Command of active matter by topological defects and patterns

NASA Astrophysics Data System (ADS)

Peng, Chenhui; Turiv, Taras; Guo, Yubing; Wei, Qi-Huo; Lavrentovich, Oleg D.

2016-11-01

Self-propelled bacteria are marvels of nature with a potential to power dynamic materials and microsystems of the future. The challenge lies in commanding their chaotic behavior. By dispersing swimming Bacillus subtilis in a liquid crystalline environment with spatially varying orientation of the anisotropy axis, we demonstrate control over the distribution of bacterial concentration, as well as the geometry and polarity of their trajectories. Bacteria recognize subtle differences in liquid crystal deformations, engaging in bipolar swimming in regions of pure splay and bend but switching to unipolar swimming in mixed splay-bend regions. They differentiate topological defects, heading toward defects of positive topological charge and avoiding negative charges. Sensitivity of bacteria to preimposed orientational patterns represents a previously unknown facet of the interplay between hydrodynamics and topology of active matter.

Command of active matter by topological defects and patterns.

PubMed

Peng, Chenhui; Turiv, Taras; Guo, Yubing; Wei, Qi-Huo; Lavrentovich, Oleg D

2016-11-18

Self-propelled bacteria are marvels of nature with a potential to power dynamic materials and microsystems of the future. The challenge lies in commanding their chaotic behavior. By dispersing swimming Bacillus subtilis in a liquid crystalline environment with spatially varying orientation of the anisotropy axis, we demonstrate control over the distribution of bacterial concentration, as well as the geometry and polarity of their trajectories. Bacteria recognize subtle differences in liquid crystal deformations, engaging in bipolar swimming in regions of pure splay and bend but switching to unipolar swimming in mixed splay-bend regions. They differentiate topological defects, heading toward defects of positive topological charge and avoiding negative charges. Sensitivity of bacteria to preimposed orientational patterns represents a previously unknown facet of the interplay between hydrodynamics and topology of active matter. Copyright © 2016, American Association for the Advancement of Science.

Topological phase transition and the effect of Hubbard interactions on the one-dimensional topological Kondo insulator

NASA Astrophysics Data System (ADS)

Pillay, Jason C.; McCulloch, Ian P.

2018-05-01

The effect of a local Kondo coupling and Hubbard interaction on the topological phase of the one-dimensional topological Kondo insulator (TKI) is numerically investigated using the infinite matrix-product state density-matrix renormalization group algorithm. The ground state of the TKI is a symmetry-protected topological (SPT) phase protected by inversion symmetry. It is found that on its own, the Hubbard interaction that tends to force fermions into a one-charge per site order is insufficient to destroy the SPT phase. However, when the local Kondo Hamiltonian term that favors a topologically trivial ground state with a one-charge per site order is introduced, the Hubbard interaction assists in the destruction of the SPT phase. This topological phase transition occurs in the charge sector where the correlation length of the charge excitation diverges while the correlation length of the spin excitation remains finite. The critical exponents, central charge, and the phase diagram separating the SPT phase from the topologically trivial phase are presented.

Topological Edge Modes in Active Mikado Networks

NASA Astrophysics Data System (ADS)

Zhou, Di; Zhang, Leyou; Mao, Xiaoming

Mechanical properties of disordered fiber networks are not only important in understanding a broad range of natural (such as the cytoskeleton and the extracellular matrix) and manmade materials (such as aerogels and porous media) but also exhibit interesting and rich physics. In this talk, we discuss how topological floppy edge modes can emerge from these fiber networks as a result of active driving. It is known that straight fibers in a network carries a state of self-stress and bears a bulk floppy mode. We find that, interestingly, by driving the network with a tiny perturbation, the bulk modes evolve into edge modes. We introduce a new transfer matrix formulation that can be applied to this strongly disordered system, to characterize the topological edge modes. We also discuss possible implications of these edge modes in biological processes. NSF-DMR-1609051.

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

PubMed Central

Guo, Ya; Xu, Quan; Canzio, Daniele; Shou, Jia; Li, Jinhuan; Gorkin, David U.; Jung, Inkyung; Wu, Haiyang; Zhai, Yanan; Tang, Yuanxiao; Lu, Yichao; Wu, Yonghu; Jia, Zhilian; Li, Wei; Zhang, Michael Q.; Ren, Bing; Krainer, Adrian R.; Maniatis, Tom; Wu, Qiang

2015-01-01

SUMMARY CTCF/cohesin play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters, and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. The findings reveal how 3D chromosome architecture can be encoded by genome sequence. PMID:26276636

Topological pattern for the search of new active drugs against methicillin resistant Staphylococcus aureus.

PubMed

Bueso-Bordils, Jose I; Perez-Gracia, Maria T; Suay-Garcia, Beatriz; Duart, Maria J; Martin Algarra, Rafael V; Lahuerta Zamora, Luis; Anton-Fos, Gerardo M; Aleman Lopez, Pedro A

2017-09-29

Molecular topology was used to develop a mathematical model capable of classifying compounds according to antimicrobial activity against methicillin resistant Staphylococcus aureus (MRSA). Topological indices were used as structural descriptors and their relation to antimicrobial activity was determined by using linear discriminant analysis. This topological model establishes new structure activity relationships which show that the presence of cyclopropyl, chlorine and ramification pairs at a distance of two bonds favor this activity, while the presence of tertiary amines decreases it. This model was applied to a combinatorial library of a thousand and one 6-fluoroquinolones, from which 117 theoretical active molecules were obtained. The compound 10 and five new quinolones were tested against MRSA. They all showed some activity against MRSA, although compounds 6, 8 and 9 showed anti-MRSA activity similar to ciprofloxacin. This model was also applied to 263 theoretical antibacterial agents described by us in a previous work, from which 34 were predicted as theoretically active. Anti-MRSA activity was found bibliographically in 9 of them (ensuring at least 26% of success), and from the rest, 3 compounds were randomly chosen and tested, finding mitomycin C to be more active than ciprofloxacin. The results demonstrate the utility of the molecular topology approaches for identifying new drugs active against MRSA. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Interactive flare sites within an active region complex

NASA Technical Reports Server (NTRS)

Poletto, G.; Gary, G. A.; Machado, M. E.

1993-01-01

We examine here a set of images of an active region complex, acquired on June 24-25, 1980, by the Hard X-ray Imaging Spectrometer on SMM, with the purpose of establishing whether there was any interplay between the frequent activity observed at different sites in the activity center and, in such a case, how the interaction was established. By analyzing both quiet and active orbits we show that, as a rule, activity originating in one region triggers the other region's activity. However, we find little unambiguous evidence for the presence of large-scale interconnecting loops. A comparison of X-ray images with magnetic field observations suggested that we interpret the active region behavior in terms of the interaction between different loop systems, in a scenario quite analogous to the interacting bipole representation of individual flares. We conclude that active region interplay provides an easily observable case to study the time-dependent topology and the mechanisms for the spreading of activity in transient events over all energy scales.

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps

PubMed Central

2016-01-01

Abstract Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor‐preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface‐based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory‐motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory‐motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M‐I. Hum Brain Mapp 37:2784–2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:27061771

Magnetic Topology of a Long-Lived Coronal Condensation Site Lasting Eight Months

NASA Astrophysics Data System (ADS)

Sun, X.; Yu, S.; Liu, W.

2017-12-01

It is well known that cool material, such as prominences or coronal rain, can form in-situ by condensation of hot coronal plasma due to a runaway radiative cooling instability (a.k.a. thermal non-equilibrium). Recent observations and numerical simulations suggest that such condensations are quite common, but in quiet-Sun regions, they occur preferentially in locations where magnetic field is weak (e.g., null points) or discontinuous (e.g., current sheets). Such events usually have short lifetimes of hours to days. Surprisingly, we observed a high-latitude condensation site lasting over eight months in 2014 with recurrent and episodic condensations fueling a funnel-shaped prominence. We analyze the coronal magnetic topology to investigate the necessary condition of such a long-lived condensation site. We find that the site was directly above a poleward photospheric flux surge when the polar field polarity was close to its solar cycle reversal. The large-scale magnetic cancellation front may have sustained interchange reconnection at this location, creating suitable conditions for coronal plasma condensation.

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology.

PubMed

Chow, Sih Yao; Wang, Yung Lin; Hsieh, Yu Chiao; Lee, Guan Chiun; Liaw, Shwu Huey

2017-11-01

Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.

Topological antiferromagnetic spintronics

NASA Astrophysics Data System (ADS)

Šmejkal, Libor; Mokrousov, Yuriy; Yan, Binghai; MacDonald, Allan H.

2018-03-01

The recent demonstrations of electrical manipulation and detection of antiferromagnetic spins have opened up a new chapter in the story of spintronics. Here, we review the emerging research field that is exploring the links between antiferromagnetic spintronics and topological structures in real and momentum space. Active topics include proposals to realize Majorana fermions in antiferromagnetic topological superconductors, to control topological protection and Dirac points by manipulating antiferromagnetic order parameters, and to exploit the anomalous and topological Hall effects of zero-net-moment antiferromagnets. We explain the basic concepts behind these proposals, and discuss potential applications of topological antiferromagnetic spintronics.

Areas activated during naturalistic reading comprehension overlap topological visual, auditory, and somatotomotor maps.

PubMed

Sood, Mariam R; Sereno, Martin I

2016-08-01

Cortical mapping techniques using fMRI have been instrumental in identifying the boundaries of topological (neighbor-preserving) maps in early sensory areas. The presence of topological maps beyond early sensory areas raises the possibility that they might play a significant role in other cognitive systems, and that topological mapping might help to delineate areas involved in higher cognitive processes. In this study, we combine surface-based visual, auditory, and somatomotor mapping methods with a naturalistic reading comprehension task in the same group of subjects to provide a qualitative and quantitative assessment of the cortical overlap between sensory-motor maps in all major sensory modalities, and reading processing regions. Our results suggest that cortical activation during naturalistic reading comprehension overlaps more extensively with topological sensory-motor maps than has been heretofore appreciated. Reading activation in regions adjacent to occipital lobe and inferior parietal lobe almost completely overlaps visual maps, whereas a significant portion of frontal activation for reading in dorsolateral and ventral prefrontal cortex overlaps both visual and auditory maps. Even classical language regions in superior temporal cortex are partially overlapped by topological visual and auditory maps. By contrast, the main overlap with somatomotor maps is restricted to a small region on the anterior bank of the central sulcus near the border between the face and hand representations of M-I. Hum Brain Mapp 37:2784-2810, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.

Predesigned surface patterns and topological defects control the active matter.

NASA Astrophysics Data System (ADS)

Turiv, Taras; Peng, Chenhui; Guo, Yubing; Wei, Qi-Huo; Lavrentovich, Oleg

Active matter exhibits remarkable patterns of never-ending dynamics with giant fluctuations of concentration, varying order, nucleating and annihilating topological defects. These patterns can be seen in active systems of both biological and artificial origin. A fundamental question is whether and how one can control this chaotic out-of-equilibrium behavior. We demonstrate a robust control of local concentration, trajectories of active self-propelled units and the net flows of active bacteria Bacillus Substilis by imposing pre-designed surface patterns of orientational order in a water-based lyotropic chromonic liquid crystal. The patterns force the bacteria to gather into dynamic swarms with spatially modulated concentration and well-defined polarity of motion. Topological defects produce net motion of bacteria with a unidirectional circulation, while pairs of defects induce a pumping action. The qualitative features of the dynamics can be explained by interplay of curvature and activity, in particular, by ability of mixed splay-bend curvatures to generate threshold-less active flows. The demonstrated level of control opens opportunities in engineering materials and devices that mimic rich functionality of living systems. This work was supported by NSF Grants DMR-1507637, DMS-1434185, CMMI-1436565, by the Petroleum Research Grant PRF# 56046-ND7 administered by the American Chemical Society.

Detection of Active Topology Probing Deception

DTIC Science & Technology

2015-09-01

patterns in the gag traceroutes and fake topologies from the DeTracer for which we may use to improve our filtering process. In all, the findings will aid...in the /24 subnet. We find intriguing patterns in the gag traceroutes and fake topologies from the DeTracer for which we may use to improve our...Forwarding xiv Acknowledgments I would like to thank Dr. Robert Beverly for his patience during the research and thesis writing process. His deep knowledge on

Synthesizing topological structures containing RNA

NASA Astrophysics Data System (ADS)

Liu, Di; Shao, Yaming; Chen, Gang; Tse-Dinh, Yuk-Ching; Piccirilli, Joseph A.; Weizmann, Yossi

2017-03-01

Though knotting and entanglement have been observed in DNA and proteins, their existence in RNA remains an enigma. Synthetic RNA topological structures are significant for understanding the physical and biological properties pertaining to RNA topology, and these properties in turn could facilitate identifying naturally occurring topologically nontrivial RNA molecules. Here we show that topological structures containing single-stranded RNA (ssRNA) free of strong base pairing interactions can be created either by configuring RNA-DNA hybrid four-way junctions or by template-directed synthesis with a single-stranded DNA (ssDNA) topological structure. By using a constructed ssRNA knot as a highly sensitive topological probe, we find that Escherichia coli DNA topoisomerase I has low RNA topoisomerase activity and that the R173A point mutation abolishes the unknotting activity for ssRNA, but not for ssDNA. Furthermore, we discover the topological inhibition of reverse transcription (RT) and obtain different RT-PCR patterns for an ssRNA knot and circle of the same sequence.

Homology modeling and molecular dynamics simulation of N-myristoyltransferase from protozoan parasites: active site characterization and insights into rational inhibitor design

NASA Astrophysics Data System (ADS)

Sheng, Chunquan; Ji, Haitao; Miao, Zhenyuan; Che, Xiaoyin; Yao, Jianzhong; Wang, Wenya; Dong, Guoqiang; Guo, Wei; Lü, Jiaguo; Zhang, Wannian

2009-06-01

Myristoyl-CoA:protein N-myristoyltransferase (NMT) is a cytosolic monomeric enzyme that catalyzes the transfer of the myristoyl group from myristoyl-CoA to the N-terminal glycine of a number of eukaryotic cellular and viral proteins. Recent experimental data suggest NMT from parasites could be a promising new target for the design of novel antiparasitic agents with new mode of action. However, the active site topology and inhibitor specificity of these enzymes remain unclear. In this study, three-dimensional models of NMT from Plasmodium falciparum (PfNMT), Leishmania major (LmNMT) and Trypanosoma brucei (TbNMT) were constructed on the basis of the crystal structures of fungal NMTs using homology modeling method. The models were further refined by energy minimization and molecular dynamics simulations. The active sites of PfNMT, LmNMT and TbNMT were characterized by multiple copy simultaneous search (MCSS). MCSS functional maps reveal that PfNMT, LmNMT and TbNMT share a similar active site topology, which is defined by two hydrophobic pockets, a hydrogen-bonding (HB) pocket, a negatively-charged HB pocket and a positively-charged HB pocket. Flexible docking approaches were then employed to dock known inhibitors into the active site of PfNMT. The binding mode, structure-activity relationships and selectivity of inhibitors were investigated in detail. From the results of molecular modeling, the active site architecture and certain key residues responsible for inhibitor binding were identified, which provided insights for the design of novel inhibitors of parasitic NMTs.

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs

PubMed Central

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C.; Hütt, Marc-Thorsten

2017-01-01

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience. PMID:28186182

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs.

PubMed

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C; Hütt, Marc-Thorsten

2017-02-10

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience.

Topological determinants of self-sustained activity in a simple model of excitable dynamics on graphs

NASA Astrophysics Data System (ADS)

Fretter, Christoph; Lesne, Annick; Hilgetag, Claus C.; Hütt, Marc-Thorsten

2017-02-01

Simple models of excitable dynamics on graphs are an efficient framework for studying the interplay between network topology and dynamics. This topic is of practical relevance to diverse fields, ranging from neuroscience to engineering. Here we analyze how a single excitation propagates through a random network as a function of the excitation threshold, that is, the relative amount of activity in the neighborhood required for the excitation of a node. We observe that two sharp transitions delineate a region of sustained activity. Using analytical considerations and numerical simulation, we show that these transitions originate from the presence of barriers to propagation and the excitation of topological cycles, respectively, and can be predicted from the network topology. Our findings are interpreted in the context of network reverberations and self-sustained activity in neural systems, which is a question of long-standing interest in computational neuroscience.

Topology of OxlT, the oxalate transporter of Oxalobacter formigenes, determined by site-directed fluorescence labeling.

PubMed

Ye, L; Jia, Z; Jung, T; Maloney, P C

2001-04-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His(9)-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+ linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis.

Topology of OxlT, the Oxalate Transporter of Oxalobacter formigenes, Determined by Site-Directed Fluorescence Labeling

PubMed Central

Ye, Liwen; Jia, Zhenzhen; Jung, Thomas; Maloney, Peter C.

2001-01-01

The topology of OxlT, the oxalate:formate exchange protein of Oxalobacter formigenes, was established by site-directed fluorescence labeling, a simple strategy that generates topological information in the context of the intact protein. Accessibility of cysteine to the fluorescent thiol-directed probe Oregon green maleimide (OGM) was examined for a panel of 34 single-cysteine variants, each generated in a His9-tagged cysteine-less host. The reaction with OGM was readily scored by examining the fluorescence profile after sodium dodecyl sulfate-polyacrylamide gel electrophoresis of material purified by Ni2+-linked affinity chromatography. A position was assigned an external location if its single-cysteine derivative reacted with OGM added to intact cells; a position was designated internal if OGM labeling required cell lysis. We also showed that labeling of external, but not internal, positions was blocked by prior exposure of cells to the impermeable and nonfluorescent thiol-specific agent ethyltrimethylammonium methanethiosulfonate. Of the 34 positions examined in this way, 29 were assigned unambiguously to either an internal or external location; 5 positions could not be assigned, since the target cysteine failed to react with OGM. There was no evidence of false-positive assignment. Our findings document a simple and rapid method for establishing the topology of a membrane protein and show that OxlT has 12 transmembrane segments, confirming inferences from hydropathy analysis. PMID:11274108

Does the choice of nucleotide substitution models matter topologically?

PubMed

Hoff, Michael; Orf, Stefan; Riehm, Benedikt; Darriba, Diego; Stamatakis, Alexandros

2016-03-24

In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available an open-source code for testing all 203 possible nucleotide substitution models in the Maximum Likelihood (ML) setting under the common Akaike, corrected Akaike, and Bayesian information criteria. We address the question if model selection matters topologically, that is, if conducting ML inferences under the optimal, instead of a standard General Time Reversible model, yields different tree topologies. We also assess, to which degree models selected and trees inferred under the three standard criteria (AIC, AICc, BIC) differ. Finally, we assess if the definition of the sample size (#sites versus #sites × #taxa) yields different models and, as a consequence, different tree topologies. We find that, all three factors (by order of impact: nucleotide model selection, information criterion used, sample size definition) can yield topologically substantially different final tree topologies (topological difference exceeding 10 %) for approximately 5 % of the tree inferences conducted on the 39 empirical datasets used in our study. We find that, using the best-fit nucleotide substitution model may change the final ML tree topology compared to an inference under a default GTR model. The effect is less pronounced when comparing distinct information criteria. Nonetheless, in some cases we did obtain substantial topological differences.

The Dynamic Interplay Between DNA Topoisomerases and DNA Topology.

PubMed

Seol, Yeonee; Neuman, Keir C

2016-09-01

Topological properties of DNA influence its structure and biochemical interactions. Within the cell DNA topology is constantly in flux. Transcription and other essential processes including DNA replication and repair, alter the topology of the genome, while introducing additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases, is a pervasive factor that influences DNA metabolism in vivo . Building on the extensive structural and biochemical characterization over the past four decades that established the fundamental mechanistic basis of topoisomerase activity, the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases have begun to be explored. In this review we survey established and emerging DNA topology dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

The dynamic interplay between DNA topoisomerases and DNA topology.

PubMed

Seol, Yeonee; Neuman, Keir C

2016-11-01

Topological properties of DNA influence its structure and biochemical interactions. Within the cell, DNA topology is constantly in flux. Transcription and other essential processes, including DNA replication and repair, not only alter the topology of the genome but also introduce additional complications associated with DNA knotting and catenation. These topological perturbations are counteracted by the action of topoisomerases, a specialized class of highly conserved and essential enzymes that actively regulate the topological state of the genome. This dynamic interplay among DNA topology, DNA processing enzymes, and DNA topoisomerases is a pervasive factor that influences DNA metabolism in vivo. Building on the extensive structural and biochemical characterization over the past four decades that has established the fundamental mechanistic basis of topoisomerase activity, scientists have begun to explore the unique roles played by DNA topology in modulating and influencing the activity of topoisomerases. In this review we survey established and emerging DNA topology-dependent protein-DNA interactions with a focus on in vitro measurements of the dynamic interplay between DNA topology and topoisomerase activity.

Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

PubMed

Ivanciuc, Ovidiu

2013-06-01

Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance.

Nobel Lecture: Topological quantum matter*

NASA Astrophysics Data System (ADS)

Haldane, F. Duncan M.

2017-10-01

Nobel Lecture, presented December 8, 2016, Aula Magna, Stockholm University. I will describe the history and background of three discoveries cited in this Nobel Prize: The "TKNN" topological formula for the integer quantum Hall effect found by David Thouless and collaborators, the Chern insulator or quantum anomalous Hall effect, and its role in the later discovery of time-reversal-invariant topological insulators, and the unexpected topological spin-liquid state of the spin-1 quantum antiferromagnetic chain, which provided an initial example of topological quantum matter. I will summarize how these early beginnings have led to the exciting, and currently extremely active, field of "topological matter."

Exploring the free-energy landscape of carbohydrate-protein complexes: development and validation of scoring functions considering the binding-site topology

NASA Astrophysics Data System (ADS)

Eid, Sameh; Saleh, Noureldin; Zalewski, Adam; Vedani, Angelo

2014-12-01

Carbohydrates play a key role in a variety of physiological and pathological processes and, hence, represent a rich source for the development of novel therapeutic agents. Being able to predict binding mode and binding affinity is an essential, yet lacking, aspect of the structure-based design of carbohydrate-based ligands. We assembled a diverse data set comprising 273 carbohydrate-protein crystal structures with known binding affinity and evaluated the prediction accuracy of a large collection of well-established scoring and free-energy functions, as well as combinations thereof. Unfortunately, the tested functions were not capable of reproducing binding affinities in the studied complexes. To simplify the complex free-energy surface of carbohydrate-protein systems, we classified the studied proteins according to the topology and solvent exposure of the carbohydrate-binding site into five distinct categories. A free-energy model based on the proposed classification scheme reproduced binding affinities in the carbohydrate data set with an r 2 of 0.71 and root-mean-squared-error of 1.25 kcal/mol ( N = 236). The improvement in model performance underlines the significance of the differences in the local micro-environments of carbohydrate-binding sites and demonstrates the usefulness of calibrating free-energy functions individually according to binding-site topology and solvent exposure.

Site-directed fluorescence labeling reveals a revised N-terminal membrane topology and functional periplasmic residues in the Escherichia coli cell division protein FtsK.

PubMed

Berezuk, Alison M; Goodyear, Mara; Khursigara, Cezar M

2014-08-22

In Escherichia coli, FtsK is a large integral membrane protein that coordinates chromosome segregation and cell division. The N-terminal domain of FtsK (FtsKN) is essential for division, and the C terminus (FtsKC) is a well characterized DNA translocase. Although the function of FtsKN is unknown, it is suggested that FtsK acts as a checkpoint to ensure DNA is properly segregated before septation. This may occur through modulation of protein interactions between FtsKN and other division proteins in both the periplasm and cytoplasm; thus, a clear understanding of how FtsKN is positioned in the membrane is required to characterize these interactions. The membrane topology of FtsKN was initially determined using site-directed reporter fusions; however, questions regarding this topology persist. Here, we report a revised membrane topology generated by site-directed fluorescence labeling. The revised topology confirms the presence of four transmembrane segments and reveals a newly identified periplasmic loop between the third and fourth transmembrane domains. Within this loop, four residues were identified that, when mutated, resulted in the appearance of cellular voids. High resolution transmission electron microscopy of these voids showed asymmetric division of the cytoplasm in the absence of outer membrane invagination or visible cell wall ingrowth. This uncoupling reveals a novel role for FtsK in linking cell envelope septation events and yields further evidence for FtsK as a critical checkpoint of cell division. The revised topology of FtsKN also provides an important platform for future studies on essential interactions required for this process. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Various topological Mott insulators and topological bulk charge pumping in strongly-interacting boson system in one-dimensional superlattice

NASA Astrophysics Data System (ADS)

Kuno, Yoshihito; Shimizu, Keita; Ichinose, Ikuo

2017-12-01

In this paper, we study a one-dimensional boson system in a superlattice potential. This system is experimentally feasible by using ultracold atomic gases, and attracts much attention these days. It is expected that the system has a topological phase called a topological Mott insulator (TMI). We show that in strongly-interacting cases, the competition between the superlattice potential and the on-site interaction leads to various TMIs with a non-vanishing integer Chern number. Compared to the hard-core case, the soft-core boson system exhibits rich phase diagrams including various non-trivial TMIs. By using the exact diagonalization, we obtain detailed bulk-global phase diagrams including the TMIs with high Chern numbers and also various non-topological phases. We also show that in adiabatic experimental setups, the strongly-interacting bosonic TMIs exhibit the topological particle transfer, i.e., the topological charge pumping phenomenon, similarly to weakly-interacting systems. The various TMIs are characterized by topological charge pumping as it is closely related to the Chern number, and therefore the Chern number is to be observed in feasible experiments.

Symmetric Topological Phases and Tensor Network States

NASA Astrophysics Data System (ADS)

Jiang, Shenghan

Classification and simulation of quantum phases are one of main themes in condensed matter physics. Quantum phases can be distinguished by their symmetrical and topological properties. The interplay between symmetry and topology in condensed matter physics often leads to exotic quantum phases and rich phase diagrams. Famous examples include quantum Hall phases, spin liquids and topological insulators. In this thesis, I present our works toward a more systematically understanding of symmetric topological quantum phases in bosonic systems. In the absence of global symmetries, gapped quantum phases are characterized by topological orders. Topological orders in 2+1D are well studied, while a systematically understanding of topological orders in 3+1D is still lacking. By studying a family of exact solvable models, we find at least some topological orders in 3+1D can be distinguished by braiding phases of loop excitations. In the presence of both global symmetries and topological orders, the interplay between them leads to new phases termed as symmetry enriched topological (SET) phases. We develop a framework to classify a large class of SET phases using tensor networks. For each tensor class, we can write down generic variational wavefunctions. We apply our method to study gapped spin liquids on the kagome lattice, which can be viewed as SET phases of on-site symmetries as well as lattice symmetries. In the absence of topological order, symmetry could protect different topological phases, which are often referred to as symmetry protected topological (SPT) phases. We present systematic constructions of tensor network wavefunctions for bosonic symmetry protected topological (SPT) phases respecting both onsite and spatial symmetries.

Disordered topological wires in a momentum-space lattice

NASA Astrophysics Data System (ADS)

Meier, Eric; An, Fangzhao; Gadway, Bryce

2017-04-01

One of the most interesting aspects of topological systems is the presence of boundary modes which remain robust in the presence of weak disorder. We explore this feature in the context of one-dimensional (1D) topological wires where staggered tunneling strengths lead to the creation of a mid-gap state in the lattice band structure. Using Bose-condensed 87Rb atoms in a 1D momentum-space lattice, we probe the robust topological character of this model when subjected to both site energy and tunneling disorder. We observe a transition to a topologically trivial phase when tailored disorder is applied, which we detect through both charge-pumping and Hamiltonian-quenching protocols. In addition, we report on efforts to probe the influence of interactions in topological momentum-space lattices.

Hormonal induction of transfected genes depends on DNA topology.

PubMed Central

Piña, B; Haché, R J; Arnemann, J; Chalepakis, G; Slater, E P; Beato, M

1990-01-01

Plasmids containing the hormone regulatory element of mouse mammary tumor virus linked to the thymidine kinase promoter of herpes simplex virus and the reporter gene chloramphenicol acetyltransferase of Escherichia coli respond to glucocorticoids and progestins when transfected into appropriate cells. In the human mammary tumor cell line T47D, the response to progestins, but not to glucocorticoids, is highly dependent on the topology of the transfected DNA. Although negatively supercoiled plasmids respond optimally to the synthetic progestin R5020, their linearized counterparts exhibit markedly reduced progestin inducibility. This is not due to changes in the efficiency of DNA transfection, since the amount of DNA incorporated into the cell nucleus is not significantly dependent on the initial topology of the plasmids. In contrast, cotransfection experiments with glucocorticoid receptor cDNA in the same cell line show no significant influence of DNA topology on induction by dexamethasone. A similar result was obtained with fibroblasts that contain endogenous glucocorticoid receptors. When the distance between receptor-binding sites or between the binding sites and the promoter was increased, the dependence of progestin induction on DNA topology was more pronounced. In contrast to the original plasmid, these constructs also revealed a similar topological dependence for induction by glucocorticoids. The differential influence of DNA topology is not due to differences in the affinity of the two hormone receptors for DNA of various topologies, but probably reflects an influence of DNA topology on the interaction between different DNA-bound receptor molecules and between receptors and other transcription factors. Images PMID:2153920

Lattice topology dictates photon statistics.

PubMed

Kondakci, H Esat; Abouraddy, Ayman F; Saleh, Bahaa E A

2017-08-21

Propagation of coherent light through a disordered network is accompanied by randomization and possible conversion into thermal light. Here, we show that network topology plays a decisive role in determining the statistics of the emerging field if the underlying lattice is endowed with chiral symmetry. In such lattices, eigenmode pairs come in skew-symmetric pairs with oppositely signed eigenvalues. By examining one-dimensional arrays of randomly coupled waveguides arranged on linear and ring topologies, we are led to a remarkable prediction: the field circularity and the photon statistics in ring lattices are dictated by its parity while the same quantities are insensitive to the parity of a linear lattice. For a ring lattice, adding or subtracting a single lattice site can switch the photon statistics from super-thermal to sub-thermal, or vice versa. This behavior is understood by examining the real and imaginary fields on a lattice exhibiting chiral symmetry, which form two strands that interleave along the lattice sites. These strands can be fully braided around an even-sited ring lattice thereby producing super-thermal photon statistics, while an odd-sited lattice is incommensurate with such an arrangement and the statistics become sub-thermal.

Active-Site Plasticity Is Essential to Carbapenem Hydrolysis by OXA-58 Class D β-Lactamase of Acinetobacter baumannii.

PubMed

Pratap, Shivendra; Katiki, Madhusudhanarao; Gill, Preet; Kumar, Pravindra; Golemi-Kotra, Dasantila

2016-01-01

Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are a subgroup of class D β-lactamases, which are enzymes that hydrolyze β-lactams. They have attracted interest due to the emergence of multidrug-resistant Acinetobacter baumannii, which is not responsive to treatment with carbapenems, the usual antibiotics of choice for this bacterium. Unlike other class D β-lactamases, these enzymes efficiently hydrolyze carbapenem antibiotics. To explore the structural requirements for the catalysis of carbapenems by these enzymes, we determined the crystal structure of the OXA-58 CHDL of A. baumannii following acylation of its active-site serine by a 6α-hydroxymethyl penicillin derivative that is a structural mimetic for a carbapenem. In addition, several point mutation variants of the active site of OXA-58, as identified by the crystal structure analysis, were characterized kinetically. These combined studies confirm the mechanistic relevance of a hydrophobic bridge formed over the active site. This structural feature is suggested to stabilize the hydrolysis-productive acyl-enzyme species formed from the carbapenem substrates of this enzyme. Furthermore, our structural studies provide strong evidence that the hydroxyethyl group of carbapenems samples different orientations in the active sites of CHDLs, and the optimum orientation for catalysis depends on the topology of the active site allowing proper closure of the active site. We propose that CHDLs use the plasticity of the active site to drive the mechanism of carbapenem hydrolysis toward efficiency. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Topological Effects of Charge Transfer in Telomere G-Quadruplex Mechanism on Telomerase Activation and Inhibition

NASA Astrophysics Data System (ADS)

Wang, Xin; Liang, Shi-Dong

2013-02-01

We explore the charge transfer in the telomere G-Quadruplex (TG4) DNA theoretically by the nonequilibrium Green's function method, and reveal the topological effect of the charge transport in TG4 DNA. The consecutive TG4 (CTG4) is semiconducting with 0.2 0.3 eV energy gap. Charges transfer favorably in the CTG4, but are trapped in the nonconsecutive TG4 (NCTG4). The global conductance is inversely proportional to the local conductance for NCTG4. The topological structure transition from NCTG4 to CTG4 induces abruptly 3nA charge current, which provide a microscopic clue to understand the telomerase activated or inhibited by TG4. Our findings reveal the fundamental property of charge transfer in TG4 and its relationship with the topological structure of TG4.

Design of Genetic Algorithms for Topology Control of Unmanned Vehicles

DTIC Science & Technology

2010-01-01

decentralised topology control mechanism distributed among active running software agents to achieve a uniform spread of terrestrial unmanned vehicles...14. ABSTRACT We present genetic algorithms (GAs) as a decentralised topology control mechanism distributed among active running software agents to...inspired topology control algorithm. The topology control of UVs using a decentralised solution over an unknown geographical terrain is a challenging

Photoinduced Topological Phase Transitions in Topological Magnon Insulators.

PubMed

Owerre, S A

2018-03-13

Topological magnon insulators are the bosonic analogs of electronic topological insulators. They are manifested in magnetic materials with topologically nontrivial magnon bands as realized experimentally in a quasi-two-dimensional (quasi-2D) kagomé ferromagnet Cu(1-3, bdc), and they also possess protected magnon edge modes. These topological magnetic materials can transport heat as well as spin currents, hence they can be useful for spintronic applications. Moreover, as magnons are charge-neutral spin-1 bosonic quasiparticles with a magnetic dipole moment, topological magnon materials can also interact with electromagnetic fields through the Aharonov-Casher effect. In this report, we study photoinduced topological phase transitions in intrinsic topological magnon insulators in the kagomé ferromagnets. Using magnonic Floquet-Bloch theory, we show that by varying the light intensity, periodically driven intrinsic topological magnetic materials can be manipulated into different topological phases with different sign of the Berry curvatures and the thermal Hall conductivity. We further show that, under certain conditions, periodically driven gapped topological magnon insulators can also be tuned to synthetic gapless topological magnon semimetals with Dirac-Weyl magnon cones. We envision that this work will pave the way for interesting new potential practical applications in topological magnetic materials.

Topological dimension tunes activity patterns in hierarchical modular networks

NASA Astrophysics Data System (ADS)

Safari, Ali; Moretti, Paolo; Muñoz, Miguel A.

2017-11-01

Connectivity patterns of relevance in neuroscience and systems biology can be encoded in hierarchical modular networks (HMNs). Recent studies highlight the role of hierarchical modular organization in shaping brain activity patterns, providing an excellent substrate to promote both segregation and integration of neural information. Here, we propose an extensive analysis of the critical spreading rate (or ‘epidemic’ threshold)—separating a phase with endemic persistent activity from one in which activity ceases—on diverse HMNs. By employing analytical and computational techniques we determine the nature of such a threshold and scrutinize how it depends on general structural features of the underlying HMN. We critically discuss the extent to which current graph-spectral methods can be applied to predict the onset of spreading in HMNs and, most importantly, we elucidate the role played by the network topological dimension as a relevant and unifying structural parameter, controlling the epidemic threshold.

Topological Anderson insulator induced by inter-cell hopping disorder

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

Lv, Shu-Hui; College of Sciences, Hebei University of Science and Technology, Shijiazhuang 050018; Song, Juntao, E-mail: jtsong@mail.hebtu.edu.cn

We have studied in detail the influence of same-orbit and different-orbit hopping disorders in HgTe/CdTe quantum wells. Intriguingly, similar to the behavior of the on-site Anderson disorder, a phase transition from a topologically trivial phase to a topological phase is induced at a proper strength of the same-orbit hopping disorder. For different-orbit hopping disorder, however, the phase transition does not occur. The results have been analytically verified by using effective medium theory. A consistent conclusion can be obtained by comparing phase diagrams, conductance, and conductance fluctuations. In addition, the influence of Rashba spin-orbit interaction (RSOI) on the system has beenmore » studied for different types of disorder, and the RSOI shows different influence on topological phase at different disorders. The topological phase induced by same-orbit hopping disorder is more robust against the RSOI than that induced by on-site Anderson disorder. For different-orbit hopping disorder, no matter whether the RSOI is included or not, the phase transition does not occur. The results indicate, whether or not the topological Anderson insulator can be observed depends on a competition between the different types of the disorder as well as the strength of the RSOI in a system.« less

Topological crystalline insulator SnTe nanoribbons

NASA Astrophysics Data System (ADS)

Dahal, Bishnu R.; Dulal, Rajendra P.; Pegg, Ian L.; Philip, John

2017-03-01

Topological crystalline insulators are systems in which a band inversion that is protected by crystalline mirror symmetry gives rise to nontrivial topological surface states. SnTe is a topological crystalline insulator. It exhibits p-type conductivity due to Sn vacancies and Te antisites, which leads to high carrier density in the bulk. Thus growth of high quality SnTe is a prerequisite for understanding the topological crystalline insulating behavior. We have grown SnTe nanoribbons using a solution method. The width of the SnTe ribbons varies from 500 nm to 2 μm. They exhibit rock salt crystal structure with a lattice parameter of 6.32 Å. The solution method that we have adapted uses low temperature, so the Sn vacancies can be controlled. The solution grown SnTe nanoribbons exhibit strong semiconducting behavior with an activation energy of 240 meV. This activation energy matches with the calculated band gap for SnTe with a lattice parameter of 6.32 Å, which is higher than that reported for bulk SnTe. The higher activation energy makes the thermal excitation of bulk charges very difficult on the surface. As a result, the topological surfaces will be free from the disturbance caused by the thermal excitations

The topology of geology 1: Topological analysis

NASA Astrophysics Data System (ADS)

Thiele, Samuel T.; Jessell, Mark W.; Lindsay, Mark; Ogarko, Vitaliy; Wellmann, J. Florian; Pakyuz-Charrier, Evren

2016-10-01

Topology has been used to characterise and quantify the properties of complex systems in a diverse range of scientific domains. This study explores the concept and applications of topological analysis in geology. We have developed an automatic system for extracting first order 2D topological information from geological maps, and 3D topological information from models built with the Noddy kinematic modelling system, and equivalent analyses should be possible for other implicit modelling systems. A method is presented for describing the spatial and temporal topology of geological models using a set of adjacency relationships that can be expressed as a topology network, thematic adjacency matrix or hive diagram. We define three types of spatial topology (cellular, structural and lithological) that allow us to analyse different aspects of the geology, and then apply them to investigate the geology of the Hamersley Basin, Western Australia.

QSAR models based on quantum topological molecular similarity.

PubMed

Popelier, P L A; Smith, P J

2006-07-01

A new method called quantum topological molecular similarity (QTMS) was fairly recently proposed [J. Chem. Inf. Comp. Sc., 41, 2001, 764] to construct a variety of medicinal, ecological and physical organic QSAR/QSPRs. QTMS method uses quantum chemical topology (QCT) to define electronic descriptors drawn from modern ab initio wave functions of geometry-optimised molecules. It was shown that the current abundance of computing power can be utilised to inject realistic descriptors into QSAR/QSPRs. In this article we study seven datasets of medicinal interest : the dissociation constants (pK(a)) for a set of substituted imidazolines , the pK(a) of imidazoles , the ability of a set of indole derivatives to displace [(3)H] flunitrazepam from binding to bovine cortical membranes , the influenza inhibition constants for a set of benzimidazoles , the interaction constants for a set of amides and the enzyme liver alcohol dehydrogenase , the natriuretic activity of sulphonamide carbonic anhydrase inhibitors and the toxicity of a series of benzyl alcohols. A partial least square analysis in conjunction with a genetic algorithm delivered excellent models. They are also able to highlight the active site, of the ligand or the molecule whose structure determines the activity. The advantages and limitations of QTMS are discussed.

Laser-irradiated Kondo insulators: Controlling the Kondo effect and topological phases

NASA Astrophysics Data System (ADS)

Takasan, Kazuaki; Nakagawa, Masaya; Kawakami, Norio

2017-09-01

We investigate theoretically the nature of laser-irradiated Kondo insulators. Using Floquet theory and the slave-boson approach, we study a periodic Anderson model and derive an effective model that describes laser-irradiated Kondo insulators. In this model, we find two generic effects induced by laser light. One is dynamical localization, which suppresses hopping and hybridization. The other is laser-induced hopping and hybridization, which can be interpreted as synthetic spin-orbit coupling or a magnetic field. The first effect drastically changes the behavior of the Kondo effect. In particular, the Kondo effect under laser light qualitatively changes its character depending on whether the hybridization is on-site or off-site. The second effect triggers topological phase transitions. In topological Kondo insulators, linearly polarized laser light realizes phase transitions between trivial, weak topological, and strong topological Kondo insulators. Moreover, circularly polarized laser light breaks time-reversal symmetry and induces Weyl semimetallic phases. Our results make it possible to dynamically control the Kondo effect and topological phases in heavy-fermion systems. We also discuss experimental setups to detect the signatures.

Membrane Topology Mapping of the Na+-Pumping NADH: Quinone Oxidoreductase from Vibrio cholerae by PhoA- Green Fluorescent Protein Fusion Analysis▿

PubMed Central

Duffy, Ellen B.; Barquera, Blanca

2006-01-01

The membrane topologies of the six subunits of Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) from Vibrio cholerae were determined by a combination of topology prediction algorithms and the construction of C-terminal fusions. Fusion expression vectors contained either bacterial alkaline phosphatase (phoA) or green fluorescent protein (gfp) genes as reporters of periplasmic and cytoplasmic localization, respectively. A majority of the topology prediction algorithms did not predict any transmembrane helices for NqrA. A lack of PhoA activity when fused to the C terminus of NqrA and the observed fluorescence of the green fluorescent protein C-terminal fusion confirm that this subunit is localized to the cytoplasmic side of the membrane. Analysis of four PhoA fusions for NqrB indicates that this subunit has nine transmembrane helices and that residue T236, the binding site for flavin mononucleotide (FMN), resides in the cytoplasm. Three fusions confirm that the topology of NqrC consists of two transmembrane helices with the FMN binding site at residue T225 on the cytoplasmic side. Fusion analysis of NqrD and NqrE showed almost mirror image topologies, each consisting of six transmembrane helices; the results for NqrD and NqrE are consistent with the topologies of Escherichia coli homologs YdgQ and YdgL, respectively. The NADH, flavin adenine dinucleotide, and Fe-S center binding sites of NqrF were localized to the cytoplasm. The determination of the topologies of the subunits of Na+-NQR provides valuable insights into the location of cofactors and identifies targets for mutagenesis to characterize this enzyme in more detail. The finding that all the redox cofactors are localized to the cytoplasmic side of the membrane is discussed. PMID:17041063

Synthetic topological Kondo insulator in a pumped optical cavity

NASA Astrophysics Data System (ADS)

Zheng, Zhen; Zou, Xu-Bo; Guo, Guang-Can

2018-02-01

Motivated by experimental advances on ultracold atoms coupled to a pumped optical cavity, we propose a scheme for synthesizing and observing the Kondo insulator in Fermi gases trapped in optical lattices. The synthetic Kondo phase arises from the screening of localized atoms coupled to mobile ones, which in our proposal is generated via the pumping laser as well as the cavity. By designing the atom-cavity coupling, it can engineer a nearest-neighbor-site Kondo coupling that plays an essential role for supporting topological Kondo phase. Therefore, the cavity-induced Kondo transition is associated with a nontrivial topological features, resulting in the coexistence of the superradiant and topological Kondo state. Our proposal can be realized with current technique, and thus has potential applications in quantum simulation of the topological Kondo insulator in ultracold atoms.

Evidence for fish dispersal from spatial analysis of stream network topology

USGS Publications Warehouse

Hitt, N.P.; Angermeier, P.L.

2008-01-01

Developing spatially explicit conservation strategies for stream fishes requires an understanding of the spatial structure of dispersal within stream networks. We explored spatial patterns of stream fish dispersal by evaluating how the size and proximity of connected streams (i.e., stream network topology) explained variation in fish assemblage structure and how this relationship varied with local stream size. We used data from the US Environmental Protection Agency's Environmental Monitoring and Assessment Program in wadeable streams of the Mid-Atlantic Highlands region (n = 308 sites). We quantified stream network topology with a continuous analysis based on the rate of downstream flow accumulation from sites and with a discrete analysis based on the presence of mainstem river confluences (i.e., basin area >250 km2) within 20 fluvial km (fkm) from sites. Continuous variation in stream network topology was related to local species richness within a distance of ???10 fkm, suggesting an influence of fish dispersal within this spatial grain. This effect was explained largely by catostomid species, cyprinid species, and riverine species, but was not explained by zoogeographic regions, ecoregions, sampling period, or spatial autocorrelation. Sites near mainstem river confluences supported greater species richness and abundance of catostomid, cyprinid, and ictalurid fishes than did sites >20 fkm from such confluences. Assemblages at sites on the smallest streams were not related to stream network topology, consistent with the hypothesis that local stream size regulates the influence of regional dispersal. These results demonstrate that the size and proximity of connected streams influence the spatial distribution of fish and suggest that these influences can be incorporated into the designs of stream bioassessments and reserves to enhance management efficacy. ?? 2008 by The North American Benthological Society.

Combining Topological Hardware and Topological Software: Color-Code Quantum Computing with Topological Superconductor Networks

NASA Astrophysics Data System (ADS)

Litinski, Daniel; Kesselring, Markus S.; Eisert, Jens; von Oppen, Felix

2017-07-01

We present a scalable architecture for fault-tolerant topological quantum computation using networks of voltage-controlled Majorana Cooper pair boxes and topological color codes for error correction. Color codes have a set of transversal gates which coincides with the set of topologically protected gates in Majorana-based systems, namely, the Clifford gates. In this way, we establish color codes as providing a natural setting in which advantages offered by topological hardware can be combined with those arising from topological error-correcting software for full-fledged fault-tolerant quantum computing. We provide a complete description of our architecture, including the underlying physical ingredients. We start by showing that in topological superconductor networks, hexagonal cells can be employed to serve as physical qubits for universal quantum computation, and we present protocols for realizing topologically protected Clifford gates. These hexagonal-cell qubits allow for a direct implementation of open-boundary color codes with ancilla-free syndrome read-out and logical T gates via magic-state distillation. For concreteness, we describe how the necessary operations can be implemented using networks of Majorana Cooper pair boxes, and we give a feasibility estimate for error correction in this architecture. Our approach is motivated by nanowire-based networks of topological superconductors, but it could also be realized in alternative settings such as quantum-Hall-superconductor hybrids.

Mutational analysis of the active site flap (20s loop) of mandelate racemase.

PubMed

Bourque, Jennifer R; Bearne, Stephen L

2008-01-15

Mandelate racemase from Pseudomonas putida catalyzes the Mg2+-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Residues of the 20s and 50s loops determine, in part, the topology and polarity of the active site and hence the substrate specificity. Previously, we proposed that, during racemization, the phenyl ring of mandelate moves between an S-pocket comprised of residues from the 50s loop and an R-pocket comprised of residues from the 20s loop [Siddiqi, F., Bourque, J. R., Jiang, H., Gardner, M., St. Maurice, M., Blouin, C., and Bearne, S. L. (2005) Biochemistry 44, 9013-9021]. The 20s loop constitutes a mobile beta-meander flap that covers the active site cavity shielding it from solvent and controlling entry and egress of ligands. To understand the role of the 20s loop in catalysis and substrate specificity, we constructed a series of mutants (V22A, V22I, V22F, T24S, A25V, V26A, V26L, V26F, V29A, V29L, V29F, V26A/V29L, and V22I/V29L) in which the sizes of hydrophobic side chains of the loop residues were varied. Catalytic efficiencies (kcat/Km) for all mutants were reduced between 6- and 40-fold with the exception of those of V22I, V26A, V29L, and V22I/V29L which had near wild-type efficiencies with mandelate. Thr 24 and Ala 25, located at the tip of the 20s loop, were particularly sensitive to minor alterations in the size of their hydrophobic side chains; however, most mutations were tolerated quite well, suggesting that flap mobility could compensate for increases in the steric bulk of hydrophobic side chains. With the exception of V29L, with mandelate as the substrate, and V22F and V26A/V29L, with 2-naphthylglycolate (2-NG) as the substrate, the values of kcat and Km were not altered in a manner consistent with steric obstruction of the R-pocket, perhaps due to flap mobility compensating for the increased size of the hydrophobic side chains. Surprisingly, V22I and V29L catalyzed the racemization of the bulkier substrate 2-NG

Exploring photonic topological insulator states in a circuit-QED lattice

NASA Astrophysics Data System (ADS)

Li, Jing-Ling; Shan, Chuan-Jia; Zhao, Feng

2018-04-01

We propose a simple protocol to explore the topological properties of photonic integer quantum Hall states in a one-dimensional circiut-QED lattice. By periodically modulating the on-site photonic energies in such a lattice, we demonstrate that this one-dimensional lattice model can be mapped into a two-dimensional integer quantum Hall insulator model. Based on the lattice-based cavity input-output theory, we show that both the photonic topological protected edge states and topological invariants can be clearly measured from the final steady state of the resonator lattice after taking into account cavity dissipation. Interestingly, we also find that the measurement signals associated with the above topological features are quite unambitious even in five coupled dissipative resonators. Our work opens up a new prospect of exploring topological states with a small-size dissipative quantum artificial lattice, which is quite attractive to the current quantum optics community.

Topological phases protected by point group symmetry

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

Song, Hao; Huang, Sheng -Jie; Fu, Liang

We consider symmetry-protected topological (SPT) phases with crystalline point group symmetry, dubbed point group SPT (pgSPT) phases. We show that such phases can be understood in terms of lower-dimensional topological phases with on-site symmetry and that they can be constructed as stacks and arrays of these lower-dimensional states. This provides the basis for a general framework to classify and characterize bosonic and fermionic pgSPT phases, which can be applied for arbitrary crystalline point group symmetry and in arbitrary spatial dimensions. We develop and illustrate this framework by means of a few examples, focusing on three-dimensional states. We classify bosonic pgSPTmore » phases and fermionic topological crystalline superconductors with Z P 2 (reflection) symmetry, electronic topological crystalline insulators (TCIs) with U(1)×Z P 2 symmetry, and bosonic pgSPT phases with C 2v symmetry, which is generated by two perpendicular mirror reflections. We also study surface properties, with a focus on gapped, topologically ordered surface states. For electronic TCIs, we find a Z 8 × Z 2 classification, where the Z 8 corresponds to known states obtained from noninteracting electrons, and the Z 2 corresponds to a “strongly correlated” TCI that requires strong interactions in the bulk. Lastly, our approach may also point the way toward a general theory of symmetry-enriched topological phases with crystalline point group symmetry.« less

Dimensional crossover and cold-atom realization of topological Mott insulators

PubMed Central

Scheurer, Mathias S.; Rachel, Stephan; Orth, Peter P.

2015-01-01

Interacting cold-atomic gases in optical lattices offer an experimental approach to outstanding problems of many body physics. One important example is the interplay of interaction and topology which promises to generate a variety of exotic phases such as the fractionalized Chern insulator or the topological Mott insulator. Both theoretically understanding these states of matter and finding suitable systems that host them have proven to be challenging problems. Here we propose a cold-atom setup where Hubbard on-site interactions give rise to spin liquid-like phases: weak and strong topological Mott insulators. They represent the celebrated paradigm of an interacting and topological quantum state with fractionalized spinon excitations that inherit the topology of the non-interacting system. Our proposal shall help to pave the way for a controlled experimental investigation of this exotic state of matter in optical lattices. Furthermore, it allows for the investigation of a dimensional crossover from a two-dimensional quantum spin Hall insulating phase to a three-dimensional strong topological insulator by tuning the hopping between the layers. PMID:25669431

Topological Quantum Information Processing Mediated Via Hybrid Topological Insulator Structures

DTIC Science & Technology

2013-11-13

manipulation, entanglement and detection ofMajorana fermions in diamond-topological insulator - superconductor heterojunctions. Furthennore, we propose to...the formation, manipulation, entanglement and detection of Majorana fermions in diamond-topological insulator - superconductor heterojunctions...Interactions between Superconductors and Topological Insulators Recent advances have revealed a new type of information processing, topological quantum

Adiabatic topological quantum computing

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

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

Adiabatic topological quantum computing

DOE PAGES

Cesare, Chris; Landahl, Andrew J.; Bacon, Dave; ...

2015-07-31

Topological quantum computing promises error-resistant quantum computation without active error correction. However, there is a worry that during the process of executing quantum gates by braiding anyons around each other, extra anyonic excitations will be created that will disorder the encoded quantum information. Here, we explore this question in detail by studying adiabatic code deformations on Hamiltonians based on topological codes, notably Kitaev’s surface codes and the more recently discovered color codes. We develop protocols that enable universal quantum computing by adiabatic evolution in a way that keeps the energy gap of the system constant with respect to the computationmore » size and introduces only simple local Hamiltonian interactions. This allows one to perform holonomic quantum computing with these topological quantum computing systems. The tools we develop allow one to go beyond numerical simulations and understand these processes analytically.« less

A Novel Topology Link-Controlling Approach for Active Defense of Nodes in Networks

PubMed Central

Li, Jun; Hu, HanPing; Ke, Qiao; Xiong, Naixue

2017-01-01

With the rapid development of virtual machine technology and cloud computing, distributed denial of service (DDoS) attacks, or some peak traffic, poses a great threat to the security of the network. In this paper, a novel topology link control technique and mitigation attacks in real-time environments is proposed. Firstly, a non-invasive method of deploying virtual sensors in the nodes is built, which uses the resource manager of each monitored node as a sensor. Secondly, a general topology-controlling approach of resisting the tolerant invasion is proposed. In the proposed approach, a prediction model is constructed by using copula functions for predicting the peak of a resource through another resource. The result of prediction determines whether or not to initiate the active defense. Finally, a minority game with incomplete strategy is employed to suppress attack flows and improve the permeability of the normal flows. The simulation results show that the proposed approach is very effective in protecting nodes. PMID:28282962

Topologically Allowed Nonsixfold Vortices in a Sixfold Multiferroic Material: Observation and Classification

DOE PAGES

Cheng, Shaobo; Li, Jun; Han, Myung-Geun; ...

2017-04-05

Here, we report structural transformation of sixfold vortex domains into two-, four-, and eightfold vortices via a different type of topological defect in hexagonal manganites. Combining high-resolution electron microscopy and Landau-theory-based numerical simulations, we also investigate the remarkable atomic arrangement and the intertwined relationship between the vortex structures and the topological defects. The roles of their displacement field, formation temperature, and nucleation sites are revealed. All conceivable vortices in the system are topologically classified using homotopy group theory, and their origins are identified.

A novel artificial condensed matter lattice and a new platform for one-dimensional topological phases

DOE PAGES

Belopolski, Ilya; Xu, Su -Yang; Koirala, Nikesh; ...

2017-03-24

Engineered lattices in condensed matter physics, such as cold-atom optical lattices or photonic crystals, can have properties that are fundamentally different from those of naturally occurring electronic crystals. We report a novel type of artificial quantum matter lattice. Our lattice is a multilayer heterostructure built from alternating thin films of topological and trivial insulators. Each interface within the heterostructure hosts a set of topologically protected interface states, and by making the layers sufficiently thin, we demonstrate for the first time a hybridization of interface states across layers. In this way, our heterostructure forms an emergent atomic chain, where the interfacesmore » act as lattice sites and the interface states act as atomic orbitals, as seen from our measurements by angle-resolved photoemission spectroscopy. By changing the composition of the heterostructure, we can directly control hopping between lattice sites. We realize a topological and a trivial phase in our superlattice band structure. We argue that the superlattice may be characterized in a significant way by a one-dimensional topological invariant, closely related to the invariant of the Su-Schrieffer-Heeger model. Our topological insulator heterostructure demonstrates a novel experimental platform where we can engineer band structures by directly controlling how electrons hop between lattice sites.« less

A novel artificial condensed matter lattice and a new platform for one-dimensional topological phases

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

Belopolski, Ilya; Xu, Su -Yang; Koirala, Nikesh

Engineered lattices in condensed matter physics, such as cold-atom optical lattices or photonic crystals, can have properties that are fundamentally different from those of naturally occurring electronic crystals. We report a novel type of artificial quantum matter lattice. Our lattice is a multilayer heterostructure built from alternating thin films of topological and trivial insulators. Each interface within the heterostructure hosts a set of topologically protected interface states, and by making the layers sufficiently thin, we demonstrate for the first time a hybridization of interface states across layers. In this way, our heterostructure forms an emergent atomic chain, where the interfacesmore » act as lattice sites and the interface states act as atomic orbitals, as seen from our measurements by angle-resolved photoemission spectroscopy. By changing the composition of the heterostructure, we can directly control hopping between lattice sites. We realize a topological and a trivial phase in our superlattice band structure. We argue that the superlattice may be characterized in a significant way by a one-dimensional topological invariant, closely related to the invariant of the Su-Schrieffer-Heeger model. Our topological insulator heterostructure demonstrates a novel experimental platform where we can engineer band structures by directly controlling how electrons hop between lattice sites.« less

Active sites of the cytochrome p450cam (CYP101) F87W and F87A mutants. Evidence for significant structural reorganization without alteration of catalytic regiospecificity.

PubMed

Tuck, S F; Graham-Lorence, S; Peterson, J A; Ortiz de Montellano, P R

1993-01-05

Ferricyanide oxidation of the aryl-iron complexes formed by the reaction of cytochrome P450 enzymes with arylhydrazines causes in situ migration of the aryl group from the iron to the porphyrin nitrogen atoms. The regiochemistry of this migration, defined by the ratio of the four possible N-arylprotoporphyrin IX isomers, provides a method for mapping the topologies of cytochrome P450 active sites. The method has been validated by using it to examine the active site of cytochrome P450cam (CYP101), for which a crystal structure is available. In agreement with the crystal structure, reaction with phenylhydrazine gives a 5:25:70 ratio of the NA:NC:ND (subscript indicates pyrrole ring) N-phenylprotoporphyrin IX isomers. Naphthylhydrazine, however, yields exclusively the NC regioisomer and 4-(phenyl)phenylhydrazine the NA:NC:ND isomers in a 14:40:46 ratio. These isomer ratio differences are readily explained by topological differences between the upper and lower reaches of the active site. Having validated the aryl-iron shift as a topological probe, we used it to investigate the structural changes caused by mutation of Phe-87, a residue that provides the ceiling over pyrrole ring D in the crystal structure of cytochrome P450cam. Mutation of Phe-87 to a tryptophan causes no detectable change in the regiochemistry of camphor hydroxylation and only minor changes in the N-aryl isomer ratios. However, mutation of Phe-87 to an alanine, which was expected to open up the region above pyrrole ring D, severely decreased the proportion of the ND in favor of the NA isomer. Less rather than more space is therefore available over pyrrole ring D in the F87A mutant despite the fact that the regiochemistry of camphor hydroxylation remains unchanged. These results provide evidence for significant structural reorganization in the upper regions of the substrate binding site without alteration of the camphor hydroxylation regiospecificity in the F87A mutant.

Topological Interaction by Entanglement of DNA

NASA Astrophysics Data System (ADS)

Feng, Lang; Sha, Ruojie; Seeman, Nadrian; Chaikin, Paul

2012-02-01

We find and study a new type of interaction between colloids, Topological Interaction by Entanglement of DNA (TIED), due to concatenation of loops formed by palindromic DNA. Consider a particle coated with palindromic DNA of sequence ``P1.'' Below the DNA hybridization temperature (Tm), loops of the self-complementary DNA form on the particle surface. Direct hybridization with similar particle covered with a different sequence P2 do not occur. However when particles are held together at T > Tm, then cooled to T < Tm, some of the loops entangle and link, similar to a Olympic Gel. We quantitatively observe and measure this topological interaction between colloids in a ˜5^o C temperature window, ˜6^o C lower than direct binding of complementary DNA with similar strength and introduce the concept of entanglement binding free energy. To prove our interaction to be topological, we unknot the purely entangled binding sites between colloids by adding Topoisomerase I which unconcatenates our loops. This research suggests novel history dependent ways of binding particles and serves as a new design tool in colloidal self-assembly.

Topological-insulator-based terahertz modulator

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

Wang, X. B.; Cheng, L.; Wu, Y.

Three dimensional topological insulators, as a new phase of quantum matters, are characterized by an insulating gap in the bulk and a metallic state on the surface. Particularly, most of the topological insulators have narrow band gaps, and hence have promising applications in the area of terahertz optoelectronics. In this work, we experimentally demonstrate an electronically-tunable terahertz intensity modulator based on Bi 1:5Sb 0:5Te 1:8Se 1:2 single crystal, one of the most insulating topological insulators. A relative frequency-independent modulation depth of ~62% over a wide frequency range from 0.3 to 1.4 THz has been achieved at room temperature, by applyingmore » a bias current of 100 mA. The modulation in the low current regime can be further enhanced at low temperature. We propose that the extraordinarily large modulation is a consequence of thermally-activated carrier absorption in the semiconducting bulk states. Our work provides a new application of topological insulators for terahertz technology.« less

Topological-insulator-based terahertz modulator

DOE PAGES

Wang, X. B.; Cheng, L.; Wu, Y.; ...

2017-10-18

Three dimensional topological insulators, as a new phase of quantum matters, are characterized by an insulating gap in the bulk and a metallic state on the surface. Particularly, most of the topological insulators have narrow band gaps, and hence have promising applications in the area of terahertz optoelectronics. In this work, we experimentally demonstrate an electronically-tunable terahertz intensity modulator based on Bi 1:5Sb 0:5Te 1:8Se 1:2 single crystal, one of the most insulating topological insulators. A relative frequency-independent modulation depth of ~62% over a wide frequency range from 0.3 to 1.4 THz has been achieved at room temperature, by applyingmore » a bias current of 100 mA. The modulation in the low current regime can be further enhanced at low temperature. We propose that the extraordinarily large modulation is a consequence of thermally-activated carrier absorption in the semiconducting bulk states. Our work provides a new application of topological insulators for terahertz technology.« less

Topological Gyroscopic Metamaterials

NASA Astrophysics Data System (ADS)

Nash, Lisa Michelle

Topological materials are generally insulating in their bulk, with protected conducting states on their boundaries that are robust against disorder and perturbation of material property. The existence of these conducting edge states is characterized by an integer topological invariant. Though the phenomenon was first discovered in electronic systems, recent years have shown that topological states exist in classical systems as well. In this thesis we are primarily concerned with the topological properties of gyroscopic materials, which are created by coupling networks of fast-spinning objects. Through a series of simulations, numerical calculations, and experiments, we show that these materials can support topological edge states. We find that edge states in these gyroscopic metamaterials bear the hallmarks of topology related to broken time reversal symmetry: they transmit excitations unidirectionally and are extremely robust against experimental disorder. We also explore requirements for topology by studying several lattice configurations and find that topology emerges naturally in gyroscopic systems.A simple prescription can be used to create many gyroscopic lattices. Though many of our gyroscopic networks are periodic, we explore amorphous point-sets and find that topology also emerges in these networks.

Emergent Topological order from Spin-Orbit Density wave

NASA Astrophysics Data System (ADS)

Gupta, Gaurav; Das, Tanmoy

We study the emergence of a Z2 -type topological order because of Landau type symmetry breaking order parameter. When two Rashba type SOC bands of different chirality become nested by a magic wavevector [(0, ∖pi) or (∖pi,0)], it introduces the inversion of chirality between different lattice sites. Such a density wave state is known as spin-orbit density wave. The resulting quantum order is associated with the topological order which is classified by a Z2 invariant. So, this system can simultaneously be classified by both a symmetry breaking order parameter and the associated Z2 topological invariant. This order parameter can be realized or engineered in two- or quasi-two-dimensional fermionic lattices, quantum wires, with tunable RSOC and correlation strength. The work is facilitated by the computer cluster facility at Department of Physics, Indian Institute of Science.

Determination of the topology of endoplasmic reticulum membrane proteins using redox-sensitive green-fluorescence protein fusions.

PubMed

Tsachaki, Maria; Birk, Julia; Egert, Aurélie; Odermatt, Alex

2015-07-01

Membrane proteins of the endoplasmic reticulum (ER) are involved in a wide array of essential cellular functions. Identification of the topology of membrane proteins can provide significant insight into their mechanisms of action and biological roles. This is particularly important for membrane enzymes, since their topology determines the subcellular site where a biochemical reaction takes place and the dependence on luminal or cytosolic co-factor pools and substrates. The methods currently available for the determination of topology of proteins are rather laborious and require post-lysis or post-fixation manipulation of cells. In this work, we have developed a simple method for defining intracellular localization and topology of ER membrane proteins in living cells, based on the fusion of the respective protein with redox-sensitive green-fluorescent protein (roGFP). We validated the method and demonstrated that roGFP fusion proteins constitute a reliable tool for the study of ER membrane protein topology, using as control microsomal 11β-hydroxysteroid dehydrogenase (11β-HSD) proteins whose topology has been resolved, and comparing with an independent approach. We then implemented this method to determine the membrane topology of six microsomal members of the 17β-hydroxysteroid dehydrogenase (17β-HSD) family. The results revealed a luminal orientation of the catalytic site for three enzymes, i.e. 17β-HSD6, 7 and 12. Knowledge of the intracellular location of the catalytic site of these enzymes will enable future studies on their biological functions and on the role of the luminal co-factor pool. Copyright © 2015 Elsevier B.V. All rights reserved.

Designed topology and site-selective metal composition in tetranuclear [MM'...M'M] linear complexes.

PubMed

Barrios, Leoní A; Aguilà, David; Roubeau, Olivier; Gamez, Patrick; Ribas-Ariño, Jordi; Teat, Simon J; Aromí, Guillem

2009-10-26

The ligand 1,3-bis[3-oxo-3-(2-hydroxyphenyl)propionyl]benzene (H(4)L), designed to align transition metals into tetranuclear linear molecules, reacts with M(II) salts (M=Ni, Co, Cu) to yield complexes with the expected [MMMM] topology. The novel complexes [Co(4)L(2)(py)(6)] (2; py=pyridine) and [Na(py)(2)][Cu(4)L(2)(py)(4)](ClO(4)) (3) have been crystallographically characterised. The metal sites in complexes 2 and 3, together with previously characterised [Ni(4)L(2)(py)(6)] (1), favour different coordination geometries. These have been exploited for the deliberate synthesis of the heterometallic complex [Cu(2)Ni(2)L(2)(py)(6)] (4). Complexes 1, 2, 3 and 4 exhibit antiferromagnetic interactions between pairs of metals within each cluster, leading to S=0 spin ground states, except for the latter cluster, which features two quasi-independent S=1/2 moieties within the molecule. Complex 4 gathers the structural and physical conditions, thus allowing it to be considered as prototype of a two-qbit quantum gate.

Membrane topology of rat sodium-coupled neutral amino acid transporter 2 (SNAT2).

PubMed

Ge, Yudan; Gu, Yanting; Wang, Jiahong; Zhang, Zhou

2018-07-01

Sodium-coupled neutral amino acid transporter 2 (SNAT2) is a subtype of the amino acid transport system A that is widely expressed in mammalian tissues. It plays critical roles in glutamic acid-glutamine circulation, liver gluconeogenesis and other biological pathway. However, the topology of the SNAT2 amino acid transporter is unknown. Here we identified the topological structure of SNAT2 using bioinformatics analysis, Methoxy-polyethylene glycol maleimide (mPEG-Mal) chemical modification, protease cleavage assays, immunofluorescence and examination of glycosylation. Our results show that SNAT2 contains 11 transmembrane domains (TMDs) with an intracellular N terminus and an extracellular C terminus. Three N-glycosylation sites were verified at the largest extracellular loop. This model is consistent with the previous model of SNAT2 with the exception of a difference in number of glycosylation sites. This is the first time to confirm the SNAT2 membrane topology using experimental methods. Our study on SNAT2 topology provides valuable structural information of one of the solute carrier family 38 (SLC38) members. Copyright © 2018 Elsevier B.V. All rights reserved.

Strongly Correlated Topological Insulators

DTIC Science & Technology

2016-02-03

Strongly Correlated Topological Insulators In the past year, the grant was used for work in the field of topological phases, with emphasis on finding...surface of topological insulators . In the past 3 years, we have started a new direction, that of fractional topological insulators . These are materials...Strongly Correlated Topological Insulators Report Title In the past year, the grant was used for work in the field of topological phases, with emphasis

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

PubMed Central

Brackley, Chris A.; Johnson, James; Kelly, Steven; Cook, Peter R.; Marenduzzo, Davide

2016-01-01

Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a fitting-free, minimal model: bivalent or multivalent red and green ‘transcription factors’ bind to cognate sites in strings of beads (‘chromatin’) to form molecular bridges stabilizing loops. In the absence of additional explicit forces, molecular dynamic simulations reveal that bound factors spontaneously cluster—red with red, green with green, but rarely red with green—to give structures reminiscent of transcription factories. Binding of just two transcription factors (or proteins) to active and inactive regions of human chromosomes yields rosettes, topological domains and contact maps much like those seen experimentally. This emergent ‘bridging-induced attraction’ proves to be a robust, simple and generic force able to organize interphase chromosomes at all scales. PMID:27060145

Global topological dominance in the left hemisphere.

PubMed

Wang, Bo; Zhou, Tian Gang; Zhuo, Yan; Chen, Lin

2007-12-26

A series of experiments with right-handers demonstrated that the left hemisphere (LH) is reliably and consistently superior to the right hemisphere (RH) for global topological perception. These experiments generalized the topological account of lateralization to different kinds of topological properties (including holes, inside/outside relation, and "presence vs. absence") in comparison with a broad spectrum of geometric properties, including orientation, distance, size, mirror-symmetry, parallelism, collinearity, etc. The stimuli and paradigms used were also designed to prevent subjects from using various nontopological properties in performing the tasks of topological discrimination. Furthermore, task factors commonly considered in the study of hemispheric asymmetry, such as response latency vs. accuracy, vertical vs. horizontal presentation, detection vs. recognition, and simultaneous vs. sequential judgment, were manipulated to not be confounding factors. Moreover, left-handed subjects were tested and showed the right lateralization of topological perception, in the opposite direction of lateralization compared with right-handers. In addition, the functional magnetic resonance imaging measure revealed that only a region in the left temporal gyrus was consistently more activated across subjects in the task of topological discrimination, consistent with the behavioral results. In summary, the global topological dominance in the LH is well supported by the converging evidence from the variety of paradigms and techniques, and it suggests a unified solution to the current major controversies on visual lateralization.

Topological BF field theory description of topological insulators

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

Cho, Gil Young; Moore, Joel E., E-mail: jemoore@berkeley.edu; Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720

2011-06-15

Research Highlights: > We show that a BF theory is the effective theory of 2D and 3D topological insulators. > The non-gauge-invariance of the bulk theory yields surface terms for a bosonized Dirac fermion. > The 'axion' term in electromagnetism is correctly obtained from gapped surfaces. > Generalizations to possible fractional phases are discussed in closing. - Abstract: Topological phases of matter are described universally by topological field theories in the same way that symmetry-breaking phases of matter are described by Landau-Ginzburg field theories. We propose that topological insulators in two and three dimensions are described by a version ofmore » abelian BF theory. For the two-dimensional topological insulator or quantum spin Hall state, this description is essentially equivalent to a pair of Chern-Simons theories, consistent with the realization of this phase as paired integer quantum Hall effect states. The BF description can be motivated from the local excitations produced when a {pi} flux is threaded through this state. For the three-dimensional topological insulator, the BF description is less obvious but quite versatile: it contains a gapless surface Dirac fermion when time-reversal-symmetry is preserved and yields 'axion electrodynamics', i.e., an electromagnetic E . B term, when time-reversal symmetry is broken and the surfaces are gapped. Just as changing the coefficients and charges of 2D Chern-Simons theory allows one to obtain fractional quantum Hall states starting from integer states, BF theory could also describe (at a macroscopic level) fractional 3D topological insulators with fractional statistics of point-like and line-like objects.« less

Normal Modes Expose Active Sites in Enzymes.

PubMed

Glantz-Gashai, Yitav; Meirson, Tomer; Samson, Abraham O

2016-12-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes.

Normal Modes Expose Active Sites in Enzymes

PubMed Central

Glantz-Gashai, Yitav; Samson, Abraham O.

2016-01-01

Accurate prediction of active sites is an important tool in bioinformatics. Here we present an improved structure based technique to expose active sites that is based on large changes of solvent accessibility accompanying normal mode dynamics. The technique which detects EXPOsure of active SITes through normal modEs is named EXPOSITE. The technique is trained using a small 133 enzyme dataset and tested using a large 845 enzyme dataset, both with known active site residues. EXPOSITE is also tested in a benchmark protein ligand dataset (PLD) comprising 48 proteins with and without bound ligands. EXPOSITE is shown to successfully locate the active site in most instances, and is found to be more accurate than other structure-based techniques. Interestingly, in several instances, the active site does not correspond to the largest pocket. EXPOSITE is advantageous due to its high precision and paves the way for structure based prediction of active site in enzymes. PMID:28002427

Topological Aspects of Information Retrieval.

ERIC Educational Resources Information Center

Egghe, Leo; Rousseau, Ronald

1998-01-01

Discusses topological aspects of theoretical information retrieval, including retrieval topology; similarity topology; pseudo-metric topology; document spaces as topological spaces; Boolean information retrieval as a subsystem of any topological system; and proofs of theorems. (LRW)

The effect of the neural activity on topological properties of growing neural networks.

PubMed

Gafarov, F M; Gafarova, V R

2016-09-01

The connectivity structure in cortical networks defines how information is transmitted and processed, and it is a source of the complex spatiotemporal patterns of network's development, and the process of creation and deletion of connections is continuous in the whole life of the organism. In this paper, we study how neural activity influences the growth process in neural networks. By using a two-dimensional activity-dependent growth model we demonstrated the neural network growth process from disconnected neurons to fully connected networks. For making quantitative investigation of the network's activity influence on its topological properties we compared it with the random growth network not depending on network's activity. By using the random graphs theory methods for the analysis of the network's connections structure it is shown that the growth in neural networks results in the formation of a well-known "small-world" network.

Glycosylatable GFP as a compartment-specific membrane topology reporter

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

Lee, Hunsang; Min, Jisoo; Heijne, Gunnar von

2012-11-02

Highlights: Black-Right-Pointing-Pointer An N-linked glycosylation site is introduced near the GFP fluorophore. Black-Right-Pointing-Pointer gGFP is not glycosylated and is fully fluorescent in the cytosol. Black-Right-Pointing-Pointer gGFP is glycosylated and non-fluorescent in the lumen of the ER. Black-Right-Pointing-Pointer gGFP is fused to membrane proteins of known topology. Black-Right-Pointing-Pointer Its applicability as a membrane topology reporter is demonstrated. -- Abstract: Determination of the membrane topology is an essential step in structural and functional studies of integral membrane proteins, yet the choices of membrane topology reporters are limited and the experimental analysis can be laborious, especially in eukaryotic cells. Here, we present amore » robust membrane topology reporter, glycosylatable green fluorescent protein (gGFP). gGFP is fully fluorescent in the yeast cytosol but becomes glycosylated and does not fluoresce in the lumen of the endoplasmic reticulum (ER). Thus, by assaying fluorescence and the glycosylation status of C-terminal fusions of gGFP to target membrane proteins in whole-cell lysates, the localization of the gGFP moiety (and hence the fusion joint) relative to the ER membrane can be unambiguously determined.« less

Optical and Casimir effects in topological materials

NASA Astrophysics Data System (ADS)

Wilson, Justin H.

Two major electromagnetic phenomena, magneto-optical effects and the Casimir effect, have seen much theoretical and experimental use for many years. On the other hand, recently there has been an explosion of theoretical and experimental work on so-called topological materials, and a natural question to ask is how such electromagnetic phenomena change with these novel materials. Specifically, we will consider are topological insulators and Weyl semimetals. When Dirac electrons on the surface of a topological insulator are gapped or Weyl fermions in the bulk of a Weyl semimetal appear due to time-reversal symmetry breaking, there is a resulting quantum anomalous Hall effect (2D in one case and bulk 3D in the other, respectively). For topological insulators, we investigate the role of localized in-gap states which can leave their own fingerprints on the magneto-optics and can therefore be probed. We have shown that these states resonantly contribute to the Hall conductivity and are magneto-optically active. For Weyl semimetals we investigate the Casimir force and show that with thickness, chemical potential, and magnetic field, a repulsive and tunable Casimir force can be obtained. Additionally, various values of the parameters can give various combinations of traps and antitraps. We additionally probe the topological transition called a Lifshitz transition in the band structure of a material and show that in a Casimir experiment, one can observe a non-analytic "kink'' in the Casimir force across such a transition. The material we propose is a spin-orbit coupled semiconductor with large g-factor that can be magnetically tuned through such a transition. Additionally, we propose an experiment with a two-dimensional metal where weak localization is tuned with an applied field in order to definitively test the effect of diffusive electrons on the Casimir force---an issue that is surprisingly unresolved to this day. Lastly, we show how the time-continuous coherent state

Simulating quantum spin Hall effect in the topological Lieb lattice of a linear circuit network

NASA Astrophysics Data System (ADS)

Zhu, Weiwei; Hou, Shanshan; Long, Yang; Chen, Hong; Ren, Jie

2018-02-01

Inspired by the topological insulator circuit experimentally proposed by Jia Ningyuan et al. [Phys. Rev. X 5, 021031 (2015), 10.1103/PhysRevX.5.021031], we theoretically realize the topological Lieb lattice, a line-centered square lattice with rich topological properties, in a radio-frequency circuit. We design a specific capacitor-inductor connection to resemble the intrinsic spin-orbit coupling and construct the analog spin by mixing degrees of freedom of voltages. As such, we are able to simulate the quantum spin Hall effect in the topological Lieb lattice of linear circuits. We then investigate the spin-resolved topological edge mode and the topological phase transition of the band structure varied with capacitances. Finally, we discuss the extension of the π /2 phase change of hopping between sites to arbitrary phase values. Our results may find implications in engineering microwave topological metamaterials for signal transmission and energy harvesting.

Fluconazole Binding and Sterol Demethylation in Three CYP51 Isoforms Indicate Differences in Active Site Topology

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

Bellamine, A.; Lepesheva, Galina I.; Waterman, Mike

2010-11-16

14{alpha}-Demethylase (CYP51) is a key enzyme in all sterol biosynthetic pathways (animals, fungi, plants, protists, and some bacteria), catalyzing the removal of the C-14 methyl group following cyclization of squalene. Based on mutations found in CYP51 genes from Candida albicans azole-resistant isolates obtained after fluconazole treatment of fungal infections, and using site-directed mutagenesis, we have found that fluconazole binding and substrate metabolism vary among three different CYP51 isoforms: human, fungal, and mycobacterial. In C. albicans, the Y132H mutant from isolates shows no effect on fluconazole binding, whereas the F145L mutant results in a 5-fold increase in its IC{sub 50} formore » fluconazole, suggesting that F145 (conserved only in fungal 14{alpha}-demethylases) interacts with this azole. In C. albicans, F145L accounts, in part, for the difference in fluconazole sensitivity reported between mammals and fungi, providing a basis for treatment of fungal infections. The C. albicans Y132H and human Y145H CYP51 mutants show essentially no effect on substrate metabolism, but the Mycobacterium tuberculosis F89H CYP51 mutant loses both its substrate binding and metabolism. Because these three residues align in the three isoforms, the results indicate that their active sites contain important structural differences, and further emphasize that fluconazole and substrate binding are uncoupled properties.« less

Neural Representation of Spatial Topology in the Rodent Hippocampus

PubMed Central

Chen, Zhe; Gomperts, Stephen N.; Yamamoto, Jun; Wilson, Matthew A.

2014-01-01

Pyramidal cells in the rodent hippocampus often exhibit clear spatial tuning in navigation. Although it has been long suggested that pyramidal cell activity may underlie a topological code rather than a topographic code, it remains unclear whether an abstract spatial topology can be encoded in the ensemble spiking activity of hippocampal place cells. Using a statistical approach developed previously, we investigate this question and related issues in greater details. We recorded ensembles of hippocampal neurons as rodents freely foraged in one and two-dimensional spatial environments, and we used a “decode-to-uncover” strategy to examine the temporally structured patterns embedded in the ensemble spiking activity in the absence of observed spatial correlates during periods of rodent navigation or awake immobility. Specifically, the spatial environment was represented by a finite discrete state space. Trajectories across spatial locations (“states”) were associated with consistent hippocampal ensemble spiking patterns, which were characterized by a state transition matrix. From this state transition matrix, we inferred a topology graph that defined the connectivity in the state space. In both one and two-dimensional environments, the extracted behavior patterns from the rodent hippocampal population codes were compared against randomly shuffled spike data. In contrast to a topographic code, our results support the efficiency of topological coding in the presence of sparse sample size and fuzzy space mapping. This computational approach allows us to quantify the variability of ensemble spiking activity, to examine hippocampal population codes during off-line states, and to quantify the topological complexity of the environment. PMID:24102128

Localized topological states in Bragg multihelicoidal fibers with twist defects

NASA Astrophysics Data System (ADS)

Alexeyev, C. N.; Lapin, B. P.; Milione, G.; Yavorsky, M. A.

2016-06-01

We have studied the influence of a twist defect in multihelicoidal Bragg fibers on the emerging of localized defect modes. We have shown that if such a fiber is excited with a Gaussian beam this leads to the appearance of a defect-localized topological state, whose topological charge coincides with the order of rotational symmetry of the fiber's refractive index. We have shown that this effect has a pronounced crossover behavior. We have also formulated a principle of creating the systems that can nestle defect-localized topologically charged modes. According to this principle, such systems have to possess topological activity, that is, the ability to change the topological charge of the incoming field, and operate in the Bragg regime.

High power density dc/dc converter: Selection of converter topology

NASA Technical Reports Server (NTRS)

Divan, Deepakraj M.

1990-01-01

The work involved in the identification and selection of a suitable converter topology is described. Three new dc/dc converter topologies are proposed: Phase-Shifted Single Active Bridge DC/DC Converter; Single Phase Dual Active Bridges DC/DC Converter; and Three Phase Dual Active Bridges DC/DC Converter (Topology C). The salient features of these topologies are: (1) All are minimal in structure, i.e., each consists of an input and output bridge, input and output filter and a transformer, all components essential for a high power dc/dc conversion process; (2) All devices of both the bridges can operate under near zero-voltage conditions, making possible a reduction of device switching losses and hence, an increase in switching frequency; (3) All circuits operate at a constant frequency, thus simplifying the task of the magnetic and filter elements; (4) Since, the leakage inductance of the transformer is used as the main current transfer element, problems associated with the diode reverse recovery are eliminated. Also, this mode of operation allows easy paralleling of multiple modules for extending the power capacity of the system; (5) All circuits are least sensitive to parasitic impedances, infact the parasitics are efficently utilized; and (6) The soft switching transitions, result in low electromagnetic interference. A detailed analysis of each topology was carried out. Based on the analysis, the various device and component ratings for each topology operating at an optimum point, and under the given specifications, are tabulated and discussed.

Topological mirror superconductivity.

PubMed

Zhang, Fan; Kane, C L; Mele, E J

2013-08-02

We demonstrate the existence of topological superconductors (SCs) protected by mirror and time-reversal symmetries. D-dimensional (D=1, 2, 3) crystalline SCs are characterized by 2(D-1) independent integer topological invariants, which take the form of mirror Berry phases. These invariants determine the distribution of Majorana modes on a mirror symmetric boundary. The parity of total mirror Berry phase is the Z(2) index of a class DIII SC, implying that a DIII topological SC with a mirror line must also be a topological mirror SC but not vice versa and that a DIII SC with a mirror plane is always time-reversal trivial but can be mirror topological. We introduce representative models and suggest experimental signatures in feasible systems. Advances in quantum computing, the case for nodal SCs, the case for class D, and topological SCs protected by rotational symmetries are pointed out.

Long-range doublon transfer in a dimer chain induced by topology and ac fields

NASA Astrophysics Data System (ADS)

Bello, M.; Creffield, C. E.; Platero, G.

2016-03-01

The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain’s end-points. This has the appealing feature that the transfer occurs only between the end-points - the particle does not pass through the intermediate sites-making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving.

Cosmic Topology

NASA Astrophysics Data System (ADS)

Luminet, Jean-Pierre

2015-08-01

Cosmic Topology is the name given to the study of the overall shape of the universe, which involves both global topological features and more local geometrical properties such as curvature. Whether space is finite or infinite, simply-connected or multi-connected like a torus, smaller or greater than the portion of the universe that we can directly observe, are questions that refer to topology rather than curvature. A striking feature of some relativistic, multi-connected "small" universe models is to create multiples images of faraway cosmic sources. While the most recent cosmological data fit the simplest model of a zero-curvature, infinite space model, they are also consistent with compact topologies of the three homogeneous and isotropic geometries of constant curvature, such as, for instance, the spherical Poincaré Dodecahedral Space, the flat hypertorus or the hyperbolic Picard horn. After a "dark age" period, the field of Cosmic Topology has recently become one of the major concerns in cosmology, not only for theorists but also for observational astronomers, leaving open a number of unsolved issues.

Fracton topological order from nearest-neighbor two-spin interactions and dualities

NASA Astrophysics Data System (ADS)

Slagle, Kevin; Kim, Yong Baek

2017-10-01

Fracton topological order describes a remarkable phase of matter, which can be characterized by fracton excitations with constrained dynamics and a ground-state degeneracy that increases exponentially with the length of the system on a three-dimensional torus. However, previous models exhibiting this order require many-spin interactions, which may be very difficult to realize in a real material or cold atom system. In this work, we present a more physically realistic model which has the so-called X-cube fracton topological order [Vijay, Haah, and Fu, Phys. Rev. B 94, 235157 (2016), 10.1103/PhysRevB.94.235157] but only requires nearest-neighbor two-spin interactions. The model lives on a three-dimensional honeycomb-based lattice with one to two spin-1/2 degrees of freedom on each site and a unit cell of six sites. The model is constructed from two orthogonal stacks of Z2 topologically ordered Kitaev honeycomb layers [Kitaev, Ann. Phys. 321, 2 (2006), 10.1016/j.aop.2005.10.005], which are coupled together by a two-spin interaction. It is also shown that a four-spin interaction can be included to instead stabilize 3+1D Z2 topological order. We also find dual descriptions of four quantum phase transitions in our model, all of which appear to be discontinuous first-order transitions.

The enzymatic processing of α-dystroglycan by MMP-2 is controlled by two anchoring sites distinct from the active site

PubMed Central

Fasciglione, Giovanni Francesco; Sbardella, Diego; Sciandra, Francesca; Casella, MariaLuisa; Camerini, Serena; Crescenzi, Marco; Gori, Alessandro; Tarantino, Umberto; Cozza, Paola; Brancaccio, Andrea; Coletta, Massimo; Bozzi, Manuela

2018-01-01

Dystroglycan (DG) is a membrane receptor, belonging to the dystrophin-glycoprotein complex (DGC) and formed by two subunits, α-dystroglycan (α-DG) and β-dystroglycan (β -DG). The C-terminal domain of α-DG and the N-terminal extracellular domain of β -DG are connected, providing a link between the extracellular matrix and the cytosol. Under pathological conditions, such as cancer and muscular dystrophies, DG may be the target of metalloproteinases MMP-2 and MMP-9, contributing to disease progression. Previously, we reported that the C-terminal domain α-DG (483–628) domain is particularly susceptible to the catalytic activity of MMP-2; here we show that the α-DG 621–628 region is required to carry out its complete digestion, suggesting that this portion may represent a MMP-2 anchoring site. Following this observation, we synthesized an α-DG based-peptide, spanning the (613–651) C-terminal region. The analysis of the kinetic and thermodynamic parameters of the whole and the isolated catalytic domain of MMP-2 (cdMMP-2) has shown its inhibitory properties, indicating the presence of (at least) two binding sites for the peptide, both located within the catalytic domain, only one of the two being topologically distinct from the catalytic active groove. However, the different behavior between whole MMP-2 and cdMMP-2 envisages the occurrence of an additional binding site for the peptide on the hemopexin-like domain of MMP-2. Interestingly, mass spectrometry analysis has shown that α-DG (613–651) peptide is cleavable even though it is a very poor substrate of MMP-2, a feature that renders this molecule a promising template for developing a selective MMP-2 inhibitor. PMID:29447293

Study of the docking of competitive inhibitors at a model of tyrosinase active site: insights from joint broken-symmetry/Spin-Flip DFT computations and ELF topological analysis

PubMed Central

de la Lande, A.; Maddaluno, J.; Parisel, O.; Darden, T. A.; Piquemal, J-P

2010-01-01

Following our previous study (Piquemal et al., New J. Chem., 2003, 27, 909), we present here a DFT study of the inhibition of the Tyrosinase enzyme. Broken-symmetry DFT computations are supplemented with Spin-Flip TD-DFT calculations, which, for the first time, are applied to such a dicopper enzyme. The chosen biomimetic model encompasses a dioxygen molecule, two Cu(II) cations, and six imidazole rings. The docking energy of a natural substrate, namely phenolate, together with those of several inhibitor and non-inhibitor compounds, are reported and show the ability of the model to rank the most potent inhibitors in agreement with experimental data. With respect to broken-symmetry calculations, the Spin-Flip TD-DFT approach reinforces the possibility for theory to point out potent inhibitors: the need for the deprotonation of the substrates, natural or inhibitors, is now clearly established. Moreover, Electron Localization Function (ELF) topological analysis computations are used to deeply track the particular electronic distribution of the Cu-O-Cu three-center bonds involved in the enzymatic Cu2O2 metallic core (Piquemal and Pilmé, J. Mol. Struct.: Theochem, 2006, 77, 764). It is shown that such bonds exhibit very resilient out-of-plane density expansions that play a key role in docking interactions: their 3D-orientation could be the topological electronic signature of oxygen activation within such systems. PMID:20396590

Topological superconductors: a review.

PubMed

Sato, Masatoshi; Ando, Yoichi

2017-07-01

This review elaborates pedagogically on the fundamental concept, basic theory, expected properties, and materials realizations of topological superconductors. The relation between topological superconductivity and Majorana fermions are explained, and the difference between dispersive Majorana fermions and a localized Majorana zero mode is emphasized. A variety of routes to topological superconductivity are explained with an emphasis on the roles of spin-orbit coupling. Present experimental situations and possible signatures of topological superconductivity are summarized with an emphasis on intrinsic topological superconductors.

Topological superconductors: a review

NASA Astrophysics Data System (ADS)

Sato, Masatoshi; Ando, Yoichi

2017-07-01

This review elaborates pedagogically on the fundamental concept, basic theory, expected properties, and materials realizations of topological superconductors. The relation between topological superconductivity and Majorana fermions are explained, and the difference between dispersive Majorana fermions and a localized Majorana zero mode is emphasized. A variety of routes to topological superconductivity are explained with an emphasis on the roles of spin-orbit coupling. Present experimental situations and possible signatures of topological superconductivity are summarized with an emphasis on intrinsic topological superconductors.

Topological magnetoplasmon

PubMed Central

Jin, Dafei; Lu, Ling; Wang, Zhong; Fang, Chen; Joannopoulos, John D.; Soljačić, Marin; Fu, Liang; Fang, Nicholas X.

2016-01-01

Classical wave fields are real-valued, ensuring the wave states at opposite frequencies and momenta to be inherently identical. Such a particle–hole symmetry can open up new possibilities for topological phenomena in classical systems. Here we show that the historically studied two-dimensional (2D) magnetoplasmon, which bears gapped bulk states and gapless one-way edge states near-zero frequency, is topologically analogous to the 2D topological p+ip superconductor with chiral Majorana edge states and zero modes. We further predict a new type of one-way edge magnetoplasmon at the interface of opposite magnetic domains, and demonstrate the existence of zero-frequency modes bounded at the peripheries of a hollow disk. These findings can be readily verified in experiment, and can greatly enrich the topological phases in bosonic and classical systems. PMID:27892453

Topological magnetoplasmon

DOE PAGES

Jin, Dafei; Lu, Ling; Wang, Zhong; ...

2016-11-28

Classical wave fields are real-valued, ensuring the wave states at opposite frequencies and momenta to be inherently identical. Such a particle–hole symmetry can open up new possibilities for topological phenomena in classical systems. Here we show that the historically studied two-dimensional (2D) magnetoplasmon, which bears gapped bulk states and gapless one-way edge states near-zero frequency, is topologically analogous to the 2D topological p+ip superconductor with chiral Majorana edge states and zero modes. We further predict a new type of one-way edge magnetoplasmon at the interface of opposite magnetic domains, and demonstrate the existence of zero-frequency modes bounded at the peripheriesmore » of a hollow disk. Finally, these findings can be readily verified in experiment, and can greatly enrich the topological phases in bosonic and classical systems.« less

Topological Materials: Weyl Semimetals

NASA Astrophysics Data System (ADS)

Yan, Binghai; Felser, Claudia

2017-03-01

Topological insulators and topological semimetals are both new classes of quantum materials, which are characterized by surface states induced by the topology of the bulk band structure. Topological Dirac or Weyl semimetals show linear dispersion around nodes, termed the Dirac or Weyl points, as the three-dimensional analog of graphene. We review the basic concepts and compare these topological states of matter from the materials perspective with a special focus on Weyl semimetals. The TaAs family is the ideal materials class to introduce the signatures of Weyl points in a pedagogical way, from Fermi arcs to the chiral magnetotransport properties, followed by hunting for the type-II Weyl semimetals in WTe2, MoTe2, and related compounds. Many materials are members of big families, and topological properties can be tuned. As one example, we introduce the multifunctional topological materials, Heusler compounds, in which both topological insulators and magnetic Weyl semimetals can be found. Instead of a comprehensive review, this article is expected to serve as a helpful introduction and summary by taking a snapshot of the quickly expanding field.

A Novel Topology Link-Controlling Approach for Active Defense of a Node in a Network.

PubMed

Li, Jun; Hu, HanPing; Ke, Qiao; Xiong, Naixue

2017-03-09

With the rapid development of virtual machine technology and cloud computing, distributed denial of service (DDoS) attacks, or some peak traffic, poses a great threat to the security of the network. In this paper, a novel topology link control technique and mitigation attacks in real-time environments is proposed. Firstly, a non-invasive method of deploying virtual sensors in the nodes is built, which uses the resource manager of each monitored node as a sensor. Secondly, a general topology-controlling approach of resisting the tolerant invasion is proposed. In the proposed approach, a prediction model is constructed by using copula functions for predicting the peak of a resource through another resource. The result of prediction determines whether or not to initiate the active defense. Finally, a minority game with incomplete strategy is employed to suppress attack flows and improve the permeability of the normal flows. The simulation results show that the proposed approach is very effective in protecting nodes.

Condensin-driven remodelling of X chromosome topology during dosage compensation

NASA Astrophysics Data System (ADS)

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-07-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure. Here we perform genome-wide chromosome conformation capture analysis, fluorescent in situ hybridization (FISH), and RNA-seq to obtain comprehensive three-dimensional (3D) maps of the Caenorhabditis elegans genome and to dissect X chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian topologically associating domains (TADs). TADs on X chromosomes have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X chromosomes coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X chromosomes by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using

Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation

PubMed Central

Crane, Emily; Bian, Qian; McCord, Rachel Patton; Lajoie, Bryan R.; Wheeler, Bayly S.; Ralston, Edward J.; Uzawa, Satoru; Dekker, Job; Meyer, Barbara J.

2015-01-01

The three-dimensional organization of a genome plays a critical role in regulating gene expression, yet little is known about the machinery and mechanisms that determine higher-order chromosome structure1,2. Here we perform genome-wide chromosome conformation capture analysis, FISH, and RNA-seq to obtain comprehensive 3D maps of the Caenorhabditis elegans genome and to dissect X-chromosome dosage compensation, which balances gene expression between XX hermaphrodites and XO males. The dosage compensation complex (DCC), a condensin complex, binds to both hermaphrodite X chromosomes via sequence-specific recruitment elements on X (rex sites) to reduce chromosome-wide gene expression by half3–7. Most DCC condensin subunits also act in other condensin complexes to control the compaction and resolution of all mitotic and meiotic chromosomes5,6. By comparing chromosome structure in wild-type and DCC-defective embryos, we show that the DCC remodels hermaphrodite X chromosomes into a sex-specific spatial conformation distinct from autosomes. Dosage-compensated X chromosomes consist of self-interacting domains (~1 Mb) resembling mammalian Topologically Associating Domains (TADs)8,9. TADs on X have stronger boundaries and more regular spacing than on autosomes. Many TAD boundaries on X coincide with the highest-affinity rex sites and become diminished or lost in DCC-defective mutants, thereby converting the topology of X to a conformation resembling autosomes. rex sites engage in DCC-dependent long-range interactions, with the most frequent interactions occurring between rex sites at DCC-dependent TAD boundaries. These results imply that the DCC reshapes the topology of X by forming new TAD boundaries and reinforcing weak boundaries through interactions between its highest-affinity binding sites. As this model predicts, deletion of an endogenous rex site at a DCC-dependent TAD boundary using CRISPR/Cas9 greatly diminished the boundary. Thus, the DCC imposes a distinct

Dial-in Topological Metamaterials Based on Bistable Stewart Platform.

PubMed

Wu, Ying; Chaunsali, Rajesh; Yasuda, Hiromi; Yu, Kaiping; Yang, Jinkyu

2018-01-08

Recently, there have been significant efforts to guide mechanical energy in structures by relying on a novel topological framework popularized by the discovery of topological insulators. Here, we propose a topological metamaterial system based on the design of the Stewart Platform, which can not only guide mechanical waves robustly in a desired path, but also can be tuned in situ to change this wave path at will. Without resorting to any active materials, the current system harnesses bistablilty in its unit cells, such that tuning can be performed simply by a dial-in action. Consequently, a topological transition mechanism inspired by the quantum valley Hall effect can be achieved. We show the possibility of tuning in a variety of topological and traditional waveguides in the same system, and numerically investigate key qualitative and quantitative differences between them. We observe that even though both types of waveguides can lead to significant wave transmission for a certain frequency range, topological waveguides are distinctive as they support robust, back scattering immune, one-way wave propagation.

Topological Acoustics

NASA Astrophysics Data System (ADS)

Yang, Zhaoju; Gao, Fei; Shi, Xihang; Lin, Xiao; Gao, Zhen; Chong, Yidong; Zhang, Baile

2015-03-01

The manipulation of acoustic wave propagation in fluids has numerous applications, including some in everyday life. Acoustic technologies frequently develop in tandem with optics, using shared concepts such as waveguiding and metamedia. It is thus noteworthy that an entirely novel class of electromagnetic waves, known as "topological edge states," has recently been demonstrated. These are inspired by the electronic edge states occurring in topological insulators, and possess a striking and technologically promising property: the ability to travel in a single direction along a surface without backscattering, regardless of the existence of defects or disorder. Here, we develop an analogous theory of topological fluid acoustics, and propose a scheme for realizing topological edge states in an acoustic structure containing circulating fluids. The phenomenon of disorder-free one-way sound propagation, which does not occur in ordinary acoustic devices, may have novel applications for acoustic isolators, modulators, and transducers.

Machine learning topological states

NASA Astrophysics Data System (ADS)

Deng, Dong-Ling; Li, Xiaopeng; Das Sarma, S.

2017-11-01

Artificial neural networks and machine learning have now reached a new era after several decades of improvement where applications are to explode in many fields of science, industry, and technology. Here, we use artificial neural networks to study an intriguing phenomenon in quantum physics—the topological phases of matter. We find that certain topological states, either symmetry-protected or with intrinsic topological order, can be represented with classical artificial neural networks. This is demonstrated by using three concrete spin systems, the one-dimensional (1D) symmetry-protected topological cluster state and the 2D and 3D toric code states with intrinsic topological orders. For all three cases, we show rigorously that the topological ground states can be represented by short-range neural networks in an exact and efficient fashion—the required number of hidden neurons is as small as the number of physical spins and the number of parameters scales only linearly with the system size. For the 2D toric-code model, we find that the proposed short-range neural networks can describe the excited states with Abelian anyons and their nontrivial mutual statistics as well. In addition, by using reinforcement learning we show that neural networks are capable of finding the topological ground states of nonintegrable Hamiltonians with strong interactions and studying their topological phase transitions. Our results demonstrate explicitly the exceptional power of neural networks in describing topological quantum states, and at the same time provide valuable guidance to machine learning of topological phases in generic lattice models.

A role for chromatin topology in imprinted domain regulation.

PubMed

MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

2016-02-01

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

Topological Quantum Phase Transition and Local Topological Order in a Strongly Interacting Light-Matter System.

PubMed

Sarkar, Sujit

2017-05-12

An attempt is made to understand the topological quantum phase transition, emergence of relativistic modes and local topological order of light in a strongly interacting light-matter system. We study this system, in a one dimensional array of nonlinear cavities. Topological quantum phase transition occurs with massless excitation only for the finite detuning process. We present a few results based on the exact analytical calculations along with the physical explanations. We observe the emergence of massive Majorana fermion mode at the topological state, massless Majorana-Weyl fermion mode during the topological quantum phase transition and Dirac fermion mode for the non-topological state. Finally, we study the quantized Berry phase (topological order) and its connection to the topological number (winding number).

Topological phases of topological-insulator thin films

NASA Astrophysics Data System (ADS)

Asmar, Mahmoud M.; Sheehy, Daniel E.; Vekhter, Ilya

2018-02-01

We study the properties of a thin film of topological insulator material. We treat the coupling between helical states at opposite surfaces of the film in the properly-adapted tunneling approximation, and show that the tunneling matrix element oscillates as a function of both the film thickness and the momentum in the plane of the film for Bi2Se3 and Bi2Te3 . As a result, while the magnitude of the matrix element at the center of the surface Brillouin zone gives the gap in the energy spectrum, the sign of the matrix element uniquely determines the topological properties of the film, as demonstrated by explicitly computing the pseudospin textures and the Chern number. We find a sequence of transitions between topological and nontopological phases, separated by semimetallic states, as the film thickness varies. In the topological phase, the edge states of the film always exist but only carry a spin current if the edge potentials break particle-hole symmetry. The edge states decay very slowly away from the boundary in Bi2Se3 , making Bi2Te3 , where this scale is shorter, a more promising candidate for the observation of these states. Our results hold for free-standing films as well as heterostructures with large-gap insulators.

Fine topology and locally Minkowskian manifolds

NASA Astrophysics Data System (ADS)

Agrawal, Gunjan; Sinha, Soami Pyari

2018-05-01

Fine topology is one of the several well-known topologies of physical and mathematical relevance. In the present paper, it is obtained that the nonempty open sets of different dimensional Minkowski spaces with the fine topology are not homeomorphic. This leads to the introduction of a new class of manifolds. It turns out that the technique developed here is also applicable to some other topologies, namely, the s-topology, space topology, f-topology, and A-topology.

Anomalous resistivity and the evolution of magnetic field topology

NASA Technical Reports Server (NTRS)

Parker, E. N.

1993-01-01

This paper explores the topological restructuring of a force-free magnetic field caused by the hypothetical sudden onset of a localized region of strong anomalous resistivity. It is shown that the topological complexity increases, with the primitive planar force-free field with straight field lines developing field lines that wrap half a turn around each other, evidently providing a surface of tangential discontinuity in the wraparound region. It is suggested that the topological restructuring contributes to the complexity of the geomagnetic substorm, the aurora, and perhaps some of the flare activity on the sun, or other star, and the Galactic halo.

Topology of the membrane protein LamB by epitope tagging and a comparison with the X-ray model.

PubMed

Newton, S M; Klebba, P E; Michel, V; Hofnung, M; Charbit, A

1996-06-01

We previously developed a genetic approach to study, with a single antibody, the topology of the outer membrane protein LamB, an Escherichia coli porin with specificity towards maltodextrins and a receptor for bacteriophage lambda. Our initial procedure consisted of inserting at random the same reporter epitope (the C3 neutralization epitope from poliovirus) into permissive sites of LamB (i.e., sites which tolerate insertions without deleterious effects on the protein activities or the cell). A specific monoclonal antibody was then used to examine the position of the inserted epitope with respect to the protein and the membrane. In the present work, we set up a site-directed procedure to insert the C3 epitope at new sites in order to distinguish between two-dimensional folding models. This allowed us to identify two new surface loops of LamB and to predict another periplasmic exposed region. The results obtained by random and directed epitope tagging are analyzed in light of the recently published X-ray structure of the LamB protein. Study of 23 hybrid LamB-C3 proteins led to the direct identification of five of the nine external loops (L4, L5, L6, L7, and L9) and led to the prediction of four periplasmic loops (I1, I4, I5, and I8) of LamB. Nine of the hybrid proteins did not lead to topological conclusions, and none led to the wrong predictions or conclusions. The comparison indicates that parts of models based on secondary structure predictions alone are not reliable and points to the importance of experimental data in the establishment of outer membrane protein topological models. The advantages and limitations of genetic foreign epitope insertion for the study of integral membrane proteins are discussed.

Topological Quantum Buses: Coherent Quantum Information Transfer between Topological and Conventional Qubits

NASA Astrophysics Data System (ADS)

Bonderson, Parsa; Lutchyn, Roman M.

2011-04-01

We propose computing bus devices that enable quantum information to be coherently transferred between topological and conventional qubits. We describe a concrete realization of such a topological quantum bus acting between a topological qubit in a Majorana wire network and a conventional semiconductor double quantum dot qubit. Specifically, this device measures the joint (fermion) parity of these two different qubits by using the Aharonov-Casher effect in conjunction with an ancilliary superconducting flux qubit that facilitates the measurement. Such a parity measurement, together with the ability to apply Hadamard gates to the two qubits, allows one to produce states in which the topological and conventional qubits are maximally entangled and to teleport quantum states between the topological and conventional quantum systems.

Topological quantum buses: coherent quantum information transfer between topological and conventional qubits.

PubMed

Bonderson, Parsa; Lutchyn, Roman M

2011-04-01

We propose computing bus devices that enable quantum information to be coherently transferred between topological and conventional qubits. We describe a concrete realization of such a topological quantum bus acting between a topological qubit in a Majorana wire network and a conventional semiconductor double quantum dot qubit. Specifically, this device measures the joint (fermion) parity of these two different qubits by using the Aharonov-Casher effect in conjunction with an ancilliary superconducting flux qubit that facilitates the measurement. Such a parity measurement, together with the ability to apply Hadamard gates to the two qubits, allows one to produce states in which the topological and conventional qubits are maximally entangled and to teleport quantum states between the topological and conventional quantum systems. © 2011 American Physical Society

Topologies on directed graphs

NASA Technical Reports Server (NTRS)

Lieberman, R. N.

1972-01-01

Given a directed graph, a natural topology is defined and relationships between standard topological properties and graph theoretical concepts are studied. In particular, the properties of connectivity and separatedness are investigated. A metric is introduced which is shown to be related to separatedness. The topological notions of continuity and homeomorphism. A class of maps is studied which preserve both graph and topological properties. Applications involving strong maps and contractions are also presented.

Symmetry-protected topological insulator and its symmetry-enriched topologically ordered boundary

NASA Astrophysics Data System (ADS)

Wang, Juven; Wen, Xiao-Gang; Witten, Edward

We propose a mechanism for achieving symmetry-enriched topologically ordered boundaries for symmetry-protected topological states, including those of topological insulators. Several different boundary phases and their phase transitions are considered, including confined phases, deconfined phases, symmetry-breaking, gapped and gapless phases. National Science Foundation PHY-1606531, Corning Glass Works Foundation Fellowship, NSF Grant DMR- 1506475 and NSFC 11274192, the BMO Financial Group and the John Templeton Foundation No. 39901.

Dissecting the active site of a photoreceptor protein

NASA Astrophysics Data System (ADS)

Hoff, Wouter; Hara, Miwa; Ren, Jie; Moghadam, Farzaneh; Xie, Aihua; Kumauchi, Masato

While enzymes are quite large molecules, functionally important chemical events are often limited to a small region of the protein: the active site. The physical and chemical properties of residues at such active sites are often strongly altered compared to the same groups dissolved in water. Understanding such effects is important for unraveling the mechanisms underlying protein function and for protein engineering, but has proven challenging. Here we report on our ongoing efforts on using photoactive yellow protein (PYP), a bacterial photoreceptor, as a model system for such effects. We will report on the following questions: How many residues affect active site properties? Are these residues in direct physical contact with the active site? Can functionally important residues be recognized in the crystal structure of a protein? What structural resolution is needed to understand active sites? What spectroscopic techniques are most informative? Which weak interactions dominate active site properties?

Topological modes bound to dislocations in mechanical metamaterials

NASA Astrophysics Data System (ADS)

Paulose, Jayson; Chen, Bryan Gin-Ge; Vitelli, Vincenzo

2015-02-01

Mechanical metamaterials are artificial structures with unusual properties, such as negative Poisson ratio, bistability or tunable vibrational properties, that originate in the geometry of their unit cell. Often at the heart of such unusual behaviour is a soft mode: a motion that does not significantly stretch or compress the links between constituent elements. When activated by motors or external fields, soft modes become the building blocks of robots and smart materials. Here, we demonstrate the existence of topological soft modes that can be positioned at desired locations in a metamaterial while being robust against a wide range of structural deformations or changes in material parameters. These protected modes, localized at dislocations in deformed kagome and square lattices, are the mechanical analogue of topological states bound to defects in electronic systems. We create physical realizations of the topological modes in prototypes of kagome lattices built out of rigid triangular plates. We show mathematically that they originate from the interplay between two Berry phases: the Burgers vector of the dislocation and the topological polarization of the lattice. Our work paves the way towards engineering topologically protected nanomechanical structures for molecular robotics or information storage and read-out.

Spontaneous topological charging of tactoids in a living nematic

NASA Astrophysics Data System (ADS)

Genkin, Mikhail M.; Sokolov, Andrey; Aranson, Igor S.

2018-04-01

Living nematic is a realization of an active matter combining a nematic liquid crystal with swimming bacteria. The material exhibits a remarkable tendency towards spatio-temporal self-organization manifested in formation of dynamic textures of self-propelled half-integer topological defects (disclinations). Here we report on the study of such living nematic near normal inclusions, or tactoids, naturally realized in liquid crystals close to the isotropic-nematic (I–N) phase transition. On the basis of the computational analysis, we have established that tactoid’s I–N interface spontaneously acquire negative topological charge which is proportional to the tactoid’s size and depends on the concentration of bacteria. The observed negative charging is attributed to the drastic difference in the mobilities of +1/2 and ‑1/2 topological defects in active systems. The effect is described in the framework of a kinetic theory for point-like weakly-interacting defects with different mobilities. Our dedicated experiment fully confirmed the theoretical prediction. The results hint into new strategies for control of active matter.

Spontaneous topological charging of tactoids in a living nematic

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

Genkin, Mikhail M.; Sokolov, Andrey; Aranson, Igor S.

Living nematic is a realization of an active matter combining a nematic liquid crystal with swimming bacteria. The material exhibits a remarkable tendency towards spatio-temporal self-organization manifested in formation of dynamic textures of self-propelled half-integer topological defects (disclinations). Here we report on the study of such living nematic near normal inclusions, or tactoids, naturally realized in liquid crystals close to the isotropic-nematic (I-N) phase transition. On the basis of the computational analysis, we have established that tactoid's I-Ninterface spontaneously acquire negative topological charge which is proportional to the tactoid's size and depends on the concentration of bacteria. The observed negativemore » charging is attributed to the drastic difference in the mobilities of +1/2 and -1/2 topological defects in active systems. The effect is described in the framework of a kinetic theory for point-like weakly-interacting defects with different mobilities. Our dedicated experiment fully confirmed the theoretical prediction. Here, the results hint into new strategies for control of active matter.« less

Spontaneous topological charging of tactoids in a living nematic

DOE PAGES

Genkin, Mikhail M.; Sokolov, Andrey; Aranson, Igor S.

2018-04-13

Living nematic is a realization of an active matter combining a nematic liquid crystal with swimming bacteria. The material exhibits a remarkable tendency towards spatio-temporal self-organization manifested in formation of dynamic textures of self-propelled half-integer topological defects (disclinations). Here we report on the study of such living nematic near normal inclusions, or tactoids, naturally realized in liquid crystals close to the isotropic-nematic (I-N) phase transition. On the basis of the computational analysis, we have established that tactoid's I-Ninterface spontaneously acquire negative topological charge which is proportional to the tactoid's size and depends on the concentration of bacteria. The observed negativemore » charging is attributed to the drastic difference in the mobilities of +1/2 and -1/2 topological defects in active systems. The effect is described in the framework of a kinetic theory for point-like weakly-interacting defects with different mobilities. Our dedicated experiment fully confirmed the theoretical prediction. Here, the results hint into new strategies for control of active matter.« less

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Topology of large-scale structure. IV - Topology in two dimensions

NASA Technical Reports Server (NTRS)

Melott, Adrian L.; Cohen, Alexander P.; Hamilton, Andrew J. S.; Gott, J. Richard, III; Weinberg, David H.

1989-01-01

In a recent series of papers, an algorithm was developed for quantitatively measuring the topology of the large-scale structure of the universe and this algorithm was applied to numerical models and to three-dimensional observational data sets. In this paper, it is shown that topological information can be derived from a two-dimensional cross section of a density field, and analytic expressions are given for a Gaussian random field. The application of a two-dimensional numerical algorithm for measuring topology to cross sections of three-dimensional models is demonstrated.

Conserved Loop Cysteines of Vitamin K Epoxide Reductase Complex Subunit 1-like 1 (VKORC1L1) Are Involved in Its Active Site Regeneration*

PubMed Central

Tie, Jian-Ke; Jin, Da-Yun; Stafford, Darrel W.

2014-01-01

Vitamin K epoxide reductase complex subunit 1 (VKORC1) reduces vitamin K epoxide in the vitamin K cycle for post-translational modification of proteins that are involved in a variety of biological functions. However, the physiological function of VKORC1-like 1 (VKORC1L1), a paralogous enzyme sharing about 50% protein identity with VKORC1, is unknown. Here we determined the structural and functional differences of these two enzymes using fluorescence protease protection (FPP) assay and an in vivo cell-based activity assay. We show that in vivo VKORC1L1 reduces vitamin K epoxide to support vitamin K-dependent carboxylation as efficiently as does VKORC1. However, FPP assays show that unlike VKORC1, VKORC1L1 is a four-transmembrane domain protein with both its termini located in the cytoplasm. Moreover, the conserved loop cysteines, which are not required for VKORC1 activity, are essential for VKORC1L1's active site regeneration. Results from domain exchanges between VKORC1L1 and VKORC1 suggest that it is VKORC1L1's overall structure that uniquely allows for active site regeneration by the conserved loop cysteines. Intermediate disulfide trapping results confirmed an intra-molecular electron transfer pathway for VKORC1L1's active site reduction. Our results allow us to propose a concerted action of the four conserved cysteines of VKORC1L1 for active site regeneration; the second loop cysteine, Cys-58, attacks the active site disulfide, forming an intermediate disulfide with Cys-139; the first loop cysteine, Cys-50, attacks the intermediate disulfide resulting in active site reduction. The different membrane topologies and reaction mechanisms between VKORC1L1 and VKORC1 suggest that these two proteins might have different physiological functions. PMID:24532791

Conserved loop cysteines of vitamin K epoxide reductase complex subunit 1-like 1 (VKORC1L1) are involved in its active site regeneration.

PubMed

Tie, Jian-Ke; Jin, Da-Yun; Stafford, Darrel W

2014-03-28

Vitamin K epoxide reductase complex subunit 1 (VKORC1) reduces vitamin K epoxide in the vitamin K cycle for post-translational modification of proteins that are involved in a variety of biological functions. However, the physiological function of VKORC1-like 1 (VKORC1L1), a paralogous enzyme sharing about 50% protein identity with VKORC1, is unknown. Here we determined the structural and functional differences of these two enzymes using fluorescence protease protection (FPP) assay and an in vivo cell-based activity assay. We show that in vivo VKORC1L1 reduces vitamin K epoxide to support vitamin K-dependent carboxylation as efficiently as does VKORC1. However, FPP assays show that unlike VKORC1, VKORC1L1 is a four-transmembrane domain protein with both its termini located in the cytoplasm. Moreover, the conserved loop cysteines, which are not required for VKORC1 activity, are essential for VKORC1L1's active site regeneration. Results from domain exchanges between VKORC1L1 and VKORC1 suggest that it is VKORC1L1's overall structure that uniquely allows for active site regeneration by the conserved loop cysteines. Intermediate disulfide trapping results confirmed an intra-molecular electron transfer pathway for VKORC1L1's active site reduction. Our results allow us to propose a concerted action of the four conserved cysteines of VKORC1L1 for active site regeneration; the second loop cysteine, Cys-58, attacks the active site disulfide, forming an intermediate disulfide with Cys-139; the first loop cysteine, Cys-50, attacks the intermediate disulfide resulting in active site reduction. The different membrane topologies and reaction mechanisms between VKORC1L1 and VKORC1 suggest that these two proteins might have different physiological functions.

Topological nearly entropy

NASA Astrophysics Data System (ADS)

Gulamsarwar, Syazwani; Salleh, Zabidin

2017-08-01

The purpose of this paper is to generalize the notions of Adler's topological entropy along with their several fundamental properties. A function f : X → Y is said to be R-map if f-1 (V) is regular open in X for every regular open set V in Y. Thus, we initiated a notion of topological nearly entropy for topological R-dynamical systems which is based on nearly compact relative to the space by using R-map.

On Topological Indices of Certain Families of Nanostar Dendrimers.

PubMed

Husin, Mohamad Nazri; Hasni, Roslan; Arif, Nabeel Ezzulddin; Imran, Muhammad

2016-06-24

A topological index of graph G is a numerical parameter related to G which characterizes its molecular topology and is usually graph invariant. In the field of quantitative structure-activity (QSAR)/quantitative structure-activity structure-property (QSPR) research, theoretical properties of the chemical compounds and their molecular topological indices such as the Randić connectivity index, atom-bond connectivity (ABC) index and geometric-arithmetic (GA) index are used to predict the bioactivity of different chemical compounds. A dendrimer is an artificially manufactured or synthesized molecule built up from the branched units called monomers. In this paper, the fourth version of ABC index and the fifth version of GA index of certain families of nanostar dendrimers are investigated. We derive the analytical closed formulas for these families of nanostar dendrimers. The obtained results can be of use in molecular data mining, particularly in researching the uniqueness of tested (hyper-branched) molecular graphs.

Low dielectric response in enzyme active site

PubMed Central

Mertz, Edward L.; Krishtalik, Lev I.

2000-01-01

The kinetics of charge transfer depend crucially on the dielectric reorganization of the medium. In enzymatic reactions that involve charge transfer, atomic dielectric response of the active site and of its surroundings determines the efficiency of the protein as a catalyst. We report direct spectroscopic measurements of the reorganization energy associated with the dielectric response in the active site of α-chymotrypsin. A chromophoric inhibitor of the enzyme is used as a spectroscopic probe. We find that water strongly affects the dielectric reorganization in the active site of the enzyme in solution. The reorganization energy of the protein matrix in the vicinity of the active site is similar to that of low-polarity solvents. Surprisingly, water exhibits an anomalously high dielectric response that cannot be described in terms of the dielectric continuum theory. As a result, sequestering the active site from the aqueous environment inside low-dielectric enzyme body dramatically reduces the dielectric reorganization. This reduction is particularly important for controlling the rate of enzymatic reactions. PMID:10681440

Methanopyrus kandleri topoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

PubMed Central

Rajan, Rakhi; Osterman, Amy; Mondragón, Alfonso

2016-01-01

Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide. PMID:26908655

Impact of network topology on self-organized criticality

NASA Astrophysics Data System (ADS)

Hoffmann, Heiko

2018-02-01

The general mechanisms behind self-organized criticality (SOC) are still unknown. Several microscopic and mean-field theory approaches have been suggested, but they do not explain the dependence of the exponents on the underlying network topology of the SOC system. Here, we first report the phenomena that in the Bak-Tang-Wiesenfeld (BTW) model, sites inside an avalanche area largely return to their original state after the passing of an avalanche, forming, effectively, critically arranged clusters of sites. Then, we hypothesize that SOC relies on the formation process of these clusters, and present a model of such formation. For low-dimensional networks, we show theoretically and in simulation that the exponent of the cluster-size distribution is proportional to the ratio of the fractal dimension of the cluster boundary and the dimensionality of the network. For the BTW model, in our simulations, the exponent of the avalanche-area distribution matched approximately our prediction based on this ratio for two-dimensional networks, but deviated for higher dimensions. We hypothesize a transition from cluster formation to the mean-field theory process with increasing dimensionality. This work sheds light onto the mechanisms behind SOC, particularly, the impact of the network topology.

Exploring 4D quantum Hall physics with a 2D topological charge pump

NASA Astrophysics Data System (ADS)

Lohse, Michael; Schweizer, Christian; Price, Hannah M.; Zilberberg, Oded; Bloch, Immanuel

2018-01-01

The discovery of topological states of matter has greatly improved our understanding of phase transitions in physical systems. Instead of being described by local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example is the two-dimensional (2D) integer quantum Hall effect: it is characterized by the first Chern number, which manifests in the quantized Hall response that is induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional (4D) systems leads to the appearance of an additional quantized Hall response, but one that is nonlinear and described by a 4D topological invariant—the second Chern number. Here we report the observation of a bulk response with intrinsic 4D topology and demonstrate its quantization by measuring the associated second Chern number. By implementing a 2D topological charge pump using ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small cloud of atoms as a local probe, we fully characterize the nonlinear response of the system via in situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probing higher-dimensional quantum Hall systems, in which additional strongly correlated topological phases, exotic collective excitations and boundary phenomena such as isolated Weyl fermions are predicted.

Exploring 4D quantum Hall physics with a 2D topological charge pump.

PubMed

Lohse, Michael; Schweizer, Christian; Price, Hannah M; Zilberberg, Oded; Bloch, Immanuel

2018-01-03

The discovery of topological states of matter has greatly improved our understanding of phase transitions in physical systems. Instead of being described by local order parameters, topological phases are described by global topological invariants and are therefore robust against perturbations. A prominent example is the two-dimensional (2D) integer quantum Hall effect: it is characterized by the first Chern number, which manifests in the quantized Hall response that is induced by an external electric field. Generalizing the quantum Hall effect to four-dimensional (4D) systems leads to the appearance of an additional quantized Hall response, but one that is nonlinear and described by a 4D topological invariant-the second Chern number. Here we report the observation of a bulk response with intrinsic 4D topology and demonstrate its quantization by measuring the associated second Chern number. By implementing a 2D topological charge pump using ultracold bosonic atoms in an angled optical superlattice, we realize a dynamical version of the 4D integer quantum Hall effect. Using a small cloud of atoms as a local probe, we fully characterize the nonlinear response of the system via in situ imaging and site-resolved band mapping. Our findings pave the way to experimentally probing higher-dimensional quantum Hall systems, in which additional strongly correlated topological phases, exotic collective excitations and boundary phenomena such as isolated Weyl fermions are predicted.

Reconfigurable topological photonic crystal

NASA Astrophysics Data System (ADS)

Shalaev, Mikhail I.; Desnavi, Sameerah; Walasik, Wiktor; Litchinitser, Natalia M.

2018-02-01

Topological insulators are materials that conduct on the surface and insulate in their interior due to non-trivial topology of the band structure. The edge states on the interface between topological (non-trivial) and conventional (trivial) insulators are topologically protected from scattering due to structural defects and disorders. Recently, it was shown that photonic crystals (PCs) can serve as a platform for realizing a scatter-free propagation of light waves. In conventional PCs, imperfections, structural disorders, and surface roughness lead to significant losses. The breakthrough in overcoming these problems is likely to come from the synergy of the topological PCs and silicon-based photonics technology that enables high integration density, lossless propagation, and immunity to fabrication imperfections. For many applications, reconfigurability and capability to control the propagation of these non-trivial photonic edge states is essential. One way to facilitate such dynamic control is to use liquid crystals (LCs), which allow to modify the refractive index with external electric field. Here, we demonstrate dynamic control of topological edge states by modifying the refractive index of a LC background medium. Background index is changed depending on the orientation of a LC, while preserving the topology of the system. This results in a change of the spectral position of the photonic bandgap and the topological edge states. The proposed concept might be implemented using conventional semiconductor technology, and can be used for robust energy transport in integrated photonic devices, all-optical circuity, and optical communication systems.

Topological crystalline magnets: Symmetry-protected topological phases of fermions

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

Watanabe, Haruki; Fu, Liang

Here, we introduce a novel class of interaction-enabled topological crystalline insulators in two- and three-dimensional electronic systems, which we call “topological crystalline magnet.” It is protected by the product of the time-reversal symmetry T and a mirror symmetry or a rotation symmetry R. A topological crystalline magnet exhibits two intriguing features: (i) it cannot be adiabatically connected to any Slater insulator and (ii) the edge state is robust against coupling electrons to the edge. These features are protected by the anomalous symmetry transformation property ( RT) 2 = -1 of the edge state. Finally, an anisotropic response to the externalmore » magnetic field can be an experimental signature.« less

Topological crystalline magnets: Symmetry-protected topological phases of fermions

DOE PAGES

Watanabe, Haruki; Fu, Liang

2017-02-27

Here, we introduce a novel class of interaction-enabled topological crystalline insulators in two- and three-dimensional electronic systems, which we call “topological crystalline magnet.” It is protected by the product of the time-reversal symmetry T and a mirror symmetry or a rotation symmetry R. A topological crystalline magnet exhibits two intriguing features: (i) it cannot be adiabatically connected to any Slater insulator and (ii) the edge state is robust against coupling electrons to the edge. These features are protected by the anomalous symmetry transformation property ( RT) 2 = -1 of the edge state. Finally, an anisotropic response to the externalmore » magnetic field can be an experimental signature.« less

Nanoscale electron transport at the surface of a topological insulator.

PubMed

Bauer, Sebastian; Bobisch, Christian A

2016-04-21

The use of three-dimensional topological insulators for disruptive technologies critically depends on the dissipationless transport of electrons at the surface, because of the suppression of backscattering at defects. However, in real devices, defects are unavoidable and scattering at angles other than 180° is allowed for such materials. Until now, this has been studied indirectly by bulk measurements and by the analysis of the local density of states in close vicinity to defect sites. Here, we directly measure the nanoscale voltage drop caused by the scattering at step edges, which occurs if a lateral current flows along a three-dimensional topological insulator. The experiments were performed using scanning tunnelling potentiometry for thin Bi2Se3 films. So far, the observed voltage drops are small because of large contributions of the bulk to the electronic transport. However, for the use of ideal topological insulating thin films in devices, these contributions would play a significant role.

Nanoscale electron transport at the surface of a topological insulator

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Bobisch, Christian A.

2016-04-01

The use of three-dimensional topological insulators for disruptive technologies critically depends on the dissipationless transport of electrons at the surface, because of the suppression of backscattering at defects. However, in real devices, defects are unavoidable and scattering at angles other than 180° is allowed for such materials. Until now, this has been studied indirectly by bulk measurements and by the analysis of the local density of states in close vicinity to defect sites. Here, we directly measure the nanoscale voltage drop caused by the scattering at step edges, which occurs if a lateral current flows along a three-dimensional topological insulator. The experiments were performed using scanning tunnelling potentiometry for thin Bi2Se3 films. So far, the observed voltage drops are small because of large contributions of the bulk to the electronic transport. However, for the use of ideal topological insulating thin films in devices, these contributions would play a significant role.

Topological Electride Y2C.

PubMed

Huang, Huaqing; Jin, Kyung-Hwan; Zhang, Shunhong; Liu, Feng

2018-03-14

Two-dimensional (2D) electrides are layered ionic crystals in which anionic electrons are confined in the interlayer space. Here, we report a discovery of nontrivial [Formula: see text] topology in the electronic structures of 2D electride Y 2 C. Based on first-principles calculations, we found a topological [Formula: see text] invariant of (1; 111) for the bulk band and topologically protected surface states in the surfaces of Y 2 C, signifying its nontrivial electronic topology. We suggest a spin-resolved angle-resolved photoemission spectroscopy (ARPES) measurement to detect the unique helical spin texture of the spin-polarized topological surface state, which will provide characteristic evidence for the nontrivial electronic topology of Y 2 C. Furthermore, the coexistence of 2D surface electride states and topological surface state enables us to explain the outstanding discrepancy between the recent ARPES experiments and theoretical calculations. Our findings establish a preliminary link between the electride in chemistry and the band topology in condensed-matter physics, which are expected to inspire further interdisciplinary research between these fields.

Homeostatic structural plasticity can account for topology changes following deafferentation and focal stroke.

PubMed

Butz, Markus; Steenbuck, Ines D; van Ooyen, Arjen

2014-01-01

After brain lesions caused by tumors or stroke, or after lasting loss of input (deafferentation), inter- and intra-regional brain networks respond with complex changes in topology. Not only areas directly affected by the lesion but also regions remote from the lesion may alter their connectivity-a phenomenon known as diaschisis. Changes in network topology after brain lesions can lead to cognitive decline and increasing functional disability. However, the principles governing changes in network topology are poorly understood. Here, we investigated whether homeostatic structural plasticity can account for changes in network topology after deafferentation and brain lesions. Homeostatic structural plasticity postulates that neurons aim to maintain a desired level of electrical activity by deleting synapses when neuronal activity is too high and by providing new synaptic contacts when activity is too low. Using our Model of Structural Plasticity, we explored how local changes in connectivity induced by a focal loss of input affected global network topology. In accordance with experimental and clinical data, we found that after partial deafferentation, the network as a whole became more random, although it maintained its small-world topology, while deafferentated neurons increased their betweenness centrality as they rewired and returned to the homeostatic range of activity. Furthermore, deafferentated neurons increased their global but decreased their local efficiency and got longer tailed degree distributions, indicating the emergence of hub neurons. Together, our results suggest that homeostatic structural plasticity may be an important driving force for lesion-induced network reorganization and that the increase in betweenness centrality of deafferentated areas may hold as a biomarker for brain repair.

Topologically massive magnetic monopoles

NASA Astrophysics Data System (ADS)

Aliev, A. N.; Nutku, Y.; Saygili, K.

2000-10-01

We show that in the Maxwell-Chern-Simons theory of topologically massive electrodynamics the Dirac string of a monopole becomes a cone in anti-de Sitter space with the opening angle of the cone determined by the topological mass, which in turn is related to the square root of the cosmological constant. This proves to be an example of a physical system, a priori completely unrelated to gravity, which nevertheless requires curved spacetime for its very existence. We extend this result to topologically massive gravity coupled to topologically massive electrodynamics within the framework of the theory of Deser, Jackiw and Templeton. The two-component spinor formalism, which is a Newman-Penrose type approach for three dimensions, is extended to include both the electrodynamical and gravitational topologically massive field equations. Using this formalism exact solutions of the coupled Deser-Jackiw-Templeton and Maxwell-Chern-Simons field equations for a topologically massive monopole are presented. These are homogeneous spaces with conical deficit. Pure Einstein gravity coupled to the Maxwell-Chern-Simons field does not admit such a monopole solution.

Recipe for Topological Polaritons

NASA Astrophysics Data System (ADS)

Karzig, Torsten; Bardyn, Charles-Edouard; Lindner, Netanel; Refael, Gil

2015-03-01

The interaction between light and matter can give rise to novel topological states. This principle was recently exemplified in Floquet topological insulators, where classical light was used to induce a topological electronic band structure. Here, in contrast, we show that mixing single photons with excitons can result in new topological polaritonic states -- or ``topolaritons''. Taken separately, the underlying photons and excitons are topologically trivial. Combined appropriately, however, they give rise to non-trivial polaritonic bands with chiral edge modes allowing for unidirectional polariton propagation. The main ingredient in our construction is an exciton-photon coupling with a phase that winds in momentum space. We demonstrate how this winding emerges from spin-orbit coupling in the electronic system and an applied Zeeman field. We discuss the requirements for obtaining a sizable topological gap in the polariton spectrum. Funded by the Institute for Quantum Information and Matter, the Bi-National Science Foundation and I-Core: the Israeli Excellence Center ``Circle of Light'', and Darpa under funding for FENA, and the Swiss National Science Foundation.

The Coordinated Positive Regulation of Topoisomerase Genes Maintains Topological Homeostasis in Streptomyces coelicolor

PubMed Central

Gongerowska, Martyna; Gutkowski, Paweł; Zakrzewska-Czerwińska, Jolanta; Jakimowicz, Dagmara

2016-01-01

ABSTRACT Maintaining an optimal level of chromosomal supercoiling is critical for the progression of DNA replication and transcription. Moreover, changes in global supercoiling affect the expression of a large number of genes and play a fundamental role in adapting to stress. Topoisomerase I (TopA) and gyrase are key players in the regulation of bacterial chromosomal topology through their respective abilities to relax and compact DNA. Soil bacteria such as Streptomyces species, which grow as branched, multigenomic hyphae, are subject to environmental stresses that are associated with changes in chromosomal topology. The topological fluctuations modulate the transcriptional activity of a large number of genes and in Streptomyces are related to the production of antibiotics. To better understand the regulation of topological homeostasis in Streptomyces coelicolor, we investigated the interplay between the activities of the topoisomerase-encoding genes topA and gyrBA. We show that the expression of both genes is supercoiling sensitive. Remarkably, increased chromosomal supercoiling induces the topA promoter but only slightly influences gyrBA transcription, while DNA relaxation affects the topA promoter only marginally but strongly activates the gyrBA operon. Moreover, we showed that exposure to elevated temperatures induces rapid relaxation, which results in changes in the levels of both topoisomerases. We therefore propose a unique mechanism of S. coelicolor chromosomal topology maintenance based on the supercoiling-dependent stimulation, rather than repression, of the transcription of both topoisomerase genes. These findings provide important insight into the maintenance of topological homeostasis in an industrially important antibiotic producer. IMPORTANCE We describe the unique regulation of genes encoding two topoisomerases, topoisomerase I (TopA) and gyrase, in a model Streptomyces species. Our studies demonstrate the coordination of topoisomerase gene

Topological nodal superconducting phases and topological phase transition in the hyperhoneycomb lattice

NASA Astrophysics Data System (ADS)

Bouhon, Adrien; Schmidt, Johann; Black-Schaffer, Annica M.

2018-03-01

We establish the topology of the spin-singlet superconducting states in the bare hyperhoneycomb lattice, and we derive analytically the full phase diagram using only symmetry and topology in combination with simple energy arguments. The phase diagram is dominated by two states preserving time-reversal symmetry. We find a line-nodal state dominating at low doping levels that is topologically nontrivial and exhibits surface Majorana flatbands, which we show perfectly match the bulk-boundary correspondence using the Berry phase approach. At higher doping levels, we find a fully gapped state with trivial topology. By analytically calculating the topological invariant of the nodal lines, we derive the critical point between the line-nodal and fully gapped states as a function of both pairing parameters and doping. We find that the line-nodal state is favored not only at lower doping levels but also if symmetry-allowed deformations of the lattice are present. Adding simple energy arguments, we establish that a fully gapped state with broken time-reversal symmetry likely appears covering the actual phase transition. We find this fully gapped state to be topologically trivial, while we find an additional point-nodal state at very low doing levels that also break time-reversal symmetry and has nontrivial topology with associated Fermi surface arcs. We eventually address the robustness of the phase diagram to generalized models also including adiabatic spin-orbit coupling, and we show how all but the point-nodal state are reasonably stable.

Topological states of condensed matter

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

Wang, Jing; Zhang, Shou-Cheng

Topological states of quantum matter have been investigated intensively in recent years in materials science and condensed matter physics. The field developed explosively largely because of the precise theoretical predictions, well-controlled materials processing, and novel characterization techniques. In this Perspective, we review recent progress in topological insulators, the quantum anomalous Hall effect, chiral topological superconductors, helical topological superconductors and Weyl semimetals.

Topological states of condensed matter

DOE PAGES

Wang, Jing; Zhang, Shou-Cheng

2017-10-25

Topological states of quantum matter have been investigated intensively in recent years in materials science and condensed matter physics. The field developed explosively largely because of the precise theoretical predictions, well-controlled materials processing, and novel characterization techniques. In this Perspective, we review recent progress in topological insulators, the quantum anomalous Hall effect, chiral topological superconductors, helical topological superconductors and Weyl semimetals.

Floquet topological insulators for sound

NASA Astrophysics Data System (ADS)

Fleury, Romain; Khanikaev, Alexander B.; Alù, Andrea

2016-06-01

The unique conduction properties of condensed matter systems with topological order have recently inspired a quest for the similar effects in classical wave phenomena. Acoustic topological insulators, in particular, hold the promise to revolutionize our ability to control sound, allowing for large isolation in the bulk and broadband one-way transport along their edges, with topological immunity against structural defects and disorder. So far, these fascinating properties have been obtained relying on moving media, which may introduce noise and absorption losses, hindering the practical potential of topological acoustics. Here we overcome these limitations by modulating in time the acoustic properties of a lattice of resonators, introducing the concept of acoustic Floquet topological insulators. We show that acoustic waves provide a fertile ground to apply the anomalous physics of Floquet topological insulators, and demonstrate their relevance for a wide range of acoustic applications, including broadband acoustic isolation and topologically protected, nonreciprocal acoustic emitters.

Floquet topological insulators for sound

PubMed Central

Fleury, Romain; Khanikaev, Alexander B; Alù, Andrea

2016-01-01

The unique conduction properties of condensed matter systems with topological order have recently inspired a quest for the similar effects in classical wave phenomena. Acoustic topological insulators, in particular, hold the promise to revolutionize our ability to control sound, allowing for large isolation in the bulk and broadband one-way transport along their edges, with topological immunity against structural defects and disorder. So far, these fascinating properties have been obtained relying on moving media, which may introduce noise and absorption losses, hindering the practical potential of topological acoustics. Here we overcome these limitations by modulating in time the acoustic properties of a lattice of resonators, introducing the concept of acoustic Floquet topological insulators. We show that acoustic waves provide a fertile ground to apply the anomalous physics of Floquet topological insulators, and demonstrate their relevance for a wide range of acoustic applications, including broadband acoustic isolation and topologically protected, nonreciprocal acoustic emitters. PMID:27312175

Topological Acoustic Delay Line

NASA Astrophysics Data System (ADS)

Zhang, Zhiwang; Tian, Ye; Cheng, Ying; Wei, Qi; Liu, Xiaojun; Christensen, Johan

2018-03-01

Topological protected wave engineering in artificially structured media is at the frontier of ongoing metamaterials research that is inspired by quantum mechanics. Acoustic analogues of electronic topological insulators have recently led to a wealth of new opportunities in manipulating sound propagation with strikingly unconventional acoustic edge modes immune to backscattering. Earlier fabrications of topological insulators are characterized by an unreconfigurable geometry and a very narrow frequency response, which severely hinders the exploration and design of useful devices. Here we establish topologically protected sound in reconfigurable phononic crystals that can be switched on and off simply by rotating its three-legged "atoms" without altering the lattice structure. In particular, we engineer robust phase delay defects that take advantage of the ultrabroadband reflection-free sound propagation. Such topological delay lines serve as a paradigm in compact acoustic devices, interconnects, and electroacoustic integrated circuits.

Topological phase transitions and chiral inelastic transport induced by the squeezing of light

PubMed Central

Peano, Vittorio; Houde, Martin; Brendel, Christian; Marquardt, Florian; Clerk, Aashish A.

2016-01-01

There is enormous interest in engineering topological photonic systems. Despite intense activity, most works on topological photonic states (and more generally bosonic states) amount in the end to replicating a well-known fermionic single-particle Hamiltonian. Here we show how the squeezing of light can lead to the formation of qualitatively new kinds of topological states. Such states are characterized by non-trivial Chern numbers, and exhibit protected edge modes, which give rise to chiral elastic and inelastic photon transport. These topological bosonic states are not equivalent to their fermionic (topological superconductor) counterparts and, in addition, cannot be mapped by a local transformation onto topological states found in particle-conserving models. They thus represent a new type of topological system. We study this physics in detail in the case of a kagome lattice model, and discuss possible realizations using nonlinear photonic crystals or superconducting circuits. PMID:26931620

Topological phase transitions and chiral inelastic transport induced by the squeezing of light

NASA Astrophysics Data System (ADS)

Peano, Vittorio; Houde, Martin; Brendel, Christian; Marquardt, Florian; Clerk, Aashish A.

2016-03-01

There is enormous interest in engineering topological photonic systems. Despite intense activity, most works on topological photonic states (and more generally bosonic states) amount in the end to replicating a well-known fermionic single-particle Hamiltonian. Here we show how the squeezing of light can lead to the formation of qualitatively new kinds of topological states. Such states are characterized by non-trivial Chern numbers, and exhibit protected edge modes, which give rise to chiral elastic and inelastic photon transport. These topological bosonic states are not equivalent to their fermionic (topological superconductor) counterparts and, in addition, cannot be mapped by a local transformation onto topological states found in particle-conserving models. They thus represent a new type of topological system. We study this physics in detail in the case of a kagome lattice model, and discuss possible realizations using nonlinear photonic crystals or superconducting circuits.

A structural topological optimization method for multi-displacement constraints and any initial topology configuration

NASA Astrophysics Data System (ADS)

Rong, J. H.; Yi, J. H.

2010-10-01

In density-based topological design, one expects that the final result consists of elements either black (solid material) or white (void), without any grey areas. Moreover, one also expects that the optimal topology can be obtained by starting from any initial topology configuration. An improved structural topological optimization method for multi- displacement constraints is proposed in this paper. In the proposed method, the whole optimization process is divided into two optimization adjustment phases and a phase transferring step. Firstly, an optimization model is built to deal with the varied displacement limits, design space adjustments, and reasonable relations between the element stiffness matrix and mass and its element topology variable. Secondly, a procedure is proposed to solve the optimization problem formulated in the first optimization adjustment phase, by starting with a small design space and advancing to a larger deign space. The design space adjustments are automatic when the design domain needs expansions, in which the convergence of the proposed method will not be affected. The final topology obtained by the proposed procedure in the first optimization phase, can approach to the vicinity of the optimum topology. Then, a heuristic algorithm is given to improve the efficiency and make the designed structural topology black/white in both the phase transferring step and the second optimization adjustment phase. And the optimum topology can finally be obtained by the second phase optimization adjustments. Two examples are presented to show that the topologies obtained by the proposed method are of very good 0/1 design distribution property, and the computational efficiency is enhanced by reducing the element number of the design structural finite model during two optimization adjustment phases. And the examples also show that this method is robust and practicable.

Topological X-Rays Revisited

ERIC Educational Resources Information Center

Lynch, Mark

2012-01-01

We continue our study of topological X-rays begun in Lynch ["Topological X-rays and MRI's," iJMEST 33(3) (2002), pp. 389-392]. We modify our definition of a topological magnetic resonance imaging and give an affirmative answer to the question posed there: Can we identify a closed set in a box by defining X-rays to probe the interior and without…

Classical topological paramagnetism

NASA Astrophysics Data System (ADS)

Bondesan, R.; Ringel, Z.

2017-05-01

Topological phases of matter are one of the hallmarks of quantum condensed matter physics. One of their striking features is a bulk-boundary correspondence wherein the topological nature of the bulk manifests itself on boundaries via exotic massless phases. In classical wave phenomena, analogous effects may arise; however, these cannot be viewed as equilibrium phases of matter. Here, we identify a set of rules under which robust equilibrium classical topological phenomena exist. We write simple and analytically tractable classical lattice models of spins and rotors in two and three dimensions which, at suitable parameter ranges, are paramagnetic in the bulk but nonetheless exhibit some unusual long-range or critical order on their boundaries. We point out the role of simplicial cohomology as a means of classifying, writing, and analyzing such models. This opens an experimental route for studying strongly interacting topological phases of spins.

Nonlinear conduction via solitons in a topological mechanical insulator.

PubMed

Chen, Bryan Gin-ge; Upadhyaya, Nitin; Vitelli, Vincenzo

2014-09-09

Networks of rigid bars connected by joints, termed linkages, provide a minimal framework to design robotic arms and mechanical metamaterials built of folding components. Here, we investigate a chain-like linkage that, according to linear elasticity, behaves like a topological mechanical insulator whose zero-energy modes are localized at the edge. Simple experiments we performed using prototypes of the chain vividly illustrate how the soft motion, initially localized at the edge, can in fact propagate unobstructed all of the way to the opposite end. Using real prototypes, simulations, and analytical models, we demonstrate that the chain is a mechanical conductor, whose carriers are nonlinear solitary waves, not captured within linear elasticity. Indeed, the linkage prototype can be regarded as the simplest example of a topological metamaterial whose protected mechanical excitations are solitons, moving domain walls between distinct topological mechanical phases. More practically, we have built a topologically protected mechanism that can perform basic tasks such as transporting a mechanical state from one location to another. Our work paves the way toward adopting the principle of topological robustness in the design of robots assembled from activated linkages as well as in the fabrication of complex molecular nanostructures.

Topological surface states in nodal superconductors.

PubMed

Schnyder, Andreas P; Brydon, Philip M R

2015-06-24

Topological superconductors have become a subject of intense research due to their potential use for technical applications in device fabrication and quantum information. Besides fully gapped superconductors, unconventional superconductors with point or line nodes in their order parameter can also exhibit nontrivial topological characteristics. This article reviews recent progress in the theoretical understanding of nodal topological superconductors, with a focus on Weyl and noncentrosymmetric superconductors and their protected surface states. Using selected examples, we review the bulk topological properties of these systems, study different types of topological surface states, and examine their unusual properties. Furthermore, we survey some candidate materials for topological superconductivity and discuss different experimental signatures of topological surface states.

Considerations for Multiprocessor Topologies

NASA Technical Reports Server (NTRS)

Byrd, Gregory T.; Delagi, Bruce A.

1987-01-01

Choosing a multiprocessor interconnection topology may depend on high-level considerations, such as the intended application domain and the expected number of processors. It certainly depends on low-level implementation details, such as packaging and communications protocols. The authors first use rough measures of cost and performance to characterize several topologies. They then examine how implementation details can affect the realizable performance of a topology.

Transmembrane topology of the arsenite permease Acr3 from Saccharomyces cerevisiae.

PubMed

Wawrzycka, Donata; Markowska, Katarzyna; Maciaszczyk-Dziubinska, Ewa; Migocka, Magdalena; Wysocki, Robert

2017-01-01

Acr3 is a plasma membrane transporter, a member of the bile/arsenite/riboflavin transporter (BART) superfamily, which confers high-level resistance to arsenicals in the yeast Saccharomyces cerevisiae. We have previously shown that the yeast Acr3 acts as a low affinity As(III)/H + and Sb(III)/H + antiporter. We have also identified several amino acid residues that are localized in putative transmembrane helices (TM) and appeared to be critical for the Acr3 activity. In the present study, the topology of Acr3 was investigated by insertion of glycosylation and factor Xa protease cleavage sites at predicted hydrophilic regions. The analysis of the glycosylation pattern and factor Xa cleavage products of resulting Acr3 fusion constructs provide evidence supporting a topological model of Acr3 with 10 TM segments and cytoplasmically oriented N- and C-terminal domains. Next, we investigated the role of the hydrophilic loop connecting TM8 and TM9, the large size of which is unique to members of the yeast Acr3 family of metalloid transporters. We found that a 28 amino acid deletion in this region does not affect Acr3 folding, trafficking substrate binding, or transport activity. Finally, we constructed a homology-based structural model of Acr3 using the crystal structure of the Yersinia frederiksenii homologue of the human bile acid sodium symporter ASBT. Copyright © 2016 Elsevier B.V. All rights reserved.

M-Polynomials and topological indices of V-Phenylenic Nanotubes and Nanotori.

PubMed

Kwun, Young Chel; Munir, Mobeen; Nazeer, Waqas; Rafique, Shazia; Min Kang, Shin

2017-08-18

V-Phenylenic nanotubes and nanotori are most comprehensively studied nanostructures due to widespread applications in the production of catalytic, gas-sensing and corrosion-resistant materials. Representing chemical compounds with M-polynomial is a recent idea and it produces nice formulas of degree-based topological indices which correlate chemical properties of the material under investigation. These indices are used in the development of quantitative structure-activity relationships (QSARs) in which the biological activity and other properties of molecules like boiling point, stability, strain energy etc. are correlated with their structures. In this paper, we determine general closed formulae for M-polynomials of V-Phylenic nanotubes and nanotori. We recover important topological degree-based indices. We also give different graphs of topological indices and their relations with the parameters of structures.

Application of sensitivity-analysis techniques to the calculation of topological quantities

NASA Astrophysics Data System (ADS)

Gilchrist, Stuart

2017-08-01

Magnetic reconnection in the corona occurs preferentially at sites where the magnetic connectivity is either discontinuous or has a large spatial gradient. Hence there is a general interest in computing quantities (like the squashing factor) that characterize the gradient in the field-line mapping function. Here we present an algorithm for calculating certain (quasi)topological quantities using mathematical techniques from the field of ``sensitivity-analysis''. The method is based on the calculation of a three dimensional field-line mapping Jacobian from which all the present topological quantities of interest can be derived. We will present the algorithm and the details of a publicly available set of libraries that implement the algorithm.

Duality and topology

NASA Astrophysics Data System (ADS)

Sacramento, P. D.; Vieira, V. R.

2018-04-01

Mappings between models may be obtained by unitary transformations with preservation of the spectra but in general a change in the states. Non-canonical transformations in general also change the statistics of the operators involved. In these cases one may expect a change of topological properties as a consequence of the mapping. Here we consider some dualities resulting from mappings, by systematically using a Majorana fermion representation of spin and fermionic problems. We focus on the change of topological invariants that results from unitary transformations taking as examples the mapping between a spin system and a topological superconductor, and between different fermionic systems.

The inside and outside: topological issues in plant cell wall biosynthesis and the roles of nucleotide sugar transporters.

PubMed

Temple, Henry; Saez-Aguayo, Susana; Reyes, Francisca C; Orellana, Ariel

2016-09-01

The cell wall is a complex extracellular matrix composed primarily of polysaccharides. Noncellulosic polysaccharides, glycoproteins and proteoglycans are synthesized in the Golgi apparatus by glycosyltransferases (GTs), which use nucleotide sugars as donors to glycosylate nascent glycan and glycoprotein acceptors that are subsequently exported to the extracellular space. Many nucleotide sugars are synthesized in the cytosol, leading to a topological issue because the active sites of most GTs are located in the Golgi lumen. Nucleotide sugar transporters (NSTs) overcome this problem by translocating nucleoside diphosphate sugars from the cytosol into the lumen of the organelle. The structures of the cell wall components synthesized in the Golgi are diverse and complex; therefore, transporter activities are necessary so that the nucleotide sugars can provide substrates for the GTs. In this review, we describe the topology of reactions involved in polysaccharide biosynthesis in the Golgi and focus on the roles of NSTs as well as their impacts on cell wall structure when they are altered. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Fuzzy topological digital space and their properties of flat electroencephalography in epilepsy disease

NASA Astrophysics Data System (ADS)

Muzafar Shah, Mazlina; Fatah Wahab, Abdul

2017-09-01

There are an abnormal electric activities or irregular interference in brain of epilepsy patient. Then a sensor will be put in patient’s scalp to measure and records all electric activities in brain. The result of the records known as Electroencephalography (EEG). The EEG has been transfer to flat EEG because it’s easier to analyze. In this study, the uncertainty in flat EEG data will be considered as fuzzy digital space. The purpose of this research is to show that the flat EEG is fuzzy topological digital space. Therefore, the main focus for this research is to introduce fuzzy topological digital space concepts with their properties such as neighbourhood, interior and closure by using fuzzy set digital concept and Chang’s fuzzy topology approach. The product fuzzy topology digital also will be shown. By introduce this concept, the data in flat EEG can considering having fuzzy topology digital properties and can identify the area in fuzzy digital space that has been affected by epilepsy seizure in epileptic patient’s brain.

Topological Sachdev-Ye-Kitaev model

NASA Astrophysics Data System (ADS)

Zhang, Pengfei; Zhai, Hui

2018-05-01

In this Rapid Communication, we construct a large-N exactly solvable model to study the interplay between interaction and topology, by connecting the Sachdev-Ye-Kitaev (SYK) model with constant hopping. The hopping forms a band structure that can exhibit both topologically trivial and nontrivial phases. Starting from a topologically trivial insulator with zero Hall conductance, we show that the interaction can drive a phase transition to a topologically nontrivial insulator with quantized nonzero Hall conductance, and a single gapless Dirac fermion emerges when the interaction is fine tuned to the critical point. The finite temperature effect is also considered, and we show that the topological phase with a stronger interaction is less stable against temperature. Our model provides a concrete example to illustrate the interacting topological phases and phase transitions, and can shed light on similar problems in physical systems.

Generation of 3D templates of active sites of proteins with rigid prosthetic groups.

PubMed

Nebel, Jean-Christophe

2006-05-15

With the increasing availability of protein structures, the generation of biologically meaningful 3D patterns from the simultaneous alignment of several protein structures is an exciting prospect: active sites could be better understood, protein functions and protein 3D structures could be predicted more accurately. Although patterns can already be generated at the fold and topological levels, no system produces high-resolution 3D patterns including atom and cavity positions. To address this challenge, our research focuses on generating patterns from proteins with rigid prosthetic groups. Since these groups are key elements of protein active sites, the generated 3D patterns are expected to be biologically meaningful. In this paper, we present a new approach which allows the generation of 3D patterns from proteins with rigid prosthetic groups. Using 237 protein chains representing proteins containing porphyrin rings, our method was validated by comparing 3D templates generated from homologues with the 3D structure of the proteins they model. Atom positions were predicted reliably: 93% of them had an accuracy of 1.00 A or less. Moreover, similar results were obtained regarding chemical group and cavity positions. Results also suggested our system could contribute to the validation of 3D protein models. Finally, a 3D template was generated for the active site of human cytochrome P450 CYP17, the 3D structure of which is unknown. Its analysis showed that it is biologically meaningful: our method detected the main patterns of the cytochrome P450 superfamily and the motifs linked to catalytic reactions. The 3D template also suggested the position of a residue, which could be involved in a hydrogen bond with CYP17 substrates and the shape and location of a cavity. Comparisons with independently generated 3D models comforted these hypotheses. Alignment software (Nestor3D) is available at http://www.kingston.ac.uk/~ku33185/Nestor3D.html

The active site of hen egg-white lysozyme: flexibility and chemical bonding

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

Held, Jeanette, E-mail: jeanette.netzel@uni-bayreuth.de; Smaalen, Sander van

Chemical bonding at the active site of lysozyme is analyzed on the basis of a multipole model employing transferable multipole parameters from a database. Large B factors at low temperatures reflect frozen-in disorder, but therefore prevent a meaningful free refinement of multipole parameters. Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader’s quantum theory of atoms in molecules [QTAIM; Bader (1994 ▶), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) ofmore » HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254–1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337–351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C�

Topology optimized permanent magnet systems

NASA Astrophysics Data System (ADS)

Bjørk, R.; Bahl, C. R. H.; Insinga, A. R.

2017-09-01

Topology optimization of permanent magnet systems consisting of permanent magnets, high permeability iron and air is presented. An implementation of topology optimization for magnetostatics is discussed and three examples are considered. The Halbach cylinder is topology optimized with iron and an increase of 15% in magnetic efficiency is shown. A topology optimized structure to concentrate a homogeneous field is shown to increase the magnitude of the field by 111%. Finally, a permanent magnet with alternating high and low field regions is topology optimized and a Λcool figure of merit of 0.472 is reached, which is an increase of 100% compared to a previous optimized design.

Activation of phenylalanine hydroxylase by phenylalanine does not require binding in the active site.

PubMed

Roberts, Kenneth M; Khan, Crystal A; Hinck, Cynthia S; Fitzpatrick, Paul F

2014-12-16

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein's regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The k(cat)/K(phe) value is down 10⁴ for the mutant enzyme, and the K(m) value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain.

Activation of Phenylalanine Hydroxylase by Phenylalanine Does Not Require Binding in the Active Site

PubMed Central

2015-01-01

Phenylalanine hydroxylase (PheH), a liver enzyme that catalyzes the hydroxylation of excess phenylalanine in the diet to tyrosine, is activated by phenylalanine. The lack of activity at low levels of phenylalanine has been attributed to the N-terminus of the protein’s regulatory domain acting as an inhibitory peptide by blocking substrate access to the active site. The location of the site at which phenylalanine binds to activate the enzyme is unknown, and both the active site in the catalytic domain and a separate site in the N-terminal regulatory domain have been proposed. Binding of catecholamines to the active-site iron was used to probe the accessibility of the active site. Removal of the regulatory domain increases the rate constants for association of several catecholamines with the wild-type enzyme by ∼2-fold. Binding of phenylalanine in the active site is effectively abolished by mutating the active-site residue Arg270 to lysine. The kcat/Kphe value is down 104 for the mutant enzyme, and the Km value for phenylalanine for the mutant enzyme is >0.5 M. Incubation of the R270K enzyme with phenylalanine also results in a 2-fold increase in the rate constants for catecholamine binding. The change in the tryptophan fluorescence emission spectrum seen in the wild-type enzyme upon activation by phenylalanine is also seen with the R270K mutant enzyme in the presence of phenylalanine. Both results establish that activation of PheH by phenylalanine does not require binding of the amino acid in the active site. This is consistent with a separate allosteric site, likely in the regulatory domain. PMID:25453233

Non-competitive inhibition by active site binders.

PubMed

Blat, Yuval

2010-06-01

Classical enzymology has been used for generations to understand the interactions of inhibitors with their enzyme targets. Enzymology tools enabled prediction of the biological impact of inhibitors as well as the development of novel, more potent, ones. Experiments designed to examine the competition between the tested inhibitor and the enzyme substrate(s) are the tool of choice to identify inhibitors that bind in the active site. Competition between an inhibitor and a substrate is considered a strong evidence for binding of the inhibitor in the active site, while the lack of competition suggests binding to an alternative site. Nevertheless, exceptions to this notion do exist. Active site-binding inhibitors can display non-competitive inhibition patterns. This unusual behavior has been observed with enzymes utilizing an exosite for substrate binding, isomechanism enzymes, enzymes with multiple substrates and/or products and two-step binding inhibitors. In many of these cases, the mechanisms underlying the lack of competition between the substrate and the inhibitor are well understood. Tools like alternative substrates, testing the enzyme reaction in the reverse direction and monitoring inhibition time dependence can be applied to enable distinction between 'badly behaving' active site binders and true exosite inhibitors.

Safety Oversight of Decommissioning Activities at DOE Nuclear Sites

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

Zull, Lawrence M.; Yeniscavich, William

2008-01-15

The Defense Nuclear Facilities Safety Board (Board) is an independent federal agency established by Congress in 1988 to provide nuclear safety oversight of activities at U.S. Department of Energy (DOE) defense nuclear facilities. The activities under the Board's jurisdiction include the design, construction, startup, operation, and decommissioning of defense nuclear facilities at DOE sites. This paper reviews the Board's safety oversight of decommissioning activities at DOE sites, identifies the safety problems observed, and discusses Board initiatives to improve the safety of decommissioning activities at DOE sites. The decommissioning of former defense nuclear facilities has reduced the risk of radioactive materialmore » contamination and exposure to the public and site workers. In general, efforts to perform decommissioning work at DOE defense nuclear sites have been successful, and contractors performing decommissioning work have a good safety record. Decommissioning activities have recently been completed at sites identified for closure, including the Rocky Flats Environmental Technology Site, the Fernald Closure Project, and the Miamisburg Closure Project (the Mound site). The Rocky Flats and Fernald sites, which produced plutonium parts and uranium materials for defense needs (respectively), have been turned into wildlife refuges. The Mound site, which performed R and D activities on nuclear materials, has been converted into an industrial and technology park called the Mound Advanced Technology Center. The DOE Office of Legacy Management is responsible for the long term stewardship of these former EM sites. The Board has reviewed many decommissioning activities, and noted that there are valuable lessons learned that can benefit both DOE and the contractor. As part of its ongoing safety oversight responsibilities, the Board and its staff will continue to review the safety of DOE and contractor decommissioning activities at DOE defense nuclear sites.« less

Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering

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

MacCarthy, Brian; Carr, Hamish; Weber, Gunther H.

2011-06-30

Existing topological interfaces to volume rendering are limited by their reliance on sophisticated knowledge of topology by the user. We extend previous work by describing topological galleries, an interface for novice users that is based on the design galleries approach. We report three contributions: an interface based on hierarchical thumbnail galleries to display the containment relationships between topologically identifiable features, the use of the pruning hierarchy instead of branch decomposition for contour tree simplification, and drag-and-drop transfer function assignment for individual components. Initial results suggest that this approach suffers from limitations due to rapid drop-off of feature size in themore » pruning hierarchy. We explore these limitations by providing statistics of feature size as function of depth in the pruning hierarchy of the contour tree.« less

Minimal Network Topologies for Signal Processing during Collective Cell Chemotaxis.

PubMed

Yue, Haicen; Camley, Brian A; Rappel, Wouter-Jan

2018-06-19

Cell-cell communication plays an important role in collective cell migration. However, it remains unclear how cells in a group cooperatively process external signals to determine the group's direction of motion. Although the topology of signaling pathways is vitally important in single-cell chemotaxis, the signaling topology for collective chemotaxis has not been systematically studied. Here, we combine mathematical analysis and simulations to find minimal network topologies for multicellular signal processing in collective chemotaxis. We focus on border cell cluster chemotaxis in the Drosophila egg chamber, in which responses to several experimental perturbations of the signaling network are known. Our minimal signaling network includes only four elements: a chemoattractant, the protein Rac (indicating cell activation), cell protrusion, and a hypothesized global factor responsible for cell-cell interaction. Experimental data on cell protrusion statistics allows us to systematically narrow the number of possible topologies from more than 40,000,000 to only six minimal topologies with six interactions between the four elements. This analysis does not require a specific functional form of the interactions, and only qualitative features are needed; it is thus robust to many modeling choices. Simulations of a stochastic biochemical model of border cell chemotaxis show that the qualitative selection procedure accurately determines which topologies are consistent with the experiment. We fit our model for all six proposed topologies; each produces results that are consistent with all experimentally available data. Finally, we suggest experiments to further discriminate possible pathway topologies. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Concept Model on Topological Learning

NASA Astrophysics Data System (ADS)

Ae, Tadashi; Kioi, Kazumasa

2010-11-01

We discuss a new model for concept based on topological learning, where the learning process on the neural network is represented by mathematical topology. The topological learning of neural networks is summarized by a quotient of input space and the hierarchical step induces a tree where each node corresponds to a quotient. In general, the concept acquisition is a difficult problem, but the emotion for a subject is represented by providing the questions to a person. Therefore, a kind of concept is captured by such data and the answer sheet can be mapped into a topology consisting of trees. In this paper, we will discuss a way of mapping the emotional concept to a topological learning model.

On the Prognostic Efficiency of Topological Descriptors for Magnetograms of Active Regions

NASA Astrophysics Data System (ADS)

Knyazeva, I. S.; Urtiev, F. A.; Makarenko, N. G.

2017-12-01

Solar flare prediction remains an important practical task of space weather. An increase in the amount and quality of observational data and the development of machine-learning methods has led to an improvement in prediction techniques. Additional information has been retrieved from the vector magnetograms; these have been recently supplemented by traditional line-of-sight (LOS) magnetograms. In this work, the problem of the comparative prognostic efficiency of features obtained on the basis of vector data and LOS magnetograms is discussed. Invariants obtained from a topological analysis of LOS magnetograms are used as complexity characteristics of magnetic patterns. Alternatively, the so-called SHARP parameters were used; they were calculated by the data analysis group of the Stanford University Laboratory on the basis of HMI/SDO vector magnetograms and are available online at the website (http://jsoc.stanford.edu/) with the solar dynamics observatory (SDO) database for the entire history of SDO observations. It has been found that the efficiency of large-flare prediction based on topological descriptors of LOS magnetograms in epignosis mode is at least s no worse than the results of prognostic schemes based on vector features. The advantages of the use of topological invariants based on LOS data are discussed.

Artificial gravity field, astrophysical analogues, and topological phase transitions in strained topological semimetals

NASA Astrophysics Data System (ADS)

Yu, Zhiming; Guan, Shan; Yao, Yugui; Yang, Shengyuan

Effective gravity and gauge fields are emergent properties intrinsic for low-energy quasiparticles in topological semimetals. Here, taking two Dirac semimetals as examples, we demonstrate that applied lattice strain can generate warped spacetime, with fascinating analogues in astrophysics. Particularly, we study the possibility of simulating black-hole/white-hole event horizons and gravitational lensing effect. Furthermore, we discover strain-induced topological phase transitions, both in the bulk materials and in their thin films. Especially in thin films, the transition between the quantum spin Hall and the trivial insulating phases can be achieved by a small strain, naturally leading to the proposition of a novel piezo-topological transistor device. Our result not only bridges multiple disciplines, revealing topological semimetals as a unique table-top platform for exploring interesting phenomena in astrophysics and general relativity; it also suggests realistic materials and methods to achieve controlled topological phase transitions with great potential for device applications.

Topological defects in epithelia govern cell death and extrusion

NASA Astrophysics Data System (ADS)

Saw, Thuan Beng; Doostmohammadi, Amin; Nier, Vincent; Kocgozlu, Leyla; Thampi, Sumesh; Toyama, Yusuke; Marcq, Philippe; Lim, Chwee Teck; Yeomans, Julia M.; Ladoux, Benoit

2017-04-01

Epithelial tissues (epithelia) remove excess cells through extrusion, preventing the accumulation of unnecessary or pathological cells. The extrusion process can be triggered by apoptotic signalling, oncogenic transformation and overcrowding of cells. Despite the important linkage of cell extrusion to developmental, homeostatic and pathological processes such as cancer metastasis, its underlying mechanism and connections to the intrinsic mechanics of the epithelium are largely unexplored. We approach this problem by modelling the epithelium as an active nematic liquid crystal (that has a long range directional order), and comparing numerical simulations to strain rate and stress measurements within monolayers of MDCK (Madin Darby canine kidney) cells. Here we show that apoptotic cell extrusion is provoked by singularities in cell alignments in the form of comet-shaped topological defects. We find a universal correlation between extrusion sites and positions of nematic defects in the cell orientation field in different epithelium types. The results confirm the active nematic nature of epithelia, and demonstrate that defect-induced isotropic stresses are the primary precursors of mechanotransductive responses in cells, including YAP (Yes-associated protein) transcription factor activity, caspase-3-mediated cell death, and extrusions. Importantly, the defect-driven extrusion mechanism depends on intercellular junctions, because the weakening of cell-cell interactions in an α-catenin knockdown monolayer reduces the defect size and increases both the number of defects and extrusion rates, as is also predicted by our model. We further demonstrate the ability to control extrusion hotspots by geometrically inducing defects through microcontact printing of patterned monolayers. On the basis of these results, we propose a mechanism for apoptotic cell extrusion: spontaneously formed topological defects in epithelia govern cell fate. This will be important in predicting

Two-dimensional topological photonics

NASA Astrophysics Data System (ADS)

Khanikaev, Alexander B.; Shvets, Gennady

2017-12-01

Originating from the studies of two-dimensional condensed-matter states, the concept of topological order has recently been expanded to other fields of physics and engineering, particularly optics and photonics. Topological photonic structures have already overturned some of the traditional views on wave propagation and manipulation. The application of topological concepts to guided wave propagation has enabled novel photonic devices, such as reflection-free sharply bent waveguides, robust delay lines, spin-polarized switches and non-reciprocal devices. Discrete degrees of freedom, widely used in condensed-matter physics, such as spin and valley, are now entering the realm of photonics. In this Review, we summarize the latest advances in this highly dynamic field, with special emphasis on the experimental work on two-dimensional photonic topological structures.

Topological quantum distillation.

PubMed

Bombin, H; Martin-Delgado, M A

2006-11-03

We construct a class of topological quantum codes to perform quantum entanglement distillation. These codes implement the whole Clifford group of unitary operations in a fully topological manner and without selective addressing of qubits. This allows us to extend their application also to quantum teleportation, dense coding, and computation with magic states.

Chiral topological insulator of magnons

NASA Astrophysics Data System (ADS)

Li, Bo; Kovalev, Alexey A.

2018-05-01

We propose a magnon realization of 3D topological insulator in the AIII (chiral symmetry) topological class. The topological magnon gap opens due to the presence of Dzyaloshinskii-Moriya interactions. The existence of the topological invariant is established by calculating the bulk winding number of the system. Within our model, the surface magnon Dirac cone is protected by the sublattice chiral symmetry. By analyzing the magnon surface modes, we confirm that the backscattering is prohibited. By weakly breaking the chiral symmetry, we observe the magnon Hall response on the surface due to opening of the gap. Finally, we show that by changing certain parameters, the system can be tuned between the chiral topological insulator, three-dimensional magnon anomalous Hall, and Weyl magnon phases.

Ionizable Side Chains at Catalytic Active Sites of Enzymes

PubMed Central

Jimenez-Morales, David; Liang, Jie

2012-01-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1072 Å3. The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes. PMID:22484856

Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Ion beam modification of topological insulator bismuth selenide

DOE PAGES

Sharma, Peter Anand; Sharma, A. L. Lima; Hekmaty, Michelle A.; ...

2014-12-17

In this study, we demonstrate chemical doping of a topological insulator Bi 2Se 3 using ion implantation. Ion beam-induced structural damage was characterized using grazing incidence X-ray diffraction and transmission electron microscopy. Ion damage was reversed using a simple thermal annealing step. Carrier-type conversion was achieved using ion implantation followed by an activation anneal in Bi 2Se 3 thin films. These two sets of experiments establish the feasibility of ion implantation for chemical modification of Bi 2Se 3, a prototypical topological insulator. Ion implantation can, in principle, be used for any topological insulator. The direct implantation of dopants should allowmore » better control over carrier concentrations for the purposes of achieving low bulk conductivity. Ion implantation also enables the fabrication of inhomogeneously doped structures, which in turn should make possible new types of device designs.« less

Two-dimensional topological photonic systems

NASA Astrophysics Data System (ADS)

Sun, Xiao-Chen; He, Cheng; Liu, Xiao-Ping; Lu, Ming-Hui; Zhu, Shi-Ning; Chen, Yan-Feng

2017-09-01

The topological phase of matter, originally proposed and first demonstrated in fermionic electronic systems, has drawn considerable research attention in the past decades due to its robust transport of edge states and its potential with respect to future quantum information, communication, and computation. Recently, searching for such a unique material phase in bosonic systems has become a hot research topic worldwide. So far, many bosonic topological models and methods for realizing them have been discovered in photonic systems, acoustic systems, mechanical systems, etc. These discoveries have certainly yielded vast opportunities in designing material phases and related properties in the topological domain. In this review, we first focus on some of the representative photonic topological models and employ the underlying Dirac model to analyze the edge states and geometric phase. On the basis of these models, three common types of two-dimensional topological photonic systems are discussed: 1) photonic quantum Hall effect with broken time-reversal symmetry; 2) photonic topological insulator and the associated pseudo-time-reversal symmetry-protected mechanism; 3) time/space periodically modulated photonic Floquet topological insulator. Finally, we provide a summary and extension of this emerging field, including a brief introduction to the Weyl point in three-dimensional systems.

Topology of Document Retrieval Systems.

ERIC Educational Resources Information Center

Everett, Daniel M.; Cater, Steven C.

1992-01-01

Explains the use of a topological structure to examine the closeness between documents in retrieval systems and analyzes the topological structure of a vector-space model, a fuzzy-set model, an extended Boolean model, a probabilistic model, and a TIRS (Topological Information Retrieval System) model. Proofs for the results are appended. (17…

Effects of topologies on signal propagation in feedforward networks

NASA Astrophysics Data System (ADS)

Zhao, Jia; Qin, Ying-Mei; Che, Yan-Qiu

2018-01-01

We systematically investigate the effects of topologies on signal propagation in feedforward networks (FFNs) based on the FitzHugh-Nagumo neuron model. FFNs with different topological structures are constructed with same number of both in-degrees and out-degrees in each layer and given the same input signal. The propagation of firing patterns and firing rates are found to be affected by the distribution of neuron connections in the FFNs. Synchronous firing patterns emerge in the later layers of FFNs with identical, uniform, and exponential degree distributions, but the number of synchronous spike trains in the output layers of the three topologies obviously differs from one another. The firing rates in the output layers of the three FFNs can be ordered from high to low according to their topological structures as exponential, uniform, and identical distributions, respectively. Interestingly, the sequence of spiking regularity in the output layers of the three FFNs is consistent with the firing rates, but their firing synchronization is in the opposite order. In summary, the node degree is an important factor that can dramatically influence the neuronal network activity.

Effects of topologies on signal propagation in feedforward networks.

PubMed

Zhao, Jia; Qin, Ying-Mei; Che, Yan-Qiu

2018-01-01

We systematically investigate the effects of topologies on signal propagation in feedforward networks (FFNs) based on the FitzHugh-Nagumo neuron model. FFNs with different topological structures are constructed with same number of both in-degrees and out-degrees in each layer and given the same input signal. The propagation of firing patterns and firing rates are found to be affected by the distribution of neuron connections in the FFNs. Synchronous firing patterns emerge in the later layers of FFNs with identical, uniform, and exponential degree distributions, but the number of synchronous spike trains in the output layers of the three topologies obviously differs from one another. The firing rates in the output layers of the three FFNs can be ordered from high to low according to their topological structures as exponential, uniform, and identical distributions, respectively. Interestingly, the sequence of spiking regularity in the output layers of the three FFNs is consistent with the firing rates, but their firing synchronization is in the opposite order. In summary, the node degree is an important factor that can dramatically influence the neuronal network activity.

Topological Edge Floppy Modes in Disordered Fiber Networks

NASA Astrophysics Data System (ADS)

Zhou, Di; Zhang, Leyou; Mao, Xiaoming

2018-02-01

Disordered fiber networks are ubiquitous in a broad range of natural (e.g., cytoskeleton) and manmade (e.g., aerogels) materials. In this Letter, we discuss the emergence of topological floppy edge modes in two-dimensional fiber networks as a result of deformation or active driving. It is known that a network of straight fibers exhibits bulk floppy modes which only bend the fibers without stretching them. We find that, interestingly, with a perturbation in geometry, these bulk modes evolve into edge modes. We introduce a topological index for these edge modes and discuss their implications in biology.

Photochemical Water Splitting by Bismuth Chalcogenide Topological Insulators.

PubMed

Rajamathi, Catherine R; Gupta, Uttam; Pal, Koushik; Kumar, Nitesh; Yang, Hao; Sun, Yan; Shekhar, Chandra; Yan, Binghai; Parkin, Stuart; Waghmare, Umesh V; Felser, Claudia; Rao, C N R

2017-09-06

As one of the major areas of interest in catalysis revolves around 2D materials based on molybdenum sulfide, we have examined the catalytic properties of bismuth selenides and tellurides, which are among the first chalcogenides to be proven as topological insulators (TIs). We find significant photochemical H 2 evolution activity with these TIs as catalysts. H 2 evolution increases drastically in nanosheets of Bi 2 Te 3 compared to single crystals. First-principles calculations show that due to the topology, surface states participate and promote the hydrogen evolution. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ionizable side chains at catalytic active sites of enzymes.

PubMed

Jimenez-Morales, David; Liang, Jie; Eisenberg, Bob

2012-05-01

Catalytic active sites of enzymes of known structure can be well defined by a modern program of computational geometry. The CASTp program was used to define and measure the volume of the catalytic active sites of 573 enzymes in the Catalytic Site Atlas database. The active sites are identified as catalytic because the amino acids they contain are known to participate in the chemical reaction catalyzed by the enzyme. Acid and base side chains are reliable markers of catalytic active sites. The catalytic active sites have 4 acid and 5 base side chains, in an average volume of 1,072 Å(3). The number density of acid side chains is 8.3 M (in chemical units); the number density of basic side chains is 10.6 M. The catalytic active site of these enzymes is an unusual electrostatic and steric environment in which side chains and reactants are crowded together in a mixture more like an ionic liquid than an ideal infinitely dilute solution. The electrostatics and crowding of reactants and side chains seems likely to be important for catalytic function. In three types of analogous ion channels, simulation of crowded charges accounts for the main properties of selectivity measured in a wide range of solutions and concentrations. It seems wise to use mathematics designed to study interacting complex fluids when making models of the catalytic active sites of enzymes.

Visualizing vector field topology in fluid flows

NASA Technical Reports Server (NTRS)

Helman, James L.; Hesselink, Lambertus

1991-01-01

Methods of automating the analysis and display of vector field topology in general and flow topology in particular are discussed. Two-dimensional vector field topology is reviewed as the basis for the examination of topology in three-dimensional separated flows. The use of tangent surfaces and clipping in visualizing vector field topology in fluid flows is addressed.

Electronic-topological study of the structure-activity relationships in a series of steroids with mineralocorticoid binding affinity.

PubMed

Kandemirli, Fatma; Tokay, Nesrin; Shvets, Nataly M; Dimoglo, Anatoly S

2003-01-01

Conformational analysis and quantum chemical calculations were carried out using molecular mechanics (MMP2) and semi-empirical quantum chemistry (CNDO/2) methods for 51 steroid homologues belonging to a series of 17-spirolactones. Matrices called Electronic-Topological Matrices of Conjunction (ETMCs) were formed using data obtained from quantum chemical calculations. A structural fragment of activity was identified in the series of steroids. As seen from the fragment's properties, active compounds are characterized by the presence of two atoms of oxygen, O1 and O3, which are situated at a distance of 13.5 A and possess high negative charges (-0.29 to -0.31 e).

Atomic-Ordering-Induced Quantum Phase Transition between Topological Crystalline Insulator and Z 2 Topological Insulator

NASA Astrophysics Data System (ADS)

Deng, Hui-Xiong; Song, Zhi-Gang; Li, Shu-Shen; Wei, Su-Huai; Luo, Jun-Wei

2018-05-01

Topological phase transition in a single material usually refers to transitions between a trivial band insulator and a topological Dirac phase, but the transition may also occur between different classes of topological Dirac phases. However, it is a fundamental challenge to realize quantum transition between Z2 nontrivial topological insulator (TI) and topological crystalline insulator (TCI) in one material because Z2 TI and TCI are hardly both co-exist in a single material due to their contradictory requirement on the number of band inversions. The Z2 TIs must have an odd number of band inversions over all the time-reversal invariant momenta, whereas, the newly discovered TCIs, as a distinct class of the topological Dirac materials protected by the underlying crystalline symmetry, owns an even number of band inversions. Here, take PbSnTe2 alloy as an example, we show that at proper alloy composition the atomic-ordering is an effective way to tune the symmetry of the alloy so that we can electrically switch between TCI phase and Z2 TI phase when the alloy is ordered from a random phase into a stable CuPt phase. Our results suggest that atomic-ordering provides a new platform to switch between different topological phases.

Site- and bond-percolation thresholds in K_{n,n}-based lattices: Vulnerability of quantum annealers to random qubit and coupler failures on chimera topologies.

PubMed

Melchert, O; Katzgraber, Helmut G; Novotny, M A

2016-04-01

We estimate the critical thresholds of bond and site percolation on nonplanar, effectively two-dimensional graphs with chimeralike topology. The building blocks of these graphs are complete and symmetric bipartite subgraphs of size 2n, referred to as K_{n,n} graphs. For the numerical simulations we use an efficient union-find-based algorithm and employ a finite-size scaling analysis to obtain the critical properties for both bond and site percolation. We report the respective percolation thresholds for different sizes of the bipartite subgraph and verify that the associated universality class is that of standard two-dimensional percolation. For the canonical chimera graph used in the D-Wave Systems Inc. quantum annealer (n=4), we discuss device failure in terms of network vulnerability, i.e., we determine the critical fraction of qubits and couplers that can be absent due to random failures prior to losing large-scale connectivity throughout the device.

Heparin/heparan sulfate 6-O-sulfatase from Flavobacterium heparinum: integrated structural and biochemical investigation of enzyme active site and substrate specificity.

PubMed

Myette, James R; Soundararajan, Venkataramanan; Shriver, Zachary; Raman, Rahul; Sasisekharan, Ram

2009-12-11

Heparin and heparan sulfate glycosaminoglycans (HSGAGs) comprise a chemically heterogeneous class of sulfated polysaccharides. The development of structure-activity relationships for this class of polysaccharides requires the identification and characterization of degrading enzymes with defined substrate specificity and enzymatic activity. Toward this end, we report here the molecular cloning and extensive structure-function analysis of a 6-O-sulfatase from the Gram-negative bacterium Flavobacterium heparinum. In addition, we report the recombinant expression of this enzyme in Escherichia coli in a soluble, active form and identify it as a specific HSGAG sulfatase. We further define the mechanism of action of the enzyme through biochemical and structural studies. Through the use of defined substrates, we investigate the kinetic properties of the enzyme. This analysis was complemented by homology-based molecular modeling studies that sought to rationalize the substrate specificity of the enzyme and mode of action through an analysis of the active-site topology of the enzyme including identifying key enzyme-substrate interactions and assigning key amino acids within the active site of the enzyme. Taken together, our structural and biochemical studies indicate that 6-O-sulfatase is a predominantly exolytic enzyme that specifically acts on N-sulfated or N-acetylated 6-O-sulfated glucosamines present at the non-reducing end of HSGAG oligosaccharide substrates. This requirement for the N-acetyl or N-sulfo groups on the glucosamine substrate can be explained through eliciting favorable interactions with key residues within the active site of the enzyme. These findings provide a framework that enables the use of 6-O-sulfatase as a tool for HSGAG structure-activity studies as well as expand our biochemical and structural understanding of this important class of enzymes.

Topological phase diagram and saddle point singularity in a tunable topological crystalline insulator

DOE PAGES

Neupane, Madhab; Xu, Su-Yang; Sankar, R.; ...

2015-08-20

Here we report the evolution of the surface electronic structure and surface material properties of a topological crystalline insulator (TCI), Pb 1more » $${-}$$xSnxSe, as a function of various material parameters including composition x, temperature T , and crystal structure. Our spectroscopic data demonstrate the electronic ground-state condition for the saddle point singularity, the tunability of surface chemical potential, and the surface states’ response to circularly polarized light. Our results show that each material parameter can tune the system between the trivial and topological phase in a distinct way, unlike that seen in Bi 2Se 3 and related compounds, leading to a rich topological phase diagram. Our systematic studies of the TCI Pb 1$${-}$$xSnxSe are a valuable materials guide to realize new topological phenomena.« less

Robustness against non-magnetic impurities in topological superconductors

NASA Astrophysics Data System (ADS)

Nagai, Y.; Ota, Y.; Machida, M.

2014-12-01

We study the robustness against non-magnetic impurities in a three-dimensional topological superconductor, focusing on an effective model (massive Dirac Bogoliubov-de Gennes (BdG) Hamiltonian with s-wave on-site pairing) of CuxBi2Se3 with the parameter set determined by the first-principles calculation. With the use of the self-consistent T- matrix approximation for impurity scattering, we discuss the impurity-concentration dependence of the zero-energy density of states. We show that a single material variable, measuring relativistic effects in the Dirac-BdG Hamiltonian, well characterizes the numerical results. In the nonrelativistic limit, the odd-parity fully-gapped topological superconductivity is fragile against non-magnetic impurities, since this superconductivity can be mapped onto the p-wave superconductivity. On the other hand, in the ultrarelativistic limit, the superconductivity is robust against the non-magnetic impurities, since the effective model has the s-wave superconductivity. We derive the effective Hamiltonian in the both limit.

Topological order following a quantum quench

NASA Astrophysics Data System (ADS)

Tsomokos, Dimitris I.; Hamma, Alioscia; Zhang, Wen; Haas, Stephan; Fazio, Rosario

2009-12-01

We determine the conditions under which topological order survives a rapid quantum quench. Specifically, we consider the case where a quantum spin system is prepared in the ground state of the toric code model and, after the quench, it evolves with a Hamiltonian that does not support topological order. We provide analytical results supported by numerical evidence for a variety of quench Hamiltonians. The robustness of topological order under nonequilibrium situations is tested by studying the topological entropy and a dynamical measure, which makes use of the similarity between partial density matrices obtained from different topological sectors.

Topological transitions induced by antiferromagnetism in a thin-film topological insulator

NASA Astrophysics Data System (ADS)

Yin, Gen; He, Qinglin; Yu, Luyan; Pan, Lei; Wang, Kang

Ferromagnetism introduced in topological insulators (TIs) opens a non-trivial exchange band gap, providing an exciting platform to control the topological order through an external magnetic field. The magnetization induces a topological transition that breaks time-reversal symmetry, resulting in anomalous Hall effects. Recently, it was experimentally shown that the surface of an antiferromagnetic (AFM) thin film can magnetize the surface Dirac fermions in a TI thin film similar to the case induced by ferromagnetism. Here, we show that when a TI thin film is sandwiched between two antiferromagnetic layers, an unsynchronized magnetic reversal introduces two intermediate spin configurations during the scan of the external field, resulting in a new topological phase with second Chern numbers. This topological phase introduces two counter-propagating chiral edge modes inside the exchange gap, changing the total number of transport channels drastically when the fermi level is close to the Dirac point. Induced by this change, the magnetoresistance of the channel presents an antisymmetric feature during the field scan. With the the help of the high ordering temperature of AFM layers, this transport signature of the phase transition persists up to 90K experimentally. This work is supported by (i) SHINES, an EFRC by US-DOE, Office of Science, BES, #SC0012670. (ii) US-NSF (DMR-1411085), (iii) ARO program W911NF-15-1-10561, and (iv) FAME Center in STARnet, an SRC program by MARCO and DARPA.

Metal active site elasticity linked to activation of homocysteine in methionine synthases

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

Koutmos, Markos; Pejchal, Robert; Bomer, Theresa M.

2008-04-02

Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry uponmore » binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.« less

A molecular topology approach to predicting pesticide pollution of groundwater

USGS Publications Warehouse

Worrall , Fred

2001-01-01

Various models have proposed methods for the discrimination of polluting and nonpolluting compounds on the basis of simple parameters, typically adsorption and degradation constants. However, such attempts are prone to site variability and measurement error to the extent that compounds cannot be reliably classified nor the chemistry of pollution extrapolated from them. Using observations of pesticide occurrence in U.S. groundwater it is possible to show that polluting from nonpolluting compounds can be distinguished purely on the basis of molecular topology. Topological parameters can be derived without measurement error or site-specific variability. A logistic regression model has been developed which explains 97% of the variation in the data, with 86% of the variation being explained by the rule that a compound will be found in groundwater if 6 < 0.55. Where 6χp is the sixth-order molecular path connectivity. One group of compounds cannot be classified by this rule and prediction requires reference to higher order connectivity parameters. The use of molecular approaches for understanding pollution at the molecular level and their application to agrochemical development and risk assessment is discussed.

Topology optimization under stochastic stiffness

NASA Astrophysics Data System (ADS)

Asadpoure, Alireza

Topology optimization is a systematic computational tool for optimizing the layout of materials within a domain for engineering design problems. It allows variation of structural boundaries and connectivities. This freedom in the design space often enables discovery of new, high performance designs. However, solutions obtained by performing the optimization in a deterministic setting may be impractical or suboptimal when considering real-world engineering conditions with inherent variabilities including (for example) variabilities in fabrication processes and operating conditions. The aim of this work is to provide a computational methodology for topology optimization in the presence of uncertainties associated with structural stiffness, such as uncertain material properties and/or structural geometry. Existing methods for topology optimization under deterministic conditions are first reviewed. Modifications are then proposed to improve the numerical performance of the so-called Heaviside Projection Method (HPM) in continuum domains. Next, two approaches, perturbation and Polynomial Chaos Expansion (PCE), are proposed to account for uncertainties in the optimization procedure. These approaches are intrusive, allowing tight and efficient coupling of the uncertainty quantification with the optimization sensitivity analysis. The work herein develops a robust topology optimization framework aimed at reducing the sensitivity of optimized solutions to uncertainties. The perturbation-based approach combines deterministic topology optimization with a perturbation method for the quantification of uncertainties. The use of perturbation transforms the problem of topology optimization under uncertainty to an augmented deterministic topology optimization problem. The PCE approach combines the spectral stochastic approach for the representation and propagation of uncertainties with an existing deterministic topology optimization technique. The resulting compact representations

Topology of polymer chains under nanoscale confinement.

PubMed

Satarifard, Vahid; Heidari, Maziar; Mashaghi, Samaneh; Tans, Sander J; Ejtehadi, Mohammad Reza; Mashaghi, Alireza

2017-08-24

Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of l p under a spherical confinement of radius R c . At low values of l p /R c , the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high l p /R c , the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of l p /R c , at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross

The topology of large-scale structure. I - Topology and the random phase hypothesis. [galactic formation models

NASA Technical Reports Server (NTRS)

Weinberg, David H.; Gott, J. Richard, III; Melott, Adrian L.

1987-01-01

Many models for the formation of galaxies and large-scale structure assume a spectrum of random phase (Gaussian), small-amplitude density fluctuations as initial conditions. In such scenarios, the topology of the galaxy distribution on large scales relates directly to the topology of the initial density fluctuations. Here a quantitative measure of topology - the genus of contours in a smoothed density distribution - is described and applied to numerical simulations of galaxy clustering, to a variety of three-dimensional toy models, and to a volume-limited sample of the CfA redshift survey. For random phase distributions the genus of density contours exhibits a universal dependence on threshold density. The clustering simulations show that a smoothing length of 2-3 times the mass correlation length is sufficient to recover the topology of the initial fluctuations from the evolved galaxy distribution. Cold dark matter and white noise models retain a random phase topology at shorter smoothing lengths, but massive neutrino models develop a cellular topology.

Quenched dynamics and spin-charge separation in an interacting topological lattice

NASA Astrophysics Data System (ADS)

Barbiero, L.; Santos, L.; Goldman, N.

2018-05-01

We analyze the static and dynamical properties of a one-dimensional topological lattice, the fermionic Su-Schrieffer-Heeger model, in the presence of on-site interactions. Based on a study of charge and spin correlation functions, we elucidate the nature of the topological edge modes, which, depending on the sign of the interactions, either display particles of opposite spin on opposite edges, or a pair and a holon. This study of correlation functions also highlights the strong entanglement that exists between the opposite edges of the system. This last feature has remarkable consequences upon subjecting the system to a quench, where an instantaneous edge-to-edge signal appears in the correlation functions characterizing the edge modes. Besides, other correlation functions are shown to propagate in the bulk according to the light cone imposed by the Lieb-Robinson bound. Our study reveals how one-dimensional lattices exhibiting entangled topological edge modes allow for a nontrivial correlation spreading, while providing an accessible platform to detect spin-charge separation using state-of-the-art experimental techniques.

Topological strings in d < 1

NASA Astrophysics Data System (ADS)

Dijkgraaf, Robbert; Verlinde, Herman; Verlinde, Erik

1991-03-01

We calculate correlation functions in minimal topological field theories. These twisted versions of N = 2 minimal models have recently been proposed to describe d < 1 matrix models, once coupled to topological gravity. In our calculation we make use of the Landau-Ginzburg formulation of the N = 2 models, and we find a direct relation between the Landau-Ginzburg superpotential and the KdV differential operator. Using this correspondence we show that the minimal topological models are in perfect agreement with the matrix models as solved in terms of the KdV hierarchy. This proves the equivalence at tree-level of topological and ordinary string thoery in d < 1.

Design and Comparison of Cascaded H-Bridge, Modular Multilevel Converter, and 5-L Active Neutral Point Clamped Topologies for Motor Drive Applications

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

Marzoughi, Alinaghi; Burgos, Rolando; Boroyevich, Dushan

This paper presents the design procedure and comparison of converters currently used in medium-voltage high-power motor drive applications. For this purpose, the cascaded H-bridge (CHB), modular multilevel converter (MMC), and five-level active neutral point clamped (5-L ANPC) topologies are targeted. The design is performed using 1.7-kV insulated gate bipolar transistors (IGBTs) for CHB and MMC converters, and utilizing 3.3- and 4.5-kV IGBTs for 5-L ANPC topology as normally done in industry. The comparison is done between the designed converter topologies at three different voltage levels (4.16, 6.9, and 13.8 kV, with only the first two voltage levels in case ofmore » the 5-L ANPC) and two different power levels (3 and 5 MVA), in order to elucidate the dependence of different parameters on voltage and power rating. Finally, the comparison is done from several points of view such as efficiency, capacitive energy storage, semiconductor utilization, parts count (for measure of reliability), and power density.« less

Noncommuting Momenta of Topological Solitons

NASA Astrophysics Data System (ADS)

Watanabe, Haruki; Murayama, Hitoshi

2014-05-01

We show that momentum operators of a topological soliton may not commute among themselves when the soliton is associated with the second cohomology H2 of the target space. The commutation relation is proportional to the winding number, taking a constant value within each topological sector. The noncommutativity makes it impossible to specify the momentum of a topological soliton, and induces a Magnus force.

Nicotinamide Cofactors Suppress Active-Site Labeling of Aldehyde Dehydrogenases.

PubMed

Stiti, Naim; Chandrasekar, Balakumaran; Strubl, Laura; Mohammed, Shabaz; Bartels, Dorothea; van der Hoorn, Renier A L

2016-06-17

Active site labeling by (re)activity-based probes is a powerful chemical proteomic tool to globally map active sites in native proteomes without using substrates. Active site labeling is usually taken as a readout for the active state of the enzyme because labeling reflects the availability and reactivity of active sites, which are hallmarks for enzyme activities. Here, we show that this relationship holds tightly, but we also reveal an important exception to this rule. Labeling of Arabidopsis ALDH3H1 with a chloroacetamide probe occurs at the catalytic Cys, and labeling is suppressed upon nitrosylation and oxidation, and upon treatment with other Cys modifiers. These experiments display a consistent and strong correlation between active site labeling and enzymatic activity. Surprisingly, however, labeling is suppressed by the cofactor NAD(+), and this property is shared with other members of the ALDH superfamily and also detected for unrelated GAPDH enzymes with an unrelated hydantoin-based probe in crude extracts of plant cell cultures. Suppression requires cofactor binding to its binding pocket. Labeling is also suppressed by ALDH modulators that bind at the substrate entrance tunnel, confirming that labeling occurs through the substrate-binding cavity. Our data indicate that cofactor binding adjusts the catalytic Cys into a conformation that reduces the reactivity toward chloroacetamide probes.

On the Topological Changes of Local Hurst Exponent in Polar Regions

NASA Astrophysics Data System (ADS)

Consolini, G.; De Michelis, P.

2014-12-01

Geomagnetic activity during magnetic substorms and storms is related to the dinamical and topological changes of the current systems flowing in the Earth's magnetosphere-ionosphere. This is particularly true in the case of polar regions where the enhancement of auroral electrojet current system is responsible for the observed geomagnetic perturbations. Here, using the DMA-technique we evaluate the local Hurst exponent (H"older exponent) for a set of 46 geomagnetic observatories, widely distributed in the northern hemisphere, during one of the most famous and strong geomagnetic storm, the Bastille event, and reconstruct a sequence of polar maps showing the dinamical changes of the topology of the local Hurst exponent with the geomagnetic activity level. The topological evolution of local Hurst exponent maps is discussed in relation to the dinamical changes of the current systems flowing in the polar ionosphere. G. Consolini has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under Grant agreement no. 313038/STORM for this research.

Minimum curvilinearity to enhance topological prediction of protein interactions by network embedding

PubMed Central

Cannistraci, Carlo Vittorio; Alanis-Lobato, Gregorio; Ravasi, Timothy

2013-01-01

Motivation: Most functions within the cell emerge thanks to protein–protein interactions (PPIs), yet experimental determination of PPIs is both expensive and time-consuming. PPI networks present significant levels of noise and incompleteness. Predicting interactions using only PPI-network topology (topological prediction) is difficult but essential when prior biological knowledge is absent or unreliable. Methods: Network embedding emphasizes the relations between network proteins embedded in a low-dimensional space, in which protein pairs that are closer to each other represent good candidate interactions. To achieve network denoising, which boosts prediction performance, we first applied minimum curvilinear embedding (MCE), and then adopted shortest path (SP) in the reduced space to assign likelihood scores to candidate interactions. Furthermore, we introduce (i) a new valid variation of MCE, named non-centred MCE (ncMCE); (ii) two automatic strategies for selecting the appropriate embedding dimension; and (iii) two new randomized procedures for evaluating predictions. Results: We compared our method against several unsupervised and supervisedly tuned embedding approaches and node neighbourhood techniques. Despite its computational simplicity, ncMCE-SP was the overall leader, outperforming the current methods in topological link prediction. Conclusion: Minimum curvilinearity is a valuable non-linear framework that we successfully applied to the embedding of protein networks for the unsupervised prediction of novel PPIs. The rationale for our approach is that biological and evolutionary information is imprinted in the non-linear patterns hidden behind the protein network topology, and can be exploited for predicting new protein links. The predicted PPIs represent good candidates for testing in high-throughput experiments or for exploitation in systems biology tools such as those used for network-based inference and prediction of disease-related functional modules

Insights into the surface topology of polyhydroxyalkanoate synthase: self-assembly of functionalized inclusions.

PubMed

Hooks, David O; Rehm, Bernd H A

2015-10-01

The polyhydroxyalkanoate (PHA) synthase catalyzes the synthesis of PHA and remains attached to the hydrophobic PHA inclusions it creates. Although this feature is actively exploited to generate functionalized biobeads via protein engineering, little is known about the structure of the PHA synthase. Here, the surface topology of Ralstonia eutropha PHA synthase was probed to inform rational protein engineering toward the production of functionalized PHA beads. Surface-exposed residues were detected by conjugating biotin to inclusion-bound PHA synthase and identifying the biotin-conjugated lysine and cysteine residues using peptide fingerprinting analysis. The identified sites (K77, K90, K139, C382, C459, and K518) were investigated as insertion sites for the generation of new protein fusions. Insertions of FLAG epitopes into exposed sites K77, K90, K139, and K518 were tolerated, retaining >65 % of in vivo activity. Sites K90, K139, and K518 were also tested by insertion of the immunoglobulin G (IgG)-binding domain (ZZ), successfully producing PHA inclusions able to bind human IgG in vitro. Although simultaneous insertions of the ZZ domain into two sites was permissive, insertion at all three lysine sites inactivated the synthase. The K90/K139 double ZZ insertion had the optimum IgG-binding capacity of 16 mg IgG/g wet PHA beads and could selectively purify the IgG fraction from human serum. Overall, this study identified surface-exposed flexible regions of the PHA synthase which either tolerate protein/peptide insertions or are critical for protein function. This further elucidates the structure and function of PHA synthase and provides new opportunities for generating functionalized PHA biobeads.

Quantum mechanical design of enzyme active sites.

PubMed

Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

2008-02-01

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Trimeric Structure of (+)-Pinoresinol-forming Dirigent Protein at 1.95 Å Resolution with Three Isolated Active Sites

DOE PAGES

Kim, Kye-Won; Smith, Clyde A.; Daily, Michael D.; ...

2014-11-19

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcoholmore » radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (₋)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. We find DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition.« less

Stability and Topology of Scale-Free Networks under Attack and Defense Strategies

NASA Astrophysics Data System (ADS)

Gallos, Lazaros K.; Cohen, Reuven; Argyrakis, Panos; Bunde, Armin; Havlin, Shlomo

2005-05-01

We study tolerance and topology of random scale-free networks under attack and defense strategies that depend on the degree k of the nodes. This situation occurs, for example, when the robustness of a node depends on its degree or in an intentional attack with insufficient knowledge of the network. We determine, for all strategies, the critical fraction pc of nodes that must be removed for disintegrating the network. We find that, for an intentional attack, little knowledge of the well-connected sites is sufficient to strongly reduce pc. At criticality, the topology of the network depends on the removal strategy, implying that different strategies may lead to different kinds of percolation transitions.

Topological Defects in Topological Insulators and Bound States at Topological Superconductor Vortices.

PubMed

Parente, Vincenzo; Campagnano, Gabriele; Giuliano, Domenico; Tagliacozzo, Arturo; Guinea, Francisco

2014-03-04

The scattering of Dirac electrons by topological defects could be one of the most relevant sources of resistance in graphene and at the boundary surfaces of a three-dimensional topological insulator (3D TI). In the long wavelength, continuous limit of the Dirac equation, the topological defect can be described as a distortion of the metric in curved space, which can be accounted for by a rotation of the Gamma matrices and by a spin connection inherited with the curvature. These features modify the scattering properties of the carriers. We discuss the self-energy of defect formation with this approach and the electron cross-section for intra-valley scattering at an edge dislocation in graphene, including corrections coming from the local stress. The cross-section contribution to the resistivity, ρ, is derived within the Boltzmann theory of transport. On the same lines, we discuss the scattering of a screw dislocation in a two-band 3D TI, like Bi 1-x Sb x , and we present the analytical simplified form of the wavefunction for gapless helical states bound at the defect. When a 3D TI is sandwiched between two even-parity superconductors, Dirac boundary states acquire superconductive correlations by proximity. In the presence of a magnetic vortex piercing the heterostructure, two Majorana states are localized at the two interfaces and bound to the vortex core. They have a half integer total angular momentum each, to match with the unitary orbital angular momentum of the vortex charge.

A topology visualization early warning distribution algorithm for large-scale network security incidents.

PubMed

He, Hui; Fan, Guotao; Ye, Jianwei; Zhang, Weizhe

2013-01-01

It is of great significance to research the early warning system for large-scale network security incidents. It can improve the network system's emergency response capabilities, alleviate the cyber attacks' damage, and strengthen the system's counterattack ability. A comprehensive early warning system is presented in this paper, which combines active measurement and anomaly detection. The key visualization algorithm and technology of the system are mainly discussed. The large-scale network system's plane visualization is realized based on the divide and conquer thought. First, the topology of the large-scale network is divided into some small-scale networks by the MLkP/CR algorithm. Second, the sub graph plane visualization algorithm is applied to each small-scale network. Finally, the small-scale networks' topologies are combined into a topology based on the automatic distribution algorithm of force analysis. As the algorithm transforms the large-scale network topology plane visualization problem into a series of small-scale network topology plane visualization and distribution problems, it has higher parallelism and is able to handle the display of ultra-large-scale network topology.

Proton spin: A topological invariant

NASA Astrophysics Data System (ADS)

Tiwari, S. C.

2016-11-01

Proton spin problem is given a new perspective with the proposition that spin is a topological invariant represented by a de Rham 3-period. The idea is developed generalizing Finkelstein-Rubinstein theory for Skyrmions/kinks to topological defects, and using non-Abelian de Rham theorems. Two kinds of de Rham theorems are discussed applicable to matrix-valued differential forms, and traces. Physical and mathematical interpretations of de Rham periods are presented. It is suggested that Wilson lines and loop operators probe the local properties of the topology, and spin as a topological invariant in pDIS measurements could appear with any value from 0 to ℏ 2, i.e. proton spin decomposition has no meaning in this approach.

A topological quantum optics interface

NASA Astrophysics Data System (ADS)

Barik, Sabyasachi; Karasahin, Aziz; Flower, Christopher; Cai, Tao; Miyake, Hirokazu; DeGottardi, Wade; Hafezi, Mohammad; Waks, Edo

2018-02-01

The application of topology in optics has led to a new paradigm in developing photonic devices with robust properties against disorder. Although considerable progress on topological phenomena has been achieved in the classical domain, the realization of strong light-matter coupling in the quantum domain remains unexplored. We demonstrate a strong interface between single quantum emitters and topological photonic states. Our approach creates robust counterpropagating edge states at the boundary of two distinct topological photonic crystals. We demonstrate the chiral emission of a quantum emitter into these modes and establish their robustness against sharp bends. This approach may enable the development of quantum optics devices with built-in protection, with potential applications in quantum simulation and sensing.

Persistent topological features of dynamical systems

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

Maletić, Slobodan, E-mail: slobodan@hitsz.edu.cn; Institute of Nuclear Sciences Vinča, University of Belgrade, Belgrade; Zhao, Yi, E-mail: zhao.yi@hitsz.edu.cn

Inspired by an early work of Muldoon et al., Physica D 65, 1–16 (1993), we present a general method for constructing simplicial complex from observed time series of dynamical systems based on the delay coordinate reconstruction procedure. The obtained simplicial complex preserves all pertinent topological features of the reconstructed phase space, and it may be analyzed from topological, combinatorial, and algebraic aspects. In focus of this study is the computation of homology of the invariant set of some well known dynamical systems that display chaotic behavior. Persistent homology of simplicial complex and its relationship with the embedding dimensions are examinedmore » by studying the lifetime of topological features and topological noise. The consistency of topological properties for different dynamic regimes and embedding dimensions is examined. The obtained results shed new light on the topological properties of the reconstructed phase space and open up new possibilities for application of advanced topological methods. The method presented here may be used as a generic method for constructing simplicial complex from a scalar time series that has a number of advantages compared to the mapping of the same time series to a complex network.« less

Pavement cells and the topology puzzle.

PubMed

Carter, Ross; Sánchez-Corrales, Yara E; Hartley, Matthew; Grieneisen, Verônica A; Marée, Athanasius F M

2017-12-01

D'Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is established early during leaf development, already before the typical pavement cell shapes emerge, with topological homeostasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw piece-like shape of the cells, but rather owes itself to a strongly life history-driven process, with limited impact from cell-surface mechanics. © 2017. Published by The Company of Biologists Ltd.

Pavement cells and the topology puzzle

PubMed Central

2017-01-01

D'Arcy Thompson emphasised the importance of surface tension as a potential driving force in establishing cell shape and topology within tissues. Leaf epidermal pavement cells grow into jigsaw-piece shapes, highly deviating from such classical forms. We investigate the topology of developing Arabidopsis leaves composed solely of pavement cells. Image analysis of around 50,000 cells reveals a clear and unique topological signature, deviating from previously studied epidermal tissues. This topological distribution is established early during leaf development, already before the typical pavement cell shapes emerge, with topological homeostasis maintained throughout growth and unaltered between division and maturation zones. Simulating graph models, we identify a heuristic cellular division rule that reproduces the observed topology. Our parsimonious model predicts how and when cells effectively place their division plane with respect to their neighbours. We verify the predicted dynamics through in vivo tracking of 800 mitotic events, and conclude that the distinct topology is not a direct consequence of the jigsaw piece-like shape of the cells, but rather owes itself to a strongly life history-driven process, with limited impact from cell-surface mechanics. PMID:29084800

Soft connectedness of soft topological space

NASA Astrophysics Data System (ADS)

Mishra, Sanjay

2017-07-01

Recently, Shabir and Naz in [4] introduced the notion of Soft Topological Spaces (STS). They defined and studied about soft topology on the collection τ of soft sets over X. After the initiation of soft topological space many researcher developed its basic theory as like soft continuity, soft compactness and soft countability. Our main objective in this paper is to study the soft connectedness properties of soft topological space and also establish relations of soft connectedness with other properties of STS.

Topological Photonics for Continuous Media

NASA Astrophysics Data System (ADS)

Silveirinha, Mario

Photonic crystals have revolutionized light-based technologies during the last three decades. Notably, it was recently discovered that the light propagation in photonic crystals may depend on some topological characteristics determined by the manner how the light states are mutually entangled. The usual topological classification of photonic crystals explores the fact that these structures are periodic. The periodicity is essential to ensure that the underlying wave vector space is a closed surface with no boundary. In this talk, we prove that it is possible calculate Chern invariants for a wide class of continuous bianisotropic electromagnetic media with no intrinsic periodicity. The nontrivial topology of the relevant continuous materials is linked with the emergence of edge states. Moreover, we will demonstrate that continuous photonic media with the time-reversal symmetry can be topologically characterized by a Z2 integer. This novel classification extends for the first time the theory of electronic topological insulators to a wide range of photonic platforms, and is expected to have an impact in the design of novel photonic systems that enable a topologically protected transport of optical energy. This work is supported in part by Fundacao para a Ciencia e a Tecnologia Grant Number PTDC/EEI-TEL/4543/2014.

Characterization of emergent synaptic topologies in noisy neural networks

NASA Astrophysics Data System (ADS)

Miller, Aaron James

Learned behaviors are one of the key contributors to an animal's ultimate survival. It is widely believed that the brain's microcircuitry undergoes structural changes when a new behavior is learned. In particular, motor learning, during which an animal learns a sequence of muscular movements, often requires precisely-timed coordination between muscles and becomes very natural once ingrained. Experiments show that neurons in the motor cortex exhibit precisely-timed spike activity when performing a learned motor behavior, and constituent stereotypical elements of the behavior can last several hundred milliseconds. The subject of this manuscript concerns how organized synaptic structures that produce stereotypical spike sequences emerge from random, dynamical networks. After a brief introduction in Chapter 1, we begin Chapter 2 by introducing a spike-timing-dependent plasticity (STDP) rule that defines how the activity of the network drives changes in network topology. The rule is then applied to idealized networks of leaky integrate-and-fire neurons (LIF). These neurons are not subjected to the variability that typically characterize neurons in vivo. In noiseless networks, synapses develop closed loops of strong connectivity that reproduce stereotypical, precisely-timed spike patterns from an initially random network. We demonstrate the characteristics of the asymptotic synaptic configuration are dependent on the statistics of the initial random network. The spike timings of the neurons simulated in Chapter 2 are generated exactly by a computationally economical, nonlinear mapping which is extended to LIF neurons injected with fluctuating current in Chapter 3. Development of an economical mapping that incorporates noise provides a practical solution to the long simulation times required to produce asymptotic synaptic topologies in networks with STDP in the presence of realistic neuronal variability. The mapping relies on generating numerical solutions to the dynamics

Characteristics, location and origin of flare activity in a complex active region

NASA Technical Reports Server (NTRS)

Machado, M. E.; Gary, G. A.; Hagyard, M. J.; Hernandez, A. M.; Rovira, M. G.

1986-01-01

The observational characteristics of series of multiple-loop flares from a complex active region are summarized. The location of the highest observed photospheric magnetic shear is found to be the commonly observed site of flare onset, but not, in many cases, the magnetic region where the largest time-integrated energy release is observed. The observations thus reveal a consistent pattern of energy-release processes related to the magnetic-field topology.

Synaptic connectivity and spatial memory: a topological approach

NASA Astrophysics Data System (ADS)

Milton, Russell; Babichev, Andrey; Dabaghian, Yuri

2015-03-01

In the hippocampus, a network of place cells generates a cognitive map of space, in which each cell is responsive to a particular area of the environment - its place field. The peak response of each cell and the size of each place field have considerable variability. Experimental evidence suggests that place cells encode a topological map of space that serves as a basis of spatial memory and spatial awareness. Using a computational model based on Persistent Homology Theory we demonstrate that if the parameters of the place cells spiking activity fall inside of the physiological range, the network correctly encodes the topological features of the environment. We next introduce parameters of synaptic connectivity into the model and demonstrate that failures in synapses that detect coincident neuronal activity lead to spatial learning deficiencies similar to the ones that are observed in rodent models of neurodegenerative diseases. Moreover, we show that these learning deficiencies may be mitigated by increasing the number of active cells and/or by increasing their firing rate, suggesting the existence of a compensatory mechanism inherent to the cognitive map.

Robust transport signatures of topological superconductivity in topological insulator nanowires.

PubMed

de Juan, Fernando; Ilan, Roni; Bardarson, Jens H

2014-09-05

Finding a clear signature of topological superconductivity in transport experiments remains an outstanding challenge. In this work, we propose exploiting the unique properties of three-dimensional topological insulator nanowires to generate a normal-superconductor junction in the single-mode regime where an exactly quantized 2e2/h zero-bias conductance can be observed over a wide range of realistic system parameters. This is achieved by inducing superconductivity in half of the wire, which can be tuned at will from trivial to topological with a parallel magnetic field, while a perpendicular field is used to gap out the normal part, except for two spatially separated chiral channels. The combination of chiral mode transport and perfect Andreev reflection makes the measurement robust to moderate disorder, and the quantization of conductance survives to much higher temperatures than in tunnel junction experiments. Our proposal may be understood as a variant of a Majorana interferometer which is easily realizable in experiments.

Topological charge algebra of optical vortices in nonlinear interactions.

PubMed

Zhdanova, Alexandra A; Shutova, Mariia; Bahari, Aysan; Zhi, Miaochan; Sokolov, Alexei V

2015-12-28

We investigate the transfer of orbital angular momentum among multiple beams involved in a coherent Raman interaction. We use a liquid crystal light modulator to shape pump and Stokes beams into optical vortices with various integer values of topological charge, and cross them in a Raman-active crystal to produce multiple Stokes and anti-Stokes sidebands. We measure the resultant vortex charges using a tilted-lens technique. We verify that in every case the generated beams' topological charges obey a simple relationship, resulting from angular momentum conservation for created and annihilated photons, or equivalently, from phase-matching considerations for multiple interacting beams.

Photoinduced topological phase transition and spin polarization in a two-dimensional topological insulator

NASA Astrophysics Data System (ADS)

Chen, M. N.; Su, W.; Deng, M. X.; Ruan, Jiawei; Luo, W.; Shao, D. X.; Sheng, L.; Xing, D. Y.

2016-11-01

A great deal of attention has been paid to the topological phases engineered by photonics over the past few years. Here, we propose a topological quantum phase transition to a quantum anomalous Hall (QAH) phase induced by off-resonant circularly polarized light in a two-dimensional system that is initially in a quantum spin Hall phase or a trivial insulator phase. This provides an alternative method to realize the QAH effect, other than magnetic doping. The circularly polarized light effectively creates a Zeeman exchange field and a renormalized Dirac mass, which are tunable by varying the intensity of the light and drive the quantum phase transition. Both the transverse and longitudinal Hall conductivities are studied, and the former is consistent with the topological phase transition when the Fermi level lies in the band gap. A highly controllable spin-polarized longitudinal electrical current can be generated when the Fermi level is in the conduction band, which may be useful for designing topological spintronics.

Topological superconductivity in an ultrathin, magnetically-doped topological insulator proximity coupled to a conventional superconductor

NASA Astrophysics Data System (ADS)

Kim, Youngseok; Philip, Timothy M.; Park, Moon Jip; Gilbert, Matthew J.; University of Illinois at Urbana; Champaign Team

As a promising candidate system to realize topological superconductivity (SC), 3D time-reversal invariant topological insulators (TI) proximity-coupled to s-wave superconductors have been intensively studied. Recent experiments on proximity-coupled TI have shown that superconductivity may be induced in ultrathin TI. One proposal to observe the topological SC in proximity-coupled ultrathin TI system is to add magnetic dopants to the TI. However, detailed study on the impact of the experimental parameters on possible topological phase is sparse. In this work, we investigate ultrathin, magnetically-doped, proximity-coupled TI in order to determine the experimentally relevant parameters needed to observe topological SC. We find that, due to the spin-momentum locked nature of the surface states in TI, the induced s-wave order parameter within the surface states persists even at large magnitudes of the Zeeman energy, allowing us to explore the system in parameter space. We elucidate the phase diagram as a function of: the hybridization gap, Zeeman energy, and chemical potential of the TI system. Our findings provide a useful guide in choosing relevant parameters to facilitate the observation of topological SC in thin film TI-superconductor hybrid systems. National Science Foundation (NSF) under Grant CAREER ECCS-1351871.

Active and regulatory sites of cytosolic 5'-nucleotidase.

PubMed

Pesi, Rossana; Allegrini, Simone; Careddu, Maria Giovanna; Filoni, Daniela Nicole; Camici, Marcella; Tozzi, Maria Grazia

2010-12-01

Cytosolic 5'-nucleotidase (cN-II), which acts preferentially on 6-hydroxypurine nucleotides, is essential for the survival of several cell types. cN-II catalyses both the hydrolysis of nucleotides and transfer of their phosphate moiety to a nucleoside acceptor through formation of a covalent phospho-intermediate. Both activities are regulated by a number of phosphorylated compounds, such as diadenosine tetraphosphate (Ap₄A), ADP, ATP, 2,3-bisphosphoglycerate (BPG) and phosphate. On the basis of a partial crystal structure of cN-II, we mutated two residues located in the active site, Y55 and T56. We ascertained that the ability to catalyse the transfer of phosphate depends on the presence of a bulky residue in the active site very close to the aspartate residue that forms the covalent phospho-intermediate. The molecular model indicates two possible sites at which adenylic compounds may interact. We mutated three residues that mediate interaction in the first activation site (R144, N154, I152) and three in the second (F127, M436 and H428), and found that Ap₄A and ADP interact with the same site, but the sites for ATP and BPG remain uncertain. The structural model indicates that cN-II is a homotetrameric protein that results from interaction through a specific interface B of two identical dimers that have arisen from interaction of two identical subunits through interface A. Point mutations in the two interfaces and gel-filtration experiments indicated that the dimer is the smallest active oligomerization state. Finally, gel-filtration and light-scattering experiments demonstrated that the native enzyme exists as a tetramer, and no further oligomerization is required for enzyme activation. © 2010 The Authors Journal compilation © 2010 FEBS.

Water in the Active Site of Ketosteroid Isomerase

PubMed Central

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-01-01

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two waters in the Y16S mutant, one water in the Y16F and FFF mutants, and intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of 1H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less

Water in the active site of ketosteroid isomerase.

PubMed

Hanoian, Philip; Hammes-Schiffer, Sharon

2011-08-09

Classical molecular dynamics simulations were utilized to investigate the structural and dynamical properties of water in the active site of ketosteroid isomerase (KSI) to provide insight into the role of these water molecules in the enzyme-catalyzed reaction. This reaction is thought to proceed via a dienolate intermediate that is stabilized by hydrogen bonding with residues Tyr16 and Asp103. A comparative study was performed for the wild-type (WT) KSI and the Y16F, Y16S, and Y16F/Y32F/Y57F (FFF) mutants. These systems were studied with three different bound ligands: equilenin, which is an intermediate analog, and the intermediate states of two steroid substrates. Several distinct water occupation sites were identified in the active site of KSI for the WT and mutant systems. Three additional sites were identified in the Y16S mutant that were not occupied in WT KSI or the other mutants studied. The number of water molecules directly hydrogen bonded to the ligand oxygen was approximately two in the Y16S mutant and one in the Y16F and FFF mutants, with intermittent hydrogen bonding of one water molecule in WT KSI. The molecular dynamics trajectories of the Y16F and FFF mutants reproduced the small conformational changes of residue 16 observed in the crystal structures of these two mutants. Quantum mechanical/molecular mechanical calculations of (1)H NMR chemical shifts of the protons in the active site hydrogen-bonding network suggest that the presence of water in the active site does not prevent the formation of short hydrogen bonds with far-downfield chemical shifts. The molecular dynamics simulations indicate that the active site water molecules exchange much more frequently for WT KSI and the FFF mutant than for the Y16F and Y16S mutants. This difference is most likely due to the hydrogen-bonding interaction between Tyr57 and an active site water molecule that is persistent in the Y16F and Y16S mutants but absent in the FFF mutant and significantly less probable

Mechanical topological insulator in zero dimensions

NASA Astrophysics Data System (ADS)

Lera, Natalia; Alvarez, J. V.

2018-04-01

We study linear vibrational modes in finite isostatic Maxwell lattices, mechanical systems where the number of degrees of freedom matches the number of constraints. Recent progress in topological mechanics exploits the nontrivial topology of BDI class Hamiltonians in one dimenson and arising topological floppy modes at the edges. A finite frame, or zero-dimensional system, also exhibits a nonzero topological index according to the classification table. We construct mechanical insulating models in zero dimensions that complete the BDI classification in the available real space dimensions. We compute and interpret its nontrivial invariant Z2.

Active Site Characterization of Proteases Sequences from Different Species of Aspergillus.

PubMed

Morya, V K; Yadav, Virendra K; Yadav, Sangeeta; Yadav, Dinesh

2016-09-01

A total of 129 proteases sequences comprising 43 serine proteases, 36 aspartic proteases, 24 cysteine protease, 21 metalloproteases, and 05 neutral proteases from different Aspergillus species were analyzed for the catalytically active site residues using MEROPS database and various bioinformatics tools. Different proteases have predominance of variable active site residues. In case of 24 cysteine proteases of Aspergilli, the predominant active site residues observed were Gln193, Cys199, His364, Asn384 while for 43 serine proteases, the active site residues namely Asp164, His193, Asn284, Ser349 and Asp325, His357, Asn454, Ser519 were frequently observed. The analysis of 21 metalloproteases of Aspergilli revealed Glu298 and Glu388, Tyr476 as predominant active site residues. In general, Aspergilli species-specific active site residues were observed for different types of protease sequences analyzed. The phylogenetic analysis of these 129 proteases sequences revealed 14 different clans representing different types of proteases with diverse active site residues.

Half-of-the-sites reactivity of outer-membrane phospholipase A against an active-site-directed inhibitor.

PubMed

Ubarretxena-Belandia, I; Cox, R C; Dijkman, R; Egmond, M R; Verheij, H M; Dekker, N

1999-03-01

The reaction of a novel active-site-directed phospholipase A1 inhibitor with the outer-membrane phospholipase A (OMPLA) was investigated. The inhibitor 1-p-nitrophenyl-octylphosphonate-2-tridecylcarbamoyl-3-et hanesulfonyl -amino-3-deoxy-sn-glycerol irreversibly inactivated OMPLA. The inhibition reaction did not require the cofactor calcium or an unprotonated active-site His142. The inhibition of the enzyme solubilized in hexadecylphosphocholine micelles was characterized by a rapid (t1/2 = 20 min) and complete loss of enzymatic activity, concurrent with the covalent modification of 50% of the active-site serines, as judged from the amount of p-nitrophenolate (PNP) released. Modification of the remaining 50% occurred at a much lower rate, indicative of half-of-the-sites reactivity against the inhibitor of this dimeric enzyme. Inhibition of monomeric OMPLA solubilized in hexadecyl-N,N-dimethyl-1-ammonio-3-propanesulfonate resulted in an equimolar monophasic release of PNP, concurrent with the loss of enzymatic activity (t1/2 = 14 min). The half-of-the-sites reactivity is discussed in view of the dimeric nature of this enzyme.

Physical activity and cancer risk: dose-response and cancer, all sites and site-specific.

PubMed

Thune, I; Furberg, A S

2001-06-01

The association between physical activity and overall and site-specific cancer risk is elaborated in relation to whether any observed dose-response association between physical activity and cancer can be interpreted in terms of how much physical activity (type, intensity, duration, frequency) is needed to influence site- and gender-specific cancer risk. Observational studies were reviewed that have examined the independent effect of the volume of occupational physical activity (OPA) and/or leisure time physical activity (LPA) on overall and site-specific cancer risk. The evidence of cohort and case-control studies suggests that both leisure time and occupational physical activity protect against overall cancer risk, with a graded dose-response association suggested in both sexes. Confounding effects such as diet, body weight, and parity are often included as a covariate in the analyses, with little influence on the observed associations. A crude graded inverse dose-response association was observed between physical activity and colon cancer in 48 studies including 40,674 colon/colorectal cancer cases for both sexes. A dose-response effect of physical activity on colon cancer risk was especially observed, when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed as MET-hours per week. An observed inverse association with a dose-response relationship between physical activity and breast cancer was also identified in the majority of the 41 studies including 108,031 breast cancer cases. The dose-response relationship was in particular observed in case-control studies and supported by observations in cohort studies when participation in activities of at least moderate activity (>4.5 MET) and demonstrated by activities expressed by MET-hours per week. This association between physical activity and breast cancer risk is possibly dependent on age at exposure, age at diagnosis, menopausal status and other effect

Topological Phases in the Real World

NASA Astrophysics Data System (ADS)

Hsu, Yi-Ting

The experimental discovery and subsequent theoretical understanding of the integer quantum Hall effect, the first known topological phase, has started a revolutionary breakthrough in understanding states of matter since its discovery four decades ago. Topological phases are predicted to have many generic signatures resulting from their underlying topological nature, such as quantized Hall transport, robust boundary states, and possible fractional excitations. The intriguing nature of these signatures and their potential applications in quantum computation has intensely fueled the efforts of the physics community to materialize topological phases. Among various topological phases initially predicted on theoretical grounds, chiral topological superconductors and time-reversal symmetric topological insulators (TI) in three dimension (3D) are two promising candidates for experimental realization and application. The family of materials, Bi2X3 (X = Se, Te), has been predicted and shown experimentally to be time-reversal symmetric 3D TIs through the observation of robust Dirac surface states with Rashba-type spin-winding. Due to their robust surface states with spin-windings, these 3D TIs are expected to be promising materials for producing large spin-transfer torques which are advantageous for spintronics application. As for topological superconductors, despite the exotic excitations that have been extensively proposed as qubits for topological quantum computing, materials hosting topological superconductivity are rare to date and the leading candidate in two dimensions (2D), Sr 2RuO4, has a low transition temperature (Tc ). The goal of my phd study is to push forward the current status of realization of topological phases by materializing higher Tc topological superconductors and investigating the stability of Dirac surface states in 3D TIs. In the first part of this thesis, I will discuss our double-pronged objective for topological superconductors: to propose how to

Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP.

PubMed

Miner, Kyle D; Kurtz, Donald M

2016-02-16

HD-GYPs make up a subclass of the metal-dependent HD phosphohydrolase superfamily and catalyze conversion of cyclic di(3',5')-guanosine monophosphate (c-di-GMP) to 5'-phosphoguanylyl-(3'→5')-guanosine (pGpG) and GMP. Until now, the only reported crystal structure of an HD-GYP that also exhibits c-di-GMP phosphodiesterase activity contains a His/carboxylate ligated triiron active site. However, other structural and phylogenetic correlations indicate that some HD-GYPs contain dimetal active sites. Here we provide evidence that an HD-GYP c-di-GMP phosphodiesterase, TM0186, from Thermotoga maritima can accommodate both di- and trimetal active sites. We show that an as-isolated iron-containing TM0186 has an oxo/carboxylato-bridged diferric site, and that the reduced (diferrous) form is necessary and sufficient to catalyze conversion of c-di-GMP to pGpG, but that conversion of pGpG to GMP requires more than two metals per active site. Similar c-di-GMP phosphodiesterase activities were obtained with divalent iron or manganese. On the basis of activity correlations with several putative metal ligand residue variants and molecular dynamics simulations, we propose that TM0186 can accommodate both di- and trimetal active sites. Our results also suggest that a Glu residue conserved in a subset of HD-GYPs is required for formation of the trimetal site and can also serve as a labile ligand to the dimetal site. Given the anaerobic growth requirement of T. maritima, we suggest that this HD-GYP can function in vivo with either divalent iron or manganese occupying di- and trimetal sites.

Topological interface modes in graphene multilayer arrays

NASA Astrophysics Data System (ADS)

Wang, Feng; Ke, Shaolin; Qin, Chengzhi; Wang, Bing; Long, Hua; Wang, Kai; Lu, Peixiang

2018-07-01

We investigate the topological interface modes of surface plasmon polaritons in a multilayer system composed of graphene waveguide arrays. The topological interface modes emerge when two topologically distinct graphene multilayer arrays are connected. In such multilayer system, the non-trivial topological interface modes and trivial modes coexist. By tuning the configuration of the graphene multilayer arrays, the associated non-trivial interface modes present robust against structural disorder. The total number of topological modes is related to that of graphene layers in a unit cell of the graphene multilayer array. The results provide a new paradigm for topologically protected plasmonics in the graphene multilayer arrays. The study suggests a promising approach to realize light transport and optical switching on a deep-subwavelength scale.

Topology and Oligomerization of Mono- and Oligomeric Proteins Regulate Their Half-Lives in the Cell.

PubMed

Mallik, Saurav; Kundu, Sudip

2018-06-05

To find additional structural constraints (besides disordered segments) that regulate protein half-life in the cell, we herein assess the influence of native topology of monomeric and sequestration of oligomeric proteins into multimeric complexes in yeast, human, and mouse. Native topology acts as a molecular marker of globular protein's mechanical resistance and consequently captures their half-life variations on genome scale. Sequestration into multimeric complexes elongates oligomeric protein half-life in the cell, presumably by burying ubiquitinoylation sites and disordered segments required for proteasomal recognition. The latter effect is stronger for proteins associated with multiple complexes and for those binding early during complex self-assembly, including proteins that oligomerize with large proportions of surface buried. After gene duplication, diversification of topology and sequestration into non-identical sets of complexes alter half-lives of paralogous proteins during the course of evolution. Thus, native topology and sequestration into multimeric complexes reflect designing principles of proteins to regulate their half-lives. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fermionic Symmetry-Protected Topological Phase in a Two-Dimensional Hubbard Model

DOE PAGES

Chen, Cheng-Chien; Muechler, Lukas; Car, Roberto; ...

2016-08-25

We study the two-dimensional (2D) Hubbard model using exact diagonalization for spin-1/2 fermions on the triangular and honeycomb lattices decorated with a single hexagon per site. In certain parameter ranges, the Hubbard model maps to a quantum compass model on those lattices. On the triangular lattice, the compass model exhibits collinear stripe antiferromagnetism, implying d-density wave charge order in the original Hubbard model. On the honeycomb lattice, the compass model has a unique, quantum disordered ground state that transforms nontrivially under lattice reflection. The ground state of the Hubbard model on the decorated honeycomb lattice is thus a 2D fermionicmore » symmetry-protected topological phase. This state—protected by time-reversal and reflection symmetries—cannot be connected adiabatically to a free-fermion topological phase.« less

Topological Defects in Topological Insulators and Bound States at Topological Superconductor Vortices

PubMed Central

Parente, Vincenzo; Campagnano, Gabriele; Giuliano, Domenico; Tagliacozzo, Arturo; Guinea, Francisco

2014-01-01

The scattering of Dirac electrons by topological defects could be one of the most relevant sources of resistance in graphene and at the boundary surfaces of a three-dimensional topological insulator (3D TI). In the long wavelength, continuous limit of the Dirac equation, the topological defect can be described as a distortion of the metric in curved space, which can be accounted for by a rotation of the Gamma matrices and by a spin connection inherited with the curvature. These features modify the scattering properties of the carriers. We discuss the self-energy of defect formation with this approach and the electron cross-section for intra-valley scattering at an edge dislocation in graphene, including corrections coming from the local stress. The cross-section contribution to the resistivity, ρ, is derived within the Boltzmann theory of transport. On the same lines, we discuss the scattering of a screw dislocation in a two-band 3D TI, like Bi1−xSbx, and we present the analytical simplified form of the wavefunction for gapless helical states bound at the defect. When a 3D TI is sandwiched between two even-parity superconductors, Dirac boundary states acquire superconductive correlations by proximity. In the presence of a magnetic vortex piercing the heterostructure, two Majorana states are localized at the two interfaces and bound to the vortex core. They have a half integer total angular momentum each, to match with the unitary orbital angular momentum of the vortex charge. PMID:28788537

Expediting topology data gathering for the TOPDB database.

PubMed

Dobson, László; Langó, Tamás; Reményi, István; Tusnády, Gábor E

2015-01-01

The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM. Results of global topology analysis of various organisms as well as topology data generated by high throughput techniques, like the sequential positions of N- or O-glycosylations were incorporated into the TOPDB database. Moreover, a new algorithm was developed to integrate scattered topology data from various publicly available databases and a new method was introduced to measure the reliability of predicted topologies. We show that reliability values highly correlate with the per protein topology accuracy of the utilized prediction method. Altogether, more than 52,000 new topology data and more than 2600 new transmembrane proteins have been collected since the last public release of the TOPDB database. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Plasmonics of magnetic and topological graphene-based nanostructures

NASA Astrophysics Data System (ADS)

Kuzmin, Dmitry A.; Bychkov, Igor V.; Shavrov, Vladimir G.; Temnov, Vasily V.

2018-02-01

Graphene is a unique material in the study of the fundamental limits of plasmonics. Apart from the ultimate single-layer thickness, its carrier concentration can be tuned by chemical doping or applying an electric field. In this manner, the electrodynamic properties of graphene can be varied from highly conductive to dielectric. Graphene supports strongly confined, propagating surface plasmon polaritons (SPPs) in a broad spectral range from terahertz to mid-infrared frequencies. It also possesses a strong magneto-optical response and thus provides complimentary architectures to conventional magneto-plasmonics based on magneto-optically active metals or dielectrics. Despite a large number of review articles devoted to plasmonic properties and applications of graphene, little is known about graphene magneto-plasmonics and topological effects in graphene-based nanostructures, which represent the main subject of this review. We discuss several strategies to enhance plasmonic effects in topologically distinct closed surface landscapes, i.e. graphene nanotubes, cylindrical nanocavities and toroidal nanostructures. A novel phenomenon of the strongly asymmetric SPP propagation on chiral meta-structures and the fundamental relations between structural and plasmonic topological indices are reviewed.

Continuity and Separation in Symmetric Topologies

ERIC Educational Resources Information Center

Harris, J.; Lynch, M.

2007-01-01

In this note, it is shown that in a symmetric topological space, the pairs of sets separated by the topology determine the topology itself. It is then shown that when the codomain is symmetric, functions which separate only those pairs of sets that are already separated are continuous, generalizing a result found by M. Lynch.

Chemical disorder in topological insulators: A route to magnetism tolerant topological surface states

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

Martínez-Velarte, M. Carmen; Kretz, Bernhard; Moro-Lagares, Maria

Here, we show that the chemical inhomogeneity in ternary three-dimensional topological insulators preserves the topological spin texture of their surface states against a net surface magnetization. The spin texture is that of a Dirac cone with helical spin structure in the reciprocal space, which gives rise to spin-polarized and dissipation-less charge currents. Thanks to the nontrivial topology of the bulk electronic structure, this spin texture is robust against most types of surface defects. However, magnetic perturbations break the time-reversal symmetry, enabling magnetic scattering and loss of spin coherence of the charge carriers. This intrinsic incompatibility precludes the design of magnetoelectronicmore » devices based on the coupling between magnetic materials and topological surface states. We demonstrate that the magnetization coming from individual Co atoms deposited on the surface can disrupt the spin coherence of the carriers in the archetypal topological insulator Bi 2Te 3, while in Bi 2Se 2Te the spin texture remains unperturbed. This is concluded from the observation of elastic backscattering events in quasiparticle interference patterns obtained by scanning tunneling spectroscopy. The mechanism responsible for the protection is investigated by energy resolved spectroscopy and ab initio calculations, and it is ascribed to the distorted adsorption geometry of localized magnetic moments due to Se–Te disorder, which suppresses the Co hybridization with the surface states.« less

Chemical disorder in topological insulators: A route to magnetism tolerant topological surface states

DOE PAGES

Martínez-Velarte, M. Carmen; Kretz, Bernhard; Moro-Lagares, Maria; ...

2017-06-13

Here, we show that the chemical inhomogeneity in ternary three-dimensional topological insulators preserves the topological spin texture of their surface states against a net surface magnetization. The spin texture is that of a Dirac cone with helical spin structure in the reciprocal space, which gives rise to spin-polarized and dissipation-less charge currents. Thanks to the nontrivial topology of the bulk electronic structure, this spin texture is robust against most types of surface defects. However, magnetic perturbations break the time-reversal symmetry, enabling magnetic scattering and loss of spin coherence of the charge carriers. This intrinsic incompatibility precludes the design of magnetoelectronicmore » devices based on the coupling between magnetic materials and topological surface states. We demonstrate that the magnetization coming from individual Co atoms deposited on the surface can disrupt the spin coherence of the carriers in the archetypal topological insulator Bi 2Te 3, while in Bi 2Se 2Te the spin texture remains unperturbed. This is concluded from the observation of elastic backscattering events in quasiparticle interference patterns obtained by scanning tunneling spectroscopy. The mechanism responsible for the protection is investigated by energy resolved spectroscopy and ab initio calculations, and it is ascribed to the distorted adsorption geometry of localized magnetic moments due to Se–Te disorder, which suppresses the Co hybridization with the surface states.« less

TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions

PubMed Central

2017-01-01

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the geometric and biological complexity. To address this problem we introduce the element-specific persistent homology (ESPH) method. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains important biological information via a multichannel image-like representation. This representation reveals hidden structure-function relationships in biomolecules. We further integrate ESPH and deep convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the deep learning limitations from small and noisy training sets, we propose a multi-task multichannel topological convolutional neural network (MM-TCNN). We demonstrate that TopologyNet outperforms the latest methods in the prediction of protein-ligand binding affinities, mutation induced globular protein folding free energy changes, and mutation induced membrane protein folding free energy changes. Availability: weilab.math.msu.edu/TDL/ PMID:28749969

Towards topological quantum computer

NASA Astrophysics Data System (ADS)

Melnikov, D.; Mironov, A.; Mironov, S.; Morozov, A.; Morozov, An.

2018-01-01

Quantum R-matrices, the entangling deformations of non-entangling (classical) permutations, provide a distinguished basis in the space of unitary evolutions and, consequently, a natural choice for a minimal set of basic operations (universal gates) for quantum computation. Yet they play a special role in group theory, integrable systems and modern theory of non-perturbative calculations in quantum field and string theory. Despite recent developments in those fields the idea of topological quantum computing and use of R-matrices, in particular, practically reduce to reinterpretation of standard sets of quantum gates, and subsequently algorithms, in terms of available topological ones. In this paper we summarize a modern view on quantum R-matrix calculus and propose to look at the R-matrices acting in the space of irreducible representations, which are unitary for the real-valued couplings in Chern-Simons theory, as the fundamental set of universal gates for topological quantum computer. Such an approach calls for a more thorough investigation of the relation between topological invariants of knots and quantum algorithms.

Topological Material-Based Spin Devices

NASA Astrophysics Data System (ADS)

Zhang, Minhao; Wang, Xuefeng

Three-dimensional topological insulators have insulating bulk and gapless helical surface states. One of the most fascinating properties of the metallic surface states is the spin-momentum helical locking. The giant current-driven torques on the magnetic layer have been discovered in TI/ferromagnet bilayers originating from the spin-momentum helical locking, enabling the efficient magnetization switching with a low current density. We demonstrated the current-direction dependent on-off state in TIs-based spin valve devices for memory and logic applications. Further, we demonstrated the Bi2Se3 system will go from a topologically nontrivial state to a topologically trivial state when Bi atoms are replaced by lighter In atoms. Here, topologically trivial metal (BixIny)2 Se3 with high mobility also facilitates the realization of its application in multifunctional spintronic devices.

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Topological Qubits from Valence Bond Solids

NASA Astrophysics Data System (ADS)

Wang, Dong-Sheng; Affleck, Ian; Raussendorf, Robert

2018-05-01

Topological qubits based on S U (N )-symmetric valence-bond solid models are constructed. A logical topological qubit is the ground subspace with twofold degeneracy, which is due to the spontaneous breaking of a global parity symmetry. A logical Z rotation by an angle 2 π /N , for any integer N >2 , is provided by a global twist operation, which is of a topological nature and protected by the energy gap. A general concatenation scheme with standard quantum error-correction codes is also proposed, which can lead to better codes. Generic error-correction properties of symmetry-protected topological order are also demonstrated.

Gating Topology of the Proton-Coupled Oligopeptide Symporters

PubMed Central

Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

2015-01-01

Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

Topological phonon modes in filamentary structures

NASA Astrophysics Data System (ADS)

Berg, Nina; Joel, Kira; Koolyk, Miriam; Prodan, Emil

2011-02-01

This work describes a class of topological phonon modes, that is, mechanical vibrations localized at the edges of special structures that are robust against the deformations of the structures. A class of topological phonons was recently found in two-dimensional structures similar to that of microtubules. The present work introduces another class of topological phonons, this time occurring in quasi-one-dimensional filamentary structures with inversion symmetry. The phenomenon is exemplified using a structure inspired from that of actin microfilaments, present in most live cells. The system discussed here is probably the simplest structure that supports topological phonon modes, a fact that allows detailed analysis in both time and frequency domains. We advance the hypothesis that the topological phonon modes are ubiquitous in the biological world and that living organisms make use of them during various processes.

Color confinement from fluctuating topology

DOE PAGES

Kharzeev, Dmitri E.

2016-10-19

QCD possesses a compact gauge group, and this implies a non-trivial topological structure of the vacuum. In this contribution to the Gribov-85 Memorial volume, we first discuss the origin of Gribov copies and their interpretation in terms of fluctuating topology in the QCD vacuum. We then describe the recent work with E. Levin that links the confinement of gluons and color screening to the fluctuating topology, and discuss implications for spin physics, high energy scattering, and the physics of quark-gluon plasma.

Semilinear (topological) spaces and applications

NASA Technical Reports Server (NTRS)

Prakash, P.; Sertel, M. R.

1971-01-01

Semivector spaces are defined and some of their algebraic aspects are developed including some structure theory. These spaces are then topologized to obtain semilinear topological spaces for which a hierarchy of local convexity axioms is identified. A number of fixed point and minmax theorems for spaces with various local convexity properties are established. The spaces of concern arise naturally as various hyperspaces of linear and semilinear (topological) spaces. It is indicated briefly how all this can be applied in socio-economic analysis and optimization.

Topological nonsymmorphic metals from band inversion

DOE PAGES

Muechler, Lukas; Alexandradinata, A.; Neupert, Titus; ...

2016-12-29

Here, we expand the phase diagram of two-dimensional, nonsymmorphic crystals at integer fillings that do not guarantee gaplessness. In addition to the trivial, gapped phase that is expected, we find that band inversion leads to a class of topological, gapless phases. These topological phases are exemplified by the monolayers of MTe 2 (M ¼ W; Mo) if spin-orbit coupling is neglected. We characterize the Dirac band touching of these topological metals by theWilson loop of the non-Abelian Berry gauge field. Furthermore, we develop a criterion for the proximity of these topological metals to 2D and 3D Z 2 topological insulatorsmore » when spinorbit coupling is included; our criterion is based on nonsymmorphic symmetry eigenvalues, and may be used to identify topological materials without inversion symmetry. An additional feature of the Dirac cone in monolayer MTe 2 is that it tilts over in a Lifshitz transition to produce electron and hole pockets—a type-II Dirac cone. These pockets, together with the pseudospin structure of the Dirac electrons, suggest a unified, topological explanation for the recently reported, nonsaturating magnetoresistance in WTe 2, as well as its circular dichroism in photoemission. We complement our analysis and first-principles band structure calculations with an ab-initio-derived tight-binding model for the WTe 2 monolayer.« less

Synaptic Impairment and Robustness of Excitatory Neuronal Networks with Different Topologies

PubMed Central

Mirzakhalili, Ehsan; Gourgou, Eleni; Booth, Victoria; Epureanu, Bogdan

2017-01-01

Synaptic deficiencies are a known hallmark of neurodegenerative diseases, but the diagnosis of impaired synapses on the cellular level is not an easy task. Nonetheless, changes in the system-level dynamics of neuronal networks with damaged synapses can be detected using techniques that do not require high spatial resolution. This paper investigates how the structure/topology of neuronal networks influences their dynamics when they suffer from synaptic loss. We study different neuronal network structures/topologies by specifying their degree distributions. The modes of the degree distribution can be used to construct networks that consist of rich clubs and resemble small world networks, as well. We define two dynamical metrics to compare the activity of networks with different structures: persistent activity (namely, the self-sustained activity of the network upon removal of the initial stimulus) and quality of activity (namely, percentage of neurons that participate in the persistent activity of the network). Our results show that synaptic loss affects the persistent activity of networks with bimodal degree distributions less than it affects random networks. The robustness of neuronal networks enhances when the distance between the modes of the degree distribution increases, suggesting that the rich clubs of networks with distinct modes keep the whole network active. In addition, a tradeoff is observed between the quality of activity and the persistent activity. For a range of distributions, both of these dynamical metrics are considerably high for networks with bimodal degree distribution compared to random networks. We also propose three different scenarios of synaptic impairment, which may correspond to different pathological or biological conditions. Regardless of the network structure/topology, results demonstrate that synaptic loss has more severe effects on the activity of the network when impairments are correlated with the activity of the neurons. PMID

Robust interface between flying and topological qubits

PubMed Central

Xue, Zheng-Yuan; Gong, Ming; Liu, Jia; Hu, Yong; Zhu, Shi-Liang; Wang, Z. D.

2015-01-01

Hybrid architectures, consisting of conventional and topological qubits, have recently attracted much attention due to their capability in consolidating robustness of topological qubits and universality of conventional qubits. However, these two kinds of qubits are normally constructed in significantly different energy scales, and thus the energy mismatch is a major obstacle for their coupling, which can support the exchange of quantum information between them. Here we propose a microwave photonic quantum bus for a strong direct coupling between the topological and conventional qubits, where the energy mismatch is compensated by an external driving field. In the framework of tight-binding simulation and perturbation approach, we show that the energy splitting of Majorana fermions in a finite length nanowire, which we use to define topological qubits, is still robust against local perturbations due to the topology of the system. Therefore, the present scheme realizes a rather robust interface between the flying and topological qubits. Finally, we demonstrate that this quantum bus can also be used to generate multipartitie entangled states with the topological qubits. PMID:26216201

A topological quantum optics interface.

PubMed

Barik, Sabyasachi; Karasahin, Aziz; Flower, Christopher; Cai, Tao; Miyake, Hirokazu; DeGottardi, Wade; Hafezi, Mohammad; Waks, Edo

2018-02-09

The application of topology in optics has led to a new paradigm in developing photonic devices with robust properties against disorder. Although considerable progress on topological phenomena has been achieved in the classical domain, the realization of strong light-matter coupling in the quantum domain remains unexplored. We demonstrate a strong interface between single quantum emitters and topological photonic states. Our approach creates robust counterpropagating edge states at the boundary of two distinct topological photonic crystals. We demonstrate the chiral emission of a quantum emitter into these modes and establish their robustness against sharp bends. This approach may enable the development of quantum optics devices with built-in protection, with potential applications in quantum simulation and sensing. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Comprehensible Presentation of Topological Information

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

Weber, Gunther H.; Beketayev, Kenes; Bremer, Peer-Timo

2012-03-05

Topological information has proven very valuable in the analysis of scientific data. An important challenge that remains is presenting this highly abstract information in a way that it is comprehensible even if one does not have an in-depth background in topology. Furthermore, it is often desirable to combine the structural insight gained by topological analysis with complementary information, such as geometric information. We present an overview over methods that use metaphors to make topological information more accessible to non-expert users, and we demonstrate their applicability to a range of scientific data sets. With the increasingly complex output of exascale simulations,more » the importance of having effective means of providing a comprehensible, abstract overview over data will grow. The techniques that we present will serve as an important foundation for this purpose.« less

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

PubMed

Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

2013-01-01

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

Recent Progress in the Study of Topological Semimetals

NASA Astrophysics Data System (ADS)

Bernevig, Andrei; Weng, Hongming; Fang, Zhong; Dai, Xi

2018-04-01

The topological semimetal is a new, theoretically predicted and experimentally discovered, topological state of matter. In one of its several realizations, the topological semimetal hosts Weyl fermions, elusive particles predicted more than 85 years ago, sought after in high-energy experiments, but only recently found in a condensed-matter setting. In the present review, we catalogue the most recent progress in this fast-developing research field. We give special attention to topological invariants and the material realization of three different types of topological semimetal. We also discuss various photo emission, transport and optical experimental observables that characterize the appearance of topological semimetal phases.

Colloquium: Zoo of quantum-topological phases of matter

NASA Astrophysics Data System (ADS)

Wen, Xiao-Gang

2017-10-01

What are topological phases of matter? First, they are phases of matter at zero temperature. Second, they have a nonzero energy gap for the excitations above the ground state. Third, they are disordered liquids that seem to have no feature. But those disordered liquids actually can have rich patterns of many-body entanglement representing new kinds of order. This Colloquium gives a simple introduction and a brief survey of topological phases of matter. First topological phases with topological order (i.e., with long-range entanglement) are discussed. Then topological phases without topological order (i.e., with short-range entanglement) are covered.

Circuit topology of proteins and nucleic acids.

PubMed

Mashaghi, Alireza; van Wijk, Roeland J; Tans, Sander J

2014-09-02

Folded biomolecules display a bewildering structural complexity and diversity. They have therefore been analyzed in terms of generic topological features. For instance, folded proteins may be knotted, have beta-strands arranged into a Greek-key motif, or display high contact order. In this perspective, we present a method to formally describe the topology of all folded linear chains and hence provide a general classification and analysis framework for a range of biomolecules. Moreover, by identifying the fundamental rules that intrachain contacts must obey, the method establishes the topological constraints of folded linear chains. We also briefly illustrate how this circuit topology notion can be applied to study the equivalence of folded chains, the engineering of artificial RNA structures and DNA origami, the topological structure of genomes, and the role of topology in protein folding. Copyright © 2014 Elsevier Ltd. All rights reserved.

Chemistry explained by topology: an alternative approach.

PubMed

Galvez, Jorge; Villar, Vincent M; Galvez-Llompart, Maria; Amigó, José M

2011-05-01

Molecular topology can be considered an application of graph theory in which the molecular structure is characterized through a set of graph-theoretical descriptors called topological indices. Molecular topology has found applications in many different fields, particularly in biology, chemistry, and pharmacology. The first topological index was introduced by H. Wiener in 1947 [1]. Although its very first application was the prediction of the boiling points of the alkanes, the Wiener index has demonstrated since then a predictive capability far beyond that. Along with the Wiener index, in this paper we focus on a few pioneering topological indices, just to illustrate the connection between physicochemical properties and molecular connectivity.

Trimeric structure of (+)-pinoresinol-forming dirigent protein at 1.95 Å resolution with three isolated active sites.

PubMed

Kim, Kye-Won; Smith, Clyde A; Daily, Michael D; Cort, John R; Davin, Laurence B; Lewis, Norman G

2015-01-16

Control over phenoxy radical-radical coupling reactions in vivo in vascular plants was enigmatic until our discovery of dirigent proteins (DPs, from the Latin dirigere, to guide or align). The first three-dimensional structure of a DP ((+)-pinoresinol-forming DP, 1.95 Å resolution, rhombohedral space group H32)) is reported herein. It has a tightly packed trimeric structure with an eight-stranded β-barrel topology for each DP monomer. Each putative substrate binding and orientation coupling site is located on the trimer surface but too far apart for intermolecular coupling between sites. It is proposed that each site enables stereoselective coupling (using either two coniferyl alcohol radicals or a radical and a monolignol). Interestingly, there are six differentially conserved residues in DPs affording either the (+)- or (-)-antipodes in the vicinity of the putative binding site and region known to control stereoselectivity. DPs are involved in lignan biosynthesis, whereas dirigent domains/sites have been implicated in lignin deposition. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Direct instrumental identification of catalytically active surface sites

NASA Astrophysics Data System (ADS)

Pfisterer, Jonas H. K.; Liang, Yunchang; Schneider, Oliver; Bandarenka, Aliaksandr S.

2017-09-01

The activity of heterogeneous catalysts—which are involved in some 80 per cent of processes in the chemical and energy industries—is determined by the electronic structure of specific surface sites that offer optimal binding of reaction intermediates. Directly identifying and monitoring these sites during a reaction should therefore provide insight that might aid the targeted development of heterogeneous catalysts and electrocatalysts (those that participate in electrochemical reactions) for practical applications. The invention of the scanning tunnelling microscope (STM) and the electrochemical STM promised to deliver such imaging capabilities, and both have indeed contributed greatly to our atomistic understanding of heterogeneous catalysis. But although the STM has been used to probe and initiate surface reactions, and has even enabled local measurements of reactivity in some systems, it is not generally thought to be suited to the direct identification of catalytically active surface sites under reaction conditions. Here we demonstrate, however, that common STMs can readily map the catalytic activity of surfaces with high spatial resolution: we show that by monitoring relative changes in the tunnelling current noise, active sites can be distinguished in an almost quantitative fashion according to their ability to catalyse the hydrogen-evolution reaction or the oxygen-reduction reaction. These data allow us to evaluate directly the importance and relative contribution to overall catalyst activity of different defects and sites at the boundaries between two materials. With its ability to deliver such information and its ready applicability to different systems, we anticipate that our method will aid the rational design of heterogeneous catalysts.

Probing topological protection using a designer surface plasmon structure

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

Gao, Fei; Gao, Zhen; Shi, Xihang

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

Probing topological protection using a designer surface plasmon structure

DOE PAGES

Gao, Fei; Gao, Zhen; Shi, Xihang; ...

2016-05-20

Topological photonic states, inspired by robust chiral edge states in topological insulators, have recently been demonstrated in a few photonic systems, including an array of coupled on-chip ring resonators at communication wavelengths. However, the intrinsic difference between electrons and photons determines that the 'topological protection' in time-reversal-invariant photonic systems does not share the same robustness as its counterpart in electronic topological insulators. Here in a designer surface plasmon platform consisting of tunable metallic sub-wavelength structures, we construct photonic topological edge states and probe their robustness against a variety of defect classes, including some common time-reversal-invariant photonic defects that can breakmore » the topological protection, but do not exist in electronic topological insulators. Furthermore, this is also an experimental realization of anomalous Floquet topological edge states, whose topological phase cannot be predicted by the usual Chern number topological invariants.« less

The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations1

PubMed Central

Just, Victoria J.; Burrell, Matthew R.; Bowater, Laura; McRobbie, Iain; Stevenson, Clare E. M.; Lawson, David M.; Bornemann, Stephen

2007-01-01

Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Δ162–163 or Δ162–164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Δ162–163 and S161A) strongly support the hypothesis that site 2 is purely structural. PMID:17680775

Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

PubMed

Kamal, Md Zahid; Mohammad, Tabrez Anwar Shamim; Krishnamoorthy, G; Rao, Nalam Madhusudhana

2012-01-01

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

Topological Phases of Sound and Light

NASA Astrophysics Data System (ADS)

Peano, V.; Brendel, C.; Schmidt, M.; Marquardt, F.

2015-07-01

Topological states of matter are particularly robust, since they exploit global features of a material's band structure. Topological states have already been observed for electrons, atoms, and photons. It is an outstanding challenge to create a Chern insulator of sound waves in the solid state. In this work, we propose an implementation based on cavity optomechanics in a photonic crystal. The topological properties of the sound waves can be wholly tuned in situ by adjusting the amplitude and frequency of a driving laser that controls the optomechanical interaction between light and sound. The resulting chiral, topologically protected phonon transport can be probed completely optically. Moreover, we identify a regime of strong mixing between photon and phonon excitations, which gives rise to a large set of different topological phases and offers an example of a Chern insulator produced from the interaction between two physically distinct particle species, photons and phonons.

Identifying Two-Dimensional Z 2 Antiferromagnetic Topological Insulators

NASA Astrophysics Data System (ADS)

Bègue, F.; Pujol, P.; Ramazashvili, R.

2018-01-01

We revisit the question of whether a two-dimensional topological insulator may arise in a commensurate Néel antiferromagnet, where staggered magnetization breaks the symmetry with respect to both elementary translation and time reversal, but retains their product as a symmetry. In contrast to the so-called Z 2 topological insulators, an exhaustive characterization of antiferromagnetic topological phases with the help of topological invariants has been missing. We analyze a simple model of an antiferromagnetic topological insulator and chart its phase diagram, using a recently proposed criterion for centrosymmetric systems [13]. We then adapt two methods, originally designed for paramagnetic systems, and make antiferromagnetic topological phases manifest. The proposed methods apply far beyond the particular examples treated in this work, and admit straightforward generalization. We illustrate this by two examples of non-centrosymmetric systems, where no simple criteria have been known to identify topological phases. We also present, for some cases, an explicit construction of edge states in an antiferromagnetic topological insulator.

Topologically Associating Domains: An invariant framework or a dynamic scaffold?

PubMed

Cubeñas-Potts, Caelin; Corces, Victor G

2015-01-01

Metazoan genomes are organized into regions of topologically associating domains (TADs). TADs are demarcated by border elements, which are enriched for active genes and high occupancy architectural protein binding sites. We recently demonstrated that 3D chromatin architecture is dynamic in response to heat shock, a physiological stress that downregulates transcription and causes a global redistribution of architectural proteins. We utilized a quantitative measure of border strength after heat shock, transcriptional inhibition, and architectural protein knockdown to demonstrate that changes in both transcription and architectural protein occupancy contribute to heat shock-induced TAD dynamics. Notably, architectural proteins appear to play a more important role in altering 3D chromatin architecture. Here, we discuss the implications of our findings on previous studies evaluating the dynamics of TAD structure during cellular differentiation. We propose that the subset of variable TADs observed after differentiation are representative of cell-type specific gene expression and are biologically significant.

A split ubiquitin system to reveal topology and released peptides of membrane proteins.

PubMed

Li, Qiu-Ping; Wang, Shuai; Gou, Jin-Ying

2017-09-02

Membrane proteins define biological functions of membranes in cells. Extracellular peptides of transmembrane proteins receive signals from pathogens or environments, and are the major targets of drug developments. Despite of their essential roles, membrane proteins remain elusive in topological studies due to technique difficulties in their expressions and purifications. First, the target gene is cloned into a destination vector to fuse with C terminal ubiquitin at the N or C terminus. Then, Cub vector with target gene and Nub WT or Nub G vectors are transformed into AP4 or AP5 yeast cells, respectively. After mating, the diploid cells are dipped onto selection medium to check the growth. Topology of the target protein is determined according to Table 1. We present a split ubiquitin topology (SUT) analysis system to study the topology and truncation peptide of membrane proteins in a simple yeast experiment. In the SUT system, transcription activator (TA) fused with a nucleo-cytoplasmic protein shows strong auto-activation with both positive and negative control vectors. TA fused with the cytoplasmic end of membrane proteins activates reporter genes only with positive control vector with a wild type N terminal ubiquitin (Nub WT ). However, TA fused with the extracellular termini of membrane proteins can't activate reporter genes even with Nub WT . Interestingly,TA fused with the released peptide of a membrane protein shows autoactivation in the SUT system. The SUT system is a simple and fast experimental procedure complementary to computational predictions and large scale proteomic techniques. The preliminary data from SUT are valuable for pathogen recognitions and new drug developments.

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 8 2011-07-01 2011-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 9 2013-07-01 2013-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 9 2012-07-01 2012-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 8 2010-07-01 2010-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

40 CFR 61.154 - Standard for active waste disposal sites.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 9 2014-07-01 2014-07-01 false Standard for active waste disposal... for Asbestos § 61.154 Standard for active waste disposal sites. Each owner or operator of an active... visible emissions to the outside air from any active waste disposal site where asbestos-containing waste...

Optoelectronic devices, plasmonics, and photonics with topological insulators

NASA Astrophysics Data System (ADS)

Politano, Antonio; Viti, Leonardo; Vitiello, Miriam S.

2017-03-01

Topological insulators are innovative materials with semiconducting bulk together with surface states forming a Dirac cone, which ensure metallic conduction in the surface plane. Therefore, topological insulators represent an ideal platform for optoelectronics and photonics. The recent progress of science and technology based on topological insulators enables the exploitation of their huge application capabilities. Here, we review the recent achievements of optoelectronics, photonics, and plasmonics with topological insulators. Plasmonic devices and photodetectors based on topological insulators in a wide energy range, from terahertz to the ultraviolet, promise outstanding impact. Furthermore, the peculiarities, the range of applications, and the challenges of the emerging fields of topological photonics and thermo-plasmonics are discussed.

Locked and proteolysis-based transcription activator-like effector (TALE) regulation.

PubMed

Lonzarić, Jan; Lebar, Tina; Majerle, Andreja; Manček-Keber, Mateja; Jerala, Roman

2016-02-18

Development of orthogonal, designable and adjustable transcriptional regulators is an important goal of synthetic biology. Their activity has been typically modulated through stimulus-induced oligomerization or interaction between the DNA-binding and activation/repression domain. We exploited a feature of the designable Transcription activator-like effector (TALE) DNA-binding domain that it winds around the DNA which allows to topologically prevent it from binding by intramolecular cyclization. This new approach was investigated through noncovalent ligand-induced cyclization or through a covalent split intein cyclization strategy, where the topological inhibition of DNA binding by cyclization and its restoration by a proteolytic release of the topologic constraint was expected. We show that locked TALEs indeed have diminished DNA binding and regain full transcriptional activity by stimulation with the rapamycin ligand or site-specific proteolysis of the peptide linker, with much higher level of activation than rapamycin-induced heterodimerization. Additionally, we demonstrated reversibility, activation of genomic targets and implemented logic gates based on combinations of protein cyclization, proteolytic cleavage and ligand-induced dimerization, where the strongest fold induction was achieved by the proteolytic cleavage of a repression domain from a linear TALE. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Enquiry into the Topology of Plasma Membrane-Localized PIN Auxin Transport Components.

PubMed

Nodzyński, Tomasz; Vanneste, Steffen; Zwiewka, Marta; Pernisová, Markéta; Hejátko, Jan; Friml, Jiří

2016-11-07

Auxin directs plant ontogenesis via differential accumulation within tissues depending largely on the activity of PIN proteins that mediate auxin efflux from cells and its directional cell-to-cell transport. Regardless of the developmental importance of PINs, the structure of these transporters is poorly characterized. Here, we present experimental data concerning protein topology of plasma membrane-localized PINs. Utilizing approaches based on pH-dependent quenching of fluorescent reporters combined with immunolocalization techniques, we mapped the membrane topology of PINs and further cross-validated our results using available topology modeling software. We delineated the topology of PIN1 with two transmembrane (TM) bundles of five α-helices linked by a large intracellular loop and a C-terminus positioned outside the cytoplasm. Using constraints derived from our experimental data, we also provide an updated position of helical regions generating a verisimilitude model of PIN1. Since the canonical long PINs show a high degree of conservation in TM domains and auxin transport capacity has been demonstrated for Arabidopsis representatives of this group, this empirically enhanced topological model of PIN1 will be an important starting point for further studies on PIN structure-function relationships. In addition, we have established protocols that can be used to probe the topology of other plasma membrane proteins in plants. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Rashba sandwiches with topological superconducting phases

NASA Astrophysics Data System (ADS)

Volpez, Yanick; Loss, Daniel; Klinovaja, Jelena

2018-05-01

We introduce a versatile heterostructure harboring various topological superconducting phases characterized by the presence of helical, chiral, or unidirectional edge states. Changing parameters, such as an effective Zeeman field or chemical potential, one can tune between these three topological phases in the same setup. Our model relies only on conventional nontopological ingredients. The bilayer setup consists of an s -wave superconductor sandwiched between two two-dimensional electron gas layers with strong Rashba spin-orbit interaction. The interplay between two different pairing mechanisms, proximity induced direct and crossed Andreev superconducting pairings, gives rise to multiple topological phases. In particular, helical edge states occur if crossed Andreev superconducting pairing is dominant. In addition, an in-plane Zeeman field leads to a two-dimensional gapless topological phase with unidirectional edge states, which were previously predicted to exist only in noncentrosymmetric superconductors. If the Zeeman field is tilted out of the plane, the system is in a topological phase hosting chiral edge states.

Topological Mechanics of Origami and Kirigami

NASA Astrophysics Data System (ADS)

Chen, Bryan Gin-ge; Liu, Bin; Evans, Arthur A.; Paulose, Jayson; Cohen, Itai; Vitelli, Vincenzo; Santangelo, C. D.

2016-04-01

Origami and kirigami have emerged as potential tools for the design of mechanical metamaterials whose properties such as curvature, Poisson ratio, and existence of metastable states can be tuned using purely geometric criteria. A major obstacle to exploiting this property is the scarcity of tools to identify and program the flexibility of fold patterns. We exploit a recent connection between spring networks and quantum topological states to design origami with localized folding motions at boundaries and study them both experimentally and theoretically. These folding motions exist due to an underlying topological invariant rather than a local imbalance between constraints and degrees of freedom. We give a simple example of a quasi-1D folding pattern that realizes such topological states. We also demonstrate how to generalize these topological design principles to two dimensions. A striking consequence is that a domain wall between two topologically distinct, mechanically rigid structures is deformable even when constraints locally match the degrees of freedom.

Topology-Optimized Multilayered Metaoptics

NASA Astrophysics Data System (ADS)

Lin, Zin; Groever, Benedikt; Capasso, Federico; Rodriguez, Alejandro W.; Lončar, Marko

2018-04-01

We propose a general topology-optimization framework for metasurface inverse design that can automatically discover highly complex multilayered metastructures with increased functionalities. In particular, we present topology-optimized multilayered geometries exhibiting angular phase control, including a single-piece nanophotonic metalens with angular aberration correction, as well as an angle-convergent metalens that focuses light onto the same focal spot regardless of the angle of incidence.

Quasi-topological Ricci polynomial gravities

NASA Astrophysics Data System (ADS)

Li, Yue-Zhou; Liu, Hai-Shan; Lü, H.

2018-02-01

Quasi-topological terms in gravity can be viewed as those that give no contribution to the equations of motion for a special subclass of metric ansätze. They therefore play no rôle in constructing these solutions, but can affect the general perturbations. We consider Einstein gravity extended with Ricci tensor polynomial invariants, which admits Einstein metrics with appropriate effective cosmological constants as its vacuum solutions. We construct three types of quasi-topological gravities. The first type is for the most general static metrics with spherical, toroidal or hyperbolic isometries. The second type is for the special static metrics where g tt g rr is constant. The third type is the linearized quasitopological gravities on the Einstein metrics. We construct and classify results that are either dependent on or independent of dimensions, up to the tenth order. We then consider a subset of these three types and obtain Lovelock-like quasi-topological gravities, that are independent of the dimensions. The linearized gravities on Einstein metrics on all dimensions are simply Einstein and hence ghost free. The theories become quasi-topological on static metrics in one specific dimension, but non-trivial in others. We also focus on the quasi-topological Ricci cubic invariant in four dimensions as a specific example to study its effect on holography, including shear viscosity, thermoelectric DC conductivities and butterfly velocity. In particular, we find that the holographic diffusivity bounds can be violated by the quasi-topological terms, which can induce an extra massive mode that yields a butterfly velocity unbound above.

Topology-function conservation in protein-protein interaction networks.

PubMed

Davis, Darren; Yaveroğlu, Ömer Nebil; Malod-Dognin, Noël; Stojmirovic, Aleksandar; Pržulj, Nataša

2015-05-15

Proteins underlay the functioning of a cell and the wiring of proteins in protein-protein interaction network (PIN) relates to their biological functions. Proteins with similar wiring in the PIN (topology around them) have been shown to have similar functions. This property has been successfully exploited for predicting protein functions. Topological similarity is also used to guide network alignment algorithms that find similarly wired proteins between PINs of different species; these similarities are used to transfer annotation across PINs, e.g. from model organisms to human. To refine these functional predictions and annotation transfers, we need to gain insight into the variability of the topology-function relationships. For example, a function may be significantly associated with specific topologies, while another function may be weakly associated with several different topologies. Also, the topology-function relationships may differ between different species. To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis. Using the graphlet degrees to represent the wiring around proteins in PINs and gene ontology (GO) annotations to describe their functions, our framework: (i) characterizes statistically significant topology-function relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions. We apply our framework to PINs of yeast and human, identifying seven biological process and two cellular component GO terms to be topologically orthologous for the two organisms. © The Author 2015. Published by Oxford University Press.

Probing topological order with Rényi entropy

NASA Astrophysics Data System (ADS)

Halász, Gábor B.; Hamma, Alioscia

2012-12-01

We present an analytical study of the quantum phase transition between the topologically ordered toric-code-model ground state and the disordered spin-polarized state. The phase transition is induced by applying an external magnetic field, and the variation in topological order is detected via two nonlocal quantities: the Wilson loop and the topological Rényi entropy of order 2. By exploiting an equivalence with the transverse-field Ising model and considering two different variants of the problem, we investigate the field dependence of these quantities by means of an exact treatment in the exactly solvable variant and complementary perturbation theories around the limits of zero and infinite fields in both variants. We find strong evidence that the phase transition point between topological order and disorder is marked by a discontinuity in the topological Rényi entropy and that the two phases around the phase transition point are characterized by its different constant values. Our results therefore indicate that the topological Rényi entropy is a proper topological invariant: its allowed values are discrete and can be used to distinguish between different phases of matter.

On the topological sensitivity of cellular automata

NASA Astrophysics Data System (ADS)

Baetens, Jan M.; De Baets, Bernard

2011-06-01

Ever since the conceptualization of cellular automata (CA), much attention has been paid to the dynamical properties of these discrete dynamical systems, and, more in particular, to their sensitivity to the initial condition from which they are evolved. Yet, the sensitivity of CA to the topology upon which they are based has received only minor attention, such that a clear insight in this dependence is still lacking and, furthermore, a quantification of this so-called topological sensitivity has not yet been proposed. The lack of attention for this issue is rather surprising since CA are spatially explicit, which means that their dynamics is directly affected by their topology. To overcome these shortcomings, we propose topological Lyapunov exponents that measure the divergence of two close trajectories in phase space originating from a topological perturbation, and we relate them to a measure grasping the sensitivity of CA to their topology that relies on the concept of topological derivatives, which is introduced in this paper. The validity of the proposed methodology is illustrated for the 256 elementary CA and for a family of two-state irregular totalistic CA.

Effective field theories for topological insulators by functional bosonization

NASA Astrophysics Data System (ADS)

Chan, AtMa; Hughes, Taylor L.; Ryu, Shinsei; Fradkin, Eduardo

2013-02-01

Effective field theories that describe the dynamics of a conserved U(1) current in terms of “hydrodynamic” degrees of freedom of topological phases in condensed matter are discussed in general dimension D=d+1 using the functional bosonization technique. For noninteracting topological insulators (superconductors) with a conserved U(1) charge and characterized by an integer topological invariant [more specifically, they are topological insulators in the complex symmetry classes (class A and AIII), and in the “primary series” of topological insulators, in the eight real symmetry classes], we derive the BF-type topological field theories supplemented with the Chern-Simons (when D is odd) or the θ (when D is even) terms. For topological insulators characterized by a Z2 topological invariant (the first and second descendants of the primary series), their topological field theories are obtained by dimensional reduction. Building on this effective field theory description for noninteracting topological phases, we also discuss, following the spirit of the parton construction of the fractional quantum Hall effect by Block and Wen, the putative “fractional” topological insulators and their possible effective field theories, and use them to determine the physical properties of these nontrivial quantum phases.

Complete theory of symmetry-based indicators of band topology.

PubMed

Po, Hoi Chun; Vishwanath, Ashvin; Watanabe, Haruki

2017-06-30

The interplay between symmetry and topology leads to a rich variety of electronic topological phases, protecting states such as the topological insulators and Dirac semimetals. Previous results, like the Fu-Kane parity criterion for inversion-symmetric topological insulators, demonstrate that symmetry labels can sometimes unambiguously indicate underlying band topology. Here we develop a systematic approach to expose all such symmetry-based indicators of band topology in all the 230 space groups. This is achieved by first developing an efficient way to represent band structures in terms of elementary basis states, and then isolating the topological ones by removing the subset of atomic insulators, defined by the existence of localized symmetric Wannier functions. Aside from encompassing all earlier results on such indicators, including in particular the notion of filling-enforced quantum band insulators, our theory identifies symmetry settings with previously hidden forms of band topology, and can be applied to the search for topological materials.Understanding the role of topology in determining electronic structure can lead to the discovery, or appreciation, of materials with exotic properties such as protected surface states. Here, the authors present a framework for identifying topologically distinct band-structures for all 3D space groups.

When quantum optics meets topology

NASA Astrophysics Data System (ADS)

Amo, Alberto

2018-02-01

Routing photons at the micrometer scale remains one of the greatest challenges of integrated quantum optics. The main difficulty is the scattering losses at bends and splitters in the photonic circuit. Current approaches imply elaborate designs, quite sensitive to fabrication details (1). Inspired by the physics underlying the one-way transport of electrons in topological insulators, on page 666 of this issue, Barik et al. (2) report a topological photonic crystal in which single photons are emitted and routed through bends with negligible loss. The marriage between quantum optics and topology promises new opportunities for compact quantum optics gating and manipulation.

Topological phenomena in classical optical networks

PubMed Central

Shi, T.; Kimble, H. J.; Cirac, J. I.

2017-01-01

We propose a scheme to realize a topological insulator with optical-passive elements and analyze the effects of Kerr nonlinearities in its topological behavior. In the linear regime, our design gives rise to an optical spectrum with topological features and where the bandwidths and bandgaps are dramatically broadened. The resulting edge modes cover a very wide frequency range. We relate this behavior to the fact that the effective Hamiltonian describing the system’s amplitudes is long range. We also develop a method to analyze the scheme in the presence of a Kerr medium. We assess robustness and stability of the topological features and predict the presence of chiral squeezed fluctuations at the edges in some parameter regimes. PMID:29073093

Cheshire charge in (3+1)-dimensional topological phases

NASA Astrophysics Data System (ADS)

Else, Dominic V.; Nayak, Chetan

2017-07-01

We show that (3 +1 ) -dimensional topological phases of matter generically support loop excitations with topological degeneracy. The loops carry "Cheshire charge": topological charge that is not the integral of a locally defined topological charge density. Cheshire charge has previously been discussed in non-Abelian gauge theories, but we show that it is a generic feature of all (3+1)-D topological phases (even those constructed from an Abelian gauge group). Indeed, Cheshire charge is closely related to nontrivial three-loop braiding. We use a dimensional reduction argument to compute the topological degeneracy of loop excitations in the (3 +1 ) -dimensional topological phases associated with Dijkgraaf-Witten gauge theories. We explicitly construct membrane operators associated with such excitations in soluble microscopic lattice models in Z2×Z2 Dijkgraaf-Witten phases and generalize this construction to arbitrary membrane-net models. We explain why these loop excitations are the objects in the braided fusion 2-category Z (2 VectGω) , thereby supporting the hypothesis that 2-categories are the correct mathematical framework for (3 +1 ) -dimensional topological phases.

t-topology on the n-dimensional Minkowski space

NASA Astrophysics Data System (ADS)

Agrawal, Gunjan; Shrivastava, Sampada

2009-05-01

In this paper, a topological study of the n-dimensional Minkowski space, n >1, with t-topology, denoted by Mt, has been carried out. This topology, unlike the usual Euclidean one, is more physically appealing being defined by means of the Lorentzian metric. It shares many topological properties with similar candidate topologies and it has the advantage of being first countable. Compact sets of Mt and continuous maps into Mt are studied using the notion of Zeno sequences besides characterizing those sets that have the same subspace topologies induced from the Euclidean and t-topologies on n-dimensional Minkowski space. A necessary and sufficient condition for a compact set in the Euclidean n-space to be compact in Mt is obtained, thereby proving that the n-cube, n >1, as a subspace of Mt, is not compact, while a segment on a timelike line is compact in Mt. This study leads to the nonsimply connectedness of Mt, for n =2. Further, Minkowski space with s-topology has also been dealt with.

Topological superconductivity in monolayer transition metal dichalcogenides.

PubMed

Hsu, Yi-Ting; Vaezi, Abolhassan; Fischer, Mark H; Kim, Eun-Ah

2017-04-11

Theoretically, it has been known that breaking spin degeneracy and effectively realizing spinless fermions is a promising path to topological superconductors. Yet, topological superconductors are rare to date. Here we propose to realize spinless fermions by splitting the spin degeneracy in momentum space. Specifically, we identify monolayer hole-doped transition metal dichalcogenide (TMD)s as candidates for topological superconductors out of such momentum-space-split spinless fermions. Although electron-doped TMDs have recently been found superconducting, the observed superconductivity is unlikely topological because of the near spin degeneracy. Meanwhile, hole-doped TMDs with momentum-space-split spinless fermions remain unexplored. Employing a renormalization group analysis, we propose that the unusual spin-valley locking in hole-doped TMDs together with repulsive interactions selectively favours two topological superconducting states: interpocket paired state with Chern number 2 and intrapocket paired state with finite pair momentum. A confirmation of our predictions will open up possibilities for manipulating topological superconductors on the device-friendly platform of monolayer TMDs.

Electronic structure of YbB 6 : Is it a topological insulator or not?

DOE PAGES

Kang, Chang -Jong; Denlinger, J. D.; Allen, J. W.; ...

2016-03-17

Here, to finally resolve the controversial issue of whether or not the electronic structure of YbB6 is nontrivially topological, we have made a combined study using angle-resolved photoemission spectroscopy (ARPES) of the nonpolar (110) surface and density functional theory (DFT). The flat-band conditions of the (110) ARPES avoid the strong band bending effects of the polar (001) surface and definitively show that YbB 6 has a topologically trivial B 2p–Yb 5d semiconductor band gap of ~0.3 eV. Accurate determination of the low energy band topology in DFT requires the use of a modified Becke-Johnson exchange potential incorporating spin-orbit coupling andmore » an on-site Yb 4f Coulomb interaction U as large as 7 eV. The DFT result, confirmed by a more precise GW band calculation, is similar to that of a small gap non-Kondo nontopological semiconductor. Additionally, the pressure-dependent electronic structure of YbB 6 is investigated theoretically and found to transform into a p–d overlap semimetal with small Yb mixed valency.« less

Modeling Natural Anti-Inflammatory Compounds by Molecular Topology

PubMed Central

Galvez-Llompart, María; Zanni, Riccardo; García-Domenech, Ramón

2011-01-01

One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with the remaining compounds (those not used in building up the model), has been carried out. Finally, a virtual screening on natural products was performed and 74 compounds showed actual anti-inflammatory activity. From them, 54 had been previously described as anti-inflammatory in the literature. This can be seen as a plus in the model validation and as a reinforcement of the role of Molecular Topology as an efficient tool for the discovery of new anti-inflammatory natural compounds. PMID:22272145

Tensor Network Wavefunctions for Topological Phases

NASA Astrophysics Data System (ADS)

Ware, Brayden Alexander

The combination of quantum effects and interactions in quantum many-body systems can result in exotic phases with fundamentally entangled ground state wavefunctions--topological phases. Topological phases come in two types, both of which will be studied in this thesis. In topologically ordered phases, the pattern of entanglement in the ground state wavefunction encodes the statistics of exotic emergent excitations, a universal indicator of a phase that is robust to all types of perturbations. In symmetry protected topological phases, the entanglement instead encodes a universal response of the system to symmetry defects, an indicator that is robust only to perturbations respecting the protecting symmetry. Finding and creating these phases in physical systems is a motivating challenge that tests all aspects--analytical, numerical, and experimental--of our understanding of the quantum many-body problem. Nearly three decades ago, the creation of simple ansatz wavefunctions--such as the Laughlin fractional quantum hall state, the AKLT state, and the resonating valence bond state--spurred analytical understanding of both the role of entanglement in topological physics and physical mechanisms by which it can arise. However, quantitative understanding of the relevant phase diagrams is still challenging. For this purpose, tensor networks provide a toolbox for systematically improving wavefunction ansatz while still capturing the relevant entanglement properties. In this thesis, we use the tools of entanglement and tensor networks to analyze ansatz states for several proposed new phases. In the first part, we study a featureless phase of bosons on the honeycomb lattice and argue that this phase can be topologically protected under any one of several distinct subsets of the crystalline lattice symmetries. We discuss methods of detecting such phases with entanglement and without. In the second part, we consider the problem of constructing fixed-point wavefunctions for

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2012 CFR

2012-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2011 CFR

2011-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2013 CFR

2013-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2010 CFR

2010-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

10 CFR 63.16 - Review of site characterization activities. 2

Code of Federal Regulations, 2014 CFR

2014-01-01

... which such activities are carried out and to observe excavations, borings, and in situ tests, as they... IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses Preapplication Review § 63.16 Review of site characterization activities. 2 2 In addition to the review of site characterization activities...

Topological transitions in continuously deformed photonic crystals

NASA Astrophysics Data System (ADS)

Zhu, Xuan; Wang, Hai-Xiao; Xu, Changqing; Lai, Yun; Jiang, Jian-Hua; John, Sajeev

2018-02-01

We demonstrate that multiple topological transitions can occur, with high sensitivity, by continuous change of the geometry of a simple two-dimensional dielectric-frame photonic crystal consisting of circular air holes. By changing the radii of the holes and/or the distance between them, multiple transitions between normal and topological photonic band gaps (PBGs) can appear. The time-reversal symmetric topological PBGs resemble the quantum spin Hall insulator of electrons and have two counterpropagating edge states. We search for optimal topological transitions, i.e., sharp transitions sensitive to the geometry, and optimal topological PBGs, i.e., large PBGs with a clean spectrum of edge states. Such optimizations reveal that dielectric-frame photonic crystals are promising for optical sensors and unidirectional waveguides.

Negative Magnetoresistance without Chiral Anomaly in Topological Insulators.

PubMed

Dai, Xin; Du, Z Z; Lu, Hai-Zhou

2017-10-20

An intriguing phenomenon in topological semimetals and topological insulators is the negative magnetoresistance (MR) observed when a magnetic field is applied along the current direction. A prevailing understanding to the negative MR in topological semimetals is the chiral anomaly, which, however, is not well defined in topological insulators. We calculate the MR of a three-dimensional topological insulator, by using the semiclassical equations of motion, in which the Berry curvature explicitly induces an anomalous velocity and orbital moment. Our theoretical results are in quantitative agreement with the experiments. The negative MR is not sensitive to temperature and increases as the Fermi energy approaches the band edge. The orbital moment and g factors also play important roles in the negative MR. Our results give a reasonable explanation to the negative MR in 3D topological insulators and will be helpful in understanding the anomalous quantum transport in topological states of matter.

Characterization of the Martian magnetic topology response to extreme solar transient events with MGS data

NASA Astrophysics Data System (ADS)

Xu, S.; Curry, S.; Mitchell, D. L.; Luhmann, J. G.; Lillis, R. J.; Dong, C.

2017-12-01

Characterizing how the solar cycle affects the physics of the Mars-solar wind interaction can improve our understanding of Mars' atmospheric evolution and the plasma environment at Mars. In particular, solar transient events such as Interplanetary Coronal Mass Ejections (ICMEs) and Stream Interaction Regions (SIRs) significantly change the solar-wind interaction, including the magnetic topology and ion acceleration. However, both the Mars Express and Mars Atmosphere Volatile EvolutioN (MAVEN) missions have encountered relatively few extreme solar transient events due to the recent low solar activity (2004-2017). In contrast, Mars Global Surveyor (MGS) was operating during a relatively active solar maximum (1999-2003). Based on new results from MAVEN, this study reanalyzes MGS data to better understand how the Martian plasma environment responds to extreme solar events. In particular, we aim to investigate how the magnetic topology during these extreme events differs from the topology during quiet times. We conduct orbit comparisons of the magnetic topology inferred from MGS electron pitch angle distributions during quiet periods and extreme events to determine how the open and closed field patterns respond to extreme events.

Topologically protected unidirectional edge spin waves

NASA Astrophysics Data System (ADS)

Wang, Xiang Rong; Wang, Xiansi; Su, Ying

Magnetic materials are highly correlated spin systems that do not respect the time-reversal symmetry. The low-energy excitations of magnetic materials are spin waves whose quanta are magnons. Like electronic materials that can be topologically nontrivial, a magnetic material can also be topologically nontrivial with topologically protected unidirectional edge states. These edge states should be superb channels of processing and manipulating spin waves because they are robust against perturbations and geometry changes, unlike the normal spin wave states that are very sensitive to the system changes and geometry. Therefore, the magnetic topological matter is of fundamental interest and technologically useful in magnonics. Here, we show that ferromagnetically interacting spins on a two-dimensional honeycomb lattice with nearest-neighbour interactions and governed by the Landau-Lifshitz-Gilbert equation, can be topologically nontrivial with gapped bulk spin waves and gapless edge spin waves. These edge spin waves are indeed very robust against defects under topological protection. Because of the unidirectional nature of these topologically protected edge spin waves, an interesting functional magnonic device called beam splitter can be made out of a domain wall in a strip. It is shown that an in-coming spin wave beam along one edge splits into two spin wave beams propagating along two opposite directions on the other edge after passing through a domain wall. This work was supported by Hong Kong GRF Grants (Nos. 163011151 and 16301816) and the Grant from NNSF of China (No. 11374249). X.S.W acknowledge support from UESTC.

Unconventional topological Hall effect in skyrmion crystals caused by the topology of the lattice

NASA Astrophysics Data System (ADS)

Göbel, Börge; Mook, Alexander; Henk, Jürgen; Mertig, Ingrid

2017-03-01

The hallmark of a skyrmion crystal (SkX) is the topological Hall effect (THE). In this article we predict and explain an unconventional behavior of the topological Hall conductivity in SkXs. In simple terms, the spin texture of the skyrmions causes an inhomogeneous emergent magnetic field whose associated Lorentz force acts on the electrons. By making the emergent field homogeneous, the THE is mapped onto the quantum Hall effect (QHE). Consequently, each electronic band of the SkX is assigned to a Landau level. This correspondence of THE and QHE allows us to explain the unconventional behavior of the THE of electrons in SkXs. For example, a skyrmion crystal on a triangular lattice exhibits a quantized topological Hall conductivity with steps of 2 .e2/h below and with steps of 1 .e2/h above the van Hove singularity. On top of this, the conductivity shows a prominent sign change at the van Hove singularity. These unconventional features are deeply connected to the topology of the structural lattice.

Entropic manifestations of topological order in three dimensions

NASA Astrophysics Data System (ADS)

Bullivant, Alex; Pachos, Jiannis K.

2016-03-01

We evaluate the entanglement entropy of exactly solvable Hamiltonians corresponding to general families of three-dimensional topological models. We show that the modification to the entropic area law due to three-dimensional topological properties is richer than the two-dimensional case. In addition to the reduction of the entropy caused by a nonzero vacuum expectation value of contractible loop operators, a topological invariant emerges that increases the entropy if the model consists of nontrivially braiding anyons. As a result the three-dimensional topological entanglement entropy provides only partial information about the two entropic topological invariants.

Reentrant topological phase transition in a bridging model between Kitaev and Haldane chains

NASA Astrophysics Data System (ADS)

Sugimoto, Takanori; Ohtsu, Mitsuyoshi; Tohyama, Takami

2017-12-01

We present a reentrant phase transition in a bridging model between two different topological models: Kitaev and Haldane chains. This model is activated by introducing a bond alternation into the Kitaev chain [A. Y. Kitaev, Phys. Usp. 44, 131 (2001), 10.1070/1063-7869/44/10S/S29]. Without the bond alternation, the finite pairing potential induces a topological state defined by the zero-energy Majorana edge mode, while finite bond alternation without the pairing potential makes a different topological state similar to the Haldane state, which is defined by the local Berry phase in the bulk. The topologically ordered state corresponds to the Su-Schrieffer-Heeger state, which is classified as the same symmetry class. We thus find a phase transition between the two topological phases with a reentrant phenomenon, and extend the phase diagram in the plane of the pairing potential and the bond alternation by using three techniques: recursive equation, fidelity, and Pfaffian. In addition, we find that the phase transition is characterized by both the change of the position of Majorana zero-energy modes from one edge to the other edge and the emergence of a string order in the bulk, and that the reentrance is based on a sublattice U(1) rotation. Consequently, our paper and model not only open a direct way to discuss the bulk and edge topologies but demonstrate an example of the reentrant topologies.

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Topology and entanglement in quench dynamics

NASA Astrophysics Data System (ADS)

Chang, Po-Yao

2018-06-01

We classify the topology of the quench dynamics by homotopy groups. A relation between the topological invariant of a postquench order parameter and the topological invariant of a static Hamiltonian is shown in d +1 dimensions (d =1 ,2 ,3 ). The midgap states in the entanglement spectrum of the postquench states reveal their topological nature. When a trivial quantum state is under a sudden quench to a Chern insulator, the midgap states in the entanglement spectrum form rings. These rings are analogous to the boundary Fermi rings in the Hopf insulators. Finally, we show a postquench order parameter in 3+1 dimensions can be characterized by the second Chern number. The number of Dirac cones in the entanglement spectrum is equal to the second Chern number.

Topological properties of a curved spacetime

NASA Astrophysics Data System (ADS)

Agrawal, Gunjan; Shrivastava, Sampada; Godani, Nisha; Sinha, Soami Pyari

2017-12-01

The present paper aims at the study of a topology on Lorentzian manifolds, defined by Göbel [4] using the ideas of Zeeman [16]. Observing that on the Minkowski space it is the same as Zeeman's time topology, it has been found that a Lorentzian manifold with this topology is path connected, nonfirst countable and nonsimply connected while the Minkowski space with time topology is, in addition nonregular and separable. Furthermore, using the notion of Zeno sequences it is obtained that a compact set does not contain a nonempty open set and that a set is compact if and only if each of its infinite subsets has a limit point if and only if each of its sequences has a convergent subsequence.

Gapless topological order, gravity, and black holes

NASA Astrophysics Data System (ADS)

Rasmussen, Alex; Jermyn, Adam S.

2018-04-01

In this work we demonstrate that linearized gravity exhibits gapless topological order with an extensive ground state degeneracy. This phenomenon is closely related both to the topological order of the pyrochlore U (1 ) spin liquid and to recent work by Hawking and co-workers, who used the soft-photon and graviton theorems to demonstrate that the vacuum in linearized gravity is not unique. We first consider lattice models whose low-energy behavior is described by electromagnetism and linearized gravity, and then argue that the topological nature of these models carries over into the continuum. We demonstrate that these models can have many ground states without making assumptions about the topology of spacetime or about the high-energy nature of the theory, and show that the infinite family of symmetries described by Hawking and co-workers is simply the different topological sectors. We argue that in this context black holes appear as topological defects in the infrared theory, and that this suggests a potential approach to understanding both the firewall paradox and information encoding in gravitational theories. Finally, we use insights from the soft-boson theorems to make connections between deconfined gauge theories with continuous gauge groups and gapless topological order.

Manipulating topological-insulator properties using quantum confinement

NASA Astrophysics Data System (ADS)

Kotulla, M.; Zülicke, U.

2017-07-01

Recent discoveries have spurred the theoretical prediction and experimental realization of novel materials that have topological properties arising from band inversion. Such topological insulators are insulating in the bulk but have conductive surface or edge states. Topological materials show various unusual physical properties and are surmised to enable the creation of exotic Majorana-fermion quasiparticles. How the signatures of topological behavior evolve when the system size is reduced is interesting from both a fundamental and an application-oriented point of view, as such understanding may form the basis for tailoring systems to be in specific topological phases. This work considers the specific case of quantum-well confinement defining two-dimensional layers. Based on the effective-Hamiltonian description of bulk topological insulators, and using a harmonic-oscillator potential as an example for a softer-than-hard-wall confinement, we have studied the interplay of band inversion and size quantization. Our model system provides a useful platform for systematic study of the transition between the normal and topological phases, including the development of band inversion and the formation of massless-Dirac-fermion surface states. The effects of bare size quantization, two-dimensional-subband mixing, and electron-hole asymmetry are disentangled and their respective physical consequences elucidated.

Hypergraph topological quantities for tagged social networks.

PubMed

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Hypergraph topological quantities for tagged social networks

NASA Astrophysics Data System (ADS)

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Role of alveolar topology on acinar flows and convective mixing.

PubMed

Hofemeier, Philipp; Sznitman, Josué

2014-06-01

Due to experimental challenges, computational simulations are often sought to quantify inhaled aerosol transport in the pulmonary acinus. Commonly, these are performed using generic alveolar topologies, including spheres, toroids, and polyhedra, to mimic the complex acinar morphology. Yet, local acinar flows and ensuing particle transport are anticipated to be influenced by the specific morphological structures. We have assessed a range of acinar models under self-similar breathing conditions with respect to alveolar flow patterns, convective flow mixing, and deposition of fine particles (1.3 μm diameter). By tracking passive tracers over cumulative breathing cycles, we find that irreversible flow mixing correlates with the location and strength of the recirculating vortex inside the cavity. Such effects are strongest in proximal acinar generations where the ratio of alveolar to ductal flow rates is low and interalveolar disparities are most apparent. Our results for multi-alveolated acinar ducts highlight that fine 1 μm inhaled particles subject to alveolar flows are sensitive to the alveolar topology, underlining interalveolar disparities in particle deposition patterns. Despite the simplicity of the acinar models investigated, our findings suggest that alveolar topologies influence more significantly local flow patterns and deposition sites of fine particles for upper generations emphasizing the importance of the selected acinar model. In distal acinar generations, however, the alveolar geometry primarily needs to mimic the space-filling alveolar arrangement dictated by lung morphology.

Topology of Neutral Hydrogen within the Small Magellanic Cloud

NASA Astrophysics Data System (ADS)

Chepurnov, A.; Gordon, J.; Lazarian, A.; Stanimirovic, S.

2008-12-01

In this paper, genus statistics have been applied to an H I column density map of the Small Magellanic Cloud in order to study its topology. To learn how topology changes with the scale of the system, we provide topology studies for column density maps at varying resolutions. To evaluate the statistical error of the genus, we randomly reassign the phases of the Fourier modes while keeping the amplitudes. We find that at the smallest scales studied (40 pc <= λ <= 80 pc), the genus shift is negative in all regions, implying a clump topology. At the larger scales (110 pc <= λ <= 250 pc), the topology shift is detected to be negative (a "meatball" topology) in four cases and positive (a "swiss cheese" topology) in two cases. In four regions, there is no statistically significant topology shift at large scales.

Superconductivity bordering Rashba type topological transition

DOE PAGES

Jin, M. L.; Sun, F.; Xing, L. Y.; ...

2017-01-04

Strong spin orbital interaction (SOI) can induce unique quantum phenomena such as topological insulators, the Rashba effect, or p-wave superconductivity. Combining these three quantum phenomena into a single compound has important scientific implications. Here we report experimental observations of consecutive quantum phase transitions from a Rashba type topological trivial phase to topological insulator state then further proceeding to superconductivity in a SOI compound BiTeI tuned via pressures. The electrical resistivity measurement with V shape change signals the transition from a Rashba type topological trivial to a topological insulator phase at 2 GPa, which is caused by an energy gap closemore » then reopen with band inverse. Superconducting transition appears at 8 GPa with a critical temperature T C of 5.3 K. Structure refinements indicate that the consecutive phase transitions are correlated to the changes in the Bi–Te bond and bond angle as function of pressures. As a result, the Hall Effect measurements reveal an intimate relationship between superconductivity and the unusual change in carrier density that points to possible unconventional superconductivity.« less

Resting-State Network Topology Differentiates Task Signals across the Adult Life Span.

PubMed

Chan, Micaela Y; Alhazmi, Fahd H; Park, Denise C; Savalia, Neil K; Wig, Gagan S

2017-03-08

Brain network connectivity differs across individuals. For example, older adults exhibit less segregated resting-state subnetworks relative to younger adults (Chan et al., 2014). It has been hypothesized that individual differences in network connectivity impact the recruitment of brain areas during task execution. While recent studies have described the spatial overlap between resting-state functional correlation (RSFC) subnetworks and task-evoked activity, it is unclear whether individual variations in the connectivity pattern of a brain area (topology) relates to its activity during task execution. We report data from 238 cognitively normal participants (humans), sampled across the adult life span (20-89 years), to reveal that RSFC-based network organization systematically relates to the recruitment of brain areas across two functionally distinct tasks (visual and semantic). The functional activity of brain areas (network nodes) were characterized according to their patterns of RSFC: nodes with relatively greater connections to nodes in their own functional system ("non-connector" nodes) exhibited greater activity than nodes with relatively greater connections to nodes in other systems ("connector" nodes). This "activation selectivity" was specific to those brain systems that were central to each of the tasks. Increasing age was accompanied by less differentiated network topology and a corresponding reduction in activation selectivity (or differentiation) across relevant network nodes. The results provide evidence that connectional topology of brain areas quantified at rest relates to the functional activity of those areas during task. Based on these findings, we propose a novel network-based theory for previous reports of the "dedifferentiation" in brain activity observed in aging. SIGNIFICANCE STATEMENT Similar to other real-world networks, the organization of brain networks impacts their function. As brain network connectivity patterns differ across

Learning neural connectivity from firing activity: efficient algorithms with provable guarantees on topology.

PubMed

Karbasi, Amin; Salavati, Amir Hesam; Vetterli, Martin

2018-04-01

The connectivity of a neuronal network has a major effect on its functionality and role. It is generally believed that the complex network structure of the brain provides a physiological basis for information processing. Therefore, identifying the network's topology has received a lot of attentions in neuroscience and has been the center of many research initiatives such as Human Connectome Project. Nevertheless, direct and invasive approaches that slice and observe the neural tissue have proven to be time consuming, complex and costly. As a result, the inverse methods that utilize firing activity of neurons in order to identify the (functional) connections have gained momentum recently, especially in light of rapid advances in recording technologies; It will soon be possible to simultaneously monitor the activities of tens of thousands of neurons in real time. While there are a number of excellent approaches that aim to identify the functional connections from firing activities, the scalability of the proposed techniques plays a major challenge in applying them on large-scale datasets of recorded firing activities. In exceptional cases where scalability has not been an issue, the theoretical performance guarantees are usually limited to a specific family of neurons or the type of firing activities. In this paper, we formulate the neural network reconstruction as an instance of a graph learning problem, where we observe the behavior of nodes/neurons (i.e., firing activities) and aim to find the links/connections. We develop a scalable learning mechanism and derive the conditions under which the estimated graph for a network of Leaky Integrate and Fire (LIf) neurons matches the true underlying synaptic connections. We then validate the performance of the algorithm using artificially generated data (for benchmarking) and real data recorded from multiple hippocampal areas in rats.

Accurate Classification of RNA Structures Using Topological Fingerprints

PubMed Central

Li, Kejie; Gribskov, Michael

2016-01-01

While RNAs are well known to possess complex structures, functionally similar RNAs often have little sequence similarity. While the exact size and spacing of base-paired regions vary, functionally similar RNAs have pronounced similarity in the arrangement, or topology, of base-paired stems. Furthermore, predicted RNA structures often lack pseudoknots (a crucial aspect of biological activity), and are only partially correct, or incomplete. A topological approach addresses all of these difficulties. In this work we describe each RNA structure as a graph that can be converted to a topological spectrum (RNA fingerprint). The set of subgraphs in an RNA structure, its RNA fingerprint, can be compared with the fingerprints of other RNA structures to identify and correctly classify functionally related RNAs. Topologically similar RNAs can be identified even when a large fraction, up to 30%, of the stems are omitted, indicating that highly accurate structures are not necessary. We investigate the performance of the RNA fingerprint approach on a set of eight highly curated RNA families, with diverse sizes and functions, containing pseudoknots, and with little sequence similarity–an especially difficult test set. In spite of the difficult test set, the RNA fingerprint approach is very successful (ROC AUC > 0.95). Due to the inclusion of pseudoknots, the RNA fingerprint approach both covers a wider range of possible structures than methods based only on secondary structure, and its tolerance for incomplete structures suggests that it can be applied even to predicted structures. Source code is freely available at https://github.rcac.purdue.edu/mgribsko/XIOS_RNA_fingerprint. PMID:27755571

Computer simulation of the active site of human serum cholinesterase

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

Kefang Jiao; Song Li; Zhengzheng Lu

1996-12-31

The first 3D-structure of acetylchelinesterase from Torpedo California electric organ (T.AChE) was published by JL. Sussman in 1991. We have simulated 3D-structure of human serum cholinesterase (H.BuChE) and the active site of H.BuChE. It is discovered by experiment that the residue of H.BuChE is still active site after a part of H.BuChE is cut. For example, the part of 21KD + 20KD is active site of H.BuChE. The 20KD as it is. Studies on these peptides by Hemelogy indicate that two active peptides have same negative electrostatic potential maps diagram. These negative electrostatic areas attached by acetyl choline with positivemore » electrostatic potency. We predict that 147...236 peptide of AChE could be active site because it was as 20KD as with negative electrostatic potential maps. We look forward to proving from other ones.« less

Algebraic Topology of Multi-Brain Connectivity Networks Reveals Dissimilarity in Functional Patterns during Spoken Communications

PubMed Central

Tadić, Bosiljka; Andjelković, Miroslav; Boshkoska, Biljana Mileva; Levnajić, Zoran

2016-01-01

Human behaviour in various circumstances mirrors the corresponding brain connectivity patterns, which are suitably represented by functional brain networks. While the objective analysis of these networks by graph theory tools deepened our understanding of brain functions, the multi-brain structures and connections underlying human social behaviour remain largely unexplored. In this study, we analyse the aggregate graph that maps coordination of EEG signals previously recorded during spoken communications in two groups of six listeners and two speakers. Applying an innovative approach based on the algebraic topology of graphs, we analyse higher-order topological complexes consisting of mutually interwoven cliques of a high order to which the identified functional connections organise. Our results reveal that the topological quantifiers provide new suitable measures for differences in the brain activity patterns and inter-brain synchronisation between speakers and listeners. Moreover, the higher topological complexity correlates with the listener’s concentration to the story, confirmed by self-rating, and closeness to the speaker’s brain activity pattern, which is measured by network-to-network distance. The connectivity structures of the frontal and parietal lobe consistently constitute distinct clusters, which extend across the listener’s group. Formally, the topology quantifiers of the multi-brain communities exceed the sum of those of the participating individuals and also reflect the listener’s rated attributes of the speaker and the narrated subject. In the broader context, the presented study exposes the relevance of higher topological structures (besides standard graph measures) for characterising functional brain networks under different stimuli. PMID:27880802

Exotic Lifshitz transitions in topological materials

NASA Astrophysics Data System (ADS)

Volovik, G. E.

2018-01-01

Topological Lifshitz transitions involve many types of topological structures in momentum and frequency-momentum spaces, such as Fermi surfaces, Dirac lines, Dirac and Weyl points, etc., each of which has its own stability-supporting topological invariant ( N_1, N_2, N_3, {\\tilde N}_3, etc.). The topology of the shape of Fermi surfaces and Dirac lines and the interconnection of objects of different dimensionalities produce a variety of Lifshitz transition classes. Lifshitz transitions have important implications for many areas of physics. To give examples, transition-related singularities can increase the superconducting transition temperature; Lifshitz transitions are the possible origin of the small masses of elementary particles in our Universe, and a black hole horizon serves as the surface of the Lifshitz transition between vacua with type-I and type-II Weyl points.

Spintronics device made of topological materials

NASA Astrophysics Data System (ADS)

Wu, Jiansheng; Shi, Zhangsheng; Wang, Maoji

Topological Materials is a new state of matter of which the bulk states are gapped insulator or superconductor while the surface states are gapless metallic states. Such surface states are robust against local disorder and impurities due to its nontrivial topology. It induces unusual transport properties and shows nontrivial topological spin texture in real space. We have made use of these two exotic properties to make application in spintronics. For example, we propose to make spin-filter transistor using of 1D or 2D quantum anomalous Hall insulator or 2D topological Weyl semimetal, we also propose a device to measure the spin-polarization of current, a device to generate entangled entangled electron pairs. Startup funds of SUSTC, Shenzhen Peacock Plan, Shenzhen Free Exploration Plan with Grant Number JCYJ20150630145302225.

Topological protection of multiparticle dissipative transport

NASA Astrophysics Data System (ADS)

Loehr, Johannes; Loenne, Michael; Ernst, Adrian; de Las Heras, Daniel; Fischer, Thomas M.

2016-06-01

Topological protection allows robust transport of localized phenomena such as quantum information, solitons and dislocations. The transport can be either dissipative or non-dissipative. Here, we experimentally demonstrate and theoretically explain the topologically protected dissipative motion of colloidal particles above a periodic hexagonal magnetic pattern. By driving the system with periodic modulation loops of an external and spatially homogeneous magnetic field, we achieve total control over the motion of diamagnetic and paramagnetic colloids. We can transport simultaneously and independently each type of colloid along any of the six crystallographic directions of the pattern via adiabatic or deterministic ratchet motion. Both types of motion are topologically protected. As an application, we implement an automatic topologically protected quality control of a chemical reaction between functionalized colloids. Our results are relevant to other systems with the same symmetry.

Topological Semimetals Studied by Ab Initio Calculations

NASA Astrophysics Data System (ADS)

Hirayama, Motoaki; Okugawa, Ryo; Murakami, Shuichi

2018-04-01

In topological semimetals such as Weyl, Dirac, and nodal-line semimetals, the band gap closes at points or along lines in k space which are not necessarily located at high-symmetry positions in the Brillouin zone. Therefore, it is not straightforward to find these topological semimetals by ab initio calculations because the band structure is usually calculated only along high-symmetry lines. In this paper, we review recent studies on topological semimetals by ab initio calculations. We explain theoretical frameworks which can be used for the search for topological semimetal materials, and some numerical methods used in the ab initio calculations.

Trivial topological phase of CaAgP and the topological nodal-line transition in CaAg (P1 -xA sx)

NASA Astrophysics Data System (ADS)

Xu, N.; Qian, Y. T.; Wu, Q. S.; Autès, G.; Matt, C. E.; Lv, B. Q.; Yao, M. Y.; Strocov, V. N.; Pomjakushina, E.; Conder, K.; Plumb, N. C.; Radovic, M.; Yazyev, O. V.; Qian, T.; Ding, H.; Mesot, J.; Shi, M.

2018-04-01

By performing angle-resolved photoemission spectroscopy and first-principles calculations, we address the topological phase of CaAgP and investigate the topological phase transition in CaAg (P1 -xA sx) . We reveal that in CaAgP, the bulk band gap and surface states with a large bandwidth are topologically trivial, in agreement with hybrid density functional theory calculations. The calculations also indicate that application of "negative" hydrostatic pressure can transform trivial semiconducting CaAgP into an ideal topological nodal-line semimetal phase. The topological transition can be realized by partial isovalent P/As substitution at x =0.38 .

Topological superconductivity in an ultrathin, magnetically-doped topological insulator proximity coupled to a conventional superconductor

NASA Astrophysics Data System (ADS)

Kim, Youngseok; Philip, Timothy M.; Park, Moon Jip; Gilbert, Matthew J.

2016-12-01

As a promising candidate system to realize topological superconductivity, the system of a 3D topological insulator (TI) grown on top of the s -wave superconductor has been extensively studied. To access the topological superconductivity experimentally, the 3D TI sample must be thin enough to allow for Cooper pair tunneling to the exposed surface of TI. The use of magnetically ordered dopants to break time-reversal symmetry may allow the surface of a TI to host Majorana fermion, which are believed to be a signature of topological superconductivity. In this work, we study a magnetically-doped thin film TI-superconductor hybrid system. Considering the proximity induced order parameter in thin film of TI, we analyze the gap closing points of the Hamiltonian and draw the phase diagram as a function of relevant parameters: the hybridization gap, Zeeman energy, and chemical potential of the TI system. Our findings provide a useful guide in choosing relevant parameters to facilitate the observation of topological superconductivity in thin film TI-superconductor hybrid systems. In addition, we further perform numerical analysis on a TI proximity coupled to an s -wave superconductor and find that, due to the spin-momentum locked nature of the surface states in TI, the induced s -wave order parameter of the surface states persists even at large magnitude of the Zeeman energy.

Valley Topological Phases in Bilayer Sonic Crystals

NASA Astrophysics Data System (ADS)

Lu, Jiuyang; Qiu, Chunyin; Deng, Weiyin; Huang, Xueqin; Li, Feng; Zhang, Fan; Chen, Shuqi; Liu, Zhengyou

2018-03-01

Recently, the topological physics in artificial crystals for classical waves has become an emerging research area. In this Letter, we propose a unique bilayer design of sonic crystals that are constructed by two layers of coupled hexagonal array of triangular scatterers. Assisted by the additional layer degree of freedom, a rich topological phase diagram is achieved by simply rotating scatterers in both layers. Under a unified theoretical framework, two kinds of valley-projected topological acoustic insulators are distinguished analytically, i.e., the layer-mixed and layer-polarized topological valley Hall phases, respectively. The theory is evidently confirmed by our numerical and experimental observations of the nontrivial edge states that propagate along the interfaces separating different topological phases. Various applications such as sound communications in integrated devices can be anticipated by the intriguing acoustic edge states enriched by the layer information.

De novo active sites for resurrected Precambrian enzymes

NASA Astrophysics Data System (ADS)

Risso, Valeria A.; Martinez-Rodriguez, Sergio; Candel, Adela M.; Krüger, Dennis M.; Pantoja-Uceda, David; Ortega-Muñoz, Mariano; Santoyo-Gonzalez, Francisco; Gaucher, Eric A.; Kamerlin, Shina C. L.; Bruix, Marta; Gavira, Jose A.; Sanchez-Ruiz, Jose M.

2017-07-01

Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.

Adventures in Topological Field Theory

NASA Astrophysics Data System (ADS)

Horne, James H.

1990-01-01

This thesis consists of 5 parts. In part I, the topological Yang-Mills theory and the topological sigma model are presented in a superspace formulation. This greatly simplifies the field content of the theories, and makes the Q-invariance more obvious. The Feynman rules for the topological Yang -Mills theory are derived. We calculate the one-loop beta-functions of the topological sigma model in superspace. The lattice version of these theories is presented. The self-duality constraints of both models lead to spectrum doubling. In part II, we show that conformally invariant gravity in three dimensions is equivalent to the Yang-Mills gauge theory of the conformal group in three dimensions, with a Chern-Simons action. This means that conformal gravity is finite and exactly soluble. In part III, we derive the skein relations for the fundamental representations of SO(N), Sp(2n), Su(m| n), and OSp(m| 2n). These relations can be used recursively to calculate the expectation values of Wilson lines in three-dimensional Chern-Simons gauge theory with these gauge groups. A combination of braiding and tying of Wilson lines completely describes the skein relations. In part IV, we show that the k = 1 two dimensional gravity amplitudes at genus 3 agree precisely with the results from intersection theory on moduli space. Predictions for the genus 4 intersection numbers follow from the two dimensional gravity theory. In part V, we discuss the partition function in two dimensional gravity. For the one matrix model at genus 2, we use the partition function to derive a recursion relation. We show that the k = 1 amplitudes completely determine the partition function at arbitrary genus. We present a conjecture for the partition function for the arbitrary topological field theory coupled to topological gravity.

Topology of AspT, the aspartate:alanine antiporter of Tetragenococcus halophilus, determined by site-directed fluorescence labeling.

PubMed

Nanatani, Kei; Fujiki, Takashi; Kanou, Kazuhiko; Takeda-Shitaka, Mayuko; Umeyama, Hideaki; Ye, Liwen; Wang, Xicheng; Nakajima, Tasuku; Uchida, Takafumi; Maloney, Peter C; Abe, Keietsu

2007-10-01

The gram-positive lactic acid bacterium Tetragenococcus halophilus catalyzes the decarboxylation of L-aspartate (Asp) with release of L-alanine (Ala) and CO(2). The decarboxylation reaction consists of two steps: electrogenic exchange of Asp for Ala catalyzed by an aspartate:alanine antiporter (AspT) and intracellular decarboxylation of the transported Asp catalyzed by an L-aspartate-beta-decarboxylase (AspD). AspT belongs to the newly classified aspartate:alanine exchanger family (transporter classification no. 2.A.81) of transporters. In this study, we were interested in the relationship between the structure and function of AspT and thus analyzed the topology by means of the substituted-cysteine accessibility method using the impermeant, fluorescent, thiol-specific probe Oregon Green 488 maleimide (OGM) and the impermeant, nonfluorescent, thiol-specific probe [2-(trimethylammonium)ethyl]methanethiosulfonate bromide. We generated 23 single-cysteine variants from a six-histidine-tagged cysteineless AspT template. A cysteine position was assigned an external location if the corresponding single-cysteine variant reacted with OGM added to intact cells, and a position was assigned an internal location if OGM labeling required cell lysis. The topology analyses revealed that AspT has a unique topology; the protein has 10 transmembrane helices (TMs), a large hydrophilic cytoplasmic loop (about 180 amino acids) between TM5 and TM6, N and C termini that face the periplasm, and a positively charged residue (arginine 76) within TM3. Moreover, the three-dimensional structure constructed by means of the full automatic modeling system indicates that the large hydrophilic cytoplasmic loop of AspT possesses a TrkA_C domain and a TrkA_C-like domain and that the three-dimensional structures of these domains are similar to each other even though their amino acid sequences show low similarity.

Phantom stars and topology change

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

DeBenedictis, Andrew; Garattini, Remo; Lobo, Francisco S. N.

2008-11-15

In this work, we consider time-dependent dark-energy star models, with an evolving parameter {omega} crossing the phantom divide {omega}=-1. Once in the phantom regime, the null energy condition is violated, which physically implies that the negative radial pressure exceeds the energy density. Therefore, an enormous negative pressure in the center may, in principle, imply a topology change, consequently opening up a tunnel and converting the dark-energy star into a wormhole. The criteria for this topology change are discussed and, in particular, we consider a Casimir energy approach involving quasilocal energy difference calculations that may reflect or measure the occurrence ofmore » a topology change. We denote these exotic geometries consisting of dark-energy stars (in the phantom regime) and phantom wormholes as phantom stars. The final product of this topological change, namely, phantom wormholes, have far-reaching physical and cosmological implications, as in addition to being used for interstellar shortcuts, an absurdly advanced civilization may manipulate these geometries to induce closed timelike curves, consequently violating causality.« less

Topological Crystalline Superconductivity in Locally Noncentrosymmetric Multilayer Superconductors

NASA Astrophysics Data System (ADS)

Yoshida, Tomohiro; Sigrist, Manfred; Yanase, Youichi

2015-07-01

Topological crystalline superconductivity in locally noncentrosymmetric multilayer superconductors (SCs) is proposed. We study the odd-parity pair-density wave (PDW) state induced by the spin-singlet pairing interaction through the spin-orbit coupling. It is shown that the PDW state is a topological crystalline SC protected by a mirror symmetry, although it is topologically trivial according to the classification based on the standard topological periodic table. The topological property of the mirror subsectors is intuitively explained by adiabatically changing the Bogoliubov-de Gennes Hamiltonian. A subsector of the bilayer PDW state reduces to the two-dimensional noncentrosymmetric SC, while a subsector of the trilayer PDW state is topologically equivalent to the spinless p -wave SC. Chiral Majorana edge modes in trilayers can be realized without Cooper pairs in the spin-triplet channel and chemical potential tuning.

Disorder-Induced Topological State Transition in Photonic Metamaterials

NASA Astrophysics Data System (ADS)

Liu, Changxu; Gao, Wenlong; Yang, Biao; Zhang, Shuang

2017-11-01

The topological state transition has been widely studied based on the quantized topological band invariant such as the Chern number for the system without intense randomness that may break the band structures. We numerically demonstrate the disorder-induced state transition in the photonic topological systems for the first time. Instead of applying the ill-defined topological band invariant in a disordered system, we utilize an empirical parameter to unambiguously illustrate the state transition of the topological metamaterials. Before the state transition, we observe a robust surface state with well-confined electromagnetic waves propagating unidirectionally, immune to the disorder from permittivity fluctuation up to 60% of the original value. During the transition, a hybrid state composed of a quasiunidirectional surface mode and intensively localized hot spots is established, a result of the competition between the topological protection and Anderson localization.

Topological Crystalline Superconductivity in Locally Noncentrosymmetric Multilayer Superconductors.

PubMed

Yoshida, Tomohiro; Sigrist, Manfred; Yanase, Youichi

2015-07-10

Topological crystalline superconductivity in locally noncentrosymmetric multilayer superconductors (SCs) is proposed. We study the odd-parity pair-density wave (PDW) state induced by the spin-singlet pairing interaction through the spin-orbit coupling. It is shown that the PDW state is a topological crystalline SC protected by a mirror symmetry, although it is topologically trivial according to the classification based on the standard topological periodic table. The topological property of the mirror subsectors is intuitively explained by adiabatically changing the Bogoliubov-de Gennes Hamiltonian. A subsector of the bilayer PDW state reduces to the two-dimensional noncentrosymmetric SC, while a subsector of the trilayer PDW state is topologically equivalent to the spinless p-wave SC. Chiral Majorana edge modes in trilayers can be realized without Cooper pairs in the spin-triplet channel and chemical potential tuning.

Irrational Charge from Topological Order

NASA Astrophysics Data System (ADS)

Moessner, R.; Sondhi, S. L.

2010-10-01

Topological or deconfined phases of matter exhibit emergent gauge fields and quasiparticles that carry a corresponding gauge charge. In systems with an intrinsic conserved U(1) charge, such as all electronic systems where the Coulombic charge plays this role, these quasiparticles are also characterized by their intrinsic charge. We show that one can take advantage of the topological order fairly generally to produce periodic Hamiltonians which endow the quasiparticles with continuously variable, generically irrational, intrinsic charges. Examples include various topologically ordered lattice models, the three-dimensional resonating valence bond liquid on bipartite lattices as well as water and spin ice. By contrast, the gauge charges of the quasiparticles retain their quantized values.

Aeroelastic Wingbox Stiffener Topology Optimization

NASA Technical Reports Server (NTRS)

Stanford, Bret K.

2017-01-01

This work considers an aeroelastic wingbox model seeded with run-out blade stiffeners along the skins. Topology optimization is conducted within the shell webs of the stiffeners, in order to add cutouts and holes for mass reduction. This optimization is done with a global-local approach in order to moderate the computational cost: aeroelastic loads are computed at the wing-level, but the topology and sizing optimization is conducted at the panel-level. Each panel is optimized separately under stress, buckling, and adjacency constraints, and periodically reassembled to update the trimmed aeroelastic loads. The resulting topology is baselined against a design with standard full-depth solid stiffener blades, and found to weigh 7.43% less.

Structural topology optimization with fuzzy constraint

NASA Astrophysics Data System (ADS)

Rosko, Peter

2011-12-01

The paper deals with the structural topology optimization with fuzzy constraint. The optimal topology of structure is defined as a material distribution problem. The objective is the weight of the structure. The multifrequency dynamic loading is considered. The optimal topology design of the structure has to eliminate the danger of the resonance vibration. The uncertainty of the loading is defined with help of fuzzy loading. Special fuzzy constraint is created from exciting frequencies. Presented study is applicable in engineering and civil engineering. Example demonstrates the presented theory.

The Topology of Three-Dimensional Symmetric Tensor Fields

NASA Technical Reports Server (NTRS)

Lavin, Yingmei; Levy, Yuval; Hesselink, Lambertus

1994-01-01

We study the topology of 3-D symmetric tensor fields. The goal is to represent their complex structure by a simple set of carefully chosen points and lines analogous to vector field topology. The basic constituents of tensor topology are the degenerate points, or points where eigenvalues are equal to each other. First, we introduce a new method for locating 3-D degenerate points. We then extract the topological skeletons of the eigenvector fields and use them for a compact, comprehensive description of the tensor field. Finally, we demonstrate the use of tensor field topology for the interpretation of the two-force Boussinesq problem.

Molecular dynamics explorations of active site structure in designed and evolved enzymes.

PubMed

Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

2015-04-21

This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

Surface conduction of topological Dirac electrons in bulk insulating Bi2Se3

NASA Astrophysics Data System (ADS)

Fuhrer, Michael

2013-03-01

The three dimensional strong topological insulator (STI) is a new phase of electronic matter which is distinct from ordinary insulators in that it supports on its surface a conducting two-dimensional surface state whose existence is guaranteed by topology. I will discuss experiments on the STI material Bi2Se3, which has a bulk bandgap of 300 meV, much greater than room temperature, and a single topological surface state with a massless Dirac dispersion. Field effect transistors consisting of thin (3-20 nm) Bi2Se3 are fabricated from mechanically exfoliated from single crystals, and electrochemical and/or chemical gating methods are used to move the Fermi energy into the bulk bandgap, revealing the ambipolar gapless nature of transport in the Bi2Se3 surface states. The minimum conductivity of the topological surface state is understood within the self-consistent theory of Dirac electrons in the presence of charged impurities. The intrinsic finite-temperature resistivity of the topological surface state due to electron-acoustic phonon scattering is measured to be ~60 times larger than that of graphene largely due to the smaller Fermi and sound velocities in Bi2Se3, which will have implications for topological electronic devices operating at room temperature. As samples are made thinner, coherent coupling of the top and bottom topological surfaces is observed through the magnitude of the weak anti-localization correction to the conductivity, and, in the thinnest Bi2Se3 samples (~ 3 nm), in thermally-activated conductivity reflecting the opening of a bandgap.

Relocating the Active-Site Lysine in Rhodopsin: 2. Evolutionary Intermediates.

PubMed

Devine, Erin L; Theobald, Douglas L; Oprian, Daniel D

2016-08-30

The visual pigment rhodopsin is a G protein-coupled receptor that covalently binds its retinal chromophore via a Schiff base linkage to an active-site Lys residue in the seventh transmembrane helix. Although this residue is strictly conserved among all type II retinylidene proteins, we found previously that the active-site Lys in bovine rhodopsin (Lys296) can be moved to three other locations (G90K, T94K, S186K) while retaining the ability to form a pigment with retinal and to activate transducin in a light-dependent manner [ Devine et al. ( 2013 ) Proc. Natl. Acad. Sci. USA 110 , 13351 - 13355 ]. Because the active-site Lys is not functionally constrained to be in helix seven, it is possible that it could relocate within the protein, most likely via an evolutionary intermediate with two active-site Lys. Therefore, in this study we characterized potential evolutionary intermediates with two Lys in the active site. Four mutant rhodopsins were prepared in which the original Lys296 was left untouched and a second Lys residue was substituted for G90K, T94K, S186K, or F293K. All four constructs covalently bind 11-cis-retinal, form a pigment, and activate transducin in a light-dependent manner. These results demonstrate that rhodopsin can tolerate a second Lys in the retinal binding pocket and suggest that an evolutionary intermediate with two Lys could allow migration of the Schiff base Lys to a position other than the observed, highly conserved location in the seventh TM helix. From sequence-based searches, we identified two groups of natural opsins, insect UV cones and neuropsins, that contain Lys residues at two positions in their active sites and also have intriguing spectral similarities to the mutant rhodopsins studied here.

Topological nanophononic states by band inversion

NASA Astrophysics Data System (ADS)

Esmann, Martin; Lamberti, Fabrice Roland; Senellart, Pascale; Favero, Ivan; Krebs, Olivier; Lanco, Loïc; Gomez Carbonell, Carmen; Lemaître, Aristide; Lanzillotti-Kimura, Norberto Daniel

2018-04-01

Nanophononics is essential for the engineering of thermal transport in nanostructured electronic devices, it greatly facilitates the manipulation of mechanical resonators in the quantum regime, and it could unveil a new route in quantum communications using phonons as carriers of information. Acoustic phonons also constitute a versatile platform for the study of fundamental wave dynamics, including Bloch oscillations, Wannier-Stark ladders, and other localization phenomena. Many of the phenomena studied in nanophononics were inspired by their counterparts in optics and electronics. In these fields, the consideration of topological invariants to control wave dynamics has already had a great impact for the generation of robust confined states. Interestingly, the use of topological phases to engineer nanophononic devices remains an unexplored and promising field. Conversely, the use of acoustic phonons could constitute a rich platform to study topological states. Here, we introduce the concept of topological invariants to nanophononics and experimentally implement a nanophononic system supporting a robust topological interface state at 350 GHz. The state is constructed through band inversion, i.e., by concatenating two semiconductor superlattices with inverted spatial mode symmetries. The existence of this state is purely determined by the Zak phases of the constituent superlattices, i.e., the one-dimensional Berry phase. We experimentally evidenced the mode through Raman spectroscopy. The reported robust topological interface states could become part of nanophononic devices requiring resonant structures such as sensors or phonon lasers.

Relativistic Heliospheric Electrons - Source, Energization and Magnetic Topology

NASA Astrophysics Data System (ADS)

Roth, Ilan

2010-05-01

Relativistic Solar Electrons are observed in conjunction with flares or coronal mass ejections (CMEs), however their origin, energization and the underlying topology seem elusive. The existence of non-thermal electrons in the solar atmosphere and along the heliospheric field lines is deduced through emission of electromagnetic waves and via direct in situ measurements. Magnetic reconnection at the flare sites may result in short term fluxes of energetic electrons, however it cannot explain the long-term relativistic fluxes as observed at 1 AU. In contrast to ions, electrons are not observed with MeV energies at the propagating CME shock. Their spectral shapes and the relative timing with respect to imaging and spectrographic observations may identify potential acceleration topology and processes controlling the formation of the (delayed with respect to a timing of a flare or initiation of CME) relativistic electrons. It is conjectured that the acceleration occurs along the stretched, closed coronal field lines, when an anisotropic seed population of low-energy electrons is injected in conjunction with the high frequency coronal radio bursts behind the large CME, as recorded by radioheliographs. This topology allows sufficient time for incubation of the accelerated electrons while the energization proceeds as a bootstrap process due to resonant interaction with oblique whistler waves, which are excited by the seed electrons. The flare serves mainly as a time reference for the electromagnetic emissions, while the CME subsequently opens an access for the relativistic electrons to the interplanetary medium. Power-laws of the energetic electron distributions are shown to be due to statistical interaction allowing discerning of the processes, which result in the observed non-Gaussian distributions, as well as time scales of their evolution.

Topological entanglement entropy of fracton stabilizer codes

NASA Astrophysics Data System (ADS)

Ma, Han; Schmitz, A. T.; Parameswaran, S. A.; Hermele, Michael; Nandkishore, Rahul M.

2018-03-01

Entanglement entropy provides a powerful characterization of two-dimensional gapped topological phases of quantum matter, intimately tied to their description by topological quantum field theories (TQFTs). Fracton topological orders are three-dimensional gapped topologically ordered states of matter that lack a TQFT description. We show that three-dimensional fracton phases are nevertheless characterized, at least partially, by universal structure in the entanglement entropy of their ground-state wave functions. We explicitly compute the entanglement entropy for two archetypal fracton models, the "X-cube model" and "Haah's code," and demonstrate the existence of a nonlocal contribution that scales linearly in subsystem size. We show via Schrieffer-Wolff transformations that this piece of the entanglement entropy of fracton models is robust against arbitrary local perturbations of the Hamiltonian. Finally, we argue that these results may be extended to characterize localization-protected fracton topological order in excited states of disordered fracton models.

Topology optimisation for natural convection problems

NASA Astrophysics Data System (ADS)

Alexandersen, Joe; Aage, Niels; Andreasen, Casper Schousboe; Sigmund, Ole

2014-12-01

This paper demonstrates the application of the density-based topology optimisation approach for the design of heat sinks and micropumps based on natural convection effects. The problems are modelled under the assumptions of steady-state laminar flow using the incompressible Navier-Stokes equations coupled to the convection-diffusion equation through the Boussinesq approximation. In order to facilitate topology optimisation, the Brinkman approach is taken to penalise velocities inside the solid domain and the effective thermal conductivity is interpolated in order to accommodate differences in thermal conductivity of the solid and fluid phases. The governing equations are discretised using stabilised finite elements and topology optimisation is performed for two different problems using discrete adjoint sensitivity analysis. The study shows that topology optimisation is a viable approach for designing heat sink geometries cooled by natural convection and micropumps powered by natural convection.

Space-time topology and quantum gravity.

NASA Astrophysics Data System (ADS)

Friedman, J. L.

Characteristic features are discussed of a theory of quantum gravity that allows space-time with a non-Euclidean topology. The review begins with a summary of the manifolds that can occur as classical vacuum space-times and as space-times with positive energy. Local structures with non-Euclidean topology - topological geons - collapse, and one may conjecture that in asymptotically flat space-times non-Euclidean topology is hiden from view. In the quantum theory, large diffeos can act nontrivially on the space of states, leading to state vectors that transform as representations of the corresponding symmetry group π0(Diff). In particular, in a quantum theory that, at energies E < EPlanck, is a theory of the metric alone, there appear to be ground states with half-integral spin, and in higher-dimensional gravity, with the kinematical quantum numbers of fundamental fermions.

On the topology of flux transfer events

NASA Technical Reports Server (NTRS)

Hesse, Michael; Birn, Joachim; Schindler, Karl

1990-01-01

A topological analysis is made of a simple model magnetic field of a perturbation at the magnetopause that shares magnetic properties with flux transfer events. The aim is to clarify a number of topological aspects that arise in the case of fully three-dimensional magnetic fields. It is shown that a localized perturbation at the magnetopause can in principle open a closed magnetosphere by establishing magnetic connections across the magnetopause by the formation of a ropelike magnetic field structure. For this purpose a global topological model of a closed magnetosphere is considered as the unperturbed state. The topological substructure of the model flux rope is discussed in detail.

Topological Spin Glass in Diluted Spin Ice

NASA Astrophysics Data System (ADS)

Sen, Arnab; Moessner, R.

2015-06-01

It is a salient experimental fact that a large fraction of candidate spin liquid materials freeze as the temperature is lowered. The question naturally arises whether such freezing is intrinsic to the spin liquid ("disorder-free glassiness") or extrinsic, in the sense that a topological phase simply coexists with standard freezing of impurities. Here, we demonstrate a surprising third alternative, namely, that freezing and topological liquidity are inseparably linked. The topological phase reacts to the introduction of disorder by generating degrees of freedom of a new type (along with interactions between them), which in turn undergo a freezing transition while the topological phase supporting them remains intact.

Topological Spin Glass in Diluted Spin Ice.

PubMed

Sen, Arnab; Moessner, R

2015-06-19

It is a salient experimental fact that a large fraction of candidate spin liquid materials freeze as the temperature is lowered. The question naturally arises whether such freezing is intrinsic to the spin liquid ("disorder-free glassiness") or extrinsic, in the sense that a topological phase simply coexists with standard freezing of impurities. Here, we demonstrate a surprising third alternative, namely, that freezing and topological liquidity are inseparably linked. The topological phase reacts to the introduction of disorder by generating degrees of freedom of a new type (along with interactions between them), which in turn undergo a freezing transition while the topological phase supporting them remains intact.

Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination.

PubMed

Rani, Nidhi; Vijayakumar, Saravanan; P T V, Lakshmi; Arunachalam, Annamalai

2016-08-01

Recent crystallographic study revealed the involvement of allosteric site in active site inhibition of penicillin binding protein (PBP2a), where one molecule of Ceftaroline (Cef) binds to the allosteric site of PBP2a and paved way for the other molecule (Cef) to bind at the active site. Though Cef has the potency to inhibit the PBP2a, its adverse side effects are of major concern. Previous studies have reported the antibacterial property of Quercetin derivatives, a group of natural compounds. Hence, the present study aims to evaluate the effect of Quercetin 3-o-rutinoside (Rut) in allosteric site-mediated active site inhibition of PBP2a. The molecular docking studies between allosteric site and ligands (Rut, Que, and Cef) revealed a better binding efficiency (G-score) of Rut (-7.790318) and Cef (-6.194946) with respect to Que (-5.079284). Molecular dynamic (MD) simulation studies showed significant changes at the active site in the presence of ligands (Rut and Cef) at allosteric site. Four different combinations of Rut and Cef were docked and their G-scores ranged between -6.320 and -8.623. MD studies revealed the stability of the key residue (Ser403) with Rut being at both sites, compared to other complexes. Morphological analysis through electron microscopy confirmed that combination of Rut and Cefixime was able to disturb the bacterial cell membrane in a similar fashion to that of Rut and Cefixime alone. The results of this study indicate that the affinity of Rut at both sites were equally good, with further validations Rut could be considered as an alternative for inhibiting MRSA growth.

Topological BF Theories

NASA Astrophysics Data System (ADS)

Sǎraru, Silviu-Constantin

Topological field theories originate in the papers of Schwarz and Witten. Initially, Schwarz shown that one of the topological invariants, namely the Ray-Singer torsion, can be represented as the partition function of a certain quantum field theory. Subsequently, Witten constructed a framework for understanding Morse theory in terms of supersymmetric quantum mechanics. These two constructions represent the prototypes of all topological field theories. The model used by Witten has been applied to classical index theorems and, moreover, suggested some generalizations that led to new mathematical results on holomorphic Morse inequalities. Starting with these results, further developments in the domain of topological field theories have been achieved. The Becchi-Rouet-Stora-Tyutin (BRST) symmetry allowed for a new definition of topological ...eld theories as theories whose BRST-invariant Hamiltonian is also BRST-exact. An important class of topological theories of Schwarz type is the class of BF models. This type of models describes three-dimensional quantum gravity and is useful at the study of four-dimensional quantum gravity in Ashtekar-Rovelli-Smolin formulation. Two-dimensional BF models are correlated to Poisson sigma models from various two-dimensional gravities. The analysis of Poisson sigma models, including their relationship to two-dimensional gravity and the study of classical solutions, has been intensively studied in the literature. In this thesis we approach the problem of construction of some classes of interacting BF models in the context of the BRST formalism. In view of this, we use the method of the deformation of the BRST charge and BRST-invariant Hamiltonian. Both methods rely on specific techniques of local BRST cohomology. The main hypotheses in which we construct the above mentioned interactions are: space-time locality, Poincare invariance, smoothness of deformations in the coupling constant and the preservation of the number of derivatives on

Deciphering the nonlocal entanglement entropy of fracton topological orders

NASA Astrophysics Data System (ADS)

Shi, Bowen; Lu, Yuan-Ming

2018-04-01

The ground states of topological orders condense extended objects and support topological excitations. This nontrivial property leads to nonzero topological entanglement entropy Stopo for conventional topological orders. Fracton topological order is an exotic class of models which is beyond the description of TQFT. With some assumptions about the condensates and the topological excitations, we derive a lower bound of the nonlocal entanglement entropy Snonlocal (a generalization of Stopo). The lower bound applies to Abelian stabilizer models including conventional topological orders as well as type-I and type-II fracton models, and it could be used to distinguish them. For fracton models, the lower bound shows that Snonlocal could obtain geometry-dependent values, and Snonlocal is extensive for certain choices of subsystems, including some choices which always give zero for TQFT. The stability of the lower bound under local perturbations is discussed.

Influence of active site location on catalytic activity in de novo-designed zinc metalloenzymes.

PubMed

Zastrow, Melissa L; Pecoraro, Vincent L

2013-04-17

While metalloprotein design has now yielded a number of successful metal-bound and even catalytically active constructs, the question of where to put a metal site along a linear, repetitive sequence has not been thoroughly addressed. Often several possibilities in a given sequence may exist that would appear equivalent but may in fact differ for metal affinity, substrate access, or protein dynamics. We present a systematic variation of active site location for a hydrolytically active ZnHis3O site contained within a de novo-designed three-stranded coiled coil. We find that the maximal rate, substrate access, and metal-binding affinity are dependent on the selected position, while catalytic efficiency for p-nitrophenyl acetate hydrolysis can be retained regardless of the location of the active site. This achievement demonstrates how efficient, tailor-made enzymes which control rate, pKa, substrate and solvent access (and selectivity), and metal-binding affinity may be realized. These findings may be applied to the more advanced de novo design of constructs containing secondary interactions, such as hydrogen-bonding channels. We are now confident that changes to location for accommodating such channels can be achieved without location-dependent loss of catalytic efficiency. These findings bring us closer to our ultimate goal of incorporating the secondary interactions we believe will be necessary in order to improve both active site properties and the catalytic efficiency to be competitive with the native enzyme, carbonic anhydrase.

Active Sites Environmental Monitoring Program: Mid-FY 1991 report

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

Ashwood, T.L.; Wickliff, D.S.; Morrissey, C.M.

1991-10-01

This report summarizes the activities of the Active Sites Environmental Monitoring Program (ASEMP) from October 1990 through March 1991. The ASEMP was established in 1989 by Solid Waste Operations and the Environmental Sciences Division to provide early detection and performance monitoring at active low-level radioactive waste (LLW) disposal sites in Solid Waste Storage Area (SWSA) 6 and transuranic (TRU) waste storage sites in SWSA 5 as required by chapters II and III of US Department of Energy Order 5820.2A. Monitoring results continue to demonstrate the no LLW is being leached from the storage vaults on the tumulus pads. Loading ofmore » vaults on Tumulus II began during this reporting period and 115 vaults had been loaded by the end of March 1991.« less

Topological phononic insulator with robust pseudospin-dependent transport

NASA Astrophysics Data System (ADS)

Xia, Bai-Zhan; Liu, Ting-Ting; Huang, Guo-Liang; Dai, Hong-Qing; Jiao, Jun-Rui; Zang, Xian-Guo; Yu, De-Jie; Zheng, Sheng-Jie; Liu, Jian

2017-09-01

Topological phononic states, which facilitate unique acoustic transport around defects and disorders, have significantly revolutionized our scientific cognition of acoustic systems. Here, by introducing a zone folding mechanism, we realize the topological phase transition in a double Dirac cone of the rotatable triangular phononic crystal with C3 v symmetry. We then investigate the distinct topological edge states on two types of interfaces of our phononic insulators. The first one is a zigzag interface which simultaneously possesses a symmetric mode and an antisymmetric mode. Hybridization of the two modes leads to a robust pseudospin-dependent one-way propagation. The second one is a linear interface with a symmetric mode or an antisymmetric mode. The type of mode is dependent on the topological phase transition of the phononic insulators. Based on the rotatability of triangular phononic crystals, we consider several complicated contours defined by the topological zigzag interfaces. Along these contours, the acoustic waves can unimpededly transmit without backscattering. Our research develops a route for the exploration of the topological phenomena in experiments and provides an excellent framework for freely steering the acoustic backscattering-immune propagation within topological phononic structures.

Topological Oxide Insulator in Cubic Perovskite Structure

PubMed Central

Jin, Hosub; Rhim, Sonny H.; Im, Jino; Freeman, Arthur J.

2013-01-01

The emergence of topologically protected conducting states with the chiral spin texture is the most prominent feature at the surface of topological insulators. On the application side, large band gap and high resistivity to distinguish surface from bulk degrees of freedom should be guaranteed for the full usage of the surface states. Here, we suggest that the oxide cubic perovskite YBiO3, more than just an oxide, defines itself as a new three-dimensional topological insulator exhibiting both a large bulk band gap and a high resistivity. Based on first-principles calculations varying the spin-orbit coupling strength, the non-trivial band topology of YBiO3 is investigated, where the spin-orbit coupling of the Bi 6p orbital plays a crucial role. Taking the exquisite synthesis techniques in oxide electronics into account, YBiO3 can also be used to provide various interface configurations hosting exotic topological phenomena combined with other quantum phases. PMID:23575973

Topological entanglement Rényi entropy and reduced density matrix structure.

PubMed

Flammia, Steven T; Hamma, Alioscia; Hughes, Taylor L; Wen, Xiao-Gang

2009-12-31

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter alpha, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of alpha for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Topological Entanglement Rényi Entropy and Reduced Density Matrix Structure

NASA Astrophysics Data System (ADS)

Flammia, Steven T.; Hamma, Alioscia; Hughes, Taylor L.; Wen, Xiao-Gang

2009-12-01

We generalize the topological entanglement entropy to a family of topological Rényi entropies parametrized by a parameter α, in an attempt to find new invariants for distinguishing topologically ordered phases. We show that, surprisingly, all topological Rényi entropies are the same, independent of α for all nonchiral topological phases. This independence shows that topologically ordered ground-state wave functions have reduced density matrices with a certain simple structure, and no additional universal information can be extracted from the entanglement spectrum.

Hg-Based Epitaxial Materials for Topological Insulators

DTIC Science & Technology

2014-07-01

Research Laboratory for investigation of properties. 15. SUBJECT TERMS EOARD, topological insulator , diluted magnetic ...topological superconductors and spintronics to quantum computation (e.g. see C.L.Kane and J.E.Moore "Topological Insulators " Physics World (2011) 24...tetradymite semiconductors Bi2Te3, Bi2Se3, and Sb2Te3 which form magnetically ordered insulators when doped with transition metal elements Cr or Fe (Rui Yu et

Algebra and topology for applications to physics

NASA Technical Reports Server (NTRS)

Rozhkov, S. S.

1987-01-01

The principal concepts of algebra and topology are examined with emphasis on applications to physics. In particular, attention is given to sets and mapping; topological spaces and continuous mapping; manifolds; and topological groups and Lie groups. The discussion also covers the tangential spaces of the differential manifolds, including Lie algebras, vector fields, and differential forms, properties of differential forms, mapping of tangential spaces, and integration of differential forms.

Evolving neural networks through augmenting topologies.

PubMed

Stanley, Kenneth O; Miikkulainen, Risto

2002-01-01

An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixed-topology method on a challenging benchmark reinforcement learning task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies that demonstrate that each component is necessary to the system as a whole and to each other. What results is significantly faster learning. NEAT is also an important contribution to GAs because it shows how it is possible for evolution to both optimize and complexify solutions simultaneously, offering the possibility of evolving increasingly complex solutions over generations, and strengthening the analogy with biological evolution.

Optical isolation with nonlinear topological photonics

NASA Astrophysics Data System (ADS)

Zhou, Xin; Wang, You; Leykam, Daniel; Chong, Y. D.

2017-09-01

It is shown that the concept of topological phase transitions can be used to design nonlinear photonic structures exhibiting power thresholds and discontinuities in their transmittance. This provides a novel route to devising nonlinear optical isolators. We study three representative designs: (i) a waveguide array implementing a nonlinear 1D Su-Schrieffer-Heeger model, (ii) a waveguide array implementing a nonlinear 2D Haldane model, and (iii) a 2D lattice of coupled-ring waveguides. In the first two cases, we find a correspondence between the topological transition of the underlying linear lattice and the power threshold of the transmittance, and show that the transmission behavior is attributable to the emergence of a self-induced topological soliton. In the third case, we show that the topological transition produces a discontinuity in the transmittance curve, which can be exploited to achieve sharp jumps in the power-dependent isolation ratio.

Measuring topology of low-intensity DNA methylation sites for high-throughput assessment of epigenetic drug-induced effects in cancer cells

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

Gertych, Arkadiusz, E-mail: gertycha@cshs.org; Bioinformatics, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA; Farkas, Daniel L., E-mail: dlfarkas@gmail.com

2010-11-15

Epigenetic anti-cancer drugs with demethylating effects have shown to alter genome organization in mammalian cell nuclei. The interest in the development of novel epigenetic drugs has increased the demand for cell-based assays to evaluate drug performance in pre-clinical studies. An imaging-based cytometrical approach that can measure demethylation effects as changes in the spatial nuclear distributions of methylated cytosine and global DNA in cancer cells is introduced in this paper. The cells were studied by immunofluorescence with a specific antibody against 5-methylcytosine (MeC), and 4,6-diamidino-2-phenylindole (DAPI) for delineation of methylated sites and global DNA in nuclei. In the preprocessing step themore » segmentation of nuclei in three-dimensional images (3-D) is followed by an automated assessment of nuclear DAPI/MeC patterns to exclude dissimilar entities. Next, low-intensity MeC (LIM) and low-intensity DNA (LID) sites of similar nuclei are localized and processed to obtain specific nuclear density profiles. These profiles sampled at half of the total nuclear volume yielded two parameters: LIM{sub 0.5} and LID{sub 0.5}. The analysis shows that zebularine and 5-azacytidine-the two tested epigenetic drugs introduce changes in the spatial distribution of low-intensity DNA and MeC signals. LIM{sub 0.5} and LID{sub 0.5} were significantly different (p < 0.001) in 5-azacytidine treated (n = 660) and zebularine treated (n = 496) vs. untreated (n = 649) DU145 human prostate cancer cells. In the latter case the LIM sites were predominantly found at the nuclear border, whereas treated populations showed different degrees of increase in LIMs towards the interior nuclear space, in which a large portion of heterochromatin is located. The cell-by-cell evaluation of changes in the spatial reorganization of MeC/DAPI signals revealed that zebularine is a more gentle demethylating agent than 5-azacytidine. Measuring changes in the topology of low-intensity sites

Quark-parton model from dual topological unitarization

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

Cohen-Tannoudji, G.; El Hassouni, A.; Kalinowski, J.

1979-06-01

Topology, which occurs in the topological expansion of quantum chromodynamics (QCD) and in the dual topological unitarization (DTU) schemes, allows us to establish a quantitative correspondence between QCD and the dual S-matrix approaches. This topological correspondence, proposed by Veneziano and made more explicit in a recent paper for current-induced reactions, provides a clarifying and unifying quark-parton interpretation of soft inclusive processes. Precise predictions for inclusive cross sections in hadron-hadron collisions, structure functions of hadrons, and quark fragmentation functions including absolute normalizations are shown to agree with data. On a more theoretical ground the proposed scheme suggests a new approach tomore » the confinement problem.« less

Quantifying the Topology and Evolution of a Magnetic Flux Rope Associated with Multi-flare Activities

NASA Astrophysics Data System (ADS)

Yang, Kai; Guo, Yang; Ding, M. D.

2016-06-01

Magnetic flux ropes (MFRs) play an important role in solar activities. The quantitative assessment of the topology of an MFR and its evolution is crucial for a better understanding of the relationship between the MFR and associated activities. In this paper, we investigate the magnetic field of active region (AR) 12017 from 2014 March 28-29, during which time 12 flares were triggered by intermittent eruptions of a filament (either successful or confined). Using vector magnetic field data from the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we calculate the magnetic energy and helicity injection in the AR, and extrapolate the 3D magnetic field with a nonlinear force-free field model. From the extrapolations, we find an MFR that is cospatial with the filament. We further determine the configuration of this MFR from the closed quasi-separatrix layer (QSL) around it. Then, we calculate the twist number and the magnetic helicity for the field lines composing the MFR. The results show that the closed QSL structure surrounding the MFR becomes smaller as a consequence of flare occurrence. We also find that the flares in our sample are mainly triggered by kink instability. Moreover, the twist number varies more sensitively than other parameters with the occurrence of flares.

Topological Rényi Entropy after a Quantum Quench

NASA Astrophysics Data System (ADS)

Halász, Gábor B.; Hamma, Alioscia

2013-04-01

We present an analytical study on the resilience of topological order after a quantum quench. The system is initially prepared in the ground state of the toric-code model, and then quenched by switching on an external magnetic field. During the subsequent time evolution, the variation in topological order is detected via the topological Rényi entropy of order 2. We consider two different quenches: the first one has an exact solution, while the second one requires perturbation theory. In both cases, we find that the long-term time average of the topological Rényi entropy in the thermodynamic limit is the same as its initial value. Based on our results, we argue that topological order is resilient against a wide range of quenches.

Local characterization of one-dimensional topologically ordered states

NASA Astrophysics Data System (ADS)

Cui, Jian; Amico, Luigi; Fan, Heng; Gu, Mile; Hamma, Alioscia; Vedral, Vlatko

2013-09-01

We consider one-dimensional Hamiltonian systems whose ground states display symmetry-protected topological order. We show that ground states within the topological phase cannot be connected with each other through local operations and classical communication between a bipartition of the system. Our claim is demonstrated by analyzing the entanglement spectrum and Rényi entropies of different physical systems that provide examples for symmetry-protected topological phases. Specifically, we consider the spin-1/2 cluster-Ising model and a class of spin-1 models undergoing quantum phase transitions to the Haldane phase. Our results provide a probe for symmetry-protected topological order. Since the picture holds even at the system's local scale, our analysis can serve as a local experimental test for topological order.

Topological Rényi entropy after a quantum quench.

PubMed

Halász, Gábor B; Hamma, Alioscia

2013-04-26

We present an analytical study on the resilience of topological order after a quantum quench. The system is initially prepared in the ground state of the toric-code model, and then quenched by switching on an external magnetic field. During the subsequent time evolution, the variation in topological order is detected via the topological Rényi entropy of order 2. We consider two different quenches: the first one has an exact solution, while the second one requires perturbation theory. In both cases, we find that the long-term time average of the topological Rényi entropy in the thermodynamic limit is the same as its initial value. Based on our results, we argue that topological order is resilient against a wide range of quenches.

Superconductivity and ferromagnetism in topological insulators

NASA Astrophysics Data System (ADS)

Zhang, Duming

Topological insulators, a new state of matter discovered recently, have attracted great interest due to their novel properties. They are insulating inside the bulk, but conducting at the surface or edges. This peculiar behavior is characterized by an insulating bulk energy gap and gapless surface or edge states, which originate from strong spin-orbit coupling and time-reversal symmetry. The spin and momentum locked surface states not only provide a model system to study fundamental physics, but can also lead to applications in spintronics and dissipationless electronics. While topological insulators are interesting by themselves, more exotic behaviors are predicted when an energy gap is induced at the surface. This dissertation explores two types of surface state gap in topological insulators, a superconducting gap induced by proximity effect and a magnetic gap induced by chemical doping. The first three chapters provide introductory theory and experimental details of my research. Chapter 1 provides a brief introduction to the theoretical background of topological insulators. Chapter 2 is dedicated to material synthesis principles and techniques. I will focus on two major synthesis methods: molecular beam epitaxy for the growth of Bi2Se3 thin films and chemical vapor deposition for the growth of Bi2Se3 nanoribbons and nanowires. Material characterization is discussed in Chapter 3. I will describe structural, morphological, magnetic, electrical, and electronic characterization techniques used to study topological insulators. Chapter 4 discusses the experiments on proximity-induced superconductivity in topological insulator (Bi2Se3) nanoribbons. This work is motivated by the search for the elusive Majorana fermions, which act as their own antiparticles. They were proposed by Ettore Majorara in 1937, but have remained undiscovered. Recently, Majorana's concept has been revived in condensed matter physics: a condensed matter analog of Majorana fermions is predicted to

Topology of molecular interaction networks.

PubMed

Winterbach, Wynand; Van Mieghem, Piet; Reinders, Marcel; Wang, Huijuan; de Ridder, Dick

2013-09-16

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks.Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs.Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes.Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further.

Topology of molecular interaction networks

PubMed Central

2013-01-01

Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over the last decade after evidence was found that they share underlying design principles with many other types of networks. Initial studies suggested that molecular interaction network topology is related to biological function and evolution. However, further whole-network analyses did not lead to a unified view on what this relation may look like, with conclusions highly dependent on the type of molecular interactions considered and the metrics used to study them. It is unclear whether global network topology drives function, as suggested by some researchers, or whether it is simply a byproduct of evolution or even an artefact of representing complex molecular interaction networks as graphs. Nevertheless, network biology has progressed significantly over the last years. We review the literature, focusing on two major developments. First, realizing that molecular interaction networks can be naturally decomposed into subsystems (such as modules and pathways), topology is increasingly studied locally rather than globally. Second, there is a move from a descriptive approach to a predictive one: rather than correlating biological network topology to generic properties such as robustness, it is used to predict specific functions or phenotypes. Taken together, this change in focus from globally descriptive to locally predictive points to new avenues of research. In particular, multi-scale approaches are developments promising to drive the study of molecular interaction networks further. PMID:24041013

Topology and the universe

NASA Astrophysics Data System (ADS)

Gott, J. Richard, III

1998-09-01

Topology may play an important role in cosmology in several different ways. First, Einstein's field equations tell us about the local geometry of the universe but not about its topology. Therefore, the universe may be multiply connected. Inflation predicts that the fluctuations that made clusters and groups of galaxies arose from random quantum fluctuations in the early universe. These should be Gaussian random phase. This can be tested by quantitatively measuring the topology of large-scale structure in the universe using the genus statistic. If the original fluctuations were Gaussian random phase then the structure we see today should have a spongelike topology. A number of studies by our group and others have shown that this is indeed the case. Future tests using the Sloan Digital Sky Survey should be possible. Microwave background fluctuations should also exhibit a characteristic symmetric pattern of hot and cold spots. The COBE data are consistent with this pattern and the MAP and PLANCK satellites should provide a definitive test. If the original inflationary state was metastable then it should decay by making an infinite number of open inflationary bubble universes. This model makes a specific prediction for the power spectrum of fluctuations in the microwave background which can be checked by the MAP and PLANCK satellites. Finally, Gott and Li have proposed how a multiply connected cosmology with an early epoch of closed timelike curves might allow the universe to be its own mother.

Painlevé equations, topological type property and reconstruction by the topological recursion

NASA Astrophysics Data System (ADS)

Iwaki, K.; Marchal, O.; Saenz, A.

2018-01-01

In this article we prove that Lax pairs associated with ħ-dependent six Painlevé equations satisfy the topological type property proposed by Bergère, Borot and Eynard for any generic choice of the monodromy parameters. Consequently we show that one can reconstruct the formal ħ-expansion of the isomonodromic τ-function and of the determinantal formulas by applying the so-called topological recursion to the spectral curve attached to the Lax pair in all six Painlevé cases. Finally we illustrate the former results with the explicit computations of the first orders of the six τ-functions.

Topological Phase Transitions in the Photonic Spin Hall Effect

DOE PAGES

Kort-Kamp, Wilton Junior de Melo

2017-10-04

The recent synthesis of two-dimensional staggered materials opens up burgeoning opportunities to study optical spin-orbit interactions in semiconducting Dirac-like systems. In this work, we unveil topological phase transitions in the photonic spin Hall effect in the graphene family materials. It is shown that an external static electric field and a high frequency circularly polarized laser allow for active on-demand manipulation of electromagnetic beam shifts. The spin Hall effect of light presents a rich dependence with radiation degrees of freedom, and material properties, and features nontrivial topological properties. Finally, we discover that photonic Hall shifts are sensitive to spin and valleymore » properties of the charge carriers, providing an unprecedented pathway to investigate spintronics and valleytronics in staggered 2D semiconductors.« less

Dynamically enriched topological orders in driven two-dimensional systems

NASA Astrophysics Data System (ADS)

Potter, Andrew C.; Morimoto, Takahiro

2017-04-01

Time-periodic driving of a quantum system can enable new dynamical topological phases of matter that could not exist in thermal equilibrium. We investigate two related classes of dynamical topological phenomena in 2D systems: Floquet symmetry-protected topological phases (FSPTs) and Floquet enriched topological orders (FETs). By constructing solvable lattice models for a complete set of 2D bosonic FSPT phases, we show that bosonic FSPTs can be understood as topological pumps which deposit loops of 1D SPT chains onto the boundary during each driving cycle, which protects a nontrivial edge state by dynamically tuning the edge to a self-dual point poised between the 1D SPT and trivial phases of the edge. By coupling these FSPT models to dynamical gauge fields, we construct solvable models of FET orders in which anyon excitations are dynamically transmuted into topologically distinct anyon types during each driving period. These bosonic FSPT and gauged FSPT models are classified by group cohomology methods. In addition, we also construct examples of "beyond cohomology" FET orders, which can be viewed as topological pumps of 1D topological chains formed of emergent anyonic quasiparticles.

Using heteroclinic orbits to quantify topological entropy in fluid flows

NASA Astrophysics Data System (ADS)

Sattari, Sulimon; Chen, Qianting; Mitchell, Kevin A.

2016-03-01

Topological approaches to mixing are important tools to understand chaotic fluid flows, ranging from oceanic transport to the design of micro-mixers. Typically, topological entropy, the exponential growth rate of material lines, is used to quantify topological mixing. Computing topological entropy from the direct stretching rate is computationally expensive and sheds little light on the source of the mixing. Earlier approaches emphasized that topological entropy could be viewed as generated by the braiding of virtual, or "ghost," rods stirring the fluid in a periodic manner. Here, we demonstrate that topological entropy can also be viewed as generated by the braiding of ghost rods following heteroclinic orbits instead. We use the machinery of homotopic lobe dynamics, which extracts symbolic dynamics from finite-length pieces of stable and unstable manifolds attached to fixed points of the fluid flow. As an example, we focus on the topological entropy of a bounded, chaotic, two-dimensional, double-vortex cavity flow. Over a certain parameter range, the topological entropy is primarily due to the braiding of a period-three orbit. However, this orbit does not explain the topological entropy for parameter values where it does not exist, nor does it explain the excess of topological entropy for the entire range of its existence. We show that braiding by heteroclinic orbits provides an accurate computation of topological entropy when the period-three orbit does not exist, and that it provides an explanation for some of the excess topological entropy when the period-three orbit does exist. Furthermore, the computation of symbolic dynamics using heteroclinic orbits has been automated and can be used to compute topological entropy for a general 2D fluid flow.

Probing the Topology of Density Matrices

NASA Astrophysics Data System (ADS)

Bardyn, Charles-Edouard; Wawer, Lukas; Altland, Alexander; Fleischhauer, Michael; Diehl, Sebastian

2018-01-01

The mixedness of a quantum state is usually seen as an adversary to topological quantization of observables. For example, exact quantization of the charge transported in a so-called Thouless adiabatic pump is lifted at any finite temperature in symmetry-protected topological insulators. Here, we show that certain directly observable many-body correlators preserve the integrity of topological invariants for mixed Gaussian quantum states in one dimension. Our approach relies on the expectation value of the many-body momentum-translation operator and leads to a physical observable—the "ensemble geometric phase" (EGP)—which represents a bona fide geometric phase for mixed quantum states, in the thermodynamic limit. In cyclic protocols, the EGP provides a topologically quantized observable that detects encircled spectral singularities ("purity-gap" closing points) of density matrices. While we identify the many-body nature of the EGP as a key ingredient, we propose a conceptually simple, interferometric setup to directly measure the latter in experiments with mesoscopic ensembles of ultracold atoms.

Scaling theory of topological phase transitions

NASA Astrophysics Data System (ADS)

Chen, Wei

2016-02-01

Topologically ordered systems are characterized by topological invariants that are often calculated from the momentum space integration of a certain function that represents the curvature of the many-body state. The curvature function may be Berry curvature, Berry connection, or other quantities depending on the system. Akin to stretching a messy string to reveal the number of knots it contains, a scaling procedure is proposed for the curvature function in inversion symmetric systems, from which the topological phase transition can be identified from the flow of the driving energy parameters that control the topology (hopping, chemical potential, etc) under scaling. At an infinitesimal operation, one obtains the renormalization group (RG) equations for the driving energy parameters. A length scale defined from the curvature function near the gap-closing momentum is suggested to characterize the scale invariance at critical points and fixed points, and displays a universal critical behavior in a variety of systems examined.

Topological photonic orbital-angular-momentum switch

NASA Astrophysics Data System (ADS)

Luo, Xi-Wang; Zhang, Chuanwei; Guo, Guang-Can; Zhou, Zheng-Wei

2018-04-01

The large number of available orbital-angular-momentum (OAM) states of photons provides a unique resource for many important applications in quantum information and optical communications. However, conventional OAM switching devices usually rely on precise parameter control and are limited by slow switching rate and low efficiency. Here we propose a robust, fast, and efficient photonic OAM switch device based on a topological process, where photons are adiabatically pumped to a target OAM state on demand. Such topological OAM pumping can be realized through manipulating photons in a few degenerate main cavities and involves only a limited number of optical elements. A large change of OAM at ˜10q can be realized with only q degenerate main cavities and at most 5 q pumping cycles. The topological photonic OAM switch may become a powerful device for broad applications in many different fields and motivate a topological design of conventional optical devices.

Aerothermoelastic Topology Optimization with Flutter and Buckling Metrics (Postprint)

DTIC Science & Technology

2013-07-01

topologies of an unheated panel, thermal buckling-optimal topologies, and flutter- optimality of a heated panel (where the latter case presents a...topological compromise between the former two). The effect of various constraint boundaries, temperature gradients, and (for the flutter of the heated panel...optimality of a heated panel (where the latter case presents a topological compromise between the former two). The effect of various constraint boundaries

Topologically-protected one-way leaky waves in nonreciprocal plasmonic structures

NASA Astrophysics Data System (ADS)

Hassani Gangaraj, S. Ali; Monticone, Francesco

2018-03-01

We investigate topologically-protected unidirectional leaky waves on magnetized plasmonic structures acting as homogeneous photonic topological insulators. Our theoretical analyses and numerical experiments aim at unveiling the general properties of these exotic surface waves, and their nonreciprocal and topological nature. In particular, we study the behavior of topological leaky modes in stratified structures composed of a magnetized plasma at the interface with isotropic conventional media, and we show how to engineer their propagation and radiation properties, leading to topologically-protected backscattering-immune wave propagation, and highly directive and tunable radiation. Taking advantage of the non-trivial topological properties of these leaky modes, we also theoretically demonstrate advanced functionalities, including arbitrary re-routing of leaky waves on the surface of bodies with complex shapes, as well as the realization of topological leaky-wave (nano)antennas with isolated channels of radiation that are completely independent and separately tunable. Our findings help shedding light on the behavior of topologically-protected modes in open wave-guiding structures, and may open intriguing directions for future antenna generations based on topological structures, at microwaves and optical frequencies.

Topological computation based on direct magnetic logic communication.

PubMed

Zhang, Shilei; Baker, Alexander A; Komineas, Stavros; Hesjedal, Thorsten

2015-10-28

Non-uniform magnetic domains with non-trivial topology, such as vortices and skyrmions, are proposed as superior state variables for nonvolatile information storage. So far, the possibility of logic operations using topological objects has not been considered. Here, we demonstrate numerically that the topology of the system plays a significant role for its dynamics, using the example of vortex-antivortex pairs in a planar ferromagnetic film. Utilising the dynamical properties and geometrical confinement, direct logic communication between the topological memory carriers is realised. This way, no additional magnetic-to-electrical conversion is required. More importantly, the information carriers can spontaneously travel up to ~300 nm, for which no spin-polarised current is required. The derived logic scheme enables topological spintronics, which can be integrated into large-scale memory and logic networks capable of complex computations.

Magnetic second-order topological insulators and semimetals

NASA Astrophysics Data System (ADS)

Ezawa, Motohiko

2018-04-01

We propose magnetic second-order topological insulators (SOTIs). First, we study a three-dimensional model. It is pointed out that the previously proposed topological hinge insulator has actually surface states along the [001] direction in addition to hinge states. We gap out these surface states by introducing magnetization, obtaining a SOTI only with hinge states. The bulk topological number is the Z2 index protected by the combined symmetry of the fourfold rotation and the inversion symmetry. We next study two-dimensional magnetic SOTIs, where the corner states are robust also in the presence of the magnetization. Finally, we construct a magnetic second-order topological semimetal by layering the two-dimensional magnetic SOTIs, where hinge-arc states are robust also in the presence of the magnetization.

Topological Band Theory for Non-Hermitian Hamiltonians

NASA Astrophysics Data System (ADS)

Shen, Huitao; Zhen, Bo; Fu, Liang

2018-04-01

We develop the topological band theory for systems described by non-Hermitian Hamiltonians, whose energy spectra are generally complex. After generalizing the notion of gapped band structures to the non-Hermitian case, we classify "gapped" bands in one and two dimensions by explicitly finding their topological invariants. We find nontrivial generalizations of the Chern number in two dimensions, and a new classification in one dimension, whose topology is determined by the energy dispersion rather than the energy eigenstates. We then study the bulk-edge correspondence and the topological phase transition in two dimensions. Different from the Hermitian case, the transition generically involves an extended intermediate phase with complex-energy band degeneracies at isolated "exceptional points" in momentum space. We also systematically classify all types of band degeneracies.

Quantum friction in two-dimensional topological materials

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

Farias, M. Belén; Kort-Kamp, Wilton J. M.; Dalvit, Diego A. R.

In this paper, we develop the theory of quantum friction in two-dimensional topological materials. The quantum drag force on a metallic nanoparticle moving above such systems is sensitive to the nontrivial topology of their electronic phases, shows a novel distance scaling law, and can be manipulated through doping or via the application of external fields. We use the developed framework to investigate quantum friction due to the quantum Hall effect in magnetic field biased graphene, and to topological phase transitions in the graphene family materials. Finally, it is shown that topologically nontrivial states in two-dimensional materials enable an increase ofmore » two orders of magnitude in the quantum drag force with respect to conventional neutral graphene systems.« less

Quantum friction in two-dimensional topological materials

DOE PAGES

Farias, M. Belén; Kort-Kamp, Wilton J. M.; Dalvit, Diego A. R.

2018-04-24

In this paper, we develop the theory of quantum friction in two-dimensional topological materials. The quantum drag force on a metallic nanoparticle moving above such systems is sensitive to the nontrivial topology of their electronic phases, shows a novel distance scaling law, and can be manipulated through doping or via the application of external fields. We use the developed framework to investigate quantum friction due to the quantum Hall effect in magnetic field biased graphene, and to topological phase transitions in the graphene family materials. Finally, it is shown that topologically nontrivial states in two-dimensional materials enable an increase ofmore » two orders of magnitude in the quantum drag force with respect to conventional neutral graphene systems.« less

Topological quantization in units of the fine structure constant.

PubMed

Maciejko, Joseph; Qi, Xiao-Liang; Drew, H Dennis; Zhang, Shou-Cheng

2010-10-15

Fundamental topological phenomena in condensed matter physics are associated with a quantized electromagnetic response in units of fundamental constants. Recently, it has been predicted theoretically that the time-reversal invariant topological insulator in three dimensions exhibits a topological magnetoelectric effect quantized in units of the fine structure constant α=e²/ℏc. In this Letter, we propose an optical experiment to directly measure this topological quantization phenomenon, independent of material details. Our proposal also provides a way to measure the half-quantized Hall conductances on the two surfaces of the topological insulator independently of each other.

Switching chiral solitons for algebraic operation of topological quaternary digits

NASA Astrophysics Data System (ADS)

Kim, Tae-Hwan; Cheon, Sangmo; Yeom, Han Woong

2017-02-01

Chiral objects can be found throughout nature; in condensed matter chiral objects are often excited states protected by a system's topology. The use of chiral topological excitations to carry information has been demonstrated, where the information is robust against external perturbations. For instance, reading, writing, and transfer of binary information have been demonstrated with chiral topological excitations in magnetic systems, skyrmions, for spintronic devices. The next step is logic or algebraic operations of such topological bits. Here, we show experimentally the switching between chiral topological excitations or chiral solitons of different chirality in a one-dimensional electronic system with Z4 topological symmetry. We found that a fast-moving achiral soliton merges with chiral solitons to switch their handedness. This can lead to the realization of algebraic operation of Z4 topological charges. Chiral solitons could be a platform for storage and operation of robust topological multi-digit information.

Observation of topologically protected bound states in photonic quantum walks.

PubMed

Kitagawa, Takuya; Broome, Matthew A; Fedrizzi, Alessandro; Rudner, Mark S; Berg, Erez; Kassal, Ivan; Aspuru-Guzik, Alán; Demler, Eugene; White, Andrew G

2012-06-06

Topological phases exhibit some of the most striking phenomena in modern physics. Much of the rich behaviour of quantum Hall systems, topological insulators, and topological superconductors can be traced to the existence of robust bound states at interfaces between different topological phases. This robustness has applications in metrology and holds promise for future uses in quantum computing. Engineered quantum systems--notably in photonics, where wavefunctions can be observed directly--provide versatile platforms for creating and probing a variety of topological phases. Here we use photonic quantum walks to observe bound states between systems with different bulk topological properties and demonstrate their robustness to perturbations--a signature of topological protection. Although such bound states are usually discussed for static (time-independent) systems, here we demonstrate their existence in an explicitly time-dependent situation. Moreover, we discover a new phenomenon: a topologically protected pair of bound states unique to periodically driven systems.

Latest advances in molecular topology applications for drug discovery.

PubMed

Zanni, Riccardo; Galvez-Llompart, Maria; García-Domenech, Ramón; Galvez, Jorge

2015-01-01

Molecular topology (MT) has emerged in recent years as a powerful approach for the in silico generation of new drugs. In the last decade, its application has become more and more popular among the leading research groups in the field of quantitative structure-activity relationships (QSAR) and drug design. This has, in turn, contributed to the rapid development of new techniques and applications of MT in QSAR studies, as well as the introduction of new topological indices. This review collates the main innovative techniques in the field of MT and provides a description of the novel topological indices recently introduced, through an exhaustive recompilation of the most significant works carried out by the leading research groups in the field of drug design and discovery. The objective is to show the importance of MT methods combined with the effectiveness of the descriptors. Recent years have witnessed a remarkable rise in QSAR methods based on MT and its application to drug design. New methodologies have been introduced in the area such as QSAR multi-target, Markov networks or perturbation methods. Moreover, novel topological indices, such as Bourgas' descriptors and other new concepts as the derivative of a graph or cliques capable to distinguish between conformers, have also been introduced. New drugs have also been discovered, including anticonvulsants, anineoplastics, antimalarials or antiallergics, just to name a few. In the authors' opinion, MT and QSAR have moved from an attractive possibility to representing a foundation stone in the process of drug discovery.

Birman—Wenzl—Murakami Algebra and Topological Basis

NASA Astrophysics Data System (ADS)

Zhou, Cheng-Cheng; Xue, Kang; Wang, Gang-Cheng; Sun, Chun-Fang; Du, Gui-Jiao

2012-02-01

In this paper, we use entangled states to construct 9 × 9-matrix representations of Temperley—Lieb algebra (TLA), then a family of 9 × 9-matrix representations of Birman—Wenzl—Murakami algebra (BWMA) have been presented. Based on which, three topological basis states have been found. And we apply topological basis states to recast nine-dimensional BWMA into its three-dimensional counterpart. Finally, we find the topological basis states are spin singlet states in special case.

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology.

PubMed

DeBlasio, Stacy L; Chavez, Juan D; Alexander, Mariko M; Ramsey, John; Eng, Jimmy K; Mahoney, Jaclyn; Gray, Stewart M; Bruce, James E; Cilia, Michelle

2016-02-15

Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection-hallmarks of host-pathogen interactions-were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used protein interaction

Visualization of Host-Polerovirus Interaction Topologies Using Protein Interaction Reporter Technology

PubMed Central

DeBlasio, Stacy L.; Chavez, Juan D.; Alexander, Mariko M.; Ramsey, John; Eng, Jimmy K.; Mahoney, Jaclyn; Gray, Stewart M.; Bruce, James E.

2015-01-01

ABSTRACT Demonstrating direct interactions between host and virus proteins during infection is a major goal and challenge for the field of virology. Most protein interactions are not binary or easily amenable to structural determination. Using infectious preparations of a polerovirus (Potato leafroll virus [PLRV]) and protein interaction reporter (PIR), a revolutionary technology that couples a mass spectrometric-cleavable chemical cross-linker with high-resolution mass spectrometry, we provide the first report of a host-pathogen protein interaction network that includes data-derived, topological features for every cross-linked site that was identified. We show that PLRV virions have hot spots of protein interaction and multifunctional surface topologies, revealing how these plant viruses maximize their use of binding interfaces. Modeling data, guided by cross-linking constraints, suggest asymmetric packing of the major capsid protein in the virion, which supports previous epitope mapping studies. Protein interaction topologies are conserved with other species in the Luteoviridae and with unrelated viruses in the Herpesviridae and Adenoviridae. Functional analysis of three PLRV-interacting host proteins in planta using a reverse-genetics approach revealed a complex, molecular tug-of-war between host and virus. Structural mimicry and diversifying selection—hallmarks of host-pathogen interactions—were identified within host and viral binding interfaces predicted by our models. These results illuminate the functional diversity of the PLRV-host protein interaction network and demonstrate the usefulness of PIR technology for precision mapping of functional host-pathogen protein interaction topologies. IMPORTANCE The exterior shape of a plant virus and its interacting host and insect vector proteins determine whether a virus will be transmitted by an insect or infect a specific host. Gaining this information is difficult and requires years of experimentation. We used

All the catalytic active sites of MoS 2 for hydrogen evolution

DOE PAGES

Li, Guoqing; Zhang, Du; Qiao, Qiao; ...

2016-11-29

MoS 2 presents a promising low-cost catalyst for the hydrogen evolution reaction (HER), but the understanding about its active sites has remained limited. Here we present an unambiguous study of the catalytic activities of all possible reaction sites of MoS 2, including edge sites, sulfur vacancies, and grain boundaries. We demonstrate that, in addition to the well-known catalytically active edge sites, sulfur vacancies provide another major active site for the HER, while the catalytic activity of grain boundaries is much weaker. Here, the intrinsic turnover frequencies (Tafel slopes) of the edge sites, sulfur vacancies, and grain boundaries are estimated tomore » be 7.5 s –1 (65–75 mV/dec), 3.2 s –1 (65–85 mV/dec), and 0.1 s –1 (120–160 mV/dec), respectively. We also demonstrate that the catalytic activity of sulfur vacancies strongly depends on the density of the vacancies and the local crystalline structure in proximity to the vacancies. Unlike edge sites, whose catalytic activity linearly depends on the length, sulfur vacancies show optimal catalytic activities when the vacancy density is in the range of 7–10%, and the number of sulfur vacancies in high crystalline quality MoS 2 is higher than that in low crystalline quality MoS 2, which may be related with the proximity of different local crystalline structures to the vacancies.« less

Thermalization of topological entropy after a quantum quench

NASA Astrophysics Data System (ADS)

Zeng, Yu; Hamma, Alioscia; Fan, Heng

2016-09-01

Topologically ordered quantum phases are robust in the sense that perturbations in the Hamiltonian of the system will not change the topological nature of the ground-state wave function. However, in order to exploit topological order for applications such as self-correcting quantum memories and information processing, these states need to be also robust both dynamically and at finite temperature in the presence of an environment. It is well known that systems like the toric code in two spatial dimensions are fragile in temperature. In this paper, we show a completely analytic treatment of the toric code away from equilibrium, after a quantum quench of the system Hamiltonian. We show that, despite being subject to unitary evolution (and at zero temperature), the long-time behavior of the topological entropy is thermal, therefore vanishing. If the quench preserves a local gauge structure, there is a residual long-lived topological entropy. This also is the thermal behavior in presence of such gauge constraints. The result is obtained by studying the time evolution of the topological 2-Rényi entropy in a fully analytical, exact way.

Multiple topological electronic phases in superconductor MoC

NASA Astrophysics Data System (ADS)

Huang, Angus; Smith, Adam D.; Schwinn, Madison; Lu, Qiangsheng; Chang, Tay-Rong; Xie, Weiwei; Jeng, Horng-Tay; Bian, Guang

2018-05-01

The search for a superconductor with non-s -wave pairing is important not only for understanding unconventional mechanisms of superconductivity but also for finding new types of quasiparticles such as Majorana bound states. Materials with both topological band structure and superconductivity are promising candidates as p +i p superconducting states can be generated through pairing the spin-polarized topological surface states. In this work, the electronic and phonon properties of the superconductor molybdenum carbide (MoC) are studied with first-principles methods. Our calculations show that nontrivial band topology and s -wave Bardeen-Cooper-Schrieffer superconductivity coexist in two structural phases of MoC, namely the cubic α and hexagonal γ phases. The α phase is a strong topological insulator and the γ phase is a topological nodal-line semimetal with drumhead surface states. In addition, hole doping can stabilize the crystal structure of the α phase and elevate the transition temperature in the γ phase. Therefore, MoC in different structural forms can be a practical material platform for studying topological superconductivity.

Topological Landscapes: A Terrain Metaphor for ScientificData

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

Weber, Gunther H.; Bremer, Peer-Timo; Pascucci, Valerio

2007-08-01

Scientific visualization and illustration tools are designed to help people understand the structure and complexity of scientific data with images that are as informative and intuitive as possible. In this context, the use of metaphors plays an important role, since they make complex information easily accessible by using commonly known concepts. In this paper we propose a new metaphor, called 'Topological Landscapes', which facilitates understanding the topological structure of scalar functions. The basic idea is to construct a terrain with the same topology as a given dataset and to display the terrain as an easily understood representation of the actualmore » input data. In this projection from an n-dimensional scalar function to a two-dimensional (2D) model we preserve function values of critical points, the persistence (function span) of topological features, and one possible additional metric property (in our examples volume). By displaying this topologically equivalent landscape together with the original data we harness the natural human proficiency in understanding terrain topography and make complex topological information easily accessible.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

DOE PAGES

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping; ...

2017-07-27

Bimetallic catalysts are promising for the most difficult thermal and electrochemical reactions, but modeling the many diverse active sites on polycrystalline samples is an open challenge. Here, we present a general framework for addressing this complexity in a systematic and predictive fashion. Active sites for every stable low-index facet of a bimetallic crystal are enumerated and cataloged, yielding hundreds of possible active sites. The activity of these sites is explored in parallel using a neural-network-based surrogate model to share information between the many density functional theory (DFT) relaxations, resulting in activity estimates with an order of magnitude fewer explicit DFTmore » calculations. Sites with interesting activity were found and provide targets for follow-up calculations. This process was applied to the electrochemical reduction of CO 2 on nickel gallium bimetallics and indicated that most facets had similar activity to Ni surfaces, but a few exposed Ni sites with a very favorable on-top CO configuration. This motif emerged naturally from the predictive modeling and represents a class of intermetallic CO 2 reduction catalysts. These sites rationalize recent experimental reports of nickel gallium activity and why previous materials screens missed this exciting material. Most importantly these methods suggest that bimetallic catalysts will be discovered by studying facet reactivity and diversity of active sites more systematically.« less

Machine-Learning Methods Enable Exhaustive Searches for Active Bimetallic Facets and Reveal Active Site Motifs for CO 2 Reduction

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

Ulissi, Zachary W.; Tang, Michael T.; Xiao, Jianping