampered by low maximum wall velocities and/or a need for prohibitively high current densities. Here, using time-resolved magnetotransport measurements, we show that vertical injection of spin currents through a magnetic tunnel junction can drive domain walls over hundreds of nanometers at ~500 m/s using current densities on the order of 6 MA/cm(2). Moreover, these measurements provide information about the stochastic and deterministic aspects of current driven domain wall mediated switching. PMID:23670402

  1. High domain wall velocities via spin transfer torque using vertical current injection

    NASA Astrophysics Data System (ADS)

    Metaxas, Peter J.; Sampaio, Joao; Chanthbouala, André; Matsumoto, Rie; Anane, Abdelmadjid; Fert, Albert; Zvezdin, Konstantin A.; Yakushiji, Kay; Kubota, Hitoshi; Fukushima, Akio; Yuasa, Shinji; Nishimura, Kazumasa; Nagamine, Yoshinori; Maehara, Hiroki; Tsunekawa, Koji; Cros, Vincent; Grollier, Julie

    2013-05-01

    Domain walls, nanoscale transition regions separating oppositely oriented ferromagnetic domains, have significant promise for use in spintronic devices for data storage and memristive applications. The state of these devices is related to the wall position and thus rapid operation will require a controllable onset of domain wall motion and high speed wall displacement. These processes are traditionally driven by spin transfer torque due to lateral injection of spin polarized current through a ferromagnetic nanostrip. However, this geometry is often hampered by low maximum wall velocities and/or a need for prohibitively high current densities. Here, using time-resolved magnetotransport measurements, we show that vertical injection of spin currents through a magnetic tunnel junction can drive domain walls over hundreds of nanometers at ~500 m/s using current densities on the order of 6 MA/cm2. Moreover, these measurements provide information about the stochastic and deterministic aspects of current driven domain wall mediated switching.

  2. Effect of crystallographic orientation on hillock formation in thermally cycled large grain tin films

    NASA Astrophysics Data System (ADS)

    Koppes, John Patrick

    Tin whiskers and hillocks grow spontaneously from the surfaces of polycrystalline Sn films at room temperature. Whiskers can grow long enough to cause short circuits in electronic devices. We hypothesized that the anisotropies of the crystal structure lead to locally high strain energies that are relieved by the growth of whiskers and hillocks. This research studies hillock formations on large grain Sn-alloy films relative to the crystallographic orientations of the adjacent grains. Large grain films were produced by solidifying 96.5wt% Sn - 3wt% Ag - 0.5wt% Cu solder alloy on a Cu substrate. These surface defects (hillocks) grew predominately at grain boundaries during thermal cycling. The formation of the surface defects between two grains created a pseudo-bi-crystal sample geometry, making it ideal for studying surface defects relative to the local crystallographic orientations and the grains' corresponding anisotropic properties. The crystallographic orientations of the grains were studied with Electron Backscatter Diffraction (EBSD) and Laue micro-diffraction at the Lawrence Berkeley National Laboratory Advanced Light Source. Local orientation studies of the surface defects and the surrounding grains indicated that the surface defects nucleated and grew with low dislocation densities. In addition, the linear surface defect densities along the grain boundaries were measured and observed to change as a function of orientation. The change in linear defect density with respect to orientation was due, in part, to the anisotropy of the coefficient of thermal expansion of β-Sn. In addition, it was important to account for elastic anisotropies. The elastic stresses, strains, and strain energy densities of the microstructures were determined with Object Oriented Finite element analysis. The simulations indicated that during thermal cycling the local stresses exceeded the yield strength. As a result, the highest linear defect densities did not occur at orientations

  3. Discontinuous properties of current-induced magnetic domain wall depinning

    PubMed Central

    Hu, X. F.; Wu, J.; Niu, D. X.; Chen, L.; Morton, S. A.; Scholl, A.; Huang, Z. C.; Zhai, Y.; Zhang, W.; Will, I.; Xu, Y. B.; Zhang, R.; van der Laan, G.

    2013-01-01

    The current-induced motion of magnetic domain walls (DWs) confined to nanostructures is of great interest for fundamental studies as well as for technological applications in spintronic devices. Here, we present magnetic images showing the depinning properties of pulse-current-driven domain walls in well-shaped Permalloy nanowires obtained using photoemission electron microscopy combined with x-ray magnetic circular dichroism. In the vicinity of the threshold current density (Jth = 4.2 × 1011 A.m−2) for the DW motion, discontinuous DW depinning and motion have been observed as a sequence of “Barkhausen jumps”. A one-dimensional analytical model with a piecewise parabolic pinning potential has been introduced to reproduce the DW hopping between two nearest neighbour sites, which reveals the dynamical nature of the current-driven DW motion in the depinning regime. PMID:24170087

  4. Tunable chiral spin texture in magnetic domain-walls.

    PubMed

    Franken, J H; Herps, M; Swagten, H J M; Koopmans, B

    2014-01-01

    Magnetic domain-walls (DWs) with a preferred chirality exhibit very efficient current-driven motion. Since structural inversion asymmetry (SIA) is required for their stability, the observation of chiral domain walls in highly symmetric Pt/Co/Pt is intriguing. Here, we tune the layer asymmetry in this system and observe, by current-assisted DW depinning experiments, a small chiral field which sensitively changes. Moreover, we convincingly link the observed efficiency of DW motion to the DW texture, using DW resistance as a direct probe for the internal orientation of the DW under the influence of in-plane fields. The very delicate effect of capping layer thickness on the chiral field allows for its accurate control, which is important in designing novel materials for optimal spin-orbit-torque-driven DW motion. PMID:24919162

  5. Tunable chiral spin texture in magnetic domain-walls

    NASA Astrophysics Data System (ADS)

    Franken, J. H.; Herps, M.; Swagten, H. J. M.; Koopmans, B.

    2014-06-01

    Magnetic domain-walls (DWs) with a preferred chirality exhibit very efficient current-driven motion. Since structural inversion asymmetry (SIA) is required for their stability, the observation of chiral domain walls in highly symmetric Pt/Co/Pt is intriguing. Here, we tune the layer asymmetry in this system and observe, by current-assisted DW depinning experiments, a small chiral field which sensitively changes. Moreover, we convincingly link the observed efficiency of DW motion to the DW texture, using DW resistance as a direct probe for the internal orientation of the DW under the influence of in-plane fields. The very delicate effect of capping layer thickness on the chiral field allows for its accurate control, which is important in designing novel materials for optimal spin-orbit-torque-driven DW motion.

  6. Simplified Parallel Domain Traversal

    SciTech Connect

    Erickson III, David J

    2011-01-01

    Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel programming approaches, we have designed DStep, a flexible system that greatly simplifies efficient parallelization of domain traversal techniques at scale. In order to deliver both simplicity to users as well as scalability on HPC platforms, we introduce a novel two-tiered communication architecture for managing and exploiting asynchronous communication loads. We also integrate our design with advanced parallel I/O techniques that operate directly on native simulation output. We demonstrate DStep by performing teleconnection analysis across ensemble runs of terascale atmospheric CO{sub 2} and climate data, and we show scalability results on up to 65,536 IBM BlueGene/P cores.

  7. Bleb-driven chemotaxis of Dictyostelium cells.

    PubMed

    Zatulovskiy, Evgeny; Tyson, Richard; Bretschneider, Till; Kay, Robert R

    2014-03-17

    Blebs and F-actin-driven pseudopods are alternative ways of extending the leading edge of migrating cells. We show that Dictyostelium cells switch from using predominantly pseudopods to blebs when migrating under agarose overlays of increasing stiffness. Blebs expand faster than pseudopods leaving behind F-actin scars, but are less persistent. Blebbing cells are strongly chemotactic to cyclic-AMP, producing nearly all of their blebs up-gradient. When cells re-orientate to a needle releasing cyclic-AMP, they stereotypically produce first microspikes, then blebs and pseudopods only later. Genetically, blebbing requires myosin-II and increases when actin polymerization or cortical function is impaired. Cyclic-AMP induces transient blebbing independently of much of the known chemotactic signal transduction machinery, but involving PI3-kinase and downstream PH domain proteins, CRAC and PhdA. Impairment of this PI3-kinase pathway results in slow movement under agarose and cells that produce few blebs, though actin polymerization appears unaffected. We propose that mechanical resistance induces bleb-driven movement in Dictyostelium, which is chemotactic and controlled through PI3-kinase. PMID:24616222

  8. Accelerating Science Driven System Design With RAMP

    SciTech Connect

    Wawrzynek, John

    2015-05-01

    Researchers from UC Berkeley, in collaboration with the Lawrence Berkeley National Lab, are engaged in developing an Infrastructure for Synthesis with Integrated Simulation (ISIS). The ISIS Project was a cooperative effort for “application-driven hardware design” that engages application scientists in the early parts of the hardware design process for future generation supercomputing systems. This project served to foster development of computing systems that are better tuned to the application requirements of demanding scientific applications and result in more cost-effective and efficient HPC system designs. In order to overcome long conventional design-cycle times, we leveraged reconfigurable devices to aid in the design of high-efficiency systems, including conventional multi- and many-core systems. The resulting system emulation/prototyping environment, in conjunction with the appropriate intermediate abstractions, provided both a convenient user programming experience and retained flexibility, and thus efficiency, of a reconfigurable platform. We initially targeted the Berkeley RAMP system (Research Accelerator for Multiple Processors) as that hardware emulation environment to facilitate and ultimately accelerate the iterative process of science-driven system design. Our goal was to develop and demonstrate a design methodology for domain-optimized computer system architectures. The tangible outcome is a methodology and tools for rapid prototyping and design-space exploration, leading to highly optimized and efficient HPC systems.

  9. Bleb-driven chemotaxis of Dictyostelium cells

    PubMed Central

    Zatulovskiy, Evgeny; Tyson, Richard; Bretschneider, Till

    2014-01-01

    Blebs and F-actin–driven pseudopods are alternative ways of extending the leading edge of migrating cells. We show that Dictyostelium cells switch from using predominantly pseudopods to blebs when migrating under agarose overlays of increasing stiffness. Blebs expand faster than pseudopods leaving behind F-actin scars, but are less persistent. Blebbing cells are strongly chemotactic to cyclic-AMP, producing nearly all of their blebs up-gradient. When cells re-orientate to a needle releasing cyclic-AMP, they stereotypically produce first microspikes, then blebs and pseudopods only later. Genetically, blebbing requires myosin-II and increases when actin polymerization or cortical function is impaired. Cyclic-AMP induces transient blebbing independently of much of the known chemotactic signal transduction machinery, but involving PI3-kinase and downstream PH domain proteins, CRAC and PhdA. Impairment of this PI3-kinase pathway results in slow movement under agarose and cells that produce few blebs, though actin polymerization appears unaffected. We propose that mechanical resistance induces bleb-driven movement in Dictyostelium, which is chemotactic and controlled through PI3-kinase. PMID:24616222

  10. Magnetic bubble domain memories

    NASA Technical Reports Server (NTRS)

    Ypma, J. E.

    1974-01-01

    Some attractive features of Bubble Domain Memory and its relation to existing technologies are discussed. Two promising applications are block access mass memory and tape recorder replacement. The required chip capabilities for these uses are listed, and the specifications for a block access mass memory designed to fit between core and HPT disk are presented. A feasibility model for a tape recorder replacement is introduced.

  11. Graphene films with large domain size by a two-step chemical vapor deposition process.

    PubMed

    Li, Xuesong; Magnuson, Carl W; Venugopal, Archana; An, Jinho; Suk, Ji Won; Han, Boyang; Borysiak, Mark; Cai, Weiwei; Velamakanni, Aruna; Zhu, Yanwu; Fu, Lianfeng; Vogel, Eric M; Voelkl, Edgar; Colombo, Luigi; Ruoff, Rodney S

    2010-11-10

    The fundamental properties of graphene are making it an attractive material for a wide variety of applications. Various techniques have been developed to produce graphene and recently we discovered the synthesis of large area graphene by chemical vapor deposition (CVD) of methane on Cu foils. We also showed that graphene growth on Cu is a surface-mediated process and the films were polycrystalline with domains having an area of tens of square micrometers. In this paper, we report on the effect of growth parameters such as temperature, and methane flow rate and partial pressure on the growth rate, domain size, and surface coverage of graphene as determined by Raman spectroscopy, and transmission and scanning electron microscopy. On the basis of the results, we developed a two-step CVD process to synthesize graphene films with domains having an area of hundreds of square micrometers. Scanning electron microscopy and Raman spectroscopy clearly show an increase in domain size by changing the growth parameters. Transmission electron microscopy further shows that the domains are crystallographically rotated with respect to each other with a range of angles from about 13 to nearly 30°. Electrical transport measurements performed on back-gated FETs show that overall films with larger domains tend to have higher carrier mobility up to about 16,000 cm(2) V(-1) s(-1) at room temperature. PMID:20957985

  12. Crystallographic growth and alignment of carbon nanotubes on few-layer graphene

    NASA Astrophysics Data System (ADS)

    Arash, Aram; Hunley, Patrick D.; Nasseri, Mohsen; Boland, Mathias J.; Sundararajan, Abhishek; Hudak, Bethany M.; Guiton, Beth S.; Strachan, Douglas R.

    2015-03-01

    Hybrid carbon nanotube and graphene structures are emerging as an exciting material system built from a common sp2 carbon backbone. Such hybrid systems have promise for use in improving the performance of energy storage and high-speed electronic applications. Towards the attainment of such hybrid materials, the catalytic growth and crystallographic alignment of these integrated structures are investigated along with the atomic-scale features of their interfaces. The catalytic activity of nanoparticles to form carbon nanotubes on the surface of few-layer graphene is tuned through precise feedstock application. Through careful materials synthesis, the interfaces of these hybrid carbon nanotube - graphene systems are investigated through ultra-high resolution electron microscopy.

  13. Anomalous polarization dependence of Raman scattering and crystallographic orientation of black phosphorus.

    PubMed

    Kim, Jungcheol; Lee, Jae-Ung; Lee, Jinhwan; Park, Hyo Ju; Lee, Zonghoon; Lee, Changgu; Cheong, Hyeonsik

    2015-11-28

    We investigated polarization dependence of the Raman modes in black phosphorus (BP) using five different excitation wavelengths. The crystallographic orientation was determined by comparing polarized optical microscopy with high-resolution transmission electron microscopy analysis. In polarized Raman spectroscopy, the B2g mode shows the same polarization dependence regardless of the excitation wavelength or the sample thickness. On the other hand, the Ag(1) and Ag(2) modes show a peculiar polarization behavior that depends on the excitation wavelength and the sample thickness. The thickness dependence can be explained by considering the anisotropic interference effect due to the birefringence and dichroism of the BP crystal, but the wavelength dependence cannot be explained. We propose a simple and fail-proof procedure to determine the orientation of a BP crystal by combining polarized Raman scattering with polarized optical microscopy. PMID:26503032

  14. EBSD study on crystallographic texture and microstructure development of cold-rolled FePd alloy

    SciTech Connect

    Lin, Hung-Pin; Ng, Tin-San; Kuo, Jui-Chao; Chen, Yen-Chun; Chen, Chun-Liang; Ding, Shi-Xuan

    2014-07-01

    The crystallographic texture and microstructure of FePd alloy after cold-rolling deformation were investigated using electron backscatter diffraction. The major orientations of twin copper and copper after 50% thickness reduction were observed in face-centered cubic-disordered FePd alloy, whereas the main orientation was obtained from brass type after 90% cold rolling. Increase in cold rolling resulted in the change of preferred orientation from copper to brass. Decrease in orientation intensity of copper also increased that of Goss and brass. - Highlights: • The evolution of texture and microstructure in FePd alloy was investigated after cold rolling using EBSD. • Increasing in reduction leads to the change of texture from Copper-type to Brass-type. • The reduction of Copper orientation results in increasing in Goss and Brass orientations.

  15. Crystallization and preliminary X-ray crystallographic analysis of rabbit l-gulonate 3-dehydrogenase

    SciTech Connect

    Asada, Yukuhiko; Kuroishi, Chizu; Ukita, Yoko; Sumii, Rie; Endo, Satoshi; Matsunaga, Toshiyuki; Hara, Akira; Kunishima, Naoki

    2008-03-01

    The preliminary X-ray crystallographic study of rabbit l-gulonate 3-dehydrogenase is described. Rabbit l-gulonate 3-dehydrogenase was crystallized using the oil-microbatch method at 295 K. X-ray diffraction data were collected to 1.70 Å resolution from a crystal at 100 K using synchrotron radiation. The crystal belongs to the C-centred monoclinic space group C2, with unit-cell parameters a = 71.81, b = 69.08, c = 65.64 Å, β = 102.7°. Assuming the presence of a monomeric protomer in the asymmetric unit gives a V{sub M} value of 2.21 Å{sup 3} Da{sup −1} and a solvent content of 44.4%. A cocrystal with NADH, which was isomorphous to the apo form, was also prepared and diffraction data were collected to 1.85 Å resolution using Cu Kα radiation at 100 K.

  16. Intrinsic Compressibility of Sperm Whale Myoglobin Determined from High-Pressure Crystallographic Structures

    NASA Astrophysics Data System (ADS)

    Clark, Jeremy

    2005-04-01

    Myoglobin, considered a paradigm for biocomplexity, may serve as a model system for studying the role of cavities and volume fluctuations in proteins. Volume fluctuations are directly probed by pressure via the compressibility. While the physico-chemical basis for pressure effects is well established, effects in structurally complex systems have yet to be fully explored. Biocomplexity can lead to significant effects at moderate, kilo-atmosphere pressures, and is the reason detailed structural information under pressure is needed to understand pressure effects in proteins and other biological systems. Structural determination of proteins at kilo-atmosphere pressures using x-ray crystallography is a powerful method for investigating the effects of pressure on structure. Here we present results quantifying the spatial distribution of intrinsic compressibility in sperm whale myoglobin calculated from crystallographic structures solved at ambient and at 1500 atm pressures.

  17. A new systematic framework for crystallographic analysis of atom probe data.

    PubMed

    Araullo-Peters, Vicente J; Breen, Andrew; Ceguerra, Anna V; Gault, Baptiste; Ringer, Simon P; Cairney, Julie M

    2015-07-01

    In this article, after a brief introduction to the principles behind atom probe crystallography, we introduce methods for unambiguously determining the presence of crystal planes within atom probe datasets, as well as their characteristics: location; orientation and interplanar spacing. These methods, which we refer to as plane orientation extraction (POE) and local crystallography mapping (LCM) make use of real-space data and allow for systematic analyses. We present here application of POE and LCM to datasets of pure Al, industrial aluminium alloys and doped-silicon. Data was collected both in DC voltage mode and laser-assisted mode (in the latter of which extracting crystallographic information is known to be more difficult due to distortions). The nature of the atomic planes in both datasets was extracted and analysed. PMID:25747179

  18. Purification, identification and preliminary crystallographic studies of a 2S albumin seed protein from Lens culinaris

    SciTech Connect

    Gupta, Pankaj; Gaur, Vineet; Salunke, Dinakar M.

    2008-08-01

    A 2S albumin from L. culinaris was purified and crystallized and preliminary crystallographic studies were carried out. Lens culinaris (lentil) is a widely consumed high-protein-content leguminous crop. A 2S albumin protein (26.5 kDa) has been identified using NH{sub 2}-terminal sequencing from a 90% ammonium sulfate saturation fraction of total L. culinaris seed protein extract. The NH{sub 2}-terminal sequence shows very high homology to PA2, an allergy-related protein from Pisum sativum. The 2S albumin protein was purified using a combination of size-exclusion and ion-exchange chromatography. Crystals of the 2S seed albumin obtained using the hanging-drop vapour-diffusion method diffracted to 2.5 Å resolution and were indexed in space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 78.6, c = 135.2 Å.

  19. Crystallization and preliminary X-ray crystallographic studies of Mycobacterium tuberculosis chorismate mutase

    SciTech Connect

    Qamra, Rohini; Prakash, Prachee; Aruna, Bandi; Hasnain, Seyed E.; Mande, Shekhar C.

    2005-05-01

    Chorismate mutase from M. tuberculosis has been crystallized. Preliminary X-ray crystallographic studies reveal the occurrence of a dimeric molecule in the crystal asymmetric unit. Chorismate mutase catalyzes the first committed step in the biosynthesis of the aromatic amino acids phenylalanine and tyrosine in bacteria, fungi and higher plants. The recent re-annotation of the Mycobacterium tuberculosis genome has revealed the presence of a duplicate set of genes coding for chorismate mutase. The mycobacterial gene Rv1885c bears <20% sequence homology to other bacterial chorismate mutases, thus serving as a potential target for the development of inhibitors specific to the pathogen. The M. tuberculosis chorismate mutase was crystallized in space group C2 and the crystals diffracted to a resolution of 2.2 Å. Matthews coefficient and self-rotation function calculations revealed the presence of two monomers in the asymmetric unit.

  20. Influence of crystallographic orientation on the response of copper crystallites to nanoindentation

    SciTech Connect

    Korchuganov, Aleksandr V.; Kryzhevich, Dmitrij S. E-mail: kost@ispms.tsc.ru; Zolnikov, Konstantin P. E-mail: kost@ispms.tsc.ru; Psakhie, Sergey G.

    2014-11-14

    Molecular dynamics simulation was performed to study the features of nucleation and development of plastic deformation in copper crystallites in nanoindentation with different crystallographic orientations of their loaded surface: (011), (001), and (111). Atomic interaction was described by a potential constructed in terms of the embedded atom method. It is shown that behavior of the crystallite reaction force correlates well with a change in the fraction of atoms involved in local structural rearrangements. The generation of local structural changes decreases the slope of the crystallite reaction force curve or results in an extremum due to internal stress relaxation. Analysis of structural changes in the material being indented demonstrates that the orientation of its loaded surface greatly affects the features of nucleation and development of plastic deformation.

  1. Vibrational algorithms for quantitative crystallographic analyses of hydroxyapatite-based biomaterials: I, theoretical foundations.

    PubMed

    Pezzotti, Giuseppe; Zhu, Wenliang; Boffelli, Marco; Adachi, Tetsuya; Ichioka, Hiroaki; Yamamoto, Toshiro; Marunaka, Yoshinori; Kanamura, Narisato

    2015-05-01

    The Raman spectroscopic method has quantitatively been applied to the analysis of local crystallographic orientation in both single-crystal hydroxyapatite and human teeth. Raman selection rules for all the vibrational modes of the hexagonal structure were expanded into explicit functions of Euler angles in space and six Raman tensor elements (RTE). A theoretical treatment has also been put forward according to the orientation distribution function (ODF) formalism, which allows one to resolve the statistical orientation patterns of the nm-sized hydroxyapatite crystallite comprised in the Raman microprobe. Close-form solutions could be obtained for the Euler angles and their statistical distributions resolved with respect to the direction of the average texture axis. Polarized Raman spectra from single-crystalline hydroxyapatite and textured polycrystalline (teeth enamel) samples were compared, and a validation of the proposed Raman method could be obtained through confirming the agreement between RTE values obtained from different samples. PMID:25673243

  2. Bacteriological and crystallographical analysis of urinary calculi: aid to patient management.

    PubMed

    Rosenstein, I; Osborn, R S; Hopewell, J P; Hamilton-Miller, J M; Brumfitt, W

    1984-06-01

    In an analysis, by both crystallographic and microbiological methods, of 50 urinary calculi recently removed by surgical operation, 33 proved to be of metabolic origin (mostly calcium oxalate and some uric acid or urate) and 17 of 'infective' origin (struvite, apatite or a mixture of the two). Metabolic stones were usually bacteriologically sterile or contained only small numbers (less than 10(3)/g of stone) of bacteria which did not produce urease, while infective stones always contained urease-producing organisms, usually Proteus mirabilis, in large numbers (greater than 10(5)/g). The combined approach of stone analysis by crystallography and microbiological culture yields more information than conventional techniques on which to base the treatment of urinary calculi and the prevention of their recurrence. PMID:6737406

  3. Mechanistic, crystallographic, and computational studies on the catalytic, enantioselective sulfenofunctionalization of alkenes

    NASA Astrophysics Data System (ADS)

    Denmark, Scott E.; Hartmann, Eduard; Kornfilt, David J. P.; Wang, Hao

    2014-12-01

    The stereocontrolled introduction of vicinal heteroatomic substituents into organic molecules is one of the most powerful ways of adding value and function. Although many methods exist for the introduction of oxygen- and nitrogen-containing substituents, the number of stereocontrolled methods for the introduction of sulfur-containing substituents pales by comparison. Previous reports from our laboratories have described sulfenofunctionalizations of alkenes that construct carbon-sulfur bonds vicinal to carbon-oxygen, carbon-nitrogen or carbon-carbon bonds with high levels of diastereospecificity and enantioselectivity. This process is enabled by the concept of Lewis-base activation of Lewis acids, which provides activation of Group 16 electrophiles. To provide a foundation for the 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.

  4. Crystallographic study on natural gas hydrates recovered from the eastern Nankai Trough

    NASA Astrophysics Data System (ADS)

    Kida, Masato; Suzuki, Hiroyuki; Suzuki, Kiyofumi; Nagao, Jiro; Narita, Hideo

    2010-05-01

    Natural gas hydrates are crystalline clathrate compounds, which encage a large amount of natural gas. The crystallographic structure of natural gas hydrates depends on the encaged natural gas components. In addition, the amount of hydrate-bound natural gas is attributed to the crystallographic structure. Massive and pore-space natural gas hydrates were obtained from the eastern Nankai Trough area during Japan's Methane Hydrate R&D Program conducted by the Ministry of Economy, Trade and Industry (METI) of Japan, aboard the RV JOIDES Resolution. In this study, hydrate-bound gas, crystal structure, and cage occupancies, and hydration number of the natural gas hydrates were characterized. The pore-space natural gas hydrates recovered from the eastern Nankai Trough area existed in pore-spaces of sandy sediments with median diameters of approximately 80-180 μm. The PXRD profiles of the massive and pore-space natural gas hydrates revealed that the crystallographic structures of the all natural gas hydrates studied were structure I. The lattice constants of the pore-space natural gas hydrates were ranging from 1.183-1.207 nm, depending on the content of fine sediment particles less than 40 μm in the sandy samples. All samples contained CH4 as a main hydrocarbon component, indicating that the natural gas in marine sediment at the study areas is mainly CH4. The hydrocarbon compositions agreed well with those reported for microbial (CO2 reduction) natural gas in gas hydrate-bearing sediments recovered previously from the eastern Nankai Trough area. In this study, on the other hand, although almost all samples contained small amounts of C2H6 (less than 200 ppm), C3H8 (less than 50 ppm), and i-C4H10 (less than 20 ppm), large concentrations of heavier hydrocarbons such as C3H8 or i-C4H10 were found in three of 15 samples. 13C NMR and Raman spectroscopic techniques were used to obtain molecular information on the encaged hydrocarbon molecules. The 13C NMR chemical shifts and

  5. Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi

    SciTech Connect

    Sugiyama, Shigeru; Tokuoka, Keiji; Uchiyama, Nahoko; Okamoto, Naoki; Okano, Yousuke; Matsumura, Hiroyoshi; Inaka, Koji; Urade, Yoshihiro; Inoue, Tsuyoshi

    2007-10-01

    Old yellow enzyme from Trypanosoma cruzi, has been crystallized using the hanging-drop vapour-diffusion method. Old yellow enzyme (OYE) is an NADPH oxidoreductase that contains a flavin mononucleotide as a prosthetic group. The OYE from Trypanosoma cruzi, which produces prostaglandin F{sub 2α}, a potent mediator of various physiological and pathological processes, from prostaglandin H2. The protein was recombinantly expressed and purified from Escherichia coli and was crystallized using the hanging-drop vapour-diffusion method. The crystal belongs to the monoclinic space group P2{sub 1}, with unit-cell parameters a = 56.3, b = 78.8, c = 78.8 Å, β = 93.4° and two molecules per asymmetric unit. The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 Å resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model.

  6. Purification, identification and preliminary crystallographic studies of Pru du amandin, an allergenic protein from Prunus dulcis

    SciTech Connect

    Gaur, Vineet; Sethi, Dhruv K.; Salunke, Dinakar M.

    2008-01-01

    The purification, identification, crystallization and preliminary crystallographic studies of an allergy-related protein, Pru du amandin, from P. dulcis nuts are reported. Food allergies appear to be one of the foremost causes of hypersensitivity reactions. Nut allergies account for most food allergies and are often permanent. The 360 kDa hexameric protein Pru du amandin, a known allergen, was purified from almonds (Prunus dulcis) by ammonium sulfate fractionation and ion-exchange chromatography. The protein was identified by a BLAST homology search against the nonredundant sequence database. Pru du amandin belongs to the 11S legumin family of seed storage proteins characterized by the presence of a cupin motif. Crystals were obtained by the hanging-drop vapour-diffusion method. The crystals belong to space group P4{sub 1} (or P4{sub 3}), with unit-cell parameters a = b = 150.7, c = 164.9 Å.

  7. Magnetoresistance in granular CrO2: Effects of variation in crystallographic and magnetic microstructure

    NASA Astrophysics Data System (ADS)

    Bajpai, A.; Nigam, A. K.

    2007-05-01

    We report magnetotransport measurements up to 5 Tesla on high purity sintered samples of granular CrO2 with a significantly enhanced grain size. The negative magnetoresistance (MR) as derived from RH isotherms is observed to be unhysteretic up to temperatures as high as 200 K. RH isotherms exhibit some unusual features between 240 and 290 K, including a positive MR and strong pinning effects. These features disappear above 290 K and are apparently related with the magnetic state of the insulating grain boundary. Qualitatively similar features with significantly enhanced MR are also observed when CrO2 is diluted with two antiferromagnetic oxides, Cr2O3 or Cr2O5. These results bring out the role played by the magnetic and crystallographic microstructure on the magnitude, sign, and hysteresis of the magnetoresistance in this technologically important material.

  8. Investigation of rail wheel steel crystallographic texture changes due to modification and thermomechanical treatment

    NASA Astrophysics Data System (ADS)

    Lychagina, T.; Nikolayev, D.; Sanin, A.; Tatarko, J.; Ullemeyer, K.

    2015-04-01

    In this work crystallographic texture for a set of rail wheel steel samples with different regimes of thermo-mechanical treatment and with and without modification by system Al-Mg-Si- Fe-C-Ca-Ti-Ce was measured by neutron diffraction. The texture measurements were carried out by using time-of-flight technique at SKAT diffractometer situated at IBR-2 reactor (Dubna, JINR, Russia). The three complete pole figures (110), (200), (211) of α-Fe phase in 5°×5°grid were extracted from a set of 1368 spectra measured for each sample. The samples were cut from rail wheel rim and from transitional zone (between rail wheel hub and wheel disk). It was concluded that the steel modification and some changes in the heat treatment modes of the rail wheels from the experimental (modified) and the conventional (non-modified) steel lead to reorientation of texture component.

  9. Conformational analysis of environmental agents: use of X-ray crystallographic data to determine molecular reactivity.

    PubMed Central

    Cody, V

    1985-01-01

    This paper explores the use of crystallographic techniques as an aid in understanding the molecular reactivities of a number of agents that are of concern to pharmacologists and toxicologists. The selected examples demonstrate the role of structural data in the determination of absolute configuration, configurational flexibility and active-site topology for a reactive species. For example, the role of absolute stereochemistry in understanding synthetic pyrethroid structure-activity relationships is shown from analysis of their crystal structures; conformational flexibility among DDT analogues, and the importance of conformational and electronic properties in phenylalkanoic acid herbicides are shown from systematic analysis of their crystal structures; and interpretation of active-site stereochemistry is made by study of computer modeling of enzyme inhibitors in the active sites of related protein crystal structures. Thus, the observed patterns in conformational flexibility and their resultant effects on substrate pharmacological profile can be interpreted in understanding the molecular level events that influence biological reactivity. PMID:3905372

  10. Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins

    SciTech Connect

    Tronrud, Dale E.; Berkholz, Donald S.; Karplus, P. Andrew

    2010-07-02

    The major macromolecular crystallographic refinement packages restrain models to ideal geometry targets defined as single values that are independent of molecular conformation. However, ultrahigh-resolution X-ray models of proteins are not consistent with this concept of ideality and have been used to develop a library of ideal main-chain bond lengths and angles that are parameterized by the {phi}/{psi} angle of the residue [Berkholz et al. (2009), Structure, 17, 1316-1325]. Here, it is first shown that the new conformation-dependent library does not suffer from poor agreement with ultrahigh-resolution structures, whereas current libraries have this problem. Using the TNT refinement package, it is then shown that protein structure refinement using this conformation-dependent library results in models that have much better agreement with library values of bond angles with little change in the R values. These tests support the value of revising refinement software to account for this new paradigm.

  11. XAFS and crystallographic studies of Ni(II) porphyrins in single crystals and in solution

    SciTech Connect

    Renner, M.W.; Furenlid, L.R.; Barkigia, K.M.; Fajer, J.

    1996-09-01

    Abstract. Nickel porphyrins serve as models for the active sites of several biological processes. Crystallographic and EXAFS results for a Ni meso-tetrapropyl porphyrin (NiTPrP) yield different Ni-N distances in solution and in the solid state. The Ni-N distances determined by single crystal polarized XAS and X-ray diffraction agree well. Polarized XANES experiments further establish that the pre-edge feature observed in square planar Ni(II) complexes is a ls-4pz transition. The single crystal and solution EXAFS results demonstrate that conformational variations of the porphyrin macrocycle can readily be imposed by environmental and/or packing forces and can thereby modulate the chemical and physical properties of porphyrinic chromophores and prosthetic groups.

  12. Maximum a posteriori estimation of crystallographic phases in X-ray diffraction tomography

    PubMed Central

    Gürsoy, Doĝa; Biçer, Tekin; Almer, Jonathan D.; Kettimuthu, Raj; Stock, Stuart R.; De Carlo, Francesco

    2015-01-01

    A maximum a posteriori approach is proposed for X-ray diffraction tomography for reconstructing three-dimensional spatial distribution of crystallographic phases and orientations of polycrystalline materials. The approach maximizes the a posteriori density which includes a Poisson log-likelihood and an a priori term that reinforces expected solution properties such as smoothness or local continuity. The reconstruction method is validated with experimental data acquired from a section of the spinous process of a porcine vertebra collected at the 1-ID-C beamline of the Advanced Photon Source, at Argonne National Laboratory. The reconstruction results show significant improvement in the reduction of aliasing and streaking artefacts, and improved robustness to noise and undersampling compared to conventional analytical inversion approaches. The approach has the potential to reduce data acquisition times, and significantly improve beamtime efficiency. PMID:25939627

  13. Sensitivity of ion induced charge pulses to the electrical and crystallographic properties of 60° dislocations

    NASA Astrophysics Data System (ADS)

    Breese, M. B. H.; King, P. J. C.; Grime, G. W.

    1994-12-01

    This letter reports evidence that the size of MeV ion induced charge pulses measured from epitaxial Si0.875Ge0.125/Si depends on both the crystallographic and electrical properties of the 60° misfit dislocations present. The results are correlated with both backscattered and transmission ion channeling analysis. With the sample in nonchanneled alignment the measured ion induced charge pulses depend on the number of charge carriers which recombine at the dislocations. With the sample in channeled alignment the rotated (110) and (11¯0) planes around the 60° dislocations affect the local rate of carrier generation and so alter the size of the measured ion induced charge pulses.

  14. Processing and crystallographic structure of non-equilibrium Si-doped HfO{sub 2}

    SciTech Connect

    Hou, Dong; Fancher, Chris M.; Esteves, Giovanni; Jones, Jacob L.; Zhao, Lili

    2015-06-28

    Si-doped HfO{sub 2} was confirmed to exist as a non-equilibrium state. The crystallographic structures of Si-doped HfO{sub 2} were studied using high-resolution synchrotron X-ray diffraction and the Rietveld refinement method. Incorporation of Si into HfO{sub 2} and diffusion of Si out of (Hf,Si)O{sub 2} were determined as a function of calcination temperature. Higher thermal energy input at elevated calcination temperatures resulted in the formation of HfSiO{sub 4}, which is the expected major secondary phase in Si-doped HfO{sub 2}. The effect of SiO{sub 2} particle size (nano- and micron-sized) on the formation of Si-doped HfO{sub 2} was also determined. Nano-crystalline SiO{sub 2} was found to incorporate into HfO{sub 2} more readily.

  15. Crystallographic and chiroptical studies on tetraarylferrocenes for use as chiral rotary modules for molecular machines.

    PubMed

    Muraoka, Takahiro; Kinbara, Kazushi; Wakamiya, Atsushi; Yamaguchi, Shigehiro; Aida, Takuzo

    2007-01-01

    A crystal structure of the racemic form of chiral molecular scissors 1 with a trans configuration at the azobenzene unit (rac-trans-1), in which the scissors adopt a closed geometry with two blade phenyl groups that overlap each other, was successfully determined. X-ray crystallographic determination of the structure of (1S,1'S)-10, which is a derivative of the key precursor of trans-1, was also successful. On the basis of the crystal structure of (1S,1'S)-10, the absolute configuration of 1 and related molecular machines, such as molecular pedal 2, and self-locking rotor 3, which all contain a chiral tetrasubstituted ferrocene module, were determined. A correlation between the absolute configuration and the circular dichroism properties of these molecular machines and their synthetic precursors was also determined. PMID:17146829

  16. Platinum Group Thiophenoxyimine Complexes: Syntheses,Crystallographic and Computational Studies of Structural Properties

    SciTech Connect

    Krinsky, Jamin L.; Arnold, John; Bergman, Robert G.

    2006-10-03

    Monomeric thiosalicylaldiminate complexes of rhodium(I) and iridium(I) were prepared by ligand transfer from the homoleptic zinc(II) species. In the presence of strongly donating ligands, the iridium complexes undergo insertion of the metal into the imine carbon-hydrogen bond. Thiophenoxyketimines were prepared by non-templated reaction of o-mercaptoacetophenone with anilines, and were complexed with rhodium(I), iridium(I), nickel(II) and platinum(II). X-ray crystallographic studies showed that while the thiosalicylaldiminate complexes display planar ligand conformations, those of the thiophenoxyketiminates are strongly distorted. Results of a computational study were consistent with a steric-strain interpretation of the difference in preferred ligand geometries.

  17. Dianthraceno[a,e]pentalenes: synthesis, crystallographic structures and applications in organic field-effect transistors.

    PubMed

    Dai, Gaole; Chang, Jingjing; Zhang, Wenhua; Bai, Shiqiang; Huang, Kuo-Wei; Xu, Jianwei; Chi, Chunyan

    2015-01-11

    Two soluble and stable dianthraceno[a,e]pentalenes with two (DAP1) and six (DAP2) phenyl substituents were synthesized. Both compounds possess a small energy band gap and show amphoteric redox behaviour due to intramolecular donor-accepter interactions. X-ray crystallographic analysis revealed that DAP2 has a closely packed structure with multi-dimensional [C-H···π] interactions although there are no π-π interactions between the dianthraceno[a,e]pentalene cores. As a result, solution-processed field effect transistors based on DAP2 exhibited an average hole mobility of 0.65 cm(2) V(-1) s(-1). Under similar conditions, DAP1 showed an average field effect hole mobility of 0.001 cm(2) V(-1) s(-1). PMID:25406768

  18. MRI driven magnetic microswimmers.

    PubMed

    Kósa, Gábor; Jakab, Péter; Székely, Gábor; Hata, Nobuhiko

    2012-02-01

    Capsule endoscopy is a promising technique for diagnosing diseases in the digestive system. Here we design and characterize a miniature swimming mechanism that uses the magnetic fields of the MRI for both propulsion and wireless powering of the capsule. Our method uses both the static and the radio frequency (RF) magnetic fields inherently available in MRI to generate a propulsive force. Our study focuses on the evaluation of the propulsive force for different swimming tails and experimental estimation of the parameters that influence its magnitude. We have found that an approximately 20 mm long, 5 mm wide swimming tail is capable of producing 0.21 mN propulsive force in water when driven by a 20 Hz signal providing 0.85 mW power and the tail located within the homogeneous field of a 3 T MRI scanner. We also analyze the parallel operation of the swimming mechanism and the scanner imaging. We characterize the size of artifacts caused by the propulsion system. We show that while the magnetic micro swimmer is propelling the capsule endoscope, the operator can locate the capsule on the image of an interventional scene without being obscured by significant artifacts. Although this swimming method does not scale down favorably, the high magnetic field of the MRI allows self propulsion speed on the order of several millimeter per second and can propel an endoscopic capsule in the stomach. PMID:22037673

  19. Gradient Driven Fluctuations

    NASA Technical Reports Server (NTRS)

    Cannell, David

    2005-01-01

    We have worked with our collaborators at the University of Milan (Professor Marzio Giglio and his group-supported by ASI) to define the science required to measure gradient driven fluctuations in the microgravity environment. Such a study would provide an accurate test of the extent to which the theory of fluctuating hydrodynamics can be used to predict the properties of fluids maintained in a stressed, non-equilibrium state. As mentioned above, the results should also provide direct visual insight into the behavior of a variety of fluid systems containing gradients or interfaces, when placed in the microgravity environment. With support from the current grant, we have identified three key systems for detailed investigation. These three systems are: 1) A single-component fluid to be studied in the presence of a temperature gradient; 2) A mixture of two organic liquids to be studied both in the presence of a temperature gradient, which induces a steady-state concentration gradient, and with the temperature gradient removed, but while the concentration gradient is dying by means of diffusion; 3) Various pairs of liquids undergoing free diffusion, including a proteidbuffer solution and pairs of mixtures having different concentrations, to allow us to vary the differences in fluid properties in a controlled manner.

  20. Compositionally Driven Dynamos

    NASA Astrophysics Data System (ADS)

    Soderlund, K. M.; Schubert, G.

    2014-12-01

    It is generally believed that compositional convection driven by inner core solidification is the main driver of the geodynamo. Thermal evolution considerations make it likely that compositional convection is also behind the present dynamos of Mercury and Ganymede as well as the early dynamos in the Moon, Mars and smaller solar system bodies. Compositional buoyancy can arise in several different ways, for example, through inner core solidification and FeS flotation with upward mixing and through freezing out and sinking of iron snow near the core-mantle boundary or deeper within the core. The mode of core cooling and freezing depends on conditions of temperature and pressure in the core and the concentration of light elements such as sulfur. Different distributions of compositional buoyancy will give rise to different patterns of core convection and dynamo magnetic fields. We report here the first results of a systematic study of the distribution of compositional buoyancy on the dynamo-generated magnetic fields, with an emphasis on Mars' core evolution due to iron rain.