WorldWideScience

Sample records for symmetric biomolecular assemblies

  1. Orientation of biomolecular assemblies in a microfluidic jet

    International Nuclear Information System (INIS)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T; Koester, S; Abel, B; Davies, R J

    2010-01-01

    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10 7 s -1 . Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  2. Charge patterns as templates for the assembly of layered biomolecular structures.

    Science.gov (United States)

    Naujoks, Nicola; Stemmer, Andreas

    2006-08-01

    Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

  3. Binary self-assembly of highly symmetric DNA nanocages via sticky-end engineering

    Institute of Scientific and Technical Information of China (English)

    Xiao-Rong Wu; Chen-Wei Wu; Fei Ding; Cheng Tian; Wen Jiang; Cheng-De Mao; Chuan Zhang

    2017-01-01

    Discrete and symmetric three-dimensional (3D) DNA nanocages have been revoked as excellent candidates for various applications,such as guest component encapsulation and organization (e.g.dye molecules,proteins,inorganic nanoparticles,etc.) to construct new materials and devices.To date,a large variety of DNA nanocages has been synthesized through assembling small individual DNA motifs into predesigned structures in a bottom-up fashion.Most of them rely on the assembly using multiple copies of single type of motifs and a few sophisticated nanostructures have been engineered by co-assembling multi-types of DNA tiles simultaneously.However,the availability of complex DNA nanocages is still limited.Herein,we demonstrate that highly symmetric DNA nanocages consisted of binary DNA pointstar motifs can be easily assembled by deliberately engineering the sticky-end interaction between the component building blocks.As such,DNA nanocages with new geometries,including elongated tetrahedron (E-TET),rhombic dodecahedron (R-DOD),and rhombic triacontahedron (R-TRI) are successfully synthesized.Moreover,their design principle,assembly process,and structural features are revealed by polyacryalmide gel electrophoresis (PAGE),atomic force microscope (AFM) imaging,and cryogenic transmission electron microscope imaging (cryo-TEM) associated with single particle reconstruction.

  4. Biomolecular condensates: organizers of cellular biochemistry.

    Science.gov (United States)

    Banani, Salman F; Lee, Hyun O; Hyman, Anthony A; Rosen, Michael K

    2017-05-01

    Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated.

  5. Nanotrumpets and circularly polarized luminescent nanotwists hierarchically self-assembled from an achiral C3-symmetric ester.

    Science.gov (United States)

    Sang, Yutao; Duan, Pengfei; Liu, Minghua

    2018-04-17

    An achiral C3-symmetric molecule was found to self-assemble into various hierarchical nanostructures such as nanotwists, nanotrumpets and nanobelts, in which the twisted fibers showed supramolecular chirality as well as circularly polarized luminescence although the compound is achiral.

  6. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang

    2013-07-01

    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  7. Biomolecular Sciences: uniting Biology and Chemistry

    NARCIS (Netherlands)

    Vrieling, Engel

    2017-01-01

    Biomolecular Sciences: uniting Biology and Chemistry www.rug.nl/research/gbb The scientific discoveries in biomolecular sciences have benefitted enormously from technological innovations. At the Groningen Biomolecular Science and Biotechnology Institute (GBB) we now sequence a genome in days,

  8. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Directory of Open Access Journals (Sweden)

    Clarisse Gravina Ricci

    2018-02-01

    Full Text Available Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes.

  9. Tailoring the Variational Implicit Solvent Method for New Challenges: Biomolecular Recognition and Assembly

    Science.gov (United States)

    Ricci, Clarisse Gravina; Li, Bo; Cheng, Li-Tien; Dzubiella, Joachim; McCammon, J. Andrew

    2018-01-01

    Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes. PMID:29484300

  10. Programmed Nanomaterial Assemblies in Large Scales: Applications of Synthetic and Genetically- Engineered Peptides to Bridge Nano-Assemblies and Macro-Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Matsui, Hiroshi

    2014-09-09

    Work is reported in these areas: Large-scale & reconfigurable 3D structures of precise nanoparticle assemblies in self-assembled collagen peptide grids; Binary QD-Au NP 3D superlattices assembled with collagen-like peptides and energy transfer between QD and Au NP in 3D peptide frameworks; Catalytic peptides discovered by new hydrogel-based combinatorial phage display approach and their enzyme-mimicking 2D assembly; New autonomous motors of metal-organic frameworks (MOFs) powered by reorganization of self-assembled peptides at interfaces; Biomimetic assembly of proteins into microcapsules on oil-in-water droplets with structural reinforcement via biomolecular recognition-based cross-linking of surface peptides; and Biomimetic fabrication of strong freestanding genetically-engineered collagen peptide films reinforced by quantum dot joints. We gained the broad knowledge about biomimetic material assembly from nanoscale to microscale ranges by coassembling peptides and NPs via biomolecular recognition. We discovered: Genetically-engineered collagen-like peptides can be self-assembled with Au NPs to generate 3D superlattices in large volumes (> μm{sup 3}); The assembly of the 3D peptide-Au NP superstructures is dynamic and the interparticle distance changes with assembly time as the reconfiguration of structure is triggered by pH change; QDs/NPs can be assembled with the peptide frameworks to generate 3D superlattices and these QDs/NPs can be electronically coupled for the efficient energy transfer; The controlled assembly of catalytic peptides mimicking the catalytic pocket of enzymes can catalyze chemical reactions with high selectivity; and, For the bacteria-mimicking swimmer fabrication, peptide-MOF superlattices can power translational and propellant motions by the reconfiguration of peptide assembly at the MOF-liquid interface.

  11. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna; Oliva, Romina; Cavallo, Luigi; Bonvin, Alexandre M. J. J.

    2017-01-01

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  12. Prediction of Biomolecular Complexes

    KAUST Repository

    Vangone, Anna

    2017-04-12

    Almost all processes in living organisms occur through specific interactions between biomolecules. Any dysfunction of those interactions can lead to pathological events. Understanding such interactions is therefore a crucial step in the investigation of biological systems and a starting point for drug design. In recent years, experimental studies have been devoted to unravel the principles of biomolecular interactions; however, due to experimental difficulties in solving the three-dimensional (3D) structure of biomolecular complexes, the number of available, high-resolution experimental 3D structures does not fulfill the current needs. Therefore, complementary computational approaches to model such interactions are necessary to assist experimentalists since a full understanding of how biomolecules interact (and consequently how they perform their function) only comes from 3D structures which provide crucial atomic details about binding and recognition processes. In this chapter we review approaches to predict biomolecular complexesBiomolecular complexes, introducing the concept of molecular dockingDocking, a technique which uses a combination of geometric, steric and energetics considerations to predict the 3D structure of a biological complex starting from the individual structures of its constituent parts. We provide a mini-guide about docking concepts, its potential and challenges, along with post-docking analysis and a list of related software.

  13. Biomolecular Science (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2012-04-01

    A brief fact sheet about NREL Photobiology and Biomolecular Science. The research goal of NREL's Biomolecular Science is to enable cost-competitive advanced lignocellulosic biofuels production by understanding the science critical for overcoming biomass recalcitrance and developing new product and product intermediate pathways. NREL's Photobiology focuses on understanding the capture of solar energy in photosynthetic systems and its use in converting carbon dioxide and water directly into hydrogen and advanced biofuels.

  14. Converting biomolecular modelling data based on an XML representation.

    Science.gov (United States)

    Sun, Yudong; McKeever, Steve

    2008-08-25

    Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  15. Converting Biomolecular Modelling Data Based on an XML Representation

    Directory of Open Access Journals (Sweden)

    Sun Yudong

    2008-06-01

    Full Text Available Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language. BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

  16. Small-angle X-ray scattering investigations of biomolecular confinement, loading, and release from liquid-crystalline nanochannel assemblies

    Czech Academy of Sciences Publication Activity Database

    Angelova, A.; Angelov, Borislav; Garamus, V. M.; Couvreur, P.; Lesieur, S.

    2012-01-01

    Roč. 3, č. 3 (2012), s. 445-457 ISSN 1948-7185 Institutional research plan: CEZ:AV0Z40500505 Keywords : nanochannels * biomolecular nanostructures * SAXS Subject RIV: CD - Macromolecular Chemistry Impact factor: 6.585, year: 2012

  17. One-dimensional Confinement Effect on the Self-assembly of Symmetric H-shaped Copolymers in a Thin Film.

    Science.gov (United States)

    Mu, Dan; Li, Jian-Quan; Feng, Sheng-Yu

    2017-10-19

    The self-assembly of a reformed symmetric H-shaped copolymer with four hydrophilic branches and one hydrophobic stem was systematically investigated. The existence of vacancies is vital to regulate the sizes of self-assembled cylinders to be able to form a hexagonal arrangement. With the introduction of horizontal-orientated confinement, a micellar structure is formed through a coalescence mechanism. The short acting distance and large influencing area of the confinement produces numerous small-sized micelles. Additionally, the cycled "contraction-expansion" change helps achieve hexagonal arrangement. In contrast, the introduction of lateral-oriented confinement with long acting distance and small influencing area cannot change the cylindrical structure. Under the fission mechanism, in which the larger cylinder splits into smaller ones, it is quite efficient to generate hierarchical-sized cylinders from larger-sized cylinders in the middle region and smaller-sized cylinders near both walls. The results indicate the possibility of regulating the characteristics of a nanomaterial by tuning the molecular structure of the copolymer and the parameters of the introduced confinement, which are closely related to the self-assembly structure.

  18. Biomolecular engineering for nanobio/bionanotechnology

    Science.gov (United States)

    Nagamune, Teruyuki

    2017-04-01

    Biomolecular engineering can be used to purposefully manipulate biomolecules, such as peptides, proteins, nucleic acids and lipids, within the framework of the relations among their structures, functions and properties, as well as their applicability to such areas as developing novel biomaterials, biosensing, bioimaging, and clinical diagnostics and therapeutics. Nanotechnology can also be used to design and tune the sizes, shapes, properties and functionality of nanomaterials. As such, there are considerable overlaps between nanotechnology and biomolecular engineering, in that both are concerned with the structure and behavior of materials on the nanometer scale or smaller. Therefore, in combination with nanotechnology, biomolecular engineering is expected to open up new fields of nanobio/bionanotechnology and to contribute to the development of novel nanobiomaterials, nanobiodevices and nanobiosystems. This review highlights recent studies using engineered biological molecules (e.g., oligonucleotides, peptides, proteins, enzymes, polysaccharides, lipids, biological cofactors and ligands) combined with functional nanomaterials in nanobio/bionanotechnology applications, including therapeutics, diagnostics, biosensing, bioanalysis and biocatalysts. Furthermore, this review focuses on five areas of recent advances in biomolecular engineering: (a) nucleic acid engineering, (b) gene engineering, (c) protein engineering, (d) chemical and enzymatic conjugation technologies, and (e) linker engineering. Precisely engineered nanobiomaterials, nanobiodevices and nanobiosystems are anticipated to emerge as next-generation platforms for bioelectronics, biosensors, biocatalysts, molecular imaging modalities, biological actuators, and biomedical applications.

  19. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software

    National Research Council Canada - National Science Library

    Frazier, John; Chusak, Yaroslav; Foy, Brent

    2008-01-01

    .... The software uses either exact or approximate stochastic simulation algorithms for generating Monte Carlo trajectories that describe the time evolution of the behavior of biomolecular reaction networks...

  20. A statistical nanomechanism of biomolecular patterning actuated by surface potential

    Science.gov (United States)

    Lin, Chih-Ting; Lin, Chih-Hao

    2011-02-01

    Biomolecular patterning on a nanoscale/microscale on chip surfaces is one of the most important techniques used in vitro biochip technologies. Here, we report upon a stochastic mechanics model we have developed for biomolecular patterning controlled by surface potential. The probabilistic biomolecular surface adsorption behavior can be modeled by considering the potential difference between the binding and nonbinding states. To verify our model, we experimentally implemented a method of electroactivated biomolecular patterning technology and the resulting fluorescence intensity matched the prediction of the developed model quite well. Based on this result, we also experimentally demonstrated the creation of a bovine serum albumin pattern with a width of 200 nm in 5 min operations. This submicron noncovalent-binding biomolecular pattern can be maintained for hours after removing the applied electrical voltage. These stochastic understandings and experimental results not only prove the feasibility of submicron biomolecular patterns on chips but also pave the way for nanoscale interfacial-bioelectrical engineering.

  1. Thermodynamic properties of water solvating biomolecular surfaces

    Science.gov (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  2. Solution scattering studies on a virus capsid protein as a building block for nanoscale assemblies

    NARCIS (Netherlands)

    Comellas Aragones, M.; Comellas-Aragones, Marta; Sikkema, Friso D.; Delaittre, Guillaume; Terry, Ann E.; King, Stephen M.; Visser, Dirk; Heenan, Richard K.; Nolte, Roeland J.M.; Cornelissen, Jeroen Johannes Lambertus Maria; Feiters, Martin C.

    2011-01-01

    Self-assembled protein cages are versatile building blocks in the construction of biomolecular nanostructures. Because of the defined assembly behaviour the cowpea chlorotic mottle virus (CCMV) protein is often used for such applications. Here we report a detailed solution scattering study of the

  3. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond

    2008-01-01

    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  4. Extending the self-assembly of coiled-coil hybrids

    NARCIS (Netherlands)

    Robson Marsden, Hana

    2009-01-01

    Of the various biomolecular building blocks in use in nature, coiled-coil forming peptides are amongst those with the most potential as building blocks for the synthetic self-assembly of nanostructures. Native coiled coils have the ability to function in, and influence, complex systems composed of

  5. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

    2011-01-01

    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem...... conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined...... by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways...

  6. Improvements to the APBS biomolecular solvation software suite.

    Science.gov (United States)

    Jurrus, Elizabeth; Engel, Dave; Star, Keith; Monson, Kyle; Brandi, Juan; Felberg, Lisa E; Brookes, David H; Wilson, Leighton; Chen, Jiahui; Liles, Karina; Chun, Minju; Li, Peter; Gohara, David W; Dolinsky, Todd; Konecny, Robert; Koes, David R; Nielsen, Jens Erik; Head-Gordon, Teresa; Geng, Weihua; Krasny, Robert; Wei, Guo-Wei; Holst, Michael J; McCammon, J Andrew; Baker, Nathan A

    2018-01-01

    The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that have provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses the three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this article, we discuss the models and capabilities that have recently been implemented within the APBS software package including a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory-based algorithm for determining pK a values, and an improved web-based visualization tool for viewing electrostatics. © 2017 The Protein Society.

  7. Biomolecular Assembly of Gold Nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Micheel, Christine Marya [Univ. of California, Berkeley, CA (United States)

    2005-05-20

    Over the past ten years, methods have been developed to construct discrete nanostructures using nanocrystals and biomolecules. While these frequently consist of gold nanocrystals and DNA, semiconductor nanocrystals as well as antibodies and enzymes have also been used. One example of discrete nanostructures is dimers of gold nanocrystals linked together with complementary DNA. This type of nanostructure is also known as a nanocrystal molecule. Discrete nanostructures of this kind have a number of potential applications, from highly parallel self-assembly of electronics components and rapid read-out of DNA computations to biological imaging and a variety of bioassays. My research focused in three main areas. The first area, the refinement of electrophoresis as a purification and characterization method, included application of agarose gel electrophoresis to the purification of discrete gold nanocrystal/DNA conjugates and nanocrystal molecules, as well as development of a more detailed understanding of the hydrodynamic behavior of these materials in gels. The second area, the development of methods for quantitative analysis of transmission electron microscope data, used computer programs written to find pair correlations as well as higher order correlations. With these programs, it is possible to reliably locate and measure nanocrystal molecules in TEM images. The final area of research explored the use of DNA ligase in the formation of nanocrystal molecules. Synthesis of dimers of gold particles linked with a single strand of DNA possible through the use of DNA ligase opens the possibility for amplification of nanostructures in a manner similar to polymerase chain reaction. These three areas are discussed in the context of the work in the Alivisatos group, as well as the field as a whole.

  8. Separator-Integrated, Reversely Connectable Symmetric Lithium-Ion Battery.

    Science.gov (United States)

    Wang, Yuhang; Zeng, Jiren; Cui, Xiaoqi; Zhang, Lijuan; Zheng, Gengfeng

    2016-02-24

    A separator-integrated, reversely connectable, symmetric lithium-ion battery is developed based on carbon-coated Li3V2(PO4)3 nanoparticles and polyvinylidene fluoride-treated separators. The Li3V2(PO4)3 nanoparticles are synthesized via a facile solution route followed by calcination in Ar/H2 atmosphere. Sucrose solution is used as the carbon source for uniform carbon coating on the Li3V2(PO4)3 nanoparticles. Both the carbon and the polyvinylidene fluoride treatments substantially improve the cycling life of the symmetric battery by preventing the dissolution and shuttle of the electroactive Li3V2(PO4)3. The obtained symmetric full cell exhibits a reversible capacity of ≈ 87 mA h g(-1), good cycling stability, and capacity retention of ≈ 70% after 70 cycles. In addition, this type of symmetric full cell can be operated in both forward and reverse connection modes, without any influence on the cycling of the battery. Furthermore, a new separator integration approach is demonstrated, which enables the direct deposition of electroactive materials for the battery assembly and does not affect the electrochemical performance. A 10-tandem-cell battery assembled without differentiating the electrode polarity exhibits a low thickness of ≈ 4.8 mm and a high output voltage of 20.8 V. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Strong orientational coordinates and orientational order parameters for symmetric objects

    International Nuclear Information System (INIS)

    Haji-Akbari, Amir; Glotzer, Sharon C

    2015-01-01

    Recent advancements in the synthesis of anisotropic macromolecules and nanoparticles have spurred an immense interest in theoretical and computational studies of self-assembly. The cornerstone of such studies is the role of shape in self-assembly and in inducing complex order. The problem of identifying different types of order that can emerge in such systems can, however, be challenging. Here, we revisit the problem of quantifying orientational order in systems of building blocks with non-trivial rotational symmetries. We first propose a systematic way of constructing orientational coordinates for such symmetric building blocks. We call the arising tensorial coordinates strong orientational coordinates (SOCs) as they fully and exclusively specify the orientation of a symmetric object. We then use SOCs to describe and quantify local and global orientational order, and spatiotemporal orientational correlations in systems of symmetric building blocks. The SOCs and the orientational order parameters developed in this work are not only useful in performing and analyzing computer simulations of symmetric molecules or particles, but can also be utilized for the efficient storage of rotational information in long trajectories of evolving many-body systems. (paper)

  10. Proteins evolve on the edge of supramolecular self-assembly

    Science.gov (United States)

    Garcia-Seisdedos, Hector; Empereur-Mot, Charly; Elad, Nadav; Levy, Emmanuel D.

    2017-08-01

    The self-association of proteins into symmetric complexes is ubiquitous in all kingdoms of life. Symmetric complexes possess unique geometric and functional properties, but their internal symmetry can pose a risk. In sickle-cell disease, the symmetry of haemoglobin exacerbates the effect of a mutation, triggering assembly into harmful fibrils. Here we examine the universality of this mechanism and its relation to protein structure geometry. We introduced point mutations solely designed to increase surface hydrophobicity among 12 distinct symmetric complexes from Escherichia coli. Notably, all responded by forming supramolecular assemblies in vitro, as well as in vivo upon heterologous expression in Saccharomyces cerevisiae. Remarkably, in four cases, micrometre-long fibrils formed in vivo in response to a single point mutation. Biophysical measurements and electron microscopy revealed that mutants self-assembled in their folded states and so were not amyloid-like. Structural examination of 73 mutants identified supramolecular assembly hot spots predictable by geometry. A subsequent structural analysis of 7,471 symmetric complexes showed that geometric hot spots were buffered chemically by hydrophilic residues, suggesting a mechanism preventing mis-assembly of these regions. Thus, point mutations can frequently trigger folded proteins to self-assemble into higher-order structures. This potential is counterbalanced by negative selection and can be exploited to design nanomaterials in living cells.

  11. Biomolecular electrostatics and solvation: a computational perspective.

    Science.gov (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A

    2012-11-01

    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  12. Direct Electron Transfer of Enzymes in a Biologically Assembled Conductive Nanomesh Enzyme Platform.

    Science.gov (United States)

    Lee, Seung-Woo; Lee, Ki-Young; Song, Yong-Won; Choi, Won Kook; Chang, Joonyeon; Yi, Hyunjung

    2016-02-24

    Nondestructive assembly of a nanostructured enzyme platform is developed in combination of the specific biomolecular attraction and electrostatic coupling for highly efficient direct electron transfer (DET) of enzymes with unprecedented applicability and versatility. The biologically assembled conductive nanomesh enzyme platform enables DET-based flexible integrated biosensors and DET of eight different enzyme with various catalytic activities. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

    Science.gov (United States)

    Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

    2017-10-01

    The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  14. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly.

    Directory of Open Access Journals (Sweden)

    Andreas I Andreou

    Full Text Available Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.

  15. Membrane-based biomolecular smart materials

    International Nuclear Information System (INIS)

    Sarles, Stephen A; Leo, Donald J

    2011-01-01

    Membrane-based biomolecular materials are a new class of smart material that feature networks of artificial lipid bilayers contained within durable synthetic substrates. Bilayers contained within this modular material platform provide an environment that can be tailored to host an enormous diversity of functional biomolecules, where the functionality of the global material system depends on the type(s) and organization(s) of the biomolecules that are chosen. In this paper, we review a series of biomolecular material platforms developed recently within the Leo Group at Virginia Tech and we discuss several novel coupling mechanisms provided by these hybrid material systems. The platforms developed demonstrate that the functions of biomolecules and the properties of synthetic materials can be combined to operate in concert, and the examples provided demonstrate how the formation and properties of a lipid bilayer can respond to a variety of stimuli including mechanical forces and electric fields

  16. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    Conducting polymers; LB films; biosensor microactuators; monolayers. ... have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices.

  17. Aligning Biomolecular Networks Using Modular Graph Kernels

    Science.gov (United States)

    Towfic, Fadi; Greenlee, M. Heather West; Honavar, Vasant

    Comparative analysis of biomolecular networks constructed using measurements from different conditions, tissues, and organisms offer a powerful approach to understanding the structure, function, dynamics, and evolution of complex biological systems. We explore a class of algorithms for aligning large biomolecular networks by breaking down such networks into subgraphs and computing the alignment of the networks based on the alignment of their subgraphs. The resulting subnetworks are compared using graph kernels as scoring functions. We provide implementations of the resulting algorithms as part of BiNA, an open source biomolecular network alignment toolkit. Our experiments using Drosophila melanogaster, Saccharomyces cerevisiae, Mus musculus and Homo sapiens protein-protein interaction networks extracted from the DIP repository of protein-protein interaction data demonstrate that the performance of the proposed algorithms (as measured by % GO term enrichment of subnetworks identified by the alignment) is competitive with some of the state-of-the-art algorithms for pair-wise alignment of large protein-protein interaction networks. Our results also show that the inter-species similarity scores computed based on graph kernels can be used to cluster the species into a species tree that is consistent with the known phylogenetic relationships among the species.

  18. Biomolecular simulation: historical picture and future perspectives.

    Science.gov (United States)

    van Gunsteren, Wilfred F; Dolenc, Jozica

    2008-02-01

    Over the last 30 years, computation based on molecular models is playing an increasingly important role in biology, biological chemistry and biophysics. Since only a very limited number of properties of biomolecular systems are actually accessible to measurement by experimental means, computer simulation complements experiments by providing not only averages, but also distributions and time series of any definable, observable or non-observable, quantity. Biomolecular simulation may be used (i) to interpret experimental data, (ii) to provoke new experiments, (iii) to replace experiments and (iv) to protect intellectual property. Progress over the last 30 years is sketched and perspectives are outlined for the future.

  19. PREFACE: Radiation Damage in Biomolecular Systems (RADAM07)

    Science.gov (United States)

    McGuigan, Kevin G.

    2008-03-01

    , which include: theoretical, experimental, medical and computational physicists, radiation chemists, radiation biologists and microbiologists, among others. An important aspect of the previous 3 conferences in this series was to remove barriers between the different working groups and to encourage a more interdisciplinary approach to research collaborations. During RADAM_07 we could observe the success of these efforts. A large number of presentations were based on new collaborations, many funded under the COST STSM programme, and all presentations led to lively discussions. It is clear from the discussions following many of the presentations and at the poster sessions that Radiation Damage in Biomolecular Systems remains a topic of increasing interest, relevance and importance. The success of this conference as well as of the whole RADAM conference series reflects the growing international interest in the area of interactions of ionizing radiation with biomolecules. Despite the scheduled conclusion in September 2007 of COST Action P9 which has part-funded this, and previous RADAM meetings, the nature of the cross-disciplinary interactions and opportunities for collaborative research was deemed so successful and valuable by the assembled delegates that it was agreed that another such meeting should be held in Debrecen in Hungary from 13-15 June 2008 http://www.isa.au.dk/meetings/radam2008/programme.html. Additional information about RADAM07 programme is available on the conference web-page http://www.isa.au.dk/networks/cost/radam07/index.html. The Organizing Committee would like to thank all speakers, contributors, session chairs, referees and meeting staff for their efforts in making the RADAM07 successful. The local Organization Committee would like to thank Lorraine Monard and Margaret Nolan for their invaluable expertise in conference management. We also gratefully acknowledge the financial support of our sponsors - The Royal, College of Surgeons in Ireland (RCSI

  20. Symmetric Pin Diversion Detection using a Partial Defect Detector (PDET)

    International Nuclear Information System (INIS)

    Sitaraman, S.; Ham, Y.S.

    2009-01-01

    Since the signature from the Partial Defect Detector (PDET) is principally dependent on the geometric layout of the guide tube locations, the capability of the technique in detecting symmetric diversion of pins needs to be determined. The Monte Carlo simulation study consisted of cases where pins were removed in a symmetric manner and the resulting signatures were examined. In addition to the normalized gamma-to-neutron ratios, the neutron and gamma signatures normalized to their maximum values, were also examined. Examination of the shape of the three curves as well as of the peak-to-valley differences in excess of the maximum expected in intact assemblies, indicated pin diversion. A set of simulations with various symmetric patterns of diversion were examined. The results from these studies indicated that symmetric diversions as low as twelve percent could be detected by this methodology

  1. Cucurbit[8]uril ternary complexes for biomolecular assemblies in solution and at interfaces

    NARCIS (Netherlands)

    Cavatorta, E.

    2016-01-01

    Self-assembly allows for rationally designed molecular platforms that exploit specific, directional, tunable and reversible non-covalent interactions. The dynamic nature of such supramolecular interactions gives rise to self-assembled systems that can sense and respond to physiological cues, or that

  2. Zwitterionic Silane Copolymer for Ultra-Stable and Bright Biomolecular Probes Based on Fluorescent Quantum Dot Nanoclusters.

    Science.gov (United States)

    Dembele, Fatimata; Tasso, Mariana; Trapiella-Alfonso, Laura; Xu, Xiangzhen; Hanafi, Mohamed; Lequeux, Nicolas; Pons, Thomas

    2017-05-31

    Fluorescent semiconductor quantum dots (QDs) exhibit several unique properties that make them suitable candidates for biomolecular sensing, including high brightness, photostability, broad excitation, and narrow emission spectra. Assembling these QDs into robust and functionalizable nanosized clusters (QD-NSCs) can provide fluorescent probes that are several orders of magnitude brighter than individual QDs, thus allowing an even greater sensitivity of detection with simplified instrumentation. However, the formation of compact, antifouling, functionalizable, and stable QD-NSCs remains a challenging task, especially for a use at ultralow concentrations for single-molecule detection. Here, we describe the development of fluorescent QD-NSCs envisioned as a tool for fast and sensitive biomolecular recognition. First, QDs were assembled into very compact 100-150 nm diameter spherical aggregates; the final QD-NSCs were obtained by growing a cross-linked silica shell around these aggregates. Hydrolytic stability in several concentration and pH conditions is a key requirement for a potential and efficient single-molecule detection tool. However, the hydrolysis of Si-O-Si bonds leads to desorption of monosilane-based surface groups at very low silica concentrations or in a slightly basic medium. Thus, we designed a novel multidentate copolymer composed of multiple silane as well as zwitterionic monomers. Coating silica beads with this multidentate copolymer provided a robust surface chemistry that was demonstrated to be stable against hydrolysis, even at low concentrations. Copolymer-coated silica beads also showed low fouling properties and high colloidal stability in saline solutions. Furthermore, incorporation of additional azido-monomers enabled easy functionalization of QD-NSCs using copper-free bio-orthogonal cyclooctyne-azide click chemistry, as demonstrated by a biotin-streptavidin affinity test.

  3. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng

    2010-03-01

    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  4. Laser photodissociation and spectroscopy of mass-separated biomolecular ions

    CERN Document Server

    Polfer, Nicolas C

    2014-01-01

    This lecture notes book presents how enhanced structural information of biomolecular ions can be obtained from interaction with photons of specific frequency - laser light. The methods described in the book ""Laser photodissociation and spectroscopy of mass-separated biomolecular ions"" make use of the fact that the discrete energy and fast time scale of photoexcitation can provide more control in ion activation. This activation is the crucial process producing structure-informative product ions that cannot be generated with more conventional heating methods, such as collisional activation. Th

  5. Vibrational dynamics of icosahedrally symmetric biomolecular assemblies compared with predictions based on continuum elasticity.

    Science.gov (United States)

    Yang, Zheng; Bahar, Ivet; Widom, Michael

    2009-06-03

    Coarse-grained elastic network models elucidate the fluctuation dynamics of proteins around their native conformations. Low-frequency collective motions derived by simplified normal mode analysis are usually involved in biological function, and these motions often possess noteworthy symmetries related to the overall shape of the molecule. Here, insights into these motions and their frequencies are sought by considering continuum models with appropriate symmetry and boundary conditions to approximately represent the true atomistic molecular structure. We solve the elastic wave equations analytically for the case of spherical symmetry, yielding a symmetry-based classification of molecular motions together with explicit predictions for their vibrational frequencies. We address the case of icosahedral symmetry as a perturbation to the spherical case. Applications to lumazine synthase, satellite tobacco mosaic virus, and brome mosaic virus show that the spherical elastic model efficiently provides insights on collective motions that are otherwise obtained by detailed elastic network models. A major utility of the continuum models is the possibility of estimating macroscopic material properties such as the Young's modulus or Poisson's ratio for different types of viruses.

  6. Swell Gels to Dumbbell Micelles: Construction of Materials and Nanostructure with Self-assembly

    Science.gov (United States)

    Pochan, Darrin

    2007-03-01

    Bionanotechnology, the emerging field of using biomolecular and biotechnological tools for nanostructure or nanotecnology development, provides exceptional opportunity in the design of new materials. Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic or charged synthetic polymer molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic interactions; in addition to more traditional self-assembling molecular attributes such as amphiphilicty, to define hierarchical material structure and consequent properties. Several molecular systems will be discussed. Synthetic block copolymers with charged corona blocks can be assembled in dilute solution containing multivalent organic counterions to produce micelle structures such as toroids. These ring-like micelles are similar to the toroidal bundling of charged semiflexible biopolymers like DNA in the presence of multivalent counterions. Micelle structure can be tuned between toroids, cylinders, and disks simply by using different concentrations or molecular volumes of organic counterion. In addition, these charged blocks can consist of amino acids as monomers producing block copolypeptides. In addition to the above attributes, block copolypeptides provide the control of block secondary structure to further control self-assembly. Design strategies based on small (less than 24 amino acids) beta-hairpin peptides will be discussed. Self-assembly of the peptides is predicated on an intramolecular folding event caused by desired solution properties. Importantly, the intramolecular folding event impart a molecular-level mechanism for environmental responsiveness at the material level (e.g. infinite change in viscosity of a solution to a gel with changes in pH, ionic strength, temperature).

  7. NMRbox: A Resource for Biomolecular NMR Computation.

    Science.gov (United States)

    Maciejewski, Mark W; Schuyler, Adam D; Gryk, Michael R; Moraru, Ion I; Romero, Pedro R; Ulrich, Eldon L; Eghbalnia, Hamid R; Livny, Miron; Delaglio, Frank; Hoch, Jeffrey C

    2017-04-25

    Advances in computation have been enabling many recent advances in biomolecular applications of NMR. Due to the wide diversity of applications of NMR, the number and variety of software packages for processing and analyzing NMR data is quite large, with labs relying on dozens, if not hundreds of software packages. Discovery, acquisition, installation, and maintenance of all these packages is a burdensome task. Because the majority of software packages originate in academic labs, persistence of the software is compromised when developers graduate, funding ceases, or investigators turn to other projects. To simplify access to and use of biomolecular NMR software, foster persistence, and enhance reproducibility of computational workflows, we have developed NMRbox, a shared resource for NMR software and computation. NMRbox employs virtualization to provide a comprehensive software environment preconfigured with hundreds of software packages, available as a downloadable virtual machine or as a Platform-as-a-Service supported by a dedicated compute cloud. Ongoing development includes a metadata harvester to regularize, annotate, and preserve workflows and facilitate and enhance data depositions to BioMagResBank, and tools for Bayesian inference to enhance the robustness and extensibility of computational analyses. In addition to facilitating use and preservation of the rich and dynamic software environment for biomolecular NMR, NMRbox fosters the development and deployment of a new class of metasoftware packages. NMRbox is freely available to not-for-profit users. Copyright © 2017 Biophysical Society. All rights reserved.

  8. Quantifying the topography of the intrinsic energy landscape of flexible biomolecular recognition

    Science.gov (United States)

    Chu, Xiakun; Gan, Linfeng; Wang, Erkang; Wang, Jin

    2013-01-01

    Biomolecular functions are determined by their interactions with other molecules. Biomolecular recognition is often flexible and associated with large conformational changes involving both binding and folding. However, the global and physical understanding for the process is still challenging. Here, we quantified the intrinsic energy landscapes of flexible biomolecular recognition in terms of binding–folding dynamics for 15 homodimers by exploring the underlying density of states, using a structure-based model both with and without considering energetic roughness. By quantifying three individual effective intrinsic energy landscapes (one for interfacial binding, two for monomeric folding), the association mechanisms for flexible recognition of 15 homodimers can be classified into two-state cooperative “coupled binding–folding” and three-state noncooperative “folding prior to binding” scenarios. We found that the association mechanism of flexible biomolecular recognition relies on the interplay between the underlying effective intrinsic binding and folding energy landscapes. By quantifying the whole global intrinsic binding–folding energy landscapes, we found strong correlations between the landscape topography measure Λ (dimensionless ratio of energy gap versus roughness modulated by the configurational entropy) and the ratio of the thermodynamic stable temperature versus trapping temperature, as well as between Λ and binding kinetics. Therefore, the global energy landscape topography determines the binding–folding thermodynamics and kinetics, crucial for the feasibility and efficiency of realizing biomolecular function. We also found “U-shape” temperature-dependent kinetic behavior and a dynamical cross-over temperature for dividing exponential and nonexponential kinetics for two-state homodimers. Our study provides a unique way to bridge the gap between theory and experiments. PMID:23754431

  9. Biomolecular modelling and simulations

    CERN Document Server

    Karabencheva-Christova, Tatyana

    2014-01-01

    Published continuously since 1944, the Advances in Protein Chemistry and Structural Biology series is the essential resource for protein chemists. Each volume brings forth new information about protocols and analysis of proteins. Each thematically organized volume is guest edited by leading experts in a broad range of protein-related topics. Describes advances in biomolecular modelling and simulations Chapters are written by authorities in their field Targeted to a wide audience of researchers, specialists, and students The information provided in the volume is well supported by a number of high quality illustrations, figures, and tables.

  10. Modeling, Analysis, Simulation, and Synthesis of Biomolecular Networks

    National Research Council Canada - National Science Library

    Ruben, Harvey; Kumar, Vijay; Sokolsky, Oleg

    2006-01-01

    ...) a first example of reachability analysis applied to a biomolecular system (lactose induction), 4) a model of tetracycline resistance that discriminates between two possible mechanisms for tetracycline diffusion through the cell membrane, and 5...

  11. Biomolecular structure refinement using the GROMOS simulation software

    International Nuclear Information System (INIS)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jožica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van

    2011-01-01

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  12. Biomolecular structure refinement using the GROMOS simulation software

    Energy Technology Data Exchange (ETDEWEB)

    Schmid, Nathan; Allison, Jane R.; Dolenc, Jozica; Eichenberger, Andreas P.; Kunz, Anna-Pitschna E.; Gunsteren, Wilfred F. van, E-mail: wfvgn@igc.phys.chem.ethz.ch [Swiss Federal Institute of Technology ETH, Laboratory of Physical Chemistry (Switzerland)

    2011-11-15

    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, {sup 3}J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

  13. A compact hard X-ray source for medical imaging and biomolecular studies

    International Nuclear Information System (INIS)

    Cline, D.B.; Green, M.A.; Kolonko, J.

    1995-01-01

    There are a large number of synchrotron light sources in the world. However, these sources are designed for physics, chemistry, and engineering studies. To our knowledge, none have been optimized for either medical imaging or biomolecular studies. There are special needs for these applications. We present here a preliminary design of a very compact source, small enough for a hospital or a biomolecular laboratory, that is suitable for these applications. (orig.)

  14. Biomolecular strategies for cell surface engineering

    Science.gov (United States)

    Wilson, John Tanner

    Islet transplantation has emerged as a promising cell-based therapy for the treatment of diabetes, but its clinical efficacy remains limited by deleterious host responses that underlie islet destruction. In this dissertation, we describe the assembly of ultrathin conformal coatings that confer molecular-level control over the composition and biophysicochemical properties of the islet surface with implications for improving islet engraftment. Significantly, this work provides novel biomolecular strategies for cell surface engineering with broad biomedical and biotechnological applications in cell-based therapeutics and beyond. Encapsulation of cells and tissue offers a rational approach for attenuating deleterious host responses towards transplanted cells, but a need exists to develop cell encapsulation strategies that minimize transplant volume. Towards this end, we endeavored to generate nanothin films of diverse architecture with tunable properties on the extracellular surface of individual pancreatic islets through a process of layer-by-layer (LbL) self assembly. We first describe the formation of poly(ethylene glycol) (PEG)-rich conformal coatings on islets via LbL self assembly of poly(L-lysine)-g-PEG(biotin) and streptavidin. Multilayer thin films conformed to the geometrically and chemically heterogeneous islet surface, and could be assembled without loss of islet viability or function. Significantly, coated islets performed comparably to untreated controls in a murine model of allogenic intraportal islet transplantation, and, to our knowledge, this is the first study to report in vivo survival and function of nanoencapsulated cells or cell aggregates. Based on these findings, we next postulated that structurally similar PLL-g-PEG copolymers comprised of shorter PEG grafts might be used to initiate and propagate the assembly of polyelectrolyte multilayer (PEM) films on pancreatic islets, while simultaneously preserving islet viability. Through control of PLL

  15. Causal symmetric spaces

    CERN Document Server

    Olafsson, Gestur; Helgason, Sigurdur

    1996-01-01

    This book is intended to introduce researchers and graduate students to the concepts of causal symmetric spaces. To date, results of recent studies considered standard by specialists have not been widely published. This book seeks to bring this information to students and researchers in geometry and analysis on causal symmetric spaces.Includes the newest results in harmonic analysis including Spherical functions on ordered symmetric space and the holmorphic discrete series and Hardy spaces on compactly casual symmetric spacesDeals with the infinitesimal situation, coverings of symmetric spaces, classification of causal symmetric pairs and invariant cone fieldsPresents basic geometric properties of semi-simple symmetric spacesIncludes appendices on Lie algebras and Lie groups, Bounded symmetric domains (Cayley transforms), Antiholomorphic Involutions on Bounded Domains and Para-Hermitian Symmetric Spaces

  16. Improvements to the APBS biomolecular solvation software suite: Improvements to the APBS Software Suite

    Energy Technology Data Exchange (ETDEWEB)

    Jurrus, Elizabeth [Pacific Northwest National Laboratory, Richland Washington; Engel, Dave [Pacific Northwest National Laboratory, Richland Washington; Star, Keith [Pacific Northwest National Laboratory, Richland Washington; Monson, Kyle [Pacific Northwest National Laboratory, Richland Washington; Brandi, Juan [Pacific Northwest National Laboratory, Richland Washington; Felberg, Lisa E. [University of California, Berkeley California; Brookes, David H. [University of California, Berkeley California; Wilson, Leighton [University of Michigan, Ann Arbor Michigan; Chen, Jiahui [Southern Methodist University, Dallas Texas; Liles, Karina [Pacific Northwest National Laboratory, Richland Washington; Chun, Minju [Pacific Northwest National Laboratory, Richland Washington; Li, Peter [Pacific Northwest National Laboratory, Richland Washington; Gohara, David W. [St. Louis University, St. Louis Missouri; Dolinsky, Todd [FoodLogiQ, Durham North Carolina; Konecny, Robert [University of California San Diego, San Diego California; Koes, David R. [University of Pittsburgh, Pittsburgh Pennsylvania; Nielsen, Jens Erik [Protein Engineering, Novozymes A/S, Copenhagen Denmark; Head-Gordon, Teresa [University of California, Berkeley California; Geng, Weihua [Southern Methodist University, Dallas Texas; Krasny, Robert [University of Michigan, Ann Arbor Michigan; Wei, Guo-Wei [Michigan State University, East Lansing Michigan; Holst, Michael J. [University of California San Diego, San Diego California; McCammon, J. Andrew [University of California San Diego, San Diego California; Baker, Nathan A. [Pacific Northwest National Laboratory, Richland Washington; Brown University, Providence Rhode Island

    2017-10-24

    The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining pKa values, and an improved web-based visualization tool for viewing electrostatics.

  17. Terminating DNA Tile Assembly with Nanostructured Caps.

    Science.gov (United States)

    Agrawal, Deepak K; Jiang, Ruoyu; Reinhart, Seth; Mohammed, Abdul M; Jorgenson, Tyler D; Schulman, Rebecca

    2017-10-24

    Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes. We find that nanostructures that present binding interfaces for all of the binding sites on a growing facet can bind selectively to growing ends and stop growth when these interfaces are presented on either a rigid or floppy scaffold. In contrast, nucleation of nanotubes requires the presentation of binding sites in an arrangement that matches the shape of the structure's facet. As a result, it is possible to build nanostructures that can terminate the growth of existing nanotubes but cannot nucleate a new structure. The resulting design principles for constructing structures that direct nucleation and termination of the growth of one-dimensional nanostructures can also serve as a starting point for programmatically directing two- and three-dimensional crystallization processes using nanostructure design.

  18. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    International Nuclear Information System (INIS)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong

    2009-01-01

    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml -1 -100 ng ml -1 at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  19. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    Science.gov (United States)

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations.

  20. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  1. FY 2000 report on the results of the R and D of the fusion domain. Volume 3. Biomolecular mechanism and design; 2000 nendo yugo ryoiki kenkyu kaihatsu. 3. Biomolecular mechanism and design

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-03-01

    For the purpose of creating cells/tissue assemblies and the molecular machine that substitute for self-organizing and self-repairing functions of a living body outside the body, the basic technology research was conducted, and the FY 2000 results were reported. In the study of 3D cell and tissue module engineering, the following were conducted: study of the surface modification and functional expression of biomaterials, study of the mechanical stress to cartilaginous cells and the response, development of the production method of biodegradable synthetic polymer porous materials, study of organism hard tissue materials/bone remodeling and cultured bone transportation, development of zinc-releasing calcium phosphate ceramics. In the study of biomolecular mechanism and design, 1D unidirectional movement of microtubules by applying microlithography technology, structural study of kinesin-family molecular motor by low temperature microscope, ribozyme and the application to leukemia, basic study on assessment of chemical substances by human cultured cells, study of a low molecule detection system using nucleic acid and peptide. (NEDO)

  2. Gigadalton-scale shape-programmable DNA assemblies

    Science.gov (United States)

    Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik

    2017-12-01

    Natural biomolecular assemblies such as molecular motors, enzymes, viruses and subcellular structures often form by self-limiting hierarchical oligomerization of multiple subunits. Large structures can also assemble efficiently from a few components by combining hierarchical assembly and symmetry, a strategy exemplified by viral capsids. De novo protein design and RNA and DNA nanotechnology aim to mimic these capabilities, but the bottom-up construction of artificial structures with the dimensions and complexity of viruses and other subcellular components remains challenging. Here we show that natural assembly principles can be combined with the methods of DNA origami to produce gigadalton-scale structures with controlled sizes. DNA sequence information is used to encode the shapes of individual DNA origami building blocks, and the geometry and details of the interactions between these building blocks then control their copy numbers, positions and orientations within higher-order assemblies. We illustrate this strategy by creating planar rings of up to 350 nanometres in diameter and with atomic masses of up to 330 megadaltons, micrometre-long, thick tubes commensurate in size to some bacilli, and three-dimensional polyhedral assemblies with sizes of up to 1.2 gigadaltons and 450 nanometres in diameter. We achieve efficient assembly, with yields of up to 90 per cent, by using building blocks with validated structure and sufficient rigidity, and an accurate design with interaction motifs that ensure that hierarchical assembly is self-limiting and able to proceed in equilibrium to allow for error correction. We expect that our method, which enables the self-assembly of structures with sizes approaching that of viruses and cellular organelles, can readily be used to create a range of other complex structures with well defined sizes, by exploiting the modularity and high degree of addressability of the DNA origami building blocks used.

  3. DNA algorithms of implementing biomolecular databases on a biological computer.

    Science.gov (United States)

    Chang, Weng-Long; Vasilakos, Athanasios V

    2015-01-01

    In this paper, DNA algorithms are proposed to perform eight operations of relational algebra (calculus), which include Cartesian product, union, set difference, selection, projection, intersection, join, and division, on biomolecular relational databases.

  4. Smartphones for cell and biomolecular detection.

    Science.gov (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B

    2014-11-01

    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  5. Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

    Science.gov (United States)

    Mallik, Saurav; Kundu, Sudip

    2017-07-01

    Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  6. Final Scientific Report - Electromagnetic Interactions in Self-Assembled Metallo-Dielectric Biomaterials

    Energy Technology Data Exchange (ETDEWEB)

    Dragnea, Bogdan G. [Indiana Univ., Bloomington, IN (United States)

    2017-05-03

    Achievements which resulted from previous DOE funding include: templated virus-like particle assembly thermodynamics, development of single particle photothermal absorption spectroscopy and dark- field spectroscopy instrumentation for the measurement of optical properties of virus-like nanoparticles, electromagnetic simulations of coupled nanoparticle cluster systems, virus contact mechanics, energy transfer and fluorescence quenching in multichromophore systems supported on biomolecular templates, and photo physical work on virus-aptamer systems. A current total of eight published research articles and a book chapter are acknowledging DOE support for the period 2013-2016.

  7. Synthesis and Structure of D3h-Symmetric Triptycene Trimaleimide

    Directory of Open Access Journals (Sweden)

    Anthony Linden

    2010-01-01

    Full Text Available A new D3h symmetric triptycene derivative has been synthesized with the aim of obtaining molecules that are able to assemble into porous structures, and can be used in the development of new ligands. The synthesis involves a Diels-Alder reaction as the key step, followed by an oxidation and the formation of a maleimide ring. Triptycene trimaleimide furnished single crystals which have been analyzed by means of X-ray diffraction.

  8. Facade Layout Symmetrization

    KAUST Repository

    Jiang, Haiyong

    2016-04-11

    We present an automatic algorithm for symmetrizing facade layouts. Our method symmetrizes a given facade layout while minimally modifying the original layout. Based on the principles of symmetry in urban design, we formulate the problem of facade layout symmetrization as an optimization problem. Our system further enhances the regularity of the final layout by redistributing and aligning boxes in the layout. We demonstrate that the proposed solution can generate symmetric facade layouts efficiently. © 2015 IEEE.

  9. Facade Layout Symmetrization

    KAUST Repository

    Jiang, Haiyong; Dong, Weiming; Yan, Dongming; Zhang, Xiaopeng

    2016-01-01

    We present an automatic algorithm for symmetrizing facade layouts. Our method symmetrizes a given facade layout while minimally modifying the original layout. Based on the principles of symmetry in urban design, we formulate the problem of facade layout symmetrization as an optimization problem. Our system further enhances the regularity of the final layout by redistributing and aligning boxes in the layout. We demonstrate that the proposed solution can generate symmetric facade layouts efficiently. © 2015 IEEE.

  10. Symmetric cryptographic protocols

    CERN Document Server

    Ramkumar, Mahalingam

    2014-01-01

    This book focuses on protocols and constructions that make good use of symmetric pseudo random functions (PRF) like block ciphers and hash functions - the building blocks for symmetric cryptography. Readers will benefit from detailed discussion of several strategies for utilizing symmetric PRFs. Coverage includes various key distribution strategies for unicast, broadcast and multicast security, and strategies for constructing efficient digests of dynamic databases using binary hash trees.   •        Provides detailed coverage of symmetric key protocols •        Describes various applications of symmetric building blocks •        Includes strategies for constructing compact and efficient digests of dynamic databases

  11. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.|info:eu-repo/dai/nl/304837717; van Dijk, M.|info:eu-repo/dai/nl/325811113; Bonvin, A.M.J.J.|info:eu-repo/dai/nl/113691238

    2010-01-01

    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  12. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

    Science.gov (United States)

    Papini, Christina; Royer, Catherine A

    2018-02-01

    Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

  13. GROMOS++Software for the Analysis of Biomolecular Simulation Trajectories

    NARCIS (Netherlands)

    Eichenberger, A.P.; Allison, J.R.; Dolenc, J.; Geerke, D.P.; Horta, B.A.C.; Meier, K; Oostenbrink, B.C.; Schmid, N.; Steiner, D; Wang, D.; van Gunsteren, W.F.

    2011-01-01

    GROMOS++ is a set of C++ programs for pre- and postprocessing of molecular dynamics simulation trajectories and as such is part of the GROningen MOlecular Simulation software for (bio)molecular simulation. It contains more than 70 programs that can be used to prepare data for the production of

  14. Unique temporal and spatial biomolecular emission profile on individual zinc oxide nanorods

    Science.gov (United States)

    Singh, Manpreet; Song, Sheng; Hahm, Jong-In

    2013-12-01

    Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical signal-enhancing platforms in DNA and protein detection. Although the use of ZnO NRs in biodetection has been demonstrated so far in systems involving many ZnO NRs per detection element, their future applications will likely take place in a miniaturized setting while exploiting single ZnO NRs in a low-volume, high-throughput bioanalysis. In this paper, we investigate temporal and spatial characteristics of the biomolecular fluorescence on individual ZnO NR systems. Quantitative and qualitative examinations of the biomolecular intensity and photostability are carried out as a function of two important criteria, the time and position along the long axis (length) of NRs. Photostability profiles are also measured with respect to the position on NRs and compared to those characteristics of biomolecules on polymeric control platforms. Unlike the uniformly distributed signal observed on the control platforms, both the fluorescence intensity and photostability are position-dependent on individual ZnO NRs. We have identified a unique phenomenon of highly localized, fluorescence intensification on the nanorod ends (FINE) of well-characterized, individual ZnO nanostructures. When compared to the polymeric controls, the biomolecular fluorescence intensity and photostability are determined to be higher on individual ZnO NRs regardless of the position on NRs. We have also carried out finite-difference time-domain simulations the results of which are in good agreement with the observed FINE. The outcomes of our investigation will offer a much needed basis for signal interpretation for biodetection devices and platforms consisting of single ZnO NRs and, at the same time, contribute significantly to provide insight in understanding the biomolecular fluorescence observed from ZnO NR ensemble-based systems.Zinc oxide nanorods (ZnO NRs) have emerged in recent years as extremely useful, optical

  15. Effect of intermolecular dipole-dipole interactions on interfacial supramolecular structures of C3-symmetric hexa-peri-hexabenzocoronene derivatives.

    Science.gov (United States)

    Mu, Zhongcheng; Shao, Qi; Ye, Jun; Zeng, Zebing; Zhao, Yang; Hng, Huey Hoon; Boey, Freddy Yin Chiang; Wu, Jishan; Chen, Xiaodong

    2011-02-15

    Two-dimensional (2D) supramolecular assemblies of a series of novel C(3)-symmetric hexa-peri-hexabenzocoronene (HBC) derivatives bearing different substituents adsorbed on highly oriented pyrolytic graphite were studied by using scanning tunneling microscopy at a solid-liquid interface. It was found that the intermolecular dipole-dipole interactions play a critical role in controlling the interfacial supramolecular assembly of these C(3)-symmetric HBC derivatives at the solid-liquid interface. The HBC molecule bearing three -CF(3) groups could form 2D honeycomb structures because of antiparallel dipole-dipole interactions, whereas HBC molecules bearing three -CN or -NO(2) groups could form hexagonal superstructures because of a special trimeric arrangement induced by dipole-dipole interactions and weak hydrogen bonding interactions ([C-H···NC-] or [C-H···O(2)N-]). Molecular mechanics and dynamics simulations were performed to reveal the physics behind the 2D structures as well as detailed functional group interactions. This work provides an example of how intermolecular dipole-dipole interactions could enable fine control over the self-assembly of disklike π-conjugated molecules.

  16. Biomolecular logic systems: applications to biosensors and bioactuators

    Science.gov (United States)

    Katz, Evgeny

    2014-05-01

    The paper presents an overview of recent advances in biosensors and bioactuators based on the biocomputing concept. Novel biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce output in the form of YES/NO response. Compared to traditional single-analyte sensing devices, biocomputing approach enables a high-fidelity multi-analyte biosensing, particularly beneficial for biomedical applications. Multi-signal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert to medical emergencies, along with an immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly exemplified for liver injury. Wide-ranging applications of multi-analyte digital biosensors in medicine, environmental monitoring and homeland security are anticipated. "Smart" bioactuators, for example for signal-triggered drug release, were designed by interfacing switchable electrodes and biocomputing systems. Integration of novel biosensing and bioactuating systems with the biomolecular information processing systems keeps promise for further scientific advances and numerous practical applications.

  17. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel

    2016-01-01

    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  18. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    Science.gov (United States)

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  19. hPDB – Haskell library for processing atomic biomolecular structures in protein data bank format

    OpenAIRE

    Gajda, Michał Jan

    2013-01-01

    Background Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. Findings I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The propo...

  20. Biologic Constraints on Modelling Virus Assembly

    Directory of Open Access Journals (Sweden)

    Robert L. Garcea

    2008-01-01

    Full Text Available The mathematic modelling of icosahedral virus assembly has drawn increasing interest because of the symmetric geometry of the outer shell structures. Many models involve equilibrium expressions of subunit binding, with reversible subunit additions forming various intermediate structures. The underlying assumption is that a final lowest energy state drives the equilibrium toward assembly. In their simplest forms, these models have explained why high subunit protein concentrations and strong subunit association constants can result in kinetic traps forming off pathway partial and aberrant structures. However, the cell biology of virus assembly is exceedingly complex. The biochemistry and biology of polyoma and papillomavirus assembly described here illustrates many of these specific issues. Variables include the use of cellular ‘chaperone’ proteins as mediators of assembly fidelity, the coupling of assembly to encapsidation of a specific nucleic acid genome, the use of cellular structures as ‘workbenches’ upon which assembly occurs, and the underlying problem of making a capsid structure that is metastable and capable of rapid disassembly upon infection. Although formidable to model, incorporating these considerations could advance the relevance of mathematical models of virus assembly to the real world.

  1. An Overview of Biomolecular Event Extraction from Scientific Documents.

    Science.gov (United States)

    Vanegas, Jorge A; Matos, Sérgio; González, Fabio; Oliveira, José L

    2015-01-01

    This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  2. An Overview of Biomolecular Event Extraction from Scientific Documents

    Directory of Open Access Journals (Sweden)

    Jorge A. Vanegas

    2015-01-01

    Full Text Available This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

  3. Role of biomolecular logic systems in biosensors and bioactuators

    Science.gov (United States)

    Mailloux, Shay; Katz, Evgeny

    2014-09-01

    An overview of recent advances in biosensors and bioactuators based on biocomputing systems is presented. Biosensors digitally process multiple biochemical signals through Boolean logic networks of coupled biomolecular reactions and produce an output in the form of a YES/NO response. Compared to traditional single-analyte sensing devices, the biocomputing approach enables high-fidelity multianalyte biosensing, which is particularly beneficial for biomedical applications. Multisignal digital biosensors thus promise advances in rapid diagnosis and treatment of diseases by processing complex patterns of physiological biomarkers. Specifically, they can provide timely detection and alert medical personnel of medical emergencies together with immediate therapeutic intervention. Application of the biocomputing concept has been successfully demonstrated for systems performing logic analysis of biomarkers corresponding to different injuries, particularly as exemplified for liver injury. Wide-ranging applications of multianalyte digital biosensors in medicine, environmental monitoring, and homeland security are anticipated. "Smart" bioactuators, for signal-triggered drug release, for example, were designed by interfacing switchable electrodes with biocomputing systems. Integration of biosensing and bioactuating systems with biomolecular information processing systems advances the potential for further scientific innovations and various practical applications.

  4. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert

    2010-05-01

    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  5. On Symmetric Polynomials

    OpenAIRE

    Golden, Ryan; Cho, Ilwoo

    2015-01-01

    In this paper, we study structure theorems of algebras of symmetric functions. Based on a certain relation on elementary symmetric polynomials generating such algebras, we consider perturbation in the algebras. In particular, we understand generators of the algebras as perturbations. From such perturbations, define injective maps on generators, which induce algebra-monomorphisms (or embeddings) on the algebras. They provide inductive structure theorems on algebras of symmetric polynomials. As...

  6. Combinatorial Models for Assembly and Decomposition of Products

    OpenAIRE

    A. N. Bojko

    2015-01-01

    The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the...

  7. Self-powered in-core neutron detector assembly with uniform perturbation characteristics

    International Nuclear Information System (INIS)

    Todt, W.H.; Playfoot, K.C.

    1979-01-01

    Disclosed is a self-powered in-core neutron detector assembly in which a plurality of longitudinally extending self-powered detectors have neutron responsive active portions spaced along a longitudinal path. A low neutron absorptive extension extends from the active portions of the spaced active portions of the detectors in symmetrical longitudinal relationship with the spaced active detector portions of each succeeding detector. The detector extension terminates with the detector assembly to provide a uniform perturbation characteristic over the entire assembly length

  8. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.

    2007-01-01

    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation

  9. Symmetrization of Facade Layouts

    KAUST Repository

    Jiang, Haiyong; Yan, Dong-Ming; Dong, Weiming; Wu, Fuzhang; Nan, Liangliang; Zhang, Xiaopeng

    2016-01-01

    We present an automatic approach for symmetrizing urban facade layouts. Our method can generate a symmetric layout through minimally modifying the original input layout. Based on the principles of symmetry in urban design, we formulate facade layout symmetrization as an optimization problem. Our method further enhances the regularity of the final layout by redistributing and aligning elements in the layout. We demonstrate that the proposed solution can effectively generate symmetric facade layouts.

  10. Symmetrization of Facade Layouts

    KAUST Repository

    Jiang, Haiyong

    2016-02-26

    We present an automatic approach for symmetrizing urban facade layouts. Our method can generate a symmetric layout through minimally modifying the original input layout. Based on the principles of symmetry in urban design, we formulate facade layout symmetrization as an optimization problem. Our method further enhances the regularity of the final layout by redistributing and aligning elements in the layout. We demonstrate that the proposed solution can effectively generate symmetric facade layouts.

  11. Single-molecule imaging and manipulation of biomolecular machines and systems.

    Science.gov (United States)

    Iino, Ryota; Iida, Tatsuya; Nakamura, Akihiko; Saita, Ei-Ichiro; You, Huijuan; Sako, Yasushi

    2018-02-01

    Biological molecular machines support various activities and behaviors of cells, such as energy production, signal transduction, growth, differentiation, and migration. We provide an overview of single-molecule imaging methods involving both small and large probes used to monitor the dynamic motions of molecular machines in vitro (purified proteins) and in living cells, and single-molecule manipulation methods used to measure the forces, mechanical properties and responses of biomolecules. We also introduce several examples of single-molecule analysis, focusing primarily on motor proteins and signal transduction systems. Single-molecule analysis is a powerful approach to unveil the operational mechanisms both of individual molecular machines and of systems consisting of many molecular machines. Quantitative, high-resolution single-molecule analyses of biomolecular systems at the various hierarchies of life will help to answer our fundamental question: "What is life?" This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Changes in biomolecular profile in a single nucleolus during cell fixation.

    Science.gov (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N

    2014-11-04

    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  13. Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces

    Science.gov (United States)

    Szent-Gyorgyi, Chris; Stanfield, Robyn L.; Andreko, Susan; Dempsey, Alison; Ahmed, Mushtaq; Capek, Sara; Waggoner, Alan; Wilson, Ian A.; Bruchez, Marcel P.

    2013-01-01

    We report that a symmetric small molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* Fluorogen Activating Protein (FAP) is a VL domain that binds malachite green dye (MG) to activate intense fluorescence. Crystallography of liganded L5* reveals a 2:1 protein:ligand complex with inclusive C2 symmetry, where MG is almost entirely encapsulated between an antiparallel arrangement of the two VL domains. Unliganded L5* VL domains crystallize as a similar antiparallel VL/VL homodimer. The complementarity determining regions (CDRs) are spatially oriented to form novel VL/VL and VL/ligand interfaces that tightly constrain a propeller conformer of MG. Binding equilibrium analysis suggests highly cooperative assembly to form a very stable VL/MG/VL complex, such that MG behaves as a strong chemical inducer of dimerization. Fusion of two VL domains into a single protein tightens MG binding over 1,000-fold to low picomolar affinity without altering the large binding enthalpy, suggesting that bonding interactions with ligand and restriction of domain movements make independent contributions to binding. Fluorescence activation of a symmetrical fluorogen provides a selection mechanism for the isolation and directed evolution of ternary complexes where unnatural symmetric binding interfaces are favored over canonical antibody interfaces. As exemplified by L5*, these self-reporting complexes may be useful as modulators of protein association or as high affinity protein tags and capture reagents. PMID:23978698

  14. Uniqueness of flat spherically symmetric spacelike hypersurfaces admitted by spherically symmetric static spacetimes

    Science.gov (United States)

    Beig, Robert; Siddiqui, Azad A.

    2007-11-01

    It is known that spherically symmetric static spacetimes admit a foliation by flat hypersurfaces. Such foliations have explicitly been constructed for some spacetimes, using different approaches, but none of them have proved or even discussed the uniqueness of these foliations. The issue of uniqueness becomes more important due to suitability of flat foliations for studying black hole physics. Here, flat spherically symmetric spacelike hypersurfaces are obtained by a direct method. It is found that spherically symmetric static spacetimes admit flat spherically symmetric hypersurfaces, and that these hypersurfaces are unique up to translation under the timelike Killing vector. This result guarantees the uniqueness of flat spherically symmetric foliations for such spacetimes.

  15. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis.

    Science.gov (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie

    2013-12-15

    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. Affinity Capillary Electrophoresis – A Powerful Tool to Investigate Biomolecular Interactions

    Czech Academy of Sciences Publication Activity Database

    Kašička, Václav

    2017-01-01

    Roč. 30, č. 5 (2017), s. 248 ISSN 1471-6577 Institutional support: RVO:61388963 Keywords : capillary affinity electrophoresis * biomolecular interactions * binding constants Subject RIV: CB - Analytical Chemistry, Separation OBOR OECD: Analytical chemistry Impact factor: 0.663, year: 2016

  17. An optics-based variable-temperature assay system for characterizing thermodynamics of biomolecular reactions on solid support

    Energy Technology Data Exchange (ETDEWEB)

    Fei, Yiyan; Landry, James P.; Zhu, X. D., E-mail: xdzhu@physics.ucdavis.edu [Department of Physics, University of California, One Shields Avenue, Davis, California 95616 (United States); Li, Yanhong; Yu, Hai; Lau, Kam; Huang, Shengshu; Chokhawala, Harshal A.; Chen, Xi [Department of Chemistry, University of California, One Shields Avenue, Davis, California 95616 (United States)

    2013-11-15

    A biological state is equilibrium of multiple concurrent biomolecular reactions. The relative importance of these reactions depends on physiological temperature typically between 10 °C and 50 °C. Experimentally the temperature dependence of binding reaction constants reveals thermodynamics and thus details of these biomolecular processes. We developed a variable-temperature opto-fluidic system for real-time measurement of multiple (400–10 000) biomolecular binding reactions on solid supports from 10 °C to 60 °C within ±0.1 °C. We illustrate the performance of this system with investigation of binding reactions of plant lectins (carbohydrate-binding proteins) with 24 synthetic glycans (i.e., carbohydrates). We found that the lectin-glycan reactions in general can be enthalpy-driven, entropy-driven, or both, and water molecules play critical roles in the thermodynamics of these reactions.

  18. HPDB-Haskell library for processing atomic biomolecular structures in Protein Data Bank format.

    Science.gov (United States)

    Gajda, Michał Jan

    2013-11-23

    Protein DataBank file format is used for the majority of biomolecular data available today. Haskell is a lazy functional language that enjoys a high-level class-based type system, a growing collection of useful libraries and a reputation for efficiency. I present a fast library for processing biomolecular data in the Protein Data Bank format. I present benchmarks indicating that this library is faster than other frequently used Protein Data Bank parsing programs. The proposed library also features a convenient iterator mechanism, and a simple API modeled after BioPython. I set a new standard for convenience and efficiency of Protein Data Bank processing in a Haskell library, and release it to open source.

  19. Symmetric q-Bessel functions

    Directory of Open Access Journals (Sweden)

    Giuseppe Dattoli

    1996-05-01

    Full Text Available q analog of bessel functions, symmetric under the interchange of q and q^ −1 are introduced. The definition is based on the generating function realized as product of symmetric q-exponential functions with appropriate arguments. Symmetric q-Bessel function are shown to satisfy various identities as well as second-order q-differential equations, which in the limit q → 1 reproduce those obeyed by the usual cylindrical Bessel functions. A brief discussion on the possible algebraic setting for symmetric q-Bessel functions is also provided.

  20. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics

    Science.gov (United States)

    Likic, Vladimir A.

    2006-01-01

    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  1. Dynamic and label-free high-throughput detection of biomolecular interactions based on phase-shift interferometry

    Science.gov (United States)

    Li, Qiang; Huang, Guoliang; Gan, Wupeng; Chen, Shengyi

    2009-08-01

    Biomolecular interactions can be detected by many established technologies such as fluorescence imaging, surface plasmon resonance (SPR)[1-4], interferometry and radioactive labeling of the analyte. In this study, we have designed and constructed a label-free, real-time sensing platform and its operating imaging instrument that detects interactions using optical phase differences from the accumulation of biological material on solid substrates. This system allows us to monitor biomolecular interactions in real time and quantify concentration changes during micro-mixing processes by measuring the changes of the optical path length (OPD). This simple interferometric technology monitors the optical phase difference resulting from accumulated biomolecular mass. A label-free protein chip that forms a 4×4 probe array was designed and fabricated using a commercial microarray robot spotter on solid substrates. Two positive control probe lines of BSA (Bovine Serum Albumin) and two experimental human IgG and goat IgG was used. The binding of multiple protein targets was performed and continuously detected by using this label-free and real-time sensing platform.

  2. Weakly Interacting Symmetric and Anti-Symmetric States in the Bilayer Systems

    Science.gov (United States)

    Marchewka, M.; Sheregii, E. M.; Tralle, I.; Tomaka, G.; Ploch, D.

    We have studied the parallel magneto-transport in DQW-structures of two different potential shapes: quasi-rectangular and quasi-triangular. The quantum beats effect was observed in Shubnikov-de Haas (SdH) oscillations for both types of the DQW structures in perpendicular magnetic filed arrangement. We developed a special scheme for the Landau levels energies calculation by means of which we carried out the necessary simulations of beating effect. In order to obtain the agreement between our experimental data and the results of simulations, we introduced two different quasi-Fermi levels which characterize symmetric and anti-symmetric states in DQWs. The existence of two different quasi Fermi-Levels simply means, that one can treat two sub-systems (charge carriers characterized by symmetric and anti-symmetric wave functions) as weakly interacting and having their own rate of establishing the equilibrium state.

  3. Scanning probe and optical tweezer investigations of biomolecular interactions

    International Nuclear Information System (INIS)

    Rigby-Singleton, Shellie

    2002-01-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ∼0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have

  4. Spin valve sensor for biomolecular identification: Design, fabrication, and characterization

    Science.gov (United States)

    Li, Guanxiong

    Biomolecular identification, e.g., DNA recognition, has broad applications in biology and medicine such as gene expression analysis, disease diagnosis, and DNA fingerprinting. Therefore, we have been developing a magnetic biodetection technology based on giant magnetoresistive spin valve sensors and magnetic nanoparticle (developed for the magnetic nanoparticle detection, assuming the equivalent average field of magnetic nanoparticles and the coherent rotation of spin valve free layer magnetization. Micromagnetic simulations have also been performed for the spin valve sensors. The analytical model and micromagnetic simulations are found consistent with each other and are in good agreement with experiments. The prototype spin valve sensors have been fabricated at both micron and submicron scales. We demonstrated the detection of a single 2.8-mum magnetic microbead by micron-sized spin valve sensors. Based on polymer-mediated self-assembly and fine lithography, a bilayer lift-off process was developed to deposit magnetic nanoparticles onto the sensor surface in a controlled manner. With the lift-off deposition method, we have successfully demonstrated the room temperature detection of monodisperse 16-nm Fe3O 4 nanoparticles in a quantity from a few tens to several hundreds by submicron spin valve sensors, proving the feasibility of the nanoparticle detection. As desired for quantitative biodetection, a fairly linear dependence of sensor signal on the number of nanoparticles has been confirmed. The initial detection of DNA hybridization events labeled by magnetic nanoparticles further proved the magnetic biodetection concept.

  5. Application of biomolecular recognition via magnetic nanoparticle in nanobiotechnology

    Science.gov (United States)

    Shen, Wei-Zheng; Cetinel, Sibel; Montemagno, Carlo

    2018-05-01

    The marriage of biomolecular recognition and magnetic nanoparticle creates tremendous opportunities in the development of advanced technology both in academic research and in industrial sectors. In this paper, we review current progress on the magnetic nanoparticle-biomolecule hybrid systems, particularly employing the recognition pairs of DNA-DNA, DNA-protein, protein-protein, and protein-inorganics in several nanobiotechnology application areas, including molecular biology, diagnostics, medical treatment, industrial biocatalysts, and environmental separations.

  6. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner

    2000-01-01

    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  7. Symmetric vectors and algebraic classification

    International Nuclear Information System (INIS)

    Leibowitz, E.

    1980-01-01

    The concept of symmetric vector field in Riemannian manifolds, which arises in the study of relativistic cosmological models, is analyzed. Symmetric vectors are tied up with the algebraic properties of the manifold curvature. A procedure for generating a congruence of symmetric fields out of a given pair is outlined. The case of a three-dimensional manifold of constant curvature (''isotropic universe'') is studied in detail, with all its symmetric vector fields being explicitly constructed

  8. Self-Assembly in the Ferritin Nano-Cage Protein Superfamily

    Directory of Open Access Journals (Sweden)

    Yu Zhang

    2011-08-01

    Full Text Available Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins.

  9. Synthetic Approach to biomolecular science by cyborg supramolecular chemistry.

    Science.gov (United States)

    Kurihara, Kensuke; Matsuo, Muneyuki; Yamaguchi, Takumi; Sato, Sota

    2018-02-01

    To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems. This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules. Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Self-powered in-core neutron detector assembly with uniform perturbation characteristics

    International Nuclear Information System (INIS)

    1981-01-01

    An in-core neutron detector assembly consisting of a number of longitudinally extending self-powered detectors is described. The uniform mechanical structures and materials are placed symmetrically at each active detector portion thus ensuring that local perturbation factors are uniform. (U.K.)

  11. Synergy of Two Highly Specific Biomolecular Recognition Events

    DEFF Research Database (Denmark)

    Ejlersen, Maria; Christensen, Niels Johan; Sørensen, Kasper K

    2018-01-01

    Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino......-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA...

  12. Representations of locally symmetric spaces

    International Nuclear Information System (INIS)

    Rahman, M.S.

    1995-09-01

    Locally symmetric spaces in reference to globally and Hermitian symmetric Riemannian spaces are studied. Some relations between locally and globally symmetric spaces are exhibited. A lucid account of results on relevant spaces, motivated by fundamental problems, are formulated as theorems and propositions. (author). 10 refs

  13. Foreword [IJEGMBE 2015: India-Japan expert group meeting on biomolecular electronics and organic nanotechnology for environment preservation, Fukuoka (Japan), 23-26 December 2015

    International Nuclear Information System (INIS)

    2016-01-01

    -established field are several emerging technologies with innovative mechanisms and functions that utilize the mixed ionic/electronic conducting character of conjugated organic materials. These techniques are based around flexible or printed electronics. Ionic functionalization influences many of the key properties of conductive polymers through its impacts on molecular order, the injection and transport of charge, optical excitations, and interactions with other molecules. Consequently, it is an important tool in the development of electronic and photonic devices based on conductive polymers. We have considered that to focus exclusively on the iontronics, ionic carriers in organic electronic materials and devices in organic electronic materials seems timely. Therefore, this report reviews the scientific understanding and important scientific discoveries made in the electrochemistry of conductive polymers based on our experience. The main purpose of IJEGMBE is to provide an opportunity for researchers, who are interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange their technical information and experience. We are sure that this meeting will be very useful and fruitful for all participants to summarize the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and prepare the next step for future generations. Many papers have been submitted from India and Japan and more than 20 papers have been accepted for presentation. All the papers accepted will be presented. The main topics of interest are as follows; Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled monolayers Nano sensors Environmental monitoring Organic devices Organic Functional Materials Others The program of this meeting consists of Invited Lectures and oral presentations. We hope all participants benefited from this meeting. We would

  14. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations.

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  15. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations

    Science.gov (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo

    2016-01-01

    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  16. Application of Hidden Markov Models in Biomolecular Simulations.

    Science.gov (United States)

    Shukla, Saurabh; Shamsi, Zahra; Moffett, Alexander S; Selvam, Balaji; Shukla, Diwakar

    2017-01-01

    Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process.

  17. Biomolecular solid state NMR with magic-angle spinning at 25K.

    Science.gov (United States)

    Thurber, Kent R; Tycko, Robert

    2008-12-01

    A magic-angle spinning (MAS) probe has been constructed which allows the sample to be cooled with helium, while the MAS bearing and drive gases are nitrogen. The sample can be cooled to 25K using roughly 3 L/h of liquid helium, while the 4-mm diameter rotor spins at 6.7 kHz with good stability (+/-5 Hz) for many hours. Proton decoupling fields up to at least 130 kHz can be applied. This helium-cooled MAS probe enables a variety of one-dimensional and two-dimensional NMR experiments on biomolecular solids and other materials at low temperatures, with signal-to-noise proportional to 1/T. We show examples of low-temperature (13)C NMR data for two biomolecular samples, namely the peptide Abeta(14-23) in the form of amyloid fibrils and the protein HP35 in frozen glycerol/water solution. Issues related to temperature calibration, spin-lattice relaxation at low temperatures, paramagnetic doping of frozen solutions, and (13)C MAS NMR linewidths are discussed.

  18. Investigating biomolecular recognition at the cell surface using atomic force microscopy.

    Science.gov (United States)

    Wang, Congzhou; Yadavalli, Vamsi K

    2014-05-01

    Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. In-situ visualization and order quantification of symmetric diblock copolymer directed self-assembly

    International Nuclear Information System (INIS)

    Salaün, M.; Le Gallic, M.; Picard, E.; Zelsmann, M.

    2013-01-01

    In this work, atomic force microscopy (AFM) investigations of lamellar PS-b-PMMA block copolymer layers are performed during the self-assembly process. These in-situ experiments are made on both un-patterned planar substrates and topographical substrates (graphoepitaxy experiments) at different temperatures and for different durations. Image processing software is used to produce AFM movies of the same location on the sample and to measure polymer micro-phase domain lengths versus annealing time. We observed that micro-domain formation starts after only a few minutes of heating. On planar substrates, the micro-domain length evolution with time (t) is in accordance with the literature, following a power law ∼ t 0.29 . On the other hand, in substrate channels and in conditions used, we show that the domain length dependence follows a two-step process. Initially, the system adopts a similar kinetic dependence as that of the planar substrate, but at longer times, drastically reduced time dependence is observed due to the topographical confinement of the domains. - Highlights: ► Live atomic force microscopy of block copolymer directed self-assembly is performed. ► Values of polymer self-assembly kinetic in topographical trenches are measured. ► Opens the way to a better understanding of graphoepitaxy order nucleation and growth

  20. Integrative NMR for biomolecular research

    International Nuclear Information System (INIS)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L.

    2016-01-01

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download_packages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  1. Integrative NMR for biomolecular research

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Woonghee, E-mail: whlee@nmrfam.wisc.edu; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R.; Tonelli, Marco; Westler, William M.; Butcher, Samuel E.; Henzler-Wildman, Katherine A.; Markley, John L., E-mail: markley@nmrfam.wisc.edu [University of Wisconsin-Madison, National Magnetic Resonance Facility at Madison and Biochemistry Department (United States)

    2016-04-15

    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( http://pine.nmrfam.wisc.edu/download-packages.html http://pine.nmrfam.wisc.edu/download{sub p}ackages.html ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( http://pine.nmrfam.wisc.edu/integrative.html http://pine.nmrfam.wisc.edu/integrative.html ).

  2. Dual formulation of covariant nonlinear duality-symmetric action of kappa-symmetric D3-brane

    Science.gov (United States)

    Vanichchapongjaroen, Pichet

    2018-02-01

    We study the construction of covariant nonlinear duality-symmetric actions in dual formulation. Essentially, the construction is the PST-covariantisation and nonlinearisation of Zwanziger action. The covariantisation made use of three auxiliary scalar fields. Apart from these, the construction proceed in a similar way to that of the standard formulation. For example, the theories can be extended to include interactions with external fields, and that the theories possess two local PST symmetries. We then explicitly demonstrate the construction of covariant nonlinear duality-symmetric actions in dual formulation of DBI theory, and D3-brane. For each of these theories, the twisted selfduality condition obtained from duality-symmetric actions are explicitly shown to match with the duality relation between field strength and its dual from the one-potential actions. Their on-shell actions between the duality-symmetric and the one-potential versions are also shown to match. We also explicitly prove kappa-symmetry of the covariant nonlinear duality-symmetric D3-brane action in dual formulation.

  3. The symmetric extendibility of quantum states

    International Nuclear Information System (INIS)

    Nowakowski, Marcin L

    2016-01-01

    Studies on the symmetric extendibility of quantum states have become particularly important in the context of the analysis of one-way quantum measures of entanglement, and the distillability and security of quantum protocols. In this paper we analyze composite systems containing a symmetric extendible part, with particular attention devoted to the one-way security of such systems. Further, we introduce a new one-way entanglement monotone based on the best symmetric approximation of a quantum state and the extendible number of a quantum state. We underpin these results with geometric observations about the structures of multi-party settings which posses substantial symmetric extendible components in their subspaces. The impossibility of reducing the maximal symmetric extendibility by means of the one-way local operations and classical communication method is pointed out on multiple copies. Finally, we state a conjecture linking symmetric extendibility with the one-way distillability and security of all quantum states, analyzing the behavior of a private key in the neighborhood of symmetric extendible states. (paper)

  4. Symmetric Tensor Decomposition

    DEFF Research Database (Denmark)

    Brachat, Jerome; Comon, Pierre; Mourrain, Bernard

    2010-01-01

    We present an algorithm for decomposing a symmetric tensor, of dimension n and order d, as a sum of rank-1 symmetric tensors, extending the algorithm of Sylvester devised in 1886 for binary forms. We recall the correspondence between the decomposition of a homogeneous polynomial in n variables...... of polynomial equations of small degree in non-generic cases. We propose a new algorithm for symmetric tensor decomposition, based on this characterization and on linear algebra computations with Hankel matrices. The impact of this contribution is two-fold. First it permits an efficient computation...... of the decomposition of any tensor of sub-generic rank, as opposed to widely used iterative algorithms with unproved global convergence (e.g. Alternate Least Squares or gradient descents). Second, it gives tools for understanding uniqueness conditions and for detecting the rank....

  5. Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

    International Nuclear Information System (INIS)

    Wang, Jianhao; Jiang, Pengju; Gao, Liqian; Yu, Yongsheng; Lu, Yao; Qiu, Lin; Wang, Cheli; Xia, Jiang

    2013-01-01

    How protein–protein interaction affects protein–nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein–nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD–protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD–protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD–His-tag interaction and protein–protein interaction can result in unique properties of protein–nanoparticle assembly for the first time

  6. Unique self-assembly properties of a bridge-shaped protein dimer with quantum dots

    Science.gov (United States)

    Wang, Jianhao; Jiang, Pengju; Gao, Liqian; Yu, Yongsheng; Lu, Yao; Qiu, Lin; Wang, Cheli; Xia, Jiang

    2013-09-01

    How protein-protein interaction affects protein-nanoparticle self-assembly is the key to the understanding of biomolecular coating of nanoparticle in biological fluids. However, the relationship between protein shape and its interaction with nanoparticles is still under-exploited because of lack of a well-conceived binding system and a method to detect the subtle change in the protein-nanoparticle assemblies. Noticing this unresolved need, we cloned and expressed a His-tagged SpeA protein that adopts a bridge-shaped dimer structure, and utilized a high-resolution capillary electrophoresis method to monitor assembly formation between the protein and quantum dots (QDs, 5 nm in diameter). We observed that the bridge-shaped structure rendered a low SpeA:QD stoichiometry at saturation. Also, close monitoring of imidazole (Im) displacement of surface-bound protein revealed a unique two-step process. High-concentration Im could displace surface-bound SpeA protein and form a transient QD-protein intermediate, through a kinetically controlled displacement process. An affinity-driven equilibrium step then followed, resulting in re-assembling of the QD-protein complex in about 1 h. Through a temporarily formed intermediate, Im causes a rearrangement of His-tagged proteins on the surface. Thus, our work showcases that the synergistic interplay between QD-His-tag interaction and protein-protein interaction can result in unique properties of protein-nanoparticle assembly for the first time.

  7. Structure and assembly of scalable porous protein cages

    Science.gov (United States)

    Sasaki, Eita; Böhringer, Daniel; van de Waterbeemd, Michiel; Leibundgut, Marc; Zschoche, Reinhard; Heck, Albert J. R.; Ban, Nenad; Hilvert, Donald

    2017-03-01

    Proteins that self-assemble into regular shell-like polyhedra are useful, both in nature and in the laboratory, as molecular containers. Here we describe cryo-electron microscopy (EM) structures of two versatile encapsulation systems that exploit engineered electrostatic interactions for cargo loading. We show that increasing the number of negative charges on the lumenal surface of lumazine synthase, a protein that naturally assembles into a ~1-MDa dodecahedron composed of 12 pentamers, induces stepwise expansion of the native protein shell, giving rise to thermostable ~3-MDa and ~6-MDa assemblies containing 180 and 360 subunits, respectively. Remarkably, these expanded particles assume unprecedented tetrahedrally and icosahedrally symmetric structures constructed entirely from pentameric units. Large keyhole-shaped pores in the shell, not present in the wild-type capsid, enable diffusion-limited encapsulation of complementarily charged guests. The structures of these supercharged assemblies demonstrate how programmed electrostatic effects can be effectively harnessed to tailor the architecture and properties of protein cages.

  8. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.; Elshenawy, M. M.; Takahashi, Masateru; Whitman, B. H.; Walter, N. G.; Hamdan, S. M.

    2011-01-01

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation

  9. Ion induced fragmentation of biomolecular systems at low collision energies

    International Nuclear Information System (INIS)

    Bernigaud, V; Adoui, L; Chesnel, J Y; Rangama, J; Huber, B A; Manil, B; Alvarado, F; Bari, S; Hoekstra, R; Postma, J; Schlathoelter, T

    2009-01-01

    In this paper, we present results of different collision experiments between multiply charged ions at low collision energies (in the keV-region) and biomolecular systems. This kind of interaction allows to remove electrons form the biomolecule without transferring a large amount of vibrational excitation energy. Nevertheless, following the ionization of the target, fragmentation of biomolecular species may occur. It is the main objective of this work to study the physical processes involved in the dissociation of highly electronically excited systems. In order to elucidate the intrinsic properties of certain biomolecules (porphyrins and amino acids) we have performed experiments in the gas phase with isolated systems. The obtained results demonstrate the high stability of porphyrins after electron removal. Furthermore, a dependence of the fragmentation pattern produced by multiply charged ions on the isomeric structure of the alanine molecule has been shown. By considering the presence of other surrounding biomolecules (clusters of nucleobases), a strong influence of the environment of the biomolecule on the fragmentation channels and their modification, has been clearly proven. This result is explained, in the thymine and uracil case, by the formation of hydrogen bonds between O and H atoms, which is known to favor planar cluster geometries.

  10. Biomolecular simulations on petascale: promises and challenges

    International Nuclear Information System (INIS)

    Agarwal, Pratul K; Alam, Sadaf R

    2006-01-01

    Proteins work as highly efficient machines at the molecular level and are responsible for a variety of processes in all living cells. There is wide interest in understanding these machines for implications in biochemical/biotechnology industries as well as in health related fields. Over the last century, investigations of proteins based on a variety of experimental techniques have provided a wealth of information. More recently, theoretical and computational modeling using large scale simulations is providing novel insights into the functioning of these machines. The next generation supercomputers with petascale computing power, hold great promises as well as challenges for the biomolecular simulation scientists. We briefly discuss the progress being made in this area

  11. Electrostatics in biomolecular simulations : where are we now and where are we heading?

    NARCIS (Netherlands)

    Karttunen, M.E.J.; Rottler, J.; Vattulainen, I.; Sagui, C.

    2008-01-01

    Chapter 2. In this review, we discuss current methods and developments in the treatment of electrostatic interactions in biomolecular and soft matter simulations. We review the current ‘work horses’, namely, Ewald summation based methods such the Particle-Mesh Ewald, and others, and also newer

  12. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  13. Self assembled linear polymeric chains with tuneable semiflexibility using isotropic interactions

    Science.gov (United States)

    Abraham, Alex; Chatterji, Apratim

    2018-04-01

    We propose a two-body spherically symmetric (isotropic) potential such that particles interacting by the potential self-assemble into linear semiflexible polymeric chains without branching. By suitable control of the potential parameters, we can control the persistence length of the polymer and can even introduce a controlled number of branches. Thus we show how to achieve effective directional interactions starting from spherically symmetric potentials. The self-assembled polymers have an exponential distribution of chain lengths akin to what is observed for worm-like micellar systems. On increasing particle density, the polymeric chains self-organize to an ordered line-hexagonal phase where every chain is surrounded by six parallel chains, the transition is first order. On further increase in monomer density, the order is destroyed and we get a branched gel-like phase. This potential can be used to model semi-flexible equilibrium polymers with tunable semiflexibility and excluded volume. The use of the potential is computationally cheap and hence can be used to simulate and probe equilibrium polymer dynamics with long chains. The potential also gives a plausible method of tuning colloidal interactions in experiments such that one can obtain self-assembling polymeric chains made up of colloids and probe polymer dynamics using an optical microscope. Furthermore, we show how a modified potential leads to the observation of an intermediate nematic phase of self-assembled chains in between the low density disordered phase and the line-ordered hexagonal phase.

  14. Biomolecular Chemistry of Isopropyl Fibrates

    Science.gov (United States)

    Rath, Niharika; Kotheimer, Amenda; Miller, Chad; Zeller, Matthias; Rath, Nigam P.

    2012-01-01

    Isopropyl 2-[4-(4-chlorobenzoyl)-phenoxy]-2-methylpropanoic acid and isopropyl 2-(4-chlorophenoxy)-2-methylpropanoate, also known as fenofibrate and isopropyl clofibrate, are hypolipidemic agents of the fibrate family. In a previously reported triclinic structure of fenofibrate (polymorph I) the methyl groups of the isopropyl moiety (iPr) are located symmetrically about the carboxylate group. We report a new monoclinic form (polymorph II) of fenofibrate and a first structural description of isopropyl clofibrate, and in these the methyl groups are placed asymmetrically about the carboxylate group. In particular the dihedral (torsion) angle between the hydrogen atom on the secondary C and the C atom of the carboxyl group makes a 2.74° angle about the ester O-C bond in the symmetric fenofibrate structure of polymorph I, whereas the same dihedral angle is 45.94° in polymorph II and -30.9° in the crystal structure of isopropyl clofibrate. Gas phase DFT geometry minimizations of fenofibrate and isopropyl clofibrate result in lowest energy conformations for both molecules with a value of about ± 30° for this same angle between the O=C-O-C plane and the C-H bond of the iPr group. A survey of crystal structures containing an iPr ester group reveals that the asymmetric conformation is predominant. Although the hydrogen atom on the secondary C atom of the isopropyl group is located at a comparable distance from the carbonyl oxygen in the symmetric and asymmetric fenofibrate (2.52 and 2.28 Å) and the isopropyl clofibrate (2.36 Å) structures, this hydrogen atom participates in a puckered five membered ring arrangement in the latter two that is unlike the planar arrangement found in symmetric fenofibrate (polymorph I). Polar molecular surface area (PSA) values indicate fenofibrate and isopropyl clofibrate are less able to act as acceptors of hydrogen bonds than their corresponding acid derivatives. Surface area calculations show dynamic polar molecular surface area (PSAd

  15. A compact imaging spectroscopic system for biomolecular detections on plasmonic chips.

    Science.gov (United States)

    Lo, Shu-Cheng; Lin, En-Hung; Wei, Pei-Kuen; Tsai, Wan-Shao

    2016-10-17

    In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing. Both the curved grating and the plasmonic chips are fabricated on flexible plastic substrates using a gas-assisted thermal-embossing method. A fiber-coupled broadband light source and a camera are included in the system. Spectral resolution within 1 nm is achieved in sensing environmental index solutions and protein bindings. The detected sensitivities of the plasmonic chip are comparable with a commercial spectrometer. An extra one-dimensional scanning stage enables high-throughput detection of protein binding on a designed plasmonic chip consisting of several nanoslit arrays with different periods. The detected resonance wavelengths match well with the grating equation under an air environment. Wavelength shifts between 1 and 9 nm are detected for antigens of various concentrations binding with antibodies. A simple, mass-productive and cost-effective method has been demonstrated on the imaging spectroscopic system for real-time, label-free, highly sensitive and high-throughput screening of biomolecular interactions.

  16. Symmetric extendibility of quantum states

    OpenAIRE

    Nowakowski, Marcin L.

    2015-01-01

    Studies on symmetric extendibility of quantum states become especially important in a context of analysis of one-way quantum measures of entanglement, distilabillity and security of quantum protocols. In this paper we analyse composite systems containing a symmetric extendible part with a particular attention devoted to one-way security of such systems. Further, we introduce a new one-way monotone based on the best symmetric approximation of quantum state. We underpin those results with geome...

  17. Symmetric eikonal expansion

    International Nuclear Information System (INIS)

    Matsuki, Takayuki

    1976-01-01

    Symmetric eikonal expansion for the scattering amplitude is formulated for nonrelativistic and relativistic potential scatterings and also for the quantum field theory. The first approximations coincide with those of Levy and Sucher. The obtained scattering amplitudes are time reversal invariant for all cases and are crossing symmetric for the quantum field theory in each order of approximation. The improved eikonal phase introduced by Levy and Sucher is also derived from the different approximation scheme from the above. (auth.)

  18. On symmetric structures of order two

    Directory of Open Access Journals (Sweden)

    Michel Bousquet

    2008-04-01

    Full Text Available Let (ω n 0 < n be the sequence known as Integer Sequence A047749 http://www.research.att.com/ njas/sequences/A047749 In this paper, we show that the integer ω n enumerates various kinds of symmetric structures of order two. We first consider ternary trees having a reflexive symmetry and we relate all symmetric combinatorial objects by means of bijection. We then generalize the symmetric structures and correspondences to an infinite family of symmetric objects.

  19. Grain-boundary free energy in an assembly of elastic disks.

    Science.gov (United States)

    Lusk, Mark T; Beale, Paul D

    2004-02-01

    Grain-boundary free energy is estimated as a function of misoriention for symmetric tilt boundaries in an assembly of nearly hard disks. Fluctuating cell theory is used to accomplish this since the most common techniques for calculating interfacial free energy cannot be applied to such assemblies. The results are analogous to those obtained using a Leonard-Jones potential, but in this case the interfacial energy is dominated by an entropic contribution. Disk assemblies colorized with free and specific volume elucidate differences between these two characteristics of boundary structure. Profiles are also provided of the Helmholtz and Gibbs free energies as a function of distance from the grain boundaries. Low angle grain boundaries are shown to follow the classical relationship between dislocation orientation/spacing and misorientation angle.

  20. Rapid prototyping of nanofluidic systems using size-reduced electrospun nanofibers for biomolecular analysis.

    Science.gov (United States)

    Park, Seung-Min; Huh, Yun Suk; Szeto, Kylan; Joe, Daniel J; Kameoka, Jun; Coates, Geoffrey W; Edel, Joshua B; Erickson, David; Craighead, Harold G

    2010-11-05

    Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.

  1. Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes.

    Science.gov (United States)

    Foo, Mathias; Kim, Jongrae; Sawlekar, Rucha; Bates, Declan G

    2017-04-06

    Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a 'subtractor' that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a biomolecular controller that allows tracking of required changes in the outputs of enzymatic reaction processes can be designed and implemented within the framework of chemical reaction network theory. The controller architecture employs an inversion-based feedforward controller that compensates for the limitations of the one-sided subtractor that generates the error signals for a feedback controller. The proposed approach requires significantly fewer chemical reactions to implement than alternative designs, and should have wide applicability throughout the fields of synthetic biology and biological engineering.

  2. Self-assembling morphologies of symmetrical PS-b-PMMA in different sized confining grooves

    DEFF Research Database (Denmark)

    Chen, Wenhui; Luo, Jun; Shi, Peixiong

    2014-01-01

    Directed self-assembly (DSA), an emerging lithographic technique, has attracted increasing attention as a result of its advantages of low cost, high throughput and convenient processing. However, DSA still presents some challenges, such as the control of defects, the fabrication of complex patterns...

  3. Instrumental biosensors: new perspectives for the analysis of biomolecular interactions.

    Science.gov (United States)

    Nice, E C; Catimel, B

    1999-04-01

    The use of instrumental biosensors in basic research to measure biomolecular interactions in real time is increasing exponentially. Applications include protein-protein, protein-peptide, DNA-protein, DNA-DNA, and lipid-protein interactions. Such techniques have been applied to, for example, antibody-antigen, receptor-ligand, signal transduction, and nuclear receptor studies. This review outlines the principles of two of the most commonly used instruments and highlights specific operating parameters that will assist in optimising experimental design, data generation, and analysis.

  4. NMR paves the way for atomic level descriptions of sparsely populated, transiently formed biomolecular conformers.

    Science.gov (United States)

    Sekhar, Ashok; Kay, Lewis E

    2013-08-06

    The importance of dynamics to biomolecular function is becoming increasingly clear. A description of the structure-function relationship must, therefore, include the role of motion, requiring a shift in paradigm from focus on a single static 3D picture to one where a given biomolecule is considered in terms of an ensemble of interconverting conformers, each with potentially diverse activities. In this Perspective, we describe how recent developments in solution NMR spectroscopy facilitate atomic resolution studies of sparsely populated, transiently formed biomolecular conformations that exchange with the native state. Examples of how this methodology is applied to protein folding and misfolding, ligand binding, and molecular recognition are provided as a means of illustrating both the power of the new techniques and the significant roles that conformationally excited protein states play in biology.

  5. Mesotherapy for benign symmetric lipomatosis.

    Science.gov (United States)

    Hasegawa, Toshio; Matsukura, Tomoyuki; Ikeda, Shigaku

    2010-04-01

    Benign symmetric lipomatosis, also known as Madelung disease, is a rare disorder characterized by fat distribution around the shoulders, arms, and neck in the context of chronic alcoholism. Complete excision of nonencapsulated lipomas is difficult. However, reports describing conservative therapeutic measures for lipomatosis are rare. The authors present the case of a 42-year-old man with a diagnosis of benign symmetric lipomatosis who had multiple, large, symmetrical masses in his neck. Multiple phosphatidylcholine injections in the neck were administered 4 weeks apart, a total of seven times to achieve lipolysis. The patient's lipomatosis improved in response to the injections, and he achieved good cosmetic results. Intralesional injection, termed mesotherapy, using phosphatidylcholine is a potentially effective therapy for benign symmetric lipomatosis that should be reconsidered as a therapeutic option for this disease.

  6. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches

    Directory of Open Access Journals (Sweden)

    Max Hirte

    2018-04-01

    Full Text Available Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially

  7. Insights Into the Bifunctional Aphidicolan-16-ß-ol Synthase Through Rapid Biomolecular Modeling Approaches.

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B

    2018-01-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modeling techniques offer an alternative route to study the enzyme's reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modeling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modeling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789, and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modeling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location of

  8. Insights into the bifunctional Aphidicolan-16-ß-ol synthase through rapid biomolecular modelling approaches

    Science.gov (United States)

    Hirte, Max; Meese, Nicolas; Mertz, Michael; Fuchs, Monika; Brück, Thomas B.

    2018-04-01

    Diterpene synthases catalyze complex, multi-step C-C coupling reactions thereby converting the universal, aliphatic precursor geranylgeranyl diphosphate into diverse olefinic macrocylces that form the basis for the structural diversity of the diterpene natural product family. Since catalytically relevant crystal structures of diterpene synthases are scarce, homology based biomolecular modelling techniques offer an alternative route to study the enzyme’s reaction mechanism. However, precise identification of catalytically relevant amino acids is challenging since these models require careful preparation and refinement techniques prior to substrate docking studies. Targeted amino acid substitutions in this protein class can initiate premature quenching of the carbocation centered reaction cascade. The structural characterization of those alternative cyclization products allows for elucidation of the cyclization reaction cascade and provides a new source for complex macrocyclic synthons. In this study, new insights into structure and function of the fungal, bifunctional Aphidicolan-16-ß-ol synthase were achieved using a simplified biomolecular modelling strategy. The applied refinement methodologies could rapidly generate a reliable protein-ligand complex, which provides for an accurate in silico identification of catalytically relevant amino acids. Guided by our modelling data, ACS mutations lead to the identification of the catalytically relevant ACS amino acid network I626, T657, Y658, A786, F789 and Y923. Moreover, the ACS amino acid substitutions Y658L and D661A resulted in a premature termination of the cyclization reaction cascade en-route from syn-copalyl diphosphate to Aphidicolan-16-ß-ol. Both ACS mutants generated the diterpene macrocycle syn-copalol and a minor, non-hydroxylated labdane related diterpene, respectively. Our biomolecular modelling and mutational studies suggest that the ACS substrate cyclization occurs in a spatially restricted location

  9. iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

    Science.gov (United States)

    Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

    2017-08-01

    Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

  10. Symmetric analysis, categorization, and optical spectrum of ideal pyramid quantum dots

    Science.gov (United States)

    Li, Wei; Belling, Samuel W.

    2017-11-01

    Self-assembled quantum dots possess an intrinsic geometric symmetry. Applying group representation theory, we systematically analyze the symmetric properties of the bound states for ideal pyramid quantum dots, which neglect band mixing and strain effects. We label each bound state by its symmetry group’s corresponding irreducible representation and define a concept called the quantum dots’ symmetry category. A class of quantum dots with the same irreducible representation sequence of bound states are characterized as belonging to a specific symmetry category. This category concept generally describes the symmetric order of Hilbert space or wavefunction space. We clearly identify the connection between the symmetry category and the geometry of quantum dots by the symmetry category graph or map. The symmetry category change or transition corresponds to an accidental degeneracy of the bound states. The symmetry category and category transition are observable from the photocurrent spectroscopy or optical spectrum. For simplicity’s sake, in this paper, we only focus on inter-subband transition spectra, but the methodology can be extended to the inter-band transition cases. We predict that from the spectral measurements, the quantum dots’ geometric information may be inversely extracted.

  11. Biomolecular surface construction by PDE transform.

    Science.gov (United States)

    Zheng, Qiong; Yang, Siyang; Wei, Guo-Wei

    2012-03-01

    This work proposes a new framework for the surface generation based on the partial differential equation (PDE) transform. The PDE transform has recently been introduced as a general approach for the mode decomposition of images, signals, and data. It relies on the use of arbitrarily high-order PDEs to achieve the time-frequency localization, control the spectral distribution, and regulate the spatial resolution. The present work provides a new variational derivation of high-order PDE transforms. The fast Fourier transform is utilized to accomplish the PDE transform so as to avoid stringent stability constraints in solving high-order PDEs. As a consequence, the time integration of high-order PDEs can be done efficiently with the fast Fourier transform. The present approach is validated with a variety of test examples in two-dimensional and three-dimensional settings. We explore the impact of the PDE transform parameters, such as the PDE order and propagation time, on the quality of resulting surfaces. Additionally, we utilize a set of 10 proteins to compare the computational efficiency of the present surface generation method and a standard approach in Cartesian meshes. Moreover, we analyze the present method by examining some benchmark indicators of biomolecular surface, that is, surface area, surface-enclosed volume, solvation free energy, and surface electrostatic potential. A test set of 13 protein molecules is used in the present investigation. The electrostatic analysis is carried out via the Poisson-Boltzmann equation model. To further demonstrate the utility of the present PDE transform-based surface method, we solve the Poisson-Nernst-Planck equations with a PDE transform surface of a protein. Second-order convergence is observed for the electrostatic potential and concentrations. Finally, to test the capability and efficiency of the present PDE transform-based surface generation method, we apply it to the construction of an excessively large biomolecule, a

  12. Interdependency of formation and localisation of the Min complex controls symmetric plastid division.

    Science.gov (United States)

    Maple, Jodi; Møller, Simon G

    2007-10-01

    Plastid division represents a fundamental biological process essential for plant development; however, the molecular basis of symmetric plastid division is unclear. AtMinE1 plays a pivotal role in selection of the plastid division site in concert with AtMinD1. AtMinE1 localises to discrete foci in chloroplasts and interacts with AtMinD1, which shows a similar localisation pattern. Here, we investigate the importance of Min protein complex formation during the chloroplast division process. Dissection of the assembly of the Min protein complex and determination of the interdependency of complex assembly and localisation in planta allow us to present a model of the molecular basis of selection of the division site in plastids. Moreover, functional analysis of AtMinE1 in bacteria demonstrates the level of functional conservation and divergence of the plastidic MinE proteins.

  13. A new approach to implement absorbing boundary condition in biomolecular electrostatics.

    Science.gov (United States)

    Goni, Md Osman

    2013-01-01

    This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

  14. Multiparty symmetric sum types

    DEFF Research Database (Denmark)

    Nielsen, Lasse; Yoshida, Nobuko; Honda, Kohei

    2010-01-01

    This paper introduces a new theory of multiparty session types based on symmetric sum types, by which we can type non-deterministic orchestration choice behaviours. While the original branching type in session types can represent a choice made by a single participant and accepted by others...... determining how the session proceeds, the symmetric sum type represents a choice made by agreement among all the participants of a session. Such behaviour can be found in many practical systems, including collaborative workflow in healthcare systems for clinical practice guidelines (CPGs). Processes...... with the symmetric sums can be embedded into the original branching types using conductor processes. We show that this type-driven embedding preserves typability, satisfies semantic soundness and completeness, and meets the encodability criteria adapted to the typed setting. The theory leads to an efficient...

  15. High-speed AFM for Studying Dynamic Biomolecular Processes

    Science.gov (United States)

    Ando, Toshio

    2008-03-01

    Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

  16. Symmetric splitting of very light systems

    International Nuclear Information System (INIS)

    Grotowski, K.; Majka, Z.; Planeta, R.

    1985-01-01

    Fission reactions that produce fragments close to one half the mass of the composite system are traditionally observed in heavy nuclei. In light systems, symmetric splitting is rarely observed and poorly understood. It would be interesting to verify the existence of the symmetric splitting of compound nuclei with A 12 C + 40 Ca, 141 MeV 9 Be + 40 Ca and 153 MeV 6 Li + 40 Ca. The out-of-plane correlation of symmetric products was also measured for the reaction 186 MeV 12 C + 40 Ca. The coincidence measurements of the 12 C + 40 Ca system demonstrated that essentially all of the inclusive yield of symmetric products around 40 0 results from a binary decay. To characterize the dependence of the symmetric splitting process on the excitation energy of the 12 C + 40 C system, inclusive measurements were made at bombarding energies of 74, 132, 162, and 185 MeV

  17. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery

    Science.gov (United States)

    Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K.; Smith, Douglas Y.; Söderberg, Christopher A. G.; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

    2016-01-01

    The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. PMID:26941001

  18. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven

    2009-10-01

    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from http://www.haptimol.co.uk, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  19. Analysis of coolant flow in central tube of WWER-440 fuel assemblies

    International Nuclear Information System (INIS)

    Zsiros, G.; Toth, S.; Attila Aszodi, A.

    2011-01-01

    Three dimensional computational fluid dynamics model has been built to investigate the coolant flow in the central tube of the WWER-440 fuel assemblies. The model was verified based on measured data of the Kurchatov Institute. With the model calculations were performed for two fuel assemblies used in PAKS NPP. One of them has symmetrical and another has inclined pin power profile. Ratios of the outlet mass fluxes of the central tube to the inlet mass fluxes of the rod bundle were determined. Heat up ratios of the tube and rod bundle flows were calculated too. Sensitivity of the results on the assembly power distribution, inlet temperature and mass flow rate was investigated. The results of these simulations can be used as boundary conditions of central tube in studies of coolant mixing in fuel assembly heads. (Authors)

  20. Propagation of symmetric and anti-symmetric surface waves in aself-gravitating magnetized dusty plasma layer with generalized (r, q) distribution

    Science.gov (United States)

    Lee, Myoung-Jae; Jung, Young-Dae

    2018-05-01

    The dispersion properties of surface dust ion-acoustic waves in a self-gravitating magnetized dusty plasma layer with the (r, q) distribution are investigated. The result shows that the wave frequency of the symmetric mode in the plasma layer decreases with an increase in the wave number. It is also shown that the wave frequency of the symmetric mode decreases with an increase in the spectral index r. However, the wave frequency of the anti-symmetric mode increases with an increase in the wave number. It is also found that the anti-symmetric mode wave frequency increases with an increase in the spectral index r. In addition, it is found that the influence of the self-gravitation on the symmetric mode wave frequency decreases with increasing scaled Jeans frequency. Moreover, it is found that the wave frequency of the symmetric mode increases with an increase in the dust charge; however, the anti-symmetric mode shows opposite behavior.

  1. Three's company: co-crystallization of a self-assembled S(4) metallacyclophane with two diastereomeric metallacycle intermediates.

    Science.gov (United States)

    Lindquist, Nathan R; Carter, Timothy G; Cangelosi, Virginia M; Zakharov, Lev N; Johnson, Darren W

    2010-05-28

    Three discrete supramolecular self-assembled arsenic(iii) complexes including an unusual S(4)-symmetric tetranuclear [As(4)L(2)Cl(4)] metallacyclophane and two diastereomeric cis/trans-[As(2)LCl(2)] metallacycle intermediates co-crystallize within a single crystal lattice.

  2. Facial One-Pot Synthesis of D 3h Symmetric Bicyclocalix[2]arene[2]triazines and Their Layered Comb Self-Assembly

    KAUST Repository

    Chen, Yin

    2017-11-23

    A number of D3h symmetric bicyclocalix[2]arene[2]triazine core compounds were synthesized via a general and good-yielding (43-48% yield) facile protocol starting from cyanuric halides, phloroglucinol and K2CO3 under very mild reaction conditions. These cage-like compounds are tolerate with different reaction conditions and can be derived with other functional groups in high yield. The X-ray crystal structures show these compounds have slightly distorted D3h symmetric structures. Due to the unique molecular topological structure, bicyclocalix[2]arene[2]triazine molecules form unique layered comb networks when hydrogen bond groups exist (such as CO2H, B(OH)2), which represent a new kind of building block unit for supramolecular architectures.

  3. Symmetric textures

    International Nuclear Information System (INIS)

    Ramond, P.

    1993-01-01

    The Wolfenstein parametrization is extended to the quark masses in the deep ultraviolet, and an algorithm to derive symmetric textures which are compatible with existing data is developed. It is found that there are only five such textures

  4. Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors.

    Science.gov (United States)

    Zhmurov, A; Dima, R I; Kholodov, Y; Barsegov, V

    2010-11-01

    Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package. © 2010 Wiley-Liss, Inc.

  5. A new strategy for imaging biomolecular events through interactions between liquid crystals and oil-in-water emulsions.

    Science.gov (United States)

    Hu, Qiong-Zheng; Jang, Chang-Hyun

    2012-11-21

    In this study, we demonstrate a new strategy to image biomolecular events through interactions between liquid crystals (LCs) and oil-in-water emulsions. The optical response had a dark appearance when a nematic LC, 4-cyano-4'-pentylbiphenyl (5CB), is in contact with emulsion droplets of glyceryl trioleate (GT). In contrast, the optical response had a bright appearance when 5CB is in contact with GT emulsions decorated with surfactants such as sodium oleate. Since lipase can hydrolyze GT and produce oleic acid, the optical response also displays a bright appearance after 5CB has been in contact with a mixture of lipase and GT emulsions. These results indicate the feasibility of monitoring biomolecular events through interactions between LCs and oil-in-water emulsions.

  6. Combinatorial Models for Assembly and Decomposition of Products

    Directory of Open Access Journals (Sweden)

    A. N. Bojko

    2015-01-01

    Full Text Available The paper discusses the most popular combinatorial models that are used for the synthesis of design solutions at the stage of the assembly process flow preparation. It shows that while assembling the product the relations of parts can be represented as a structure of preferences, which is formed on the basis of objective design restrictions put in at the stage of the product design. This structure is a binary preference relation pre-order. Its symmetrical part is equivalence and describes the entry of parts into the assembly unit. The asymmetric part is a partial order. It specifies part- ordering time in in the course of the assembly process. The structure of preferences is a minimal description of the restrictions and constraints in the assembly process. It can serve as a source for generating multiple assembly sequences of a product and its components, which are allowed by design. This multiplicity increases the likelihood of rational choice under uncertainty, unpredictable changes in the properties of technological or industrial systems.Incomplete dominance relation gives grounds for further examination and better understanding of the project situation. Operation field of the study is limited to a set of disparate elements of the partial order. Different strategies for processing the disparate elements may be offered, e.g. selection of the most informative pairs, comparison of which foremost linearizes the original partial order.

  7. Supramolecular ribbons from amphiphilic trisamides self-assembly.

    Science.gov (United States)

    García, Fátima; Buendía, Julia; Sánchez, Luis

    2011-08-05

    Two amphiphilic C(3)-symmetric OPE-based trisamides have been synthesized and their self-assembling features investigated in solution and on surface. Variable-temperature UV-vis experiments demonstrate the cooperative supramolecular polymerization of these trisamides that self-assemble by the operation of triple C═O···H-N H-bonding arrays between the amide functional groups and π-π stacking between the aromatic units. The helical organization of the aggregates has been demonstrated by circular dichroism at a concentration as low as 1 × 10(-4) M in acetonitrile. In the reported trisamides, the large hydrophobic aromatic core acts as a solvophobic module impeding the interaction between the polar TEG chains and the amide H-bonds. This strategy makes unnecessary the separation of the amide functional groups to the polar tri(ethylene glycol) chains by paraffinic fragments. Achiral trisamide 1 self-assembles into flat ribbon-like structures that experience an amplification of chirality by the addition of a small amount of chiral 2 that generates twisted stripes.

  8. Probabilistic cloning of three symmetric states

    International Nuclear Information System (INIS)

    Jimenez, O.; Bergou, J.; Delgado, A.

    2010-01-01

    We study the probabilistic cloning of three symmetric states. These states are defined by a single complex quantity, the inner product among them. We show that three different probabilistic cloning machines are necessary to optimally clone all possible families of three symmetric states. We also show that the optimal cloning probability of generating M copies out of one original can be cast as the quotient between the success probability of unambiguously discriminating one and M copies of symmetric states.

  9. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng

    2015-04-01

    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  10. Resonant Raman spectroscopy of PAH-Os self-assembled multilayers

    International Nuclear Information System (INIS)

    Tognalli, N.; Fainstein, A.; Bonazzola, C.; Calvo, E.

    2004-01-01

    We present a resonant Raman scattering study of (PAH-Os/PVS) n and (PAH-Os/GOx) m self-assembled multilayers (n=1-11 and m=1-3). These Os polymer multilayers can be used in electrodes as efficient molecular wires for biomolecular recognition. The Raman intensity dependence on the number of self-assembly cycles provides information on the deposition process. The spectra are identical to that observed for PAH-Os in aqueous solution, indicating that the PAH-Os metal complex structure is conserved in the multilayers. We observe at ∼500 nm incoming and outgoing Raman resonances of osmium and bipyridine vibrational modes. These resonances are associated to the metal-to-ligand charge transfer (MLCT) transition. We study the evolution of these Raman modes as a function of the Os oxidation state during in situ electrochemistry. During the oxidation process, Os(II)→Os(III), the Raman resonance related to the MLCT disappears and the bipyridine related modes harden by ∼10 cm-1. These results are correlated with optical transmission measurements which show the disappearance of the visible region absorption when the Os complex is oxidized. We also find partial quenching of the Raman mode intensity after in situ voltamperometric cycles which demonstrates the existence of photo-electro-chemical processes

  11. A symmetrical rail accelerator

    International Nuclear Information System (INIS)

    Igenbergs, E.

    1991-01-01

    This paper reports on the symmetrical rail accelerator that has four rails, which are arranged symmetrically around the bore. The opposite rails have the same polarity and the adjacent rails the opposite polarity. In this configuration the radial force acting upon the individual rails is significantly smaller than in a conventional 2-rail configuration and a plasma armature is focussed towards the axis of the barrel. Experimental results indicate a higher efficiency compared to a conventional rail accelerator

  12. Micro- and nanodevices integrated with biomolecular probes.

    Science.gov (United States)

    Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A

    2015-12-01

    Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. Copyright © 2015 Elsevier Inc. All rights reserved.

  13. Self-Assembly Carbon Nanotubes on Cantilever Biosensor for Sensitivity Enhancement

    Energy Technology Data Exchange (ETDEWEB)

    He, Johnny H [Institute of Microelectronics, 11 Science Park Road, Science Park II, Singapore 117685 (Singapore); Sun Shaoqing [Institute of Microelectronics, 11 Science Park Road, Science Park II, Singapore 117685 (Singapore); Ye Jianshan [Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore); Lim, T M [Department of Biological Science, National University of Singapore, 14 Science Drive 4, Singapore 117543 (Singapore)

    2006-04-01

    In recent years, highly sensitive and selective as well as cost-effective sensing and detection of biomolecules (e.g. virus, bacterial, DNA and protein) by MEMS/NEMS (Micro- /Nano Electro- Mechanical-System) structures have attracted extensive attention for its importance in clinical diagnostics, treatment, and various genome projects. Meanwhile, Substantial research efforts have been spent on the improvement of sensitivity of bioMEMS structures. Among a variety of methods that have been investigated, surface modification by nanoparticles (NPs) turns out to be an attractive way, which provides a platform for the enhancement of the sensitivity for biosensor devices. However, conventional applications for surface modification were mostly implemented on microelectrodes. Thus, in this paper, we demonstrate a new approach for surface enhancement on Au-coated silicon microcantilevers in micro-/nano-system. By self-assembly surface binding of multi-walled carbon nanotubes (MWCNTs) on the Au monolayer on top of the Si microcantilever surfaces, much larger surface area could be created for bio-molecular binding (such as antibodies or single DNA strands, which act as probes to capture target molecules). Therefore, this could enable specific interactions and selective binding to target biomolecules with a very low sample size, which greatly increases the sensitivity of detection. It should be noted that functionalization of MWCNTs with terminal carboxylic functionalities (in DCC solution) onto the Au surfaces of Si microchips have been introduced in our study. Further applications of MWCNTs functionalization are worth exploring in biomolecular detection for their exceptional mechanical and unique electronic properties. The successful binding of MWCNTs was testified as shown obviously on AFM image.

  14. Proceedings of the international advisory committee on 'biomolecular dynamics instrument DNA' and the workshop on 'biomolecular dynamics backscattering spectrometers'

    International Nuclear Information System (INIS)

    Arai, Masatoshi; Aizawa, Kazuya; Nakajima, Kenji; Shibata, Kaoru; Takahashi, Nobuaki

    2008-08-01

    A workshop entitled 'Biomolecular Dynamics Backscattering Spectrometers' was held on February 27th - 29th, 2008 at J-PARC Center, Japan Atomic Energy Agency. This workshop was planned to be held for aiming to realize an innovative neutron backscattering instrument, namely DNA, in the MLF and thus four leading scientists in the field of neutron backscattering instruments were invited as the International Advisory Committee (IAC member: Dr. Dan Neumann (Chair); Prof. Ferenc Mezei; Dr. Hannu Mutka; Dr. Philip Tregenna-Piggott) for DNA from institutes in the United States, France and Switzerland, where backscattering instruments are in-service. It was therefore held in the form of lecture anterior and then in the form of the committee posterior. This report includes the executive summary of the IAC and materials of the presentations in the IAC and the workshop. (author)

  15. Homotheties of cylindrically symmetric static spacetimes

    International Nuclear Information System (INIS)

    Qadir, A.; Ziad, M.; Sharif, M.

    1998-08-01

    In this note we consider the homotheties of cylindrically symmetric static spacetimes. We find that we can provide a complete list of all metrics that admit non-trivial homothetic motions and are cylindrically symmetric static. (author)

  16. Counting with symmetric functions

    CERN Document Server

    Mendes, Anthony

    2015-01-01

    This monograph provides a self-contained introduction to symmetric functions and their use in enumerative combinatorics.  It is the first book to explore many of the methods and results that the authors present. Numerous exercises are included throughout, along with full solutions, to illustrate concepts and also highlight many interesting mathematical ideas. The text begins by introducing fundamental combinatorial objects such as permutations and integer partitions, as well as generating functions.  Symmetric functions are considered in the next chapter, with a unique emphasis on the combinatorics of the transition matrices between bases of symmetric functions.  Chapter 3 uses this introductory material to describe how to find an assortment of generating functions for permutation statistics, and then these techniques are extended to find generating functions for a variety of objects in Chapter 4.  The next two chapters present the Robinson-Schensted-Knuth algorithm and a method for proving Pólya’s enu...

  17. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis

    International Nuclear Information System (INIS)

    Gurushankar, K; Gohulkumar, M; Krishnakumar, N; Kumar, Piyush; Murali Krishna, C

    2016-01-01

    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800–500 cm −1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC–LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  18. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes.

    Science.gov (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J

    2016-02-22

    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at http://haddock.science.uu.nl/services/HADDOCK2.2. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  19. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    International Nuclear Information System (INIS)

    Zhou, Peipei; Cai, Shuiming; Liu, Zengrong; Chen, Luonan; Wang, Ruiqi

    2013-01-01

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks

  20. Coupling switches and oscillators as a means to shape cellular signals in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Peipei [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Cai, Shuiming [Faculty of Science, Jiangsu University, Zhenjiang, Jiangsu 212013 (China); Liu, Zengrong [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China); Chen, Luonan [Key Laboratory of Systems Biology, SIBS-Novo Nordisk Translational Research Center for PreDiabetes, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031 (China); Collaborative Research Center for Innovative Mathematical Modeling, Institute of Industrial Science, University of Tokyo, Tokyo 153-8505 (Japan); Wang, Ruiqi [Institute of Systems Biology, Shanghai University, Shanghai 200444 (China)

    2013-05-15

    To understand how a complex biomolecular network functions, a decomposition or a reconstruction process of the network is often needed so as to provide new insights into the regulatory mechanisms underlying various dynamical behaviors and also to gain qualitative knowledge of the network. Unfortunately, it seems that there are still no general rules on how to decompose a complex network into simple modules. An alternative resolution is to decompose a complex network into small modules or subsystems with specified functions such as switches and oscillators and then integrate them by analyzing the interactions between them. The main idea of this approach can be illustrated by considering a bidirectionally coupled network in this paper, i.e., coupled Toggle switch and Repressilator, and analyzing the occurrence of various dynamics, although the theoretical principle may hold for a general class of networks. We show that various biomolecular signals can be shaped by regulating the coupling between the subsystems. The approach presented here can be expected to simplify and analyze even more complex biological networks.

  1. Characteristic function-based semiparametric inference for skew-symmetric models

    KAUST Repository

    Potgieter, Cornelis J.

    2012-12-26

    Skew-symmetric models offer a very flexible class of distributions for modelling data. These distributions can also be viewed as selection models for the symmetric component of the specified skew-symmetric distribution. The estimation of the location and scale parameters corresponding to the symmetric component is considered here, with the symmetric component known. Emphasis is placed on using the empirical characteristic function to estimate these parameters. This is made possible by an invariance property of the skew-symmetric family of distributions, namely that even transformations of random variables that are skew-symmetric have a distribution only depending on the symmetric density. A distance metric between the real components of the empirical and true characteristic functions is minimized to obtain the estimators. The method is semiparametric, in that the symmetric component is specified, but the skewing function is assumed unknown. Furthermore, the methodology is extended to hypothesis testing. Two tests for a hypothesis of specific parameter values are considered, as well as a test for the hypothesis that the symmetric component has a specific parametric form. A resampling algorithm is described for practical implementation of these tests. The outcomes of various numerical experiments are presented. © 2012 Board of the Foundation of the Scandinavian Journal of Statistics.

  2. Symmetric metamaterials based on flower-shaped structure

    International Nuclear Information System (INIS)

    Tuong, P.V.; Park, J.W.; Rhee, J.Y.; Kim, K.W.; Cheong, H.; Jang, W.H.; Lee, Y.P.

    2013-01-01

    We proposed new models of metamaterials (MMs) based on a flower-shaped structure (FSS), whose “meta-atoms” consist of two flower-shaped metallic parts separated by a dielectric layer. Like the non-symmetric MMs based on cut-wire-pairs or electric ring resonators, the symmetrical FSS demonstrates the negative permeability at GHz frequencies. Employing the results, we designed a symmetric negative-refractive-index MM [a symmetric combined structure (SCS)], which is composed of FSSs and cross continuous wires. The MM properties of the FSS and the SCS are presented numerically and experimentally. - Highlights: • A new designed of sub-wavelength metamaterial, flower-shaped structure was proposed. • Flower-shaped meta-atom illustrated effective negative permeability. • Based on the meta-atom, negative refractive index was conventionally gained. • Negative refractive index was demonstrated with symmetric properties for electromagnetic wave. • Dimensional parameters were studied under normal electromagnetic wave

  3. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari

    2009-01-01

    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  4. Towards sensitive, high-throughput, biomolecular assays based on fluorescence lifetime

    Science.gov (United States)

    Ioanna Skilitsi, Anastasia; Turko, Timothé; Cianfarani, Damien; Barre, Sophie; Uhring, Wilfried; Hassiepen, Ulrich; Léonard, Jérémie

    2017-09-01

    Time-resolved fluorescence detection for robust sensing of biomolecular interactions is developed by implementing time-correlated single photon counting in high-throughput conditions. Droplet microfluidics is used as a promising platform for the very fast handling of low-volume samples. We illustrate the potential of this very sensitive and cost-effective technology in the context of an enzymatic activity assay based on fluorescently-labeled biomolecules. Fluorescence lifetime detection by time-correlated single photon counting is shown to enable reliable discrimination between positive and negative control samples at a throughput as high as several hundred samples per second.

  5. Super-symmetric informationally complete measurements

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Huangjun, E-mail: hzhu@pitp.ca

    2015-11-15

    Symmetric informationally complete measurements (SICs in short) are highly symmetric structures in the Hilbert space. They possess many nice properties which render them an ideal candidate for fiducial measurements. The symmetry of SICs is intimately connected with the geometry of the quantum state space and also has profound implications for foundational studies. Here we explore those SICs that are most symmetric according to a natural criterion and show that all of them are covariant with respect to the Heisenberg–Weyl groups, which are characterized by the discrete analog of the canonical commutation relation. Moreover, their symmetry groups are subgroups of the Clifford groups. In particular, we prove that the SIC in dimension 2, the Hesse SIC in dimension 3, and the set of Hoggar lines in dimension 8 are the only three SICs up to unitary equivalence whose symmetry groups act transitively on pairs of SIC projectors. Our work not only provides valuable insight about SICs, Heisenberg–Weyl groups, and Clifford groups, but also offers a new approach and perspective for studying many other discrete symmetric structures behind finite state quantum mechanics, such as mutually unbiased bases and discrete Wigner functions.

  6. Integration of biomolecular logic gates with field-effect transducers

    Energy Technology Data Exchange (ETDEWEB)

    Poghossian, A., E-mail: a.poghossian@fz-juelich.de [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Malzahn, K. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Abouzar, M.H. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany); Mehndiratta, P. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Katz, E. [Department of Chemistry and Biomolecular Science, NanoBio Laboratory (NABLAB), Clarkson University, Potsdam, NY 13699-5810 (United States); Schoening, M.J. [Institute of Nano- and Biotechnologies, Aachen University of Applied Sciences, Campus Juelich, Heinrich-Mussmann-Str. 1, D-52428 Juelich (Germany); Institute of Bio- and Nanosystems, Research Centre Juelich GmbH, D-52425 Juelich (Germany)

    2011-11-01

    Highlights: > Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. > The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. > Logic gates were activated by different combinations of chemical inputs (analytes). > The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO{sub 2}-Ta{sub 2}O{sub 5} structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta{sub 2}O{sub 5}) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  7. Integration of biomolecular logic gates with field-effect transducers

    International Nuclear Information System (INIS)

    Poghossian, A.; Malzahn, K.; Abouzar, M.H.; Mehndiratta, P.; Katz, E.; Schoening, M.J.

    2011-01-01

    Highlights: → Enzyme-based AND/OR logic gates are integrated with a capacitive field-effect sensor. → The AND/OR logic gates compose of multi-enzyme system immobilised on sensor surface. → Logic gates were activated by different combinations of chemical inputs (analytes). → The logic output (pH change) produced by the enzymes was read out by the sensor. - Abstract: The integration of biomolecular logic gates with field-effect devices - the basic element of conventional electronic logic gates and computing - is one of the most attractive and promising approaches for the transformation of biomolecular logic principles into macroscopically useable electrical output signals. In this work, capacitive field-effect EIS (electrolyte-insulator-semiconductor) sensors based on a p-Si-SiO 2 -Ta 2 O 5 structure modified with a multi-enzyme membrane have been used for electronic transduction of biochemical signals processed by enzyme-based OR and AND logic gates. The realised OR logic gate composes of two enzymes (glucose oxidase and esterase) and was activated by ethyl butyrate or/and glucose. The AND logic gate composes of three enzymes (invertase, mutarotase and glucose oxidase) and was activated by two chemical input signals: sucrose and dissolved oxygen. The developed integrated enzyme logic gates produce local pH changes at the EIS sensor surface as a result of biochemical reactions activated by different combinations of chemical input signals, while the pH value of the bulk solution remains unchanged. The pH-induced charge changes at the gate-insulator (Ta 2 O 5 ) surface of the EIS transducer result in an electronic signal corresponding to the logic output produced by the immobilised enzymes. The logic output signals have been read out by means of a constant-capacitance method.

  8. Perspective: Markov models for long-timescale biomolecular dynamics

    International Nuclear Information System (INIS)

    Schwantes, C. R.; McGibbon, R. T.; Pande, V. S.

    2014-01-01

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics

  9. Perspective: Markov models for long-timescale biomolecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Schwantes, C. R.; McGibbon, R. T. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Pande, V. S., E-mail: pande@stanford.edu [Department of Chemistry, Stanford University, Stanford, California 94305 (United States); Department of Computer Science, Stanford University, Stanford, California 94305 (United States); Department of Structural Biology, Stanford University, Stanford, California 94305 (United States); Biophysics Program, Stanford University, Stanford, California 94305 (United States)

    2014-09-07

    Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.

  10. Facial One-Pot Synthesis of D 3h Symmetric Bicyclocalix[2]arene[2]triazines and Their Layered Comb Self-Assembly

    KAUST Repository

    Chen, Yin; Jiahui, Wang; Xu, Hai; Qianqian, Li; Jing, Jiang

    2017-01-01

    A number of D3h symmetric bicyclocalix[2]arene[2]triazine core compounds were synthesized via a general and good-yielding (43-48% yield) facile protocol starting from cyanuric halides, phloroglucinol and K2CO3 under very mild reaction conditions

  11. Techniques of biomolecular quantification through AMS detection of radiocarbon

    International Nuclear Information System (INIS)

    Vogel, S.J.; Turteltaub, K.W.; Frantz, C.; Felton, J.S.; Gledhill, B.L.

    1992-01-01

    Accelerator mass spectrometry offers a large gain over scintillation counting in sensitivity for detecting radiocarbon in biomolecular tracing. Application of this sensitivity requires new considerations of procedures to extract or isolate the carbon fraction to be quantified, to inventory all carbon in the sample, to prepare graphite from the sample for use in the spectrometer, and to derive a meaningful quantification from the measured isotope ratio. These procedures need to be accomplished without contaminating the sample with radiocarbon, which may be ubiquitous in laboratories and on equipment previously used for higher dose, scintillation experiments. Disposable equipment, materials and surfaces are used to control these contaminations. Quantification of attomole amounts of labeled substances are possible through these techniques

  12. Linac design algorithm with symmetric segments

    International Nuclear Information System (INIS)

    Takeda, Harunori; Young, L.M.; Nath, S.; Billen, J.H.; Stovall, J.E.

    1996-01-01

    The cell lengths in linacs of traditional design are typically graded as a function of particle velocity. By making groups of cells and individual cells symmetric in both the CCDTL AND CCL, the cavity design as well as mechanical design and fabrication is simplified without compromising the performance. We have implemented a design algorithm in the PARMILA code in which cells and multi-cavity segments are made symmetric, significantly reducing the number of unique components. Using the symmetric algorithm, a sample linac design was generated and its performance compared with a similar one of conventional design

  13. PT symmetric Aubry–Andre model

    International Nuclear Information System (INIS)

    Yuce, C.

    2014-01-01

    PT symmetric Aubry–Andre model describes an array of N coupled optical waveguides with position-dependent gain and loss. We show that the reality of the spectrum depends sensitively on the degree of quasi-periodicity for small number of lattice sites. We obtain the Hofstadter butterfly spectrum and discuss the existence of the phase transition from extended to localized states. We show that rapidly changing periodical gain/loss materials almost conserve the total intensity. - Highlights: • We show that PT symmetric Aubry–Andre model may have real spectrum. • We show that the reality of the spectrum depends sensitively on the degree of disorder. • We obtain the Hofstadter butterfly spectrum for PT symmetric Aubry–Andre model. • We discuss that phase transition from extended to localized states exists

  14. PT symmetric Aubry–Andre model

    Energy Technology Data Exchange (ETDEWEB)

    Yuce, C., E-mail: cyuce@anadolu.edu.tr

    2014-06-13

    PT symmetric Aubry–Andre model describes an array of N coupled optical waveguides with position-dependent gain and loss. We show that the reality of the spectrum depends sensitively on the degree of quasi-periodicity for small number of lattice sites. We obtain the Hofstadter butterfly spectrum and discuss the existence of the phase transition from extended to localized states. We show that rapidly changing periodical gain/loss materials almost conserve the total intensity. - Highlights: • We show that PT symmetric Aubry–Andre model may have real spectrum. • We show that the reality of the spectrum depends sensitively on the degree of disorder. • We obtain the Hofstadter butterfly spectrum for PT symmetric Aubry–Andre model. • We discuss that phase transition from extended to localized states exists.

  15. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  16. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Science.gov (United States)

    Caravagna, Giulio; Mauri, Giancarlo; d'Onofrio, Alberto

    2013-01-01

    After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i) the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii) a model of enzymatic futile cycle and (iii) a genetic toggle switch. In (ii) and (iii) we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  17. Stereochemistry in subcomponent self-assembly.

    Science.gov (United States)

    Castilla, Ana M; Ramsay, William J; Nitschke, Jonathan R

    2014-07-15

    CONSPECTUS: As Pasteur noted more than 150 years ago, asymmetry exists in matter at all organization levels. Biopolymers such as proteins or DNA adopt one-handed conformations, as a result of the chirality of their constituent building blocks. Even at the level of elementary particles, asymmetry exists due to parity violation in the weak nuclear force. While the origin of homochirality in living systems remains obscure, as does the possibility of its connection with broken symmetries at larger or smaller length scales, its centrality to biomolecular structure is clear: the single-handed forms of bio(macro)molecules interlock in ways that depend upon their handednesses. Dynamic artificial systems, such as helical polymers and other supramolecular structures, have provided a means to study the mechanisms of transmission and amplification of stereochemical information, which are key processes to understand in the context of the origins and functions of biological homochirality. Control over stereochemical information transfer in self-assembled systems will also be crucial for the development of new applications in chiral recognition and separation, asymmetric catalysis, and molecular devices. In this Account, we explore different aspects of stereochemistry encountered during the use of subcomponent self-assembly, whereby complex structures are prepared through the simultaneous formation of dynamic coordinative (N → metal) and covalent (N═C) bonds. This technique provides a useful method to study stereochemical information transfer processes within metal-organic assemblies, which may contain different combinations of fixed (carbon) and labile (metal) stereocenters. We start by discussing how simple subcomponents with fixed stereogenic centers can be incorporated in the organic ligands of mononuclear coordination complexes and communicate stereochemical information to the metal center, resulting in diastereomeric enrichment. Enantiopure subcomponents were then

  18. Comprehensive asynchronous symmetric rendezvous algorithm in ...

    Indian Academy of Sciences (India)

    Meenu Chawla

    2017-11-10

    Nov 10, 2017 ... Simulation results affirm that CASR algorithm performs better in terms of average time-to-rendezvous as compared ... process; neighbour discovery; symmetric rendezvous algorithm. 1. .... dezvous in finite time under the symmetric model. The CH ..... CASR algorithm in Matlab 7.11 and performed several.

  19. Performance evaluation of symmetric supercapacitor based on cobalt hydroxide [Co(OH)2] thin film electrodes

    International Nuclear Information System (INIS)

    Jagadale, A.D.; Kumbhar, V.S.; Dhawale, D.S.; Lokhande, C.D.

    2013-01-01

    In the present investigation, we have successfully assembled symmetric supercapacitor device based on cobalt hydroxide [Co(OH) 2 ] thin film electrodes using 1 M KOH as an electrolyte. Initially, potentiodynamic electrodeposition method is employed for the preparation of Co(OH) 2 thin films onto stainless steel substrate. These films are characterized for structural and morphological elucidations using X-ray diffraction (XRD) and scanning electron microscopy (SEM), respectively. The XRD reveals formation of β-Co(OH) 2 material with hexagonal crystal structure. The SEM images show formation of nanoflakes like microstructure with average flake width 100 nm. Electrochemical characterizations of Co(OH) 2 based symmetric supercapacitor cell are carried out using cyclic voltammetry, charge–discharge and electrochemical impedance spectroscopy (EIS) techniques. In the performance evaluation the maximum values of specific capacitance, specific energy and specific power are encountered as 44 F g −1 , 3.96 Wh kg −1 and 42 kW kg −1 . The value of equivalent series resistance (ESR) is estimated as 2.3 Ω using EIS

  20. Parallel assembling and equation solving via graph algorithms with an application to the FE simulation of metal extrusion processes

    CERN Document Server

    Unterkircher, A

    2005-01-01

    We propose methods for parallel assembling and iterative equation solving based on graph algorithms. The assembling technique is independent of dimension, element type and model shape. As a parallel solving technique we construct a multiplicative symmetric Schwarz preconditioner for the conjugate gradient method. Both methods have been incorporated into a non-linear FE code to simulate 3D metal extrusion processes. We illustrate the efficiency of these methods on shared memory computers by realistic examples.

  1. Peptide-based biosensors: From self-assembled interfaces to molecular probes in electrochemical assays.

    Science.gov (United States)

    Puiu, Mihaela; Bala, Camelia

    2018-04-01

    Redox-tagged peptides have emerged as functional materials with multiple applications in the area of sensing and biosensing applications due to their high stability, excellent redox properties and versatility of biomolecular interactions. They allow direct observation of molecular interactions in a wide range of affinity and enzymatic assays and act as electron mediators. Short helical peptides possess the ability to self-assemble in specific configurations with the possibility to develop in highly-ordered, stable 1D, 2D and 3D architectures in a hierarchical controlled manner. We provide here a brief overview of the electrochemical techniques available to study the electron transfer in peptide films with particular interest in developing biosensors with immobilized peptide motifs, for biological and clinical applications. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Integrated Spintronic Platforms for Biomolecular Recognition Detection

    Science.gov (United States)

    Martins, V. C.; Cardoso, F. A.; Loureiro, J.; Mercier, M.; Germano, J.; Cardoso, S.; Ferreira, R.; Fonseca, L. P.; Sousa, L.; Piedade, M. S.; Freitas, P. P.

    2008-06-01

    This paper covers recent developments in magnetoresistive based biochip platforms fabricated at INESC-MN, and their application to the detection and quantification of pathogenic waterborn microorganisms in water samples for human consumption. Such platforms are intended to give response to the increasing concern related to microbial contaminated water sources. The presented results concern the development of biological active DNA chips and protein chips and the demonstration of the detection capability of the present platforms. Two platforms are described, one including spintronic sensors only (spin-valve based or magnetic tunnel junction based), and the other, a fully scalable platform where each probe site consists of a MTJ in series with a thin film diode (TFD). Two microfluidic systems are described, for cell separation and concentration, and finally, the read out and control integrated electronics are described, allowing the realization of bioassays with a portable point of care unit. The present platforms already allow the detection of complementary biomolecular target recognition with 1 pM concentration.

  3. The Symmetric Rudin-Shapiro Transform

    DEFF Research Database (Denmark)

    Harbo, Anders La-Cour

    2003-01-01

    A method for constructing spread spectrum sequences is presented. The method is based on a linear, orthogonal, symmetric transform, the Rudin-Shapiro transform (RST), which is in many respects quite similar to the Haar wavelet packet transform. The RST provides the means for generating large sets...... of spread spectrum signals. This presentation provides a simple definition of the symmetric RST that leads to a fast N log(N) and numerically stable implementation of the transform....

  4. Perspective: Watching low-frequency vibrations of water in biomolecular recognition by THz spectroscopy

    Science.gov (United States)

    Xu, Yao; Havenith, Martina

    2015-11-01

    Terahertz (THz) spectroscopy has turned out to be a powerful tool which is able to shed new light on the role of water in biomolecular processes. The low frequency spectrum of the solvated biomolecule in combination with MD simulations provides deep insights into the collective hydrogen bond dynamics on the sub-ps time scale. The absorption spectrum between 1 THz and 10 THz of solvated biomolecules is sensitive to changes in the fast fluctuations of the water network. Systematic studies on mutants of antifreeze proteins indicate a direct correlation between biological activity and a retardation of the (sub)-ps hydration dynamics at the protein binding site, i.e., a "hydration funnel." Kinetic THz absorption studies probe the temporal changes of THz absorption during a biological process, and give access to the kinetics of the coupled protein-hydration dynamics. When combined with simulations, the observed results can be explained in terms of a two-tier model involving a local binding and a long range influence on the hydration bond dynamics of the water around the binding site that highlights the significance of the changes in the hydration dynamics at recognition site for biomolecular recognition. Water is shown to assist molecular recognition processes.

  5. Thermal characterization of indirectly heated axi-symmetric solid cathode electron beam gun for melting application

    International Nuclear Information System (INIS)

    Prakash, B.; Gupta, S.; Malik, P.; Mishra, K.K.; Jha, M.N.; Kandaswamy, E.; Martin, M.

    2015-01-01

    Electron beam melting gun with indirectly heated axi-symmetric solid cathode was designed, fabricated and characterized experimentally. The thermal simulation and optical analysis of the electron gun was carried out to estimate the power required to achieve the emission temperature of the solid cathode, to obtain the temperature distribution in the assembly and the beam transportation. On the basis of the thermal simulation and electron optics, the electron gun design was finalised. The electron gun assembly was fabricated and installed in the vacuum chamber for carrying out the experiment to find the actual temperature distribution. Thermocouple and two colour pyrometer were used to measure the temperature at various locations in the electron gun. The attenuation effect of the viewing port glass of the vacuum chamber was compensated in the final reading of the temperature measured by the pyrometer. The temperature of solid cathode obtained by the experiment was found to be 2800K which is the emission temperature of solid cathode. (author)

  6. Research on the rolling moment in the symmetrical and asymmetrical rolling process

    Science.gov (United States)

    Alexa, V.; Raţiu, S. A.; Kiss, I.; Cioată, C. G.

    2017-01-01

    Research distribution the rolling moments symmetrical and asymmetrical report presents great importance both in theory and to introduce clarifications to the calculation of rolling resistance line assemblies. Clarifying individuals of metallic material deformation between the rolls single cylinder diameters act of any difference of work and analysis of advance and delay phenomena. Torque drive value for each of the rolling cylinders was done by reducing the thickness of the laminate samples, an experimental facility located in the laboratory of plastic deformation of the Faculty of Engineering Hunedoara. The analysis of research results show that in terms of power consumption for deformation and safety equipment in operation is rational for mills which require such a difference between the work rolls to execute about one cylinder operated.

  7. Symmetric imaging findings in neuroradiology

    International Nuclear Information System (INIS)

    Zlatareva, D.

    2015-01-01

    Full text: Learning objectives: to make a list of diseases and syndromes which manifest as bilateral symmetric findings on computed tomography and magnetic resonance imaging; to discuss the clinical and radiological differential diagnosis for these diseases; to explain which of these conditions necessitates urgent therapy and when additional studies and laboratory can precise diagnosis. There is symmetry in human body and quite often we compare the affected side to the normal one but in neuroradiology we might have bilateral findings which affected pair structures or corresponding anatomic areas. It is very rare when clinical data prompt diagnosis. Usually clinicians suspect such an involvement but Ct and MRI can reveal symmetric changes and are one of the leading diagnostic tool. The most common location of bilateral findings is basal ganglia and thalamus. There are a number of diseases affecting these structures symmetrically: metabolic and systemic diseases, intoxication, neurodegeneration and vascular conditions, toxoplasmosis, tumors and some infections. Malformations of cortical development and especially bilateral perisylvian polymicrogyria requires not only exact report on the most affected parts but in some cases genetic tests or combination with other clinical symptoms. In the case of herpes simplex encephalitis bilateral temporal involvement is common and this finding very often prompt therapy even before laboratory results. Posterior reversible encephalopathy syndrome (PReS) and some forms of hypoxic ischemic encephalopathy can lead to symmetric changes. In these acute conditions MR plays a crucial role not only in diagnosis but also in monitoring of the therapeutic effect. Patients with neurofibromatosis type 1 or type 2 can demonstrate bilateral optic glioma combined with spinal neurofibroma and bilateral acoustic schwanoma respectively. Mirror-image aneurysm affecting both internal carotid or middle cerebral arteries is an example of symmetry in

  8. ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.

    Science.gov (United States)

    Parvatikar, Akash; Vacaliuc, Gabriel S; Ramanathan, Arvind; Chennubhotla, S Chakra

    2018-05-08

    Anharmonicity in time-dependent conformational fluctuations is noted to be a key feature of functional dynamics of biomolecules. Although anharmonic events are rare, long-timescale (μs-ms and beyond) simulations facilitate probing of such events. We have previously developed quasi-anharmonic analysis to resolve higher-order spatial correlations and characterize anharmonicity in biomolecular simulations. In this article, we have extended this toolbox to resolve higher-order temporal correlations and built a scalable Python package called anharmonic conformational analysis (ANCA). ANCA has modules to: 1) measure anharmonicity in the form of higher-order statistics and its variation as a function of time, 2) output a storyboard representation of the simulations to identify key anharmonic conformational events, and 3) identify putative anharmonic conformational substates and visualization of transitions between these substates. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  9. Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes

    OpenAIRE

    Foo, Mathias; Kim, Jongrae; Sawlekar, Rucha; Bates, Declan G.

    2017-01-01

    Feedback control is widely used in chemical engineering to improve the performance and robustness of chemical processes. Feedback controllers require a ‘subtractor’ that is able to compute the error between the process output and the reference signal. In the case of embedded biomolecular control circuits, subtractors designed using standard chemical reaction network theory can only realise one-sided subtraction, rendering standard controller design approaches inadequate. Here, we show how a b...

  10. Introduction to a Protein Interaction System Used for Quantitative Evaluation of Biomolecular Interactions

    OpenAIRE

    Yamniuk, Aaron

    2013-01-01

    A central goal of molecular biology is the determination of biomolecular function. This comes largely from a knowledge of the non-covalent interactions that biological small and macro-molecules experience. The fundamental mission of the Molecular Interactions Research Group (MIRG) of the ABRF is to show how solution biophysical tools are used to quantitatively characterize molecular interactions, and to educate the ABRF members and scientific community on the utility and limitations of core t...

  11. Looking for symmetric Bell inequalities

    OpenAIRE

    Bancal, Jean-Daniel; Gisin, Nicolas; Pironio, Stefano

    2010-01-01

    Finding all Bell inequalities for a given number of parties, measurement settings and measurement outcomes is in general a computationally hard task. We show that all Bell inequalities which are symmetric under the exchange of parties can be found by examining a symmetrized polytope which is simpler than the full Bell polytope. As an illustration of our method, we generate 238 885 new Bell inequalities and 1085 new Svetlichny inequalities. We find, in particular, facet inequalities for Bell e...

  12. The Symmetric Rudin-Shapiro Transform

    DEFF Research Database (Denmark)

    Harbo, Anders La-Cour

    2003-01-01

    A method for constructing spread spectrum sequences is presented. The method is based on a linear, orthogonal, and symmetric transform given as the Rudin-Shapiro transform (RST), which is in many respects quite similar to the Haar wavelet packet transform. The RST provides the means for generatin...... large sets of spread spectrum signals. This presentation provides a simple definition of the symmetric RST that leads to a fast N log(N) and numerically stable implementation of the transform....

  13. Review of MEMS differential scanning calorimetry for biomolecular study

    Science.gov (United States)

    Yu, Shifeng; Wang, Shuyu; Lu, Ming; Zuo, Lei

    2017-12-01

    Differential scanning calorimetry (DSC) is one of the few techniques that allow direct determination of enthalpy values for binding reactions and conformational transitions in biomolecules. It provides the thermodynamics information of the biomolecules which consists of Gibbs free energy, enthalpy and entropy in a straightforward manner that enables deep understanding of the structure function relationship in biomolecules such as the folding/unfolding of protein and DNA, and ligand bindings. This review provides an up to date overview of the applications of DSC in biomolecular study such as the bovine serum albumin denaturation study, the relationship between the melting point of lysozyme and the scanning rate. We also introduce the recent advances of the development of micro-electro-mechanic-system (MEMS) based DSCs.

  14. Harmonic analysis on symmetric spaces

    CERN Document Server

    Terras, Audrey

    This text explores the geometry and analysis of higher rank analogues of the symmetric spaces introduced in volume one. To illuminate both the parallels and differences of the higher rank theory, the space of positive matrices is treated in a manner mirroring that of the upper-half space in volume one. This concrete example furnishes motivation for the general theory of noncompact symmetric spaces, which is outlined in the final chapter. The book emphasizes motivation and comprehensibility, concrete examples and explicit computations (by pen and paper, and by computer), history, and, above all, applications in mathematics, statistics, physics, and engineering. The second edition includes new sections on Donald St. P. Richards’s central limit theorem for O(n)-invariant random variables on the symmetric space of GL(n, R), on random  matrix theory, and on advances in the theory of automorphic forms on arithmetic groups.

  15. On isotropic cylindrically symmetric stellar models

    International Nuclear Information System (INIS)

    Nolan, Brien C; Nolan, Louise V

    2004-01-01

    We attempt to match the most general cylindrically symmetric vacuum spacetime with a Robertson-Walker interior. The matching conditions show that the interior must be dust filled and that the boundary must be comoving. Further, we show that the vacuum region must be polarized. Imposing the condition that there are no trapped cylinders on an initial time slice, we can apply a result of Thorne's and show that trapped cylinders never evolve. This results in a simplified line element which we prove to be incompatible with the dust interior. This result demonstrates the impossibility of the existence of an isotropic cylindrically symmetric star (or even a star which has a cylindrically symmetric portion). We investigate the problem from a different perspective by looking at the expansion scalars of invariant null geodesic congruences and, applying to the cylindrical case, the result that the product of the signs of the expansion scalars must be continuous across the boundary. The result may also be understood in relation to recent results about the impossibility of the static axially symmetric analogue of the Einstein-Straus model

  16. RNA Packing Specificity and Folding during Assembly of the Bacteriophage MS2

    Directory of Open Access Journals (Sweden)

    Ottar Rolfsson

    2008-01-01

    Full Text Available Using a combination of biochemistry, mass spectrometry, NMR spectroscopy and cryo-electron microscopy (cryo-EM, we have been able to show that quasi-equivalent conformer switching in the coat protein (CP of an RNA bacteriophage (MS2 is controlled by a sequence-specific RNA–protein interaction. The RNA component of this complex is an RNA stem-loop encompassing just 19 nts from the phage genomic RNA, which is 3569 nts in length. This binding results in the conversion of a CP dimer from a symmetrical conformation to an asymmetric one. Only when both symmetrical and asymmetrical dimers are present in solution is assembly of the T = 3 phage capsid efficient. This implies that the conformers, we have characterized by NMR correspond to the two distinct quasi-equivalent conformers seen in the 3D structure of the virion. An icosahedrally-averaged single particle cryo-EM reconstruction of the wild-type phage (to ∼9 Å resolution has revealed icosahedrally ordered density encompassing up to 90% of the single-stranded RNA genome. The RNA is seen with a novel arrangement of two concentric shells, with connections between them along the 5-fold symmetry axes. RNA in the outer shell interacts with each of the 90 CP dimers in the T = 3 capsid and although the density is icosahedrally averaged, there appears to be a different average contact at the different quasi-equivalent protein dimers: precisely the result that would be expected if protein conformer switching is RNA-mediated throughout the assembly pathway. This unprecedented RNA structure provides new constraints for models of viral assembly and we describe experiments aimed at probing these. Together, these results suggest that viral genomic RNA folding is an important factor in efficient assembly, and further suggest that RNAs that could sequester viral CPs but not fold appropriately could act as potent inhibitors of viral assembly.

  17. Multiscale Persistent Functions for Biomolecular Structure Characterization

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin [Nanyang Technological University (Singapore). Division of Mathematical Sciences, School of Physical, Mathematical Sciences and School of Biological Sciences; Li, Zhiming [Central China Normal University, Wuhan (China). Key Laboratory of Quark and Lepton Physics (MOE) and Institute of Particle Physics; Mu, Lin [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computer Science and Mathematics Division

    2017-11-02

    Here in this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions (MRFs) with persistent homology analysis, so as to construct a series of multiscale persistent functions, particularly multiscale persistent entropies, for structure characterization. To clarify the fundamental idea of our method, the multiscale persistent entropy (MPE) model is discussed in great detail. Mathematically, unlike the previous persistent entropy (Chintakunta et al. in Pattern Recognit 48(2):391–401, 2015; Merelli et al. in Entropy 17(10):6872–6892, 2015; Rucco et al. in: Proceedings of ECCS 2014, Springer, pp 117–128, 2016), a special resolution parameter is incorporated into our model. Various scales can be achieved by tuning its value. Physically, our MPE can be used in conformational entropy evaluation. More specifically, it is found that our method incorporates in it a natural classification scheme. This is achieved through a density filtration of an MRF built from angular distributions. To further validate our model, a systematical comparison with the traditional entropy evaluation model is done. Additionally, it is found that our model is able to preserve the intrinsic topological features of biomolecular data much better than traditional approaches, particularly for resolutions in the intermediate range. Moreover, by comparing with traditional entropies from various grid sizes, bond angle-based methods and a persistent homology-based support vector machine method (Cang et al. in Mol Based Math Biol 3:140–162, 2015), we find that our MPE method gives the best results in terms of average true positive rate in a classic protein structure classification test. More interestingly, all-alpha and all-beta protein classes can be clearly separated from each other with zero error only in our model. Finally, a special protein structure index (PSI) is proposed, for the first

  18. First assembly phase for the ATLAS toroid coils

    CERN Multimedia

    Maximilien Brice

    2003-01-01

    The ATLAS barrel toroid system consists of eight coils, each of axial length 25.3 m, assembled radially and symmetrically around the beam axis. The coils are of a flat racetrack type with two double-pancake windings made of 20.5 kA aluminium-stabilized niobium-titanium superconductor. In the first phase of assembly, the two 'pancakes' are packed into their vacuum vessel. This is done using bladders filled with resin and glass microbeads under pressure. The resin is heated and, once cooled, holds the pancakes in place. The operation has to be performed on both sides of the coil, which necessitated a special technique to turn the coils over and then transport them to the heating table. Photos 01, 02, 03: Transporting the coil to the heating table using a special lifting gantry manufactured at JINR-Dubna, Russia in preparation for the 'bladderisation' operation.

  19. Globally optimal superconducting magnets part II: symmetric MSE coil arrangement.

    Science.gov (United States)

    Tieng, Quang M; Vegh, Viktor; Brereton, Ian M

    2009-01-01

    A globally optimal superconducting magnet coil design procedure based on the Minimum Stored Energy (MSE) current density map is outlined. The method has the ability to arrange coils in a manner that generates a strong and homogeneous axial magnetic field over a predefined region, and ensures the stray field external to the assembly and peak magnetic field at the wires are in acceptable ranges. The outlined strategy of allocating coils within a given domain suggests that coils should be placed around the perimeter of the domain with adjacent coils possessing alternating winding directions for optimum performance. The underlying current density maps from which the coils themselves are derived are unique, and optimized to possess minimal stored energy. Therefore, the method produces magnet designs with the lowest possible overall stored energy. Optimal coil layouts are provided for unshielded and shielded short bore symmetric superconducting magnets.

  20. On the harmonic starlike functions with respect to symmetric ...

    African Journals Online (AJOL)

    In the present paper, we introduce the notions of functions harmonic starlike with respect to symmetric, conjugate and symmetric conjugate points. Such results as coefficient inequalities and structural formulae for these function classes are proved. Keywords: Harmonic functions, harmonic starlike functions, symmetric points, ...

  1. Native fluorescence detection of biomolecular and pharmaceutical compounds in capillary electrophoresis: detector designs, performance and applications: A review

    NARCIS (Netherlands)

    de Kort, B.J.; de Jong, G.J.; Somsen, G.W.

    2013-01-01

    This review treats the coupling of capillary electrophoresis (CE) with fluorescence detection (Flu) for the analysis of natively fluorescent biomolecular and pharmaceutical compounds. CE-Flu combines the excellent separation efficiency of CE with the high selectivity and sensitivity of Flu. In

  2. Cotangent bundles over all the Hermitian symmetric spaces

    International Nuclear Information System (INIS)

    Arai, Masato; Baba, Kurando

    2016-01-01

    We construct the N = 2 supersymmetric nonlinear sigma models on the cotangent bundles over all the compact and non-compact Hermitian symmetric spaces. In order to construct them we use the projective superspace formalism which is an N = 2 off-shell superfield formulation in four-dimensional space-time. This formalism allows us to obtain the explicit expression of N = 2 supersymmetric nonlinear sigma models on the cotangent bundles over any Hermitian symmetric spaces in terms of the N =1 superfields, once the Kähler potentials of the base manifolds are obtained. Starting with N = 1 supersymmetric Kähler nonlinear sigma models on the Hermitian symmetric spaces, we extend them into the N = 2 supersymmetric models by using the projective superspace formalism and derive the general formula for the cotangent bundles over all the compact and non-compact Hermitian symmetric spaces. We apply to the formula for the non-compact Hermitian symmetric space E 7 /E 6 × U(1) 1 . (paper)

  3. Symmetric waterbomb origami.

    Science.gov (United States)

    Chen, Yan; Feng, Huijuan; Ma, Jiayao; Peng, Rui; You, Zhong

    2016-06-01

    The traditional waterbomb origami, produced from a pattern consisting of a series of vertices where six creases meet, is one of the most widely used origami patterns. From a rigid origami viewpoint, it generally has multiple degrees of freedom, but when the pattern is folded symmetrically, the mobility reduces to one. This paper presents a thorough kinematic investigation on symmetric folding of the waterbomb pattern. It has been found that the pattern can have two folding paths under certain circumstance. Moreover, the pattern can be used to fold thick panels. Not only do the additional constraints imposed to fold the thick panels lead to single degree of freedom folding, but the folding process is also kinematically equivalent to the origami of zero-thickness sheets. The findings pave the way for the pattern being readily used to fold deployable structures ranging from flat roofs to large solar panels.

  4. Symmetric modular torsatron

    Science.gov (United States)

    Rome, J.A.; Harris, J.H.

    1984-01-01

    A fusion reactor device is provided in which the magnetic fields for plasma confinement in a toroidal configuration is produced by a plurality of symmetrical modular coils arranged to form a symmetric modular torsatron referred to as a symmotron. Each of the identical modular coils is helically deformed and comprise one field period of the torsatron. Helical segments of each coil are connected by means of toroidally directed windbacks which may also provide part of the vertical field required for positioning the plasma. The stray fields of the windback segments may be compensated by toroidal coils. A variety of magnetic confinement flux surface configurations may be produced by proper modulation of the winding pitch of the helical segments of the coils, as in a conventional torsatron, winding the helix on a noncircular cross section and varying the poloidal and radial location of the windbacks and the compensating toroidal ring coils.

  5. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1

    Directory of Open Access Journals (Sweden)

    S. Iachettini

    2015-10-01

    Full Text Available Myotonic dystrophy type 1 (DM1 is a neuromuscular disorder caused by a CTG repeat expansion in 3’UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  6. Performance limitations of translationally symmetric nonimaging devices

    Science.gov (United States)

    Bortz, John C.; Shatz, Narkis E.; Winston, Roland

    2001-11-01

    The component of the optical direction vector along the symmetry axis is conserved for all rays propagated through a translationally symmetric optical device. This quality, referred to herein as the translational skew invariant, is analogous to the conventional skew invariant, which is conserved in rotationally symmetric optical systems. The invariance of both of these quantities is a consequence of Noether's theorem. We show how performance limits for translationally symmetric nonimaging optical devices can be derived from the distributions of the translational skew invariant for the optical source and for the target to which flux is to be transferred. Examples of computed performance limits are provided. In addition, we show that a numerically optimized non-tracking solar concentrator utilizing symmetry-breaking surface microstructure can overcome the performance limits associated with translational symmetry. The optimized design provides a 47.4% increase in efficiency and concentration relative to an ideal translationally symmetric concentrator.

  7. Hybrid organic semiconductor lasers for bio-molecular sensing.

    Science.gov (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas

    2014-01-01

    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  8. Symmetric Imidazolium-Based Paramagnetic Ionic Liquids

    Science.gov (United States)

    2017-11-29

    Charts N/A Unclassified Unclassified Unclassified SAR 14 Kamran Ghiassi N/A 1 Symmetric Imidazolium-Based Paramagnetic Ionic Liquids Kevin T. Greeson...NUMBER (Include area code) 29 November 2017 Briefing Charts 01 November 2017 - 30 November 2017 Symmetric Imidazolium-Based Paramagnetic Ionic ... Liquids K. Greeson, K. Ghiassi, J. Alston, N. Redeker, J. Marcischak, L. Gilmore, A. Guenthner Air Force Research Laboratory (AFMC) AFRL/RQRP 9 Antares

  9. Design rules for biomolecular adhesion: lessons from force measurements.

    Science.gov (United States)

    Leckband, Deborah

    2010-01-01

    Cell adhesion to matrix, other cells, or pathogens plays a pivotal role in many processes in biomolecular engineering. Early macroscopic methods of quantifying adhesion led to the development of quantitative models of cell adhesion and migration. The more recent use of sensitive probes to quantify the forces that alter or manipulate adhesion proteins has revealed much greater functional diversity than was apparent from population average measurements of cell adhesion. This review highlights theoretical and experimental methods that identified force-dependent molecular properties that are central to the biological activity of adhesion proteins. Experimental and theoretical methods emphasized in this review include the surface force apparatus, atomic force microscopy, and vesicle-based probes. Specific examples given illustrate how these tools have revealed unique properties of adhesion proteins and their structural origins.

  10. Symmetric autocompensating quantum key distribution

    Science.gov (United States)

    Walton, Zachary D.; Sergienko, Alexander V.; Levitin, Lev B.; Saleh, Bahaa E. A.; Teich, Malvin C.

    2004-08-01

    We present quantum key distribution schemes which are autocompensating (require no alignment) and symmetric (Alice and Bob receive photons from a central source) for both polarization and time-bin qubits. The primary benefit of the symmetric configuration is that both Alice and Bob may have passive setups (neither Alice nor Bob is required to make active changes for each run of the protocol). We show that both the polarization and the time-bin schemes may be implemented with existing technology. The new schemes are related to previously described schemes by the concept of advanced waves.

  11. Magnetospectroscopy of symmetric and anti-symmetric states in double quantum wells

    Science.gov (United States)

    Marchewka, M.; Sheregii, E. M.; Tralle, I.; Ploch, D.; Tomaka, G.; Furdak, M.; Kolek, A.; Stadler, A.; Mleczko, K.; Zak, D.; Strupinski, W.; Jasik, A.; Jakiela, R.

    2008-02-01

    The experimental results obtained for magnetotransport in the InGaAs/InAlAs double quantum well (DQW) structures of two different shapes of wells are reported. A beating effect occurring in the Shubnikov-de Haas (SdH) oscillations was observed for both types of structures at low temperatures in the parallel transport when the magnetic field was perpendicular to the layers. An approach for the calculation of the Landau level energies for DQW structures was developed and then applied to the analysis and interpretation of the experimental data related to the beating effect. We also argue that in order to account for the observed magnetotransport phenomena (SdH and integer quantum Hall effect), one should introduce two different quasi-Fermi levels characterizing two electron subsystems regarding the symmetry properties of their states, symmetric and anti-symmetric ones, which are not mixed by electron-electron interaction.

  12. Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery*

    Science.gov (United States)

    Gakh, Oleksandr; Ranatunga, Wasantha; Smith, Douglas Y.; Ahlgren, Eva-Christina; Al-Karadaghi, Salam; Thompson, James R.; Isaya, Grazia

    2016-01-01

    Fe-S clusters, essential cofactors needed for the activity of many different enzymes, are assembled by conserved protein machineries inside bacteria and mitochondria. As the architecture of the human machinery remains undefined, we co-expressed in Escherichia coli the following four proteins involved in the initial step of Fe-S cluster synthesis: FXN42–210 (iron donor); [NFS1]·[ISD11] (sulfur donor); and ISCU (scaffold upon which new clusters are assembled). We purified a stable, active complex consisting of all four proteins with 1:1:1:1 stoichiometry. Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional model of the complex with ∼14 Å resolution. Molecular dynamics flexible fitting of protein structures docked into the EM map of the model revealed a [FXN42–210]24·[NFS1]24·[ISD11]24·[ISCU]24 complex, consistent with the measured 1:1:1:1 stoichiometry of its four components. The complex structure fulfills distance constraints obtained from chemical cross-linking of the complex at multiple recurring interfaces, involving hydrogen bonds, salt bridges, or hydrophobic interactions between conserved residues. The complex consists of a central roughly cubic [FXN42–210]24·[ISCU]24 sub-complex with one symmetric ISCU trimer bound on top of one symmetric FXN42–210 trimer at each of its eight vertices. Binding of 12 [NFS1]2·[ISD11]2 sub-complexes to the surface results in a globular macromolecule with a diameter of ∼15 nm and creates 24 Fe-S cluster assembly centers. The organization of each center recapitulates a previously proposed conserved mechanism for sulfur donation from NFS1 to ISCU and reveals, for the first time, a path for iron donation from FXN42–210 to ISCU. PMID:27519411

  13. A multiscale modeling approach for biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Bowling, Alan, E-mail: bowling@uta.edu; Haghshenas-Jaryani, Mahdi, E-mail: mahdi.haghshenasjaryani@mavs.uta.edu [The University of Texas at Arlington, Department of Mechanical and Aerospace Engineering (United States)

    2015-04-15

    This paper presents a new multiscale molecular dynamic model for investigating the effects of external interactions, such as contact and impact, during stepping and docking of motor proteins and other biomolecular systems. The model retains the mass properties ensuring that the result satisfies Newton’s second law. This idea is presented using a simple particle model to facilitate discussion of the rigid body model; however, the particle model does provide insights into particle dynamics at the nanoscale. The resulting three-dimensional model predicts a significant decrease in the effect of the random forces associated with Brownian motion. This conclusion runs contrary to the widely accepted notion that the motor protein’s movements are primarily the result of thermal effects. This work focuses on the mechanical aspects of protein locomotion; the effect ATP hydrolysis is estimated as internal forces acting on the mechanical model. In addition, the proposed model can be numerically integrated in a reasonable amount of time. Herein, the differences between the motion predicted by the old and new modeling approaches are compared using a simplified model of myosin V.

  14. Filtering microfluidic bubble trains at a symmetric junction.

    Science.gov (United States)

    Parthiban, Pravien; Khan, Saif A

    2012-02-07

    We report how a nominally symmetric microfluidic junction can be used to sort all bubbles of an incoming train exclusively into one of its arms. The existence of this "filter" regime is unexpected, given that the junction is symmetric. We analyze this behavior by quantifying how bubbles modulate the hydrodynamic resistance in microchannels and show how speeding up a bubble train whilst preserving its spatial periodicity can lead to filtering at a nominally symmetric junction. We further show how such an asymmetric traffic of bubble trains can be triggered in symmetric geometries by identifying conditions wherein the resistance to flow decreases with an increase in the number of bubbles in the microchannel and derive an exact criterion to predict the same.

  15. Crankshafts: using simple, flat C2h-symmetric molecules to direct the assembly of chiral 2D nanopatterns.

    Science.gov (United States)

    Zhou, Hui; Wuest, James D

    2013-06-18

    Linear D2h-symmetric bisisophthalic acids 1 and 2 and related substances have well-defined flattened structures, high affinities for graphite, and strong abilities to engage in specific intermolecular interactions. Their adsorption produces characteristic nanopatterns that reveal how 2D molecular organization can be controlled by reliable interadsorbate interactions such as hydrogen bonds when properly oriented by molecular geometry. In addition, the behavior of these compounds shows how large-scale organization can be obstructed by programming molecules to associate strongly according to competing motifs that have similar stability and can coexist smoothly without creating significant defects. Analogous new bisisophthalic acids 3a and 4a have similar associative properties, and their unique C2h-symmetric crankshaft geometry gives them the added ability to probe the poorly understood effect of chirality on molecular organization. Their adsorption shows how nanopatterns composed predictably of a single enantiomer can be obtained by depositing molecules that can respect established rules of association only by accepting neighbors of the same configuration. In addition, an analysis of the adsorption of crankshaft compounds 3a and 4a and their derivatives by STM reveals directly on the molecular level how kinetics and thermodynamics compete to control the crystallization of chiral compounds. In such ways, detailed studies of the adsorption of properly designed compounds on surfaces are proving to be a powerful way to discover and test rules that broadly govern molecular organization in both 2D and 3D.

  16. Entangling capabilities of symmetric two-qubit gates

    Indian Academy of Sciences (India)

    Com- putational investigation of entanglement of such ensembles is therefore impractical for ... the computational complexity. Pairs of spin-1 ... tensor operators which can also provide different symmetric logic gates for quantum pro- ... that five of the eight, two-qubit symmetric quantum gates expressed in terms of our newly.

  17. Pion condensation in symmetric nuclear matter

    Science.gov (United States)

    Kabir, K.; Saha, S.; Nath, L. M.

    1988-01-01

    Using a model which is based essentially on the chiral SU(2)×SU(2) symmetry of the pion-nucleon interaction, we examine the possibility of pion condensation in symmetric nucleon matter. We find that the pion condensation is not likely to occur in symmetric nuclear matter for any finite value of the nuclear density. Consequently, no critical opalescence phenomenom is expected to be seen in the pion-nucleus interaction.

  18. A cascaded three-phase symmetrical multistage voltage multiplier

    International Nuclear Information System (INIS)

    Iqbal, Shahid; Singh, G K; Besar, R; Muhammad, G

    2006-01-01

    A cascaded three-phase symmetrical multistage Cockcroft-Walton voltage multiplier (CW-VM) is proposed in this report. It consists of three single-phase symmetrical voltage multipliers, which are connected in series at their smoothing columns like string of batteries and are driven by three-phase ac power source. The smoothing column of each voltage multiplier is charged twice every cycle independently by respective oscillating columns and discharged in series through load. The charging discharging process completes six times a cycle and therefore the output voltage ripple's frequency is of sixth order of the drive signal frequency. Thus the proposed approach eliminates the first five harmonic components of load generated voltage ripples and sixth harmonic is the major ripple component. The proposed cascaded three-phase symmetrical voltage multiplier has less than half the voltage ripple, and three times larger output voltage and output power than the conventional single-phase symmetrical CW-VM. Experimental and simulation results of the laboratory prototype are given to show the feasibility of proposed cascaded three-phase symmetrical CW-VM

  19. Transport synthetic acceleration for long-characteristics assembly-level transport problems

    Energy Technology Data Exchange (ETDEWEB)

    Zika, M R; Adams, M L

    2000-02-01

    The authors apply the transport synthetic acceleration (TSA) scheme to the long-characteristics spatial discretization for the two-dimensional assembly-level transport problem. This synthetic method employs a simplified transport operator as its low-order approximation. Thus, in the acceleration step, the authors take advantage of features of the long-characteristics discretization that make it particularly well suited to assembly-level transport problems. The main contribution is to address difficulties unique to the long-characteristics discretization and produce a computationally efficient acceleration scheme. The combination of the long-characteristics discretization, opposing reflecting boundary conditions (which are present in assembly-level transport problems), and TSA presents several challenges. The authors devise methods for overcoming each of them in a computationally efficient way. Since the boundary angular data exist on different grids in the high- and low-order problems, they define restriction and prolongation operations specific to the method of long characteristics to map between the two grids. They implement the conjugate gradient (CG) method in the presence of opposing reflection boundary conditions to solve the TSA low-order equations. The CG iteration may be applied only to symmetric positive definite (SPD) matrices; they prove that the long-characteristics discretization yields an SPD matrix. They present results of the acceleration scheme on a simple test problem, a typical pressurized water reactor assembly, and a typical boiling water reactor assembly.

  20. Transport synthetic acceleration for long-characteristics assembly-level transport problems

    International Nuclear Information System (INIS)

    Zika, M.R.; Adams, M.L.

    2000-01-01

    The authors apply the transport synthetic acceleration (TSA) scheme to the long-characteristics spatial discretization for the two-dimensional assembly-level transport problem. This synthetic method employs a simplified transport operator as its low-order approximation. Thus, in the acceleration step, the authors take advantage of features of the long-characteristics discretization that make it particularly well suited to assembly-level transport problems. The main contribution is to address difficulties unique to the long-characteristics discretization and produce a computationally efficient acceleration scheme. The combination of the long-characteristics discretization, opposing reflecting boundary conditions (which are present in assembly-level transport problems), and TSA presents several challenges. The authors devise methods for overcoming each of them in a computationally efficient way. Since the boundary angular data exist on different grids in the high- and low-order problems, they define restriction and prolongation operations specific to the method of long characteristics to map between the two grids. They implement the conjugate gradient (CG) method in the presence of opposing reflection boundary conditions to solve the TSA low-order equations. The CG iteration may be applied only to symmetric positive definite (SPD) matrices; they prove that the long-characteristics discretization yields an SPD matrix. They present results of the acceleration scheme on a simple test problem, a typical pressurized water reactor assembly, and a typical boiling water reactor assembly

  1. Transport Synthetic Acceleration for Long-Characteristics Assembly-Level Transport Problems

    International Nuclear Information System (INIS)

    Zika, Michael R.; Adams, Marvin L.

    2000-01-01

    We apply the transport synthetic acceleration (TSA) scheme to the long-characteristics spatial discretization for the two-dimensional assembly-level transport problem. This synthetic method employs a simplified transport operator as its low-order approximation. Thus, in the acceleration step, we take advantage of features of the long-characteristics discretization that make it particularly well suited to assembly-level transport problems. Our main contribution is to address difficulties unique to the long-characteristics discretization and produce a computationally efficient acceleration scheme.The combination of the long-characteristics discretization, opposing reflecting boundary conditions (which are present in assembly-level transport problems), and TSA presents several challenges. We devise methods for overcoming each of them in a computationally efficient way. Since the boundary angular data exist on different grids in the high- and low-order problems, we define restriction and prolongation operations specific to the method of long characteristics to map between the two grids. We implement the conjugate gradient (CG) method in the presence of opposing reflection boundary conditions to solve the TSA low-order equations. The CG iteration may be applied only to symmetric positive definite (SPD) matrices; we prove that the long-characteristics discretization yields an SPD matrix. We present results of our acceleration scheme on a simple test problem, a typical pressurized water reactor assembly, and a typical boiling water reactor assembly

  2. Centrioles in Symmetric Spaces

    OpenAIRE

    Quast, Peter

    2011-01-01

    We describe all centrioles in irreducible simply connected pointed symmetric spaces of compact type in terms of the root system of the ambient space, and we study some geometric properties of centrioles.

  3. THz time domain spectroscopy of biomolecular conformational modes

    International Nuclear Information System (INIS)

    Markelz, Andrea; Whitmire, Scott; Hillebrecht, Jay; Birge, Robert

    2002-01-01

    We discuss the use of terahertz time domain spectroscopy for studies of conformational flexibility and conformational change in biomolecules. Protein structural dynamics are vital to biological function with protein flexibility affecting enzymatic reaction rates and sensory transduction cycling times. Conformational mode dynamics occur on the picosecond timescale and with the collective vibrational modes associated with these large scale structural motions in the 1-100 cm -1 range. We have performed THz time domain spectroscopy (TTDS) of several biomolecular systems to explore the sensitivity of TTDS to distinguish different molecular species, different mutations within a single species and different conformations of a given biomolecule. We compare the measured absorbances to normal mode calculations and find that the TTDS absorbance reflects the density of normal modes determined by molecular mechanics calculations, and is sensitive to both conformation and mutation. These early studies demonstrate some of the advantages and limitations of using TTDS for the study of biomolecules

  4. Pion condensation in symmetric nuclear matter

    International Nuclear Information System (INIS)

    Kabir, K.; Saha, S.; Nath, L.M.

    1987-09-01

    Using a model which is based essentially on the chiral SU(2)xSU(2) symmetry of the pion-nucleon interaction, we examine the possibility of pion condensation in symmetric nucleon matter. We find that the pion condensation is not likely to occur in symmetric nuclear matter for any finite value of the nuclear density. Consequently, no critical opalescence phenomenon is expected to be seen in the pion-nucleus interaction. (author). 20 refs

  5. Topologically protected bound states in photonic parity-time-symmetric crystals.

    Science.gov (United States)

    Weimann, S; Kremer, M; Plotnik, Y; Lumer, Y; Nolte, S; Makris, K G; Segev, M; Rechtsman, M C; Szameit, A

    2017-04-01

    Parity-time (PT)-symmetric crystals are a class of non-Hermitian systems that allow, for example, the existence of modes with real propagation constants, for self-orthogonality of propagating modes, and for uni-directional invisibility at defects. Photonic PT-symmetric systems that also support topological states could be useful for shaping and routing light waves. However, it is currently debated whether topological interface states can exist at all in PT-symmetric systems. Here, we show theoretically and demonstrate experimentally the existence of such states: states that are localized at the interface between two topologically distinct PT-symmetric photonic lattices. We find analytical closed form solutions of topological PT-symmetric interface states, and observe them through fluorescence microscopy in a passive PT-symmetric dimerized photonic lattice. Our results are relevant towards approaches to localize light on the interface between non-Hermitian crystals.

  6. Synthesis & Characterization of New bis-Symmetrical Adipoyl ...

    African Journals Online (AJOL)

    Full Title: Synthesis and Characterization of New bis-Symmetrical Adipoyl, Terepthaloyl, Chiral Diimido-di-L-alanine Diesters and Chiral Phthaloyl-L-alanine Ester of Tripropoxy p-tert-Butyl Calix[4]arene and Study of Their Hosting Ability for Alanine and Na+. Bis-symmetrical tripropoxy p-tert-butyl calix[4]arene esters were ...

  7. Looking for symmetric Bell inequalities

    Energy Technology Data Exchange (ETDEWEB)

    Bancal, Jean-Daniel; Gisin, Nicolas [Group of Applied Physics, University of Geneva, 20 rue de l' Ecole-de Medecine, CH-1211 Geneva 4 (Switzerland); Pironio, Stefano, E-mail: jean-daniel.bancal@unige.c [Laboratoire d' Information Quantique, Universite Libre de Bruxelles (Belgium)

    2010-09-24

    Finding all Bell inequalities for a given number of parties, measurement settings and measurement outcomes is in general a computationally hard task. We show that all Bell inequalities which are symmetric under the exchange of parties can be found by examining a symmetrized polytope which is simpler than the full Bell polytope. As an illustration of our method, we generate 238 885 new Bell inequalities and 1085 new Svetlichny inequalities. We find, in particular, facet inequalities for Bell experiments involving two parties and two measurement settings that are not of the Collins-Gisin-Linden-Massar-Popescu type.

  8. Looking for symmetric Bell inequalities

    International Nuclear Information System (INIS)

    Bancal, Jean-Daniel; Gisin, Nicolas; Pironio, Stefano

    2010-01-01

    Finding all Bell inequalities for a given number of parties, measurement settings and measurement outcomes is in general a computationally hard task. We show that all Bell inequalities which are symmetric under the exchange of parties can be found by examining a symmetrized polytope which is simpler than the full Bell polytope. As an illustration of our method, we generate 238 885 new Bell inequalities and 1085 new Svetlichny inequalities. We find, in particular, facet inequalities for Bell experiments involving two parties and two measurement settings that are not of the Collins-Gisin-Linden-Massar-Popescu type.

  9. Diagrams for symmetric product orbifolds

    International Nuclear Information System (INIS)

    Pakman, Ari; Rastelli, Leonardo; Razamat, Shlomo S.

    2009-01-01

    We develop a diagrammatic language for symmetric product orbifolds of two-dimensional conformal field theories. Correlation functions of twist operators are written as sums of diagrams: each diagram corresponds to a branched covering map from a surface where the fields are single-valued to the base sphere where twist operators are inserted. This diagrammatic language facilitates the study of the large N limit and makes more transparent the analogy between symmetric product orbifolds and free non-abelian gauge theories. We give a general algorithm to calculate the leading large N contribution to four-point correlators of twist fields.

  10. Symmetric normalisation for intuitionistic logic

    DEFF Research Database (Denmark)

    Guenot, Nicolas; Straßburger, Lutz

    2014-01-01

    We present two proof systems for implication-only intuitionistic logic in the calculus of structures. The first is a direct adaptation of the standard sequent calculus to the deep inference setting, and we describe a procedure for cut elimination, similar to the one from the sequent calculus......, but using a non-local rewriting. The second system is the symmetric completion of the first, as normally given in deep inference for logics with a DeMorgan duality: all inference rules have duals, as cut is dual to the identity axiom. We prove a generalisation of cut elimination, that we call symmetric...

  11. The Axially Symmetric One-Monopole

    International Nuclear Information System (INIS)

    Wong, K.-M.; Teh, Rosy

    2009-01-01

    We present new classical generalized one-monopole solution of the SU(2) Yang-Mills-Higgs theory with the Higgs field in the adjoint representation. We show that this solution with θ-winding number m = 1 and φ-winding number n = 1 is an axially symmetric generalization of the 't Hooft-Polyakov one-monopole. We construct this axially symmetric one-monopole solution by generalizing the large distance asymptotic solutions of the 't Hooft-Polyakov one-monopole to the Jacobi elliptic functions and solving the second order equations of motion numerically when the Higgs potential is vanishing. This solution is a non-BPS solution.

  12. Commutative curvature operators over four-dimensional generalized symmetric

    Directory of Open Access Journals (Sweden)

    Ali Haji-Badali

    2014-12-01

    Full Text Available Commutative properties of four-dimensional generalized symmetric pseudo-Riemannian manifolds were considered. Specially, in this paper, we studied Skew-Tsankov and Jacobi-Tsankov conditions in 4-dimensional pseudo-Riemannian generalized symmetric manifolds.

  13. A biomolecular recognition approach for the functionalization of cellulose with gold nanoparticles.

    Science.gov (United States)

    Almeida, A; Rosa, A M M; Azevedo, A M; Prazeres, D M F

    2017-09-01

    Materials with new and improved functionalities can be obtained by modifying cellulose with gold nanoparticles (AuNPs) via the in situ reduction of a gold precursor or the deposition or covalent immobilization of pre-synthesized AuNPs. Here, we present an alternative biomolecular recognition approach to functionalize cellulose with biotin-AuNPs that relies on a complex of 2 recognition elements: a ZZ-CBM3 fusion that combines a carbohydrate-binding module (CBM) with the ZZ fragment of the staphylococcal protein A and an anti-biotin antibody. Paper and cellulose microparticles with AuNPs immobilized via the ZZ-CBM3:anti-biotin IgG supramolecular complex displayed an intense red color, whereas essentially no color was detected when AuNPs were deposited over the unmodified materials. Scanning electron microscopy analysis revealed a homogeneous distribution of AuNPs when immobilized via ZZ-CBM3:anti-biotin IgG complexes and aggregation of AuNPs when deposited over paper, suggesting that color differences are due to interparticle plasmon coupling effects. The approach could be used to functionalize paper substrates and cellulose nanocrystals with AuNPs. More important, however, is the fact that the occurrence of a biomolecular recognition event between the CBM-immobilized antibody and its specific, AuNP-conjugated antigen is signaled by red color. This opens up the way for the development of simple and straightforward paper/cellulose-based tests where detection of a target analyte can be made by direct use of color signaling. Copyright © 2017 John Wiley & Sons, Ltd.

  14. Radial power distribution shaping within a PWR fuel assembly utilizing asymmetrically loaded gadolinia-bearing fuel pins

    International Nuclear Information System (INIS)

    Stone, I.Z.

    1992-01-01

    As in-core fuel management designs evolve to meet the demands of increasing energy output, more innovative methods are developed to maintain power peaking within acceptable thermal margin limits. In-core fuel management staff must utilize various loading pattern strategies such as cross-core movement of fuel assemblies, multibatch enrichment schemes, and burnable absorbers as the primary means of controlling the radial power distribution. The utilization of fresh asymmetrically loaded gadolinia-bearing assemblies as a fuel management tool provides an additional means of controlling the radial power distribution. At Siemens Nuclear Power Corporation (SNP), fresh fuel assemblies fabricated with asymmetrically loaded gadolinia-bearing fuel rods have been used successfully for several cycles of reactor operation. Asymmetric assemblies are neutronically modeled using the same tools and models that SNP uses to model symmetrically loaded gadolinia-bearing fuel assemblies. The CASMO-2E code is used to produce the homogenized macroscopic assembly cross sections for the nodal core simulator. Optimum fuel pin locations within the asymmetrical assembly are determined using the pin-by-pin PDQ7 assembly core model for each new assembly design. The optimum pin location is determined by the rod loading that minimizes the peak-to-average pin power

  15. Crossing-symmetric solutions to low equations

    International Nuclear Information System (INIS)

    McLeod, R.J.; Ernst, D.J.

    1985-01-01

    Crossing symmetric models of the pion-nucleon interaction in which crossing symmetry is kept to lowest order in msub(π)/msub(N) are investigated. Two iterative techniques are developed to solve the crossing-symmetric Low equation. The techniques are used to solve the original Chew-Low equations and their generalizations to include the coupling to the pion-production channels. Small changes are found in comparison with earlier results which used an iterative technique proposed by Chew and Low and which did not produce crossing-symmetric results. The iterative technique of Chew and Low is shown to fail because of its inability to produce zeroes in the amplitude at complex energies while physical solutions to the model require such zeroes. We also prove that, within the class of solutions such that phase shifts approach zero for infinite energy, the solution to the Low equation is unique. (orig.)

  16. Radon transformation on reductive symmetric spaces:Support theorems

    DEFF Research Database (Denmark)

    Kuit, Job Jacob

    2013-01-01

    We introduce a class of Radon transforms for reductive symmetric spaces, including the horospherical transforms, and derive support theorems for these transforms. A reductive symmetric space is a homogeneous space G/H for a reductive Lie group G of the Harish-Chandra class, where H is an open sub...... is based on the relation between the Radon transform and the Fourier transform on G/H, and a Paley–Wiener-shift type argument. Our results generalize the support theorem of Helgason for the Radon transform on a Riemannian symmetric space....

  17. Optimal number of coarse-grained sites in different components of large biomolecular complexes.

    Science.gov (United States)

    Sinitskiy, Anton V; Saunders, Marissa G; Voth, Gregory A

    2012-07-26

    The computational study of large biomolecular complexes (molecular machines, cytoskeletal filaments, etc.) is a formidable challenge facing computational biophysics and biology. To achieve biologically relevant length and time scales, coarse-grained (CG) models of such complexes usually must be built and employed. One of the important early stages in this approach is to determine an optimal number of CG sites in different constituents of a complex. This work presents a systematic approach to this problem. First, a universal scaling law is derived and numerically corroborated for the intensity of the intrasite (intradomain) thermal fluctuations as a function of the number of CG sites. Second, this result is used for derivation of the criterion for the optimal number of CG sites in different parts of a large multibiomolecule complex. In the zeroth-order approximation, this approach validates the empirical rule of taking one CG site per fixed number of atoms or residues in each biomolecule, previously widely used for smaller systems (e.g., individual biomolecules). The first-order corrections to this rule are derived and numerically checked by the case studies of the Escherichia coli ribosome and Arp2/3 actin filament junction. In different ribosomal proteins, the optimal number of amino acids per CG site is shown to differ by a factor of 3.5, and an even wider spread may exist in other large biomolecular complexes. Therefore, the method proposed in this paper is valuable for the optimal construction of CG models of such complexes.

  18. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis

    Science.gov (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith

    2013-01-01

    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  19. Applications of atomic force microscopy to the studies of biomaterials in biomolecular systems

    Science.gov (United States)

    Ma, Xiang

    Atomic force microscopy (AFM) is a unique tool for the studies of nanoscale structures and interactions. In this dissertation, I applied AFM to study transitions among multiple states of biomaterials in three different microscopic biomolecular systems: MukB-dependent DNA condensation, holdfast adhesion, and virus elasticity. To elucidate the mechanism of MukB-dependent DNA condensation, I have studied the conformational changes of MukB proteins as indicators for the strength of interactions between MukB, DNA and other molecular factors, such as magnesium and ParC proteins, using high-resolution AFM imaging. To determine the physical origins of holdfast adhesion, I have investigated the dynamics of adhesive force development of the holdfast, employing AFM force spectroscopy. By measuring rupture forces between the holdfast and the substrate, I showed that the holdfast adhesion is strongly time-dependent and involves transformations at multiple time scales. Understanding the mechanisms of adhesion force development of the holdfast will be critical for future engineering of holdfasts properties for various applications. Finally, I have examined the elasticity of self-assembled hepatitis B virus-like particles (HBV VLPs) and brome mosaic virus (BMV) in response to changes of pH and salinity, using AFM nanoindentation. The distributions of elasticity were mapped on a single particle level and compared between empty, RNA- and gold-filled HBV VLPs. I found that a single HBV VLP showed heterogeneous distribution of elasticity and a two-step buckling transition, suggesting a discrete property of HBV capsids. For BMV, I have showed that viruses containing different RNA molecules can be distinguished by mechanical measurements, while they are indistinguishable by morphology. I also studied the effect of pH on the elastic behaviors of three-particle BMV and R3/4 BMV. This study can yield insights into RNA presentation/release mechanisms, and could help us to design novel drug

  20. Young—Capelli symmetrizers in superalgebras†

    Science.gov (United States)

    Brini, Andrea; Teolis, Antonio G. B.

    1989-01-01

    Let Supern[U [unk] V] be the nth homogeneous subspace of the supersymmetric algebra of U [unk] V, where U and V are Z2-graded vector spaces over a field K of characteristic zero. The actions of the general linear Lie superalgebras pl(U) and pl(V) span two finite-dimensional K-subalgebras B and [unk] of EndK(Supern[U [unk] V]) that are the centralizers of each other. Young—Capelli symmetrizers and Young—Capelli *-symmetrizers give rise to K-linear bases of B and [unk] containing orthogonal systems of idempotents; thus they yield complete decompositions of B and [unk] into minimal left and right ideals, respectively. PMID:16594014

  1. Symmetric splitting of very light systems

    International Nuclear Information System (INIS)

    Grotowski, K.; Majka, Z.; Planeta, R.

    1984-01-01

    Inclusive and coincidence measurements have been performed to study symmetric products from the reactions 74--186 MeV 12 C+ 40 Ca, 141 MeV 9 Be+ 40 Ca, and 153 MeV 6 Li+ 40 Ca. The binary decay of the composite system has been verified. Energy spectra, angular distributions, and fragment correlations are presented. The total kinetic energies for the symmetric products from these very light composite systems are compared to liquid drop model calculations and fission systematics

  2. 2-d and 1-d Nanomaterials Construction through Peptide Computational Design and Solution Assembly

    Science.gov (United States)

    Pochan, Darrin

    Self-assembly of molecules is an attractive materials construction strategy due to its simplicity in application. By considering peptidic molecules in the bottom-up materials self-assembly design process, one can take advantage of inherently biomolecular attributes; intramolecular folding events, secondary structure, and electrostatic/H-bonding/hydrophobic interactions to define hierarchical material structure and consequent properties. Importantly, while biomimicry has been a successful strategy for the design of new peptide molecules for intermolecular assembly, computational tools have been developed to de novo design peptide molecules required for construction of pre-determined, desired nanostructures and materials. A new system comprised of coiled coil bundle motifs theoretically designed to assemble into designed, one and two-dimensional nanostructures will be introduced. The strategy provides the opportunity for arbitrary nanostructure formation, i.e. structures not observed in nature, with peptide molecules. Importantly, the desired nanostructure was chosen first while the peptides needed for coiled coil formation and subsequent nanomaterial formation were determined computationally. Different interbundle, two-dimensional nanostructures are stabilized by differences in amino acid composition exposed on the exterior of the coiled coil bundles. Computation was able to determine molecules required for different interbundle symmetries within two-dimensional sheets stabilized by subtle differences in amino acid composition of the inherent peptides. Finally, polymers were also created through covalent interactions between bundles that allowed formation of architectures spanning flexible network forming chains to ultra-stiff polymers, all with the same building block peptides. The success of the computational design strategy is manifested in the nanomaterial results as characterized by electron microscopy, scattering methods, and biophysical techniques. Support

  3. Radon transformation on reductive symmetric spaces: support theorems

    NARCIS (Netherlands)

    Kuit, J.J.|info:eu-repo/dai/nl/313872589

    2011-01-01

    In this thesis we introduce a class of Radon transforms for reductive symmetric spaces, including the horospherical transforms, and study some of their properties. In particular we obtain a generalization of Helgason's support theorem for the horospherical transform on a Riemannian symmetric space.

  4. Decomposition of a symmetric second-order tensor

    Science.gov (United States)

    Heras, José A.

    2018-05-01

    In the three-dimensional space there are different definitions for the dot and cross products of a vector with a second-order tensor. In this paper we show how these products can uniquely be defined for the case of symmetric tensors. We then decompose a symmetric second-order tensor into its ‘dot’ part, which involves the dot product, and the ‘cross’ part, which involves the cross product. For some physical applications, this decomposition can be interpreted as one in which the dot part identifies with the ‘parallel’ part of the tensor and the cross part identifies with the ‘perpendicular’ part. This decomposition of a symmetric second-order tensor may be suitable for undergraduate courses of vector calculus, mechanics and electrodynamics.

  5. Revisiting the Optical PT-Symmetric Dimer

    Directory of Open Access Journals (Sweden)

    José Delfino Huerta Morales

    2016-08-01

    Full Text Available Optics has proved a fertile ground for the experimental simulation of quantum mechanics. Most recently, optical realizations of PT -symmetric quantum mechanics have been shown, both theoretically and experimentally, opening the door to international efforts aiming at the design of practical optical devices exploiting this symmetry. Here, we focus on the optical PT -symmetric dimer, a two-waveguide coupler where the materials show symmetric effective gain and loss, and provide a review of the linear and nonlinear optical realizations from a symmetry-based point of view. We go beyond a simple review of the literature and show that the dimer is just the smallest of a class of planar N-waveguide couplers that are the optical realization of the Lorentz group in 2 + 1 dimensions. Furthermore, we provide a formulation to describe light propagation through waveguide couplers described by non-Hermitian mode coupling matrices based on a non-Hermitian generalization of the Ehrenfest theorem.

  6. Parity-Time Symmetric Photonics

    KAUST Repository

    Zhao, Han

    2018-01-17

    The establishment of non-Hermitian quantum mechanics (such as parity-time (PT) symmetry) stimulates a paradigmatic shift for studying symmetries of complex potentials. Owing to the convenient manipulation of optical gain and loss in analogy to the complex quantum potentials, photonics provides an ideal platform for visualization of many conceptually striking predictions from the non-Hermitian quantum theory. A rapidly developing field has emerged, namely, PT symmetric photonics, demonstrating intriguing optical phenomena including eigenstate coalescence and spontaneous PT symmetry breaking. The advance of quantum physics, as the feedback, provides photonics with brand-new paradigms to explore the entire complex permittivity plane for novel optical functionalities. Here, we review recent exciting breakthroughs in PT symmetric photonics while systematically presenting their underlying principles guided by non-Hermitian symmetries. The potential device applications for optical communication and computing, bio-chemical sensing, and healthcare are also discussed.

  7. Parity Violation in Chiral Molecules: From Theory towards Spectroscopic Experiment and the Evolution of Biomolecular Homochirality

    CERN Multimedia

    CERN. Geneva

    2016-01-01

    The observation of biomolecular homochirality can be considered as a quasi-fossil of the evolution of life [1], the interpretation of which has been an open question for more than a century, with numerous related hypotheses, but no definitive answers. We shall briefly discuss the current status and the relation to the other two questions. The discovery of parity violation led to important developm...

  8. Crossing symmetric solution of the Chew-Low equation

    International Nuclear Information System (INIS)

    McLeod, R.J.; Ernst, D.J.

    1982-01-01

    An N/D dispersion theory is developed which solves crossing symmetric Low equations. The method is used to generate crossing symmetric solutions to the Chew-Low model. We show why the technique originally proposed by Chew and Low was incapable of producing solutions. (orig.)

  9. Emitter and absorber assembly for multiple self-dual operation and directional transparency

    Science.gov (United States)

    Kalozoumis, P. A.; Morfonios, C. V.; Kodaxis, G.; Diakonos, F. K.; Schmelcher, P.

    2017-03-01

    We demonstrate how to systematically design wave scattering systems with simultaneous coherent perfect absorbing and lasing operation at multiple and prescribed frequencies. The approach is based on the recursive assembly of non-Hermitian emitter and absorber units into self-dual emitter-absorber trimers at different composition levels, exploiting the simple structure of the corresponding transfer matrices. In particular, lifting the restriction to parity-time-symmetric setups enables the realization of emitter and absorber action at distinct frequencies and provides flexibility with respect to the choice of realistic parameters. We further show how the same assembled scatterers can be rearranged to produce unidirectional and bidirectional transparency at the selected frequencies. With the design procedure being generically applicable to wave scattering in single-channel settings, we demonstrate it with concrete examples of photonic multilayer setups.

  10. Symmetric webs, Jones-Wenzl recursions and q-Howe duality

    DEFF Research Database (Denmark)

    Rose, David; Tubbenhauer, Daniel

    We define and study the category of symmetric sl2-webs. This category is a combinatorial description of the category of all finite dimensional quantum sl2-modules. Explicitly, we show that (the additive closure of) the symmetric sl2-spider is (braided monoidally) equivalent to the latter. Our mai...... tool is a quantum version of symmetric Howe duality. As a corollary of our construction, we provide new insight into Jones-Wenzl projectors and the colored Jones polynomials....

  11. SUSY formalism for the symmetric double well potential

    Indian Academy of Sciences (India)

    symmetric double well potential barrier we have obtained a class of exactly solvable potentials subject to moving boundary condition. The eigenstates are also obtained by the same technique. Keywords. SUSY; moving boundary condition; exactly solvable; symmetric double well; NH3 molecule. PACS Nos 02.30.Ik; 03.50.

  12. Coupled dilaton and electromagnetic field in cylindrically symmetric ...

    Indian Academy of Sciences (India)

    The dilaton black hole solutions have attracted considerable attention for the ... theory and study the corresponding cylindrically symmetric spacetime, where .... where Йm and Йe are integration constants to be interpreted later as the ..... feature is apparent for the cylindrically symmetric spacetime in the presence of the dila-.

  13. First assembly phase for the ATLAS toroid coils

    CERN Document Server

    Patrice Loïez

    2003-01-01

    The ATLAS barrel toroid system consists of eight coils, each of axial length 25.3 m, assembled radially and symmetrically around the beam axis. The coils are of a flat racetrack type with two double-pancake windings made of 20.5 kA aluminium-stabilized niobium-titanium superconductor. In the first phase of assembly, the two 'pancakes' are packed into their vacuum vessel. This is done using bladders filled with resin and glass microbeads under pressure. The resin is heated and, once cooled, holds the pancakes in place. The operation has to be performed on both sides of the coil, which necessitated a special technique to turn the coils over and then transport them to the heating table. Photos 01, 02, 03: Use of the overhead travelling crane to hoist the coil up and then tilt it over, the coil frame's metal feet being used as rotational pivots, supporting half the coil's weight. Once it has been turned over, the coil, now with only half the frame, is transported to the heating table using a special lifting gant...

  14. Fibre optic sensor on robot end effector for flexible assembly

    International Nuclear Information System (INIS)

    Yung, K.L.; Lau, W.S.; Choi, C.K.; Shan, Y.Y.

    1995-01-01

    A fibre optic sensor system was constructed for use on robot end effectors for flexible assembly. The sensor detected the deviations between robot end effector and the workpiece. The signal was fed back to robot controller to shift the end effector until the centre of end effector and the centre of workpiece were aligned at the correct orientation. Then workpiece can be grasped symmetrically. Sensor fusion concept was used to guard against sensor system failure. Fuzzy linguistic variable and control rule concept were introduced in the sensor integration. The experimental setup for the sensor integrated system was shown. The accuracy was also discussed

  15. Rectified tunneling current response of bio-functionalized metal-bridge-metal junctions.

    Science.gov (United States)

    Liu, Yaqing; Offenhäusser, Andreas; Mayer, Dirk

    2010-01-15

    Biomolecular bridged nanostructures allow direct electrical addressing of electroactive biomolecules, which is of interest for the development of bioelectronic and biosensing hybrid junctions. In the present paper, the electroactive biomolecule microperoxidase-11 (MP-11) was integrated into metal-bridge-metal (MBM) junctions assembled from a scanning tunneling microscope (STM) setup. Before immobilization of MP-11, the Au working electrode was first modified by a self-assembled monolayer of 1-undecanethiol (UDT). A symmetric and potential independent response of current-bias voltage (I(t)/V(b)) was observed for the Au (substrate)/UDT/Au (tip) junction. However, the I(t)/V(b) characteristics became potential dependent and asymmetrical after binding of MP-11 between the electrodes of the junction. The rectification ratio of the asymmetric current response varies with gate electrode modulation. A resonant tunneling process between metal electrode and MP-11 enhances the tunneling current and is responsible for the observed rectification. Our investigations demonstrated that functional building blocks of proteins can be reassembled into new conceptual devices with operation modes deviating from their native function, which could prove highly useful in the design of future biosensors and bioelectronic devices. Copyright 2009 Elsevier B.V. All rights reserved.

  16. Highly-dispersive electromagnetic induced transparency in planar symmetric metamaterials.

    Science.gov (United States)

    Lu, Xiqun; Shi, Jinhui; Liu, Ran; Guan, Chunying

    2012-07-30

    We propose, design and experimentally demonstrate highly-dispersive electromagnetically induced transparency (EIT) in planar symmetric metamaterials actively switched and controlled by angles of incidence. Full-wave simulation and measurement results show EIT phenomena, trapped-mode excitations and the associated local field enhancement of two symmetric metamaterials consisting of symmetrically split rings (SSR) and a fishscale (FS) metamaterial pattern, respectively, strongly depend on angles of incidence. The FS metamaterial shows much broader spectral splitting than the SSR metamaterial due to the surface current distribution variation.

  17. Dose controlled low energy electron irradiator for biomolecular films.

    Science.gov (United States)

    Kumar, S V K; Tare, Satej T; Upalekar, Yogesh V; Tsering, Thupten

    2016-03-01

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at -20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  18. DNA-assisted swarm control in a biomolecular motor system.

    Science.gov (United States)

    Keya, Jakia Jannat; Suzuki, Ryuhei; Kabir, Arif Md Rashedul; Inoue, Daisuke; Asanuma, Hiroyuki; Sada, Kazuki; Hess, Henry; Kuzuya, Akinori; Kakugo, Akira

    2018-01-31

    In nature, swarming behavior has evolved repeatedly among motile organisms because it confers a variety of beneficial emergent properties. These include improved information gathering, protection from predators, and resource utilization. Some organisms, e.g., locusts, switch between solitary and swarm behavior in response to external stimuli. Aspects of swarming behavior have been demonstrated for motile supramolecular systems composed of biomolecular motors and cytoskeletal filaments, where cross-linkers induce large scale organization. The capabilities of such supramolecular systems may be further extended if the swarming behavior can be programmed and controlled. Here, we demonstrate that the swarming of DNA-functionalized microtubules (MTs) propelled by surface-adhered kinesin motors can be programmed and reversibly regulated by DNA signals. Emergent swarm behavior, such as translational and circular motion, can be selected by tuning the MT stiffness. Photoresponsive DNA containing azobenzene groups enables switching between solitary and swarm behavior in response to stimulation with visible or ultraviolet light.

  19. A fast mollified impulse method for biomolecular atomistic simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fath, L., E-mail: lukas.fath@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Hochbruck, M., E-mail: marlis.hochbruck@kit.edu [Institute for App. and Num. Mathematics, Karlsruhe Institute of Technology (Germany); Singh, C.V., E-mail: chandraveer.singh@utoronto.ca [Department of Materials Science & Engineering, University of Toronto (Canada)

    2017-03-15

    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice–ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  20. Dose controlled low energy electron irradiator for biomolecular films

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, S. V. K., E-mail: svkk@tifr.res.in; Tare, Satej T.; Upalekar, Yogesh V.; Tsering, Thupten [Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400 005 (India)

    2016-03-15

    We have developed a multi target, Low Energy Electron (LEE), precise dose controlled irradiator for biomolecular films. Up to seven samples can be irradiated one after another at any preset electron energy and dose under UHV conditions without venting the chamber. In addition, one more sample goes through all the steps except irradiation, which can be used as control for comparison with the irradiated samples. All the samples are protected against stray electron irradiation by biasing them at −20 V during the entire period, except during irradiation. Ethernet based communication electronics hardware, LEE beam control electronics and computer interface were developed in house. The user Graphical User Interface to control the irradiation and dose measurement was developed using National Instruments Lab Windows CVI. The working and reliability of the dose controlled irradiator has been fully tested over the electron energy range of 0.5 to 500 eV by studying LEE induced single strand breaks to ΦX174 RF1 dsDNA.

  1. Parallel coupling of symmetric and asymmetric exclusion processes

    International Nuclear Information System (INIS)

    Tsekouras, K; Kolomeisky, A B

    2008-01-01

    A system consisting of two parallel coupled channels where particles in one of them follow the rules of totally asymmetric exclusion processes (TASEP) and in another one move as in symmetric simple exclusion processes (SSEP) is investigated theoretically. Particles interact with each other via hard-core exclusion potential, and in the asymmetric channel they can only hop in one direction, while on the symmetric lattice particles jump in both directions with equal probabilities. Inter-channel transitions are also allowed at every site of both lattices. Stationary state properties of the system are solved exactly in the limit of strong couplings between the channels. It is shown that strong symmetric couplings between totally asymmetric and symmetric channels lead to an effective partially asymmetric simple exclusion process (PASEP) and properties of both channels become almost identical. However, strong asymmetric couplings between symmetric and asymmetric channels yield an effective TASEP with nonzero particle flux in the asymmetric channel and zero flux on the symmetric lattice. For intermediate strength of couplings between the lattices a vertical-cluster mean-field method is developed. This approximate approach treats exactly particle dynamics during the vertical transitions between the channels and it neglects the correlations along the channels. Our calculations show that in all cases there are three stationary phases defined by particle dynamics at entrances, at exits or in the bulk of the system, while phase boundaries depend on the strength and symmetry of couplings between the channels. Extensive Monte Carlo computer simulations strongly support our theoretical predictions. Theoretical calculations and computer simulations predict that inter-channel couplings have a strong effect on stationary properties. It is also argued that our results might be relevant for understanding multi-particle dynamics of motor proteins

  2. Confining but chirally symmetric dense and cold matter

    International Nuclear Information System (INIS)

    Glozman, L. Ya.

    2012-01-01

    The possibility for existence of cold, dense chirally symmetric matter with confinement is reviewed. The answer to this question crucially depends on the mechanism of mass generation in QCD and interconnection of confinement and chiral symmetry breaking. This question can be clarified from spectroscopy of hadrons and their axial properties. Almost systematical parity doubling of highly excited hadrons suggests that their mass is not related to chiral symmetry breaking in the vacuum and is approximately chirally symmetric. Then there is a possibility for existence of confining but chirally symmetric matter. We clarify a possible mechanism underlying such a phase at low temperatures and large density. Namely, at large density the Pauli blocking prevents the gap equation to generate a solution with broken chiral symmetry. However, the chirally symmetric part of the quark Green function as well as all color non-singlet quantities are still infrared divergent, meaning that the system is with confinement. A possible phase transition to such a matter is most probably of the first order. This is because there are no chiral partners to the lowest lying hadrons.

  3. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    International Nuclear Information System (INIS)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database

  4. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.

    1994-12-01

    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  5. Solitons in PT-symmetric potential with competing nonlinearity

    International Nuclear Information System (INIS)

    Khare, Avinash; Al-Marzoug, S.M.; Bahlouli, Hocine

    2012-01-01

    We investigate the effect of competing nonlinearities on beam dynamics in PT-symmetric potentials. In particular, we consider the stationary nonlinear Schrödinger equation (NLSE) in one dimension with competing cubic and generalized nonlinearity in the presence of a PT-symmetric potential. Closed form solutions for localized states are obtained. These solitons are shown to be stable over a wide range of potential parameters. The transverse power flow associated with these complex solitons is also examined. -- Highlights: ► Effect of competing nonlinearities on beam dynamics in PT-symmetric potentials. ► Closed form solutions for localized states are. ► The transverse power flow associated with these complex solitons is also examined.

  6. Color symmetrical superconductivity in a schematic nuclear quark model

    DEFF Research Database (Denmark)

    Bohr, Henrik; Providencia, C.; da Providencia, J.

    2010-01-01

    In this letter, a novel BCS-type formalism is constructed in the framework of a schematic QCD inspired quark model, having in mind the description of color symmetrical superconducting states. In the usual approach to color superconductivity, the pairing correlations affect only the quasi-particle...... states of two colors, the single-particle states of the third color remaining unaffected by the pairing correlations. In the theory of color symmetrical superconductivity here proposed, the pairing correlations affect symmetrically the quasi-particle states of the three colors and vanishing net color...

  7. Geometric characteristics of aberrations of plane-symmetric optical systems

    International Nuclear Information System (INIS)

    Lu Lijun; Deng Zhiyong

    2009-01-01

    The geometric characteristics of aberrations of plane-symmetric optical systems are studied in detail with a wave-aberration theory. It is dealt with as an extension of the Seidel aberrations to realize a consistent aberration theory from axially symmetric to plane-symmetric systems. The aberration distribution is analyzed with the spot diagram of a ray and an aberration curve. Moreover, the root-mean-square value and the centroid of aberration distribution are discussed. The numerical results are obtained with the focusing optics of a toroidal mirror at grazing incidence.

  8. The use of gold nanoparticle aggregation for DNA computing and logic-based biomolecular detection

    International Nuclear Information System (INIS)

    Lee, In-Hee; Yang, Kyung-Ae; Zhang, Byoung-Tak; Lee, Ji-Hoon; Park, Ji-Yoon; Chai, Young Gyu; Lee, Jae-Hoon

    2008-01-01

    The use of DNA molecules as a physical computational material has attracted much interest, especially in the area of DNA computing. DNAs are also useful for logical control and analysis of biological systems if efficient visualization methods are available. Here we present a quick and simple visualization technique that displays the results of the DNA computing process based on a colorimetric change induced by gold nanoparticle aggregation, and we apply it to the logic-based detection of biomolecules. Our results demonstrate its effectiveness in both DNA-based logical computation and logic-based biomolecular detection

  9. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan

    2015-01-01

    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA),enzyme-linkedimmunosorbentassay(EIA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...

  10. Sparse symmetric preconditioners for dense linear systems in electromagnetism

    NARCIS (Netherlands)

    Carpentieri, Bruno; Duff, Iain S.; Giraud, Luc; Monga Made, M. Magolu

    2004-01-01

    We consider symmetric preconditioning strategies for the iterative solution of dense complex symmetric non-Hermitian systems arising in computational electromagnetics. In particular, we report on the numerical behaviour of the classical incomplete Cholesky factorization as well as some of its recent

  11. Synthesis of self-assembly plasmonic silver nanoparticles with tunable luminescence color

    International Nuclear Information System (INIS)

    Al-Ghamdi, Haifa S.; Mahmoud, Waleed E.

    2014-01-01

    Assembly is an elegant and effective bottom-up approach to prepare arrays of nanoparticles from nobel metals. Noble metal nanoparticles are perfect building blocks because they can be prepared with an adequate functionalization to allow their assembly and with controlled sizes. Herein, we report a novel recipe for the synthesis of self-assembled silver nanoparticles with tunable optical properties and sizes. The synthetic route followed here based on the covalent binding among silver nanoparticles by means of poly vinyl alcohol for the first time. The size of silver nanoparticle is governed by varying the amount of sodium borohydride. The as-synthesized nanoparticles were characterized by transmission electron microscopy, x-ray diffraction, energy dispersive x-ray spectroscopy, selected area electron diffraction and UV–vis spectroscopy. Results depicted that self-assembly of mono-dispersed silver nanoparticles with different sizes have been achieved. The silver nanostructure has a single crystalline faced centered cubic structure with growth orientation along (1 1 1) facet. These nanoparticles exhibited localized surface plasmon resonance at 403 nm. The luminescence peaks were red-sifted from violet to green due to the increase of the particle sizes. -- Highlights: • Self-assembled silver nanoparticles based PVA were synthesized. • NaBH 4 amount was found particle size dependent. • Silver nanoparticles strongly affected the surface plasmon resonance. • Highly symmetric luminescence emission band narrow width is obtained. • Dark field image showed a tunable color change from violet to green

  12. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics [version 1; referees: 3 approved

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-01-01

    Full Text Available Experimentally derived structural constraints have been crucial to the implementation of computational models of biomolecular dynamics. For example, not only does crystallography provide essential starting points for molecular simulations but also high-resolution structures permit for parameterization of simplified models. Since the energy landscapes for proteins and other biomolecules have been shown to be minimally frustrated and therefore funneled, these structure-based models have played a major role in understanding the mechanisms governing folding and many functions of these systems. Structural information, however, may be limited in many interesting cases. Recently, the statistical analysis of residue co-evolution in families of protein sequences has provided a complementary method of discovering residue-residue contact interactions involved in functional configurations. These functional configurations are often transient and difficult to capture experimentally. Thus, co-evolutionary information can be merged with that available for experimentally characterized low free-energy structures, in order to more fully capture the true underlying biomolecular energy landscape.

  13. Final report for Assembling Microorganisms into Energy Converting Materials

    Energy Technology Data Exchange (ETDEWEB)

    Sahin, Ozgur

    2018-03-26

    The goal of this project was to integrate microorganisms capable of reversible energy transduction in response to changing relative humidity with non-biological materials to create hybrid energy conversion systems. While plants and many other biological organisms have developed structures that are extraordinarily effective in converting changes in relative humidity into mechanical energy, engineered energy transduction systems rarely take advantage of this powerful phenomenon. Rather than developing synthetic materials that can convert changes in relative humidity in to mechanical energy, we developed approaches to assemble bacterial spores into larger materials. These materials can convert energy from evaporation of water in dry atmospheric conditions, which we demonstrated by building energy harvesters from these materials. We have also developed experiments to investigate the interaction of water with the spore material, and to determine how this interaction imposes limits on energy conversion. In addition, we carried out theoretical calculations to investigate the limits imposed by the environmental conditions to the power available in the energy harvesting process. These calculations took into account heat and water vapor transfer in the atmosphere surrounding the spore based materials. Overall, our results suggest that biomolecular materials are promising candidates to convert energy from evaporation.

  14. Tilting-connected symmetric algebras

    OpenAIRE

    Aihara, Takuma

    2010-01-01

    The notion of silting mutation was introduced by Iyama and the author. In this paper we mainly study silting mutation for self-injective algebras and prove that any representation-finite symmetric algebra is tilting-connected. Moreover we give some sufficient conditions for a Bongartz-type Lemma to hold for silting objects.

  15. Distributed Searchable Symmetric Encryption

    NARCIS (Netherlands)

    Bösch, C.T.; Peter, Andreas; Leenders, Bram; Lim, Hoon Wei; Tang, Qiang; Wang, Huaxiong; Hartel, Pieter H.; Jonker, Willem

    Searchable Symmetric Encryption (SSE) allows a client to store encrypted data on a storage provider in such a way, that the client is able to search and retrieve the data selectively without the storage provider learning the contents of the data or the words being searched for. Practical SSE schemes

  16. Rings with involution whose symmetric elements are central

    Directory of Open Access Journals (Sweden)

    Taw Pin Lim

    1980-01-01

    Full Text Available In a ring R with involution whose symmetric elements S are central, the skew-symmetric elements K form a Lie algebra over the commutative ring S. The classification of such rings which are 2-torsion free is equivalent to the classification of Lie algebras K over S equipped with a bilinear form f that is symmetric, invariant and satisfies [[x,y],z]=f(y,zx−f(z,xy. If S is a field of char ≠2, f≠0 and dimK>1 then K is a semisimple Lie algebra if and only if f is nondegenerate. Moreover, the derived algebra K′ is either the pure quaternions over S or a direct sum of mutually orthogonal abelian Lie ideals of dim≤2.

  17. Optomechanically induced absorption in parity-time-symmetric optomechanical systems

    Science.gov (United States)

    Zhang, X. Y.; Guo, Y. Q.; Pei, P.; Yi, X. X.

    2017-06-01

    We explore the optomechanically induced absorption (OMIA) in a parity-time- (PT -) symmetric optomechanical system (OMS). By numerically calculating the Lyapunov exponents, we find out the stability border of the PT -symmetric OMS. The results show that in the PT -symmetric phase the system can be either stable or unstable depending on the coupling constant and the decay rate. In the PT -symmetric broken phase the system can have a stable state only for small gain rates. By calculating the transmission rate of the probe field, we find that there is an inverted optomechanically induced transparency (OMIT) at δ =-ωM and an OMIA at δ =ωM for the PT -symmetric optomechanical system. At each side of δ =-ωM there is an absorption window due to the resonance absorption of the two generated supermodes. Comparing with the case of optomechanics coupled to a passive cavity, we find that the active cavity can enhance the resonance absorption. The absorption rate at δ =ωM increases as the coupling strength between the two cavities increases. Our work provides us with a promising platform for controlling light propagation and light manipulation in terms of PT symmetry, which might have potential applications in quantum information processing and quantum optical devices.

  18. All-optical symmetric ternary logic gate

    Science.gov (United States)

    Chattopadhyay, Tanay

    2010-09-01

    Symmetric ternary number (radix=3) has three logical states (1¯, 0, 1). It is very much useful in carry free arithmetical operation. Beside this, the logical operation using this type of number system is also effective in high speed computation and communication in multi-valued logic. In this literature all-optical circuits for three basic symmetrical ternary logical operations (inversion, MIN and MAX) are proposed and described. Numerical simulation verifies the theoretical model. In this present scheme the different ternary logical states are represented by different polarized state of light. Terahertz optical asymmetric demultiplexer (TOAD) based interferometric switch has been used categorically in this manuscript.

  19. Symmetric spaces and the Kashiwara-Vergne method

    CERN Document Server

    Rouvière, François

    2014-01-01

    Gathering and updating results scattered in journal articles over thirty years, this self-contained monograph gives a comprehensive introduction to the subject. Its goal is to: - motivate and explain the method for general Lie groups, reducing the proof of deep results in invariant analysis to the verification of two formal Lie bracket identities related to the Campbell-Hausdorff formula (the "Kashiwara-Vergne conjecture"); - give a detailed proof of the conjecture for quadratic and solvable Lie algebras, which is relatively elementary; - extend the method to symmetric spaces; here an obstruction appears, embodied in a single remarkable object called an "e-function"; - explain the role of this function in invariant analysis on symmetric spaces, its relation to invariant differential operators, mean value operators and spherical functions; - give an explicit e-function for rank one spaces (the hyperbolic spaces); - construct an e-function for general symmetric spaces, in the spirit of Kashiwara and Vergne's or...

  20. Helically symmetric experiment, (HSX) goals, design and status

    International Nuclear Information System (INIS)

    Anderson, F.S.B.; Almagri, A.F.; Anderson, D.T.; Matthews, P.G.; Talmadge, J.N.; Shohet, J.L.

    1995-01-01

    HSX is a quasi-helically symmetric (QHS) stellarator currently under construction at the Torsatron-Stellarator Laboratory of the University of Wisconsin-Madison. This device is unique in its magnetic design in that the magnetic field spectrum possesses only a single dominant (helical) component. This design avoids the large direct orbit losses and the low-collisionality neoclassical losses associated with conventional stellarators. The restoration of symmetry to the confining magnetic field makes the neoclassical confinement in this device analogous to an axisymmetric q=1/3 tokamak. The HSX device has been designed with a clear set of primary physics goals: demonstrate the feasibility of construction of a QHS device, examine single particle confinement of injected ions with regard to magnetic field symmetry breaking, compare density and temperature profiles in this helically symmetric system to those for axisymmetric tokamaks and conventional stellarators, examine electric fields and plasma rotation with edge biasing in relation to L-H transitions in symmetric versus non-symmetric stellarator systems, investigate QHS effects on 1/v regime electron confinement, and examine how greatly-reduced neoclassical electron thermal conductivity compares to the experimental χ e profile. 3 refs., 4 figs., 1 tab

  1. Ancillary ligand-assisted assembly of C{sub 3}-symmetric 4,4′,4″-nitrilotribenzoic acid with divalent Zn{sup 2+} ions: Syntheses, topological structures, and photoluminescence properties

    Energy Technology Data Exchange (ETDEWEB)

    Cui, Li-Ting; Niu, Yan-Fei [Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062 (China); Han, Jie, E-mail: chan@ouhk.edu.hk [School of Science & Technology, The Open University of Hong Kong, Kowloon, Hong Kong SAR (China); Zhao, Xiao-Li, E-mail: xlzhao@chem.ecnu.edu.cn [Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, East China Normal University, 3663 North Zhongshan Road, Shanghai 200062 (China)

    2015-07-15

    4,4′,4″-nitrilotribenzoic acid (H{sub 3}L), a C{sub 3}-symmetric ligand, was found to self-assemble into two polymorphs driven by intermolecular hydrogen-bonding interactions. Reactions of this ligand with Zn{sup 2+} under solvothermal conditions resulted in four new coordination polymers bearing interesting structural motifs: [Zn{sub 2}(L){sub 2}(py){sub 2}]·2(H{sub 2}NMe{sub 2}){sup +}·DMF·2H{sub 2}O (1), [Zn{sub 2}(L)(H{sub 2}L)(bipy)]·1.5H{sub 2}O·Guest (2), [Zn{sub 2}(L){sub 2}(bipy)]·2(H{sub 2}NMe{sub 2}){sup +}·2DMF (3), and [Zn{sub 3}(L){sub 2}(bpa)]·2H{sub 2}O·Guest (4) (H{sub 3}L=4,4′,4′′-nitrilotribenzoic acid, DMF=dimethylformamide, py=pyridine, bipy=4,4′-bipyridine, bpa=1,2-bis(4-pyridyl)diazene). Single-crystal structural analysis revealed that compound 1 exhibits a rare example of twofold interpenetrating anionic 3D (3,3)-net framework containing helical channels, whereas in 2, the 3D pillar-layer structure generated from bipy-pillared Zn{sub 2}(L)(H{sub 2}L) layer is further reinforced by intermolecular hydrogen bonding among pairs of free –COOH units. Compound 3 shows an interesting entangled architecture of 2D→3D parallel polycatenation consisting five-coordinated Zn{sup 2+} ions. Compound 4 displays a 3D pillar-layer framework with trimeric Zn{sub 3}(CO{sub 2}){sub 6} serving as secondary building unit (SBU). The syntheses, structures, thermal stabilities, powder X-ray diffractions and solid-state photoluminescence properties for these crystalline materials have been carried out. In addition, supramolecular assembly of H{sub 3}L under solvothermal conditions will also be addressed. - Graphical abstract: Supramolecular assembly of 4,4′,4′′-nitrilotribenzoic acid and its ligand behavior toward Zn{sup 2+} were investigated, which exhibit two polymorphs of the free acid and four metal coordination polymers bearing interesting structural motifs. - Highlights: • Two polymorphs of H{sub 3}L showing different hydrogen

  2. Symmetric coupling of four spin-1/2 systems

    Science.gov (United States)

    Suzuki, Jun; Englert, Berthold-Georg

    2012-06-01

    We address the non-binary coupling of identical angular momenta based upon the representation theory for the symmetric group. A correspondence is pointed out between the complete set of commuting operators and the reference-frame-free subsystems. We provide a detailed analysis of the coupling of three and four spin-1/2 systems and discuss a symmetric coupling of four spin-1/2 systems.

  3. Biomolecular ions in superfluid helium nanodroplets

    Energy Technology Data Exchange (ETDEWEB)

    Gonzalez Florez, Ana Isabel

    2016-07-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  4. Biomolecular ions in superfluid helium nanodroplets

    International Nuclear Information System (INIS)

    Gonzalez Florez, Ana Isabel

    2016-01-01

    The function of a biological molecule is closely related to its structure. As a result, understanding and predicting biomolecular structure has become the focus of an extensive field of research. However, the investigation of molecular structure can be hampered by two main difficulties: the inherent complications that may arise from studying biological molecules in their native environment, and the potential congestion of the experimental results as a consequence of the large number of degrees of freedom present in these molecules. In this work, a new experimental setup has been developed and established in order to overcome the afore mentioned limitations combining structure-sensitive gas-phase methods with superfluid helium droplets. First, biological molecules are ionised and brought into the gas phase, often referred to as a clean-room environment, where the species of interest are isolated from their surroundings and, thus, intermolecular interactions are absent. The mass-to-charge selected biomolecules are then embedded inside clusters of superfluid helium with an equilibrium temperature of ∝0.37 K. As a result, the internal energy of the molecules is lowered, thereby reducing the number of populated quantum states. Finally, the local hydrogen bonding patterns of the molecules are investigated by probing specific vibrational modes using the Fritz Haber Institute's free electron laser as a source of infrared radiation. Although the structure of a wide variety of molecules has been studied making use of the sub-Kelvin environment provided by superfluid helium droplets, the suitability of this method for the investigation of biological molecular ions was still unclear. However, the experimental results presented in this thesis demonstrate the applicability of this experimental approach in order to study the structure of intact, large biomolecular ions and the first vibrational spectrum of the protonated pentapeptide leu-enkephalin embedded in helium

  5. New approach to solve symmetric fully fuzzy linear systems

    Indian Academy of Sciences (India)

    In this paper, we present a method to solve fully fuzzy linear systems with symmetric coefficient matrix. The symmetric coefficient matrix is decomposed into two systems of equations by using Cholesky method and then a solution can be obtained. Numerical examples are given to illustrate our method.

  6. PREFACE The physics of virus assembly The physics of virus assembly

    Science.gov (United States)

    Stockley, Peter G.; Twarock, Reidun

    2010-12-01

    Viruses are pathogens in every kingdom of life and are major causes of human disease and suffering. They are known to encompass a size range that overlaps with that of the smallest bacterial cells, and the largest viruses now seem to be hosts of their own viral pathogens. Recent genomic sequencing efforts show that many organisms have genes that are likely to be descended in evolution from viral progenitors. Even more astonishingly, analysis of the world's oceans has shown that some of the simplest viruses, the tailed dsDNA phages, are the most common biological entities on the planet, with estimates of their numbers ranging up to 1031, with ~ 1021 infection events every second, leading to a turnover of around 20% of the biomass in the sea every few days. These cycles of infection and lysis of oceanic bacteria and algae provide the nutrients for the smallest organisms lying at the bottom of the food chain. Without viruses, therefore, life on Earth would probably not be sustainable. These are remarkable facts for systems that are non-living in the strict sense, and are composed of simple materials—nucleic acids, proteins and lipids. Many viruses consist of little more than a protective protein coat surrounding their genomic nucleic acids, which can be either DNA or RNA. Their simplicity leads to highly symmetrical structures with protein containers based on helical or icosahedral lattices. Many simple viruses self-assemble rapidly and with great fidelity, and many groups are busy trying to exploit these properties to make virus-like particles for a wide range of applications, including targeted drug-delivery, medical imaging and even novel materials. This issue of Physical Biology contains a series of papers describing some of the latest experimental and theoretical research on viruses, their structures and assembly, as well as their regulated disassembly during infection. These range from a dissection of the in vivo assembly mechanism of a filamentous virus

  7. Kinetic-energy distribution for symmetric fission of 236U

    International Nuclear Information System (INIS)

    Brissot, R.; Bocquet, J.P.; Ristori, C.; Crancon, J.; Guet, C.R.; Nifenecker, H.A.; Montoya, M.

    1980-01-01

    Fission fragment kinetic-energy distributions have been measured at the Grenoble high-flux reactor with the Lohengrin facility. Spurious events were eliminated in the symmetric region by a coherence test based on a time-of-flight measurement of fragment velocities. A Monte-Carlo calculation is then performed to correct the experimental data for neutron evaporation. The difference between the most probable kinetic energy in symmetric fission and the fission in which the heavy fragment is 'magic' (Zsub(H)=50) is found to be approximately =30 MeV. The results suggest that for the symmetric case the total excitation energy available at scission is shared equally among the fragments. (author)

  8. A hydrogel-based versatile screening platform for specific biomolecular recognition in a well plate format.

    Science.gov (United States)

    Beer, Meike V; Rech, Claudia; Diederichs, Sylvia; Hahn, Kathrin; Bruellhoff, Kristina; Möller, Martin; Elling, Lothar; Groll, Jürgen

    2012-04-01

    Precise determination of biomolecular interactions in high throughput crucially depends on a surface coating technique that allows immobilization of a variety of interaction partners in a non-interacting environment. We present a one-step hydrogel coating system based on isocyanate functional six-arm poly(ethylene oxide)-based star polymers for commercially available 96-well microtiter plates that combines a straightforward and robust coating application with versatile bio-functionalization. This system generates resistance to unspecific protein adsorption and cell adhesion, as demonstrated with fluorescently labeled bovine serum albumin and primary human dermal fibroblasts (HDF), and high specificity for the assessment of biomolecular recognition processes when ligands are immobilized on this surface. One particular advantage is the wide range of biomolecules that can be immobilized and convert the per se inert coating into a specifically interacting surface. We here demonstrate the immobilization and quantification of a broad range of biochemically important ligands, such as peptide sequences GRGDS and GRGDSK-biotin, the broadly applicable coupler molecule biocytin, the protein fibronectin, and the carbohydrates N-acetylglucosamine and N-acetyllactosamine. A simplified protocol for an enzyme-linked immunosorbent assay was established for the detection and quantification of ligands on the coating surface. Cell adhesion on the peptide and protein-modified surfaces was assessed using HDF. All coatings were applied using a one-step preparation technique, including bioactivation, which makes the system suitable for high-throughput screening in a format that is compatible with the most routinely used testing systems.

  9. Symmetry theorems via the continuous steiner symmetrization

    Directory of Open Access Journals (Sweden)

    L. Ragoub

    2000-06-01

    Full Text Available Using a new approach due to F. Brock called the Steiner symmetrization, we show first that if $u$ is a solution of an overdetermined problem in the divergence form satisfying the Neumann and non-constant Dirichlet boundary conditions, then $Omega$ is an N-ball. In addition, we show that we can relax the condition on the value of the Dirichlet boundary condition in the case of superharmonicity. Finally, we give an application to positive solutions of some semilinear elliptic problems in symmetric domains for the divergence case.

  10. Molecular Design of Bioinspired Nanostructures for Biomedical Applications: Synthesis, Self-Assembly and Functional Properties

    Science.gov (United States)

    Xu, Hesheng Victor; Zheng, Xin Ting; Mok, Beverly Yin Leng; Ibrahim, Salwa Ali; Yu, Yong; Tan, Yen Nee

    2016-08-01

    Biomolecules are the nanoscale building blocks of cells, which play multifaceted roles in the critical biological processes such as biomineralization in a living organism. In these processes, the biological molecules such as protein and nucleic acids use their exclusive biorecognition properties enabled from their unique chemical composition, shape and function to initiate a cascade of cellular events. The exceptional features of these biomolecules, coupled with the recent advancement in nanotechnology, have led to the emergence of a new research field that focuses on the molecular design of bioinspired nanostructures that inherit the extraordinary function of natural biomaterials. These “bioinspired” nanostructures could be formulated by biomimetic approaches through either self-assembling of biomolecules or acting as a biomolecular template/precursor to direct the synthesis of nanocomposite. In either situation, the resulting nanomaterials exhibit phenomenal biocompatibility, superb aqueous solubility and excellent colloidal stability, branding them exceptionally desirable for both in vitro and in vivo biomedical applications. In this review, we will present the recent developments in the preparation of “bioinspired” nanostructures through biomimetic self-assembly and biotemplating synthesis, as well as highlight their functional properties and potential applications in biomedical diagnostics and therapeutic delivery. Lastly, we will conclude this topic with some personal perspective on the challenges and future outlooks of the “bioinspired” nanostructures for nanomedicine.

  11. Symmetric group representations and Z

    OpenAIRE

    Adve, Anshul; Yong, Alexander

    2017-01-01

    We discuss implications of the following statement about the representation theory of symmetric groups: every integer appears infinitely often as an irreducible character evaluation, and every nonnegative integer appears infinitely often as a Littlewood-Richardson coefficient and as a Kronecker coefficient.

  12. Quantum systems and symmetric spaces

    International Nuclear Information System (INIS)

    Olshanetsky, M.A.; Perelomov, A.M.

    1978-01-01

    Certain class of quantum systems with Hamiltonians related to invariant operators on symmetric spaces has been investigated. A number of physical facts have been derived as a consequence. In the classical limit completely integrable systems related to root systems are obtained

  13. Programming the Assembly of Unnatural Materials with Nucleic Acids

    Science.gov (United States)

    Mirkin, Chad

    Nature directs the assembly of enormously complex and highly functional materials through an encoded class of biomolecules, nucleic acids. The establishment of a similarly programmable code for the construction of synthetic, unnatural materials would allow researchers to impart functionality by precisely positioning all material components. Although it is exceedingly difficult to control the complex interactions between atomic and molecular species in such a manner, interactions between nanoscale components can be directed through the ligands attached to their surface. Our group has shown that nucleic acids can be used as highly programmable surface ligands to control the spacing and symmetry of nanoparticle building blocks in structurally sophisticated and functional materials. These nucleic acids function as programmable ``bonds'' between nanoparticle ``atoms,'' analogous to a nanoscale genetic code for assembling materials. The sequence and length tunability of nucleic acid bonds has allowed us to define a powerful set of design rules for the construction of nanoparticle superlattices with more than 30 unique lattice symmetries, tunable defect structures and interparticle spacings, and several well-defined crystal habits. Further, the nature of the nucleic acid bond enables an additional level of structural control: temporal regulation of dynamic material response to external biomolecular and chemical stimuli. This control allows for the reversible transformation between thermodynamic states with different crystal symmetries, particle stoichiometries, thermal stabilities, and interparticle spacings on demand. Notably, our unique genetic approach affords functional nanoparticle architectures that, among many other applications, can be used to systematically explore and manipulate optoelectronic material properties, such as tunable interparticle plasmonic interactions, microstructure-directed energy emission, and coupled plasmonic and photonic modes.

  14. Biosensing based on magnetically induced self-assembly of particles in magnetic colloids.

    Science.gov (United States)

    Yang, Ye; Morimoto, Yoshitaka; Takamura, Tsukasa; Sandhu, Adarsh

    2012-03-01

    Superparamagnetic beads and nonmagnetic beads of different sizes were assembled to form a "ring-structure" in a magnetorheological (MR) fluid solution by the application of external magnetic fields. For superparamagnetic beads and non-magnetic beads functionalized with probe and target molecules, respectively, the ring-structure was maintained even after removing the external magnetic field due to biomolecular bonding. Several experiments are described, including the formation process of ring-structures with and without molecular interactions, the accelerating effect of external magnetic fields, and the effect of biotin concentration on the structures of the rings. We define the small nonmagnetic particles as "petals" because the whole structure looks like a flower. The number of remnant ring petals was a function of the concentration of target molecules in the concentration range of 0.0768 ng/ml-3.8419 ng/ml which makes this protocol a promising method for biosensing. Not only was the formation process rapid, but the resulting two-dimensional colloidal system also offers a simple method for reducing reagent consumption and waste generation.

  15. Hypercyclic operators on algebra of symmetric snalytic functions on $\\ell_p$

    Directory of Open Access Journals (Sweden)

    Z. H. Mozhyrovska

    2016-06-01

    Full Text Available In the paper, it is proposed a method of construction of hypercyclic composition operators on $H(\\mathbb{C}^n$ using polynomial automorphisms of $\\mathbb{C}^n$ and symmetric analytic functions on $\\ell_p.$ In particular, we show that an ``symmetric translation'' operator is hypercyclic on a Frechet algebra of symmetric entire functions on $\\ell_p$ which are bounded on bounded subsets.

  16. A New Formulation for Symmetric Implicit Runge-Kutta-Nystrom ...

    African Journals Online (AJOL)

    In this paper we derive symmetric stable Implicit Runge-Kutta –Nystrom Method for the Integration of General Second Order ODEs by using the collocation approach.The block hybrid method obtained by the evaluation of the continuous interpolant at different nodes of the polynomial is symmetric and suitable for stiff intial ...

  17. Relativistic fluids in spherically symmetric space

    International Nuclear Information System (INIS)

    Dipankar, R.

    1977-12-01

    Some of McVittie and Wiltshire's (1977) solutions of Walker's (1935) isotropy conditions for relativistic perfect fluid spheres are generalized. Solutions are spherically symmetric and conformally flat

  18. The generalised Sylvester matrix equations over the generalised bisymmetric and skew-symmetric matrices

    Science.gov (United States)

    Dehghan, Mehdi; Hajarian, Masoud

    2012-08-01

    A matrix P is called a symmetric orthogonal if P = P T = P -1. A matrix X is said to be a generalised bisymmetric with respect to P if X = X T = PXP. It is obvious that any symmetric matrix is also a generalised bisymmetric matrix with respect to I (identity matrix). By extending the idea of the Jacobi and the Gauss-Seidel iterations, this article proposes two new iterative methods, respectively, for computing the generalised bisymmetric (containing symmetric solution as a special case) and skew-symmetric solutions of the generalised Sylvester matrix equation ? (including Sylvester and Lyapunov matrix equations as special cases) which is encountered in many systems and control applications. When the generalised Sylvester matrix equation has a unique generalised bisymmetric (skew-symmetric) solution, the first (second) iterative method converges to the generalised bisymmetric (skew-symmetric) solution of this matrix equation for any initial generalised bisymmetric (skew-symmetric) matrix. Finally, some numerical results are given to illustrate the effect of the theoretical results.

  19. Stability of transparent spherically symmetric thin shells and wormholes

    International Nuclear Information System (INIS)

    Ishak, Mustapha; Lake, Kayll

    2002-01-01

    The stability of transparent spherically symmetric thin shells (and wormholes) to linearized spherically symmetric perturbations about static equilibrium is examined. This work generalizes and systematizes previous studies and explores the consequences of including the cosmological constant. The approach shows how the existence (or not) of a domain wall dominates the landscape of possible equilibrium configurations

  20. Evolução biomolecular homoquiral: a origem e a amplificação da quiralidade nas moléculas da vida Homochiral biomolecular evolution: the origin and the amplification of chirality in life molecules

    Directory of Open Access Journals (Sweden)

    José Augusto R. Rodrigues

    2010-01-01

    Full Text Available The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symmetry breaking processes, which include autocatalytic crystallization, asymmetric autocatalysis, spontaneous crystallization, adsorption and polymerization of amino acids on mineral surfaces, provide new insights into the origin of biomolecular homochirality.

  1. Multiple symmetrical lipomatosis (Madelung's disease) - a case report

    International Nuclear Information System (INIS)

    Vieira, Marcelo Vasconcelos; Abreu, Marcelo de; Furtado, Claudia Dietz; Silveira, Marcio Fleck da; Furtado, Alvaro Porto Alegre; Genro, Carlos Horacio; Grazziotin, Rossano Ughini

    2001-01-01

    Multiple symmetrical lipomatosis (Madelung's disease) is a rare disorder characterized by deep accumulation of fat tissue, involving mainly the neck, shoulders and chest. This disease is associated with heavy alcohol intake and it is more common in men of Mediterranean origin. This disease can cause severe aesthetic deformities and progressive respiratory dysfunction. We report a case of a patient with multiple symmetrical lipomatosis and describe the clinical and radiological features of this disorder. (author)

  2. Duality, phase structures, and dilemmas in symmetric quantum games

    International Nuclear Information System (INIS)

    Ichikawa, Tsubasa; Tsutsui, Izumi

    2007-01-01

    Symmetric quantum games for 2-player, 2-qubit strategies are analyzed in detail by using a scheme in which all pure states in the 2-qubit Hilbert space are utilized for strategies. We consider two different types of symmetric games exemplified by the familiar games, the Battle of the Sexes (BoS) and the Prisoners' Dilemma (PD). These two types of symmetric games are shown to be related by a duality map, which ensures that they share common phase structures with respect to the equilibria of the strategies. We find eight distinct phase structures possible for the symmetric games, which are determined by the classical payoff matrices from which the quantum games are defined. We also discuss the possibility of resolving the dilemmas in the classical BoS, PD, and the Stag Hunt (SH) game based on the phase structures obtained in the quantum games. It is observed that quantization cannot resolve the dilemma fully for the BoS, while it generically can for the PD and SH if appropriate correlations for the strategies of the players are provided

  3. Biomolecular Structure Information from High-Speed Quantum Mechanical Electronic Spectra Calculation.

    Science.gov (United States)

    Seibert, Jakob; Bannwarth, Christoph; Grimme, Stefan

    2017-08-30

    A fully quantum mechanical (QM) treatment to calculate electronic absorption (UV-vis) and circular dichroism (CD) spectra of typical biomolecules with thousands of atoms is presented. With our highly efficient sTDA-xTB method, spectra averaged along structures from molecular dynamics (MD) simulations can be computed in a reasonable time frame on standard desktop computers. This way, nonequilibrium structure and conformational, as well as purely quantum mechanical effects like charge-transfer or exciton-coupling, are included. Different from other contemporary approaches, the entire system is treated quantum mechanically and neither fragmentation nor system-specific adjustment is necessary. Among the systems considered are a large DNA fragment, oligopeptides, and even entire proteins in an implicit solvent. We propose the method in tandem with experimental spectroscopy or X-ray studies for the elucidation of complex (bio)molecular structures including metallo-proteins like myoglobin.

  4. Bound states for non-symmetric evolution Schroedinger potentials

    Energy Technology Data Exchange (ETDEWEB)

    Corona, Gulmaro Corona [Area de Analisis Matematico y sus Aplicaciones, Universidad Autonoma Metropolitana-Azcapotalco, Atzcapotzalco, DF (Mexico)). E-mail: ccg@correo.azc.uam.mx

    2001-09-14

    We consider the spectral problem associated with the evolution Schroedinger equation, (D{sup 2}+ k{sup 2}){phi}=u{phi}, where u is a matrix-square-valued function, with entries in the Schwartz class defined on the real line. The solution {phi}, called the wavefunction, consists of a function of one real variable, matrix-square-valued with entries in the Schwartz class. This problem has been dealt for symmetric potentials u. We found for the present case that the bound states are localized similarly to the scalar and symmetric cases, but by the zeroes of an analytic matrix-valued function. If we add an extra condition to the potential u, we can determine these states by an analytic scalar function. We do this by generalizing the scalar and symmetric cases but without using the fact that the Wronskian of a pair of wavefunction is constant. (author)

  5. Theoretical restrictions on longest implicit time scales in Markov state models of biomolecular dynamics

    Science.gov (United States)

    Sinitskiy, Anton V.; Pande, Vijay S.

    2018-01-01

    Markov state models (MSMs) have been widely used to analyze computer simulations of various biomolecular systems. They can capture conformational transitions much slower than an average or maximal length of a single molecular dynamics (MD) trajectory from the set of trajectories used to build the MSM. A rule of thumb claiming that the slowest implicit time scale captured by an MSM should be comparable by the order of magnitude to the aggregate duration of all MD trajectories used to build this MSM has been known in the field. However, this rule has never been formally proved. In this work, we present analytical results for the slowest time scale in several types of MSMs, supporting the above rule. We conclude that the slowest implicit time scale equals the product of the aggregate sampling and four factors that quantify: (1) how much statistics on the conformational transitions corresponding to the longest implicit time scale is available, (2) how good the sampling of the destination Markov state is, (3) the gain in statistics from using a sliding window for counting transitions between Markov states, and (4) a bias in the estimate of the implicit time scale arising from finite sampling of the conformational transitions. We demonstrate that in many practically important cases all these four factors are on the order of unity, and we analyze possible scenarios that could lead to their significant deviation from unity. Overall, we provide for the first time analytical results on the slowest time scales captured by MSMs. These results can guide further practical applications of MSMs to biomolecular dynamics and allow for higher computational efficiency of simulations.

  6. Perovskite nanocrystals: across-dimensional attachment, film-scale assembly on a flexible substrate and their fluorescence properties

    Science.gov (United States)

    Huang, Wenyi; Liu, Jiajia; Bai, Bing; Huang, Liu; Xu, Meng; Liu, Jia; Rong, Hongpan; Zhang, Jiatao

    2018-03-01

    Perovskite nanocrystals (NCs), which are a good fluorescence candidate with excellent photoelectric properties, have opened new avenues in the fabrication of highly efficient solar cells, light-emitting diodes (LEDs), and other optoelectronic devices. Further advances will rely on the multitude of compositional, structural variants that enable the formation of lower-dimensionality layered and three-dimensional (3D) perovskites with architectural innovations. In this work, the perovskite film was fabricated on a flexible substrate using simple dip-coating technology and 3D assemblies of perovskite NCs were obtained through an attachment process. Original perovskite NCs had a rectangular or square morphology with high particle uniformity and the narrow and symmetric fluorescence emission peak was adjustable at 515-527 nm. The controllable self-assembly of the micron size cuboid-like 3D assembly had an apparent enhancement on peak (111) in the x-ray diffraction (XRD) pattern. Surface ligands not only play a role in the attachment process but also keep the independence of each NC in 3D assemblies. Such assembly of the perovskite film maintained the original perovskite NCs fluorescence emission peak and narrow full width at the half-maximum (FWHM), which is of great importance for the investigation of future devices.

  7. Symmetric Key Authentication Services Revisited

    NARCIS (Netherlands)

    Crispo, B.; Popescu, B.C.; Tanenbaum, A.S.

    2004-01-01

    Most of the symmetric key authentication schemes deployed today are based on principles introduced by Needham and Schroeder [15] more than twenty years ago. However, since then, the computing environment has evolved from a LAN-based client-server world to include new paradigms, including wide area

  8. Symmetric nuclear matter with Skyrme interaction

    International Nuclear Information System (INIS)

    Manisa, K.; Bicer, A.; Atav, U.

    2010-01-01

    The equation of state (EOS) and some properties of symmetric nuclear matter, such as the saturation density, saturation energy and incompressibility, are obtained by using Skyrme's density-dependent effective nucleon-nucleon interaction.

  9. On the pseudo-norm in some PT-symmetric potentials

    International Nuclear Information System (INIS)

    Levai, G.

    2005-01-01

    Complete text of publication follows. PT-symmetric quantum mechanical systems possess non-hermitian Hamiltonian, still they have some characteristics similar to hermitian problems. The most notable of these is their discrete energy spectrum, which can be partly or completely real. These systems are invariant under the simultaneous action of the P space and T time inversion operations. Perhaps the simplest PT-symmetric Hamiltonian contains a one-dimensional Schroedinger operator with a complex potential satisfying the V*(-x) = V (x) relation. Another typical feature PT-symmetric systems have in common with hermitian problems is that their basis states form an orthogonal set provided that the inner product is redefined as (ψ φ)PT ≡ (ψ Pφ). However, the norm defined by this inner product, the pseudo-norm turned out to possess indefinite sign, and this raised the question of the probabilistic interpretation of PT-symmetric systems. This problem was later put into a more general context when it was found that PT symmetry is a special case of pseudo-hermiticity, and this explains most of the peculiar features of PT-symmetric systems. There have been several attempts to link PT-symmetric, and in general, pseudo- hermitian systems with equivalent hermitian ones, and the sign of the pseudo-norm was found to play an important role in this respect. It is thus essential to evaluate the pseudo- norm for various potentials, especially considering the fact that there are some inconsistencies in the available results. Numerical studies indicated that the sign of the pseudo-norm typically alternates according to the n principal quantum number as (-1) n , and this was later proven for a class of potentials that are written in a polynomial form of ix. However, some potentials of other type did not fit into this line: this was the case for the Scarf II potential, the most well-known exactly solvable PT-symmetric potential. In contrast with the other examples, this potential is

  10. Is the Universe matter-antimatter symmetric

    International Nuclear Information System (INIS)

    Alfven, H.

    1976-09-01

    According to the symmetric cosmology there should be antimatter regions in space which are equally as large as the matter regions. The regions of different kind are separated by Leidenfrost layers, which may be very thin and not observable from a distance. This view has met resistance which in part is based on the old view that the dilute interstellar and intergalactic medium is more or less homogeneous. However, through space research in the magnetosphere and interplanetary space we know that thin layers, dividing space into regions of different magnetisation, exist and based on this it is concluded that space in general has a cellular structure. This result may break down the psychological resistance to the symmetric theory. The possibility that every second star in our galaxy consists of antimatter is discussed, and it is shown that this view is not in conflict with any observations. As most stars are likely to be surrounded by solar systems of a structure like our own, it is concluded that collisions between comets and antistars (or anticomets and stars) would be rather frequent. Such collisions would result in phenomena of the same type as the observed cosmic γ-ray bursts. Another support for the symmetric cosmology is the continuous X-ray background radiation. Also many of the observed large energy releases in cosmos are likely to be due to annihilation

  11. FACES WITH LARGE DIAMETER ON THE SYMMETRICAL TRAVELING SALESMAN POLYTOPE

    NARCIS (Netherlands)

    SIERKSMA, G; TIJSSEN, GA

    This paper deals with the symmetric traveling salesman polytope and contains three main theorems. The first one gives a new characterization of (non)adjacency. Based on this characterization a new upper bound for the diameter of the symmetric traveling salesman polytope (conjectured to be 2 by M.

  12. Symmetric relations of finite negativity

    NARCIS (Netherlands)

    Kaltenbaeck, M.; Winkler, H.; Woracek, H.; Forster, KH; Jonas, P; Langer, H

    2006-01-01

    We construct and investigate a space which is related to a symmetric linear relation S of finite negativity on an almost Pontryagin space. This space is the indefinite generalization of the completion of dom S with respect to (S.,.) for a strictly positive S on a Hilbert space.

  13. The symmetric longest queue system

    NARCIS (Netherlands)

    van Houtum, Geert-Jan; Adan, Ivo; van der Wal, Jan

    1997-01-01

    We derive the performance of the exponential symmetric longest queue system from two variants: a longest queue system with Threshold Rejection of jobs and one with Threshold Addition of jobs. It is shown that these two systems provide lower and upper bounds for the performance of the longest queue

  14. Silica biomineralization via the self-assembly of helical biomolecules.

    Science.gov (United States)

    Liu, Ben; Cao, Yuanyuan; Huang, Zhehao; Duan, Yingying; Che, Shunai

    2015-01-21

    The biomimetic synthesis of relevant silica materials using biological macromolecules as templates via silica biomineralization processes attract rapidly rising attention toward natural and artificial materials. Biomimetic synthesis studies are useful for improving the understanding of the formation mechanism of the hierarchical structures found in living organisms (such as diatoms and sponges) and for promoting significant developments in the biotechnology, nanotechnology and materials chemistry fields. Chirality is a ubiquitous phenomenon in nature and is an inherent feature of biomolecular components in organisms. Helical biomolecules, one of the most important types of chiral macromolecules, can self-assemble into multiple liquid-crystal structures and be used as biotemplates for silica biomineralization, which renders them particularly useful for fabricating complex silica materials under ambient conditions. Over the past two decades, many new silica materials with hierarchical structures and complex morphologies have been created using helical biomolecules. In this review, the developments in this field are described and the recent progress in silica biomineralization templating using several classes of helical biomolecules, including DNA, polypeptides, cellulose and rod-like viruses is summarized. Particular focus is placed on the formation mechanism of biomolecule-silica materials (BSMs) with hierarchical structures. Finally, current research challenges and future developments are discussed in the conclusion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Overlap-free symmetric D 0 Lwords

    Directory of Open Access Journals (Sweden)

    Anna Frid

    2001-12-01

    Full Text Available A D0L word on an alphabet Σ={0,1,…,q-1} is called symmetric if it is a fixed point w=φ(w of a morphism φ:Σ * → Σ * defined by φ(i= t 1 + i t 2 + i … t m + i for some word t 1 t 2 … t m (equal to φ(0 and every i ∈ Σ; here a means a mod q. We prove a result conjectured by J. Shallit: if all the symbols in φ(0 are distinct (i.e., if t i ≠ t j for i ≠ j, then the symmetric D0L word w is overlap-free, i.e., contains no factor of the form axaxa for any x ∈ Σ * and a ∈ Σ.

  16. Flat synchronizations in spherically symmetric space-times

    International Nuclear Information System (INIS)

    Herrero, Alicia; Morales-Lladosa, Juan Antonio

    2010-01-01

    It is well known that the Schwarzschild space-time admits a spacelike slicing by flat instants and that the metric is regular at the horizon in the associated adapted coordinates (Painleve-Gullstrand metric form). We consider this type of flat slicings in an arbitrary spherically symmetric space-time. The condition ensuring its existence is analyzed, and then, we prove that, for any spherically symmetric flat slicing, the densities of the Weinberg momenta vanish. Finally, we deduce the Schwarzschild solution in the extended Painleve-Gullstrand-LemaItre metric form by considering the coordinate decomposition of the vacuum Einstein equations with respect to a flat spacelike slicing.

  17. Introduction to left-right symmetric models

    International Nuclear Information System (INIS)

    Grimus, W.

    1993-01-01

    We motivate left-right symmetric models by the possibility of spontaneous parity breaking. Then we describe the multiplets and the Lagrangian of such models. Finally we discuss lower bounds on the right-handed scale. (author)

  18. Positive projections of symmetric matrices and Jordan algebras

    DEFF Research Database (Denmark)

    Fuglede, Bent; Jensen, Søren Tolver

    2013-01-01

    An elementary proof is given that the projection from the space of all symmetric p×p matrices onto a linear subspace is positive if and only if the subspace is a Jordan algebra. This solves a problem in a statistical model.......An elementary proof is given that the projection from the space of all symmetric p×p matrices onto a linear subspace is positive if and only if the subspace is a Jordan algebra. This solves a problem in a statistical model....

  19. Nilpotent orbits in real symmetric pairs and stationary black holes

    Energy Technology Data Exchange (ETDEWEB)

    Dietrich, Heiko [School of Mathematical Sciences, Monash University, VIC (Australia); De Graaf, Willem A. [Department of Mathematics, University of Trento, Povo (Italy); Ruggeri, Daniele [Universita di Torino, Dipartimento di Fisica (Italy); INFN, Sezione di Torino (Italy); Trigiante, Mario [DISAT, Politecnico di Torino (Italy)

    2017-02-15

    In the study of stationary solutions in extended supergravities with symmetric scalar manifolds, the nilpotent orbits of a real symmetric pair play an important role. In this paper we discuss two approaches to determine the nilpotent orbits of a real symmetric pair. We apply our methods to an explicit example, and thereby classify the nilpotent orbits of (SL{sub 2}(R)){sup 4} acting on the fourth tensor power of the natural 2-dimensional SL{sub 2}(R)-module. This makes it possible to classify all stationary solutions of the so-called STU-supergravity model. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  20. Nilpotent orbits in real symmetric pairs and stationary black holes

    International Nuclear Information System (INIS)

    Dietrich, Heiko; De Graaf, Willem A.; Ruggeri, Daniele; Trigiante, Mario

    2017-01-01

    In the study of stationary solutions in extended supergravities with symmetric scalar manifolds, the nilpotent orbits of a real symmetric pair play an important role. In this paper we discuss two approaches to determine the nilpotent orbits of a real symmetric pair. We apply our methods to an explicit example, and thereby classify the nilpotent orbits of (SL 2 (R)) 4 acting on the fourth tensor power of the natural 2-dimensional SL 2 (R)-module. This makes it possible to classify all stationary solutions of the so-called STU-supergravity model. (copyright 2017 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  1. Symmetrical parahiliar infiltrated, cough and dyspnoea

    International Nuclear Information System (INIS)

    Giraldo Estrada, Horacio; Escalante, Hector

    2004-01-01

    It is the case a patient to who is diagnosed symmetrical parahiliar infiltrated; initially she is diagnosed lymphoma Hodgkin, treaty with radiotherapy and chemotherapy, but the X rays of the thorax demonstrated parahiliars and paramediastinals infiltrated

  2. Self-Assembly of Narrowly Dispersed Brush Diblock Copolymers with Domain Spacing more than 100 nm

    Science.gov (United States)

    Gu, Weiyin; Sveinbjornsson, Benjamin; Hong, Sung Woo; Grubbs, Robert; Russell, Thomas

    2012-02-01

    Self-assembled structures of high molecular weight (MW), narrow molecular weight distribution brush block copolymers containing polylactic acid (PLA) and polystyrene (PS) side chains with similar MWs were studied in both the melt and thin films. The polynorbornene-backbone-based brush diblock copolymers containing approximately equal volume fractions of each block self-assembled into highly ordered lamellae with domain spacing over 100 nm, as revealed by SAXS, GISAXS and AFM. The domain size increased approximately linearly with backbone length, which indicated an extended conformation of the backbone in the ordered state. The length of side chains also played a significant role in terms of controlling the domain size. As the degree of polymerization (DP) increased, the symmetric brush diblock copolymers with longer side chains tended to form larger lamellar microdomains in comparison to those that have the same DP but shorter side chains.

  3. Stationary states of a PT symmetric two-mode Bose–Einstein condensate

    International Nuclear Information System (INIS)

    Graefe, Eva-Maria

    2012-01-01

    The understanding of nonlinear PT symmetric quantum systems, arising for example in the theory of Bose–Einstein condensates in PT symmetric potentials, is widely based on numerical investigations, and little is known about generic features induced by the interplay of PT symmetry and nonlinearity. To gain deeper insights it is important to have analytically solvable toy models at hand. In the present paper the stationary states of a simple toy model of a PT symmetric system previously introduced in [1, 2] are investigated. The model can be interpreted as a simple description of a Bose–Einstein condensate in a PT symmetric double well trap in a two-mode approximation. The eigenvalues and eigenstates of the system can be explicitly calculated in a straightforward manner; the resulting structures resemble those that have recently been found numerically for a more realistic PT symmetric double delta potential. In addition, a continuation of the system is introduced that allows an interpretation in terms of a simple linear matrix model. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Quantum physics with non-Hermitian operators’. (paper)

  4. Exploring plane-symmetric solutions in f(R) gravity

    Energy Technology Data Exchange (ETDEWEB)

    Shamir, M. F., E-mail: farasat.shamir@nu.edu.pk [National University of Computer and Emerging Sciences, Department of Sciences and Humanities (Pakistan)

    2016-02-15

    The modified theories of gravity, especially the f(R) gravity, have attracted much attention in the last decade. This paper is devoted to exploring plane-symmetric solutions in the context of metric f(R) gravity. We extend the work on static plane-symmetric vacuum solutions in f(R) gravity already available in the literature [1, 2]. The modified field equations are solved using the assumptions of both constant and nonconstant scalar curvature. Some well-known solutions are recovered with power-law and logarithmic forms of f(R) models.

  5. Integrability and symmetric spaces. II- The coset spaces

    International Nuclear Information System (INIS)

    Ferreira, L.A.

    1987-01-01

    It shown that a sufficient condition for a model describing the motion of a particle on a coset space to possess a fundamental Poisson bracket relation, and consequently charges involution, is that it must be a symmetric space. The conditions a hamiltonian, or any function of the canonical variables, has to satisfy in order to commute with these charges are studied. It is shown that, for the case of non compact symmetric space, these conditions lead to an algebraic structure which plays an important role in the construction of conserved quantities. (author) [pt

  6. Some curvature properties of quarter symmetric metric connections

    International Nuclear Information System (INIS)

    Rastogi, S.C.

    1986-08-01

    A linear connection Γ ji h with torsion tensor T j h P i -T i h P j , where T j h is an arbitrary (1,1) tensor field and P i is a 1-form, has been called a quarter-symmetric connection by Golab. Some properties of such connections have been studied by Rastogi, Mishra and Pandey, and Yano and Imai. In this paper based on the curvature tensor of quarter-symmetric metric connection we define a tensor analogous to conformal curvature tensor and study some properties of such a tensor. (author)

  7. Color-symmetric superconductivity in a phenomenological QCD model

    DEFF Research Database (Denmark)

    Bohr, Henrik; Providencia, C.; Providencia, J. da

    2009-01-01

    In this paper, we construct a theory of the NJL type where superconductivity is present, and yet the superconducting state remains, in the average, color symmetric. This shows that the present approach to color superconductivity is consistent with color singletness. Indeed, quarks are free...... in the deconfined phase, but the deconfined phase itself is believed to be a color singlet. The usual description of the color superconducting state violates color singletness. On the other hand, the color superconducting state here proposed is color symmetric in the sense that an arbitrary color rotation leads...

  8. Representations of the infinite symmetric group

    CERN Document Server

    Borodin, Alexei

    2016-01-01

    Representation theory of big groups is an important and quickly developing part of modern mathematics, giving rise to a variety of important applications in probability and mathematical physics. This book provides the first concise and self-contained introduction to the theory on the simplest yet very nontrivial example of the infinite symmetric group, focusing on its deep connections to probability, mathematical physics, and algebraic combinatorics. Following a discussion of the classical Thoma's theorem which describes the characters of the infinite symmetric group, the authors describe explicit constructions of an important class of representations, including both the irreducible and generalized ones. Complete with detailed proofs, as well as numerous examples and exercises which help to summarize recent developments in the field, this book will enable graduates to enhance their understanding of the topic, while also aiding lecturers and researchers in related areas.

  9. Symmetric vs. asymmetric stem cell divisions: an adaptation against cancer?

    Directory of Open Access Journals (Sweden)

    Leili Shahriyari

    Full Text Available Traditionally, it has been held that a central characteristic of stem cells is their ability to divide asymmetrically. Recent advances in inducible genetic labeling provided ample evidence that symmetric stem cell divisions play an important role in adult mammalian homeostasis. It is well understood that the two types of cell divisions differ in terms of the stem cells' flexibility to expand when needed. On the contrary, the implications of symmetric and asymmetric divisions for mutation accumulation are still poorly understood. In this paper we study a stochastic model of a renewing tissue, and address the optimization problem of tissue architecture in the context of mutant production. Specifically, we study the process of tumor suppressor gene inactivation which usually takes place as a consequence of two "hits", and which is one of the most common patterns in carcinogenesis. We compare and contrast symmetric and asymmetric (and mixed stem cell divisions, and focus on the rate at which double-hit mutants are generated. It turns out that symmetrically-dividing cells generate such mutants at a rate which is significantly lower than that of asymmetrically-dividing cells. This result holds whether single-hit (intermediate mutants are disadvantageous, neutral, or advantageous. It is also independent on whether the carcinogenic double-hit mutants are produced only among the stem cells or also among more specialized cells. We argue that symmetric stem cell divisions in mammals could be an adaptation which helps delay the onset of cancers. We further investigate the question of the optimal fraction of stem cells in the tissue, and quantify the contribution of non-stem cells in mutant production. Our work provides a hypothesis to explain the observation that in mammalian cells, symmetric patterns of stem cell division seem to be very common.

  10. Asymptotic properties of solvable PT-symmetric potentials

    International Nuclear Information System (INIS)

    Levai, G.

    2010-01-01

    Compete text of publication follows. The introduction of PT-symmetric quantum mechanics generated renewed interest in non-hermitian quantum mechanical systems in the past decade. PT symmetry means the invariance of a Hamiltonian under the simultaneous P space and T time reflection, the latter understood as complex conjugation. Considering the Schroedinger equation in one dimension, this corresponds to a potential with even real and odd imaginary components. This implies a delicate balance of emissive and absorptive regions that eventually manifests itself in properties that typically characterize real potentials, i.e. hermitian systems. These include partly or fully real energy spectrum and conserved (pseudo-)norm. A particularly notable feature of these systems is the spontaneous breakdown of PT symmetry, which typically occurs when the magnitude of the imaginary potential component exceeds a certain limit. At this point the real energy eigenvalues begin to merge pairwise and re-emerge as complex conjugate pairs. Another unusual property of PT-symmetric potentials is that they can, or sometimes have to be defined off the real x axis on trajectories that are symmetric with respect to the imaginary x axis. After more than a decade of theoretical investigations a remarkable recent development was the experimental verification of the existence of PT-symmetric systems in nature and the occurrence of spontaneous PT symmetry breaking in them. The experimental setup was a waveguide containing regions where loss and gain of flux occurred in a set out prescribed by PT symmetry. These experimental developments require the study of PT -symmetric potentials with various asymptotics, in which, furthermore, the complex potential component is finite in its range and/or its magnitude. Having in mind that PT symmetry allows for a wider variety of asymptotic properties than hermeticity, we studied three exactly solvable PT-symmetric potentials and compared their scattering and bound

  11. Entanglement of three-qubit Greenberger-Horne-Zeilinger-symmetric states.

    Science.gov (United States)

    Eltschka, Christopher; Siewert, Jens

    2012-01-13

    The first characterization of mixed-state entanglement was achieved for two-qubit states in Werner's seminal work [Phys. Rev. A 40, 4277 (1989)]. A physically important extension concerns mixtures of a pure entangled state [such as the Greenberger-Horne-Zeilinger (GHZ) state] and the unpolarized state. These mixed states serve as benchmark for the robustness of multipartite entanglement. They share the symmetries of the GHZ state. We call such states GHZ symmetric. Here we give a complete description of the entanglement in the family of three-qubit GHZ-symmetric states and, in particular, of the three-qubit generalized Werner states. Our method relies on the appropriate parametrization of the states and on the invariance of entanglement properties under general local operations. An application is the definition of a symmetrization witness for the entanglement class of arbitrary three-qubit states.

  12. Random matrix ensembles for PT-symmetric systems

    International Nuclear Information System (INIS)

    Graefe, Eva-Maria; Mudute-Ndumbe, Steve; Taylor, Matthew

    2015-01-01

    Recently much effort has been made towards the introduction of non-Hermitian random matrix models respecting PT-symmetry. Here we show that there is a one-to-one correspondence between complex PT-symmetric matrices and split-complex and split-quaternionic versions of Hermitian matrices. We introduce two new random matrix ensembles of (a) Gaussian split-complex Hermitian; and (b) Gaussian split-quaternionic Hermitian matrices, of arbitrary sizes. We conjecture that these ensembles represent universality classes for PT-symmetric matrices. For the case of 2 × 2 matrices we derive analytic expressions for the joint probability distributions of the eigenvalues, the one-level densities and the level spacings in the case of real eigenvalues. (fast track communication)

  13. Homochiral oligopeptides by chiral amplification within two-dimensional crystalline self-assemblies at the air-water interface; Relevance to biomolecular handedness

    DEFF Research Database (Denmark)

    Weissbuch, I.; Zepik, H.; Bolbach, G.

    2003-01-01

    -assembled into two-dimensional (2D) ordered crystallites at the air-aqueous solution interface. As model systems we studied NE-stearoyl-lysine thioethyl ester (C-18-TE-Lys), gamma-stearyl-glutamic thioethyl ester (C-18-TE-Glu), N-alpha-carboxyanhydride of gamma-stearyl-glutamic acid (C-18-Glu NCA) and gamma......-aqueous solution interface after injection of appropriate catalysts into the water subphase. The experimental relative abundance of oligopeptides with homochiral sequence generated from (R,S)-C-18-TE-Lys and (R,S)-C-18-TE-Glu, as determined by mass spectrometry on enantioselectively deuterium-labeled samples...

  14. Cancer genetics meets biomolecular mechanism-bridging an age-old gulf.

    Science.gov (United States)

    González-Sánchez, Juan Carlos; Raimondi, Francesco; Russell, Robert B

    2018-02-01

    Increasingly available genomic sequencing data are exploited to identify genes and variants contributing to diseases, particularly cancer. Traditionally, methods to find such variants have relied heavily on allele frequency and/or familial history, often neglecting to consider any mechanistic understanding of their functional consequences. Thus, while the set of known cancer-related genes has increased, for many, their mechanistic role in the disease is not completely understood. This issue highlights a wide gap between the disciplines of genetics, which largely aims to correlate genetic events with phenotype, and molecular biology, which ultimately aims at a mechanistic understanding of biological processes. Fortunately, new methods and several systematic studies have proved illuminating for many disease genes and variants by integrating sequencing with mechanistic data, including biomolecular structures and interactions. These have provided new interpretations for known mutations and suggested new disease-relevant variants and genes. Here, we review these approaches and discuss particular examples where these have had a profound impact on the understanding of human cancers. © 2018 Federation of European Biochemical Societies.

  15. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies

    International Nuclear Information System (INIS)

    Zhou Pei; Wagner, Gerhard

    2010-01-01

    Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR. We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.

  16. Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

    Directory of Open Access Journals (Sweden)

    Hassan Taghipour

    2013-01-01

    Full Text Available Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

  17. Piezoelectric tuning fork biosensors for the quantitative measurement of biomolecular interactions

    International Nuclear Information System (INIS)

    Gonzalez, Laura; Maria Benito, Angel; Puig-Vidal, Manel; Otero, Jorge; Rodrigues, Mafalda; Pérez-García, Lluïsa

    2015-01-01

    The quantitative measurement of biomolecular interactions is of great interest in molecular biology. Atomic force microscopy (AFM) has proved its capacity to act as a biosensor and determine the affinity between biomolecules of interest. Nevertheless, the detection scheme presents certain limitations when it comes to developing a compact biosensor. Recently, piezoelectric quartz tuning forks (QTFs) have been used as laser-free detection sensors for AFM. However, only a few studies along these lines have considered soft biological samples, and even fewer constitute quantified molecular recognition experiments. Here, we demonstrate the capacity of QTF probes to perform specific interaction measurements between biotin–streptavidin complexes in buffer solution. We propose in this paper a variant of dynamic force spectroscopy based on representing adhesion energies E (aJ) against pulling rates v (nm s"–"1). Our results are compared with conventional AFM measurements and show the great potential of these sensors in molecular interaction studies. (paper)

  18. XML-based approaches for the integration of heterogeneous bio-molecular data.

    Science.gov (United States)

    Mesiti, Marco; Jiménez-Ruiz, Ernesto; Sanz, Ismael; Berlanga-Llavori, Rafael; Perlasca, Paolo; Valentini, Giorgio; Manset, David

    2009-10-15

    The today's public database infrastructure spans a very large collection of heterogeneous biological data, opening new opportunities for molecular biology, bio-medical and bioinformatics research, but raising also new problems for their integration and computational processing. In this paper we survey the most interesting and novel approaches for the representation, integration and management of different kinds of biological data by exploiting XML and the related recommendations and approaches. Moreover, we present new and interesting cutting edge approaches for the appropriate management of heterogeneous biological data represented through XML. XML has succeeded in the integration of heterogeneous biomolecular information, and has established itself as the syntactic glue for biological data sources. Nevertheless, a large variety of XML-based data formats have been proposed, thus resulting in a difficult effective integration of bioinformatics data schemes. The adoption of a few semantic-rich standard formats is urgent to achieve a seamless integration of the current biological resources.

  19. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.

    Science.gov (United States)

    Anandakrishnan, Ramu; Aguilar, Boris; Onufriev, Alexey V

    2012-07-01

    The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.

  20. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems.

    Science.gov (United States)

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa

    2015-04-14

    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  1. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services.

    Science.gov (United States)

    Correa, Miria C; Deus, Helena F; Vasconcelos, Ana T; Hayashi, Yuki; Ajani, Jaffer A; Patnana, Srikrishna V; Almeida, Jonas S

    2010-10-26

    AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF), and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model). We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally) reflected into the configuration of the client's interface application. The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general purpose solution to the challenge of having interfaces

  2. AGUIA: autonomous graphical user interface assembly for clinical trials semantic data services

    Directory of Open Access Journals (Sweden)

    Hayashi Yuki

    2010-10-01

    Full Text Available Abstract Background AGUIA is a front-end web application originally developed to manage clinical, demographic and biomolecular patient data collected during clinical trials at MD Anderson Cancer Center. The diversity of methods involved in patient screening and sample processing generates a variety of data types that require a resource-oriented architecture to capture the associations between the heterogeneous data elements. AGUIA uses a semantic web formalism, resource description framework (RDF, and a bottom-up design of knowledge bases that employ the S3DB tool as the starting point for the client's interface assembly. Methods The data web service, S3DB, meets the necessary requirements of generating the RDF and of explicitly distinguishing the description of the domain from its instantiation, while allowing for continuous editing of both. Furthermore, it uses an HTTP-REST protocol, has a SPARQL endpoint, and has open source availability in the public domain, which facilitates the development and dissemination of this application. However, S3DB alone does not address the issue of representing content in a form that makes sense for domain experts. Results We identified an autonomous set of descriptors, the GBox, that provides user and domain specifications for the graphical user interface. This was achieved by identifying a formalism that makes use of an RDF schema to enable the automatic assembly of graphical user interfaces in a meaningful manner while using only resources native to the client web browser (JavaScript interpreter, document object model. We defined a generalized RDF model such that changes in the graphic descriptors are automatically and immediately (locally reflected into the configuration of the client's interface application. Conclusions The design patterns identified for the GBox benefit from and reflect the specific requirements of interacting with data generated by clinical trials, and they contain clues for a general

  3. On the Huygens principle for bianisotropic mediums with symmetric permittivity and permeability dyadics

    Energy Technology Data Exchange (ETDEWEB)

    Faryad, Muhammad, E-mail: muhammad.faryad@lums.edu.pk [Department of Physics, Lahore University of Management Sciences, Lahore 54792 (Pakistan); Lakhtakia, Akhlesh [Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802 (United States)

    2017-02-19

    Mathematical statements of the Huygens principle relate the electric and magnetic field phasors at an arbitrary location in a source-free region enclosed by a surface to the tangential components of the electric and magnetic field phasors over that surface, via the dyadic Green functions applicable to the linear homogeneous medium occupying that region. We have mathematically formulated the Huygens principle for the electric and magnetic field phasors when the permittivity and permeability dyadics of the medium are symmetric, the symmetric parts of the two magnetoelectric dyadics of the medium are negative of each other, and both magnetoelectric dyadics also contain anti-symmetric terms. We have also formulated the Huygens principle for the electric (resp. magnetic) field phasor in a medium whose permittivity (resp. permeability) is scalar, the permeability (resp. permittivity) is symmetric, the symmetric parts of the two magnetoelectric dyadics reduce to dissimilar scalars, and anti-symmetric parts of the two magnetoelectric dyadics are identical. - Highlights: • The Huygens principle was formulated for bianistropic mediums when the permittivity and permeability dyadics of the medium are symmetric. • The formulation covers isotropic, biisotropic, and gyrotropic-like uniaxial mediums for which the Huygens principle is already available. • The formulation also covers new mediums like biaxial, chiro-omega, pseudo chiral, gyrotropic-like biaxial, and Lorentz reciprocal mediums.

  4. Remitting seronegative symmetrical synovitis with pitting edema (RS3PE syndrome

    Directory of Open Access Journals (Sweden)

    Neslihan Gokcen

    2017-03-01

    Full Text Available Remitting seronegative symmetrical synovitis with pitting edema is a rare rheumatological disorder that presents with symmetrical hand and/or foot edema resembling rheumatoid arthritis. It is generally seen in male patients in older age, but atypical cases in different age groups have been documented. Although no clear mechanism has been described, certain genetic and environmental factors have been suggested for etiopathogenesis. Medical treatment is mainly focused on glucocorticoid therapy. This article aims to discuss the Remitting seronegative symmetrical synovitis with pitting edema syndrome and to review the current literature. [Cukurova Med J 2017; 42(1.000: 147-154

  5. Theorem on axially symmetric gravitational vacuum configurations

    Energy Technology Data Exchange (ETDEWEB)

    Papadopoulos, A; Le Denmat, G [Paris-6 Univ., 75 (France). Inst. Henri Poincare

    1977-01-24

    A theorem is proved which asserts the non-existence of axially symmetric gravitational vacuum configurations with non-stationary rotation only. The eventual consequences in black-hole physics are suggested.

  6. The discrete dynamics of symmetric competition in the plane.

    Science.gov (United States)

    Jiang, H; Rogers, T D

    1987-01-01

    We consider the generalized Lotka-Volterra two-species system xn + 1 = xn exp(r1(1 - xn) - s1yn) yn + 1 = yn exp(r2(1 - yn) - s2xn) originally proposed by R. M. May as a model for competitive interaction. In the symmetric case that r1 = r2 and s1 = s2, a region of ultimate confinement is found and the dynamics therein are described in some detail. The bifurcations of periodic points of low period are studied, and a cascade of period-doubling bifurcations is indicated. Within the confinement region, a parameter region is determined for the stable Hopf bifurcation of a pair of symmetrically placed period-two points, which imposes a second component of oscillation near the stable cycles. It is suggested that the symmetric competitive model contains much of the dynamical complexity to be expected in any discrete two-dimensional competitive model.

  7. Microfluidic Devices for Studying Biomolecular Interactions

    Science.gov (United States)

    Wilson, Wilbur W.; Garcia, Carlos d.; Henry, Charles S.

    2006-01-01

    Microfluidic devices for monitoring biomolecular interactions have been invented. These devices are basically highly miniaturized liquid-chromatography columns. They are intended to be prototypes of miniature analytical devices of the laboratory on a chip type that could be fabricated rapidly and inexpensively and that, because of their small sizes, would yield analytical results from very small amounts of expensive analytes (typically, proteins). Other advantages to be gained by this scaling down of liquid-chromatography columns may include increases in resolution and speed, decreases in the consumption of reagents, and the possibility of performing multiple simultaneous and highly integrated analyses by use of multiple devices of this type, each possibly containing multiple parallel analytical microchannels. The principle of operation is the same as that of a macroscopic liquid-chromatography column: The column is a channel packed with particles, upon which are immobilized molecules of the protein of interest (or one of the proteins of interest if there are more than one). Starting at a known time, a solution or suspension containing molecules of the protein or other substance of interest is pumped into the channel at its inlet. The liquid emerging from the outlet of the channel is monitored to detect the molecules of the dissolved or suspended substance(s). The time that it takes these molecules to flow from the inlet to the outlet is a measure of the degree of interaction between the immobilized and the dissolved or suspended molecules. Depending on the precise natures of the molecules, this measure can be used for diverse purposes: examples include screening for solution conditions that favor crystallization of proteins, screening for interactions between drugs and proteins, and determining the functions of biomolecules.

  8. Distinction of impedance responses of Li-ion batteries for individual electrodes using symmetric cells

    International Nuclear Information System (INIS)

    Momma, Toshiyuki; Yokoshima, Tokihiko; Nara, Hiroki; Gima, Yuhei; Osaka, Tetsuya

    2014-01-01

    Graphical abstract: - Highlights: • Impedance of lithium ion battery and symmetric cells were analyzed. • Anode symmetric cells and cathode one were prepared with ca. 7 × 7 cm 2 electrodes. • Except for R ct in cathode, electrochemical parameters did not change by reassembling. • Fitting data for symmetric cell were found to be useful for full cell analysis. • Electrochemical parameters of battery were traced during cycling degradation. - Abstract: Symmetric cells were prepared with a newly designed separable cell module, which enabled ca. 70 mm by 70 mm electrode sheets to be used for a pouch type 5 Ah class Li-ion battery (LIB). Impedance analysis of the LIB as a full cell state was successfully performed with electrochemical parameters obtained by an impedance analysis of symmetric cells of anodes and cathodes obtained from the operated Li-ion batteries. While the charge transfer resistance of the cathode was found to increase after reassembling the cells symmetrically, other electrochemical parameters were found not to change when comparing the values obtained for full cells with symmetric cells. Eelectrodes degraded by charge/discharge cycling of the battery were also investigated, and the parameter change caused by the degradation was confirmed

  9. Connections of geometric measure of entanglement of pure symmetric states to quantum state estimation

    International Nuclear Information System (INIS)

    Chen Lin; Zhu Huangjun; Wei, Tzu-Chieh

    2011-01-01

    We study the geometric measure of entanglement (GM) of pure symmetric states related to rank 1 positive-operator-valued measures (POVMs) and establish a general connection with quantum state estimation theory, especially the maximum likelihood principle. Based on this connection, we provide a method for computing the GM of these states and demonstrate its additivity property under certain conditions. In particular, we prove the additivity of the GM of pure symmetric multiqubit states whose Majorana points under Majorana representation are distributed within a half sphere, including all pure symmetric three-qubit states. We then introduce a family of symmetric states that are generated from mutually unbiased bases and derive an analytical formula for their GM. These states include Dicke states as special cases, which have already been realized in experiments. We also derive the GM of symmetric states generated from symmetric informationally complete POVMs (SIC POVMs) and use it to characterize all inequivalent SIC POVMs in three-dimensional Hilbert space that are covariant with respect to the Heisenberg-Weyl group. Finally, we describe an experimental scheme for creating the symmetric multiqubit states studied in this article and a possible scheme for measuring the permanence of the related Gram matrix.

  10. Symmetric, discrete fractional splines and Gabor systems

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel

    2006-01-01

    In this paper we consider fractional splines as windows for Gabor frames. We introduce two new types of symmetric, fractional splines in addition to one found by Unser and Blu. For the finite, discrete case we present two families of splines: One is created by sampling and periodizing the continu......In this paper we consider fractional splines as windows for Gabor frames. We introduce two new types of symmetric, fractional splines in addition to one found by Unser and Blu. For the finite, discrete case we present two families of splines: One is created by sampling and periodizing...... the continuous splines, and one is a truly finite, discrete construction. We discuss the properties of these splines and their usefulness as windows for Gabor frames and Wilson bases....

  11. On the mixing model for calculating the temperature fields in nuclear reactor fuel assemblies

    International Nuclear Information System (INIS)

    Mikhin, V.I.; Zhukov, A.V.

    1985-01-01

    One of the alternatives of the mixing model applied for calculating temperature fields in nuclear reactor fuel assemblies,including the fuel assemblies with nonequilibrium energy-release in fuel element cross section, is consistently described. The equations for both constant and variable values of coolant density and heat capacity are obtained. The mixing model is based on a set of mass, heat and longitudinal momentum balance equations. This set is closed by the ratios connecting the unknown values for gaps between fuel elements with the averaged values for neighbouring channels. The ratios to close momentum and heat balance equations, explaining, in particular, the nonequivalent heat and mass, momentum and mass transfer coefficients, are suggested. The balance equations with variable coolant density and heat capacity are reduced to the form coinciding with those of the similar equations with constant values of these parameters. Application of one of the main ratios of the mixing model relating the coolant transverse overflow in the gaps between fuel elements to the averaged coolant rates (flow rates) in the neighbouring channels is mainly limited by the coolant stabilized flow in the fuel assemblies with regular symmetrical arrangement of elements. Mass transfer coefficients for these elements are experimentally determined. The ratio in the paper is also applicable for calculation of fuel assembly temperature fields with a small relative shift of elements

  12. Non-symmetric bi-stable flow around the Ahmed body

    International Nuclear Information System (INIS)

    Meile, W.; Ladinek, T.; Brenn, G.; Reppenhagen, A.; Fuchs, A.

    2016-01-01

    Highlights: • The non-symmetric bi-stable flow around the Ahmed body is investigated experimentally. • Bi-stability, described for symmetric flow by Cadot and co-workers, was found in nonsymmetric flow also. • The flow field randomly switches between two states. • The flow is subject to a spanwise instability identified by Cadot and co-workers for symmetric flow. • Aerodynamic forces fluctuate strongly due to the bi-stability. - Abstract: The flow around the Ahmed body at varying Reynolds numbers under yawing conditions is investigated experimentally. The body geometry belongs to a regime subject to spanwise flow instability identified in symmetric flow by Cadot and co-workers (Grandemange et al., 2013b). Our experiments cover the two slant angles 25° and 35° and Reynolds numbers up to 2.784 × 10"6. Special emphasis lies on the aerodynamics under side wind influence. For the 35° slant angle, forces and moments change significantly with the yawing angle in the range 10° ≤ |β| ≤ 15°. The lift and the pitching moment exhibit strong fluctuations due to bi-stable flow around a critical angle β of ±12.5°, where the pitching moment changes sign. Time series of the forces and moments are studied and explained by PIV measurements in the flow field near the rear of the body.

  13. Frequency-scanning MALDI linear ion trap mass spectrometer for large biomolecular ion detection.

    Science.gov (United States)

    Lu, I-Chung; Lin, Jung Lee; Lai, Szu-Hsueh; Chen, Chung-Hsuan

    2011-11-01

    This study presents the first report on the development of a matrix-assisted laser desorption ionization (MALDI) linear ion trap mass spectrometer for large biomolecular ion detection by frequency scan. We designed, installed, and tested this radio frequency (RF) scan linear ion trap mass spectrometer and its associated electronics to dramatically extend the mass region to be detected. The RF circuit can be adjusted from 300 to 10 kHz with a set of operation amplifiers. To trap the ions produced by MALDI, a high pressure of helium buffer gas was employed to quench extra kinetic energy of the heavy ions produced by MALDI. The successful detection of the singly charged secretory immunoglobulin A ions indicates that the detectable mass-to-charge ratio (m/z) of this system can reach ~385 000 or beyond.

  14. Solving the generalized symmetric eigenvalue problem using tile algorithms on multicore architectures

    KAUST Repository

    Ltaief, Hatem; Luszczek, Piotr R.; Haidar, Azzam; Dongarra, Jack

    2012-01-01

    This paper proposes an efficient implementation of the generalized symmetric eigenvalue problem on multicore architecture. Based on a four-stage approach and tile algorithms, the original problem is first transformed into a standard symmetric

  15. Solving symmetric-definite quadratic lambda-matrix problems without factorization

    International Nuclear Information System (INIS)

    Scott, D.S.; Ward, R.C.

    1982-01-01

    Algorithms are presented for computing some of the eigenvalues and their associated eigenvectors of the quadratic lambda-matrix M lambda 2 C lambda + K. M, C, and K are assumed to have special symmetry-type properties which insure that theory analogous to the standard symmetric eigenproblem exists. The algorithms are based on a generalization of the Rayleigh quotient and the Lanczos method for computing eigenpairs of standard symmetric eigenproblems. Monotone quadratic convergence of the basic method is proved. Test examples are presented

  16. Analytical Study on Propagation Dynamics of Optical Beam in Parity-Time Symmetric Optical Couplers

    International Nuclear Information System (INIS)

    Zhou Zheng; Zhang Li-Juan; Zhu Bo

    2015-01-01

    We present exact analytical solutions to parity-time (PT) symmetric optical system describing light transport in PT-symmetric optical couplers. We show that light intensity oscillates periodically between two waveguides for unbroken PT-symmetric phase, whereas light always leaves the system from the waveguide experiencing gain when light is initially input at either waveguide experiencing gain or waveguide experiencing loss for broken PT-symmetric phase. These analytical results agree with the recent experimental observation reported by Rüter et al. [Nat. Phys. 6 (2010) 192]. Besides, we present a scheme for manipulating PT symmetry by applying a periodic modulation. Our results provide an efficient way to control light propagation in periodically modulated PT-symmetric system by tuning the modulation amplitude and frequency. (paper)

  17. A cosmological problem for maximally symmetric supergravity

    International Nuclear Information System (INIS)

    German, G.; Ross, G.G.

    1986-01-01

    Under very general considerations it is shown that inflationary models of the universe based on maximally symmetric supergravity with flat potentials are unable to resolve the cosmological energy density (Polonyi) problem. (orig.)

  18. Sobolev spaces on bounded symmetric domains

    Czech Academy of Sciences Publication Activity Database

    Engliš, Miroslav

    Roč. 60, č. 12 ( 2015 ), s. 1712-1726 ISSN 1747-6933 Institutional support: RVO:67985840 Keywords : bounded symmetric domain * Sobolev space * Bergman space Subject RIV: BA - General Mathematics Impact factor: 0.466, year: 2015 http://www.tandfonline.com/doi/abs/10.1080/17476933. 2015 .1043910

  19. Harmonic analysis on reductive symmetric spaces

    NARCIS (Netherlands)

    Ban, E.P. van den; Schlichtkrull, H.

    2000-01-01

    We give a relatively non-technical survey of some recent advances in the Fourier theory for semisimple symmetric spaces. There are three major results: An inversion formula for the Fourier transform, a Palley-Wiener theorem, which describes the Fourier image of the space of completely supported

  20. Analog/RF performance of two tunnel FETs with symmetric structures

    Science.gov (United States)

    Chen, Shupeng; Liu, Hongxia; Wang, Shulong; Li, Wei; Wang, Qianqiong

    2017-11-01

    In this paper, the radio frequency and analog performance of two tunnel field-effect transistors with symmetric structures are analyzed. The symmetric U-shape gate tunnel field-effect transistor (SUTFET) and symmetric tunnel field-effect transistor (STFET) are investigated by Silvaco Atlas simulation. The basic electrical properties and the parameters related to frequency and analog characteristics are analyzed. Due to the lower off-state leakage current, the STFET has better power consumption performance. The SUTFET obtains larger operating current (242 μA/μm), transconductance (490 μS/μm), output conductance (494 μS/μm), gain bandwidth product (3.2 GHz) and cut-off frequency (27.7 GHz). The simulation result of these two devices can be used as a guideline for their analog/RF applications.

  1. Electroweak Baryogenesis in R-symmetric Supersymmetry

    Energy Technology Data Exchange (ETDEWEB)

    Fok, R.; Kribs, Graham D.; Martin, Adam; Tsai, Yuhsin

    2013-03-01

    We demonstrate that electroweak baryogenesis can occur in a supersymmetric model with an exact R-symmetry. The minimal R-symmetric supersymmetric model contains chiral superfields in the adjoint representation, giving Dirac gaugino masses, and an additional set of "R-partner" Higgs superfields, giving R-symmetric \\mu-terms. New superpotential couplings between the adjoints and the Higgs fields can simultaneously increase the strength of the electroweak phase transition and provide additional tree-level contributions to the lightest Higgs mass. Notably, no light stop is present in this framework, and in fact, we require both stops to be above a few TeV to provide sufficient radiative corrections to the lightest Higgs mass to bring it up to 125 GeV. Large CP-violating phases in the gaugino/higgsino sector allow us to match the baryon asymmetry of the Universe with no constraints from electric dipole moments due to R-symmetry. We briefly discuss some of the more interesting phenomenology, particularly of the of the lightest CP-odd scalar.

  2. Axially symmetrical stresses measurement in the cylindrical tube using DIC with hole-drilling

    Science.gov (United States)

    Ma, Yinji; Yao, Xuefeng; Zhang, Danwen

    2015-03-01

    In this paper, a new method combining the digital image correlation (DIC) with the hole-drilling technology to characterize the axially symmetrical stresses of the cylindrical tube is developed. First, the theoretical expressions of the axially symmetrical stresses in the cylindrical tube are derived based on the displacement or strain fields before and after hole-drilling. Second, the release of the axially symmetrical stresses for the cylindrical tube caused by hole-drilling is simulated by the finite element method (FEM), which indicates that the axially symmetrical stresses of the cylindrical tube calculated by the cylindrical solution is more accuracy than that for traditionally planar solution. Finally, both the speckle image information and the displacement field of the cylindrical tube before and after hole-drilling are extracted by combining the DIC with the hole-drilling technology, then the axially symmetrical loading induced stresses of the cylindrical tube are obtained, which agree well with the results from the strain gauge method.

  3. Morphology-tunable and photoresponsive properties in a self-assembled two-component gel system.

    Science.gov (United States)

    Zhou, Yifeng; Xu, Miao; Yi, Tao; Xiao, Shuzhang; Zhou, Zhiguo; Li, Fuyou; Huang, Chunhui

    2007-01-02

    Photoresponsive C3-symmetrical trisurea self-assembling building blocks containing three azobenzene groups (LC10 and LC4) at the rim were designed and synthesized. By introducing a trisamide gelator (G18), which can self-aggregate through hydrogen bonds of acylamino moieties to form a fibrous network, the mixture of LC10 (or LC4) and G18 forms an organogel with coral-like supramolecular structure from 1,4-dioxane. The cooperation of hydrogen bonding and the hydrophobic diversity between these components are the main contributions to the specific superstructure. The two-component gel exhibits reversible photoisomerization from trans to cis transition without breakage of the gel state.

  4. Particle in a box in PT-symmetric quantum mechanics and an electromagnetic analog

    Science.gov (United States)

    Dasarathy, Anirudh; Isaacson, Joshua P.; Jones-Smith, Katherine; Tabachnik, Jason; Mathur, Harsh

    2013-06-01

    In PT-symmetric quantum mechanics a fundamental principle of quantum mechanics, that the Hamiltonian must be Hermitian, is replaced by another set of requirements, including notably symmetry under PT, where P denotes parity and T denotes time reversal. Here we study the role of boundary conditions in PT-symmetric quantum mechanics by constructing a simple model that is the PT-symmetric analog of a particle in a box. The model has the usual particle-in-a-box Hamiltonian but boundary conditions that respect PT symmetry rather than Hermiticity. We find that for a broad class of PT-symmetric boundary conditions the model respects the condition of unbroken PT symmetry, namely, that the Hamiltonian and the symmetry operator PT have simultaneous eigenfunctions, implying that the energy eigenvalues are real. We also find that the Hamiltonian is self-adjoint under the PT-symmetric inner product. Thus we obtain a simple soluble model that fulfills all the requirements of PT-symmetric quantum mechanics. In the second part of this paper we formulate a variational principle for PT-symmetric quantum mechanics that is the analog of the textbook Rayleigh-Ritz principle. Finally we consider electromagnetic analogs of the PT-symmetric particle in a box. We show that the isolated particle in a box may be realized as a Fabry-Perot cavity between an absorbing medium and its conjugate gain medium. Coupling the cavity to an external continuum of incoming and outgoing states turns the energy levels of the box into sharp resonances. Remarkably we find that the resonances have a Breit-Wigner line shape in transmission and a Fano line shape in reflection; by contrast, in the corresponding Hermitian case the line shapes always have a Breit-Wigner form in both transmission and reflection.

  5. Stabilization of self-mode-locked quantum dash lasers by symmetric dual-loop optical feedback

    Science.gov (United States)

    Asghar, Haroon; Wei, Wei; Kumar, Pramod; Sooudi, Ehsan; McInerney, John. G.

    2018-02-01

    We report experimental studies of the influence of symmetric dual-loop optical feedback on the RF linewidth and timing jitter of self-mode-locked two-section quantum dash lasers emitting at 1550 nm. Various feedback schemes were investigated and optimum levels determined for narrowest RF linewidth and low timing jitter, for single-loop and symmetric dual-loop feedback. Two symmetric dual-loop configurations, with balanced and unbalanced feedback ratios, were studied. We demonstrate that unbalanced symmetric dual loop feedback, with the inner cavity resonant and fine delay tuning of the outer loop, gives narrowest RF linewidth and reduced timing jitter over a wide range of delay, unlike single and balanced symmetric dual-loop configurations. This configuration with feedback lengths 80 and 140 m narrows the RF linewidth by 4-67x and 10-100x, respectively, across the widest delay range, compared to free-running. For symmetric dual-loop feedback, the influence of different power split ratios through the feedback loops was determined. Our results show that symmetric dual-loop feedback is markedly more effective than single-loop feedback in reducing RF linewidth and timing jitter, and is much less sensitive to delay phase, making this technique ideal for applications where robustness and alignment tolerance are essential.

  6. Solving the generalized symmetric eigenvalue problem using tile algorithms on multicore architectures

    KAUST Repository

    Ltaief, Hatem

    2012-01-01

    This paper proposes an efficient implementation of the generalized symmetric eigenvalue problem on multicore architecture. Based on a four-stage approach and tile algorithms, the original problem is first transformed into a standard symmetric eigenvalue problem by computing the Cholesky factorization of the right hand side symmetric definite positive matrix (first stage), and applying the inverse of the freshly computed triangular Cholesky factors to the original dense symmetric matrix of the problem (second stage). Calculating the eigenpairs of the resulting problem is then equivalent to the eigenpairs of the original problem. The computation proceeds by reducing the updated dense symmetric matrix to symmetric band form (third stage). The band structure is further reduced by applying a bulge chasing procedure, which annihilates the extra off-diagonal entries using orthogonal transformations (fourth stage). More details on the third and fourth stage can be found in Haidar et al. [Accepted at SC\\'11, November 2011]. The eigenvalues are then calculated from the tridiagonal form using the standard LAPACK QR algorithm (i.e., DTSEQR routine), while the complex and challenging eigenvector computations will be addressed in a companion paper. The tasks from the various stages can concurrently run in an out-of-order fashion. The data dependencies are cautiously tracked by the dynamic runtime system environment QUARK, which ensures the dependencies are not violated for numerical correctness purposes. The obtained tile four-stage generalized symmetric eigenvalue solver significantly outperforms the state-of-the-art numerical libraries (up to 21-fold speed up against multithreaded LAPACK with optimized multithreaded MKL BLAS and up to 4-fold speed up against the corresponding routine from the commercial numerical software Intel MKL) on four sockets twelve cores AMD system with a 24000×24000 matrix size. © 2012 The authors and IOS Press. All rights reserved.

  7. Marginal Stability Diagrams for Infinite-n Ballooning Modes in Quasi-symmetric Stellarators

    International Nuclear Information System (INIS)

    Hudson, S.R.; Hegna, C.C.; Torasso, R.; Ware, A.

    2003-01-01

    By perturbing the pressure and rotational-transform profiles at a selected surface in a given equilibrium, and by inducing a coordinate variation such that the perturbed state is in equilibrium, a family of magnetohydrodynamic equilibria local to the surface and parameterized by the pressure gradient and shear is constructed for arbitrary stellarator geometry. The geometry of the surface is not changed. The perturbed equilibria are analyzed for infinite-n ballooning stability and marginal stability diagrams are constructed that are analogous to the (s; alpha) diagrams constructed for axi-symmetric configurations. The method describes how pressure and rotational-transform gradients influence the local shear, which in turn influences the ballooning stability. Stability diagrams for the quasi-axially-symmetric NCSX (National Compact Stellarator Experiment), a quasi-poloidally-symmetric configuration and the quasi-helically-symmetric HSX (Helically Symmetric Experiment) are presented. Regions of second-stability are observed in both NCSX and the quasi-poloidal configuration, whereas no second stable region is observed for the quasi-helically symmetric device. To explain the different regions of stability, the curvature and local shear of the quasi-poloidal configuration are analyzed. The results are seemingly consistent with the simple explanation: ballooning instability results when the local shear is small in regions of bad curvature. Examples will be given that show that the structure, and stability, of the ballooning mode is determined by the structure of the potential function arising in the Schroedinger form of the ballooning equation

  8. (Anti)symmetric multivariate exponential functions and corresponding Fourier transforms

    International Nuclear Information System (INIS)

    Klimyk, A U; Patera, J

    2007-01-01

    We define and study symmetrized and antisymmetrized multivariate exponential functions. They are defined as determinants and antideterminants of matrices whose entries are exponential functions of one variable. These functions are eigenfunctions of the Laplace operator on the corresponding fundamental domains satisfying certain boundary conditions. To symmetric and antisymmetric multivariate exponential functions there correspond Fourier transforms. There are three types of such Fourier transforms: expansions into the corresponding Fourier series, integral Fourier transforms and multivariate finite Fourier transforms. Eigenfunctions of the integral Fourier transforms are found

  9. Symmetric mixed states of n qubits: Local unitary stabilizers and entanglement classes

    Energy Technology Data Exchange (ETDEWEB)

    Lyons, David W.; Walck, Scott N. [Lebanon Valley College, Annville, Pennsylvania 17003 (United States)

    2011-10-15

    We classify, up to local unitary equivalence, local unitary stabilizer Lie algebras for symmetric mixed states of n qubits into six classes. These include the stabilizer types of the Werner states, the Greenberger-Horne-Zeilinger state and its generalizations, and Dicke states. For all but the zero algebra, we classify entanglement types (local unitary equivalence classes) of symmetric mixed states that have those stabilizers. We make use of the identification of symmetric density matrices with polynomials in three variables with real coefficients and apply the representation theory of SO(3) on this space of polynomials.

  10. PT-symmetric ladders with a scattering core

    Energy Technology Data Exchange (ETDEWEB)

    D' Ambroise, J. [Department of Mathematics, Amherst College, Amherst, MA 01002-5000 (United States); Lepri, S. [CNR – Consiglio Nazionale delle Ricerche, Istituto dei Sistemi Complessi, via Madonna del piano 10, I-50019 Sesto Fiorentino (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Firenze, via G. Sansone 1, I-50019 Sesto Fiorentino (Italy); Malomed, B.A. [Department of Physical Electronics, School of Electrical Engineering, Faculty of Engineering, Tel Aviv University, Tel Aviv 69978 (Israel); Kevrekidis, P.G. [Department of Mathematics and Statistics, University of Massachusetts, Amherst, MA 01003-9305 (United States)

    2014-08-01

    We consider a PT-symmetric chain (ladder-shaped) system governed by the discrete nonlinear Schrödinger equation where the cubic nonlinearity is carried solely by two central “rungs” of the ladder. Two branches of scattering solutions for incident plane waves are found. We systematically construct these solutions, analyze their stability, and discuss non-reciprocity of the transmission associated with them. To relate the results to finite-size wavepacket dynamics, we also perform direct simulations of the evolution of the wavepackets, which confirm that the transmission is indeed asymmetric in this nonlinear system with the mutually balanced gain and loss. - Highlights: • We model a PT-symmetric ladder system with cubic nonlinearity on two central rungs. • We examine non-reciprocity and stability of incident plane waves. • Simulations of wavepackets confirm our results.

  11. An effective hierarchical model for the biomolecular covalent bond: an approach integrating artificial chemistry and an actual terrestrial life system.

    Science.gov (United States)

    Oohashi, Tsutomu; Ueno, Osamu; Maekawa, Tadao; Kawai, Norie; Nishina, Emi; Honda, Manabu

    2009-01-01

    Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

  12. Symmetric voltage-controlled variable resistance

    Science.gov (United States)

    Vanelli, J. C.

    1978-01-01

    Feedback network makes resistance of field-effect transistor (FET) same for current flowing in either direction. It combines control voltage with source and load voltages to give symmetric current/voltage characteristics. Since circuit produces same magnitude output voltage for current flowing in either direction, it introduces no offset in presense of altering polarity signals. It is therefore ideal for sensor and effector circuits in servocontrol systems.

  13. ATR-FTIR Spectroscopic Evidence for Biomolecular Phosphorus and Carboxyl Groups Facilitating Bacterial Adhesion to Iron Oxides

    Science.gov (United States)

    Parikh, Sanjai J.; Mukome, Fungai N.D.; Zhang, Xiaoming

    2014-01-01

    Attenuated total reflectance (ATR) Fourier transform infrared (FTIR) spectroscopy has been used to probe the binding of bacteria to hematite (α-Fe2O3) and goethite (α-FeOOH). In situ ATR-FTIR experiments with bacteria (Pseudomonas putida, P. aeruginosa, Escherichia coli), mixed amino acids, polypeptide extracts, deoxyribonucleic acid (DNA), and a suite of model compounds were conducted. These compounds represent carboxyl, catecholate, amide, and phosphate groups present in siderophores, amino acids, polysaccharides, phospholipids, and DNA. Due in part to the ubiquitous presence of carboxyl groups in biomolecules, numerous IR peaks corresponding to outer-sphere or unbound (1400 cm−1) and inner-sphere (1310-1320 cm−1) coordinated carboxyl groups are noted following reaction of bacteria and biomolecules with α-Fe2O3 and α-FeOOH. However, the data also reveal that the presence of low-level amounts (i.e., 0.45-0.79%) of biomolecular phosphorous groups result in strong IR bands at ~1043 cm−1, corresponding to inner-sphere Fe-O-P bonds, underscoring the importance of bacteria associated P-containing groups in biomolecule and cell adhesion. Spectral comparisons also reveal slightly greater P-O-Fe contributions for bacteria (Pseudomonad, E. coli) deposited on α-FeOOH, as compared to α-Fe2O3. This data demonstrates that slight differences in bacterial adhesion to Fe oxides can be attributed to bacterial species and Fe-oxide minerals. However, more importantly, the strong binding affinity of phosphate in all bacteria samples to both Fe-oxides results in the formation of inner-sphere Fe-O-P bonds, signifying the critical role of biomolecular P in the initiation of bacterial adhesion. PMID:24859052

  14. The Mathematics of Symmetrical Factorial Designs

    Indian Academy of Sciences (India)

    The Mathematics of Symmetrical Factorial Designs. Mausumi Bose (nee Sen) obtained her MSc degree in. Statistics from the Calcutta. University and PhD degree from the Indian Statistical. Institute. She is on the faculty of the Indian. Statistical Institute. Her main field of research interest is design and analysis of experiments.

  15. Solution of generalized shifted linear systems with complex symmetric matrices

    International Nuclear Information System (INIS)

    Sogabe, Tomohiro; Hoshi, Takeo; Zhang, Shao-Liang; Fujiwara, Takeo

    2012-01-01

    We develop the shifted COCG method [R. Takayama, T. Hoshi, T. Sogabe, S.-L. Zhang, T. Fujiwara, Linear algebraic calculation of Green’s function for large-scale electronic structure theory, Phys. Rev. B 73 (165108) (2006) 1–9] and the shifted WQMR method [T. Sogabe, T. Hoshi, S.-L. Zhang, T. Fujiwara, On a weighted quasi-residual minimization strategy of the QMR method for solving complex symmetric shifted linear systems, Electron. Trans. Numer. Anal. 31 (2008) 126–140] for solving generalized shifted linear systems with complex symmetric matrices that arise from the electronic structure theory. The complex symmetric Lanczos process with a suitable bilinear form plays an important role in the development of the methods. The numerical examples indicate that the methods are highly attractive when the inner linear systems can efficiently be solved.

  16. A comparison of lower bounds for the symmetric circulant traveling salesman problem

    NARCIS (Netherlands)

    de Klerk, E.; Dobre, C.

    2011-01-01

    When the matrix of distances between cities is symmetric and circulant, the traveling salesman problem (TSP) reduces to the so-called symmetric circulant traveling salesman problem (SCTSP), that has applications in the design of reconfigurable networks, and in minimizing wallpaper waste. The

  17. A class of non-symmetric band determinants with the Gaussian q ...

    African Journals Online (AJOL)

    A class of symmetric band matrices of bandwidth 2r+1 with the binomial coefficients entries was studied earlier. We consider a class of non-symmetric band matrices with the Gaussian q-binomial coefficients whose upper bandwith is s and lower bandwith is r. We give explicit formulæ for the determinant, the inverse (along ...

  18. Asymptotic expansions for Toeplitz operators on symmetric spaces of general type

    Czech Academy of Sciences Publication Activity Database

    Engliš, Miroslav; Upmeier, H.

    2015-01-01

    Roč. 367, č. 1 (2015), s. 423-476 ISSN 0002-9947 R&D Projects: GA ČR GA201/09/0473 Institutional support: RVO:67985840 Keywords : symmetric space * symmetric domain * Berezin quantization Subject RIV: BA - General Mathematics Impact factor: 1.196, year: 2015 http://www.ams.org/journals/tran/2015-367-01/S0002-9947-2014-06130-8/

  19. Complex {PT}-symmetric extensions of the nonlinear ultra-short light pulse model

    Science.gov (United States)

    Yan, Zhenya

    2012-11-01

    The short pulse equation u_{xt}=u+\\frac{1}{2}(u^2u_x)_x is PT symmetric, which arises in nonlinear optics for the ultra-short pulse case. We present a family of new complex PT-symmetric extensions of the short pulse equation, i[(iu_x)^{\\sigma }]_t=au+bu^m+ic[u^n(iu_x)^{\\epsilon }]_x \\,\\, (\\sigma ,\\, \\epsilon ,\\,a,\\,b,\\,c,\\,m,\\,n \\in {R}), based on the complex PT-symmetric extension principle. Some properties of these equations with some chosen parameters are studied including the Hamiltonian structures and exact solutions such as solitary wave solutions, doubly periodic wave solutions and compacton solutions. Our results may be useful to understand complex PT-symmetric nonlinear physical models. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Quantum physics with non-Hermitian operators’.

  20. Symmetric minimally entangled typical thermal states for canonical and grand-canonical ensembles

    Science.gov (United States)

    Binder, Moritz; Barthel, Thomas

    2017-05-01

    Based on the density matrix renormalization group (DMRG), strongly correlated quantum many-body systems at finite temperatures can be simulated by sampling over a certain class of pure matrix product states (MPS) called minimally entangled typical thermal states (METTS). When a system features symmetries, these can be utilized to substantially reduce MPS computation costs. It is conceptually straightforward to simulate canonical ensembles using symmetric METTS. In practice, it is important to alternate between different symmetric collapse bases to decrease autocorrelations in the Markov chain of METTS. To this purpose, we introduce symmetric Fourier and Haar-random block bases that are efficiently mixing. We also show how grand-canonical ensembles can be simulated efficiently with symmetric METTS. We demonstrate these approaches for spin-1 /2 X X Z chains and discuss how the choice of the collapse bases influences autocorrelations as well as the distribution of measurement values and, hence, convergence speeds.

  1. Holographic Spherically Symmetric Metrics

    Science.gov (United States)

    Petri, Michael

    The holographic principle (HP) conjectures, that the maximum number of degrees of freedom of any realistic physical system is proportional to the system's boundary area. The HP has its roots in the study of black holes. It has recently been applied to cosmological solutions. In this article we apply the HP to spherically symmetric static space-times. We find that any regular spherically symmetric object saturating the HP is subject to tight constraints on the (interior) metric, energy-density, temperature and entropy-density. Whenever gravity can be described by a metric theory, gravity is macroscopically scale invariant and the laws of thermodynamics hold locally and globally, the (interior) metric of a regular holographic object is uniquely determined up to a constant factor and the interior matter-state must follow well defined scaling relations. When the metric theory of gravity is general relativity, the interior matter has an overall string equation of state (EOS) and a unique total energy-density. Thus the holographic metric derived in this article can serve as simple interior 4D realization of Mathur's string fuzzball proposal. Some properties of the holographic metric and its possible experimental verification are discussed. The geodesics of the holographic metric describe an isotropically expanding (or contracting) universe with a nearly homogeneous matter-distribution within the local Hubble volume. Due to the overall string EOS the active gravitational mass-density is zero, resulting in a coasting expansion with Ht = 1, which is compatible with the recent GRB-data.

  2. Efficient small molecule bulk heterojunction solar cells with high fill factors via pyrene-directed molecular self-assembly

    KAUST Repository

    Lee, Olivia P.; Yiu, Alan T.; Beaujuge, Pierre; Woo, Claire; Holcombe, Thomas W.; Millstone, Jill E.; Douglas, Jessica D.; Chen, Mark S.; Frechet, Jean

    2011-01-01

    Efficient organic photovoltaic (OPV) materials are constructed by attaching completely planar, symmetric end-groups to donor-acceptor electroactive small molecules. Appending C2-pyrene as the small molecule end-group to a diketopyrrolopyrrole core leads to materials with a tight, aligned crystal packing and favorable morphology dictated by π-π interactions, resulting in high power conversion efficiencies and high fill factors. The use of end-groups to direct molecular self-assembly is an effective strategy for designing high-performance small molecule OPV devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Efficient small molecule bulk heterojunction solar cells with high fill factors via pyrene-directed molecular self-assembly

    KAUST Repository

    Lee, Olivia P.

    2011-10-21

    Efficient organic photovoltaic (OPV) materials are constructed by attaching completely planar, symmetric end-groups to donor-acceptor electroactive small molecules. Appending C2-pyrene as the small molecule end-group to a diketopyrrolopyrrole core leads to materials with a tight, aligned crystal packing and favorable morphology dictated by π-π interactions, resulting in high power conversion efficiencies and high fill factors. The use of end-groups to direct molecular self-assembly is an effective strategy for designing high-performance small molecule OPV devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Symmetrized neutron transport equation and the fast Fourier transform method

    International Nuclear Information System (INIS)

    Sinh, N.Q.; Kisynski, J.; Mika, J.

    1978-01-01

    The differential equation obtained from the neutron transport equation by the application of the source iteration method in two-dimensional rectangular geometry is transformed into a symmetrized form with respect to one of the angular variables. The discretization of the symmetrized equation leads to finite difference equations based on the five-point scheme and solved by use of the fast Fourier transform method. Possible advantages of the approach are shown on test calculations

  5. Invariant subspaces in some function spaces on symmetric spaces. II

    International Nuclear Information System (INIS)

    Platonov, S S

    1998-01-01

    Let G be a semisimple connected Lie group with finite centre, K a maximal compact subgroup of G, and M=G/K a Riemannian symmetric space of non-compact type. We study the problem of describing the structure of closed linear subspaces in various function spaces on M that are invariant under the quasiregular representation of the group G. We consider the case when M is a symplectic symmetric space of rank 1

  6. Ultrastrong extraordinary transmission and reflection in PT-symmetric Thue-Morse optical waveguide networks.

    Science.gov (United States)

    Wu, Jiaye; Yang, Xiangbo

    2017-10-30

    In this paper, we construct a 1D PT-symmetric Thue-Morse aperiodic optical waveguide network (PTSTMAOWN) and mainly investigate the ultrastrong extraordinary transmission and reflection. We propose an approach to study the photonic modes and solve the problem of calculating photonic modes distributions in aperiodic networks due to the lack of dispersion functions and find that in a PTSTMAOWN there exist more photonic modes and more spontaneous PT-symmetric breaking points, which are quite different from other reported PT-symmetric optical systems. Additionally, we develop a method to sort spontaneous PT-symmetric breaking point zones to seek the strongest extraordinary point and obtain that at this point the strongest extraordinary transmission and reflection arrive at 2.96316 × 10 5 and 1.32761 × 10 5 , respectively, due to the PT-symmetric coupling resonance and the special symmetry pattern of TM networks. These enormous gains are several orders of magnitude larger than the previous results. This optical system may possess potential in designing optical amplifier, optical logic elements in photon computers and ultrasensitive optical switches with ultrahigh monochromatity.

  7. Tailoring Spectral Properties of Binary PT-Symmetric Gratings by Duty-Cycle Methods

    DEFF Research Database (Denmark)

    Lupu, Anatole T.; Benisty, Henri; Lavrinenko, Andrei

    2016-01-01

    We explore the frequency selective functionalities of a nonuniform PT-symmetric Bragg grating with modulated complex index profile. We start by assessing the possibility to achieve an efficient apodization of the PT-symmetric Bragg grating spectral response by using direct adaptations of the conv...

  8. Symmetric scrolled packings of multilayered carbon nanoribbons

    Science.gov (United States)

    Savin, A. V.; Korznikova, E. A.; Lobzenko, I. P.; Baimova, Yu. A.; Dmitriev, S. V.

    2016-06-01

    Scrolled packings of single-layer and multilayer graphene can be used for the creation of supercapacitors, nanopumps, nanofilters, and other nanodevices. The full atomistic simulation of graphene scrolls is restricted to consideration of relatively small systems in small time intervals. To overcome this difficulty, a two-dimensional chain model making possible an efficient calculation of static and dynamic characteristics of nanoribbon scrolls with allowance for the longitudinal and bending stiffness of nanoribbons is proposed. The model is extended to the case of scrolls of multilayer graphene. Possible equilibrium states of symmetric scrolls of multilayer carbon nanotribbons rolled up so that all nanoribbons in the scroll are equivalent are found. Dependences of the number of coils, the inner and outer radii, lowest vibrational eigenfrequencies of rolled packages on the length L of nanoribbons are obtained. It is shown that the lowest vibrational eigenfrequency of a symmetric scroll decreases with a nanoribbon length proportionally to L -1. It is energetically unfavorable for too short nanoribbons to roll up, and their ground state is a stack of plane nanoribbons. With an increasing number k of layers, the nanoribbon length L necessary for creation of symmetric scrolls increases. For a sufficiently small number of layers k and a sufficiently large nanoribbon length L, the scrolled packing has the lowest energy as compared to that of stack of plane nanoribbons and folded structures. The results can be used for development of nanomaterials and nanodevices on the basis of graphene scrolled packings.

  9. Maximum-confidence discrimination among symmetric qudit states

    International Nuclear Information System (INIS)

    Jimenez, O.; Solis-Prosser, M. A.; Delgado, A.; Neves, L.

    2011-01-01

    We study the maximum-confidence (MC) measurement strategy for discriminating among nonorthogonal symmetric qudit states. Restricting to linearly dependent and equally likely pure states, we find the optimal positive operator valued measure (POVM) that maximizes our confidence in identifying each state in the set and minimizes the probability of obtaining inconclusive results. The physical realization of this POVM is completely determined and it is shown that after an inconclusive outcome, the input states may be mapped into a new set of equiprobable symmetric states, restricted, however, to a subspace of the original qudit Hilbert space. By applying the MC measurement again onto this new set, we can still gain some information about the input states, although with less confidence than before. This leads us to introduce the concept of sequential maximum-confidence (SMC) measurements, where the optimized MC strategy is iterated in as many stages as allowed by the input set, until no further information can be extracted from an inconclusive result. Within each stage of this measurement our confidence in identifying the input states is the highest possible, although it decreases from one stage to the next. In addition, the more stages we accomplish within the maximum allowed, the higher will be the probability of correct identification. We will discuss an explicit example of the optimal SMC measurement applied in the discrimination among four symmetric qutrit states and propose an optical network to implement it.

  10. The symmetric MSD encoder for one-step adder of ternary optical computer

    Science.gov (United States)

    Kai, Song; LiPing, Yan

    2016-08-01

    The symmetric Modified Signed-Digit (MSD) encoding is important for achieving the one-step MSD adder of Ternary Optical Computer (TOC). The paper described the symmetric MSD encoding algorithm in detail, and developed its truth table which has nine rows and nine columns. According to the truth table, the state table was developed, and the optical-path structure and circuit-implementation scheme of the symmetric MSD encoder (SME) for one-step adder of TOC were proposed. Finally, a series of experiments were designed and performed. The observed results of the experiments showed that the scheme to implement SME was correct, feasible and efficient.

  11. Quantum work relations and response theory in parity-time-symmetric quantum systems

    Science.gov (United States)

    Wei, Bo-Bo

    2018-01-01

    In this work, we show that a universal quantum work relation for a quantum system driven arbitrarily far from equilibrium extends to a parity-time- (PT -) symmetric quantum system with unbroken PT symmetry, which is a consequence of microscopic reversibility. The quantum Jarzynski equality, linear response theory, and Onsager reciprocal relations for the PT -symmetric quantum system are recovered as special cases of the universal quantum work relation in a PT -symmetric quantum system. In the regime of broken PT symmetry, the universal quantum work relation does not hold because the norm is not preserved during the dynamics.

  12. Nonstandard jump functions for radically symmetric shock waves

    International Nuclear Information System (INIS)

    Baty, Roy S.; Tucker, Don H.; Stanescu, Dan

    2008-01-01

    Nonstandard analysis is applied to derive generalized jump functions for radially symmetric, one-dimensional, magnetogasdynamic shock waves. It is assumed that the shock wave jumps occur on infinitesimal intervals and the jump functions for the physical parameters occur smoothly across these intervals. Locally integrable predistributions of the Heaviside function are used to model the flow variables across a shock wave. The equations of motion expressed in nonconservative form are then applied to derive unambiguous relationships between the jump functions for the physical parameters for two families of self-similar flows. It is shown that the microstructures for these families of radially symmetric, magnetogasdynamic shock waves coincide in a nonstandard sense for a specified density jump function.

  13. Are average and symmetric faces attractive to infants? Discrimination and looking preferences.

    Science.gov (United States)

    Rhodes, Gillian; Geddes, Keren; Jeffery, Linda; Dziurawiec, Suzanne; Clark, Alison

    2002-01-01

    Young infants prefer to look at faces that adults find attractive, suggesting a biological basis for some face preferences. However, the basis for infant preferences is not known. Adults find average and symmetric faces attractive. We examined whether 5-8-month-old infants discriminate between different levels of averageness and symmetry in faces, and whether they prefer to look at faces with higher levels of these traits. Each infant saw 24 pairs of female faces. Each pair consisted of two versions of the same face differing either in averageness (12 pairs) or symmetry (12 pairs). Data from the mothers confirmed that adults preferred the more average and more symmetric versions in each pair. The infants were sensitive to differences in both averageness and symmetry, but showed no looking preference for the more average or more symmetric versions. On the contrary, longest looks were significantly longer for the less average versions, and both longest looks and first looks were marginally longer for the less symmetric versions. Mean looking times were also longer for the less average and less symmetric versions, but those differences were not significant. We suggest that the infant looking behaviour may reflect a novelty preference rather than an aesthetic preference.

  14. Cytoscape: a software environment for integrated models of biomolecular interaction networks.

    Science.gov (United States)

    Shannon, Paul; Markiel, Andrew; Ozier, Owen; Baliga, Nitin S; Wang, Jonathan T; Ramage, Daniel; Amin, Nada; Schwikowski, Benno; Ideker, Trey

    2003-11-01

    Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

  15. REVIEW ARTICLE: How do biomolecular systems speed up and regulate rates?

    Science.gov (United States)

    Zhou, Huan-Xiang

    2005-09-01

    The viability of a biological system depends upon careful regulation of the rates of various processes. These rates have limits imposed by intrinsic chemical or physical steps (e.g., diffusion). These limits can be expanded by interactions and dynamics of the biomolecules. For example, (a) a chemical reaction is catalyzed when its transition state is preferentially bound to an enzyme; (b) the folding of a protein molecule is speeded up by specific interactions within the transition-state ensemble and may be assisted by molecular chaperones; (c) the rate of specific binding of a protein molecule to a cellular target can be enhanced by mechanisms such as long-range electrostatic interactions, nonspecific binding and folding upon binding; (d) directional movement of motor proteins is generated by capturing favorable Brownian motion through intermolecular binding energy; and (e) conduction and selectivity of ions through membrane channels are controlled by interactions and the dynamics of channel proteins. Simple physical models are presented here to illustrate these processes and provide a unifying framework for understanding speed attainment and regulation in biomolecular systems.

  16. Uma abordagem visual para análise comparativa de redes biomoleculares com apoio de diagramas de Venn

    OpenAIRE

    Henry Heberle

    2014-01-01

    Sistemas biológicos podem ser representados por redes que armazenam não apenas informações de conectividade, mas também informações de características de seus nós. No contexto biomolecular, esses nós podem representar proteínas, metabólitos, entre outros tipos de moléculas. Cada molécula possui características anotadas e armazenadas em bases de dados como o Gene Ontology. A comparação visual dessas redes depende de ferramentas que permitam o usuário identificar diferenças e semelhanças entre ...

  17. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.

    2011-11-07

    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  18. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications

    Science.gov (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  19. The 1/ N Expansion of Tensor Models with Two Symmetric Tensors

    Science.gov (United States)

    Gurau, Razvan

    2018-06-01

    It is well known that tensor models for a tensor with no symmetry admit a 1/ N expansion dominated by melonic graphs. This result relies crucially on identifying jackets, which are globally defined ribbon graphs embedded in the tensor graph. In contrast, no result of this kind has so far been established for symmetric tensors because global jackets do not exist. In this paper we introduce a new approach to the 1/ N expansion in tensor models adapted to symmetric tensors. In particular we do not use any global structure like the jackets. We prove that, for any rank D, a tensor model with two symmetric tensors and interactions the complete graph K D+1 admits a 1/ N expansion dominated by melonic graphs.

  20. Elastic-plastic analysis of an axi-symmetric problem by a finite element method

    International Nuclear Information System (INIS)

    Isozaki, Toshikuni

    1984-06-01

    Generally speaking, many structures are designed and fabricated on the basis of an axi-symmetric structure. Finite Element Method is the capable method to solve these axi-symmetric problems beyond the elastic limit. As the first step to solve these problems, the computer program for the elastic-plastic analysis of the axi-symmetric problem is composed. The basic program is based upon that described in Zienkiewicz's text book to solve the elastic plane stress problem, taking the plastic stress matrix by Yamada's method into consideration and it is converted to solve the axi-symmetric problem. For the verification of the program, the plane strain problem of a cylindrical tube under internal pressure was solved. The computed results were compared with those shown in ADINA's user's manual. They showed close agreement. (author)

  1. Evolution of lateral ordering in symmetric block copolymer thin films upon rapid thermal processing

    International Nuclear Information System (INIS)

    Ceresoli, Monica; Ferrarese Lupi, Federico; Seguini, Gabriele; Perego, Michele; Sparnacci, Katia; Gianotti, Valentina; Antonioli, Diego; Laus, Michele; Boarino, Luca

    2014-01-01

    This work reports experimental findings about the evolution of lateral ordering of lamellar microdomains in symmetric PS-b-PMMA thin films on featureless substrates. Phase separation and microdomain evolution are explored in a rather wide range of temperatures (190–340 °C) using a rapid thermal processing (RTP) system. The maximum processing temperature that enables the ordering of block copolymers without introducing any significant degradation of macromolecules is identified. The reported results clearly indicate that the range of accessible temperatures in the processing of these self-assembling materials is mainly limited by the thermal instability of the grafted random copolymer layer, which starts to degrade at T > 300 °C, inducing detachment of the block copolymer thin film. For T ⩽ 290 °C, clear dependence of correlation length (ξ) values on temperature is observed. The highest level of lateral order achievable in the current system in a quasi-equilibrium condition was obtained at the upper processing temperature limit after an annealing time as short as 60 s. (paper)

  2. Symmetric bends how to join two lengths of cord

    CERN Document Server

    Miles, Roger E

    1995-01-01

    A bend is a knot securely joining together two lengths of cord (or string or rope), thereby yielding a single longer length. There are many possible different bends, and a natural question that has probably occurred to many is: "Is there a 'best' bend and, if so, what is it?"Most of the well-known bends happen to be symmetric - that is, the two constituent cords within the bend have the same geometric shape and size, and interrelationship with the other. Such 'symmetric bends' have great beauty, especially when the two cords bear different colours. Moreover, they have the practical advantage o

  3. Characterization of Generalized Young Measures Generated by Symmetric Gradients

    Science.gov (United States)

    De Philippis, Guido; Rindler, Filip

    2017-06-01

    This work establishes a characterization theorem for (generalized) Young measures generated by symmetric derivatives of functions of bounded deformation (BD) in the spirit of the classical Kinderlehrer-Pedregal theorem. Our result places such Young measures in duality with symmetric-quasiconvex functions with linear growth. The "local" proof strategy combines blow-up arguments with the singular structure theorem in BD (the analogue of Alberti's rank-one theorem in BV), which was recently proved by the authors. As an application of our characterization theorem we show how an atomic part in a BD-Young measure can be split off in generating sequences.

  4. Algorithms for sparse, symmetric, definite quadratic lambda-matrix eigenproblems

    International Nuclear Information System (INIS)

    Scott, D.S.; Ward, R.C.

    1981-01-01

    Methods are presented for computing eigenpairs of the quadratic lambda-matrix, M lambda 2 + C lambda + K, where M, C, and K are large and sparse, and have special symmetry-type properties. These properties are sufficient to insure that all the eigenvalues are real and that theory analogous to the standard symmetric eigenproblem exists. The methods employ some standard techniques such as partial tri-diagonalization via the Lanczos Method and subsequent eigenpair calculation, shift-and- invert strategy and subspace iteration. The methods also employ some new techniques such as Rayleigh-Ritz quadratic roots and the inertia of symmetric, definite, quadratic lambda-matrices

  5. Supersymmetry and cotangent bundle over non-compact exceptional Hermitian symmetric space

    International Nuclear Information System (INIS)

    Arai, Masato; Baba, Kurando

    2015-01-01

    We construct N=2 supersymmetric nonlinear sigma models on the cotangent bundles over the non-compact exceptional Hermitian symmetric spaces M=E 6(−14) /SO(10)×U(1) and E 7(−25) /E 6 ×U(1). In order to construct them we use the projective superspace formalism which is an N=2 off-shell superfield formulation in four-dimensional space-time. This formalism allows us to obtain the explicit expression of N=2 supersymmetric nonlinear sigma models on the cotangent bundles over any Hermitian symmetric spaces in terms of the N=1 superfields, once the Kähler potentials of the base manifolds are obtained. We derive the N=1 supersymmetric nonlinear sigma models on the Kähler manifolds M. Then we extend them into the N=2 supersymmetric models with the use of the result in arXiv:1211.1537 developed in the projective superspace formalism. The resultant models are the N=2 supersymmetric nonlinear sigma models on the cotangent bundles over the Hermitian symmetric spaces M. In this work we complete constructing the cotangent bundles over all the compact and non-compact Hermitian symmetric spaces.

  6. Parametric amplification and bidirectional invisibility in PT -symmetric time-Floquet systems

    Science.gov (United States)

    Koutserimpas, Theodoros T.; Alù, Andrea; Fleury, Romain

    2018-01-01

    Parity-time (PT )-symmetric wave devices, which exploit balanced interactions between material gain and loss, exhibit extraordinary properties, including lasing and flux-conserving scattering processes. In a seemingly different research field, periodically driven systems, also known as time-Floquet systems, have been widely studied as a relevant platform for reconfigurable active wave control and manipulation. In this article, we explore the connection between PT -symmetry and parametric time-Floquet systems. Instead of relying on material gain, we use parametric amplification by considering a time-periodic modulation of the refractive index at a frequency equal to twice the incident signal frequency. We show that the scattering from a simple parametric slab, whose dynamics follows the Mathieu equation, can be described by a PT -symmetric scattering matrix, whose PT -breaking threshold corresponds to the Mathieu instability threshold. By combining different parametric slabs modulated out of phase, we create PT -symmetric time-Floquet systems that feature exceptional scattering properties, such as coherent perfect absorption (CPA)-laser operation and bidirectional invisibility. These bidirectional properties, rare for regular PT -symmetric systems, are related to a compensation of parametric amplification due to multiple scattering between two parametric systems modulated with a phase difference.

  7. Fe-substituted (La,Sr)TiO{sub 3} as potential electrodes for symmetrical fuel cells (SFCs)

    Energy Technology Data Exchange (ETDEWEB)

    Canales-Vazquez, Jesus [Renewable Energy Research Institute, University of Castilla la Mancha, 02006 Albacete (Spain); Instituto de Ciencia de los Materiales de Barcelona, ICMAB-CSIC, 01893 Bellaterra (Spain); Ruiz-Morales, Juan Carlos; Marrero-Lopez, David; Pena-Martinez, Juan; Nunez, Pedro [Dpto. Quimica Inorganica, Universidad de La Laguna, Avda. Francisco Sanchez s/n, 38200 Tenerife, Canary Islands (Spain); Gomez-Romero, Pedro [Instituto de Ciencia de los Materiales de Barcelona, ICMAB-CSIC, 01893 Bellaterra (Spain)

    2007-09-27

    In the work presented herein, the potential use of La{sub 4}Sr{sub 8}Ti{sub 12-x}Fe{sub x}O{sub 38-{delta}} (LSTF) materials as electrodes for a new concept of solid oxide fuel cells, symmetrical fuel cells (SFCs), is considered. Such fuel cells use simultaneously the same material as anode and cathode, which notably simplifies the assembly and further maintenance of the cells. Therefore, we search for materials showing high conductivity in a wide range of oxygen partial pressures in addition to certain degree of catalytic activity for the oxidation of the fuel and reduction of the oxidant, respectively. The preliminary electrochemical experiments performed reveal that the overall conductivity increases notably upon Fe substitution, being the main contribution electronic n-type. The fuel cell tests indicate that LSTF composites with YSZ and CeO{sub 2} perform reasonably well under H{sub 2} conditions, although the performance in methane is rather modest and require further optimisation. (author)

  8. Factored Facade Acquisition using Symmetric Line Arrangements

    KAUST Repository

    Ceylan, Duygu

    2012-05-01

    We introduce a novel framework for image-based 3D reconstruction of urban buildings based on symmetry priors. Starting from image-level edges, we generate a sparse and approximate set of consistent 3D lines. These lines are then used to simultaneously detect symmetric line arrangements while refining the estimated 3D model. Operating both on 2D image data and intermediate 3D feature representations, we perform iterative feature consolidation and effective outlier pruning, thus eliminating reconstruction artifacts arising from ambiguous or wrong stereo matches. We exploit non-local coherence of symmetric elements to generate precise model reconstructions, even in the presence of a significant amount of outlier image-edges arising from reflections, shadows, outlier objects, etc. We evaluate our algorithm on several challenging test scenarios, both synthetic and real. Beyond reconstruction, the extracted symmetry patterns are useful towards interactive and intuitive model manipulations.

  9. Complex group algebras of the double covers of the symmetric and alternating group

    DEFF Research Database (Denmark)

    Bessenrodt, Christine; Nguyen, Hung Ngoc; Olsson, Jørn Børling

    2015-01-01

    We prove that the double covers of the alternating and symmetric groups are determined by their complex group algebras......We prove that the double covers of the alternating and symmetric groups are determined by their complex group algebras...

  10. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

    Directory of Open Access Journals (Sweden)

    Noji Hiroyuki

    2009-01-01

    Full Text Available Abstract We have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully. (See supplementary material 1 Electronic supplementary material The online version of this article (doi:10.1007/s11671-009-9479-3 contains supplementary material, which is available to authorized users. Click here for file

  11. Exotic fermions in the left-right symmetric model

    International Nuclear Information System (INIS)

    Choi, J.; Volkas, R.R.

    1992-01-01

    A systematic study is made of non-standard fermion multiplets in left-right symmetric models with gauge group SU(3) x SU(2) L x SU(2) R x U(1) BL . Constraints from gauge anomaly cancellation and invariance of Yukawa coupling terms are used to define interesting classes of exotic fermions. The standard quark lepton spectrum of left-right symmetric models was identified as the simplest member of an infinite class. Phenomenological implications of the next simplest member of this class are then studied. Classes of exotic fermions which may couple to the standard fermions through doublet Higgs bosons were also considered, then shown that some of these exotics may be used to induce a generalised universal see-saw mechanism. 12 refs., 1 tab

  12. Pseudo-Hermitian description of PT-symmetric systems defined on a complex contour

    International Nuclear Information System (INIS)

    Mostafazadeh, Ali

    2005-01-01

    We describe a method that allows for a practical application of the theory of pseudo-Hermitian operators to PT-symmetric systems defined on a complex contour. We apply this method to study the Hamiltonians H = p 2 + x 2 (ix) ν with ν ε (-2, ∞) that are defined along the corresponding anti-Stokes lines. In particular, we reveal the intrinsic non-Hermiticity of H for the cases that ν is an even integer, so that H p 2 ± x 2+ν , and give a proof of the discreteness of the spectrum of H for all ν ε (-2, ∞). Furthermore, we study the consequences of defining a square-well Hamiltonian on a wedge-shaped complex contour. This yields a PT-symmetric system with a finite number of real eigenvalues. We present a comprehensive analysis of this system within the framework of pseudo-Hermitian quantum mechanics. We also outline a direct pseudo-Hermitian treatment of PT-symmetric systems defined on a complex contour which clarifies the underlying mathematical structure of the formulation of PT-symmetric quantum mechanics based on the charge-conjugation operator. Our results provide conclusive evidence that pseudo-Hermitian quantum mechanics provides a complete description of general PT-symmetric systems regardless of whether they are defined along the real line or a complex contour

  13. Tourist Demand Reactions: Symmetric or Asymmetric across the Business Cycle?

    Science.gov (United States)

    Bronner, Fred; de Hoog, Robert

    2017-09-01

    Economizing and spending priorities on different types of vacations are investigated during two periods: an economic downturn and returning prosperity. Two nation-wide samples of vacationers are used: one during a downturn, the other one at the start of the recovery period. Through comparing the results, conclusions can be drawn about symmetric or asymmetric tourist demand across the business cycle. The main summer holiday has an asymmetric profile: being fairly crisis-resistant during a recession and showing considerable growth during an expansion. This does not apply to short vacations and day trips, each having a symmetric profile: during a recession they experience substantial reductions and during expansion comparable growth. So when talking about tourist demand in general , one cannot say that it is symmetric or asymmetric across the business cycle: it depends on the type of vacation. Differences in tourist demand are best explained by the role of Quality-of-Life for vacationers.

  14. Phase behaviour of the symmetric binary mixture from thermodynamic perturbation theory.

    Science.gov (United States)

    Dorsaz, N; Foffi, G

    2010-03-17

    We study the phase behaviour of symmetric binary mixtures of hard core Yukawa (HCY) particles via thermodynamic perturbation theory (TPT). We show that all the topologies of phase diagram reported for the symmetric binary mixtures are correctly reproduced within the TPT approach. In a second step we use the capability of TPT to be straightforwardly extended to mixtures that are nonsymmetric in size. Starting from mixtures that belong to the different topologies of symmetric binary mixtures we investigate the effect on the phase behaviour when an asymmetry in the diameters of the two components is introduced. Interestingly, when the energy of interaction between unlike particles is weaker than the interaction between like particles, the propensity for the solution to demix is found to increase strongly with size asymmetry.

  15. Exact solutions of the spherically symmetric multidimensional ...

    African Journals Online (AJOL)

    The complete orthonormalised energy eigenfunctions and the energy eigenvalues of the spherically symmetric isotropic harmonic oscillator in N dimensions, are obtained through the methods of separation of variables. Also, the degeneracy of the energy levels are examined. KEY WORDS: - Schrödinger Equation, Isotropic ...

  16. Hardware Realization of Chaos Based Symmetric Image Encryption

    KAUST Repository

    Barakat, Mohamed L.

    2012-01-01

    This thesis presents a novel work on hardware realization of symmetric image encryption utilizing chaos based continuous systems as pseudo random number generators. Digital implementation of chaotic systems results in serious degradations

  17. Maximally Symmetric Composite Higgs Models.

    Science.gov (United States)

    Csáki, Csaba; Ma, Teng; Shu, Jing

    2017-09-29

    Maximal symmetry is a novel tool for composite pseudo Goldstone boson Higgs models: it is a remnant of an enhanced global symmetry of the composite fermion sector involving a twisting with the Higgs field. Maximal symmetry has far-reaching consequences: it ensures that the Higgs potential is finite and fully calculable, and also minimizes the tuning. We present a detailed analysis of the maximally symmetric SO(5)/SO(4) model and comment on its observational consequences.

  18. Determination of symmetrical index for 3H in river waters

    International Nuclear Information System (INIS)

    Jankovic, M.; Todorovic, D.; Jankovic, B.; Nikolic, J.; Sarap, N.

    2011-01-01

    The paper presents the results of determining the symmetric index, which describes the magnitude of the tritium content changes with time, for samples of Sava and Danube river waters and Mlaka creek water. The results cover the period from 2003 to 2008. It was shown that the value of the symmetric index is the highest for Mlaka samples, which is in accordance with the fact that in these samples the highest concentration of tritium was found in comparison with samples of the Sava and Danube. [sr

  19. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.

    Science.gov (United States)

    Prinz, Jan-Hendrik; Chodera, John D; Pande, Vijay S; Swope, William C; Smith, Jeremy C; Noé, Frank

    2011-06-28

    Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.

  20. A Derandomized Algorithm for RP-ADMM with Symmetric Gauss-Seidel Method

    OpenAIRE

    Xu, Jinchao; Xu, Kailai; Ye, Yinyu

    2017-01-01

    For multi-block alternating direction method of multipliers(ADMM), where the objective function can be decomposed into multiple block components, we show that with block symmetric Gauss-Seidel iteration, the algorithm will converge quickly. The method will apply a block symmetric Gauss-Seidel iteration in the primal update and a linear correction that can be derived in view of Richard iteration. We also establish the linear convergence rate for linear systems.

  1. Architecture of the Yeast Mitochondrial Iron-Sulfur Cluster Assembly Machinery: THE SUB-COMPLEX FORMED BY THE IRON DONOR, Yfh1 PROTEIN, AND THE SCAFFOLD, Isu1 PROTEIN.

    Science.gov (United States)

    Ranatunga, Wasantha; Gakh, Oleksandr; Galeano, Belinda K; Smith, Douglas Y; Söderberg, Christopher A G; Al-Karadaghi, Salam; Thompson, James R; Isaya, Grazia

    2016-05-06

    The biosynthesis of Fe-S clusters is a vital process involving the delivery of elemental iron and sulfur to scaffold proteins via molecular interactions that are still poorly defined. We reconstituted a stable, functional complex consisting of the iron donor, Yfh1 (yeast frataxin homologue 1), and the Fe-S cluster scaffold, Isu1, with 1:1 stoichiometry, [Yfh1]24·[Isu1]24 Using negative staining transmission EM and single particle analysis, we obtained a three-dimensional reconstruction of this complex at a resolution of ∼17 Å. In addition, via chemical cross-linking, limited proteolysis, and mass spectrometry, we identified protein-protein interaction surfaces within the complex. The data together reveal that [Yfh1]24·[Isu1]24 is a roughly cubic macromolecule consisting of one symmetric Isu1 trimer binding on top of one symmetric Yfh1 trimer at each of its eight vertices. Furthermore, molecular modeling suggests that two subunits of the cysteine desulfurase, Nfs1, may bind symmetrically on top of two adjacent Isu1 trimers in a manner that creates two putative [2Fe-2S] cluster assembly centers. In each center, conserved amino acids known to be involved in sulfur and iron donation by Nfs1 and Yfh1, respectively, are in close proximity to the Fe-S cluster-coordinating residues of Isu1. We suggest that this architecture is suitable to ensure concerted and protected transfer of potentially toxic iron and sulfur atoms to Isu1 during Fe-S cluster assembly. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Single-Cell Biomolecular Analysis of Coral Algal Symbionts Reveals Opposing Metabolic Responses to Heat Stress and Expulsion

    Directory of Open Access Journals (Sweden)

    Katherina Petrou

    2018-03-01

    Full Text Available The success of corals in nutrient poor environments is largely attributed to the symbiosis between the cnidarian host and its intracellular alga. Warm water anomalies have been shown to destabilize this symbiosis, yet detailed analysis of the effect of temperature and expulsion on cell-specific carbon and nutrient allocation in the symbiont is limited. Here, we exposed colonies of the hard coral Acropora millepora to heat stress and using synchrotron-based infrared microspectroscopy measured the biomolecular profiles of individual in hospite and expelled symbiont cells at an acute state of bleaching. Our results showed symbiont metabolic profiles to be remarkably distinct with heat stress and expulsion, where the two effectors elicited opposing metabolic adjustments independent of treatment or cell type. Elevated temperature resulted in biomolecular changes reflecting cellular stress, with relative increases in free amino acids and phosphorylation of molecules and a concomitant decline in protein content, suggesting protein modification and degradation. This contrasted with the metabolic profiles of expelled symbionts, which showed relative decreases in free amino acids and phosphorylated molecules, but increases in proteins and lipids, suggesting expulsion lessens the overall effect of heat stress on the metabolic signature of the algal symbionts. Interestingly, the combined effects of expulsion and thermal stress were additive, reducing the overall shifts in all biomolecules, with the notable exception of the significant accumulation of lipids and saturated fatty acids. This first use of a single-cell metabolomics approach on the coral symbiosis provides novel insight into coral bleaching and emphasizes the importance of a single-cell approach to demark the cell-to-cell variability in the physiology of coral cellular populations.

  3. Symmetric and asymmetric nuclear matter in the relativistic approach

    International Nuclear Information System (INIS)

    Huber, H.; Weber, F.; Weigel, M.K.

    1995-01-01

    Symmetric and asymmetric nuclear matter is studied in the framework of the relativistic Brueckner-Hartree-Fock and in the relativistic version of the so-called Λ 00 approximation. The equations are solved self-consistently in the full Dirac space, so avoiding the ambiguities in the choice of the effective scattering amplitude in matter. The calculations were performed for some modern meson-exchange potentials constructed by Brockmann and Machleidt. In some cases we used also the Groningen potentials. First, we examine the outcome for symmetric matter with respect to other calculations, which restrict themselves to positive-energy states only. The main part is devoted to the properties of asymmetric matter. In this case we obtain additionally to the good agreement with the parameters of symmetric matter, also a quite satisfactory agreement with the semiempirical macroscopic coefficients of asymmetric matter. Furthermore, we tested the assumption of a quadratic dependence of the asymmetry energy for a large range of asymmetries. Included is also the dependence of nucleon self-energies on density and neutron excess. For the purpose of comparison we discuss further the similarities and differences with relativistic Hartree and Hartree-Fock calculations and nonrelativistic Skyrme calculations

  4. The critical current of point symmetric Josephson tunnel junctions

    International Nuclear Information System (INIS)

    Monaco, Roberto

    2016-01-01

    Highlights: • We disclose some geometrical properties of the critical current field dependence that apply to a large class of Josephson junctions characterized by a point symmetric shape. • The developed theory is valid for any orientation of the applied magnetic field, therefore it allows the determine the consequences of field misalignment in the experimental setups. • We also address that the threshold curves of Josephson tunnel junctions with complex shapes can be expressed as a linear combination of the threshold curves of junctions with simpler point symmetric shapes. - Abstract: The physics of Josephson tunnel junctions drastically depends on their geometrical configurations. The shape of the junction determines the specific form of the magnetic-field dependence of its Josephson current. Here we address the magnetic diffraction patterns of specially shaped planar Josephson tunnel junctions in the presence of an in-plane magnetic field of arbitrary orientations. We focus on a wide ensemble of junctions whose shape is invariant under point reflection. We analyze the implications of this type of isometry and derive the threshold curves of junctions whose shape is the union or the relative complement of two point symmetric plane figures.

  5. Optimality and stability of symmetric evolutionary games with applications in genetic selection.

    Science.gov (United States)

    Huang, Yuanyuan; Hao, Yiping; Wang, Min; Zhou, Wen; Wu, Zhijun

    2015-06-01

    Symmetric evolutionary games, i.e., evolutionary games with symmetric fitness matrices, have important applications in population genetics, where they can be used to model for example the selection and evolution of the genotypes of a given population. In this paper, we review the theory for obtaining optimal and stable strategies for symmetric evolutionary games, and provide some new proofs and computational methods. In particular, we review the relationship between the symmetric evolutionary game and the generalized knapsack problem, and discuss the first and second order necessary and sufficient conditions that can be derived from this relationship for testing the optimality and stability of the strategies. Some of the conditions are given in different forms from those in previous work and can be verified more efficiently. We also derive more efficient computational methods for the evaluation of the conditions than conventional approaches. We demonstrate how these conditions can be applied to justifying the strategies and their stabilities for a special class of genetic selection games including some in the study of genetic disorders.

  6. Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components

    Science.gov (United States)

    Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.; Grun, Casey; Strauss, Maximilian T.; Bron, Patrick; Lai-Kee-Him, Josephine; Schueder, Florian; Wang, Bei; Wang, Pengfei; Kishi, Jocelyn Y.; Myhrvold, Cameron; Zhu, Allen; Jungmann, Ralf; Bellot, Gaetan; Ke, Yonggang; Yin, Peng

    2017-12-01

    Nucleic acids (DNA and RNA) are widely used to construct nanometre-scale structures with ever increasing complexity, with possible application in fields such as structural biology, biophysics, synthetic biology and photonics. The nanostructures are formed through one-pot self-assembly, with early kilodalton-scale examples containing typically tens of unique DNA strands. The introduction of DNA origami, which uses many staple strands to fold one long scaffold strand into a desired structure, has provided access to megadalton-scale nanostructures that contain hundreds of unique DNA strands. Even larger DNA origami structures are possible, but manufacturing and manipulating an increasingly long scaffold strand remains a challenge. An alternative and more readily scalable approach involves the assembly of DNA bricks, which each consist of four short binding domains arranged so that the bricks can interlock. This approach does not require a scaffold; instead, the short DNA brick strands self-assemble according to specific inter-brick interactions. First-generation bricks used to create three-dimensional structures are 32 nucleotides long, consisting of four eight-nucleotide binding domains. Protocols have been designed to direct the assembly of hundreds of distinct bricks into well formed structures, but attempts to create larger structures have encountered practical challenges and had limited success. Here we show that DNA bricks with longer, 13-nucleotide binding domains make it possible to self-assemble 0.1-1-gigadalton, three-dimensional nanostructures from tens of thousands of unique components, including a 0.5-gigadalton cuboid containing about 30,000 unique bricks and a 1-gigadalton rotationally symmetric tetramer. We also assembled a cuboid that contains around 10,000 bricks and about 20,000 uniquely addressable, 13-base-pair ‘voxels’ that serves as a molecular canvas for three-dimensional sculpting. Complex, user-prescribed, three-dimensional cavities can

  7. Neutrinoless double-beta decay in left-right symmetric models

    International Nuclear Information System (INIS)

    Picciotto, C.E.; Zahir, M.S.

    1982-06-01

    Neutrinoless double-beta decay is calculated via doubly charged Higgs, which occur naturally in left-right symmetric models. We find that the comparison with known half-lives yields values of phenomenological parameters which are compatible with earlier analyses of neutral current data. In particular, we obtain a right-handed gauge-boson mass lower bound of the order of 240 GeV. Using this result and expressions for neutrino masses derived in a parity non-conserving left-right symmetric model, we obtain msub(νsub(e)) < 1.5 eV, msub(νsub(μ)) < 0.05 MeV and msub(νsub(tau)) < 18 MeV

  8. SAS-6 assembly templated by the lumen of cartwheel-less centrioles precedes centriole duplication.

    Science.gov (United States)

    Fong, Chii Shyang; Kim, Minhee; Yang, T Tony; Liao, Jung-Chi; Tsou, Meng-Fu Bryan

    2014-07-28

    Centrioles are 9-fold symmetric structures duplicating once per cell cycle. Duplication involves self-oligomerization of the centriolar protein SAS-6, but how the 9-fold symmetry is invariantly established remains unclear. Here, we found that SAS-6 assembly can be shaped by preexisting (or mother) centrioles. During S phase, SAS-6 molecules are first recruited to the proximal lumen of the mother centriole, adopting a cartwheel-like organization through interactions with the luminal wall, rather than via their self-oligomerization activity. The removal or release of luminal SAS-6 requires Plk4 and the cartwheel protein STIL. Abolishing either the recruitment or the removal of luminal SAS-6 hinders SAS-6 (or centriole) assembly at the outside wall of mother centrioles. After duplication, the lumen of engaged mother centrioles becomes inaccessible to SAS-6, correlating with a block for reduplication. These results lead to a proposed model that centrioles may duplicate via a template-based process to preserve their geometry and copy number. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. On the Effect of Sphere-Overlap on Super Coarse-Grained Models of Protein Assemblies

    Science.gov (United States)

    Degiacomi, Matteo T.

    2018-05-01

    Ion mobility mass spectrometry (IM/MS) can provide structural information on intact protein complexes. Such data, including connectivity and collision cross sections (CCS) of assemblies' subunits, can in turn be used as a guide to produce representative super coarse-grained models. These models are constituted by ensembles of overlapping spheres, each representing a protein subunit. A model is considered plausible if the CCS and sphere-overlap levels of its subunits fall within predetermined confidence intervals. While the first is determined by experimental error, the latter is based on a statistical analysis on a range of protein dimers. Here, we first propose a new expression to describe the overlap between two spheres. Then we analyze the effect of specific overlap cutoff choices on the precision and accuracy of super coarse-grained models. Finally, we propose a method to determine overlap cutoff levels on a per-case scenario, based on collected CCS data, and show that it can be applied to the characterization of the assembly topology of symmetrical homo-multimers. [Figure not available: see fulltext.

  10. Symmetric configurations highlighted by collective quantum coherence

    Energy Technology Data Exchange (ETDEWEB)

    Obster, Dennis [Radboud University, Institute for Mathematics, Astrophysics and Particle Physics, Nijmegen (Netherlands); Kyoto University, Yukawa Institute for Theoretical Physics, Kyoto (Japan); Sasakura, Naoki [Kyoto University, Yukawa Institute for Theoretical Physics, Kyoto (Japan)

    2017-11-15

    Recent developments in quantum gravity have shown the Lorentzian treatment to be a fruitful approach towards the emergence of macroscopic space-times. In this paper, we discuss another related aspect of the Lorentzian treatment: we argue that collective quantum coherence may provide a simple mechanism for highlighting symmetric configurations over generic non-symmetric ones. After presenting the general framework of the mechanism, we show the phenomenon in some concrete simple examples in the randomly connected tensor network, which is tightly related to a certain model of quantum gravity, i.e., the canonical tensor model. We find large peaks at configurations invariant under Lie-group symmetries as well as a preference for charge quantization, even in the Abelian case. In future study, this simple mechanism may provide a way to analyze the emergence of macroscopic space-times with global symmetries as well as various other symmetries existing in nature, which are usually postulated. (orig.)

  11. Hardware Realization of Chaos-based Symmetric Video Encryption

    KAUST Repository

    Ibrahim, Mohamad A.

    2013-01-01

    This thesis reports original work on hardware realization of symmetric video encryption using chaos-based continuous systems as pseudo-random number generators. The thesis also presents some of the serious degradations caused by digitally

  12. Review of Transducer Principles for Label-Free Biomolecular Interaction Analysis

    Directory of Open Access Journals (Sweden)

    Janos Vörös

    2011-07-01

    Full Text Available Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM and the film bulk acoustic resonator (FBAR, calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

  13. Renormalization of period doubling in symmetric four-dimensional volume-preserving maps

    International Nuclear Information System (INIS)

    Mao, J.; Greene, J.M.

    1987-01-01

    We have determined three maps (truncated at quadratic terms) that are fixed under the renormalization operator of pitchfork period doubling in symmetric four-dimensional volume-preserving maps. Each of these contains the previously known two-dimensional area-preserving map that is fixed under the period-doubling operator. One of these three fixed maps consists of two uncoupled two-dimensional (nonlinear) area-preserving fixed maps. The other two contain also the two-dimensional area-preserving fixed map coupled (in general) with a linear two-dimensional map. The renormalization calculation recovers all numerical results for the pitchfork period doubling in the symmetric four-dimensional volume-preserving maps, reported by Mao and Helleman [Phys. Rev. A 35, 1847 (1987)]. For a large class of nonsymmetric four-dimensional volume-preserving maps, we found that the fixed maps are the same as those for the symmetric maps

  14. Experimental technique of calibration of symmetrical air pollution ...

    Indian Academy of Sciences (India)

    Based on the inherent property of symmetry of air pollution models, a Symmetrical Air Pollution. Model ... process is in compliance with air pollution regula- ..... Ground simulation is achieved through MATLAB package which is based on least-.

  15. An iteration for indefinite and non-symmetric systems and its application to the Navier-Stokes equations

    Energy Technology Data Exchange (ETDEWEB)

    Wathen, A. [Oxford Univ. (United Kingdom); Golub, G. [Stanford Univ., CA (United States)

    1996-12-31

    A simple fixed point linearisation of the Navier-Stokes equations leads to the Oseen problem which after appropriate discretisation yields large sparse linear systems with coefficient matrices of the form (A B{sup T} B -C). Here A is non-symmetric but its symmetric part is positive definite, and C is symmetric and positive semi-definite. Such systems arise in other situations. In this talk we will describe and present some analysis for an iteration based on an indefinite and symmetric preconditioner of the form (D B{sup T} B -C).

  16. Pre-Clinical Tests of an Integrated CMOS Biomolecular Sensor for Cardiac Diseases Diagnosis.

    Science.gov (United States)

    Lee, Jen-Kuang; Wang, I-Shun; Huang, Chi-Hsien; Chen, Yih-Fan; Huang, Nien-Tsu; Lin, Chih-Ting

    2017-11-26

    Coronary artery disease and its related complications pose great threats to human health. In this work, we aim to clinically evaluate a CMOS field-effect biomolecular sensor for cardiac biomarkers, cardiac-specific troponin-I (cTnI), N -terminal prohormone brain natriuretic peptide (NT-proBNP), and interleukin-6 (IL-6). The CMOS biosensor is implemented via a standard commercialized 0.35 μm CMOS process. To validate the sensing characteristics, in buffer conditions, the developed CMOS biosensor has identified the detection limits of IL-6, cTnI, and NT-proBNP as being 45 pM, 32 pM, and 32 pM, respectively. In clinical serum conditions, furthermore, the developed CMOS biosensor performs a good correlation with an enzyme-linked immuno-sorbent assay (ELISA) obtained from a hospital central laboratory. Based on this work, the CMOS field-effect biosensor poses good potential for accomplishing the needs of a point-of-care testing (POCT) system for heart disease diagnosis.

  17. Synchronous fluorescence based biosensor for albumin determination by cooperative binding of fluorescence probe in a supra-biomolecular host-protein assembly.

    Science.gov (United States)

    Patra, Digambara

    2010-01-15

    A synchronous fluorescence probe based biosensor for estimation of albumin with high sensitivity and selectivity was developed. Unlike conventional fluorescence emission or excitation spectral measurements, synchronous fluorescence measurement offered exclusively a new synchronous fluorescence peak in the shorter wavelength range upon binding of chrysene with protein making it an easy identification tool for albumin determination. The cooperative binding of a fluorescence probe, chrysene, in a supramolecular host-protein assembly during various albumin assessments was investigated. The presence of supramolecular host molecules such as beta-cyclodextrin, curucurbit[6]uril or curucurbit[7]uril have little influence on sensitivity or limit of detection during albumin determination but reduced dramatically interference from various coexisting metal ion quenchers/enhancers. Using the present method the limit of detection for BSA and gamma-Globulin was found to be 0.005 microM which is more sensitive than reported values. Copyright 2009 Elsevier B.V. All rights reserved.

  18. Focusing optical waves with a rotationally symmetric sharp-edge aperture

    Science.gov (United States)

    Hu, Yanwen; Fu, Shenhe; Li, Zhen; Yin, Hao; Zhou, Jianying; Chen, Zhenqiang

    2018-04-01

    While there has been various kinds of patterned structures proposed for wave focusing, these patterned structures usually involve complicated lithographic techniques since the element size of the patterned structures should be precisely controlled in microscale or even nanoscale. Here we propose a new and straightforward method for focusing an optical plane wave in free space with a rotationally symmetric sharp-edge aperture. The focusing phenomenon of wave is realized by superposition of a portion of the higher-order symmetric plane waves generated from the sharp edges of the apertures, in contrast to previously focusing techniques which usually depend on a curved phase. We demonstrate both experimentally and theoretically the focusing effect with a series of apertures having different rotational symmetry, and find that the intensity of the hotspots could be controlled by the symmetric strength of the sharp-edge apertures. The presented results would advance the conventional wisdom that light would diffract in all directions and become expanding when it propagates through an aperture. The proposed method is easy to be processed, and might open potential applications in interferometry, image, and superresolution.

  19. A Paley-Wiener theorem for reductive symmetric spaces

    NARCIS (Netherlands)

    Ban, E.P. van den; Schlichtkrull, H.

    2006-01-01

    Let X = G/H be a reductive symmetric space and K a maximal compact subgroup of G. The image under the Fourier transform of the space of K-finite compactly supported smooth functions on X is characterized.

  20. Symmetric and Programmable Multi-Chip Module for Low-Power Prototyping System

    OpenAIRE

    Yen, Mao-Hsu; Chen, Sao-Jie; Lan, Sanko H.

    2001-01-01

    The advantages of a Multi-Chip Module (MCM) product are its low-power and small-size. But the design of an MCM system usually requires weeks of engineering effort, thus we need a generic MCM substrate with programmable interconnections to accelerate system prototyping. In this paper, we propose a Symmetric and Programmable MCM (SPMCM) substrate for this purpose. This SPMCM substrate consists of a symmetrical array of slots for bare-chip attachment and Field Programmable Interco...

  1. Cuspidal discrete series for semisimple symmetric spaces

    DEFF Research Database (Denmark)

    Andersen, Nils Byrial; Flensted-Jensen, Mogens; Schlichtkrull, Henrik

    2012-01-01

    We propose a notion of cusp forms on semisimple symmetric spaces. We then study the real hyperbolic spaces in detail, and show that there exists both cuspidal and non-cuspidal discrete series. In particular, we show that all the spherical discrete series are non-cuspidal. (C) 2012 Elsevier Inc. All...

  2. Symmetric intersections of Rauzy fractals | Sellami | Quaestiones ...

    African Journals Online (AJOL)

    In this article we study symmetric subsets of Rauzy fractals of unimodular irreducible Pisot substitutions. The symmetry considered is re ection through the origin. Given an unimodular irreducible Pisot substitution, we consider the intersection of its Rauzy fractal with the Rauzy fractal of the reverse substitution. This set is ...

  3. Symmetrical and overloaded effect of diffusion in information filtering

    Science.gov (United States)

    Zhu, Xuzhen; Tian, Hui; Chen, Guilin; Cai, Shimin

    2017-10-01

    In physical dynamics, mass diffusion theory has been applied to design effective information filtering models on bipartite network. In previous works, researchers unilaterally believe objects' similarities are determined by single directional mass diffusion from the collected object to the uncollected, meanwhile, inadvertently ignore adverse influence of diffusion overload. It in some extent veils the essence of diffusion in physical dynamics and hurts the recommendation accuracy and diversity. After delicate investigation, we argue that symmetrical diffusion effectively discloses essence of mass diffusion, and high diffusion overload should be published. Accordingly, in this paper, we propose an symmetrical and overload penalized diffusion based model (SOPD), which shows excellent performances in extensive experiments on benchmark datasets Movielens and Netflix.

  4. Continuous symmetric reductions of the Adler-Bobenko-Suris equations

    International Nuclear Information System (INIS)

    Tsoubelis, D; Xenitidis, P

    2009-01-01

    Continuously symmetric solutions of the Adler-Bobenko-Suris class of discrete integrable equations are presented. Initially defined by their invariance under the action of both of the extended three-point generalized symmetries admitted by the corresponding equations, these solutions are shown to be determined by an integrable system of partial differential equations. The connection of this system to the Nijhoff-Hone-Joshi 'generating partial differential equations' is established and an auto-Baecklund transformation and a Lax pair for it are constructed. Applied to the H1 and Q1 δ=0 members of the Adler-Bobenko-Suris family, the method of continuously symmetric reductions yields explicit solutions determined by the Painleve trancendents

  5. RPYFMM: Parallel adaptive fast multipole method for Rotne-Prager-Yamakawa tensor in biomolecular hydrodynamics simulations

    Science.gov (United States)

    Guan, W.; Cheng, X.; Huang, J.; Huber, G.; Li, W.; McCammon, J. A.; Zhang, B.

    2018-06-01

    RPYFMM is a software package for the efficient evaluation of the potential field governed by the Rotne-Prager-Yamakawa (RPY) tensor interactions in biomolecular hydrodynamics simulations. In our algorithm, the RPY tensor is decomposed as a linear combination of four Laplace interactions, each of which is evaluated using the adaptive fast multipole method (FMM) (Greengard and Rokhlin, 1997) where the exponential expansions are applied to diagonalize the multipole-to-local translation operators. RPYFMM offers a unified execution on both shared and distributed memory computers by leveraging the DASHMM library (DeBuhr et al., 2016, 2018). Preliminary numerical results show that the interactions for a molecular system of 15 million particles (beads) can be computed within one second on a Cray XC30 cluster using 12,288 cores, while achieving approximately 54% strong-scaling efficiency.

  6. Symmetric functions and orthogonal polynomials

    CERN Document Server

    Macdonald, I G

    1997-01-01

    One of the most classical areas of algebra, the theory of symmetric functions and orthogonal polynomials has long been known to be connected to combinatorics, representation theory, and other branches of mathematics. Written by perhaps the most famous author on the topic, this volume explains some of the current developments regarding these connections. It is based on lectures presented by the author at Rutgers University. Specifically, he gives recent results on orthogonal polynomials associated with affine Hecke algebras, surveying the proofs of certain famous combinatorial conjectures.

  7. Baryon symmetric big-bang cosmology

    Energy Technology Data Exchange (ETDEWEB)

    Stecker, F.W.

    1978-04-01

    The framework of baryon-symmetric big-bang cosmology offers the greatest potential for deducing the evolution of the universe as a consequence of physical laws and processes with the minimum number of arbitrary assumptions as to initial conditions in the big-bang. In addition, it offers the possibility of explaining the photon-baryon ratio in the universe and how galaxies and galaxy clusters are formed, and also provides the only acceptable explanation at present for the origin of the cosmic gamma ray background radiation.

  8. Baryon symmetric big-bang cosmology

    International Nuclear Information System (INIS)

    Stecker, F.W.

    1978-04-01

    The framework of baryon-symmetric big-bang cosmology offers the greatest potential for deducing the evolution of the universe as a consequence of physical laws and processes with the minimum number of arbitrary assumptions as to initial conditions in the big-bang. In addition, it offers the possibility of explaining the photon-baryon ratio in the universe and how galaxies and galaxy clusters are formed, and also provides the only acceptable explanation at present for the origin of the cosmic gamma ray background radiation

  9. Bright Solitons in a PT-Symmetric Chain of Dimers

    Directory of Open Access Journals (Sweden)

    Omar B. Kirikchi

    2016-01-01

    Full Text Available We study the existence and stability of fundamental bright discrete solitons in a parity-time- (PT- symmetric coupler composed by a chain of dimers that is modelled by linearly coupled discrete nonlinear Schrödinger equations with gain and loss terms. We use a perturbation theory for small coupling between the lattices to perform the analysis, which is then confirmed by numerical calculations. Such analysis is based on the concept of the so-called anticontinuum limit approach. We consider the fundamental onsite and intersite bright solitons. Each solution has symmetric and antisymmetric configurations between the arms. The stability of the solutions is then determined by solving the corresponding eigenvalue problem. We obtain that both symmetric and antisymmetric onsite mode can be stable for small coupling, in contrast to the reported continuum limit where the antisymmetric solutions are always unstable. The instability is either due to the internal modes crossing the origin or the appearance of a quartet of complex eigenvalues. In general, the gain-loss term can be considered parasitic as it reduces the stability region of the onsite solitons. Additionally, we analyse the dynamic behaviour of the onsite and intersite solitons when unstable, where typically it is either in the form of travelling solitons or soliton blow-ups.

  10. Crosstalk properties of 36-fold segmented symmetric hexagonal HPGe detectors

    International Nuclear Information System (INIS)

    Bruyneel, Bart; Reiter, Peter; Wiens, Andreas; Eberth, Juergen; Hess, Herbert; Pascovici, Gheorghe; Warr, Nigel; Weisshaar, Dirk

    2009-01-01

    Crosstalk properties of three 36-fold segmented, symmetric, large volume, HPGe detectors from the AGATA Collaboration were deduced from coincidence measurements performed with digitized segment and core signals after interaction of γ rays with energies of 1.33 MeV. The mean energy values measured by the core signal fluctuate for γ-ray interactions with energy deposited in two segments. A regular pattern is observed depending on the hit segment combinations. The core energy shifts deviate 0.03-0.06% from the average energy calibration. The segment-sum energy is reduced with respect to the core energy as a function of the decoupling capacitance and the segment multiplicity. The deviation of the segment-sum energies from multiplicity two events fluctuates within an interval of less than 0.1% depending on the different segment combinations. The energy shifts caused by crosstalk for the core and segment signals are comparable for all three detectors. A linear electronic model of the detector and preamplifier assembly was developed to evaluate the results. The fold-dependent energy shifts of the segment-sum energies are reproduced. The model yields a constant shift in all segments, proportional to the core signal. The measured crosstalk pattern and its intensity variation in the segments agree well with the calculated values. The regular variation observed in the core energies cannot be directly related to crosstalk and may be caused by other effects like electron trapping.

  11. Application Of The Bertlmann-Martin Inequalities To Super Symmetric Partners

    International Nuclear Information System (INIS)

    IGHEZOU, F.Z.; KERRIS, A.T.; MESSAMAH, J.; LOMBARD, R.J.

    2011-01-01

    The purpose of the present study is to discuss some general aspects of the Bertlmann and Martin inequalities (BMI) in the case of the super symmetric partners. The (BMI) have been established by minoring the multipole sum rules according to a method initiated by Bertlmann and Martin. Application to different potentials and generalizations were derived and tested in various papers. We present new concepts of super symmetry in quantum mechanics (SUSYQM) and apply them to two exactly solvable potentials in the one dimensional space. We apply the (BMI) to their super symmetric partners and we examine the degree of saturation of the (BMI)

  12. Norm estimates of complex symmetric operators applied to quantum systems

    International Nuclear Information System (INIS)

    Prodan, Emil; Garcia, Stephan R; Putinar, Mihai

    2006-01-01

    This paper communicates recent results in the theory of complex symmetric operators and shows, through two non-trivial examples, their potential usefulness in the study of Schroedinger operators. In particular, we propose a formula for computing the norm of a compact complex symmetric operator. This observation is applied to two concrete problems related to quantum mechanical systems. First, we give sharp estimates on the exponential decay of the resolvent and the single-particle density matrix for Schroedinger operators with spectral gaps. Second, we provide new ways of evaluating the resolvent norm for Schroedinger operators appearing in the complex scaling theory of resonances

  13. The space-time outside a source of gravitational radiation: the axially symmetric null fluid

    Energy Technology Data Exchange (ETDEWEB)

    Herrera, L. [Universidad Central de Venezuela, Escuela de Fisica, Facultad de Ciencias, Caracas (Venezuela, Bolivarian Republic of); Universidad de Salamanca, Instituto Universitario de Fisica Fundamental y Matematicas, Salamanca (Spain); Di Prisco, A. [Universidad Central de Venezuela, Escuela de Fisica, Facultad de Ciencias, Caracas (Venezuela, Bolivarian Republic of); Ospino, J. [Universidad de Salamanca, Departamento de Matematica Aplicada and Instituto Universitario de Fisica Fundamental y Matematicas, Salamanca (Spain)

    2016-11-15

    We carry out a study of the exterior of an axially and reflection symmetric source of gravitational radiation. The exterior of such a source is filled with a null fluid produced by the dissipative processes inherent to the emission of gravitational radiation, thereby representing a generalization of the Vaidya metric for axially and reflection symmetric space-times. The role of the vorticity, and its relationship with the presence of gravitational radiation is put in evidence. The spherically symmetric case (Vaidya) is, asymptotically, recovered within the context of the 1 + 3 formalism. (orig.)

  14. The hidden symmetries and their algebraic structure of the static axially symmetric SDYM fields

    International Nuclear Information System (INIS)

    Hao Sanru

    1993-01-01

    A new explicit transformation about the static axially symmetric self-dual Yang-Mills (SDYM) fields is presented. The theory has proved that the new transformation is a symmetric one. For the two kinds of the Lie algebraic generators of the Lie group SL (N. R) /SO (N), the corresponding transformations are given. By making use of the Yang-Baxter equality and their square brackets, the loop and conformal algebraic structures of the symmetric transformations for the basic fields have been obtained. All the results obtained can be directly generalized to the other models

  15. Symmetric Stream Cipher using Triple Transposition Key Method and Base64 Algorithm for Security Improvement

    Science.gov (United States)

    Nurdiyanto, Heri; Rahim, Robbi; Wulan, Nur

    2017-12-01

    Symmetric type cryptography algorithm is known many weaknesses in encryption process compared with asymmetric type algorithm, symmetric stream cipher are algorithm that works on XOR process between plaintext and key, to improve the security of symmetric stream cipher algorithm done improvisation by using Triple Transposition Key which developed from Transposition Cipher and also use Base64 algorithm for encryption ending process, and from experiment the ciphertext that produced good enough and very random.

  16. The Lp Spectrum of Locally Symmetric Spaces with Small Fundamental Group

    International Nuclear Information System (INIS)

    Weber, Andreas

    2009-01-01

    We determine the L p spectrum of the Laplace-Beltrami operator on certain complete locally symmetric spaces M whose universal covering X is a symmetric space of non-compact type with rank one. More precisely, we show that the L p spectra of M and X coincide if the fundamental group of M is small and if the injectivity radius of M is bounded away from zero. In the L 2 case, the restriction on the injectivity radius is not needed

  17. Two-parametric PT-symmetric quartic family

    International Nuclear Information System (INIS)

    Eremenko, Alexandre; Gabrielov, Andrei

    2012-01-01

    We describe a parametrization of the real spectral locus of the two-parametric family of PT-symmetric quartic oscillators. For this family, we find a parameter region where all eigenvalues are real, extending the results of Dorey et al (2007 J. Phys. A: Math Theor. 40 R205–83) and Shin (2005 J. Phys. A: Math. Gen. 38 6147–66; 2002 Commun. Math. Phys. 229 543–64). (paper)

  18. Solution High-Energy Burst Assembly (SHEBA) results from subprompt critical experiments with uranyl fluoride fuel

    International Nuclear Information System (INIS)

    Cappiello, C.C.; Butterfield, K.B.; Sanchez, R.G.

    1997-10-01

    The Solution High-Energy Burst Assembly (SHEBA) was originally constructed during 1980 and was designed to be a clean free-field geometry, right-circular, cylindrically symmetric critical assembly employing U(5%)O 2 F 2 solution as fuel. A second version of SHEBA, employing the same fuel but equipped with a fuel pump and shielding pit, was commissioned in 1993. This report includes data and operating experience for the 1993 SHEBA only. Solution-fueled benchmark work focused on the development of experimental measurements of the characterization of SHEBA; a summary of the results are given. A description of the system and the experimental results are given in some detail in the report. Experiments were designed to: (1) study the behavior of nuclear excursions in a low-enrichment solution, (2) evaluate accidental criticality alarm detectors for fuel-processing facilities, (3) provide radiation spectra and dose measurements to benchmark radiation transport calculations on a low-enrichment solution system similar to centrifuge enrichment plants, and (4) provide radiation fields to calibrate personnel dosimetry. 15 refs., 37 figs., 10 tabs

  19. SUSY formalism for the symmetric double well potential

    Indian Academy of Sciences (India)

    Using first- and second-order supersymmetric Darboüx formalism and starting with symmetric double well potential barrier we have obtained a class of exactly solvable potentials subject to moving boundary condition. The eigenstates are also obtained by the same technique.

  20. Time-invariant PT product and phase locking in PT -symmetric lattice models

    Science.gov (United States)

    Joglekar, Yogesh N.; Onanga, Franck Assogba; Harter, Andrew K.

    2018-01-01

    Over the past decade, non-Hermitian, PT -symmetric Hamiltonians have been investigated as candidates for both a fundamental, unitary, quantum theory and open systems with a nonunitary time evolution. In this paper, we investigate the implications of the former approach in the context of the latter. Motivated by the invariance of the PT (inner) product under time evolution, we discuss the dynamics of wave-function phases in a wide range of PT -symmetric lattice models. In particular, we numerically show that, starting with a random initial state, a universal, gain-site location dependent locking between wave-function phases at adjacent sites occurs in the PT -symmetry-broken region. Our results pave the way towards understanding the physically observable implications of time invariants in the nonunitary dynamics produced by PT -symmetric Hamiltonians.

  1. Robotically Assembled Aerospace Structures: Digital Material Assembly using a Gantry-Type Assembler

    Science.gov (United States)

    Trinh, Greenfield; Copplestone, Grace; O'Connor, Molly; Hu, Steven; Nowak, Sebastian; Cheung, Kenneth; Jenett, Benjamin; Cellucci, Daniel

    2017-01-01

    This paper evaluates the development of automated assembly techniques for discrete lattice structures using a multi-axis gantry type CNC machine. These lattices are made of discrete components called "digital materials." We present the development of a specialized end effector that works in conjunction with the CNC machine to assemble these lattices. With this configuration we are able to place voxels at a rate of 1.5 per minute. The scalability of digital material structures due to the incremental modular assembly is one of its key traits and an important metric of interest. We investigate the build times of a 5x5 beam structure on the scale of 1 meter (325 parts), 10 meters (3,250 parts), and 30 meters (9,750 parts). Utilizing the current configuration with a single end effector, performing serial assembly with a globally fixed feed station at the edge of the build volume, the build time increases according to a scaling law of n4, where n is the build scale. Build times can be reduced significantly by integrating feed systems into the gantry itself, resulting in a scaling law of n3. A completely serial assembly process will encounter time limitations as build scale increases. Automated assembly for digital materials can assemble high performance structures from discrete parts, and techniques such as built in feed systems, parallelization, and optimization of the fastening process will yield much higher throughput.

  2. Mass generation for Abelian spin-1 particles via a symmetric tensor

    International Nuclear Information System (INIS)

    Dalmazi, D.; Mendonça, E.L.

    2012-01-01

    In the topologically massive BF model (TMBF) the photon becomes massive via coupling to an antisymmetric tensor, without breaking the U(1) gauge symmetry. There is no need of a Higgs field. The TMBF model is dual to a first-order (in derivatives) formulation of the Maxwell-Proca theory where the antisymmetric field plays the role of an auxiliary field. Since the Maxwell-Proca theory also admits a first-order version which makes use of an auxiliary symmetric tensor, we investigate here a possible generalization of the TMBF model where the photon acquires mass via coupling to a symmetric tensor. We show that it is indeed possible to build up dual models to the Maxwell-Proca theory where the U(1) gauge symmetry is manifest without Higgs field, but after a local field redefinition the vector field eats up the trace of the symmetric tensor and becomes massive. So the explicit U(1) symmetry can be removed unlike the TMBF model.

  3. Axion-photon conversion in space and in low symmetrical dielectric crystals

    International Nuclear Information System (INIS)

    Gorelik, V S

    2016-01-01

    The opportunities of axions detection as the result of axion-photon conversion processes in the space and in low symmetrical dielectric crystals are discussed. In accordance with the modern theory predictions, axions are pseudoscalar vacuum particles having very small (0.001-1.0 meV) rest energy. The possibility of axions conversion into photons and vice-versa processes in vacuum at the presence of outer magnetic field has been analyzed before. Pseudoscalar (axion type) modes are existing in some types of crystals. Polar pseudoscalar lattice and exciton modes in low symmetrical crystals are strongly interacted with axions. In this work, optical excitation of axion-type modes in low symmetrical crystals is proposed for observation of axion - photon conversion processes. Instead of outer magnetic field, the crystalline field of such crystals may be used. The experimental schemes for axion-photon conversion processes observation with recording the secondary emission of luminescence, infrared or Stimulated Raman Scattering in some dielectric crystals are discussed. (paper)

  4. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  5. Fourier inversion on a reductive symmetric space

    NARCIS (Netherlands)

    Ban, E.P. van den

    1999-01-01

    Let X be a semisimple symmetric space. In previous papers, [8] and [9], we have dened an explicit Fourier transform for X and shown that this transform is injective on the space C 1 c (X) ofcompactly supported smooth functions on X. In the present paper, which is a continuation of these papers, we

  6. Baryon symmetric big bang cosmology

    International Nuclear Information System (INIS)

    Stecker, F.W.

    1978-01-01

    It is stated that the framework of baryon symmetric big bang (BSBB) cosmology offers our greatest potential for deducting the evolution of the Universe because its physical laws and processes have the minimum number of arbitrary assumptions about initial conditions in the big-bang. In addition, it offers the possibility of explaining the photon-baryon ratio in the Universe and how galaxies and galaxy clusters are formed. BSBB cosmology also provides the only acceptable explanation at present for the origin of the cosmic γ-ray background radiation. (author)

  7. Symmetric lithium-ion cell based on lithium vanadium fluorophosphate with ionic liquid electrolyte

    International Nuclear Information System (INIS)

    Plashnitsa, Larisa S.; Kobayashi, Eiji; Okada, Shigeto; Yamaki, Jun-ichi

    2011-01-01

    Lithium vanadium fluorophosphate, LiVPO 4 F, was utilized as both cathode and anode for fabrication of a symmetric lithium-ion LiVPO 4 F//LiVPO 4 F cell. The electrochemical evolution of the LiVPO 4 F//LiVPO 4 F cell with the commonly used organic electrolyte LiPF 6 /EC-DMC has shown that this cell works as a secondary battery, but exhibits poor durability at room temperature and absolutely does not work at increased operating temperatures. To improve the performance and safety of this symmetric battery, we substituted a non-flammable ionic liquid (IL) LiBF 4 /EMIBF 4 electrolyte for the organic electrolyte. The symmetric battery using the IL electrolyte was examined galvanostatically at different rates and operating temperatures within the voltage range of 0.01-2.8 V. It was demonstrated that the IL-based symmetric cell worked as a secondary battery with a Coulombic efficiency of 77% at 0.1 mA cm -2 and 25 o C. It was also found that the use of the IL electrolyte instead of the organic one resulted in the general reduction of the first discharge capacity by about 20-25% but provided much more stable behavior and a longer cycle life. Moreover, an increase of the discharge capacity of the IL-based symmetric battery up to 120 mA h g -1 was observed when the operating temperature was increased up to 80 o C at 0.1 mA cm -2 . The obtained electrochemical behavior of both symmetric batteries was confirmed by complex-impedance measurements at different temperatures and cycling states. The thermal stability of LiVPO 4 F with both the IL and organic electrolytes was also examined.

  8. Conservation laws in baroclinic inertial-symmetric instabilities

    Science.gov (United States)

    Grisouard, Nicolas; Fox, Morgan B.; Nijjer, Japinder

    2017-04-01

    Submesoscale oceanic density fronts are structures in geostrophic and hydrostatic balance, but are more prone to instabilities than mesoscale flows. As a consequence, they are believed to play a large role in air-sea exchanges, near-surface turbulence and dissipation of kinetic energy of geostrophically and hydrostatically balanced flows. We will present two-dimensional (x, z) Boussinesq numerical experiments of submesoscale baroclinic fronts on the f-plane. Instabilities of the mixed inertial and symmetric types (the actual name varies across the literature) develop, with the absence of along-front variations prohibiting geostrophic baroclinic instabilities. Two new salient facts emerge. First, contrary to pure inertial and/or pure symmetric instability, the potential energy budget is affected, the mixed instability extracting significant available potential energy from the front and dissipating it locally. Second, in the submesoscale regime, the growth rate of this mixed instability is sufficiently large that significant radiation of near-inertial internal waves occurs. Although energetically small compared to e.g. local dissipation within the front, this process might be a significant source of near-inertial energy in the ocean.

  9. On some homological functors of a Bieberbach group with symmetric point group

    Science.gov (United States)

    Ting, Tan Yee; Idrus, Nor'ashiqin Mohd; Masri, Rohaidah; Ladi, Nor Fadzilah Abdul

    2017-05-01

    Bieberbach groups with symmetric point group are polycyclic. The properties of the groups can be explored by computing their homological functors. In this paper, some homological functors of a Bieberbach group with symmetric point group, such as the Schur multiplier and the G-trivial subgroup of the nonabelian tensor square, are generalized up to finite dimension and are represented in the form of direct product of cyclic groups.

  10. Information Retrieval and Criticality in Parity-Time-Symmetric Systems.

    Science.gov (United States)

    Kawabata, Kohei; Ashida, Yuto; Ueda, Masahito

    2017-11-10

    By investigating information flow between a general parity-time (PT-)symmetric non-Hermitian system and an environment, we find that the complete information retrieval from the environment can be achieved in the PT-unbroken phase, whereas no information can be retrieved in the PT-broken phase. The PT-transition point thus marks the reversible-irreversible criticality of information flow, around which many physical quantities such as the recurrence time and the distinguishability between quantum states exhibit power-law behavior. Moreover, by embedding a PT-symmetric system into a larger Hilbert space so that the entire system obeys unitary dynamics, we reveal that behind the information retrieval lies a hidden entangled partner protected by PT symmetry. Possible experimental situations are also discussed.

  11. Symmetric extension of bipartite quantum states and its use in quantum key distribution with two-way postprocessing

    Energy Technology Data Exchange (ETDEWEB)

    Myhr, Geir Ove

    2010-11-08

    Just like we can divide the set of bipartite quantum states into separable states and entangled states, we can divide it into states with and without a symmetric extension. The states with a symmetric extension - which includes all the separable states - behave classically in many ways, while the states without a symmetric extension - which are all entangled - have the potential to exhibit quantum effects. The set of states with a symmetric extension is closed under local quantum operations assisted by one-way classical communication (1-LOCC) just like the set of separable states is closed under local operations assisted by two-way classical communication (LOCC). Because of this, states with a symmetric extension often play the same role in a one-way communication setting as the separable states play in a two-way communication setting. We show that any state with a symmetric extension can be decomposed into a convex combination of states that have a pure symmetric extension. A necessary condition for a state to have a pure symmetric extension is that the spectra of the local and global density matrices are equal. This condition is also sufficient for two qubits, but not for any larger systems. We present a conjectured necessary and sufficient condition for two-qubit states with a symmetric extension. Proofs are provided for some classes of states: rank-two states, states on the symmetric subspace, Bell-diagonal states and states that are invariant under S x S, where S is a phase gate. We also show how the symmetric extension problem for multi-qubit Bell-diagonal states can be simplified and the simplified problem implemented as a semidefinite program. Quantum key distribution protocols such as the six-state protocol and the BB84 protocol effectively gives Alice and Bob Bell-diagonal states that they measure in the standard basis to obtain a raw key which they may then process further to obtain a secret error-free key. When the raw key has a high error rate, the

  12. Symmetric extension of bipartite quantum states and its use in quantum key distribution with two-way postprocessing

    International Nuclear Information System (INIS)

    Myhr, Geir Ove

    2010-01-01

    Just like we can divide the set of bipartite quantum states into separable states and entangled states, we can divide it into states with and without a symmetric extension. The states with a symmetric extension - which includes all the separable states - behave classically in many ways, while the states without a symmetric extension - which are all entangled - have the potential to exhibit quantum effects. The set of states with a symmetric extension is closed under local quantum operations assisted by one-way classical communication (1-LOCC) just like the set of separable states is closed under local operations assisted by two-way classical communication (LOCC). Because of this, states with a symmetric extension often play the same role in a one-way communication setting as the separable states play in a two-way communication setting. We show that any state with a symmetric extension can be decomposed into a convex combination of states that have a pure symmetric extension. A necessary condition for a state to have a pure symmetric extension is that the spectra of the local and global density matrices are equal. This condition is also sufficient for two qubits, but not for any larger systems. We present a conjectured necessary and sufficient condition for two-qubit states with a symmetric extension. Proofs are provided for some classes of states: rank-two states, states on the symmetric subspace, Bell-diagonal states and states that are invariant under S x S, where S is a phase gate. We also show how the symmetric extension problem for multi-qubit Bell-diagonal states can be simplified and the simplified problem implemented as a semidefinite program. Quantum key distribution protocols such as the six-state protocol and the BB84 protocol effectively gives Alice and Bob Bell-diagonal states that they measure in the standard basis to obtain a raw key which they may then process further to obtain a secret error-free key. When the raw key has a high error rate, the

  13. A differential equation for Lerch's transcendent and associated symmetric operators in Hilbert space

    International Nuclear Information System (INIS)

    Kaplitskii, V M

    2014-01-01

    The function Ψ(x,y,s)=e iy Φ(−e iy ,s,x), where Φ(z,s,v) is Lerch's transcendent, satisfies the following two-dimensional formally self-adjoint second-order hyperbolic differential equation, where s=1/2+iλ. The corresponding differential expression determines a densely defined symmetric operator (the minimal operator) on the Hilbert space L 2 (Π), where Π=(0,1)×(0,2π). We obtain a description of the domains of definition of some symmetric extensions of the minimal operator. We show that formal solutions of the eigenvalue problem for these symmetric extensions are represented by functional series whose structure resembles that of the Fourier series of Ψ(x,y,s). We discuss sufficient conditions for these formal solutions to be eigenfunctions of the resulting symmetric differential operators. We also demonstrate a close relationship between the spectral properties of these symmetric differential operators and the distribution of the zeros of some special analytic functions analogous to the Riemann zeta function. Bibliography: 15 titles

  14. Bacteriophage Assembly

    Directory of Open Access Journals (Sweden)

    Anastasia A. Aksyuk

    2011-02-01

    Full Text Available Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.

  15. Symmetrical waveguide devices fabricated by direct UV writing

    DEFF Research Database (Denmark)

    Færch, Kjartan Ullitz; Svalgaard, Mikael

    2002-01-01

    Power splitters and directional couplers fabricated by direct UV writing in index matched silica-on-silicon samples can suffer from an asymmetrical device performance, even though the UV writing is carried out in a symmetrical fashion. This effect originates from a reduced photosensitivity...

  16. Symmetric Electrode Spanning Narrows the Excitation Patterns of Partial Tripolar Stimuli in Cochlear Implants.

    Science.gov (United States)

    Luo, Xin; Wu, Ching-Chih

    2016-12-01

    In cochlear implants (CIs), standard partial tripolar (pTP) mode reduces current spread by returning a fraction of the current to two adjacent flanking electrodes within the cochlea. Symmetric electrode spanning (i.e., separating both the apical and basal return electrodes from the main electrode by one electrode) has been shown to increase the pitch of pTP stimuli, when the ratio of intracochlear return current was fixed. To explain the pitch increase caused by symmetric spanning in pTP mode, this study measured the electrical potentials of both standard and symmetrically spanned pTP stimuli on a main electrode EL8 in five CI ears using electrical field imaging (EFI). In addition, the spatial profiles of evoked compound action potentials (ECAP) and the psychophysical forward masking (PFM) patterns were also measured for both stimuli. The EFI, ECAP, and PFM patterns of a given stimulus differed in shape details, reflecting the different levels of auditory processing and different ratios of intracochlear return current across the measurement methods. Compared to the standard pTP stimuli, the symmetrically spanned pTP stimuli significantly reduced the areas under the curves of the normalized EFI and PFM patterns, without shifting the pattern peaks and centroids (both around EL8). The more focused excitation patterns with symmetric spanning may have caused the previously reported pitch increase, due to an interaction between pitch and timbre perception. Being able to reduce the spread of excitation, pTP mode symmetric spanning is a promising stimulation strategy that may further increase spectral resolution and frequency selectivity with CIs.

  17. Path integral representation of the symmetric Rosen-Morse potential

    International Nuclear Information System (INIS)

    Duru, I.H.

    1983-09-01

    An integral formula for the Green's function of symmetric Rosen-Morse potential is obtained by solving path integrals. The correctly normalized wave functions and bound state energy spectrum are derived. (author)

  18. Thermal properties of self-gravitating plane-symmetric configuration

    Energy Technology Data Exchange (ETDEWEB)

    Hara, T; Ikeuchi, S [Kyoto Univ. (Japan). Dept. of Physics; Sugimoto, D

    1976-09-01

    As a limiting case of rotating stars, thermal properties of infinite plane-symmetric self-gravitating gas are investigated. Such a configuration is characterized by surface density of the plane instead of stellar mass. In the Kelvin contraction, temperature of the interior decreases, if the surface density is kept constant. If the accretion of matter takes place, or if the angular momenta are transferred outward, the surface density will increase. In this case, the temperature of the interior may increase. When a nuclear burning is ignited, it is thermally unstable in most cases, even when electrons are non-degenerate. This thermal instability is one of the essential differences of the plane-symmetric configuration from the spherical star. Such instabilities are computed for different cases of nuclear fuels. This type of nuclear instability is the same phenomenon as thermal instability of a thin shell burning in a spherical star.

  19. The inverse spatial Laplacian of spherically symmetric spacetimes

    International Nuclear Information System (INIS)

    Fernandes, Karan; Lahiri, Amitabha

    2017-01-01

    We derive the inverse spatial Laplacian for static, spherically symmetric backgrounds by solving Poisson’s equation for a point source. This is different from the electrostatic Green function, which is defined on the four dimensional static spacetime, while the equation we consider is defined on the spatial hypersurface of such spacetimes. This Green function is relevant in the Hamiltonian dynamics of theories defined on spherically symmetric backgrounds, and closed form expressions for the solutions we find are absent in the literature. We derive an expression in terms of elementary functions for the Schwarzschild spacetime, and comment on the relation of this solution with the known Green function of the spacetime Laplacian operator. We also find an expression for the Green function on the static pure de-Sitter space in terms of hypergeometric functions. We conclude with a discussion of the constraints of the electromagnetic field. (paper)

  20. Harmonic maps of the bounded symmetric domains

    International Nuclear Information System (INIS)

    Xin, Y.L.

    1994-06-01

    A shrinking property of harmonic maps into R IV (2) is proved which is used to classify complete spacelike surfaces of the parallel mean curvature in R 4 2 with a reasonable condition on the Gauss image. Liouville-type theorems of harmonic maps from the higher dimensional bounded symmetric domains are also established. (author). 25 refs