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Sample records for automated two-dimensional protein

  1. Extraction of plant proteins for two-dimensional electrophoresis

    OpenAIRE

    Granier, Fabienne

    1988-01-01

    Three different extraction procedures for two-dimensional electrophoresis of plant proteins are compared: (i) extraction of soluble proteins with a nondenaturing Tris-buffer, (ii) denaturing extraction in presence of sodium dodecyl sulfate at elevated temperature allowing the solubilization of membrane proteins in addition to a recovery of soluble proteins, and (iii) a trichloroacetic acid-acetone procedure allowing the direct precipitation of total proteins.

  2. Human muscle proteins: analysis by two-dimensional electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Giometti, C.S.; Danon, M.J.; Anderson, N.G.

    1983-09-01

    Proteins from single frozen sections of human muscle were separated by two-dimensional gel electrophoresis and detected by fluorography or Coomassie Blue staining. The major proteins were identical in different normal muscles obtained from either sex at different ages, and in Duchenne and myotonic dystrophy samples. Congenital myopathy denervation atrophy, polymyositis, and Becker's muscular dystrophy samples, however, showed abnormal myosin light chain compositions, some with a decrease of fast-fiber myosin light chains and others with a decrease of slow-fiber light chains. These protein alterations did not correlate with any specific disease, and may be cause by generalized muscle-fiber damage.

  3. Procedures for two-dimensional electrophoresis of proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tollaksen, S.L.; Giometti, C.S.

    1996-10-01

    High-resolution two-dimensional gel electrophoresis (2DE) of proteins, using isoelectric focusing in the first dimension and sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) in the second, was first described in 1975. In the 20 years since those publications, numerous modifications of the original method have evolved. The ISO-DALT system of 2DE is a high-throughput approach that has stood the test of time. The problem of casting many isoelectric focusing gels and SDS-PAGE slab gels (up to 20) in a reproducible manner has been solved by the use of the techniques and equipment described in this manual. The ISO-DALT system of two-dimensional gel electrophoresis originated in the late 1970s and has been modified many times to improve its high-resolution, high-throughput capabilities. This report provides the detailed procedures used with the current ISO-DALT system to prepare, run, stain, and photograph two-dimensional gels for protein analysis.

  4. Analysis of soybean embryonic axis proteins by two-dimensional gel electrophoresis and mass spectrometry

    Science.gov (United States)

    A proteomic approach based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) for protein separation and subsequent mass spectrometry (MS) for protein identification was applied to establish a proteomic reference map for the soybean embryonic axis. Proteins were extracted from dissecte...

  5. Changes in muscle protein composition induced by disuse atrophy - Analysis by two-dimensional electrophoresis

    Science.gov (United States)

    Ellis, S.; Giometti, C. S.; Riley, D. A.

    1985-01-01

    Using 320 g rats, a two-dimensional electrophoretic analysis of muscle proteins in the soleus and EDL muscles from hindlimbs maintained load-free for 10 days is performed. Statistical analysis of the two-dimensional patterns of control and suspended groups reveals more protein alteration in the soleus muscle, with 25 protein differences, than the EDL muscle, with 9 protein differences, as a result of atrophy. Most of the soleus differences reside in minor components. It is suggested that the EDL may also show alteration in its two-dimensional protein map, even though no significant atrophy occurred in muscle wet weight. It is cautioned that strict interpretation of data must take into account possible endocrine perturbations.

  6. Automated multivariate analysis of comprehensive two-dimensional gas chromatograms of petroleum

    DEFF Research Database (Denmark)

    Skov, Søren Furbo

    them. Comprehensive two-dimensional gas chromatography (GCGC) is a method for analyzing the volatile parts of a sample. It can separate hundreds or thousands of compounds based on their boiling point, polarity and polarizability. This makes it ideally suited for petroleum analysis. The number...

  7. Two-dimensional Electrophoresis Analysis of Differential Protein Expression in Squamous Carcinoma of the Cervix

    Institute of Scientific and Technical Information of China (English)

    ZHU Xue-qiong; WU Jie-li; YU Li-rong; LIN Yi; L(U) Jie-qiang; ZOU Shuang-wei; HU Yue

    2008-01-01

    Objective:To establish and optimize the two-dimensional gel electrophoresis(2-DE)maps of squamous carcinoma of the cervix and to study the protein difference between squamous carcinoma of the cervix(SCC)and normal cervical tissue.Methods:Using Two-dimensional gel electrophoresis followed by computer-assisted image analysis,the differential proteins between squamous carcinoma of the cervical tissue and normal cervical tissue were compared.Then using matrix-assisted laser desorption/ionization-time of flight mass spectrometry,the differential proteins were identified.Results:The well-resolved and reproducible two-dimensional gel electrophoresis patterns of squamous carcinoma of the cervix tissue and normal cervical tissue were obtained.After silver staining.the average matching ratio of squamous carcinoma of the cervix was 86.1%.There was a good reproducibility of spot position in 2-DE map,with average deviation in IEF direction of 0.95±0.13 mm,while in SDS-PAGE direction it was 1.20±0.18 mm.Ten protein spots were identified by mass spectrometry,some of which were involved in cell proliferation,cell apoptosis,intracellular enzymes,structural proteins,cycle regulation,and tumor occurrence.Conclusion:The differentially expressed proteins provide a fundamental basis for further study of human squamous carcinoma of the cervix and screening of its specific markers.

  8. Automated detection of coherent Lagrangian vortices in two-dimensional unsteady flows

    CERN Document Server

    Karrasch, Daniel; Haller, George

    2014-01-01

    Coherent boundaries of Lagrangian vortices in fluid flows have recently been identified as closed orbits of line fields associated with the Cauchy-Green strain tensor. Here we develop a fully automated procedure for the detection of such closed orbits in large-scale velocity data sets. We illustrate the power of our method on ocean surface velocities derived from satellite altimetry.

  9. Two-dimensional crystallization of integral membrane proteins for electron crystallography.

    Science.gov (United States)

    Stokes, David L; Rice, William J; Hu, Minghui; Kim, Changki; Ubarretxena-Belandia, Iban

    2010-01-01

    Although membrane proteins make up 30% of the proteome and are a common target for therapeutic drugs, determination of their atomic structure remains a technical challenge. Electron crystallography represents an alternative to the conventional methods of X-ray diffraction and NMR and relies on the formation of two-dimensional crystals. These crystals are produced by reconstituting purified, detergent-solubilized membrane proteins back into the native environment of a lipid bilayer. This chapter reviews methods for producing two-dimensional crystals and for screening them by negative stain electron microscopy. In addition, we show examples of the different morphologies that are commonly obtained and describe basic image analysis procedures that can be used to evaluate their promise for structure determination by cryoelectron microscopy.

  10. Two-dimensional Electrophoresis Analysis of Proteins Extracted from Alexandrium sp. LC3

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Two-dimensional electrophoresis(2-DE) of protein extracted and purified from Alexandrium sp. LC3 was conducted. In the SDS-PAGE study, the relative molecular weights of the proteins were mainly in the range of 14 kDa-31 kDa and 43 kDa-66 kDa, and more proteins were detected between 14 kDa and 31 kDa. With the improved protein preparation, the two-dimensional electrophoresis patterns indicated that the relative molecular weights of the proteins were between 14 kDa and 100 kDa, and most of them ranged from 14 kDa to 31 kDa. This was consistent with the result of the SDS-PAGE analysis. The isoelectric points were found to lie between 3.0 and 8.0, and most of them were in the range of 3.0-6.0. Better separation effect was acquired with pre-prepared immobilized gradient (IPG) strip (pH 3-5.6), and about 320 protein spots could be visualized on the 2-DE map by staining. Within pH 3-10 and pH 3-5.6 strips, the protein samples of Alexandriun sp. LC3 could be separated well.

  11. Protein Conformational Change Based on a Two-dimensional Generalized Langevin Equation

    Institute of Scientific and Technical Information of China (English)

    Ying-xi Wang; Shuang-mu Linguang; Nan-rong Zhao; Yi-jing Yan

    2011-01-01

    A two-dimensional generalized Langevin equation is proposed to describe the protein conformational change,compatible to the electron transfer process governed by atomic packing density model.We assume a fractional Gaussian noise and a white noise through bond and through space coordinates respectively,and introduce the coupling effect coming from both fluctuations and equilibrium variances.The general expressions for autocorrelation functions of distance fluctuation and fluorescence lifetime variation are derived,based on which the exact conformational change dynamics can be evaluated with the aid of numerical Laplace inversion technique.We explicitly elaborate the short time and long time approximations.The relationship between the two-dimensional description and the one-dimensional theory is also discussed.

  12. Protein profile analysis of Malaysian snake venoms by two-dimensional gel electrophoresis

    Directory of Open Access Journals (Sweden)

    J Vejayan

    2010-01-01

    Full Text Available Snake venoms comprise a highly complex mixture of proteins, which requires for their characterization the use of versatile two-dimensional electrophoresis techniques. In the present study, venoms obtained from eight snakes (Ophiophagus hannah, Naja kaouthia, Naja sumatrana, Bungarus fasciatus, Trimeresurus sumatranus, Tropidolaemus wagleri, Enhydrina schistosa and Calloselasma rhodostoma commonly found in Malaysia were separated based on two independent properties, isoelectric point (pI and molecular weight (MW. Many differences in snake venoms at the inter-family, inter-subfamily, inter-genus and inter-species levels were revealed. Notably, proteins from individuals of the Viperidae family - Trimeresurus sumatranus, Tropidolaemus wagleri and Calloselasma rhodostoma - were found to be numerous and scattered by the two-dimensional gel electrophoresis (2DE specifically in regions between 37 and 100 kDa compared to the Elapidae venom proteins. The latter were clustered at the basic and lower molecular mass region (less than 20 kDa. Trains of spots were commonly observed, indicating that these proteins may be derived from post-translational modifications. Ophiophagus hannah (Elapidae revealed a great amount of protein spots in the higher molecular mass range when compared to Enhydrina schistosa, Naja kaouthia, Naja sumatrana and Bungarus fasciatus. Overall 2DE showed large differences in the venom profile of each species, which might be employed as an ancillary tool to the identification of venomous snake species.

  13. Application of Two-Dimensional Electrophoresis in the Research of Retinal Proteins of Diabetic Rat

    Institute of Scientific and Technical Information of China (English)

    Shangqing Liu; Yanyan Zhang; Xianyong Xie; Weiming Hu; Rong Cai; Jian Kang; Huijun Yang

    2007-01-01

    Diabetes mellitus (DM) is a chronic disease which is associated with numerous serious health complications such as diabetic retinopathy, and is the leading cause of new cases of blindness in adults at the age of 20-74 years old. The aim of the study was to establish and optimize a two-dimensional polyacrylamide gel electrophoresis (2-DE) technique for retina proteomics to improve the resolution and reproducibility, and to observe the proteomic changes of retinal tissues in diabetic and normal rats. Proteins were extracted from retinal tissues of normal and 8 weeks diabetic SD rats and used in two-dimensional electrophoresis. Various conditions of retina proteomic 2-DE were adjusted, optimized and protein spots of differential expression were obtained through analysis of 2-DE images with PDQuest software. By choosing appropriate sample amount, using pre-cast IPG dry strips (pH 5-8)and casting 12% equal gel, satisfactory 2-DE images of retina were obtained and a steady 2-DE technique was established. In this way, we found 36 spots in 2-DE gel of diabetic retinas that exhibited statistically significant variations, including up-regulation of 5 proteins in diabetic rat retinas, down-regulation of 23, and disappearance of 8, in comparison with normal tissues. The differences of protein expression were observed in retinas between diabetic and normal rats. Our established 2-DE technique of retina proteins could be effectively applied in proteomics of retina diseases.

  14. [Total protein analysis by two-dimensional electrophoresis in cysticerci of Taenia solium and Taenia asiatica].

    Science.gov (United States)

    Fang, Wen; Xiao, Liang-Liang; Bao, Huai-En; Mu, Rong

    2011-06-01

    Two 20-day-old three-way crossed hybrid pigs were infected with 80000 Taenia solium or T. asiatica eggs, respectively. Immature cysticerci of the two species in liver were collected at 40 days after infection. The total proteins were separated by two-dimensional electrophoresis, and differentially expressed proteins were analyzed by Image-Master 2D Platinum 6.0 software. The results showed that there were (236 +/- 12) and (231 +/- 14) protein spots in 2D electrophoresis gel images of T. solium and T. asiatica, respectively, with 3 proteins up-regulated and 7 proteins down-regulated in T. solium cysticercus by 2-fold or more compared with those in T. asiatica cysticercus.

  15. Proteomic Profiling Of Two-Dimensional Gel Electrophoresis Protein Expression Data

    Science.gov (United States)

    Ahmad, Norhaiza; Zhang, J.; Brown, P. J.; James, D. C.; Birch, J. R.; Racher, A. J.; Smales, C. M.

    2008-01-01

    We have undertaken two-dimensional gel electrophoresis (2-DE) proteomic profiling on a series of cell lines with different recombinant antibody production rates. Due to the nature of 2-DE proteomic investigations there will always be `process variability' factors in any data set collected in this way. Some of this variation will arise during sample preparation, gel running and staining, while further variation will arise from the gel analysis procedure. Therefore, in order to identify all significant changes in protein expression between biological samples when analysed by 2-DE, the system precision or `error', and how this correlates to protein abundance, must be known. Only then can the system be considered robust and investigators accurately and confidently report all observable statistically significant changes in protein expression. We introduce an expression variability test to identify protein spots whose expression correlates with increased antibody production. The results have highlighted a small number of candidate proteins for further investigation.

  16. Femtosecond X-ray Diffraction From Two-Dimensional Protein Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Frank, Matthias [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Carlson, David B. [Univ. of California, Davis, CA (United States); Hunter, Mark [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Williams, Garth J. [SLAC National Accelerator Lab., Menlo Park, CA (United States). Linac Coherent Light Source (LCLS); Messerschmidt, Marc [Univ. of California, Davis, CA (United States); Zatsepin, Nadia A. [Arizona State Univ., Tempe, AZ (United States); Barty, Anton [Univ. of Hamburg (Germany); Benner, Henry [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Chu, Kaiqin [Center for Biophotonics, Sacramento, CA (United States); Graf, Alexander [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Hau-Riege, Stefan [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Kirian, Rick [Univ. of Hamburg (Germany); Padeste, Celestino [Paul Scherrer Inst., Villigen (Switzerland); Pardini, Tommaso [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pedrini, Bill [Paul Scherrer Inst., Villigen (Switzerland); Segelke, Brent [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Seibert, M. M. [Univ. of California, Davis, CA (United States); Spence, John C. [Arizona State Univ., Tempe, AZ (United States); Tsai, Ching-Ju [Paul Scherrer Inst., Villigen (Switzerland); Lane, Steve M. [Center for Biophotonics, Sacramento, CA (United States); Li, Xiao-Dan [Paul Scherrer Inst., Villigen (Switzerland); Schertler, Gebhard [Paul Scherrer Inst., Villigen (Switzerland); Boutet, Sebastien [Univ. of California, Davis, CA (United States); Coleman, Matthew A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Evans, James E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Univ. of California, Davis, CA (United States)

    2014-02-28

    Here we present femtosecond x-ray diffraction patterns from two-dimensional (2-D) protein crystals using an x-ray free electron laser (XFEL). To date it has not been possible to acquire x-ray diffraction from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permits a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy methodology at the Linac Coherent Light Source, we observed Bragg diffraction to better than 8.5 Å resolution for two different 2-D protein crystal samples that were maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  17. Comparison of Three Methods of Protein Extraction from Dermatophagoides Pteronyssinus for Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Jin-lu Sun; Hong-yu Zhang; Zhi-yi Guo; Wan-tao Ying; Xiao-hong Qian; Jing-lan Wang

    2009-01-01

    Objective To explore an effective method of Dermatophagoides pteronyssinus protein extraction suitable for two-dimensional electrophoresis (2-DE) analysis. Methods The extracts of Dermatophagoides pteronyssinus were prepared with Coca's solution, lysis buffer of 2-DE, and Trizol reagent, respectively. Bicinchoninic acid (BCA) assay was used to determine the total protein concentration of the samples. The efficiency of different protein extraction methods were evaluated with 2-DE analysis. Results The concentrations of extracted protein by methods of Coca's solution, lysis buffer, and Trizol reagent were 0.63 g/L, 0.90 g/L, and 0.80 g/L, respectively. The 2-DE analysis results showed that some protein spots in low molecular weight (LMW) range could be detected with the Coca's solution method. With the lysis buffer of 2-DE method, more protein spots in LMW range could be detected, while the medium molecular weight (MMW) protein spots were absent. Several MMW protein spots (174-178 kD and 133 kD) and more LMW protein spots were detected with Trizol reagent method. Conclusions Among Coca's solution, lysis buffer of 2-DE, and Trizol reagent, the concentration of extracted protein of Dermatophagoides pteronyssinus by lysis buffer of 2-DE is the highest. However, most protein components of Dermatophagoides pteronyssinus purified mite bodies can be extracted by Trizol reagent, which may generally reflect the whole profile of Dermatophagoides pteronyssinus allergens.

  18. Consistent two-dimensional visualization of protein-ligand complex series

    Directory of Open Access Journals (Sweden)

    Stierand Katrin

    2011-06-01

    Full Text Available Abstract Background The comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods. Results We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. Based on the structural three-dimensional input information, a global two-dimensional layout for all residues of the complex ensemble is computed. The algorithm incorporates the three-dimensional adjacencies of the active site residues in order to find an universally valid circular arrangement of the residues around the ligand. Subsequent to a two-dimensional ligand superimposition step, a global placement for each residue is derived from the set of already placed ligands. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Application examples document an improved legibility compared to series of diagrams whose layouts are calculated independently from each other. Conclusions The presented method extends the field of complex series visualizations. A series of molecules binding to the same protein active site is drawn in a graphically consistent way. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series.

  19. Proteins of human semen. I. Two-dimensional mapping of human seminal fluid.

    Science.gov (United States)

    Edwards, J J; Tollaksen, S L; Anderson, N G

    1981-08-01

    The proteins in human seminal plasma were mapped by high-resolution two-dimensional electrophoresis (ISO-DALT and BASO-DALT systems). When analyzed under dissociating conditions, samples from normal fertile males revealed a pattern of over 200 proteins, ranging in mass from 10 000 to 100 000 daltons. Comparison of the mapped proteins from these males and those who had undergone vasectomy allowed us to identify one series of glycoproteins as missing from the semen from vasectomized individuals. Glycoproteins isolated by affinity chromatography with use of concanavalin A were also mapped. Some of the protein spots were identified either by co-electrophoresis with purified proteins or by the electrophoretic transfer of proteins to nitrocellulose sheets and subsequent detection by immunological procedures. The proteins identified include a number of serum proteins as well as prostatic acid phosphatase and creatine kinase. Proteolytic events shown to occur during the liquefaction of semen that occurs early after collection indicate the importance of carefully controlled collection and preparation methods for clinical evaluation of seminal plasma. Ethylenediaminetetraacetic acid and phenylmethylsulfonyl fluoride inhibit this proteolysis. PMID:7273394

  20. Femtosecond X-ray diffraction from two-dimensional protein crystals.

    Science.gov (United States)

    Frank, Matthias; Carlson, David B; Hunter, Mark S; Williams, Garth J; Messerschmidt, Marc; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Chu, Kaiqin; Graf, Alexander T; Hau-Riege, Stefan P; Kirian, Richard A; Padeste, Celestino; Pardini, Tommaso; Pedrini, Bill; Segelke, Brent; Seibert, M Marvin; Spence, John C H; Tsai, Ching-Ju; Lane, Stephen M; Li, Xiao-Dan; Schertler, Gebhard; Boutet, Sebastien; Coleman, Matthew; Evans, James E

    2014-03-01

    X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals. PMID:25075325

  1. Imaging Plate, a two dimensional detector, in modern protein crystallography using synchrotron radiation

    International Nuclear Information System (INIS)

    Proteins have two major structural aspects: one is static structure and the other is dynamic structure which is related with their reactions. Research on their dynamic structure started only recently as strong white X-ray became available from synchrotron radiation. Synchrotron radiation is a dream come true for protein crystallography. Theoretically, stronger rays permit the analysis of smaller structural changes. Synchrotron radiation has many good features which are useful for data collection by protein crystallography. Imaging Plate, a film-type large two-dimensional detector developed by Fuji Photo Film Co., Ltd., is very suitable for structural analysis of proteins by means of synchrotron radiation. A Weissenberg camera for macromolecules, which was developed by the author, has many advantages for data collection when used in combination with Imaging Plate. Some study results obtained by using them are outlined briefly focusing on the structure of ω-amino acid. Results of trigger experiments using a time resolved Laue camera and laser are also described. (N.K.)

  2. Femtosecond X-ray diffraction from two-dimensional protein crystals

    Directory of Open Access Journals (Sweden)

    Matthias Frank

    2014-03-01

    Full Text Available X-ray diffraction patterns from two-dimensional (2-D protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

  3. Optimization of Protein Extraction and Two-Dimensional Electrophoresis Protocols for Oil Palm Leaf.

    Science.gov (United States)

    Daim, Leona Daniela Jeffery; Ooi, Tony Eng Keong; Yusof, Hirzun Mohd; Majid, Nazia Abdul; Karsani, Saiful Anuar Bin

    2015-08-01

    Oil palm (Elaeis guineensis) is an important economic crop cultivated for its nutritional palm oil. A significant amount of effort has been undertaken to understand oil palm growth and physiology at the molecular level, particularly in genomics and transcriptomics. Recently, proteomics studies have begun to garner interest. However, this effort is impeded by technical challenges. Plant sample preparation for proteomics analysis is plagued with technical challenges due to the presence of polysaccharides, secondary metabolites and other interfering compounds. Although protein extraction methods for plant tissues exist, none work universally on all sample types. Therefore, this study aims to compare and optimize different protein extraction protocols for use with two-dimensional gel electrophoresis of young and mature leaves from the oil palm. Four protein extraction methods were evaluated: phenol-guanidine isothiocyanate, trichloroacetic acid-acetone precipitation, sucrose and trichloroacetic acid-acetone-phenol. Of these four protocols, the trichloroacetic acid-acetone-phenol method was found to give the highest resolution and most reproducible gel. The results from this study can be used in sample preparations of oil palm tissue for proteomics work.

  4. Characterization and identification of early proteins in Chlamydia trachomatis serovar L2 by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Lundemose, AG; Birkelund, Svend; Larsen, PM;

    1990-01-01

    The synthesis of early proteins from Chlamydia trachomatis serovar L2 was analyzed by two-dimensional gel electrophoresis. By pulse-label experiments, the synthesis of seven proteins was observed at 2 to 8 h postinfection before the major outer membrane protein was detected at 8 to 10 h after...

  5. Comparison of ethanol-soluble proteins from different rye (Secale cereale) varieties by two-dimensional electrophoresis

    DEFF Research Database (Denmark)

    Radzikowski, Louise; Nesic, Ljiljana; Hansen, H.B.;

    2002-01-01

    The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Ronhave, Denmark, were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2-D electrophor......The major storage proteins from six rye varieties, grown under the same conditions in 1997 and 1998 in Ronhave, Denmark, were analyzed by two-dimensional (2-D) polyacrylamide gel electrophoresis. The proteins were extracted from ground rye kernels with 70% ethanol and separated by 2-D...

  6. Protein composition of wheat gluten polymer fractions determined by quantitative two-dimensional gel electrophoresis and tandem mass spectrometry

    Science.gov (United States)

    Flour proteins from the US bread wheat Butte 86 were extracted in 0.5% SDS using a two-step procedure with and without sonication and further separated by size exclusion chromatography into monomeric and polymeric fractions. Proteins in each fraction were analyzed by quantitative two-dimensional gel...

  7. Identification of mitochondrial proteins and some of their precursors in two-dimensional electrophoretic maps of human cells.

    OpenAIRE

    Anderson, L.

    1981-01-01

    A set of at least 30 proteins disappears from the two-dimensional electrophoretic pattern of human lymphoid cells treated with various antimitochondrial agents. This set is similar to the set of proteins found in isolated mitochondria (except for the presence of action in the latter group), indicating that the inhibitor effect stops production of a majority of mature mitochondrial proteins. Several proteins having the characteristics of precursors to the major cytoplasmically synthesized mito...

  8. Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals

    Science.gov (United States)

    Suzuki, Yuta; Cardone, Giovanni; Restrepo, David; Zavattieri, Pablo D.; Baker, Timothy S.; Tezcan, F. Akif

    2016-05-01

    Two-dimensional (2D) crystalline materials possess unique structural, mechanical and electronic properties that make them highly attractive in many applications. Although there have been advances in preparing 2D materials that consist of one or a few atomic or molecular layers, bottom-up assembly of 2D crystalline materials remains a challenge and an active area of development. More challenging is the design of dynamic 2D lattices that can undergo large-scale motions without loss of crystallinity. Dynamic behaviour in porous three-dimensional (3D) crystalline solids has been exploited for stimuli-responsive functions and adaptive behaviour. As in such 3D materials, integrating flexibility and adaptiveness into crystalline 2D lattices would greatly broaden the functional scope of 2D materials. Here we report the self-assembly of unsupported, 2D protein lattices with precise spatial arrangements and patterns using a readily accessible design strategy. Three single- or double-point mutants of the C4-symmetric protein RhuA were designed to assemble via different modes of intermolecular interactions (single-disulfide, double-disulfide and metal-coordination) into crystalline 2D arrays. Owing to the flexibility of the single-disulfide interactions, the lattices of one of the variants (C98RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. C98RhuA lattices display a Poisson’s ratio of ‑1—the lowest thermodynamically possible value for an isotropic material—making them auxetic.

  9. Analysis of total proteins in pollen of Humulus scandens Lour in Wuhan Region of China by two-dimensional electrophoresis

    Institute of Scientific and Technical Information of China (English)

    LI Dongdong; HE Shaoheng

    2007-01-01

    Total proteins in the pollen of Humulus scandens Lour,one of the most popular aeroallergens in China,were analyzed by two-dimensional electrophoresis in the current study.The proteins were extracted by Trichloracetic acid (TCA) method,and then separated by isoelectric focusing as the first dimension and SDS-PAGE as the second dimension.The spots of proteins were visualized by staining with Coomassie Brilliant Blue.After analysis with software (ImageMaster 2D),122 different proteins were detected;isoelectric point (pI),Molecular weight (MW) and relativevolume of each protein in the pollen were also discovered.This is the first high-resolution,two-dimensional protein map of the pollen ofHumulus scandens Lour in China.Our finding has built a solid foundation for identification,characterization,gene cloning and standardization of allergenic proteins in the pollen ofHumulus scandens Lour for further studies.

  10. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Jessen, Flemming; Wulff, Tune

    2015-01-01

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS...

  11. Identification of two-dimensional electrophoresis-separated proteins in human hepatoma cell by electrospray ion trap mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    As one of the most important analytical methods in proteome research, mass spectrometry was utilized to identify proteins separated by two-dimensional electrophoresis in the human hepatoma cell line BEL-7404. The protein spots were excised from the gel, followed by in-gel digestion, and the peptide mappings were analyzed by liquid chromatography electrospray ion trap mass spectrometer. Nine proteins were identified via database searching, according to the molecular weights and amino acid sequences of peptides, among which two proteins have not been identified in the other liver-cell database. The sequence coverage was 21%-72%. Furthermore, the relationship between the expressed proteins and the liver carcinoma was discussed.

  12. 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source.

    Science.gov (United States)

    Pedrini, Bill; Tsai, Ching-Ju; Capitani, Guido; Padeste, Celestino; Hunter, Mark S; Zatsepin, Nadia A; Barty, Anton; Benner, W Henry; Boutet, Sébastien; Feld, Geoffrey K; Hau-Riege, Stefan P; Kirian, Richard A; Kupitz, Christopher; Messerschmitt, Marc; Ogren, John I; Pardini, Tommaso; Segelke, Brent; Williams, Garth J; Spence, John C H; Abela, Rafael; Coleman, Matthew; Evans, James E; Schertler, Gebhard F X; Frank, Matthias; Li, Xiao-Dan

    2014-07-17

    Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump-probe experiments at subpicosecond time resolution. PMID:24914166

  13. Efficient extraction of proteins from recalcitrant plant tissue for subsequent analysis by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Parkhey, Suruchi; Chandrakar, Vibhuti; Naithani, S C; Keshavkant, S

    2015-10-01

    Protein extraction for two-dimensional electrophoresis from tissues of recalcitrant species is quite problematic and challenging due to the low protein content and high abundance of contaminants. Proteomics in Shorea robusta is scarcely conducted due to the lack of a suitable protein preparation procedure. To establish an effective protein extraction protocol suitable for two-dimensional electrophoresis in Shorea robusta, four procedures (borate buffer/trichloroacetic acid extraction, organic solvent/trichloroacetic acid precipitation, sucrose/Tris/phenol, and organic solvent/phenol/sodium dodecyl sulfate) were evaluated. Following these, proteins were isolated from mature leaves and were analyzed for proteomics, and also for potential contaminants, widely reported to hinder proteomics. The borate buffer/trichloroacetic acid extraction had the lowest protein yield and did not result in any banding even in one-dimensional electrophoresis. In contrast, organic solvent/phenol/sodium dodecyl sulfate extraction allowed the highest protein yield. Moreover, during proteomics, organic solvent/phenol/sodium dodecyl sulfate extracted protein resolved the maximum number (144) of spots. Further, when proteins were evaluated for contaminants, significant (77-95%) reductions in the nucleic acids, phenol, and sugars were discernible with refinement in extraction procedure. Accumulated data suggested that the organic solvent/phenol/sodium dodecyl sulfate extraction was the most effective protocol for protein isolation for proteomics of Shorea robusta and can be used for plants that have a similar set of contaminants. PMID:26257211

  14. Two-dimensional electrophoretogram of acute brain injury-associated proteins Comparison between Injured and normal cerebral cortex

    Institute of Scientific and Technical Information of China (English)

    Xuejun Li; Xianrui Yuan; Cui Li; Zefeng Peng; Dun Yuan

    2008-01-01

    BACKGROUND:To this date,specific molecular markers for early diagnosis and prognosis monitoring ofcraniocerebral injury in clinical medicine do not exist.Therefore,differential detection of specific proteinsmight play an important role in diagnosis and treatment of this type of brain injury.OBJECTIVE:To compare differential cerebral cortical protein expression of craniocerebral injury patientsand normal subjects through the use of proteomics.DESIGN:Contrast observation.SETTING:Department of Neurosurgery,Xiangya Hospital of Central South University.PARTICIPANTS:Ten patients(6 males and 4 females,20-58 years old),with severe craniocerebral injury,were selected at the Department of Neurosurgery,Xiangya Hospital of Central South University,from June2004 to December 2006.All patients were diagnosed with CT test and Glasgow test(scores <8).Surgery was performed 4-12 hours after craniocerebral injury,and injured cortical tissues of the frontal and temporal lobes were resected for sampling.At the same time,control cortical tissues were collected from frontal and temporal lobes of 2 epileptic patients who underwent hippocampus-nucleus amygdala resection,and 2 lateral ventricular tumor patients who underwent tumor resection.The participants and their relatives provided confirmed consent,and this study received confirmed consent from the local ethics committee. METHODS:Ten samples from injured patients and 4 normal samples were compared through the use of proteomics.Total protein was separated by using two-dimensional electrophoresis with immobilized pH gradients,and the differential protein expressions were compared using image analysis after blue-sliver staining. Differential protein spot expressions were analyzed with a matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI/TOF MS) and electrospray ionization-quadrupole time of flight mass spectrometry(ESI-Qq TOF MS).MAIN OUTCOME MEASURES: ①Two-dimensional electrophoresis of protein from

  15. Molecular phylogeny of the hominoid primates as indicated by two-dimensional protein electrophoresis

    International Nuclear Information System (INIS)

    A molecular phylogeny for the hominoid primates was constructed by using genetic distances from a survey of 383 radiolabeled fibroblast polypeptides resolved by two-dimensional electrophoresis (2DE). An internally consistent matrix of Nei genetic distances was generated on the basis of variants in electrophoretic position. The derived phylogenetic tree indicated a branching sequence, from oldest to most recent, of cercopithecoids (Macaca fascicularis), gibbon-siamang, orangutan, gorilla, and human-chimpanzee. A cladistic analysis of 240 electrophoretic characters that varied between ape species produced an identical tree. Genetic distance measures obtained by 2DE are largely consistent with those generated by other molecular procedures. In addition, the 2DE data set appears to resolve the human-chimpanzee-gorilla trichotomy in favor of a more recent association of chimpanzees and humans

  16. Separation and identification of Musa acuminate Colla (banana) leaf proteins by two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Lu, Y; Qi, Y X; Zhang, H; Zhang, H Q; Pu, J J; Xie, Y X

    2013-12-19

    To establish a proteomic reference map of Musa acuminate Colla (banana) leaf, we separated and identified leaf proteins using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Tryptic digests of 44 spots were subjected to peptide mass fingerprinting (PMF) by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS. Three spots that were not identified by MALDI-TOF MS analysis were identified by searching against the NCBInr, SwissProt, and expressed sequence tag (EST) databases. We identified 41 unique proteins. The majority of the identified leaf proteins were found to be involved in energy metabolism. The results indicate that 2D-PAGE is a sensitive and powerful technique for the separation and identification of Musa leaf proteins. A summary of the identified proteins and their putative functions is discussed.

  17. Characterization of royal jelly proteins in both Africanized and European honeybees (Apis mellifera) by two-dimensional gel electrophoresis.

    Science.gov (United States)

    Sano, Osamu; Kunikata, Toshio; Kohno, Keizo; Iwaki, Kanso; Ikeda, Masao; Kurimoto, Masashi

    2004-01-14

    In this study, the proteins contained in royal jelly (RJ) produced by Africanized honeybees and European honeybees (Apis mellifera) haven been analyzed in detail and compared using two-dimensional gel electrophoresis, and the N-terminal amino acid sequence of each spot has been determined. Most spots were assigned to major royal jelly proteins (MRJPs). Remarkable differences were found in the heterogeneity of the MRJPs, in particular MRJP3, in terms of molecular weights and isoelectric points between the two species of RJ. Furthermore, during the determination of the N-terminal amino acid sequence of each spot, for the first time, MRJP4 protein has been identified, the existence of which had been only implied by cloning of its cDNA sequence. The presence of heterogeneous bands of glucose oxidase was also identified. Thus, the results suggest that two-dimensional gel electrophoresis provides a suitable method for the qualitative analysis of the proteins contained in RJ derived from different honeybee species. PMID:14709007

  18. Proteome analysis of barley seeds: Identification of major proteins from two-dimensional gels (pl 4-7)

    DEFF Research Database (Denmark)

    Østergaard, O.; Finnie, Christine; Laugesen, S.;

    2004-01-01

    Germination of monocotyledonous plants involves activation and de novo synthesis of enzymes that degrade cell walls and starch and mobilize stored endosperm reserves for embryo growth. Two-dimensional (2-D) gel electrophoresis and mass spectrometry were applied to identify major water-soluble pro......Germination of monocotyledonous plants involves activation and de novo synthesis of enzymes that degrade cell walls and starch and mobilize stored endosperm reserves for embryo growth. Two-dimensional (2-D) gel electrophoresis and mass spectrometry were applied to identify major water......-soluble proteins in extracts of mature barley (Hordeum vulgare) seeds and to follow their fate during germination. About 1200 and 600 spots of p/ 4-7 were detected on 2-D gels by silver staining and colloidal Coomassie Brilliant Blue staining, respectively. About 300 spots were selected for in-gel digestion...... followed by matrix-assisted laser desorption/ionization-mass spectrometry-peptide map fingerprint analysis. Database searches using measured peptide masses resulted in 198 identifications of 103 proteins in 177 spots. These include housekeeping enzymes, chaperones, defence proteins (including enzyme...

  19. Mapping and identification of interferon gamma-regulated HeLa cell proteins separated by immobilized pH gradient two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P;

    1999-01-01

    magnitude of IFN-gamma responsive genes has been reported previously. Our goal is to identify and map IFN-gamma-regulated HeLa cell proteins to the two-dimensional polyacrylamide gel electrophoresis with the immobilized pH gradient (IPG) two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) system...

  20. Comparison of Yeast Cell Protein Solubilization Procedures for Two-dimensional Electrophoresis

    DEFF Research Database (Denmark)

    Harder, A; Wildgruber, R; Nawrocki, A;

    1999-01-01

    with sodium dodecyl sulfate (SDS) buffer, consisting of 1% SDS and 100 mM tris(hydroxymethyl)aminomethane (Tris)-HCl, pH 7.0, followed by dilution with "standard" lysis buffer, and (iii) boiling the sample with SDS during cell lysis, followed by dilution with thiourea/urea lysis buffer (2 M thiourea/ 7 M urea...... molecular mass proteins. The procedures employed were sonication, followed by (i) protein solubilization with "standard" lysis buffer (9 M urea, 2% 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS), 1% dithiothreitol (DTT), 2% v/v carrier ampholytes, (ii) presolubilization of proteins...... sonication (method ii). Protein disaggregation and solubilization of high Mr proteins were further improved by pre-boiling with SDS and using thiourea/urea lysis buffer instead of "standard" lysis buffer (procedure iii)....

  1. Evaluation of Protein Extraction Methods for Vitis vinifera Leaf and Root Proteome Analysis by Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    Neila Jellouli; Asma Ben Salem; Abdelwahed Ghorbel; Hatem Ben Jouira

    2010-01-01

    An efficient protein extraction method is crucial to ensure successful separation by two-dimensional electrophoresis(2-DE)for recalcitrant plant species, in particular for grapevine(Vitis vinifera L.). Trichloroacetic acid-acetone(TCA-acetone)and phenol extraction methods were evaluated for proteome analysis of leaves and roots from the Tunisian cultivar 'Razegui'. The phenol-based protocol proved to give a higher protein yield,a greater spot resolution, and a minimal streaking on 2-DE gels for both leaf and root tissues compared with the TCA-based protocol. Furthermore, the highest numbers of detected proteins on 2-DE gels were observed using the phenol extraction from leaves and roots as compared with TCA-acetone extraction.

  2. Creating two-dimensional patterned substrates for protein and cell confinement.

    Science.gov (United States)

    Johnson, Dawn M; LaFranzo, Natalie A; Maurer, Joshua A

    2011-01-01

    Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.(1) While microcontact printing can be employed to directly print a large number of molecules, including proteins,(2) DNA,(3) and silanes,(4) the formation of self-assembled monolayers (SAMs) from long chain alkane thiols on gold provides a simple way to confine proteins and cells to specific patterns containing adhesive and resistant regions. This confinement can be used to control cell morphology and is useful for examining a variety of questions in protein and cell biology. Here, we describe a general method for the creation of well-defined protein patterns for cellular studies.(5) This process involves three steps: the production of a patterned master using photolithography, the creation of a PDMS stamp, and microcontact printing of a gold-coated substrate. Once patterned, these cell culture substrates are capable of confining proteins and/or cells (primary cells or cell lines) to the pattern. The use of self-assembled monolayer chemistry allows for precise control over the patterned protein/cell adhesive regions and non-adhesive regions; this cannot be achieved using direct protein stamping. Hexadecanethiol, the long chain alkane thiol used in the microcontact printing step, produces a hydrophobic surface that readily adsorbs protein from solution. The glycol-terminated thiol, used for backfilling the non-printed regions of the substrate, creates a monolayer that is resistant to protein adsorption and therefore cell growth.(6) These thiol monomers produce highly structured monolayers that precisely define regions of the substrate that can support protein adsorption and cell growth. As a result, these substrates are useful for a wide variety of applications from the study of intercellular behavior(7) to the creation of microelectronics.(8) While other types of monolayer chemistry have been used for cell culture studies, including work from

  3. Two Dimensional Electrophoresis of Proteins from Cultures of Erysiphe graminis f.sp. hordei

    DEFF Research Database (Denmark)

    Torp, J.; Andersen, Brian

    1982-01-01

    (SDS) in the second dimension. The protein patterns obtained were insensitive to environmental variations, host genotype and age of the conidia. Seven mildew cultures of diverse origin were each characterized by a unique and reproducible pattern involving 174 predominant protein spots. The average......Conidial proteins from barley powdery mildew, Erysiphe graminis f. sp. hordei, were separated by 2-dimensional electrophoresis in polyacrylamide slab gels. Isoelectric focusing was used in the first dimension and separation according to molecular weight in a gel containing sodium dodecyl sulphate...... coefficient of similarity was 0–95. A wild type culture and a mutant differing only in pathogenicity to barley lines with resistance gene Ml-g, had identical patterns....

  4. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...... on single spot differences, but on the covariance structure between proteins. However, their outcome is dependent on data scaling, and they may fail in producing valid multivariate models due to the much higher number of "irrelevant" spots present in the gels. The case where only few gels are available...... 'autoscaling' of the full data set based on within-group standard deviations is introduced and shown to be advantageous in revealing potential group-dependent proteins additional to those found by prefiltering....

  5. Triton X-114 cloud point extraction to subfractionate blood plasma proteins for two-dimensional gel electrophoresis.

    Science.gov (United States)

    Jessen, Flemming; Wulff, Tune

    2015-09-15

    A simple and reproducible procedure for enrichment of a plasma protein subfraction suitable for two-dimensional polyacrylamide gel electrophoresis (2DE) was developed, using a Triton X-114-based cloud point extraction (CPE). Appropriate conditions for such a CPE procedure were found by SDS-PAGE to be a plasma protein concentration of about 10mg/ml in 3% (w/v) Triton X-114. 2DE of proteins obtained by CPE of 400 μl of human plasma revealed about 200 spots constituting a spot pattern very different from the pattern of total plasma. The CPE procedure only had a limited contribution to the technical variation. Identification of about 60 spots, representing only 22 proteins, revealed that several proteins in the obtained subfraction were present in more isoforms or modifications. Among these were apolipoproteins (A-1, D, E, L1, and M), haptoglobin-related protein, phosphatidylcholine-sterol acyltransferase, serum amyloid A, and serum paraoxonase/arylesterase 1, which are proteins of a hydrophobic nature, as in plasma they relate to lipoprotein particles. Thus, Triton X-114-based CPE is a simple plasma prefractionation tool, attractive for detailed 2DE studies of hydrophobic plasma proteins and their isoforms or modifications.

  6. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  7. Identification and mapping of DNA binding proteins target sequences in long genomic regions by two-dimensional EMSA.

    Science.gov (United States)

    Chernov, Igor P; Akopov, Sergey B; Nikolaev, Lev G; Sverdlov, Eugene D

    2006-07-01

    Specific binding of nuclear proteins, in particular transcription factors, to target DNA sequences is a major mechanism of genome functioning and gene expression regulation in eukaryotes. Therefore, identification and mapping specific protein target sites (PTS) is necessary for understanding genomic regulation. Here we used a novel two-dimensional electrophoretic mobility shift assay (2D-EMSA) procedure for identification and mapping of 52 PTS within a 563-kb human genome region located between the FXYD5 and TZFP genes. The PTS occurred with approximately equal frequency within unique and repetitive genomic regions. PTS belonging to unique sequences tended to group together within gene introns and close to their 5' and 3' ends, whereas PTS located within repeats were evenly distributed between transcribed and intragenic regions. PMID:16869519

  8. Fast Two-Dimensional NMR Spectroscopy of High Molecular Weight Protein Assemblies

    International Nuclear Information System (INIS)

    An optimized NMR experiment that combines the advantages of methyl-TROSY and SOFAST-HMQC has been developed. It allows the recording of high quality methyl 1H-13C correlation spectra of protein assemblies of several hundreds of kDa in a few seconds. The SOFAST-methyl-TROSY-based experiment offers completely new opportunities for the study of structural and dynamic changes occurring in molecular nano-machines while they perform their biological function in vitro. (authors)

  9. Keeping Lung Surfactant Where It Belongs: Protein Regulation of Two-Dimensional Viscosity

    OpenAIRE

    Alonso, Coralie; Waring, Alan; Zasadzinski, Joseph A.

    2005-01-01

    Lung surfactant causes the surface tension, γ, in the alveoli to drop to nearly zero on exhalation; in the upper airways γ is ∼30 mN/m and constant. Hence, a surface tension gradient exists between alveoli and airways that should lead to surfactant flow out of the alveoli and elimination of the surface tension gradient. However, the lung surfactant specific protein SP-C enhances the resistance to surfactant flow by regulating the ratio of solid to fluid phase in the monolayer, leading to a ja...

  10. Protein adsorption in two-dimensional electrochromatography packed with superporous and microporous cellulose beads

    Institute of Scientific and Technical Information of China (English)

    Dongmei WANG; Guodong JIA; Liang XU; Xiaoyan DONG; Yan SUN

    2009-01-01

    Anion-exchange superporous cellulose (DEAE-SC) and microporous cellulose (DEAE-MC) adsorbents were packed in an electrochromatographic column, and the effect of external electric field (eEF) on the dynamic adsorption was investigated. The column was designed to provide longitudinal, transverse or 2-dimensional (2D) eEF. It was found that the electro-kinetic effect caused by the introduction of an electric field played an important role in the dynamic adsorption of bovine serum albumin to the adsorbents. The dynamic binding capacity (DBC) in the presence of2D eEF was higher than in the presence of a one-dimensional eEF. The effect of flow velocity on the DBC of the two adsorbents was also demonstrated. It was found that the effect of electric field. on the DEAE-MC column was more remarkable than that on the DEAE-SC column at the same flow rate, whereas the DEAE-SC column showed higher DBC and adsorption efficiency (AE) than the DEAE-MC column. With increasing flow rate, the DEAE-SC column could still offer high DBC and AE in the presence of the 2D eEF. For example, a DBC of 21.4 mg/mL and an AE of 57.7% were obtained even at a flow rate as high as 900 cm/h. The results indicate that the 2D electrochromatography packed with the superporous cellulose adsorbent is promising for high-speed protein chromatography.

  11. Avoiding acidic region streaking in two-dimensional gel electrophoresis: Case study with two bacterial whole cell protein extracts

    Indian Academy of Sciences (India)

    Arnab Roy; Umesh Varshney; Debnath Pal

    2014-09-01

    Acidic region streaking (ARS) is one of the lacunae in two-dimensional gel electrophoresis (2DE) of bacterial proteome. This streaking is primarily caused by nucleic acid (NuA) contamination and poses major problem in the downstream processes like image analysis and protein identification. Although cleanup and nuclease digestion are practiced as remedial options, these strategies may incur loss in protein recovery and perform incomplete removal of NuA. As a result, ARS has remained a common observation across publications, including the recent ones. In this work, we demonstrate how ultrasound wave can be used to shear NuA in plain ice-cooled water, facilitating the elimination of ARS in the 2DE gels without the need for any additional sample cleanup tasks. In combination with a suitable buffer recipe, IEF program and frequent paper-wick changing approach, we are able to reproducibly demonstrate the production of clean 2DE gels with improved protein recovery and negligible or no ARS. We illustrate our procedure using whole cell protein extracts from two diverse organisms, Escherichia coli and Mycobacterium smegmatis. Our designed protocols are straightforward and expected to provide good 2DE gels without ARS, with comparable times and significantly lower cost.

  12. Assessing two-dimensional crystallization trials of small membrane proteins for structural biology studies by electron crystallography.

    Science.gov (United States)

    Johnson, Matthew C; Rudolph, Frederik; Dreaden, Tina M; Zhao, Gengxiang; Barry, Bridgette A; Schmidt-Krey, Ingeborg

    2010-10-29

    Electron crystallography has evolved as a method that can be used either alternatively or in combination with three-dimensional crystallization and X-ray crystallography to study structure-function questions of membrane proteins, as well as soluble proteins. Screening for two-dimensional (2D) crystals by transmission electron microscopy (EM) is the critical step in finding, optimizing, and selecting samples for high-resolution data collection by cryo-EM. Here we describe the fundamental steps in identifying both large and ordered, as well as small 2D arrays, that can potentially supply critical information for optimization of crystallization conditions. By working with different magnifications at the EM, data on a range of critical parameters is obtained. Lower magnification supplies valuable data on the morphology and membrane size. At higher magnifications, possible order and 2D crystal dimensions are determined. In this context, it is described how CCD cameras and online-Fourier Transforms are used at higher magnifications to assess proteoliposomes for order and size. While 2D crystals of membrane proteins are most commonly grown by reconstitution by dialysis, the screening technique is equally applicable for crystals produced with the help of monolayers, native 2D crystals, and ordered arrays of soluble proteins. In addition, the methods described here are applicable to the screening for 2D crystals of even smaller as well as larger membrane proteins, where smaller proteins require the same amount of care in identification as our examples and the lattice of larger proteins might be more easily identifiable at earlier stages of the screening.

  13. Optimized sample preparation for two-dimensional gel electrophoresis of soluble proteins from chicken bursa of Fabricius

    Directory of Open Access Journals (Sweden)

    Zheng Xiaojuan

    2009-10-01

    Full Text Available Abstract Background Two-dimensional gel electrophoresis (2-DE is a powerful method to study protein expression and function in living organisms and diseases. This technique, however, has not been applied to avian bursa of Fabricius (BF, a central immune organ. Here, optimized 2-DE sample preparation methodologies were constructed for the chicken BF tissue. Using the optimized protocol, we performed further 2-DE analysis on a soluble protein extract from the BF of chickens infected with virulent avibirnavirus. To demonstrate the quality of the extracted proteins, several differentially expressed protein spots selected were cut from 2-DE gels and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS. Results An extraction buffer containing 7 M urea, 2 M thiourea, 2% (w/v 3-[(3-cholamidopropyl-dimethylammonio]-1-propanesulfonate (CHAPS, 50 mM dithiothreitol (DTT, 0.2% Bio-Lyte 3/10, 1 mM phenylmethylsulfonyl fluoride (PMSF, 20 U/ml Deoxyribonuclease I (DNase I, and 0.25 mg/ml Ribonuclease A (RNase A, combined with sonication and vortex, yielded the best 2-DE data. Relative to non-frozen immobilized pH gradient (IPG strips, frozen IPG strips did not result in significant changes in the 2-DE patterns after isoelectric focusing (IEF. When the optimized protocol was used to analyze the spleen and thymus, as well as avibirnavirus-infected bursa, high quality 2-DE protein expression profiles were obtained. 2-DE maps of BF of chickens infected with virulent avibirnavirus were visibly different and many differentially expressed proteins were found. Conclusion These results showed that method C, in concert extraction buffer IV, was the most favorable for preparing samples for IEF and subsequent protein separation and yielded the best quality 2-DE patterns. The optimized protocol is a useful sample preparation method for comparative proteomics analysis of chicken BF tissues.

  14. Fish Proteins as Targets of Ferrous-Catalyzed Oxidation: Identification of Protein Carbonyls by Fluorescent Labeling on Two-Dimensional Gels and MALDI-TOF/TOF Mass Spectrometry

    DEFF Research Database (Denmark)

    Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter;

    2011-01-01

    , indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly increased carbonylation of important structural proteins in fish muscle, mainly actin and myosin, and degradation products of those proteins were observed...... with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change...... in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe...

  15. Two-dimensional gas chromatography/mass spectrometry, physical property modeling and automated production of component maps to assess the weathering of pollutants.

    Science.gov (United States)

    Antle, Patrick M; Zeigler, Christian D; Livitz, Dimitri G; Robbat, Albert

    2014-10-17

    Local conditions influence how pollutants will weather in subsurface environments and sediment, and many of the processes that comprise environmental weathering are dependent upon these substances' physical and chemical properties. For example, the effects of dissolution, evaporation, and organic phase partitioning can be related to the aqueous solubility (SW), vapor pressure (VP), and octanol-water partition coefficient (KOW), respectively. This study outlines a novel approach for estimating these physical properties from comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC/MS) retention index-based polyparameter linear free energy relationships (LFERs). Key to robust correlation between GC measurements and physical properties is the accurate and precise generation of retention indices. Our model, which employs isovolatility curves to calculate retention indices, provides improved retention measurement accuracy for families of homologous compounds and leads to better estimates of their physical properties. Results indicate that the physical property estimates produced from this approach have the same error on a logarithmic-linear scale as previous researchers' log-log estimates, yielding a markedly improved model. The model was embedded into a new software program, allowing for automated determination of these properties from a single GC×GC analysis with minimal model training and parameter input. This process produces component maps that can be used to discern the mechanism and progression of how a particular site weathers due to dissolution, organic phase partitioning, and evaporation into the surrounding environment.

  16. Analysis of Male Sterility-Related Proteins of Young Panicle in Rice (Oryza sativa L.) by Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    HU Yao-jun; WEI Lei; LIU Shu-nan; YU Jin-hong; DING Yi

    2005-01-01

    For searching out male sterility-related proteins (polypeptides) in rice (Oryza sativa L.), we examined the difference of panicle protein (polypeptides) between hybrid rice (Wujin2A/R168, Wujin5A/R988) and their parents (male-sterile line Wujin2A, Wujin5A, and restorer line R168, R988) at the formation stage of pollen mother cell by two-dimensional electrophoresis (2-DE). The results revealed that the 2-DE polypeptide maps were similar among these experimental materials. A small group of polypeptides were disappeared in 2-DE polypeptide maps of male-sterile line (Wujin2A, Wujin5A) by comparing to restorer line (R168, R988) and the first filial (F1) generation (Wujin2A/R168, Wujin5A/R988). The isoelectric points of these polypeptides were pI 5.8-6.5, molecular weight 42.7×103-66.2×103.

  17. The master two-dimensional gel database of human AMA cell proteins: towards linking protein and genome sequence and mapping information (update 1991)

    DEFF Research Database (Denmark)

    Celis, J E; Leffers, H; Rasmussen, H H;

    1991-01-01

    autoantigens" and "cDNAs". For convenience we have included an alphabetical list of all known proteins recorded in this database. In the long run, the main goal of this database is to link protein and DNA sequencing and mapping information (Human Genome Program) and to provide an integrated picture......The master two-dimensional gel database of human AMA cells currently lists 3801 cellular and secreted proteins, of which 371 cellular polypeptides (306 IEF; 65 NEPHGE) were added to the master images during the last 10 months. These include: (i) very basic and acidic proteins that do not focus...... under normal running conditions and (ii) low-abundant proteins that can only be detected after prolonged gel exposure. Annotation categories updated in this version include "protein name", "antibody against protein", "cellular localization", and "microsequenced proteins". New entries include "human...

  18. metAlignID: A high-throughout sofware tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data

    NARCIS (Netherlands)

    Lommen, A.; Kamp, van der H.J.; Kools, H.J.; Lee, van der M.K.; Weg, van der G.

    2012-01-01

    A new alternative data processing tool set, metAlignID, is developed for automated pre-processing and library-based identification and concentration estimation of target compounds after analysis by comprehensive two-dimensional gas chromatography with mass spectrometric detection. The tool set has b

  19. Two-dimensional gel electrophoresis pattern (pH 6-11) and identification of water-soluble barley seed and malt proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Bak-Jensen, K.S.; Laugesen, S.; Roepstorff, P.;

    2004-01-01

    A protocol was established for two-dimensional gel electrophoresis (2-DE) of barley seed and malt proteins in the pH range of 6-11. Proteins extracted from flour in a low-salt buffer were focused after cup-loading onto IPG strips. Successful separation in the second dimension was achieved using...

  20. Proteomics analysis in mature seed of four peanut cultivars using two-dimensional gel electrophoresis reveals distinct differential expression of storage, anti-nutritive, and allergenic proteins

    Science.gov (United States)

    Protein profiles of total seed proteins isolated from mature seeds of four peanut cultivars, New Mexico Valencia C (NM Valencia C), Tamspan 90, Georgia Green, and NC-7, were studied using two-dimensional gel electrophoresis coupled with nano electrospray ionization liquid chromatography tandem mass ...

  1. Automated classification of single airborne particles from two-dimensional angle-resolved optical scattering (TAOS) patterns by non-linear filtering

    Science.gov (United States)

    Crosta, Giovanni Franco; Pan, Yong-Le; Aptowicz, Kevin B.; Casati, Caterina; Pinnick, Ronald G.; Chang, Richard K.; Videen, Gorden W.

    2013-12-01

    Measurement of two-dimensional angle-resolved optical scattering (TAOS) patterns is an attractive technique for detecting and characterizing micron-sized airborne particles. In general, the interpretation of these patterns and the retrieval of the particle refractive index, shape or size alone, are difficult problems. By reformulating the problem in statistical learning terms, a solution is proposed herewith: rather than identifying airborne particles from their scattering patterns, TAOS patterns themselves are classified through a learning machine, where feature extraction interacts with multivariate statistical analysis. Feature extraction relies on spectrum enhancement, which includes the discrete cosine FOURIER transform and non-linear operations. Multivariate statistical analysis includes computation of the principal components and supervised training, based on the maximization of a suitable figure of merit. All algorithms have been combined together to analyze TAOS patterns, organize feature vectors, design classification experiments, carry out supervised training, assign unknown patterns to classes, and fuse information from different training and recognition experiments. The algorithms have been tested on a data set with more than 3000 TAOS patterns. The parameters that control the algorithms at different stages have been allowed to vary within suitable bounds and are optimized to some extent. Classification has been targeted at discriminating aerosolized Bacillus subtilis particles, a simulant of anthrax, from atmospheric aerosol particles and interfering particles, like diesel soot. By assuming that all training and recognition patterns come from the respective reference materials only, the most satisfactory classification result corresponds to 20% false negatives from B. subtilis particles and <11% false positives from all other aerosol particles. The most effective operations have consisted of thresholding TAOS patterns in order to reject defective ones

  2. Identification of cellular proteins that interact with Newcastle Disease Virus and human Respiratory Syncytial Virus by a two-dimensional virus overlay protein binding assay (VOPBA).

    Science.gov (United States)

    Holguera, Javier; Villar, Enrique; Muñoz-Barroso, Isabel

    2014-10-13

    Although it is well documented that the initial attachment receptors for Newcastle Disease Virus (NDV) and Respiratory Syncytial Virus (RSV) are sialic acid-containing molecules and glycosaminoglycans respectively, the exact nature of the receptors for both viruses remains to be deciphered. Moreover, additional molecules at the host cell surface might be involved in the entry mechanism. With the aim of identifying the cellular proteins that interact with NDV and RSV at the cell surface, we performed a virus overlay protein binding assay (VOPBA). Cell membrane lysates were separated by two dimensional (2D) gel electrophoresis and electrotransferred to PVDF membranes, after which they were probed with high viral concentrations. NDV interacted with a Protein Disulfide Isomerase from chicken fibroblasts. In the case of RSV, we detected 15 reactive spots, which were identified as six different proteins, of which nucleolin was outstanding. We discuss the possible role of PDI and nucleolin in NDV and RSV entry, respectively.

  3. Fish proteins as targets of ferrous-catalyzed oxidation: identification of protein carbonyls by fluorescent labeling on two-dimensional gels and MALDI-TOF/TOF mass spectrometry.

    Science.gov (United States)

    Pazos, Manuel; da Rocha, Angela Pereira; Roepstorff, Peter; Rogowska-Wrzesinska, Adelina

    2011-07-27

    Protein oxidation in fish meat is considered to affect negatively the muscle texture. An important source of free radicals taking part in this process is Fenton's reaction dependent on ferrous ions present in the tissue. The aim of this study was to investigate the susceptibility of cod muscle proteins in sarcoplasmic and myofibril fractions to in vitro metal-catalyzed oxidation and to point out protein candidates that might play a major role in the deterioration of fish quality. Extracted control proteins and proteins subjected to free radicals generated by Fe(II)/ascorbate mixture were labeled with fluorescein-5-thiosemicarbazide (FTSC) to tag carbonyl groups and separated by two-dimensional gel electrophoresis. Consecutive visualization of protein carbonyl levels by capturing the FTSC signal and total protein levels by capturing the SyproRuby staining signal allowed us to quantify the relative change in protein carbonyl levels corrected for changes in protein content. Proteins were identified using MALDI-TOF/TOF mass spectrometry and homology-based searches. The results show that freshly extracted cod muscle proteins exhibit a detectable carbonylation background and that the incubation with Fe(II)/ascorbate triggers a further oxidation of both sarcoplasmic and myofibril proteins. Different proteins exhibited various degrees of sensitivity to oxidation processes. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), nucleoside diphosphate kinase B (NDK), triosephosphate isomerase, phosphoglycerate mutase, lactate dehydrogenase, creatine kinase, and enolase were the sarcoplasmic proteins most vulnerable to ferrous-catalyzed oxidation. Moreover, NDK, phosphoglycerate mutase, and GAPDH were identified in several spots differing by their pI, and those forms showed different susceptibilities to metal-catalyzed oxidation, indicating that post-translational modifications may change the resistance of proteins to oxidative damage. The Fe(II)/ascorbate treatment significantly

  4. CSE-MECC two-dimensional capillary electrophoresis analysis of proteins in the mouse tumor cell (AtT-20) homogenate

    OpenAIRE

    Chen, Xingguo; Fazal, Md. Abul; Dovichi, Norman J.

    2007-01-01

    Two-dimensional capillary electrophoresis was used for the separation of proteins and biogenic amines from the mouse AtT-20 cell line. The first-dimension capillary contained a TRIS-CHES-SDS-dextran buffer to perform capillary sieving electrophoresis, which is based on molecular weight of proteins. The second-dimension capillary contained a TRIS-CHES-SDS buffer for micel1ar electrokinetic capillary chromatography. After a 61 seconds preliminary separation, fractions from the first-dimension c...

  5. Proteins pattern alteration in AZT-treated K562 cells detected by two-dimensional gel electrophoresis and peptide mass fingerprinting

    Directory of Open Access Journals (Sweden)

    Mignogna Giuseppina

    2006-03-01

    Full Text Available Abstract In this study we report the effect of AZT on the whole protein expression profile both in the control and the AZT-treated K562 cells, evidenced by two-dimensional gel electrophoresis and peptide mass fingerprinting analysis. Two-dimensional gels computer digital image analysis showed two spots that appeared up-regulated in AZT-treated cells and one spot present only in the drug exposed samples. Upon extraction and analysis by peptide mass fingerprinting, the first two spots were identified as PDI-A3 and stathmin, while the third one was proved to be NDPK-A. Conversely, two protein spots were present only in the untreated K562 cells, and were identified as SOD1 and HSP-60, respectively.

  6. Comparison of a three-dimensional and two-dimensional camera system for automated measurement of back posture in dairy cows

    NARCIS (Netherlands)

    Viazzi, S.; Bahr, C.; Hertem, van T.; Schlageter-Tello, A.; Romanini, C.E.B.; Halachmi, I.; Lokhorst, C.; Berckmans, D.

    2014-01-01

    In this study, two different computer vision techniques to automatically measure the back posture in dairy cows were tested and evaluated. A two-dimensional and a three-dimensional camera system were used to extract the back posture from walking cows, which is one measurement used by experts to disc

  7. Studies on middle silkgland proteins of cocoon colour sex-limited silkworm (Bombyx mori L.) using two-dimensional polyacrylamide gel electrophoresis

    Indian Academy of Sciences (India)

    Yuan-Xiang Jin; Yu-Yin Chen; Meng-Kui Xu; Yong-Huang Jiang

    2004-03-01

    Qualitative and quantitative differences in proteins expressed in the middle silkglands of male and female silkworm larvae that differ in silk colour were investigated by high resolution two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), followed by computer assisted image analysis. About 1000 protein spots were resolved in both the sexes and most proteins were shown to be distributed in the area from 15 kDa to 70 kDa and pH 4–8. It was found that some proteins displayed higher expression in yellow cocoon, while two proteins were only expressed in female silkworm silkgland tissue through the comparison and analysis by two-D software. These proteins especially existed in female silkworm middle silkgland tissue of yellow cocoon. Furthermore, these proteins might be involved in the expression of cocoon colour phenotype.

  8. Two-dimensional blue native/SDS-PAGE analysis of whole cell lysate protein complexes of rice in response to salt stress.

    Science.gov (United States)

    Hashemi, Amenehsadat; Gharechahi, Javad; Nematzadeh, Ghorbanali; Shekari, Faezeh; Hosseini, Seyed Abdollah; Salekdeh, Ghasem Hosseini

    2016-08-01

    To understand the biology of a plant in response to stress, insight into protein-protein interactions, which almost define cell behavior, is thought to be crucial. Here, we provide a comparative complexomics analysis of leaf whole cell lysate of two rice genotypes with contrasting responses to salt using two-dimensional blue native/SDS-PAGE (2D-BN/SDS-PAGE). We aimed to identify changes in subunit composition and stoichiometry of protein complexes elicited by salt. Using mild detergent for protein complex solubilization, we were able to identify 9 protein assemblies as hetero-oligomeric and 30 as homo-oligomeric complexes. A total of 20 proteins were identified as monomers in the 2D-BN/SDS-PAGE gels. In addition to identifying known protein complexes that confirm the technical validity of our analysis, we were also able to discover novel protein-protein interactions. Interestingly, an interaction was detected for glycolytic enzymes enolase (ENO1) and triosephosphate isomerase (TPI) and also for a chlorophyll a-b binding protein and RuBisCo small subunit. To show changes in subunit composition and stoichiometry of protein assemblies during salt stress, the differential abundance of interacting proteins was compared between salt-treated and control plants. A detailed exploration of some of the protein complexes provided novel insight into the function, composition, stoichiometry and dynamics of known and previously uncharacterized protein complexes in response to salt stress. PMID:27362847

  9. Database of two-dimensional polyacrylamide gel electrophoresis of proteins labeled with CyDye DIGE Fluor saturation dye.

    Science.gov (United States)

    Fujii, Kazuyasu; Kondo, Tadashi; Yokoo, Hideki; Okano, Tetsuya; Yamada, Masayo; Yamada, Tesshi; Iwatsuki, Keiji; Hirohashi, Setsuo

    2006-03-01

    CyDye DIGE Fluor saturation dye (saturation dye, GE Healthcare Amersham Biosciences) enables highly sensitive 2-D PAGE. As the dye reacts with all reduced cysteine thiols, 2-D PAGE can be performed with a lower amount of protein, compared with CyDye DIGE Fluor minimal dye (GE Healthcare Amersham Biosciences), the sensitivity of which is equivalent to that of silver staining. We constructed a 2-D map of the saturation dye-labeled proteins of a liver cancer cell line (HepG2) and identified by MS 92 proteins corresponding to 123 protein spots. Functional classification revealed that the identified proteins had chaperone, protein binding, nucleotide binding, metal ion binding, isomerase activity, and motor activity. The functional distribution and the cysteine contents of the proteins were similar to those in the most comprehensive 2-D database of hepatoma cells (Seow et al.., Electrophoresis 2000, 21, 1787-1813), where silver staining was used for protein visualization. Hierarchical clustering on the basis of the quantitative expression profiles of the 123 characterized spots labeled with two charge- and mass-matched saturation dyes (Cy3 and Cy5) discriminated between nine hepatocellular carcinoma cell lines and primary cultured hepatocytes from five individuals, suggesting the utility of saturation dye and our database for proteomic studies of liver cancer.

  10. Proteomic analysis of halotolerant proteins under high and low salt stress in Dunaliella salina using two-dimensional differential in-gel electrophoresis

    Directory of Open Access Journals (Sweden)

    Yan-Long Jia

    2016-01-01

    Full Text Available Abstract Dunaliella salina, a single-celled marine alga with extreme salt tolerance, is an important model organism for studying fundamental extremophile survival mechanisms and their potential practical applications. In this study, two-dimensional differential in-gel electrophoresis (2D-DIGE was used to investigate the expression of halotolerant proteins under high (3 M NaCl and low (0.75 M NaCl salt concentrations. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS and bioinformatics were used to identify and characterize the differences among proteins. 2D-DIGE analysis revealed 141 protein spots that were significantly differentially expressed between the two salinities. Twenty-four differentially expressed protein spots were successfully identified by MALDI-TOF/TOF MS, including proteins in the following important categories: molecular chaperones, proteins involved in photosynthesis, proteins involved in respiration and proteins involved in amino acid synthesis. Expression levels of these proteins changed in response to the stress conditions, which suggests that they may be involved in the maintenance of intracellular osmotic pressure, cellular stress responses, physiological changes in metabolism, continuation of photosynthetic activity and other aspects of salt stress. The findings of this study enhance our understanding of the function and mechanisms of various proteins in salt stress.

  11. Evaluation and comparison of four protein extraction protocols for mono- and two-dimensional electrophoresis in Mytilus galloprovincialis

    Directory of Open Access Journals (Sweden)

    Marina Ceruso

    2015-09-01

    Full Text Available In this study, four protein extraction protocols from Mytilus galloprovincialis were evaluated with the aim to identify the most practical, efficient and reproducible method. Four extraction protocols frequently used for mussels and organic matrices were selected and compared. The methods were based on the use of: i TRIzol reagent; ii Lysis buffer; iii phenylmethanesulfonyl fluoride; iv trichloroacetic acid-acetone. Protein concentration was measured by the Bradford method. Three specimens of mussels were studied and the analysis was conducted in triplicate for each of the four protocols. Results indicated that the four methods could extract significantly different protein profiles. The highest number of protein spots resolved in 2DE gels and the best reproducibility was obtained using trichloroacetic acid-acetone protocol. Results afforded the selection of a suitable extraction protocol to be used for ecotoxicoproteomics studies from mussels and for other proteomic studies conducted by particularly complex tissues such as Mytilus galloprovincialis.

  12. Protein Extraction Methods for Two-Dimensional Electrophoresis from Baphicacanthus cusia (Nees) Bremek Leaves-A Medicinal Plant with High Contents of Interfering Compounds

    Institute of Scientific and Technical Information of China (English)

    XIANG Xiao-liang; NING Shu-ju; JIANG Xia; GONG Xiao-gui; ZHU Ren-lei; WEI Dao-zhi

    2010-01-01

    Protein extraction is a critical step for two-dimensional electrophoresis (2-DE). Different plant samples require different and adaptive protein extraction protocols. The leaves of medicinal plant, Baphicacanthus cusia (Nees) Bremek are notoriously recalcitrant to common protein extraction methods due to high levels of interfering compounds (especially the secondary metabolites and pigments). This study was aimed to establish a routine procedure for the proteomic analysis of B. cusia leaves, and a new protocol for the protein extraction was developed by optimizing tfichloroacetic acid (TCA)/acetone extraction method. The efficiency of this protocol was demonstrated by comparison with 3 published protein extraction methods (chloroform/acetone, Mg/NP-40, Tris-base/acetone). The results showed that the optimized TCA/acetone precipitation extraction method gave a relatively high protein yield (9.263 mg g fresh weight), high-resolution separation, clear protein profiles, the highest proteins spots (1 311 protein spots), and displayed less contamination in 2DE gels. Therefore, the results suggested that the optimized TCA/acetone method was the most effective among the 4 methods for B. cusia leaves.

  13. Characterisation of ribosomal proteins from HeLa and Krebs II mouse ascites tumor cells by different two-dimensional polyacrylamide gel electrophoresis techniques

    DEFF Research Database (Denmark)

    Issinger, O G; Beier, H

    1978-01-01

    Electrophoresis of ribosomal proteins according to Kaltschmidt and Wittmann, 1970a, b (pH 8.6/pH 4.5 urea system) yielded 29 proteins for the small subunits and 35 and 37 proteins for the large subunits of Krebs II ascites and HeLa ribosomes, respectively. Analysis of the proteins according...... to a modified technique by Mets and Bogorad (1974) (pH 4.5/pH 8.6 SDS system) revealed 28 and 29 proteins in the small subunits and 37 and 38 proteins in the large subunits of Krebs II ascites and HeLa ribosomes. The molecular weights of the individual proteins were determined by: 1. "three-dimensional" gel...... electrophoresis; 2. two-dimensional gel electrophoresis at pH 4.K/pH 8.6 in SDS. The molecular weights for 40S proteins ranged from 10,000 to 39,000 dalton (number average molecular weight: 21,000). The molecular weights for the 60S proteins ranged from 14,000 to 44,000 dalton (number average molecular weight: 23...

  14. Explorative data analysis of two-dimensional electrophoresis gels

    DEFF Research Database (Denmark)

    Schultz, J.; Gottlieb, D.M.; Petersen, Marianne Kjerstine;

    2004-01-01

    Methods for classification of two-dimensional (2-DE) electrophoresis gels based on multivariate data analysis are demonstrated. Two-dimensional gels of ten wheat varieties are analyzed and it is demonstrated how to classify the wheat varieties in two qualities and a method for initial screening...... of gels is presented. First, an approach is demonstrated in which no prior knowledge of the separated proteins is used. Alignment of the gels followed by a simple transformation of data makes it possible to analyze the gels in an automated explorative manner by principal component analysis, to determine...... if the gels should be further analyzed. A more detailed approach is done by analyzing spot volume lists by principal components analysis and partial least square regression. The use of spot volume data offers a mean to investigate the spot pattern and link the classified protein patterns to distinct spots...

  15. New light on protein folding: Unraveling folding and unfolding mechanisms using time-resolved and two-dimensional vibrational spectroscopy

    NARCIS (Netherlands)

    H. Meuzelaar

    2015-01-01

    How a protein folds from its one-dimensional sequence of amino acids into its three-dimensional, functional structure on biologically relevant time scales (typically on the micro- to millisecond time scale) is one of the most challenging questions currently investigated in several scientific discipl

  16. Protein identification from two-dimensional gel electrophoresis analysis of Klebsiella pneumoniae by combined use of mass spectrometry data and raw genome sequences

    Directory of Open Access Journals (Sweden)

    Zeng An-Ping

    2003-12-01

    Full Text Available Abstract Separation of proteins by two-dimensional gel electrophoresis (2-DE coupled with identification of proteins through peptide mass fingerprinting (PMF by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS is the widely used technique for proteomic analysis. This approach relies, however, on the presence of the proteins studied in public-accessible protein databases or the availability of annotated genome sequences of an organism. In this work, we investigated the reliability of using raw genome sequences for identifying proteins by PMF without the need of additional information such as amino acid sequences. The method is demonstrated for proteomic analysis of Klebsiella pneumoniae grown anaerobically on glycerol. For 197 spots excised from 2-DE gels and submitted for mass spectrometric analysis 164 spots were clearly identified as 122 individual proteins. 95% of the 164 spots can be successfully identified merely by using peptide mass fingerprints and a strain-specific protein database (ProtKpn constructed from the raw genome sequences of K. pneumoniae. Cross-species protein searching in the public databases mainly resulted in the identification of 57% of the 66 high expressed protein spots in comparison to 97% by using the ProtKpn database. 10 dha regulon related proteins that are essential for the initial enzymatic steps of anaerobic glycerol metabolism were successfully identified using the ProtKpn database, whereas none of them could be identified by cross-species searching. In conclusion, the use of strain-specific protein database constructed from raw genome sequences makes it possible to reliably identify most of the proteins from 2-DE analysis simply through peptide mass fingerprinting.

  17. Fast two-dimensional grid and transmission X-ray microscopy scanning methods for visualizing and characterizing protein crystals

    Science.gov (United States)

    Wojdyla, Justyna Aleksandra; Panepucci, Ezequiel; Martiel, Isabelle; Ebner, Simon; Huang, Chia-Ying; Caffrey, Martin; Bunk, Oliver; Wang, Meitian

    2016-01-01

    A fast continuous grid scan protocol has been incorporated into the Swiss Light Source (SLS) data acquisition and analysis software suite on the macromolecular crystallography (MX) beamlines. Its combination with fast readout single-photon counting hybrid pixel array detectors (PILATUS and EIGER) allows for diffraction-based identification of crystal diffraction hotspots and the location and centering of membrane protein microcrystals in the lipid cubic phase (LCP) in in meso in situ serial crystallography plates and silicon nitride supports. Diffraction-based continuous grid scans with both still and oscillation images are supported. Examples that include a grid scan of a large (50 nl) LCP bolus and analysis of the resulting diffraction images are presented. Scanning transmission X-ray microscopy (STXM) complements and benefits from fast grid scanning. STXM has been demonstrated at the SLS beamline X06SA for near-zero-dose detection of protein crystals mounted on different types of sample supports at room and cryogenic temperatures. Flash-cooled crystals in nylon loops were successfully identified in differential and integrated phase images. Crystals of just 10 µm thickness were visible in integrated phase images using data collected with the EIGER detector. STXM offers a truly low-dose method for locating crystals on solid supports prior to diffraction data collection at both synchrotron microfocusing and free-electron laser X-ray facilities. PMID:27275141

  18. Two-dimensional calculus

    CERN Document Server

    Osserman, Robert

    2011-01-01

    The basic component of several-variable calculus, two-dimensional calculus is vital to mastery of the broader field. This extensive treatment of the subject offers the advantage of a thorough integration of linear algebra and materials, which aids readers in the development of geometric intuition. An introductory chapter presents background information on vectors in the plane, plane curves, and functions of two variables. Subsequent chapters address differentiation, transformations, and integration. Each chapter concludes with problem sets, and answers to selected exercises appear at the end o

  19. Two-dimensional models

    CERN Document Server

    Schrör, B

    2005-01-01

    It is not possible to compactly review the overwhelming literature on two-dimensional models in a meaningful way without a specific viewpoint; I have therefore tacitly added to the above title the words ``as theoretical laboratories for general quantum field theory''. I dedicate this contribution to the memory of J. A. Swieca with whom I have shared the passion of exploring 2-dimensional models for almost one decade. A shortened version of this article is intended as a contribution to the project ``Encyclopedia of mathematical physics'' and comments, suggestions and critical remarks are welcome.

  20. Effects of essential oil treatments on the secondary protein structure of Vicia faba: A mid-infrared spectroscopic study supported by two-dimensional correlation analysis

    Science.gov (United States)

    Mecozzi, Mauro; Sturchio, Elena

    2015-02-01

    In this study we investigated the effects of essential oil treatments on the secondary protein structure of the Vicia faba roots, a bioindicator plant, in order to obtain information for the potential allelopathic uses of these oils as alternative to the use of pesticides in agriculture. We tested two mixtures of essential oils consisting of Tween 20-emulsions of tea tree oil (TTO) and Tween 20-emulsion of Clove and Rosemary (GARROM) essential oils respectively at three different oil concentrations each. The molecular modifications caused in Vicia faba by exposure to oil emulsions were investigated by FTIR spectroscopy in diffuse reflectance (DRIFT) mode. We considered the specific Amide I, Amide II and Amide VI bands by ordinary and second derivative spectroscopy and the results showed that both Tween 20-emulsion of GARROM and Tween 20-emulsion of TTO oils cause transitions among the secondary (α-helix, β-sheet and β-turn) structures with in addition the appearance of random coil structures in exposed samples. The Amide VI bands, placed between 500 and 600 cm-1, confirmed the structural transitions observed for the Amide I bands. In addition we observed the presence of a protein oxidation effect for TTO treated samples, oxidation which resulted negligible instead for the GARROM oil samples. At last, FTIR spectra were also submitted to two-dimensional correlation analysis (2DCORR) and double two-dimensional correlation analysis (D2DCORR); the results confirmed the different effects caused by the two typologies of essential oils on the secondary protein structures of Vicia faba roots.

  1. Two-dimensional ferroelectrics

    International Nuclear Information System (INIS)

    The investigation of the finite-size effect in ferroelectric crystals and films has been limited by the experimental conditions. The smallest demonstrated ferroelectric crystals had a diameter of ∼200 A and the thinnest ferroelectric films were ∼200 A thick, macroscopic sizes on an atomic scale. Langmuir-Blodgett deposition of films one monolayer at a time has produced high quality ferroelectric films as thin as 10 A, made from polyvinylidene fluoride and its copolymers. These ultrathin films permitted the ultimate investigation of finite-size effects on the atomic thickness scale. Langmuir-Blodgett films also revealed the fundamental two-dimensional character of ferroelectricity in these materials by demonstrating that there is no so-called critical thickness; films as thin as two monolayers (1 nm) are ferroelectric, with a transition temperature near that of the bulk material. The films exhibit all the main properties of ferroelectricity with a first-order ferroelectric-paraelectric phase transition: polarization hysteresis (switching); the jump in spontaneous polarization at the phase transition temperature; thermal hysteresis in the polarization; the increase in the transition temperature with applied field; double hysteresis above the phase transition temperature; and the existence of the ferroelectric critical point. The films also exhibit a new phase transition associated with the two-dimensional layers. (reviews of topical problems)

  2. Identification of proteins of human colorectal carcinoma cell line SW480 by two-dimensional electrophoresis and MALDI-TOF mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Ying-Tao Zhang; Yi-Ping Geng; Le Zhou; Bao-Chang Lai; Lv-Sheng Si; Yi-Li Wang

    2005-01-01

    AIM: To conduct the proteomic analysis of human colorectal carcinoma cell line, SW480 by using two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption /ionization-time of flight mass spectrometry (MALDITOFMS).METHODS: The total proteins of human colorectal carcinoma cell line, SW480 were separated with 2-DE by using immobilized pH gradient strips and visualized by staining with silver nitrate. The gel images were acquired by scanner and 2-DE analysis software, Image Master 2D Elite. Nineteen distinct protein spots were excised from gel randomly and digested in gel by TPCK-trypsin. Mass analysis ofthe tryptic digest peptides mixture was performed by using MALDI-TOF MS. Peptide mass fingerprints (PMFs) obtained by the MALDI-TOF analysis were used to search NCBI,SWISS-PROT and MSDB databases by using Mascot software.RESULTS: PMF maps of all spots were obtained by MALDI-TOF MS and thirteen proteins were preliminarily identified.CONCLUSION: The methods of analysis and identification of protein spots of tumor cells in 2-DE gel with silver staining by MALDI-TOF MS derived PMF have been established.Protein expression profile of SW480 has been obtained.It is demonstrated that a combination of proteomics and cell culture is a useful approach to comprehend the process of colon carcinogenesis.

  3. Two-dimensional turbulent flow chromatography coupled on-line to liquid chromatography-mass spectrometry for solution-based ligand screening against multiple proteins.

    Science.gov (United States)

    Zhou, Jian-Liang; An, Jing-Jing; Li, Ping; Li, Hui-Jun; Jiang, Yan; Cheng, Jie-Fei

    2009-03-20

    We present herein a novel bioseparation/chemical analysis strategy for protein-ligand screening and affinity ranking in compound mixtures, designed to increase screening rates and improve sensitivity and ruggedness in performance. The strategy is carried out by combining on-line two-dimensional turbulent flow chromatography (2D-TFC) with liquid chromatography-mass spectrometry (LC-MS), and accomplished through the following steps: (1) a reversed-phase TFC stage to separate the protein/ligand complex from the unbound free molecules, (2) an on-line dissociation process to release the bound ligands from the complexes, and (3) a second mixed-mode cation-exchange/reversed-phase TFC stage to trap the bound ligands and to remove the proteins and salts, followed by LC-MS analysis for identification and determination of the binding affinities. The technique can implement an ultra-fast isolation of protein/ligand complex with the retention time of a complex peak in about 5s, and on-line prepare the "clean" sample to be directly compatible with the LC-MS analysis. The improvement in performance of this 2D-TFC/LC-MS approach over the conventional approach has been demonstrated by determining affinity-selected ligands of the target proteins acetylcholinesterase and butyrylcholinesterase from a small library with known binding affinities and a steroidal alkaloid library composed of structurally similar compounds. Our results show that 2D-TFC/LC-MS is a generic and efficient tool for high-throughput screening of ligands with low-to-high binding affinities, and structure-activity relationship evaluation. PMID:19203758

  4. Comparison of fractionation strategies for offline two-dimensional liquid chromatography tandem mass spectrometry analysis of proteins from mouse adipose tissue.

    Science.gov (United States)

    Sajic, Tatjana; Varesio, Emmanuel; Szanto, Ildiko; Hopfgartner, Gérard

    2015-09-01

    In the frame of protein identification from mouse adipose tissue, two strategies were compared for the offline elution of peptides from a strong cation exchange (SCX) column in two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) analyses. First, the salt gradient (using K(+) as displacing agent) was evaluated from 25 to 500mM KCl. Then, a less investigated elution mode using a pH gradient (using citric acid and ammonium hydroxide) was carried out from pH 2.5 to 9.0. Equal amounts of peptide digest derived from mouse adipose tissue were loaded onto the SCX column and fractionated according to the two approaches. A total of 15 fractions were collected in two independent experiments for each SCX elution strategy. Then, each fraction was analyzed on a nanoLC-MS/MS platform equipped with a column-switching unit for desalting and enrichment. No substantial differences in peptide quality characteristics (molecular weight, isoelectric point, or GRAVY [grand average of hydropathicity] index distributions) were observed between the two datasets. The pH gradient approach was found to be superior, with 27.5% more unique peptide identifications and 10% more distinct protein identifications compared with the salt-based elution method. In conclusion, our data imply that the pH gradient SCX fractionation is more desirable for proteomics analysis of entire adipose tissue. PMID:26036199

  5. Mapping and identification of HeLa cell proteins separated by immobilized pH-gradient two-dimensional gel electrophoresis and construction of a two-dimensional polyacrylamide gel electrophoresis database

    DEFF Research Database (Denmark)

    Shaw, AC; Rossel Larsen, M; Roepstorff, P;

    1999-01-01

    The HeLa cell line, a human adenocarcinoma, is used in many research fields, since it can be infected with a wide range of viruses and intracellular bacteria. Therefore, the mapping of HeLa cell proteins is useful for the investigation of parasite host cell interactions. Because of the recent...

  6. An incremental approach to automated protein localisation

    Directory of Open Access Journals (Sweden)

    Kummert Franz

    2008-10-01

    Full Text Available Abstract Background The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted based on amino acid sequences. Besides increasing our knowledge about intracellular processes, this information facilitates the development of innovative therapies and new diagnostic methods. In order to perform such a localisation, the proteins under analysis are usually fused with a fluorescent protein. So, they can be observed by means of a fluorescence microscope and analysed. In recent years, several automated methods have been proposed for performing such analyses. Here, two different types of approaches can be distinguished: techniques which enable the recognition of a fixed set of protein locations and methods that identify new ones. To our knowledge, a combination of both approaches – i.e. a technique, which enables supervised learning using a known set of protein locations and is able to identify and incorporate new protein locations afterwards – has not been presented yet. Furthermore, associated problems, e.g. the recognition of cells to be analysed, have usually been neglected. Results We introduce a novel approach to automated protein localisation in living cells. In contrast to well-known techniques, the protein localisation technique presented in this article aims at combining the two types of approaches described above: After an automatic identification of unknown protein locations, a potential user is enabled to incorporate them into the pre-trained system. An incremental neural network allows the classification of a fixed set of protein location as well as the detection, clustering and incorporation of additional patterns that occur during an experiment. Here, the proposed technique achieves promising results with respect to both tasks. In addition, the protein localisation procedure has been adapted

  7. A comprehensive two-dimensional gel protein database of noncultured unfractionated normal human epidermal keratinocytes: towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Madsen, Peder; Rasmussen, H H;

    1991-01-01

    A two-dimensional (2-D) gel database of cellular proteins from noncultured, unfractionated normal human epidermal keratinocytes has been established. A total of 2651 [35S]methionine-labeled cellular proteins (1868 isoelectric focusing, 783 nonequilibrium pH gradient electrophoresis) were resolved......, melanocytes, fibroblasts, dermal microvascular endothelial cells, peripheral blood mononuclear cells and sweat duct cells. The keratinocyte 2-D gel protein database will be updated yearly in the November issue of Electrophoresis. Udgivelsesdato: 1991-Nov...

  8. Comprehensive two-dimensional gel protein databases offer a global approach to the analysis of human cells: the transformed amnion cells (AMA) master database and its link to genome DNA sequence data

    DEFF Research Database (Denmark)

    Celis, J E; Gesser, B; Rasmussen, H H;

    1990-01-01

    A total of 3430 polypeptides (2592 cellular; 838 secreted) from transformed human amnion cells (AMA) labeled with [35S]methionine were separated and recorded using computer-aided two-dimensional (2-D) gel electrophoresis. A master 2-D gel database of cellular protein information that includes both......, mitochondria, Golgi, ribosomes, intermediate filaments, microfilaments and microtubules), levels in fetal human tissues, partial protein sequences (containing information on 48 human proteins microsequenced so far), cell cycle-regulated proteins, proteins sensitive to interferons alpha, beta, and gamma, heat......-specific proteins, to microsequence them and store the information in the database, to identify the corresponding genes, to search for homology with previously characterized proteins and to study the function of groups of proteins (pathways, organelles, etc.) that exhibit interesting regulatory properties...

  9. 地衣芽孢杆菌总蛋白双向电泳方法的建立和优化%Establishment and optimization of two-dimensional gel electrophoresis of total proteins from Bacillus lincheniformis

    Institute of Scientific and Technical Information of China (English)

    江慎华; 陈惠; 陈静; 汪涛; 姚中平; 周英棠

    2013-01-01

    探索建立有效的地衣芽孢杆菌蛋白质组双向电泳体系,为进一步揭示地衣芽孢杆菌促进氧化葡萄糖酸杆菌产酸的作用机制奠定基础.以地衣芽孢杆菌为材料,比较蛋白质制备超声破壁时间、新型细胞裂解液、pH梯度和不同上样量对地衣芽孢杆菌蛋白双向电泳结果的影响.结果显示:采用15min超声破壁提取地衣芽孢杆菌总蛋白,选用新型蛋白质裂解,用长24cm、pH4~7的IPG胶条,在上样量为80μg进行等电聚焦,于60V 15min、120V 6h条件下进行SDS-PAGE垂直电泳,可以获得背景清晰、重复性好的双向电泳图谱.在探索出一种新型可行的新型细胞裂解液的同时,建立一套用于地衣芽孢杆菌蛋白质组分析的双向电泳方法.%A two dimensional gel electrophoresis protocol proteomic study of Bacillus lincheniformis and offer further information how Bacillus cereus stimulate the growth of Gluconobacter oxydans to produce 2-keto-L-gulonic acid (2-KLG) after entering into stationary phase was established.Different parameters,including protein preparation by different ultrasonic broken time,new type lysis,pH gradient and different sample of Bacillus lincheniformis protein,were used to evaluate the effect of two-dimensional electrophoresis of Bacillus lincheniformis proteins.Results showed that the clear background and reproducibility of two dimensional gel electrophoresis were established on the condition of using 15min of ultrasonic broken extraction,selection of protein cleavage I,pH4~7 24cm IPG strips,80 μg loading volume,isoelectric focus at 60V 15min,120V 6h.The aim of this study was not only to explore a novel cell lysate in two-dimensional gel electrophoresis,but also to establish a method of proteome analysis for two-dimensional electrophoresis of Bacillus licheniformis.

  10. Two dimensional unstable scar statistics.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Jorgenson, Roy Eberhardt; Kotulski, Joseph Daniel; Lee, Kelvin S. H. (ITT Industries/AES Los Angeles, CA)

    2006-12-01

    This report examines the localization of time harmonic high frequency modal fields in two dimensional cavities along periodic paths between opposing sides of the cavity. The cases where these orbits lead to unstable localized modes are known as scars. This paper examines the enhancements for these unstable orbits when the opposing mirrors are both convex and concave. In the latter case the construction includes the treatment of interior foci.

  11. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H;

    1991-01-01

    a global approach to the study of the cell. Using the integrated approach offered by 2-dimensional gel protein databases it is now possible to reveal phenotype specific protein (or proteins), to microsequence them, to search for homology with previously identified proteins, to clone the cDNAs, to assign...

  12. The human keratinocyte two-dimensional protein database (update 1994): towards an integrated approach to the study of cell proliferation, differentiation and skin diseases

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Olsen, E;

    1994-01-01

    identified (protein name, organelle components, etc.) using one or a combination of procedures that include (i) comigration with known human proteins, (ii) 2-D gel immunoblotting using specific antibodies (iii) microsequencing of Coomassie Brilliant Blue stained proteins, (iv) mass spectrometry and (v...

  13. Identification of tissue-specific DNA-protein binding sites by means of two-dimensional electrophoretic mobility shift assay display.

    Science.gov (United States)

    Chernov, Igor P; Timchenko, Kira A; Akopov, Sergey B; Nikolaev, Lev G; Sverdlov, Eugene D

    2007-05-01

    We developed a technique of differential electrophoretic mobility shift assay (EMSA) display allowing identification of tissue-specific protein-binding sites within long genomic sequences. Using this approach, we identified 10 cell type-specific protein-binding sites (protein target sites [PTSs]) within a 137-kb human chromosome 19 region. In general, tissue-specific binding of proteins from different nuclear extracts by individual PTSs did not follow the all-or-nothing principle. Most often, PTS-protein complexes were formed in all cases, but they were different for different nuclear extracts used. PMID:17359930

  14. Two-dimensional Electrophoresis Analysis of Proteins in Response to Cold Stress in Extremely Cold-resistant Winter Wheat Dongnongdongmai 1 Tillering Nodes

    Institute of Scientific and Technical Information of China (English)

    Cang Jing; Yu Jing; Liu Li-jie; Yang Yang; Cui Hong; Hao Zai-bin; Li Zhuo-fu

    2012-01-01

    The overwintering survival ratio of the cultivar Dongnongdongmai 1 with strong cold-resistance in paramos of Heilongjiang Province in China are over 85%. The tillering nodes are the most important organs for overwintering survival of winter wheat, because there are more substances associated with cold resistance in tillering nodes than those in leaves and roots. Proteins in the tillering nodes of the cold-resistant cultivar Dongnongdongmai 1 grown under field conditions with or without any lowtemperature stress were analyzed by 2-dimensional electrophoresis and identified by mass spectrometry. In the range of pH 4-7, the expression of 37 proteins showed obvious difference (±more than two fold) in the proteomic maps of cold-stressed and non-stressed tillering nodes, including a new protein spot. All proteins exhibiting the difference in expression were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, followed by a database search for protein identification and function prediction. Five groups of proteins were confirmed, namely stress-related proteins (22%), metabolism-associated proteins (35%), and signaling molecules (24%), cell wall-binding proteins (5%), unclear proteins (14%). This indicated that tillering node cells supported the energy requirements of plant growth and stress resistance by signal transduction adapting to metabolism and structure.

  15. Two-dimensional box plot

    OpenAIRE

    Phattrawan Tongkumchum

    2005-01-01

    In this paper we propose a two-dimensional box plot, a simple bivariate extension of the box plot and the scatter plot. This plot comprises a pair of trapeziums oriented in the direction of a fitted straight line, with symbols denoting extreme values. The choice for the fitted straight resistant line showing the relationship between the two variables is Tukey’s resistance line. The main components of the plot are an inner box containing 50% of the projection points of the observations on the ...

  16. Two-dimensional elastic turbulence

    CERN Document Server

    Berti, S; Boffetta, G; Celani, A; Musacchio, S; 10.1103/PhysRevE.77.055306

    2010-01-01

    We investigate the effect of polymer additives on a two-dimensional Kolmogorov flow at very low Reynolds numbers by direct numerical simulations of the Oldroyd-B viscoelastic model. We find that above the elastic instability threshold the flow develops the elastic turbulence regime recently observed in experiments. We observe that both the turbulent drag and the Lyapunov exponent increase with Weissenberg, indicating the presence of a disordered, turbulent-like mixing flow. The energy spectrum develops a power-law scaling range with an exponent close to the experimental and theoretical expectations.

  17. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V;

    1998-01-01

    -MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross......-references demonstrated that there is no obvious pattern by which the mobility of a protein in one gel system can be used to predict its mobility in the other. Thus, as laboratories adopt the immobilized pH gradient-based 2-D gel systems, the only reliable means of translating the data gained with the carrier ampholyte...

  18. Mapping of Chlamydia trachomatis proteins by immobiline-polyacrylamide two-dimensional electrophoresis: spot identification by N-terminal sequencing and immunoblotting

    DEFF Research Database (Denmark)

    Bini, L; Sanchez-Campillo, M; Santucci, A;

    1996-01-01

    reproducible and resolve ca. 600 spots. By using immunoblot analysis with specific antibodies and/or N-terminal amino acid sequencing, we established the map positions of a number of described chlamydial proteins, such as the major outer membrane protein (MOMP) the 60 kDa cystein-rich outer membrane protein...... parameters (Mr, pI and N-terminal sequence). This work provides a preliminary basis for a future and progressive compilation of a genome-linked database of chlamydial proteins....

  19. Two dimensional solid state NMR

    International Nuclear Information System (INIS)

    This thesis illustrates, by discussing some existing and newly developed 2D solid state experiments, that two-dimensional NMR of solids is a useful and important extension of NMR techniques. Chapter 1 gives an overview of spin interactions and averaging techniques important in solid state NMR. As 2D NMR is already an established technique in solutions, only the basics of two dimensional NMR are presented in chapter 2, with an emphasis on the aspects important for solid spectra. The following chapters discuss the theoretical background and applications of specific 2D solid state experiments. An application of 2D-J resolved NMR, analogous to J-resolved spectroscopy in solutions, to natural rubber is given in chapter 3. In chapter 4 the anisotropic chemical shift is mapped out against the heteronuclear dipolar interaction to obtain information about the orientation of the shielding tensor in poly-(oxymethylene). Chapter 5 concentrates on the study of super-slow molecular motions in polymers using a variant of the 2D exchange experiment developed by us. Finally chapter 6 discusses a new experiment, 2D nutation NMR, which makes it possible to study the quadrupole interaction of half-integer spins. 230 refs.; 48 figs.; 8 tabs

  20. Identification of oxidised proteins in the matrix of rice leaf mitochondria by immunoprecipitation and two-dimensional liquid chromatography-tandem mass spectrometry

    DEFF Research Database (Denmark)

    Kristensen, B.K.; Askerlund, P.; Bykova, N.V.;

    2004-01-01

    blots showed that neither the isolation of mitochondria, nor their subfractionation introduced carbonyl groups. We therefore conclude that a number of proteins are oxidised in the matrix of rice leaf mitochondria in vivo and further identify a group of proteins that are particularly susceptible to mild......Highly purified mitochondria were isolated from green 7-day-old rice leaves. The mitochondria were sonicated and the matrix fraction isolated as the 100,000g supernatant. Part of the matrix fraction was left untreated while the other part was subjected to a mild oxidative treatment (0.5 mM H2O2 + 0.......2 mM CuSO4 for 10 min at room temperature). The oxidised proteins in both samples were tagged with dinitrophenylhydrazine (DNP), which forms a covalent bond with carbonyl groups. The DNP-tagged proteins were immunoprecipitated using anti-DNP antibodies and digested with trypsin. The mixture of...

  1. Identification of DNA-binding proteins that interact with the 5'-flanking region of the human D-amino acid oxidase gene by pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry.

    Science.gov (United States)

    Tran, Diem Hong; Shishido, Yuji; Chung, Seong Pil; Trinh, Huong Thi Thanh; Yorita, Kazuko; Sakai, Takashi; Fukui, Kiyoshi

    2015-12-10

    D-Amino acid oxidase (DAO) is a flavoenzyme that metabolizes D-amino acids and is expected to be a promising therapeutic target of schizophrenia and glioblastoma. The study of DNA-binding proteins has yielded much information in the regulation of transcription and other biological processes. However, proteins interacting with DAO gene have not been elucidated. Our assessment of human DAO promoter activity using luciferase reporter system indicated the 5'-flanking region of this gene (-4289 bp from transcription initiation site) has a regulatory sequence for gene expression, which is regulated by multi-protein complexes interacting with this region. By using pull-down assay coupled with two-dimensional gel electrophoresis and mass spectrometry, we identified six proteins binding to the 5'-flanking region of the human DAO gene (zinc finger C2HC domain-containing protein 1A; histidine-tRNA ligase, cytoplasmic; molybdenum cofactor biosynthesis protein; 60S ribosomal protein L37; calponin-1; calmodulin binding protein and heterogeneous nuclear ribonucleoprotein A2/B1). These preliminary results will contribute to the advance in the understanding of the potential factors associated with the regulatory mechanism of DAO expression.

  2. Differences in alcohol-soluble protein from genetically altered wheat using capillary zone electrophoresis, one- and two-dimensional electrophoresis and a novel gluten matrix association factor analysis

    Science.gov (United States)

    Wheat protein composition and organization play interrelated roles in determining physical properties for technological purposes. In prior research, a number of isogenic wheat lines of Bobwhite that have high levels of expression of the native Dx5 and/or Dy10 high molecular weight subunits (HMW-GS)...

  3. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

    International Nuclear Information System (INIS)

    The aromatic 1H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 → Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures

  4. Two-dimensional NMR and photo-CIDNP studies of the insulin monomer: Assignment of aromatic resonances with application to protein folding, structure, and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Weiss, M.A.; Shoelson, S.E. (Harvard Medical School, Boston, MA (USA) Massachusetts General Hospital, Boston (USA)); Nguyen, D.T.; O' Shea, E.; Karplus, M. (Harvard Univ., Cambridge, MA (USA)); Khait, I.; Neuringer, L.J. (Massachusetts Institute of Technology, Cambridge (USA)); Inouye, K. (Shionogi and Co., Ltd., Osaka (Japan)); Frank, B.H.; Beckage, M. (Eli Lilly and Co., Indianapolis, IN (USA))

    1989-12-12

    The aromatic {sup 1}H NMR resonances of the insulin monomer are assigned at 500 MHz by comparative studies of chemically modified and genetically altered variants, including a mutant insulin (PheB25 {yields} Leu) associated with diabetes mellitus. The two histidines, three phenylalanines, and four tyrosines are observed to be in distinct local environments; their assignment provides sensitive markers for studies of tertiary structure, protein dynamics, and protein folding. The environments of the tyrosine residues have also been investigated by photochemically induced dynamic nuclear polarization (photo-CIDNP) and analyzed in relation to packing constrains in the crystal structures of insulin. Dimerization involving specific B-chain interactions is observed with increasing protein concentration and is shown to depend on temperature, pH, and solvent composition. The differences between proinsulin and mini-proinsulin suggest a structural mechanism for the observation that the fully reduced B29-A1 analogue folds more efficiently than proinsulin to form the correct pattern of disulfide bonds. These results are discussed in relation to molecular mechanics calculations of insulin based on the available crystal structures.

  5. High Blood Pressure Effects on the Blood to Cerebrospinal Fluid Barrier and Cerebrospinal Fluid Protein Composition: A Two-Dimensional Electrophoresis Study in Spontaneously Hypertensive Rats

    Directory of Open Access Journals (Sweden)

    Ibrahim González-Marrero

    2013-01-01

    Full Text Available The aim of the present work is to analyze the cerebrospinal fluid proteomic profile, trying to find possible biomarkers of the effects of hypertension of the blood to CSF barrier disruption in the brain and their participation in the cholesterol and β-amyloid metabolism and inflammatory processes. Cerebrospinal fluid (CSF is a system linked to the brain and its composition can be altered not only by encephalic disorder, but also by systemic diseases such as arterial hypertension, which produces alterations in the choroid plexus and cerebrospinal fluid protein composition. 2D gel electrophoresis in cerebrospinal fluid extracted from the cistern magna before sacrifice of hypertensive and control rats was performed. The results showed different proteomic profiles between SHR and WKY, that α-1-antitrypsin, apolipoprotein A1, albumin, immunoglobulin G, vitamin D binding protein, haptoglobin and α-1-macroglobulin were found to be up-regulated in SHR, and apolipoprotein E, transthyretin, α-2-HS-glycoprotein, transferrin, α-1β-glycoprotein, kininogen and carbonic anhidrase II were down-regulated in SHR. The conclusion made here is that hypertension in SHR produces important variations in cerebrospinal fluid proteins that could be due to a choroid plexus dysfunction and this fact supports the close connection between hypertension and blood to cerebrospinal fluid barrier disruption.

  6. Position Analysis of Three Recombinant Proteins of Echinococcus granulosus Protoscolex with Two-dimensional Electrophoresis%细粒棘球蚴原头节3种重组抗原的双向电泳定位分析

    Institute of Scientific and Technical Information of China (English)

    朱明星; 李君良; 巨艳; 高鹏; 赵巍

    2013-01-01

    Objective To obtain specific antibodies of the three recombinant antigens obtained previously,rEgZW-5,rEg14-3-3 and rEgP-29,for identifiying the corresponding proteins in two-dimensional electrophoretogram of Echinococcus granulosus protoscolex.Methods The distribution of proteins from E.granulosus protoscoleces was judged by SDS-PAGE previously.Two-dimensional electrophoresis was used to separate proteins from E.granulosus protoscoleces,and the result was scanned and analyzed by the PDquest software to get the information about the quantity of proteins as well as their isoelectric point (IP) and relative molecular mass (Mr).Rabbits were immunized with the 3 recombinant antigens and antibodies were purified from antisera.Western blotting was used to identify the protein as marker in two-dimensional electrophoretogram of protoscolex.Results SDS-PAGE displayed that the proteins separated from Echinococcus granulosus protoscoleces mainly distributed in the Mr region of 18 000-90000.240proteins were obtained by two-dimensional electrophoresis with Mr 15790-117050 and IP 4.0-9.5,and 85.8% (206/241) of the proteins showed the IP ranged from 5 to 9.Western blotting showed that the specific antibody of rEg14-3-3 identified the 14-3-3 protein in two-dimensional electrophoretogram of protoscolex with Mr 33 000 and IP 4.86,the specific antibody of rEgZW-5 identified the ZW-5 protein with Mr 23 000 and IP 4.98,and the specific antibody of rEg P-29 identified the P-29 protein with Mr 29 000 and IP 5.65.Conclusion The antibodies against the three recombinant proteins from Echinococcus granulosus protoscoleces can identify corresponding proteins in the two-dimensional electrophotoregrams.%目的 利用已有的细粒棘球蚴(Echinococcus granulosus)原头节3种重组抗原rEgZW-5、rEg14-3-3和rEgP-29获得特异性抗体,以识别双向电泳图谱中相应的蛋白位点. 方法 十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)初步分离细粒棘球蚴原头节

  7. On two-dimensional Bessel functions

    OpenAIRE

    Korsch, H. J.; Klumpp, A.; Witthaut, D.

    2006-01-01

    The general properties of two-dimensional generalized Bessel functions are discussed. Various asymptotic approximations are derived and applied to analyze the basic structure of the two-dimensional Bessel functions as well as their nodal lines.

  8. Spectral editing of two-dimensional magic-angle-spinning solid-state NMR spectra for protein resonance assignment and structure determination

    International Nuclear Information System (INIS)

    Several techniques for spectral editing of 2D 13C–13C correlation NMR of proteins are introduced. They greatly reduce the spectral overlap for five common amino acid types, thus simplifying spectral assignment and conformational analysis. The carboxyl (COO) signals of glutamate and aspartate are selected by suppressing the overlapping amide N–CO peaks through 13C–15N dipolar dephasing. The sidechain methine (CH) signals of valine, lecuine, and isoleucine are separated from the overlapping methylene (CH2) signals of long-chain amino acids using a multiple-quantum dipolar transfer technique. Both the COO and CH selection methods take advantage of improved dipolar dephasing by asymmetric rotational-echo double resonance (REDOR), where every other π-pulse is shifted from the center of a rotor period tr by about 0.15 tr. This asymmetry produces a deeper minimum in the REDOR dephasing curve and enables complete suppression of the undesired signals of immobile segments. Residual signals of mobile sidechains are positively identified by dynamics editing using recoupled 13C–1H dipolar dephasing. In all three experiments, the signals of carbons within a three-bond distance from the selected carbons are detected in the second spectral dimension via 13C spin exchange. The efficiencies of these spectral editing techniques range from 60 % for the COO and dynamic selection experiments to 25 % for the CH selection experiment, and are demonstrated on well-characterized model proteins GB1 and ubiquitin.

  9. Automating the determination of 3D protein structure

    Energy Technology Data Exchange (ETDEWEB)

    Rayl, K.D.

    1993-12-31

    The creation of an automated method for determining 3D protein structure would be invaluable to the field of biology and presents an interesting challenge to computer science. Unfortunately, given the current level of protein knowledge, a completely automated solution method is not yet feasible, therefore, our group has decided to integrate existing databases and theories to create a software system that assists X-ray crystallographers in specifying a particular protein structure. By breaking the problem of determining overall protein structure into small subproblems, we hope to come closer to solving a novel structure by solving each component. By generating necessary information for structure determination, this method provides the first step toward designing a program to determine protein conformation automatically.

  10. 适于双向电泳分析的酵母胞外蛋白提取方法%Procedure to Prepare Samples for Two-dimensional Electrophoresis of Secreted Proteins from Saccharomyces cerevisiae

    Institute of Scientific and Technical Information of China (English)

    杜维; 朴永哲; 黄玮; 谷月; 赵长新

    2015-01-01

    Saccraomyces cerevsiae FFC2144 was cultured in nitrogen base medium without protein. The secretory proteins of yeasts were extracted by ammonium sulfate precipitation, ultrafiltration and lyophilization-phenol extraction respectively. Extraction rates by 3 methods were calculated and the proteins were separated by two-dimensional electrophoresis. The proteins isolated were confirmed by MALDI-TOF-MS. The extraction rate by lyophilization-phenol method was 73.67% and 114 protein spots were obtained with the most protein spots and clearest electrophoretogram. Lyophilization-phenol method could be an ideal separation method for studying secretory proteomics.%采用了无蛋白酵母培养基培养FFC2144酵母细胞,用硫铵沉淀法、超滤法、冻干酚提等方法提取酵母胞外蛋白,计算3种方法的提取率并分别用双向电泳的方法对提取到的蛋白样品进行分离,同时运用质谱鉴定分离后蛋白.其中冻干-平衡酚法提取后得到114个蛋白点,提取率为73.67%,图谱识别的蛋白点最多图谱最清晰,是研究分泌类蛋白质组学理想的分离方法.

  11. Spectral editing of two-dimensional magic-angle-spinning solid-state NMR spectra for protein resonance assignment and structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt-Rohr, K.; Fritzsching, K. J.; Liao, S. Y.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry and Ames Laboratory (United States)

    2012-12-15

    Several techniques for spectral editing of 2D {sup 13}C-{sup 13}C correlation NMR of proteins are introduced. They greatly reduce the spectral overlap for five common amino acid types, thus simplifying spectral assignment and conformational analysis. The carboxyl (COO) signals of glutamate and aspartate are selected by suppressing the overlapping amide N-CO peaks through {sup 13}C-{sup 15}N dipolar dephasing. The sidechain methine (CH) signals of valine, lecuine, and isoleucine are separated from the overlapping methylene (CH{sub 2}) signals of long-chain amino acids using a multiple-quantum dipolar transfer technique. Both the COO and CH selection methods take advantage of improved dipolar dephasing by asymmetric rotational-echo double resonance (REDOR), where every other {pi}-pulse is shifted from the center of a rotor period t{sub r} by about 0.15 t{sub r}. This asymmetry produces a deeper minimum in the REDOR dephasing curve and enables complete suppression of the undesired signals of immobile segments. Residual signals of mobile sidechains are positively identified by dynamics editing using recoupled {sup 13}C-{sup 1}H dipolar dephasing. In all three experiments, the signals of carbons within a three-bond distance from the selected carbons are detected in the second spectral dimension via {sup 13}C spin exchange. The efficiencies of these spectral editing techniques range from 60 % for the COO and dynamic selection experiments to 25 % for the CH selection experiment, and are demonstrated on well-characterized model proteins GB1 and ubiquitin.

  12. In situ photo-immobilised pH gradient isoelectric focusing and zone electrophoresis integrated two-dimensional microfluidic chip electrophoresis for protein separation

    International Nuclear Information System (INIS)

    A method is introduced for open-column photo-induced site-selective immobilization of pH gradients in a layer of PEG-methacrylate in a multi-dimensional microfluidic chip for use in electrophoresis. It has several attractive features: (a) mixtures of fluorescently labelled proteins carbonic anhydrase, catalase and myoglobin in their native state can be separated by pH-gradient isoelectric focusing (IEF) and zone electrophoresis (CZE) using integrated 2D chip electrophoresis; (b) compared to strip packing or monolithic photo-immobilization, it overcomes the shortcomings of free carrier ampholyte-based 2D chip electrophoresis in an easy way; (c) larger amount of sample can be loaded into the open column-mode electrophoresis (d) immobilized pH gradients can be re-used and the chip can be recycled; (e) a multilayer 3D pH gradient is established by a layer-by-layer assembly technique to further increase the separation capacity. In our perception, this strategy has a large potential in microfluidic chip-based separation schemes because of its simplicity, separation power, re-usability, and separation capacity. (author)

  13. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, J.M. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)

    1991-01-01

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs.

  14. Analysis of Two-Dimensional Gel Electrophoresis Images of Protein from Posterior Silk Gland of Silkworm (Bombyx mori) on Day 1 and Day 4 in the 5th Instar Stage

    Institute of Scientific and Technical Information of China (English)

    WU Wei-cheng; ZHONG Bo-xiong; GAO Qi-kang; CHEN Jin-e; YE Jian; QIAN Yang-wen; LI Jian-ying; LU Hua-yun; MENG Zhi-qi; NI Chun-xiao

    2007-01-01

    The posterior silk gland (PSG) of silkworm is an important organ where fibroin is synthesized and secreted exclusively.Because fibroin constitutes 75-80% of the silk filament, the mechanism governing fibroin secretion, quality and yield of cocoon can be elucidated by the study on the PSG. Using two-dimensional gel electrophoresis (2-DE) and image analysis system, the changes in the protein composition in the PSG cell were investigated on the day 1 (D1) and day 4 (D4) in the 5th instar stage from five different strains of silkworm (Bombyx mori). While differences at protein level between days and strains were far less than those observed at the gene level using EST analysis. The change trends in protein composition from D1 to D4 were diverse among the different strains. The results suggest that the secretion of fibroin is regulated by multiple proteins. The site of regulation and the proteins responsible for the regulation vary with the strain, which leads to differences between strains in the capacity of fibroin secretion in the PSG cell.

  15. Comparison of protein patterns of xrs-5, a radiosensitive Chinese hamster ovary cell line, and CHO-K1, its radioresistant parent, using two-dimensional gel-electrophoresis

    International Nuclear Information System (INIS)

    X-ray sensitive strains of Chinese hamster ovary cell lines have been used to analyze radiation repair mechanisms. One cell line, xrs-5, has been shown to be very sensitive to ionizing radiation and radical forming chemical mutagens. This sensitivity is thought to be a result a mutation in the DNA double strand break (DSB) repair mechanism, and its characterization has been a goal of several repair mechanism studies. Using two-dimensional gel electrophoresis, we have detected a protein (MW approximately 55KD) in the DNA/Nuclear Matrix (nucleoid) cell fraction of CHO-Kl cells that is absent in the nucleoid fraction of xrs-5. This protein is present, however, in both CHO-Kl and xrs-5 whole cell protein maps. To determine whether the 55KD protein is responsible for the radiosensitive and defective DSB repair phenotype of xrs-5 cells, studies are now underway to analyze revertants of xrs-5 that are proficient in DSB repair. Furthermore, an effort to sequence the protein in question is planned. 23 refs., 2 figs

  16. 未成熟与成熟猪囊尾蚴蛋白双向电泳的图谱分析%Total Protein Analysis of Immature and Mature Cysticerci of Taenia solium by Two-dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    方文; 肖靓靓; 包怀恩; 牟荣

    2011-01-01

    为从蛋白质水平揭示猪带绦虫入侵中间宿主家猪的免疫逃避机制,应用双向电泳技术分析未成熟与成熟猪囊尾蚴蛋白质表达差异,进行双向电泳图像软件分析.结果表明:未成熟猪囊尾蚴与成熟猪囊尾蚴蛋白的双向电泳凝胶上分别有(217±13)个、(241±17)个蛋白斑点,未成熟猪囊尾蚴表达上调2倍以上的蛋白有6个,下调2倍以上的蛋白有2个.%In order to explore the immune-escape mechanisms of the T. solium cysticercus on the protein level, the differentially expressed proteins of the immature and mature T. solium cysticerci were separated by two-dimensional electrophoresis respectively and analyzed by ImageMaster 2D Plantinum 6. 0 software. The results showed that the immature and mature T. solium cysticerci have 217 13 and 241 17 protein spots respectively, the immature T. solium cysticerci have six proteins of more than two times upregulation and two proteins of more than two times downregulation compared to the mature T. solium cysticerci.

  17. RNA-protein binding kinetics in an automated microfluidic reactor.

    Science.gov (United States)

    Ridgeway, William K; Seitaridou, Effrosyni; Phillips, Rob; Williamson, James R

    2009-11-01

    Microfluidic chips can automate biochemical assays on the nanoliter scale, which is of considerable utility for RNA-protein binding reactions that would otherwise require large quantities of proteins. Unfortunately, complex reactions involving multiple reactants cannot be prepared in current microfluidic mixer designs, nor is investigation of long-time scale reactions possible. Here, a microfluidic 'Riboreactor' has been designed and constructed to facilitate the study of kinetics of RNA-protein complex formation over long time scales. With computer automation, the reactor can prepare binding reactions from any combination of eight reagents, and is optimized to monitor long reaction times. By integrating a two-photon microscope into the microfluidic platform, 5-nl reactions can be observed for longer than 1000 s with single-molecule sensitivity and negligible photobleaching. Using the Riboreactor, RNA-protein binding reactions with a fragment of the bacterial 30S ribosome were prepared in a fully automated fashion and binding rates were consistent with rates obtained from conventional assays. The microfluidic chip successfully combines automation, low sample consumption, ultra-sensitive fluorescence detection and a high degree of reproducibility. The chip should be able to probe complex reaction networks describing the assembly of large multicomponent RNPs such as the ribosome.

  18. Object Type Recognition for Automated Analysis of Protein Subcellular Location

    OpenAIRE

    Zhao, Ting; Velliste, Meel; Boland, Michael V.; Murphy, Robert F.

    2005-01-01

    The new field of location proteomics seeks to provide a comprehensive, objective characterization of the subcellular locations of all proteins expressed in a given cell type. Previous work has demonstrated that automated classifiers can recognize the patterns of all major subcellular organelles and structures in fluorescence microscope images with high accuracy. However, since some proteins may be present in more than one organelle, this paper addresses a more difficult task: recognizing a pa...

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

    Science.gov (United States)

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

    2004-12-24

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

  20. Initial research of screening for the differentially expressed proteins in beagles irradiated with 4.5 Gy 60Co γ-rays by two-dimensional gel electrophoresis and mass spectrometry

    International Nuclear Information System (INIS)

    Objective: To explore the mechanisms of cytokines on acute radiation disease in irradiation beagles. Methods: The sera of beagles irradiated with 4.5 Gy γ-rays with cytokines treatment was collected at different time points post irradiation. The two-dimensional gel electrophoresis (2-DE) was differentially expressed proteins with significance, and the amino acid sequences should be determined. Results: High resolution 2-DE gel map was obtained. There were six differentially expressed proteins in sera of irradiated beagles at different time points. Four protein spots were successfully identified by MS. A significant spot was identified as serum amyloid A (SAA) by HD-MS, with relative molecular mass of 13 077 and isoelectric point of 6.26. Expression of SAA was not found 1 d pre-irradiation and 36 d post-irradiation, but increased slightly 1 d (0.2166) and significantly 14 d post-irradiation (0.4577). Conclusions: The expression of serum amyloid A was consistent with the process of acute radiation injury, which might indicate the turnover of the disease. (authors)

  1. Comparative Study of Early Cold-Regulated Proteins by Two-Dimensional Difference Gel Electrophoresis Reveals a Key Role for Phospholipase Dα1 in Mediating Cold Acclimation Signaling Pathway in Rice.

    Science.gov (United States)

    Huo, Chenmin; Zhang, Baowen; Wang, Hui; Wang, Fawei; Liu, Meng; Gao, Yingjie; Zhang, Wenhua; Deng, Zhiping; Sun, Daye; Tang, Wenqiang

    2016-04-01

    To understand the early signaling steps that regulate cold responses in rice, two-dimensional difference gel electrophoresis (2-D DIGE)(1)was used to study early cold-regulated proteins in rice seedlings. Using mass spectrometry, 32 spots, which represent 26 unique proteins that showed an altered expression level within 5 min of cold treatment were identified. Among these proteins, Western blot analyses confirmed that the cellular phospholipase D α1 (OsPLDα1) protein level was increased as early as 1 min after cold treatment. Genetic studies showed that reducing the expression ofOsPLDα1makes rice plants more sensitive to chilling stress as well as cold acclimation increased freezing tolerance. Correspondingly, cold-regulated proteomic changes and the expression of the cold-responsive C repeat/dehydration-responsive element binding 1 (OsDREB1) family of transcription factors were inhibited in thepldα1mutant. We also found that the expression ofOsPLDα1is directly regulated by OsDREB1A. This transcriptional regulation ofOsPLDα1could provide positive feedback regulation of the cold signal transduction pathway in rice. OsPLDα1 hydrolyzes phosphatidylcholine to produce the signal molecule phosphatidic acid (PA). By lipid-overlay assay, we demonstrated that the rice cold signaling proteins, MAP kinase 6 (OsMPK6) and OsSIZ1, bind directly to PA. Taken together, our results suggest that OsPLDα1 plays a key role in transducing cold signaling in rice by producing PA and regulatingOsDREB1s' expression by OsMPK6, OsSIZ1, and possibly other PA-binding proteins. PMID:26747563

  2. Two-dimensional electrophoresis analysis of the protein expression of dental pulp in different conditions%不同状态下牙髓组织蛋白质表达的二维电泳分析

    Institute of Scientific and Technical Information of China (English)

    林晨; 聂敏; 张露; 陈智

    2008-01-01

    目的 利用蛋白质组技术探讨牙髓对中龋和热刺激的反应.方法 用双向电泳得到牙髓在中龋和热刺激状态下的二维电泳图谱,对差异点进行质谱鉴定.结果 经Image Master2-D Platinum 5.0软件分析显示,正常牙髓和中龋牙髓的蛋白表达无显著差异;热损伤牙髓有2个蛋白点缺失,8个蛋白点下调.质谱分析鉴定了7种蛋白质.结论 本实验条件下,中龋牙髓的蛋白质表达与正常牙髓无显著差异,热刺激可造成部分蛋白表达的下调.%Objective To analyze the different responses of dental pulp to moderate caries and thermal stimulation by proteomies.Methods Two-dimensional electrophoresis(2-DE)was performed to obtain the 2-D gel electrophoresis patterns of dental pulp.Mass spectrometry(MS)was used to analyze several different selected spots in the expression proteins.Results No significant difference in protein expression was found between normal and moderate carious dental.Two protein spots were absent in heatdamaged group and 8 spots showed significantly down-regulated.Seven proteins were identified by MS.Conclusions In the present study,no significant difference in the pulp protein expression was detected between the healthy and moderate carious pulp tissues.However,down-regulation of pulp protein in thermal stimulation was observed.

  3. Measuring Monotony in Two-Dimensional Samples

    Science.gov (United States)

    Kachapova, Farida; Kachapov, Ilias

    2010-01-01

    This note introduces a monotony coefficient as a new measure of the monotone dependence in a two-dimensional sample. Some properties of this measure are derived. In particular, it is shown that the absolute value of the monotony coefficient for a two-dimensional sample is between /"r"/ and 1, where "r" is the Pearson's correlation coefficient for…

  4. Topology optimization of two-dimensional waveguides

    DEFF Research Database (Denmark)

    Jensen, Jakob Søndergaard; Sigmund, Ole

    2003-01-01

    In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss.......In this work we use the method of topology optimization to design two-dimensional waveguides with low transmission loss....

  5. Two-dimensional generalized Weyl fractional calculus pertaining to two-dimensional $ \\overline{H} $-transforms

    Directory of Open Access Journals (Sweden)

    V. B. L. Chaurasia

    2006-09-01

    Full Text Available The aim of this paper is to establish a relation between the two-dimensional $ \\overline{H} $-transform involving a general polynomials and the Weyl type two-dimensional Saigo operator of fractional integration.

  6. Comparison of different cartilage protein extraction strategies used by two-dimensional electrophorosis technique%应用于双向电泳技术的不同软骨蛋白提取方案对比

    Institute of Scientific and Technical Information of China (English)

    肖军; 尹若峰; 梁锦前; 史占军; 吴志宏; 邱贵兴

    2011-01-01

    目的 探索可兼顾双向电泳凝胶图像质量和结果保真性的软骨蛋白提取方案.方法 取股骨髁软骨(n=17).分别用软骨组织直接提取总蛋白(软骨组织组)、软骨组织提取总蛋白后CPC处理(软骨+CPC组)、直接分离软骨细胞提取总蛋白(直接软骨细胞组)或培养软骨细胞提取总蛋白(培养软骨细胞组)同步进行2-DE,对比不同方案产生凝胶图像质量和结果保真性的差异.结果 软骨组织组不能形成等电聚焦.软骨+CPC组可形成等电聚焦,但蛋白点数量偏少.直接软骨细胞组可获得与培养软骨细胞组媲美的高质量等电聚焦和凝胶图像,且在高分子量和偏碱区域分离出培养软骨细胞组缺如的部分蛋白点,质谱结果显示这些蛋白分别为Ⅵ型胶原、TGF-β2和annexin等骨关节炎病因学相关蛋白.结论 从软骨组织直接提取软骨细胞用于2-DE的方案在解决等电聚焦难题的同时,还避免了细胞培养对实验结果保真性的影响,是软骨相关疾病样本的2-DE研究优化处理方案.%Objective To explore an optimal cartilage protein extraction approach that can guarantee both the image quality and the result fidelity of the two-dimensional gel electrophoresis (2-DE) technique. Methods Knee cartilage samples were obtained from femoral condyles ( n = 17 ). Approaches used for protein samples of 2-DE were grouped: ( 1 ) Extracting protein directly from cartilage samples ( Cartialge approach); ( 2 ) Total protein was treat with cetylpyridinium chloride (CPC) after being extracted from cartilage samples (Cartilage plus CPC approach);(3) Extracting protein from chondrocytes directly isolated from cartilage samples (directly extracted chondrocytes approch). (4)Extracting protein from cultured chondrocytes (cultured chondrocyters approach). Image qualities generated by 2-DE with different protein extracting approaches were compared and the capabilities of these approaches in generating

  7. Two-Dimensional Electronic Spectroscopy Using Incoherent Light: Theoretical Analysis

    CERN Document Server

    Turner, Daniel B; Sutor, Erika J; Hendrickson, Rebecca A; Gealy, M W; Ulness, Darin J

    2012-01-01

    Electronic energy transfer in photosynthesis occurs over a range of time scales and under a variety of intermolecular coupling conditions. Recent work has shown that electronic coupling between chromophores can lead to coherent oscillations in two-dimensional electronic spectroscopy measurements of pigment-protein complexes measured with femtosecond laser pulses. A persistent issue in the field is to reconcile the results of measurements performed using femtosecond laser pulses with physiological illumination conditions. Noisy-light spectroscopy can begin to address this question. In this work we present the theoretical analysis of incoherent two-dimensional electronic spectroscopy, I(4) 2D ES. Simulations reveal diagonal peaks, cross peaks, and coherent oscillations similar to those observed in femtosecond two-dimensional electronic spectroscopy experiments. The results also expose fundamental differences between the femtosecond-pulse and noisy-light techniques; the differences lead to new challenges and opp...

  8. Two-Dimensional Planetary Surface Lander

    Science.gov (United States)

    Hemmati, H.; Sengupta, A.; Castillo, J.; McElrath, T.; Roberts, T.; Willis, P.

    2014-06-01

    A systems engineering study was conducted to leverage a new two-dimensional (2D) lander concept with a low per unit cost to enable scientific study at multiple locations with a single entry system as the delivery vehicle.

  9. Comparison of protein sample preparation methods of two-dimensional electrophoresis for Skeletonema costatum%中肋骨条藻蛋白质双向电泳样品制备方法的比较

    Institute of Scientific and Technical Information of China (English)

    王秀秀; 陈纪新; 黄邦钦

    2012-01-01

    Lysis buffer method and trichloroacetic acid (TCA)-acetone precipitation method both are the common methods in algal protein abstraction. We compared the 2-DE maps of these two protein extraction methods to find out the best protocol for Skeletonema costatum. As a result, the Lysis buffer-TCA-acetone method had better effect than the other two lysis buffer methods (lysis buffer-microcon &- lysis buffer-2 D clean-up kit) in removing the intracellular interferential factors, such as salt, nucleic acid, polyphenol and polysaccharide. The lysis buffer-TCA-acetone method and straight TCA-acetone precipitation method both represented clean background and clear protein dots in 2-DE maps while the later method showed better isoelectrofocusing results. We optimized the straight TCA-acetone precipitation methods. The TCA-acetone precipitation with 12 hours precipitation and a following ultrasonic cleaning process method was confirmed to be the appropiate sample preparation method for S. costatum for two-dimensional electrophoresis.%比较了裂解液法和直接三氯乙酸(TCA)丙酮沉淀法对中肋骨条藻Skeletonema costatum蛋白双向电泳的提取效果并优化了提取条件,结果表明:裂解液-TCA丙酮沉淀法在去除胞内干扰物质方面,较裂解液-超滤管法和裂解液试剂盒法的效果都好.裂解液TCA-丙酮沉淀法和直接TCA-丙酮沉淀法都能取得背景干净、蛋白点清晰的双向电泳图谱,但后者的双向电泳图谱聚焦更完全,在进一步优化条件后(即蛋白沉淀12h并增加超声波洗涤过程),可作为提取中肋骨条藻蛋白的最适方法.

  10. 应用双向电泳和质谱联用技术研究乳源蛋白的差异性%Analysis of milk protein by two-dimensional electrophoresis combined with mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    向明霞; 王丽娜; 李昀锴; 李子超; 成希飞; 徐明芳

    2012-01-01

    Two-dimensional electrophoresiscotnbined with mass spectrometry was used for the analysis of the differences of milk proteins. 21 differential proteins which mainly distributed in areas of low abundance existed only in water buffalo milk were identified according to comparing the profiles of caseins matched with software of ImageMaster 2D Platinum. And 24 differential whey proteins only in water buffalo milk were identified. Four casein fractions belonged to water buffalo milk casein and two new fractions which were high homology components with water buffalo milk casein were determined with the further analysis by mass spectrometry( MS). Four casein fractions belonged to water buffalo milk whey and two new fractions which were high homology components with water buffalo milk whey using were also determined by the same method.%应用双向电泳和质谱联用技术,对不同乳源蛋白的差异性进行了研究.根据ImageMaster 2 DPlatinum图像分析软件对不同乳源酪蛋白和乳清蛋白的双向电泳(2-DE)图谱进行蛋白斑点的匹配分析,获得21个存在于水牛奶中主要分布在低丰度蛋白区的酪蛋白差异蛋白点和24个存在于水牛奶中乳清蛋白差异蛋白点.这些差异蛋白点经质谱鉴定分析,得到4个属于水牛奶酪蛋白的主要组分和2个与水牛奶中酪蛋白有较高同源性的新组分,同时获得4个属于水牛奶乳清蛋白的主要组分和3个与水牛奶中乳清蛋白有较高同源性的组分.

  11. Two-dimensional Topology of Cosmological Reionization

    Science.gov (United States)

    Wang, Yougang; Park, Changbom; Xu, Yidong; Chen, Xuelei; Kim, Juhan

    2015-11-01

    We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two-dimensional genus curve for the early, middle, and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometre Array.

  12. Two dimensional topology of cosmological reionization

    CERN Document Server

    Wang, Yougang; Xu, Yidong; Chen, Xuelei; Kim, Juhan

    2015-01-01

    We study the two-dimensional topology of the 21-cm differential brightness temperature for two hydrodynamic radiative transfer simulations and two semi-numerical models. In each model, we calculate the two dimensional genus curve for the early, middle and late epochs of reionization. It is found that the genus curve depends strongly on the ionized fraction of hydrogen in each model. The genus curves are significantly different for different reionization scenarios even when the ionized faction is the same. We find that the two-dimensional topology analysis method is a useful tool to constrain the reionization models. Our method can be applied to the future observations such as those of the Square Kilometer Array.

  13. Two-dimensional x-ray diffraction

    CERN Document Server

    He, Bob B

    2009-01-01

    Written by one of the pioneers of 2D X-Ray Diffraction, this useful guide covers the fundamentals, experimental methods and applications of two-dimensional x-ray diffraction, including geometry convention, x-ray source and optics, two-dimensional detectors, diffraction data interpretation, and configurations for various applications, such as phase identification, texture, stress, microstructure analysis, crystallinity, thin film analysis and combinatorial screening. Experimental examples in materials research, pharmaceuticals, and forensics are also given. This presents a key resource to resea

  14. Matching Two-dimensional Gel Electrophoresis' Spots

    DEFF Research Database (Denmark)

    Dos Anjos, António; AL-Tam, Faroq; Shahbazkia, Hamid Reza;

    2012-01-01

    This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches. This ar......This paper describes an approach for matching Two-Dimensional Electrophoresis (2-DE) gels' spots, involving the use of image registration. The number of false positive matches produced by the proposed approach is small, when compared to academic and commercial state-of-the-art approaches...

  15. Two-dimensional microstrip detector for neutrons

    Energy Technology Data Exchange (ETDEWEB)

    Oed, A. [Institut Max von Laue - Paul Langevin (ILL), 38 - Grenoble (France)

    1997-04-01

    Because of their robust design, gas microstrip detectors, which were developed at ILL, can be assembled relatively quickly, provided the prefabricated components are available. At the beginning of 1996, orders were received for the construction of three two-dimensional neutron detectors. These detectors have been completed. The detectors are outlined below. (author). 2 refs.

  16. Piezoelectricity in Two-Dimensional Materials

    KAUST Repository

    Wu, Tao

    2015-02-25

    Powering up 2D materials: Recent experimental studies confirmed the existence of piezoelectricity - the conversion of mechanical stress into electricity - in two-dimensional single-layer MoS2 nanosheets. The results represent a milestone towards embedding low-dimensional materials into future disruptive technologies. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA.

  17. Quantum theory of two-dimensional gravity

    International Nuclear Information System (INIS)

    We discuss local O(2,1)-invariant two-dimensional gravity interacting with scalar matter fields. Quantum constraints of lapse and shift functions are obtained by demanding the conformal algebra without a center. From the constraints and the covariant conservation law, we derive the semiclassical expectation value of the energy-momentum tensor of matter

  18. Kronecker Product of Two-dimensional Arrays

    Institute of Scientific and Technical Information of China (English)

    Lei Hu

    2006-01-01

    Kronecker sequences constructed from short sequences are good sequences for spread spectrum communication systems. In this paper we study a similar problem for two-dimensional arrays, and we determine the linear complexity of the Kronecker product of two arrays. Our result shows that similar good property on linear complexity holds for Kronecker product of arrays.

  19. A tracked approach for automated NMR assignments in proteins (TATAPRO)

    Energy Technology Data Exchange (ETDEWEB)

    Atreya, H.S.; Sahu, S.C.; Chary, K.V.R.; Govil, Girjesh [Tata Institute of Fundamental Research, Department of Chemical Sciences (India)

    2000-06-15

    A novel automated approach for the sequence specific NMR assignments of {sup 1}H{sup N}, {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}}, {sup 13}C'/{sup 1}H{sup {alpha}} and {sup 15}N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate {sup 1}H{sup N} and {sup 15}N chemical shifts with those of {sup 13}C{sup {alpha}}, {sup 13}C{sup {beta}} and {sup 13}C'/{sup 1}H{sup {alpha}}. The information derived from such correlations is used to create a 'master{sub l}ist' consisting of all possible sets of {sup 1}H{sup N}{sub i}, {sup 15}N{sub i}, {sup 13}C{sup {alpha}}{sub i}, {sup 13}C{sup {beta}}{sub i}, {sup 13}C'{sub i}/{sup 1}H{sup {alpha}}{sub i}, {sup 13}C{sup {alpha}}{sub i-1}, {sup 13}C{sup {beta}}{sub i-1} and {sup 13}C'{sub i-1}/ {sup 1}H{sup {alpha}}{sub i-1} chemical shifts. On the basis of an extensive statistical analysis of {sup 13}C{sup {alpha}} and {sup 13}C{sup {beta}} chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master{sub l}ist and also to translate the protein primary sequence into an array called pps{sub a}rray. The program then uses the master{sub l}ist to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig{sub a}rray, with the two-digit code assigned earlier. The assig{sub a}rray is then mapped onto the pps{sub a}rray for sequence specific resonance assignment. The program has been tested using

  20. Toward two-dimensional search engines

    International Nuclear Information System (INIS)

    We study the statistical properties of various directed networks using ranking of their nodes based on the dominant vectors of the Google matrix known as PageRank and CheiRank. On average PageRank orders nodes proportionally to a number of ingoing links, while CheiRank orders nodes proportionally to a number of outgoing links. In this way, the ranking of nodes becomes two dimensional which paves the way for the development of two-dimensional search engines of a new type. Statistical properties of information flow on the PageRank–CheiRank plane are analyzed for networks of British, French and Italian universities, Wikipedia, Linux Kernel, gene regulation and other networks. A special emphasis is done for British universities networks using the large database publicly available in the UK. Methods of spam links control are also analyzed. (paper)

  1. Two-dimensional ranking of Wikipedia articles

    Science.gov (United States)

    Zhirov, A. O.; Zhirov, O. V.; Shepelyansky, D. L.

    2010-10-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists ab aeterno. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. While PageRank highlights very well known nodes with many ingoing links, CheiRank highlights very communicative nodes with many outgoing links. In this way the ranking becomes two-dimensional. Using CheiRank and PageRank we analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

  2. Two-dimensional Kagome photonic bandgap waveguide

    DEFF Research Database (Denmark)

    Nielsen, Jens Bo; Søndergaard, Thomas; Libori, Stig E. Barkou;

    2000-01-01

    The transverse-magnetic photonic-bandgap-guidance properties are investigated for a planar two-dimensional (2-D) Kagome waveguide configuration using a full-vectorial plane-wave-expansion method. Single-moded well-localized low-index guided modes are found. The localization of the optical modes...... is investigated with respect to the width of the 2-D Kagome waveguide, and the number of modes existing for specific frequencies and waveguide widths is mapped out....

  3. Two-dimensional Einstein numbers and associativity

    OpenAIRE

    Gregor, Tomáš; Haluška, Ján

    2013-01-01

    In this paper, we deal with generalizations of real Einstein numbers to various spaces and dimensions. We search operations and their properties in generalized settings. Especially, we are interested in the generalized operation of hyperbolic addition to more-dimensional spaces, which is associative and commutative. We extend the theory to some abstract spaces, especially to Hilbert-like ones. Further, we bring two different two-dimensional generalizations of Einstein numbers and study proper...

  4. Fully Localized Two-dimensional Embedded Solitons

    OpenAIRE

    Yang, Jianke

    2010-01-01

    We report the first prediction of fully localized two-dimensional embedded solitons. These solitons are obtained in a quasi-one-dimensional waveguide array which is periodic along one spatial direction and localized along the orthogonal direction. Under appropriate nonlinearity, these solitons are found to exist inside the Bloch bands (continuous spectrum) of the waveguide, and thus are embedded solitons. These embedded solitons are fully localized along both spatial directions. In addition, ...

  5. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    Energy Technology Data Exchange (ETDEWEB)

    Fenglei Li

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  6. Two-dimensional and transient thermal model of the continuous tape laying process

    NARCIS (Netherlands)

    Skandali, M.; Jansen, K.M.B.; Koussios, S.; Sinke, J.; Benedictus, R.

    2015-01-01

    The purpose of this study is to simulate the two-dimensional, transient and continuous heat transfer during the thermoset Automated Tape Laying (ATL) process. The heat transfer analysis is coupled with a cure kinetics model of the thermoset prepreg tapes used for the process. Unlike most studies, th

  7. Two-Dimensional Synthetic-Aperture Radiometer

    Science.gov (United States)

    LeVine, David M.

    2010-01-01

    A two-dimensional synthetic-aperture radiometer, now undergoing development, serves as a test bed for demonstrating the potential of aperture synthesis for remote sensing of the Earth, particularly for measuring spatial distributions of soil moisture and ocean-surface salinity. The goal is to use the technology for remote sensing aboard a spacecraft in orbit, but the basic principles of design and operation are applicable to remote sensing from aboard an aircraft, and the prototype of the system under development is designed for operation aboard an aircraft. In aperture synthesis, one utilizes several small antennas in combination with a signal processing in order to obtain resolution that otherwise would require the use of an antenna with a larger aperture (and, hence, potentially more difficult to deploy in space). The principle upon which this system is based is similar to that of Earth-rotation aperture synthesis employed in radio astronomy. In this technology the coherent products (correlations) of signals from pairs of antennas are obtained at different antenna-pair spacings (baselines). The correlation for each baseline yields a sample point in a Fourier transform of the brightness-temperature map of the scene. An image of the scene itself is then reconstructed by inverting the sampled transform. The predecessor of the present two-dimensional synthetic-aperture radiometer is a one-dimensional one, named the Electrically Scanned Thinned Array Radiometer (ESTAR). Operating in the L band, the ESTAR employs aperture synthesis in the cross-track dimension only, while using a conventional antenna for resolution in the along-track dimension. The two-dimensional instrument also operates in the L band to be precise, at a frequency of 1.413 GHz in the frequency band restricted for passive use (no transmission) only. The L band was chosen because (1) the L band represents the long-wavelength end of the remote- sensing spectrum, where the problem of achieving adequate

  8. Evaporation of two-dimensional black holes

    International Nuclear Information System (INIS)

    An interesting two-dimensional model theory has been proposed that allows one to consider black-hole evaporation in the semiclassical approximation. The semiclassical equations will give a singularity where the dilaton field reaches a certain critical value. This singularity will be hidden behind a horizon. As the evaporation proceeds, the dilaton field on the horizon will approach the critical value but the temperature and rate of emission will remain finite. These results indicate either that there is a naked singularity, or (more likely) that the semiclassical approximation breaks down

  9. Two dimensional thick center vortex model

    Energy Technology Data Exchange (ETDEWEB)

    Rafibakhsh, Shahnoosh; Ahmadi, Alireza [Department of Physics, Science and Research Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2016-01-22

    The potential between static color source is calculated in the SU (3) gauge group by introducing a two dimensional vortex flux. To generalize the model, the length of the Wilson loop is equal to R oriented along the x axis, and the vortex flux is considered as a function of x and y. The comparison between the generalized model and the original one shows that the intermediate linear regime is increased significantly and better agreement with Casimir scaling is achieved. Furthermore, the model is applied to calculate the potential between baryons.

  10. Two dimensional thick center vortex model

    Science.gov (United States)

    Rafibakhsh, Shahnoosh; Ahmadi, Alireza

    2016-01-01

    The potential between static color source is calculated in the SU (3) gauge group by introducing a two dimensional vortex flux. To generalize the model, the length of the Wilson loop is equal to R oriented along the x axis, and the vortex flux is considered as a function of x and y. The comparison between the generalized model and the original one shows that the intermediate linear regime is increased significantly and better agreement with Casimir scaling is achieved. Furthermore, the model is applied to calculate the potential between baryons.

  11. Mobility anisotropy of two-dimensional semiconductors

    CERN Document Server

    Lang, Haifeng; Liu, Zhirong

    2016-01-01

    The carrier mobility of anisotropic two-dimensional (2D) semiconductors under longitudinal acoustic (LA) phonon scattering was theoretically studied with the deformation potential theory. Based on Boltzmann equation with relaxation time approximation, an analytic formula of intrinsic anisotropic mobility was deduced, which shows that the influence of effective mass to the mobility anisotropy is larger than that of deformation potential constant and elastic modulus. Parameters were collected for various anisotropic 2D materials (black phosphorus, Hittorf's phosphorus, BC$_2$N, MXene, TiS$_3$, GeCH$_3$) to calculate their mobility anisotropy. It was revealed that the anisotropic ratio was overestimated in the past.

  12. Two-dimensional heterogeneous photonic bandedge laser

    OpenAIRE

    Kwon, Soon-Hong; Kim, Se-Heon; Kim, Sun-Kyung; Lee, Yong-Hee; Kim, Sung-Bock

    2004-01-01

    We proposed and realized a two-dimensional (2D) photonic bandedge laser surrounded by the photonic bandgap. The heterogeneous photonic crystal structure consists of two triangular lattices of the same lattice constant with different air hole radii. The photonic crystal laser was realized by room-temperature optical pumping of air-bridge slabs of InGaAsP quantum wells emitting at 1.55 micrometer. The lasing mode was identified from its spectral positions and polarization directions. A low thre...

  13. Vector (two-dimensional) magnetic phenomena

    International Nuclear Information System (INIS)

    In this paper, some interesting phenomena were described from the viewpoint of two-dimensional magnetic property, which is reworded with the vector magnetic property. It shows imperfection of conventional magnetic property and some interested phenomena were discovered, too. We found magnetic materials had the strong nonlinearity both magnitude and spatial phase due to the relationship between the magnetic field strength H-vector and the magnetic flux density B-vector. Therefore, magnetic properties should be defined as the vector relationship. Furthermore, the new Barukhausen signal was observed under rotating flux. (Author)

  14. Sums of two-dimensional spectral triples

    DEFF Research Database (Denmark)

    Christensen, Erik; Ivan, Cristina

    2007-01-01

    construct a sum of two dimensional modules which reflects some aspects of the topological dimensions of the compact metric space, but this will only give the metric back approximately. At the end we make an explicit computation of the last module for the unit interval in. The metric is recovered exactly......, the Dixmier trace induces a multiple of the Lebesgue integral but the growth of the number of eigenvalues is different from the one found for the standard differential operator on the unit interval....

  15. Weak turbulence in two-dimensional magnetohydrodynamics

    OpenAIRE

    Tronko, Natalia; Nazarenko, Sergey; Galtier, Sebastien

    2012-01-01

    A weak wave turbulence theory is developed for two-dimensional (2D) magnetohydrodynamics (MHD). We derive and analyze the kinetic equation describing the three-wave interactions of pseudo-Alfv\\'en waves. Our analysis is greatly helped by the fortunate fact that in 2D the wave-kinetic equation is integrable. In contrast with the 3D case, in 2D the wave interactions are nonlocal. Another distinct feature is that strong derivatives of spectra tend to appear in the region of small parallel (i.e. ...

  16. Nonsingular Lagrangians for Two Dimensional Black Holes

    CERN Document Server

    Banks, T

    1993-01-01

    We introduce a large class of modifications of the standard lagrangian for two dimensional dilaton gravity, whose general solutions are nonsingular black holes. A subclass of these lagrangians have extremal solutions which are nonsingular analogues of the extremal Reissner-Nordstrom spacetime. It is possible that quantum deformations of these extremal solutions are the endpoint of Hawking evaporation when the models are coupled to matter, and that the resulting evolution may be studied entirely within the framework of the semiclassical approximation. Numerical work to verify this conjecture is in progress. We point out however that the solutions with non-negative mass always contain Cauchy horizons, and may be sensitive to small perturbations.

  17. Quasicondensation in Two-Dimensional Fermi Gases.

    Science.gov (United States)

    Wu, Chien-Te; Anderson, Brandon M; Boyack, Rufus; Levin, K

    2015-12-11

    In this paper we follow the analysis and protocols of recent experiments, combined with simple theory, to arrive at a physical understanding of quasi-condensation in two dimensional Fermi gases. A key signature of quasi-condensation, which contains aspects of Berezinskiĭ-Kosterlitz-Thouless behavior, is a strong zero momentum peak in the pair momentum distribution. Importantly, this peak emerges at a reasonably well defined onset temperature. The resulting phase diagram, pair momentum distribution, and algebraic power law decay are compatible with recent experiments throughout the continuum from BEC to BCS. PMID:26705613

  18. Two-dimensional ranking of Wikipedia articles

    CERN Document Server

    Zhirov, A O; Shepelyansky, D L

    2010-01-01

    The Library of Babel, described by Jorge Luis Borges, stores an enormous amount of information. The Library exists {\\it ab aeterno}. Wikipedia, a free online encyclopaedia, becomes a modern analogue of such a Library. Information retrieval and ranking of Wikipedia articles become the challenge of modern society. We analyze the properties of two-dimensional ranking of all Wikipedia English articles and show that it gives their reliable classification with rich and nontrivial features. Detailed studies are done for countries, universities, personalities, physicists, chess players, Dow-Jones companies and other categories.

  19. Two-Dimensional Theory of Scientific Representation

    Directory of Open Access Journals (Sweden)

    A Yaghmaie

    2013-03-01

    Full Text Available Scientific representation is an interesting topic for philosophers of science, many of whom have recently explored it from different points of view. There are currently two competing approaches to the issue: cognitive and non-cognitive, and each of them claims its own merits over the other. This article tries to provide a hybrid theory of scientific representation, called Two-Dimensional Theory of Scientific Representation, which has the merits of the two accounts and is free of their shortcomings. To do this, we will argue that although scientific representation needs to use the notion of intentionality, such a notion is defined and realized in a simply structural form contrary to what cognitive approach says about intentionality. After a short introduction, the second part of the paper is devoted to introducing theories of scientific representation briefly. In the third part, the structural accounts of representation will be criticized. The next step is to introduce the two-dimensional theory which involves two key components: fixing and structural fitness. It will be argued that fitness is an objective and non-intentional relation, while fixing is intentional.

  20. Two-dimensional shape memory graphene oxide

    Science.gov (United States)

    Chang, Zhenyue; Deng, Junkai; Chandrakumara, Ganaka G.; Yan, Wenyi; Liu, Jefferson Zhe

    2016-06-01

    Driven by the increasing demand for micro-/nano-technologies, stimuli-responsive shape memory materials at nanoscale have recently attracted great research interests. However, by reducing the size of conventional shape memory materials down to approximately nanometre range, the shape memory effect diminishes. Here, using density functional theory calculations, we report the discovery of a shape memory effect in a two-dimensional atomically thin graphene oxide crystal with ordered epoxy groups, namely C8O. A maximum recoverable strain of 14.5% is achieved as a result of reversible phase transition between two intrinsically stable phases. Our calculations conclude co-existence of the two stable phases in a coherent crystal lattice, giving rise to the possibility of constructing multiple temporary shapes in a single material, thus, enabling highly desirable programmability. With an atomic thickness, excellent shape memory mechanical properties and electric field stimulus, the discovery of a two-dimensional shape memory graphene oxide opens a path for the development of exceptional micro-/nano-electromechanical devices.

  1. Existence and Stability of Two-Dimensional Compact-Like Discrete Breathers in Discrete Two-Dimensional Monatomic Square Lattices

    Institute of Scientific and Technical Information of China (English)

    XU Quan; TIAN Qiang

    2007-01-01

    Two-dimensional compact-like discrete breathers in discrete two-dimensional monatomic square lattices are investigated by discussing a generafized discrete two-dimensional monatomic model.It is proven that the twodimensional compact-like discrete breathers exist not only in two-dimensional soft Ф4 potentials but also in hard two-dimensional Ф4 potentials and pure two-dimensional K4 lattices.The measurements of the two-dimensional compact-like discrete breather cores in soft and hard two-dimensional Ф4 potential are determined by coupling parameter K4,while those in pure two-dimensional K4 lattices have no coupling with parameter K4.The stabilities of the two-dimensional compact-like discrete breathers correlate closely to the coupling parameter K4 and the boundary condition of lattices.

  2. Analysis of Two-Dimensional Electrophoresis Gel Images

    DEFF Research Database (Denmark)

    Pedersen, Lars

    2002-01-01

    and pharmaceutical applications, e.g., drug development. The technique results in an image, where the proteins appear as dark spots on a bright background. However, the analysis of these images is very time consuming and requires a large amount of manual work so there is a great need for fast, objective, and robust...... as two-dimensional points sets and methods for point pattern matching can be applied. This thesis presents a range of state-of-the-art methods for this purpose and also suggests a regionalised scheme. The general point pattern matching methods focussed on are the Robust Point Matching methods and among...

  3. Two-Dimensional Low-Turbulence Tunnel

    Science.gov (United States)

    1938-01-01

    Manometer for the Two-Dimensional Low-Turbulence Tunnel. The Two-Dimensional Low-Turbulence Tunnel was originally called the Refrigeration or 'Ice' tunnel because it was intended to support research on aircraft icing. The tunnel was built of wood, lined with sheet steel, and heavily insulated on the outside. Refrigeration equipment was installed to generate icing conditions inside the test section. The NACA sent out a questionnaire to airline operators, asking them to detail the specific kinds of icing problems they encountered in flight. The replies became the basis for a comprehensive research program begun in 1938 when the tunnel commenced operation. Research quickly focused on the concept of using exhaust heat to prevent ice from forming on the wing's leading edge. This project was led by Lewis Rodert, who later would win the Collier Trophy for his work on deicing. By 1940, aircraft icing research had shifted to the new Ames Research Laboratory, and the Ice tunnel was refitted with screens and honeycomb. Researchers were trying to eliminate all turbulence in the test section. From TN 1283: 'The Langley two-dimensional low-turbulence pressure tunnel is a single-return closed-throat tunnel.... The tunnel is constructed of heavy steel plate so that the pressure of the air may be varied from approximately full vacuum to 10 atmospheres absolute, thereby giving a wide range of air densities. Reciprocating compressors with a capacity of 1200 cubic feet of free air per minute provide compressed air. Since the tunnel shell has a volume of about 83,000 cubic feet, a compression rate of approximately one atmosphere per hour is obtained. ... The test section is rectangular in shape, 3 feet wide, 7 1/2 feet high, and 7 1/2 feet long. ... The over-all size of the wind-tunnel shell is about 146 feet long and 58 feet wide with a maximum diameter of 26 feet. The test section and entrance and exit cones are surrounded by a 22-foot diameter section of the shell to provide a space

  4. Two-dimensional turbulence in magnetised plasmas

    CERN Document Server

    Kendl, Alexander

    2010-01-01

    In an inhomogeneous magnetised plasma the transport of energy and particles perpendicular to the magnetic field is in general mainly caused by quasi two-dimensional turbulent fluid mixing. The physics of turbulence and structure formation is of ubiquitous importance to every magnetically confined laboratory plasma for experimental or industrial application. Specifically, high temperature plasmas for fusion energy research are also dominated by the properties of this turbulent transport. Self-organisation of turbulent vortices to mesoscopic structures like zonal flows is related to the formation of transport barriers that can significantly enhance the confinement of a fusion plasma. This subject of great importance in research is rarely touched on in introductory plasma physics or continuum dynamics courses. Here a brief tutorial on 2D fluid and plasma turbulence is presented as an introduction to the field, appropriate for inclusion in undergraduate and graduate courses.

  5. Acidity of two-dimensional zeolites.

    Science.gov (United States)

    Rybicki, Marcin; Sauer, Joachim

    2015-11-01

    Hybrid quantum mechanics:molecular mechanics (QM/MM) calculations of absolute deprotonation energies are performed with periodic boundary conditions for Brønsted sites of aluminosilicate bilayers with various Al/Si ratios (two-dimensional zeolite). The supercell method is applied and density functional theory is used. Much lower values are obtained (1042, 1069 and 1091 kJ mol(-1) for Al/Si = 1/63, 1/7 and 1/3, respectively) than those for bulk zeolites (1233 kJ mol(-1) for H-chabazite with Al/Si = 1/11). We ascribe the much lower deprotonation energy to the smaller effective dielectric constant (1.6-1.9) of an ultra-thin dielectric in a vacuum compared to that of the corresponding bulk systems (3.0 for H-chabazite), which leads to a better stabilization of the charge created upon deprotonation. PMID:26437870

  6. Influence functional in two dimensional dilaton gravity

    CERN Document Server

    Lombardo, F C; Lombardo, Fernando C.; Mazzitelli, Francisco D.

    1998-01-01

    We evaluate the influence functional for two dimensional models of dilaton gravity. This functional is exactly computed when the conformal invariance is preserved, and it can be written as the difference between the Liouville actions on each closed-time-path branch plus a boundary term. From the influence action we derive the covariant form of the semiclassical field equations. We also study the quantum to classical transition in cosmological backgrounds. In the conformal case we show that the semiclassical approximation is not valid because there is no imaginary part in the influence action. Finally we show that the inclusion of the dilaton loop in the influence functional breaks conformal invariance and ensures the validity of the semiclassical approximation.

  7. Two-dimensional fourier transform spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    DeFlores, Lauren; Tokmakoff, Andrei

    2016-10-25

    The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

  8. Janus Spectra in Two-Dimensional Flows

    Science.gov (United States)

    Liu, Chien-Chia; Cerbus, Rory T.; Chakraborty, Pinaki

    2016-09-01

    In large-scale atmospheric flows, soap-film flows, and other two-dimensional flows, the exponent of the turbulent energy spectra, α , may theoretically take either of two distinct values, 3 or 5 /3 , but measurements downstream of obstacles have invariably revealed α =3 . Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which α transitions from 3 to 5 /3 for the streamwise fluctuations but remains equal to 3 for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows.

  9. Two-dimensional fourier transform spectrometer

    Science.gov (United States)

    DeFlores, Lauren; Tokmakoff, Andrei

    2013-09-03

    The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

  10. Two-dimensional position sensitive neutron detector

    Indian Academy of Sciences (India)

    A M Shaikh; S S Desai; A K Patra

    2004-08-01

    A two-dimensional position sensitive neutron detector has been developed. The detector is a 3He + Kr filled multiwire proportional counter with charge division position readout and has a sensitive area of 345 mm × 345 mm, pixel size 5 mm × 5 mm, active depth 25 mm and is designed for efficiency of 70% for 4 Å neutrons. The detector is tested with 0.5 bar 3He + 1.5 bar krypton gas mixture in active chamber and 2 bar 4He in compensating chamber. The pulse height spectrum recorded at an anode potential of 2000 V shows energy resolution of ∼ 25% for the 764 keV peak. A spatial resolution of 8 mm × 6 mm is achieved. The detector is suitable for SANS studies in the range of 0.02–0.25 Å-1.

  11. Optimal excitation of two dimensional Holmboe instabilities

    CERN Document Server

    Constantinou, Navid C

    2010-01-01

    Highly stratified shear layers are rendered unstable even at high stratifications by Holmboe instabilities when the density stratification is concentrated in a small region of the shear layer. These instabilities may cause mixing in highly stratified environments. However these instabilities occur in tongues for a limited range of parameters. We perform Generalized Stability analysis of the two dimensional perturbation dynamics of an inviscid Boussinesq stratified shear layer and show that Holmboe instabilities at high Richardson numbers can be excited by their adjoints at amplitudes that are orders of magnitude larger than by introducing initially the unstable mode itself. We also determine the optimal growth that obtains for parameters for which there is no instability. We find that there is potential for large transient growth regardless of whether the background flow is exponentially stable or not and that the characteristic structure of the Holmboe instability asymptotically emerges for parameter values ...

  12. Local doping of two-dimensional materials

    Energy Technology Data Exchange (ETDEWEB)

    Wong, Dillon; Velasco, Jr, Jairo; Ju, Long; Kahn, Salman; Lee, Juwon; Germany, Chad E.; Zettl, Alexander K.; Wang, Feng; Crommie, Michael F.

    2016-09-20

    This disclosure provides systems, methods, and apparatus related to locally doping two-dimensional (2D) materials. In one aspect, an assembly including a substrate, a first insulator disposed on the substrate, a second insulator disposed on the first insulator, and a 2D material disposed on the second insulator is formed. A first voltage is applied between the 2D material and the substrate. With the first voltage applied between the 2D material and the substrate, a second voltage is applied between the 2D material and a probe positioned proximate the 2D material. The second voltage between the 2D material and the probe is removed. The first voltage between the 2D material and the substrate is removed. A portion of the 2D material proximate the probe when the second voltage was applied has a different electron density compared to a remainder of the 2D material.

  13. Two-dimensional nuclear magnetic resonance petrophysics.

    Science.gov (United States)

    Sun, Boqin; Dunn, Keh-Jim

    2005-02-01

    Two-dimensional nuclear magnetic resonance (2D NMR) opens a wide area for exploration in petrophysics and has significant impact to petroleum logging technology. When there are multiple fluids with different diffusion coefficients saturated in a porous medium, this information can be extracted and clearly delineated from CPMG measurements of such a system either using regular pulsing sequences or modified two window sequences. The 2D NMR plot with independent variables of T2 relaxation time and diffusion coefficient allows clear separation of oil and water signals in the rocks. This 2D concept can be extended to general studies of fluid-saturated porous media involving other combinations of two or more independent variables, such as chemical shift and T1/T2 relaxation time (reflecting pore size), proton population and diffusion contrast, etc. PMID:15833623

  14. 体内 D-酸性氨基酸分析的自动二维手性高效液相色谱法的建立及应用%Establishment and Application of an Automated Chiral Two-dimensional High Performance Liquid Chromatography for Bio-analysis of D-Acidic Amino Acids

    Institute of Scientific and Technical Information of China (English)

    韩海; 王启钦; 吴慧慧; 王欢

    2014-01-01

    The physiological and bio-marker function of D-acidic amino acids is now becoming the hot topic on metabolomics study and new drug discovery. A fully automated two-dimensional high performance liquid chromatography (2D-HPLC) system was established by using monolithic ODS column as the first dimension column, acetonitrile-trifluoro acetic acid-water (9: 0. 05: 92, V/ V) as the mobile phase; micro Chiralpak QD-1-AX column as the enantiomer separation column, 10 mmol/ L citric acid in methanol-acetonitrile (50: 50, V/ V) as the mobile phase for the second dimension, 4-fluoro-7-nitro-2,1,3-benzoxadiazole (NBD-F) as the fluorometrical derivative reagent. The separation efficiency ( Rs > 2. 5), determination sensitivity ( LOD =1 fmol) of acidic amino acids enantiomers were higher than those of existing methods, and an online confirmation of the enantiomers amounts was also achieved using this system. The recoveries were around 97-104% , RSD values for intra-day and inter-day precision were less than 5% for the acidic amino acids enantiomers in the biological samples. Furthermore, by analyzing the aging model senescence accelerated mouse prone 1 (SAMP1) mice which have low immunocompetence, the amounts of D-aspartic acid in thymus and spleen were determined as (206±18) and (264±21) nmol/ g, respectively. It is the first time that an obvious trend of the increasement of D-aspartic acid (p2.5);高灵敏度检测(LOD =1 fmol)及定量值的确证,酸性氨基酸异构体回收率均在97%~104%之间,日内日间精密度的 RSD<5%。应用本系统对免疫功能低下的老年病小鼠动物模型快速老化小鼠亚系1(SAMP1)进行分析,测得 SAMP1小鼠胸腺和脾脏中 D-天门冬氨酸的含量分别为(206±18)nmol/ g 和(264±21)nmol/ g。首次发现了其胸腺和脾脏中 D-天门冬氨酸的含量较对照组同龄抗快速老化小鼠亚系1(SAMR1)有显著升高趋势(p<0.01)。

  15. Automated production of recombinant human proteins as resource for proteome research

    OpenAIRE

    Poustka Annemarie; Wiemann Stefan; Schmidt Christian; Kohl Thorsten; Korf Ulrike

    2008-01-01

    Abstract Background An arbitrary set of 96 human proteins was selected and tested to set-up a fully automated protein production strategy, covering all steps from DNA preparation to protein purification and analysis. The target proteins are encoded by functionally uncharacterized open reading frames (ORF) identified by the German cDNA consortium. Fusion proteins were produced in E. coli with four different fusion tags and tested in five different purification strategies depending on the respe...

  16. Automated production of recombinant human proteins as resource for proteome research

    Directory of Open Access Journals (Sweden)

    Poustka Annemarie

    2008-01-01

    Full Text Available Abstract Background An arbitrary set of 96 human proteins was selected and tested to set-up a fully automated protein production strategy, covering all steps from DNA preparation to protein purification and analysis. The target proteins are encoded by functionally uncharacterized open reading frames (ORF identified by the German cDNA consortium. Fusion proteins were produced in E. coli with four different fusion tags and tested in five different purification strategies depending on the respective fusion tag. The automated strategy relies on standard liquid handling and clone picking equipment. Results A robust automated strategy for the production of recombinant human proteins in E. coli was established based on a set of four different protein expression vectors resulting in NusA/His, MBP/His, GST and His-tagged proteins. The yield of soluble fusion protein was correlated with the induction temperature and the respective fusion tag. NusA/His and MBP/His fusion proteins are best expressed at low temperature (25°C, whereas the yield of soluble GST fusion proteins was higher when protein expression was induced at elevated temperature. In contrast, the induction of soluble His-tagged fusion proteins was independent of the temperature. Amylose was not found useful for affinity-purification of MBP/His fusion proteins in a high-throughput setting, and metal chelating chromatography is recommended instead. Conclusion Soluble fusion proteins can be produced in E. coli in sufficient qualities and μg/ml culture quantities for downstream applications like microarray-based assays, and studies on protein-protein interactions employing a fully automated protein expression and purification strategy. Future applications might include the optimization of experimental conditions for the large-scale production of soluble recombinant proteins from libraries of open reading frames.

  17. Janus spectra in two-dimensional flows

    CERN Document Server

    Liu, Chien-Chia; Chakraborty, Pinaki

    2016-01-01

    In theory, large-scale atmospheric flows, soap-film flows and other two-dimensional flows may host two distinct types of turbulent energy spectra---in one, $\\alpha$, the spectral exponent of velocity fluctuations, equals $3$ and the fluctuations are dissipated at the small scales, and in the other, $\\alpha=5/3$ and the fluctuations are dissipated at the large scales---but measurements downstream of obstacles have invariably revealed $\\alpha = 3$. Here we report experiments on soap-film flows where downstream of obstacles there exists a sizable interval in which $\\alpha$ has transitioned from $3$ to $5/3$ for the streamwise fluctuations but remains equal to $3$ for the transverse fluctuations, as if two mutually independent turbulent fields of disparate dynamics were concurrently active within the flow. This species of turbulent energy spectra, which we term the Janus spectra, has never been observed or predicted theoretically. Our results may open up new vistas in the study of turbulence and geophysical flows...

  18. Turbulence in two dimensional visco - elastic medium

    CERN Document Server

    Tiwari, Sanat Kumar; Das, Amita; Patel, Bhavesh G; Kaw, Predhiman

    2014-01-01

    The properties of decaying turbulence is studied with the help of a Generalized Hydrodynamic (GHD) fluid model in the context of two dimensional visco - elastic medium such as a strongly coupled dusty plasma system. For the incompressible case considered here however, the observations are valid for a wider class of visco - elastic systems not necessarily associated with plasmas only. Our observations show that an initial spectrum that is confined in a limited domain of wave numbers becomes broad, even when the Reynold's number is much less than the critical value required for the onset of turbulence in Newtonian fluids. This is a signature of elastic turbulence where Weissenberg's number also plays a role in the onset of turbulence. This has been reported in several experiments. It is also shown that the existence of memory relaxation time parameter and the transverse shear wave inhibit the normal process (for 2-D systems) of inverse spectral cascade in this case. A detailed simulation study has been carried ...

  19. Photodetectors based on two dimensional materials

    Science.gov (United States)

    Zheng, Lou; Zhongzhu, Liang; Guozhen, Shen

    2016-09-01

    Two-dimensional (2D) materials with unique properties have received a great deal of attention in recent years. This family of materials has rapidly established themselves as intriguing building blocks for versatile nanoelectronic devices that offer promising potential for use in next generation optoelectronics, such as photodetectors. Furthermore, their optoelectronic performance can be adjusted by varying the number of layers. They have demonstrated excellent light absorption, enabling ultrafast and ultrasensitive detection of light in photodetectors, especially in their single-layer structure. Moreover, due to their atomic thickness, outstanding mechanical flexibility, and large breaking strength, these materials have been of great interest for use in flexible devices and strain engineering. Toward that end, several kinds of photodetectors based on 2D materials have been reported. Here, we present a review of the state-of-the-art in photodetectors based on graphene and other 2D materials, such as the graphene, transition metal dichalcogenides, and so on. Project supported by the National Natural Science Foundation of China (Nos. 61377033, 61574132, 61504136) and the State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences.

  20. Asymptotics for Two-dimensional Atoms

    DEFF Research Database (Denmark)

    Nam, Phan Thanh; Portmann, Fabian; Solovej, Jan Philip

    2012-01-01

    We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E^{\\TF}(\\lambd......We prove that the ground state energy of an atom confined to two dimensions with an infinitely heavy nucleus of charge $Z>0$ and $N$ quantum electrons of charge -1 is $E(N,Z)=-{1/2}Z^2\\ln Z+(E^{\\TF}(\\lambda)+{1/2}c^{\\rm H})Z^2+o(Z^2)$ when $Z\\to \\infty$ and $N/Z\\to \\lambda$, where $E......^{\\TF}(\\lambda)$ is given by a Thomas-Fermi type variational problem and $c^{\\rm H}\\approx -2.2339$ is an explicit constant. We also show that the radius of a two-dimensional neutral atom is unbounded when $Z\\to \\infty$, which is contrary to the expected behavior of three-dimensional atoms....

  1. Two-dimensional transport of tokamak plasmas

    International Nuclear Information System (INIS)

    A reduced set of two-fluid transport equations is obtained from the conservation equations describing the time evolution of the differential particle number, entropy, and magnetic fluxes in an axisymmetric toroidal plasma with nested magnetic surfaces. Expanding in the small ratio of perpendicular to parallel mobilities and thermal conductivities yields as solubility constraints one-dimensional equations for the surface-averaged thermodynamic variables and magnetic fluxes. Since Ohm's law E +u x B =R', where R' accounts for any nonideal effects, only determines the particle flow relative to the diffusing magnetic surfaces, it is necessary to solve a single two-dimensional generalized differential equation, (partial/partialt) delpsi. (delp - J x B) =0, to find the absolute velocity of a magnetic surface enclosing a fixed toroidal flux. This equation is linear but nonstandard in that it involves flux surface averages of the unknown velocity. Specification of R' and the cross-field ion and electron heat fluxes provides a closed system of equations. A time-dependent coordinate transformation is used to describe the diffusion of plasma quantities through magnetic surfaces of changing shape

  2. Predicting Two-Dimensional Silicon Carbide Monolayers.

    Science.gov (United States)

    Shi, Zhiming; Zhang, Zhuhua; Kutana, Alex; Yakobson, Boris I

    2015-10-27

    Intrinsic semimetallicity of graphene and silicene largely limits their applications in functional devices. Mixing carbon and silicon atoms to form two-dimensional (2D) silicon carbide (SixC1-x) sheets is promising to overcome this issue. Using first-principles calculations combined with the cluster expansion method, we perform a comprehensive study on the thermodynamic stability and electronic properties of 2D SixC1-x monolayers with 0 ≤ x ≤ 1. Upon varying the silicon concentration, the 2D SixC1-x presents two distinct structural phases, a homogeneous phase with well dispersed Si (or C) atoms and an in-plane hybrid phase rich in SiC domains. While the in-plane hybrid structure shows uniform semiconducting properties with widely tunable band gap from 0 to 2.87 eV due to quantum confinement effect imposed by the SiC domains, the homogeneous structures can be semiconducting or remain semimetallic depending on a superlattice vector which dictates whether the sublattice symmetry is topologically broken. Moreover, we reveal a universal rule for describing the electronic properties of the homogeneous SixC1-x structures. These findings suggest that the 2D SixC1-x monolayers may present a new "family" of 2D materials, with a rich variety of properties for applications in electronics and optoelectronics. PMID:26394207

  3. Predicting Two-Dimensional Silicon Carbide Monolayers.

    Science.gov (United States)

    Shi, Zhiming; Zhang, Zhuhua; Kutana, Alex; Yakobson, Boris I

    2015-10-27

    Intrinsic semimetallicity of graphene and silicene largely limits their applications in functional devices. Mixing carbon and silicon atoms to form two-dimensional (2D) silicon carbide (SixC1-x) sheets is promising to overcome this issue. Using first-principles calculations combined with the cluster expansion method, we perform a comprehensive study on the thermodynamic stability and electronic properties of 2D SixC1-x monolayers with 0 ≤ x ≤ 1. Upon varying the silicon concentration, the 2D SixC1-x presents two distinct structural phases, a homogeneous phase with well dispersed Si (or C) atoms and an in-plane hybrid phase rich in SiC domains. While the in-plane hybrid structure shows uniform semiconducting properties with widely tunable band gap from 0 to 2.87 eV due to quantum confinement effect imposed by the SiC domains, the homogeneous structures can be semiconducting or remain semimetallic depending on a superlattice vector which dictates whether the sublattice symmetry is topologically broken. Moreover, we reveal a universal rule for describing the electronic properties of the homogeneous SixC1-x structures. These findings suggest that the 2D SixC1-x monolayers may present a new "family" of 2D materials, with a rich variety of properties for applications in electronics and optoelectronics.

  4. Two-Dimensional Crystallization of the Ca(2+)-ATPase for Electron Crystallography.

    Science.gov (United States)

    Glaves, John Paul; Primeau, Joseph O; Young, Howard S

    2016-01-01

    Electron crystallography of two-dimensional crystalline arrays is a powerful alternative for the structure determination of membrane proteins. The advantages offered by this technique include a native membrane environment and the ability to closely correlate function and dynamics with crystalline preparations and structural data. Herein, we provide a detailed protocol for the reconstitution and two-dimensional crystallization of the sarcoplasmic reticulum calcium pump (also known as Ca(2+)-ATPase or SERCA) and its regulatory subunits phospholamban and sarcolipin.

  5. Two-Dimensional Electrophoretic Analysis of Soluble Leaf Proteins of a Salt-sensitive (Triticum aestivum) and a Salt-tolerant (T. Durum) Cultivar in Response to NaCl Stress

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In this research, 3-day-old etiolated wheat seedlings of Triticum aestivum L. cv. Ceyhan-99 (salt-sensitive) and T. durum Desf. cv. Firat-93 (salt-tolerant) were grown in control and salt (150 mmol/L NaCl) treatments at a 15/25℃ temperature regime in the light for 12 days. Soluble proteins extracted from the first leaf tissues of two cultivars were analyzed by twodimensional (2-D) electrophoresis in order to detect NaCl-induced changes. The soluble leaf protein profiles of cultivars were observed to be similar. However, quantitative differences in 74 proteins were detected in the salt treatment group,compared to the control. Among the 74 protein spots, 14 were common for two cultivars. As a result of NaCl treatment, two low-molecular-weight (LMW) proteins (28.9 and 30.0 kDa) and one intermediate-molecular-weight (IMW) protein (44.3 kDa)in cv. Ceyhan-99 and six LMW proteins (18.6, 19.4, 25.7, 25.9, 26 and 27.6 kDa) in cv. Firat-93 were newly synthesized. The newly synthesized proteins were specific to each cultivar. In the Firat-93 cultivar, four proteins with LMW (24.8-27.9 kDa)were completely lost in NaCl treatment. Moreover, these four protein spots were not observed in both protein profiles of cv. Ceyhan-99. Most of these proteins were in acidic character (pi <6.0-6.9) and low molecular weight (<31.6 kDa). It is suggested that the newly synthesized or completely lost LMW proteins may be important for cultivars differing in sensitivity towards NaCl.

  6. Two-dimensional dynamic fluid bowtie attenuators.

    Science.gov (United States)

    Hermus, James R; Szczykutowicz, Timothy P

    2016-01-01

    Fluence field modulated (FFM) CT allows for improvements in image quality and dose reduction. To date, only one-dimensional modulators have been proposed, as the extension to two-dimensional (2-D) modulation is difficult with solid-metal attenuation-based fluence field modulated designs. This work proposes to use liquid and gas to attenuate the x-ray beam, as unlike solids, these materials can be arranged allowing for 2-D fluence modulation. The thickness of liquid and the pressure for a given path length of gas were determined that provided the same attenuation as 30 cm of soft tissue at 80, 100, 120, and 140 kV. Liquid iodine, zinc chloride, cerium chloride, erbium oxide, iron oxide, and gadolinium chloride were studied. Gaseous xenon, uranium hexafluoride, tungsten hexafluoride, and nickel tetracarbonyl were also studied. Additionally, we performed a proof-of-concept experiment using a 96 cell array in which the liquid thickness in each cell was adjusted manually. Liquid thickness varied as a function of kV and chemical composition, with erbium oxide allowing for the smallest thickness. For the gases, tungsten hexaflouride required the smallest pressure to compensate for 30 cm of soft tissue. The 96 cell iodine attenuator allowed for a reduction in both dynamic range to the detector and scatter-to-primary ratio. For both liquids and gases, when k-edges were located within the diagnostic energy range used for imaging, the mean beam energy exhibited the smallest change with compensation amount. The thickness of liquids and the gas pressure seem logistically implementable within the space constraints of C-arm-based cone beam CT (CBCT) and diagnostic CT systems. The gas pressures also seem logistically implementable within the space and tube loading constraints of CBCT and diagnostic CT systems. PMID:26835499

  7. Automated protein motif generation in the structure-based protein function prediction tool ProMOL.

    Science.gov (United States)

    Osipovitch, Mikhail; Lambrecht, Mitchell; Baker, Cameron; Madha, Shariq; Mills, Jeffrey L; Craig, Paul A; Bernstein, Herbert J

    2015-12-01

    ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. PMID:26573864

  8. The MRC-5 human embryonal lung fibroblast two-dimensional gel cellular protein database: quantitative identification of polypeptides whose relative abundance differs between quiescent, proliferating and SV40 transformed cells

    DEFF Research Database (Denmark)

    Celis, J E; Dejgaard, K; Madsen, Peder;

    1990-01-01

    proteins quantitated so far, the levels of 138 were up- or down-regulated (51 and 87, respectively) by two times or more in the transformed cells as compared to their normal proliferating counterparts, while only 14 behaved similarly in quiescent cells. Seven MRC-5 SV40 proteins, including plastin and two...... cells (AMA) database (Celis et al., Electrophoresis 1990, 11, 989-1071) for those polypeptides of known and unknown identity that have been matched to AMA polypeptides. As more information is gathered in this and other laboratories, including data on oncogene proteins and transcription factors......, this comprehensive database will outline an integrated picture of the expression levels and properties of the thousands of protein components of organelles, pathways and cytoskeletal systems that may be directly or indirectly involved in properties associated with the transformed state. Udgivelsesdato: 1990-Dec...

  9. Comparative proteomics of E. coli O157:H7: two-dimensional gel electrophoresis vs. two-dimensional liquid chromatography separation

    Science.gov (United States)

    The accepted method for comparing bacterial proteomes has traditionally been two-dimensional gel electrophoresis (2-D GE). However, in recent years, new procedures for protein separation have been introduced. One of these new procedures utilizes column-based liquid chromatography (2-D LC) separati...

  10. Two-dimensional vibrational-electronic spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Courtney, Trevor L.; Fox, Zachary W.; Slenkamp, Karla M.; Khalil, Munira, E-mail: mkhalil@uw.edu [Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195 (United States)

    2015-10-21

    Two-dimensional vibrational-electronic (2D VE) spectroscopy is a femtosecond Fourier transform (FT) third-order nonlinear technique that creates a link between existing 2D FT spectroscopies in the vibrational and electronic regions of the spectrum. 2D VE spectroscopy enables a direct measurement of infrared (IR) and electronic dipole moment cross terms by utilizing mid-IR pump and optical probe fields that are resonant with vibrational and electronic transitions, respectively, in a sample of interest. We detail this newly developed 2D VE spectroscopy experiment and outline the information contained in a 2D VE spectrum. We then use this technique and its single-pump counterpart (1D VE) to probe the vibrational-electronic couplings between high frequency cyanide stretching vibrations (ν{sub CN}) and either a ligand-to-metal charge transfer transition ([Fe{sup III}(CN){sub 6}]{sup 3−} dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN){sub 5}Fe{sup II}CNRu{sup III}(NH{sub 3}){sub 5}]{sup −} dissolved in formamide). The 2D VE spectra of both molecules reveal peaks resulting from coupled high- and low-frequency vibrational modes to the charge transfer transition. The time-evolving amplitudes and positions of the peaks in the 2D VE spectra report on coherent and incoherent vibrational energy transfer dynamics among the coupled vibrational modes and the charge transfer transition. The selectivity of 2D VE spectroscopy to vibronic processes is evidenced from the selective coupling of specific ν{sub CN} modes to the MMCT transition in the mixed valence complex. The lineshapes in 2D VE spectra report on the correlation of the frequency fluctuations between the coupled vibrational and electronic frequencies in the mixed valence complex which has a time scale of 1 ps. The details and results of this study confirm the versatility of 2D VE spectroscopy and its applicability to probe how vibrations modulate charge and energy transfer in a

  11. Application of Natural Isotopic Abundance ¹H-¹³C- and ¹H-¹⁵N-Correlated Two-Dimensional NMR for Evaluation of the Structure of Protein Therapeutics.

    Science.gov (United States)

    Arbogast, Luke W; Brinson, Robert G; Marino, John P

    2016-01-01

    Methods for characterizing the higher-order structure of protein therapeutics are in great demand for establishing consistency in drug manufacturing, for detecting drug product variations resulting from modifications in the manufacturing process, and for comparing a biosimilar to an innovator reference product. In principle, solution NMR can provide a robust approach for characterization of the conformation(s) of protein therapeutics in formulation at atomic resolution. However, molecular weight limitations and the perceived need for stable isotope labeling have to date limited its practical applications in the biopharmaceutical industry. Advances in NMR magnet and console technologies, cryogenically cooled probes, and new rapid acquisition methodologies, particularly selective optimized flip-angle short transient pulse schemes and nonuniform sampling, have greatly ameliorated these limitations. Here, we describe experimental methods for the collection and analysis of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra applied to protein drug products at natural isotopic abundance, including representatives from the rapidly growing class of monoclonal antibody (mAb) therapeutics. Practical aspects of experimental setup and data acquisition for both standard and rapid acquisition NMR techniques are described. Furthermore, strategies for the statistical comparison of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra are detailed. PMID:26791974

  12. CASA: An Efficient Automated Assignment of Protein Mainchain NMR Data Using an Ordered Tree Search Algorithm

    International Nuclear Information System (INIS)

    Rapid analysis of protein structure, interaction, and dynamics requires fast and automated assignments of 3D protein backbone triple-resonance NMR spectra. We introduce a new depth-first ordered tree search method of automated assignment, CASA, which uses hand-edited peak-pick lists of a flexible number of triple resonance experiments. The computer program was tested on 13 artificially simulated peak lists for proteins up to 723 residues, as well as on the experimental data for four proteins. Under reasonable tolerances, it generated assignments that correspond to the ones reported in the literature within a few minutes of CPU time. The program was also tested on the proteins analyzed by other methods, with both simulated and experimental peaklists, and it could generate good assignments in all relevant cases. The robustness was further tested under various situations

  13. The Best Method for Extracting and Concentration Detecting of Proteins Used for Two-dimensional Electrophoresis from Flowering Buds of Chinese Cabbage (Brassica rapa L. ssp. pekinensis)%适合双向电泳的大白菜花蕾蛋白提取及浓度测定方法

    Institute of Scientific and Technical Information of China (English)

    周雪; 冯辉; 冀瑞琴

    2013-01-01

    Extracting high-quality flower bud proteins is the prerequisite in studying of the floral-organ Proteome in Chinese cabbage. In this experiment, the flower buds of Chinese cabbage A/B line AB01 were used to extract the whole protein by using the following six methods (TCA acetone precipitation method, Tris-HC1 method, Phenol modified method, Trizol precipitation method, Tris-acetone-phenol method and Urea-thiourea extraction method). The 2-DE maps were generated by the two-dimensional electrophoresis approach as well. The best methods for flower bud protein extraction and concentration determination were selected by analyzing and comparing the protein spots in 2-DE maps. The results showed that the protein spots in the 2-DE maps generated by TCA-acetone precipitation were clear and even distributed, therefore the TCA-acetone precipitation method was recommended as an ideal methods for extracting the flower bud protein, while the Protein Assay kit should be more accurate to detect the protein concentration based on comparing the maps generated by the two-dimensional electrophoresis protein quantitative kit and Bradford method.%  高质量提取大白菜花蕾蛋白是大白菜花器官蛋白质组学研究的关键步骤。本试验以大白菜AB01可育花蕾为材料,采用TCA丙酮沉淀法、Tris-HC1法、酚改良法、Trizol沉淀法、Tris-丙酮-酚法和尿素-硫脲提取法等六种方法分别提取花蕾全蛋白,通过Bradford法和双向电泳蛋白定量试剂盒测定蛋白浓度,经双向电泳分离后得到2-DE图谱,经分析、比较图谱蛋白点的情况,找到花蕾全蛋白的最佳提取方法和浓度测定方法。结果显示:TCA丙酮沉淀法得到的2-DE图谱,蛋白点分布均匀、清晰,是一种较为理想的花蕾蛋白提取方法;采用蛋白定量试剂盒测定蛋白浓度更加准确。

  14. Optimization of the conditions for serum protein two-dimensional gel electrophoresis in polycystic ovary syndrome%多囊卵巢综合征患者血清蛋白质双向凝胶电泳技术条件优化

    Institute of Scientific and Technical Information of China (English)

    秦芬; 丘彦; 杨曦; 孟江萍

    2010-01-01

    目的 探讨多囊卵巢综合征(PCOS)患者外周静脉血血清蛋白质的双向凝胶电泳条件优化.方法 对去除血清中的高丰度蛋白与否、不同蛋白质上样量、固相pH梯度(IPG)胶条的pH值范围、水化上样液体积、水化时间进行双向电泳实验结果 比较.结果 将去除高丰度蛋白血清样品中300μg蛋白质溶解于终体积为400μl水化上样液,水化14 h,应用pH 4-7的IPG胶条和浓度12%的SDS-PAGE凝胶进行双向电泳,得到图象清晰,蛋白斑点数为369个蛋白质二维图谱.结论 优化了PCOS血清双向凝胶电泳的条件,得到分辨率较好的PCOS血清的蛋白图谱,创造了进一步开展PCOS血清蛋白质组图谱分析条件.%Objective To optimize the conditions of two-dimensional gel electrophoresis(2-DE) for serum protein in peripheral venous blood of patients with polycystic ovary syndrome. Methods After high-abundance proteins were removed from serum samples with AurumTM Serum Protein Mini Kit of Bio-Rad company, the amount of protein sample,pH range of IPG,the concentration of gel, the volume of sample hydration fluid, and hydration time in different conditions were used to separate the proteins. Results With the conditions of dissolving 300μg proteins to form 400μl sample fluid hydration,adjusting IPG pH from 4 to 7 and using 12% SDS-PAGE gel,some satisfactory two-dimensional maps of proteins were acquired. Conclusions The optimizated conditions for serum protein 2-DE in human being are the foundation for further study on serum diferential proteomics.

  15. Zero in on Key Open Problems in Automated NMR Protein Structure Determination

    KAUST Repository

    Abbas, Ahmed

    2015-11-12

    consensus of the B-H selected peaks from both PICKY and WaVPeak. On average, the consensus method is able to identify more than 88% of the expected true peaks, whereas less than 17% of the selected peaks are false ones. Our third contribution is to propose for the first time, the 3D extension of the Median-Modified-Wiener-Filter (MMWF), and its novel variation named MMWF*. These spatial filters have only one parameter to tune: the window-size. Unlike wavelet denoising, the higher dimensional extension of the newly proposed filters is relatively easy. Thus, they can be applied to denoise multi-dimensional NMR-spectra. We tested the proposed filters and the Wiener-filter, an adaptive variant of the mean-filter, on a benchmark set that contains 16 two-dimensional and three-dimensional NMR- spectra extracted from eight proteins. Our results demonstrate that the adaptive spatial filters significantly outperform their non-adaptive versions. The performance of the new MMWF* on 2D/3D-spectra is even better than wavelet-denoising. Finally, we propose a novel framework that simultaneously conducts slice picking and spin system forming, an essential step in resonance assignment. Our framework then employs a genetic algorithm, directed by both connectivity information and amino acid typing information from the spin systems to assign the spin systems to residues. The inputs to our framework can be as few as two commonly used spectra, i.e., CBCA(CO)NH and HNCACB. Different from existing peak picking and resonance assignment methods that treat peaks as the units, our method is based on slices, which are one-dimensional vectors in three-dimensional spectra that correspond to certain (N, H) values. Experimental results on both benchmark simulated data sets and four real protein data sets demonstrate that our method significantly outperforms the state-of-the-art methods especially on the more challenging real protein data sets, while using a less number of spectra than those methods

  16. 二维电泳分析胎儿酒精综合征斑马鱼模型蛋白表达谱%Two-dimensional electrophoresis analysis for protein profile change in zebrafish alcohol syndrome model

    Institute of Scientific and Technical Information of China (English)

    钱林溪; 孙淑娜; 蔡威; 王跃祥; 蒋缪; 宋后燕

    2011-01-01

    Objective To study the putative mechanisms underlying fetal alcohol syndrome by comparative protein-profile analysis between normal and ethanol-treated zebrafish embryo with twodimensional electrophoresis (2-DE).Methods Zebrafish embryos were exposed in 400 mmol/L ethanol at dome stage for 3 hours,and then ethanol-induced abnormalities were observed.Proteomes of zebrafish embryos at early stages including zygote stage,dome stage,shield stage and 5-somite stage,were separated by 2-DE.The subtraction analysis method was applied to eliminate the interference from maternal derived proteins.The ethanol-treated embryos at 5-somite stage was analyzed by 2-DE,and the protein profile was compared with that generated from control embryos at the same stage.The data obtained from 2-DE analysis were verified by in-situ hybridization.Results 400 mmol/L ethanol treatment caused axial malformation (62%) and cyclopia (60%) in zebrafish embryos.The 2-DE analysis showed that the expression of Collagen2al (Col2a1) and TAR DNA binding protein (TDP) was decreased in 12 hours post fertilization (12 hpf) ethanol-treated embryos by 81% and 73%,respectively.The in-situ hybridization also demonstrated that the expression of Col2al in axial mesoderm was reduced by ethanol treatment at the same stage.But for 24 hpf ethanoltreated embryos,the expression of Col2al in axis recovered to a comparable level to that in control embryos,while the structure of neural tube was disrupted severely by ethanol exposure.Conclusions It is suggested that the expressions of Col2al and TDP were disrupted by ethanol during early stage,which might induce the zebrafish developmental abnormalities.The ethanol interference on early expression of Col2al is supposed to be one of the major reasons leading to later abnormalities of axis and neutral tube.%目的 利用二维电泳分析乙醇诱导斑马鱼胚胎发育畸形的可能分子机制.方法 采用400 mmol/L乙醇在斑马鱼胚胎圆顶期处理3 h,观察乙

  17. Designing finite-height two-dimensional photonic crystal waveguides

    DEFF Research Database (Denmark)

    Søndergaard, Thomas; Bjarklev, Anders Overgaard; Kristensen, Martin;

    2000-01-01

    Guidelines for designing planar waveguides based on introducing line-defects in two-dimensional photonic-crystal slabs are obtained by comparing calculations on two-dimensional structures with dispersion relations for the media above and below the slab. (C) 2000 American Institute of Physics....

  18. The Chandrasekhar's Equation for Two-Dimensional Hypothetical White Dwarfs

    CERN Document Server

    De, Sanchari

    2014-01-01

    In this article we have extended the original work of Chandrasekhar on the structure of white dwarfs to the two-dimensional case. Although such two-dimensional stellar objects are hypothetical in nature, we strongly believe that the work presented in this article may be prescribed as Master of Science level class problem for the students in physics.

  19. Frustrated phase separation in two-dimensional charged systems

    OpenAIRE

    Ortix, C.; Lorenzana, J.; Di Castro, C.

    2005-01-01

    We study phase separation frustrated by the long-range Coulomb interaction in two dimensional electronic systems with emphasys in the case of a metallic and an insulating phase. We find that two-dimensional systems are more prone to mesoscopic frustrated phase separation than the three dimensional ones.

  20. Two-dimensional black holes and non-commutative spaces

    International Nuclear Information System (INIS)

    We study the effects of non-commutative spaces on two-dimensional black hole. The event horizon of two-dimensional black hole is obtained in non-commutative space up to second order of perturbative calculations. A lower limit for the non-commutativity parameter is also obtained. The observer in that limit in contrast to commutative case see two horizon

  1. Two Dimensional Polymerization of Graphene Oxide: Bottom-up Approach

    OpenAIRE

    Atanasov, Victor; Russev, Stoyan; Lyutov, Lyudmil; Zagranyarski, Yulian; Dimitrova, Iglika; Avdeev, Georgy; Avramova, Ivalina; Vulcheva, Evgenia; Kirilov, Kiril; Tzonev, Atanas; Abrashev, Miroslav; Tsutsumanova, Gichka

    2012-01-01

    We demonstrate a bottom-up synthesis of structures similar to graphene oxide via a two dimensional polymerization. Experimental evidence and discussion are conveyed as well as a general framework for this two dimensional polymerization. The proposed morphologies and lattice structures of these graphene oxides are derived from aldol condensation of alternating three nucleophilic and three electrophilic centers of benzenetriol.

  2. Two-dimensional electron layers in perovskite oxides

    NARCIS (Netherlands)

    Hassink, Gerrit Willem Johannes

    2009-01-01

    Two-dimensional electron systems have always attracted attention for their remarkable properties. In this thesis, two-dimensional electron layers in two correlated-electron systems were studied: LaTiO3/LaAlO3 for a possible Mott insulating state and LaAlO3/SrTiO3 for its conducting interface. Singl

  3. Mechanics of Apparent Horizon in Two Dimensional Dilaton Gravity

    CERN Document Server

    Cai, Rong-Gen

    2016-01-01

    In this article, we give a definition of apparent horizon in a two dimensional general dilaton gravity theory. With this definition, we construct the mechanics of the apparent horizon by introducing a quasi-local energy of the theory. Our discussion generalizes the apparent horizons mechanics in general spherically symmetric spactimes in four or higher dimensions to the two dimensional dilaton gravity case.

  4. Topological aspect of disclinations in two-dimensional crystals

    Institute of Scientific and Technical Information of China (English)

    Qi Wei-Kai; Zhu Tao; Chen Yong; Ren Ji-Rong

    2009-01-01

    By using topological current theory, this paper studies the inner topological structure of disclinations during the melting of two-dimensional systems. From two-dimensional elasticity theory, it finds that there are topological currents for topological defects in homogeneous equation. The evolution of disclinations is studied, and the branch conditions for generating, annihilating, crossing, splitting and merging of disclinations are given.

  5. Beginning Introductory Physics with Two-Dimensional Motion

    Science.gov (United States)

    Huggins, Elisha

    2009-01-01

    During the session on "Introductory College Physics Textbooks" at the 2007 Summer Meeting of the AAPT, there was a brief discussion about whether introductory physics should begin with one-dimensional motion or two-dimensional motion. Here we present the case that by starting with two-dimensional motion, we are able to introduce a considerable…

  6. High Resolution Quantitative Proteomics of HeLa Cells Protein Species Using Stable Isotope Labeling with Amino Acids in Cell Culture(SILAC), Two-Dimensional Gel Electrophoresis(2DE) and Nano-Liquid Chromatograpohy Coupled to an LTQ-OrbitrapMass Spectrometer*

    Science.gov (United States)

    Thiede, Bernd; Koehler, Christian J.; Strozynski, Margarita; Treumann, Achim; Stein, Robert; Zimny-Arndt, Ursula; Schmid, Monika; Jungblut, Peter R.

    2013-01-01

    The proteomics field has shifted over recent years from two-dimensional gel electrophoresis (2-DE)-based approaches to SDS-PAGE or gel-free workflows because of the tremendous developments in isotopic labeling techniques, nano-liquid chromatography, and high-resolution mass spectrometry. However, 2-DE still offers the highest resolution in protein separation. Therefore, we combined stable isotope labeling with amino acids in cell culture of controls and apoptotic HeLa cells with 2-DE and the subsequent analysis of tryptic peptides via nano-liquid chromatography coupled to an LTQ-Orbitrap mass spectrometer to obtain quantitative data using the methods with the highest resolving power on all levels of the proteomics workflow. More than 1,200 proteins with more than 2,700 protein species were identified and quantified from 816 Coomassie Brilliant Blue G-250 stained 2-DE spots. About half of the proteins were identified and quantified only in single 2-DE spots. The majority of spots revealed one to five proteins; however, in one 2-DE spot, up to 23 proteins were identified. Only half of the 2-DE spots represented a dominant protein with more than 90% of the whole protein amount. Consequently, quantification based on staining intensities in 2-DE gels would in approximately half of the spots be imprecise, and minor components could not be quantified. These problems are circumvented by quantification using stable isotope labeling with amino acids in cell culture. Despite challenges, as shown in detail for lamin A/C and vimentin, the quantitative changes of protein species can be detected. The combination of 2-DE with high-resolution nano-liquid chromatography-mass spectrometry allowed us to identify proteomic changes in apoptotic cells that would be unobservable using any of the other previously employed proteomic workflows. PMID:23033477

  7. Effect of Isoelectrofocusing Intensity on Protein Separation of Cassava Leaves by Two-Dimensional Gel Electrophoresis%等电聚焦强度对木薯叶片蛋白质双向电泳分离结果的影响

    Institute of Scientific and Technical Information of China (English)

    王海燕; 王斌; 王丹; 王东阳; 王力敏; 王红岩; 王旭初; 田维敏

    2011-01-01

    To obtain high-resolution reference of two-dimensional gel electrophoresis (2-DE)profiles of proteins from cassava leaves, the parameters of isoelectro-focusing (IEF) intensity were optimized. Results showed that the quality of 2-DE profiles under 130 000 Vhs was better than that of those under other conditions. Seven proteins among the selected 10 proteins were positively identified by MALDI TOF MS, suggesting their MS compatibility. The identified proteins were mainly involved in energy metabolic pathway and some of which appeared only in the 2-DE profiles under 130 000 Vhs condition.%通过优化等电聚焦强度改良木薯叶片蛋白质双向电泳的分离效果.结果表明,13万Vhs等电聚焦强度能很好地分离木薯叶片蛋白质,且分离的蛋白质具有良好的质谱兼容性.质谱鉴定7个蛋白点,结果显示这些蛋白主要参与能量代谢,其中有些蛋白点是在13万Vhs聚焦强度下特异出现的.

  8. Two-Dimensional Discrete Gap Breathers in a Two-Dimensional Diatomic βFermi-Pasta-Ulam Lattice

    Institute of Scientific and Technical Information of China (English)

    XU Quan; TIAN Qiang

    2008-01-01

    We study the existence of two-dimensional discrete breathers in a two-dimensional face-centred square lattice consisting of alternating light and heavy atoms, with nearest-neighbour coupling containing quartic soft or hard nonlinearity. This study is focused on two-dimensional breathers with frequency in the gap that separates the acoustic and optical bands of the phonon spectrum. We demonstrate the possibility of existence of two-dimensional gap breathers by using the numerical method, the local anharmonicity approximation and the rotating wave approximation. We obtain six types of two-dimensional gap breathers, i.e., symmetric, mirror-symmetric and asymmetric, no matter whether the centre of the breather is on a light or a heavy atom.

  9. Two-dimensional discrete gap breathers in a two-dimensional discrete diatomic Klein-Gordon lattice

    Institute of Scientific and Technical Information of China (English)

    XU Quan; QIANG Tian

    2009-01-01

    We study the existence and stability of two-dimensional discrete breathers in a two-dimensional discrete diatomic Klein-Gordon lattice consisting of alternating light and heavy atoms, with nearest-neighbor harmonic coupling.Localized solutions to the corresponding nonlinear differential equations with frequencies inside the gap of the linear wave spectrum, i.e. two-dimensional gap breathers, are investigated numerically. The numerical results of the corresponding algebraic equations demonstrate the possibility of the existence of two-dimensional gap breathers with three types of symmetries, i.e., symmetric, twin-antisymmetric and single-antisymmetric. Their stability depends on the nonlinear on-site potential (soft or hard), the interaction potential (attractive or repulsive)and the center of the two-dimensional gap breather (on a light or a heavy atom).

  10. Automated analysis of protein subcellular location in time series images

    OpenAIRE

    Hu, Yanhua; Osuna-Highley, Elvira; Hua, Juchang; Nowicki, Theodore Scott; Stolz, Robert; McKayle, Camille; Murphy, Robert F.

    2010-01-01

    Motivation: Image analysis, machine learning and statistical modeling have become well established for the automatic recognition and comparison of the subcellular locations of proteins in microscope images. By using a comprehensive set of features describing static images, major subcellular patterns can be distinguished with near perfect accuracy. We now extend this work to time series images, which contain both spatial and temporal information. The goal is to use temporal features to improve...

  11. Two-dimensional and novel quasi-two-dimensional quantum liquids

    CERN Document Server

    Nava, Marco

    2013-01-01

    In this thesis we have used Quantum Monte Carlo techniques to study two systems that can be regarded as the archetype for neutral strongly interacting systems: 4He, and its fermionic counterpart 3He.More specifically, we have used the Path Integral Ground State and the Path Integral Monte Carlo methods to study a system of two dimensional 3He (2d-3He) and a system of 4He adsorbed on Graphene-Fluoride (GF) and Graphane (GH) at both zero and finite temperature. The purpose of the study of 4He on GF (GH) was the research of new physical phenomena, whereas in the case of 2d-3He it was the application of novel methodologies for the ab-initio study of static and dynamic properties of Fermi systems. In the case of 2d-3He we have computed the spin susceptibility as function of density which turned out to be in very good agreement with experimental data; we have also obtained the first ab-initio evaluation of the zero-sound mode and the dynamic structure factor of 2d-3He that is in remarkably good agreement with exper...

  12. ONE-DIMENSIONAL AND TWO-DIMENSIONAL LEADERSHIP STYLES

    Directory of Open Access Journals (Sweden)

    Nikola Stefanović

    2007-06-01

    Full Text Available In order to motivate their group members to perform certain tasks, leaders use different leadership styles. These styles are based on leaders' backgrounds, knowledge, values, experiences, and expectations. The one-dimensional styles, used by many world leaders, are autocratic and democratic styles. These styles lie on the two opposite sides of the leadership spectrum. In order to precisely define the leadership styles on the spectrum between the autocratic leadership style and the democratic leadership style, leadership theory researchers use two dimensional matrices. The two-dimensional matrices define leadership styles on the basis of different parameters. By using these parameters, one can identify two-dimensional styles.

  13. RESEARCH ON TWO-DIMENSIONAL LDA FOR FACE RECOGNITION

    Institute of Scientific and Technical Information of China (English)

    Han Ke; Zhu Xiuchang

    2006-01-01

    The letter presents an improved two-dimensional linear discriminant analysis method for feature extraction. Compared with the current two-dimensional methods for feature extraction, the improved two-dimensional linear discriminant analysis method makes full use of not only the row and the column direction information of face images but also the discriminant information among different classes. The method is evaluated using the Nanjing University of Science and Technology (NUST) 603 face database and the Aleix Martinez and Robert Benavente (AR) face database. Experimental results show that the method in the letter is feasible and effective.

  14. Fully automated synthesis of (phosphopeptide arrays in microtiter plate wells provides efficient access to protein tyrosine kinase characterization

    Directory of Open Access Journals (Sweden)

    Goldstein David J

    2005-01-01

    Full Text Available Abstract Background Synthetic peptides have played a useful role in studies of protein kinase substrates and interaction domains. Synthetic peptide arrays and libraries, in particular, have accelerated the process. Several factors have hindered or limited the applicability of various techniques, such as the need for deconvolution of combinatorial libraries, the inability or impracticality of achieving full automation using two-dimensional or pin solid phases, the lack of convenient interfacing with standard analytical platforms, or the difficulty of compartmentalization of a planar surface when contact between assay components needs to be avoided. This paper describes a process for synthesis of peptides and phosphopeptides on microtiter plate wells that overcomes previous limitations and demonstrates utility in determination of the epitope of an autophosphorylation site phospho-motif antibody and utility in substrate utilization assays of the protein tyrosine kinase, p60c-src. Results The overall reproducibility of phospho-peptide synthesis and multiplexed EGF receptor (EGFR autophosphorylation site (pY1173 antibody ELISA (9H2 was within 5.5 to 8.0%. Mass spectrometric analyses of the released (phosphopeptides showed homogeneous peaks of the expected molecular weights. An overlapping peptide array of the complete EGFR cytoplasmic sequence revealed a high redundancy of 9H2 reactive sites. The eight reactive phospopeptides were structurally related and interestingly, the most conserved antibody reactive peptide motif coincided with a subset of other known EGFR autophosphorylation and SH2 binding motifs and an EGFR optimal substrate motif. Finally, peptides based on known substrate specificities of c-src and related enzymes were synthesized in microtiter plate array format and were phosphorylated by c-Src with the predicted specificities. The level of phosphorylation was proportional to c-Src concentration with sensitivities below 0.1 Units of

  15. ADSORPTION OF SHORT TWO-DIMENSIONAL COMPACT CHAINS

    Institute of Scientific and Technical Information of China (English)

    Jia-ye Su; Jin Chen; Zhao-yun Zhang; Lin-xi Zhang

    2006-01-01

    Short two-dimensional compact chains adsorbed on the attractive surface at different temperatures were investigated by using the enumeration calculation method. First we investigate the chain size and shape of adsorbed chains,temperatures. There are some special behaviors for the chain size and shape at low temperature, especially for strong attraction interaction. In the meantime, adsorbed compact chains have different behaviors from general adsorbed polymer chains. Some thermodynamics properties are also discussed here. Heat capacity changes non-monotonously, first increases and then reduces. The transition temperature Tc is nearly 1.0, 1.4, 2.0 and 4.2 (in the unit of T0) for the case of ε = 0, -1,-2 and -4 (in the unit of kT0), respectively. Average energy per bond increases while average Helmholtz free energy per bond decreases with increasing temperatures. From these two thermodynamics parameters we can also get another transition temperature Tc', and it is close to 0.7, 1.1, 1.5 and 3.4 for ε = 0, -1, -2, and -4, respectively. Therefore, Tc is greater than Tc'under the same condition. These investigations may provide some insights into the thermodynamics behaviors of adsorbed protein-like chains.

  16. The J-UNIO protocol for automated protein structure determination by NMR in solution

    International Nuclear Information System (INIS)

    The J-UNIO (JCSG protocol using the software UNIO) procedure for automated protein structure determination by NMR in solution is introduced. In the present implementation, J-UNIO makes use of APSY-NMR spectroscopy, 3D heteronuclear-resolved [1H,1H]-NOESY experiments, and the software UNIO. Applications with proteins from the JCSG target list with sizes up to 150 residues showed that the procedure is highly robust and efficient. In all instances the correct polypeptide fold was obtained in the first round of automated data analysis and structure calculation. After interactive validation of the data obtained from the automated routine, the quality of the final structures was comparable to results from interactive structure determination. Special advantages are that the NMR data have been recorded with 6–10 days of instrument time per protein, that there is only a single step of chemical shift adjustments to relate the backbone signals in the APSY-NMR spectra with the corresponding backbone signals in the NOESY spectra, and that the NOE-based amino acid side chain chemical shift assignments are automatically focused on those residues that are heavily weighted in the structure calculation. The individual working steps of J-UNIO are illustrated with the structure determination of the protein YP926445.1 from Shewanella amazonensis, and the results obtained with 17 JCSG targets are critically evaluated.

  17. Automated analysis of protein NMR assignments using methods from artificial intelligence.

    Science.gov (United States)

    Zimmerman, D E; Kulikowski, C A; Huang, Y; Feng, W; Tashiro, M; Shimotakahara, S; Chien, C; Powers, R; Montelione, G T

    1997-06-20

    An expert system for determining resonance assignments from NMR spectra of proteins is described. Given the amino acid sequence, a two-dimensional 15N-1H heteronuclear correlation spectrum and seven to eight three-dimensional triple-resonance NMR spectra for seven proteins, AUTOASSIGN obtained an average of 98% of sequence-specific spin-system assignments with an error rate of less than 0.5%. Execution times on a Sparc 10 workstation varied from 16 seconds for smaller proteins with simple spectra to one to nine minutes for medium size proteins exhibiting numerous extra spin systems attributed to conformational isomerization. AUTOASSIGN combines symbolic constraint satisfaction methods with a domain-specific knowledge base to exploit the logical structure of the sequential assignment problem, the specific features of the various NMR experiments, and the expected chemical shift frequencies of different amino acids. The current implementation specializes in the analysis of data derived from the most sensitive of the currently available triple-resonance experiments. Potential extensions of the system for analysis of additional types of protein NMR data are also discussed.

  18. MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

    Directory of Open Access Journals (Sweden)

    Kuczmarski Thomas A

    2006-10-01

    Full Text Available Abstract Background MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. Description MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. Conclusion MannDB comprises a large number of genomes and comprehensive protein

  19. UPWIND DISCONTINUOUS GALERKIN METHODS FOR TWO DIMENSIONAL NEUTRON TRANSPORT EQUATIONS

    Institute of Scientific and Technical Information of China (English)

    袁光伟; 沈智军; 闫伟

    2003-01-01

    In this paper the upwind discontinuous Galerkin methods with triangle meshes for two dimensional neutron transport equations will be studied.The stability for both of the semi-discrete and full-discrete method will be proved.

  20. Model of a Negatively Curved Two-Dimensional Space.

    Science.gov (United States)

    Eckroth, Charles A.

    1995-01-01

    Describes the construction of models of two-dimensional surfaces with negative curvature that are used to illustrate differences in the triangle sum rule for the various Big Bang Theories of the universe. (JRH)

  1. Entanglement Entropy for time dependent two dimensional holographic superconductor

    CERN Document Server

    Mazhari, N S; Myrzakulov, Kairat; Myrzakulov, R

    2016-01-01

    We studied entanglement entropy for a time dependent two dimensional holographic superconductor. We showed that the conserved charge of the system plays the role of the critical parameter to have condensation.

  2. Ultrafast two-dimensional THz spectroscopy of graphene

    Directory of Open Access Journals (Sweden)

    Woerner M.

    2013-03-01

    Full Text Available With two-dimensional THz spectroscopy the dynamics of low-energy carriers in graphene is determined. Both intra- and interband absorption contribute to the observed ultrafast pump-probe signals.

  3. Bound states of two-dimensional relativistic harmonic oscillators

    Institute of Scientific and Technical Information of China (English)

    Qiang Wen-Chao

    2004-01-01

    We give the exact normalized bound state wavefunctions and energy expressions of the Klein-Gordon and Dirac equations with equal scalar and vector harmonic oscillator potentials in the two-dimensional space.

  4. A study of two-dimensional magnetic polaron

    Institute of Scientific and Technical Information of China (English)

    LIU Tao; ZHANG Huaihong; FENG Mang; WANG Kelin

    2006-01-01

    By using the variational method and anneal simulation, we study in this paper the self-trapped magnetic polaron (STMP) in two-dimensional anti-ferromagnetic material and the bound magnetic polaron (BMP) in ferromagnetic material. Schwinger angular momentum theory is applied to changing the problem into a coupling problem of carriers and two types of Bosons. Our calculation shows that there are single-peak and multi-peak structures in the two-dimensional STMP. For the ferromagnetic material, the properties of the two-dimensional BMP are almost the same as that in one-dimensional case; but for the anti-ferromagnetic material, the two-dimensional STMP structure is much richer than the one-dimensional case.

  5. Decoherence in a Landau Quantized Two Dimensional Electron Gas

    Directory of Open Access Journals (Sweden)

    McGill Stephen A.

    2013-03-01

    Full Text Available We have studied the dynamics of a high mobility two-dimensional electron gas as a function of temperature. The presence of satellite reflections in the sample and magnet can be modeled in the time-domain.

  6. Second invariant for two-dimensional classical super systems

    Indian Academy of Sciences (India)

    S C Mishra; Roshan Lal; Veena Mishra

    2003-10-01

    Construction of superpotentials for two-dimensional classical super systems (for ≥ 2) is carried out. Some interesting potentials have been studied in their super form and also their integrability.

  7. Two-dimensional random tilings of large codimension: new progress

    OpenAIRE

    Destainville, N.; Widom, M.; Mosseri, R.; Bailly, F.

    1999-01-01

    Two-dimensional random tilings of rhombi can be seen as projections of two-dimensional membranes embedded in hypercubic lattices of higher dimensional spaces. Here, we consider tilings projected from a $D$-dimensional space. We study the limiting case, when the quantity $D$, and therefore the number of different species of tiles, become large. We had previously demonstrated [ICQ6] that, in this limit, the thermodynamic properties of the tiling become independent of the boundary conditions. Th...

  8. Two-Dimensionally-Modulated, Magnetic Structure of Neodymium Metal

    DEFF Research Database (Denmark)

    Lebech, Bente; Bak, P.

    1979-01-01

    The incipient magnetic order of dhcp Nd is described by a two-dimensional, incommensurably modulated structure ("triple-q" structure). The ordering is accompanied by a lattice distortion that forms a similar pattern.......The incipient magnetic order of dhcp Nd is described by a two-dimensional, incommensurably modulated structure ("triple-q" structure). The ordering is accompanied by a lattice distortion that forms a similar pattern....

  9. Oscillatory crossover from two dimensional to three dimensional topological insulators

    OpenAIRE

    Liu, Chao-Xing; Zhang, Haijun; Yan, Binghai; Qi, Xiao-Liang; Frauenheim, Thomas; Dai, Xi; Fang, Zhong; Zhang, Shou-Cheng

    2009-01-01

    We investigate the crossover regime from three dimensional topological insulators $Bi_2Te_3$ and $Bi_2Se_3$ to two dimensional topological insulators with quantum spin Hall effect when the layer thickness is reduced. Using both analytical models and first-principles calculations, we find that the crossover occurs in an oscillatory fashion as a function of the layer thickness, alternating between topologically trivial and non-trivial two dimensional behavior.

  10. Two-Dimensional Weak Pseudomanifolds on Eight Vertices

    Indian Academy of Sciences (India)

    Basudeb Datta; Nandini Nilakantan

    2002-05-01

    We explicitly determine all the two-dimensional weak pseudomanifolds on 8 vertices. We prove that there are (up to isomorphism) exactly 95 such weak pseudomanifolds, 44 of which are combinatorial 2-manifolds. These 95 weak pseudomanifolds triangulate 16 topological spaces. As a consequence, we prove that there are exactly three 8-vertex two-dimensional orientable pseudomanifolds which allow degree three maps to the 4-vertex 2-sphere.

  11. The Two-Dimensional Analogue of General Relativity

    OpenAIRE

    Lemos, José P. S.; Sá, Paulo M.

    1993-01-01

    General Relativity in three or more dimensions can be obtained by taking the limit $\\omega\\rightarrow\\infty$ in the Brans-Dicke theory. In two dimensions General Relativity is an unacceptable theory. We show that the two-dimensional closest analogue of General Relativity is a theory that also arises in the limit $\\omega\\rightarrow\\infty$ of the two-dimensional Brans-Dicke theory.

  12. The two dimensional generalized Weyl fractional calculus and special functions

    Directory of Open Access Journals (Sweden)

    V. B. L. Chaurasia

    2010-06-01

    Full Text Available The object of this present paper is to derive a relation between the two dimensional I-transform involving a general class of polynomials and the Weyl type two dimensional Saigo operators of fractional integration. The results derived here are general in nature and include the results given earlier by Saigo, Saxena and Ram [10],Saxena and Ram [8], Saxena and Kiryakova [9] and Chaurasia and Srivastava [12].

  13. Nicked-sleeve interface for two-dimensional capillary electrophoresis

    OpenAIRE

    Flaherty, Ryan J.; Huge, Bonnie J.; Bruce, Spencer M.; Dada, Oluwatosin O.; Dovichi, Norman J.

    2013-01-01

    We report an improved interface for two-dimensional capillary electrophoresis. This interface is based on capillary tubing and a Plexiglas chip, both of which were milled using a micro-dicing saw. The interface was evaluated and compared to a traditional interface design for both pseudo one-dimensional and two-dimensional capillary electrophoresis. We observe less than 70% transfer efficiency for the traditional design and greater than 90% transfer efficiency with this new interface.

  14. Two-Dimensional Materials for Sensing: Graphene and Beyond

    OpenAIRE

    Seba Sara Varghese; Saino Hanna Varghese; Sundaram Swaminathan; Krishna Kumar Singh; Vikas Mittal

    2015-01-01

    Two-dimensional materials have attracted great scientific attention due to their unusual and fascinating properties for use in electronics, spintronics, photovoltaics, medicine, composites, etc. Graphene, transition metal dichalcogenides such as MoS2, phosphorene, etc., which belong to the family of two-dimensional materials, have shown great promise for gas sensing applications due to their high surface-to-volume ratio, low noise and sensitivity of electronic properties to the changes in the...

  15. Tagging multiphoton ionization events by two-dimensional photoelectron spectroscopy

    OpenAIRE

    de Groot, Mattijs; Broos, Jaap; Buma, Wybren Jan

    2007-01-01

    Two-dimensional photoelectron spectroscopy has been used to supply process-specific labels to multiphoton ionization events. Employing these tags, the authors can construct excitation and photoelectron spectra along predefined excitation routes in the neutral manifold and ionization routes to the ionic manifold from one single two-dimensional photoelectron spectrum. These results offer a novel way to elucidate the vibronic and dynamic properties of excited and ionic states. (c) 2007 American ...

  16. Two Dimensional Hamiltonian with Generalized Shape Invariance Symmetry

    OpenAIRE

    Panahi-Talemi, H.; Jafarizadeh, M. A.

    2002-01-01

    The two dimensional Hamiltonian with generalized shape invariance symmetry over $S^2$, has been obtained via Fourier transformation over the three coordinates of the $SU(3)$ Casimir operator defined on $SU(3)/SU(2)$ symmetric space. It is shown that the generalized shape invariance is equivalent to $SU(3)$ symmetry and that there is one to one correspondence between the representations of the generalized shape invariance and $SU(3)$ Verma modules. Also the two dimensional Hamiltonian in $\\mat...

  17. Establishment and Preliminary Application of Two dimensional Electrophoresis and Mass Spectrometry in Ovary Study

    Institute of Scientific and Technical Information of China (English)

    Xiang MA; Ye-fei ZHU; Jia-hao SHA; Zuo-min ZHOU; Jia-yin LIU

    2003-01-01

    Objective To apply two-dimensional electrophoresis and mass spectrometry in the ovary proteome research Methods Protein extractions from mouse ovaries were run in IPGphor isoelectric focus system with 11 cm and 24 cm IPG strips respectively (pH 3~10, 0.3 mm thick), then the protein spots were identified by mass spectrometry.Results The ovary protein exactions separated by two-dimensional electrophoresis have got high resolution, and identifing protein by mass spectrometry was highly efficient and facilitly.These two techniques should facilitate further investigation of female reproduction proteome research.Conclusion These two rapid high resolutions and efficient techniques have a variety of applications foreground in female reproduction proteome pattern research.

  18. The theory of critical phenomena in two-dimensional systems

    International Nuclear Information System (INIS)

    An exposition of the theory of critical phenomena in two-dimensional physical systems is presented. The first six chapters deal with the mean field theory of critical phenomena, scale invariance of the thermodynamic functions, Kadanoff's spin block construction, Wilson's renormalization group treatment of critical phenomena in configuration space, and the two-dimensional Ising model on a triangular lattice. The second part of this work is made of four chapters devoted to the application of the ideas expounded in the first part to the discussion of critical phenomena in superfluid films, two-dimensional crystals and the two-dimensional XY model of magnetic systems. Chapters seven to ten are devoted to the following subjects: analysis of long range order in one, two, and three-dimensional physical systems. Topological defects in the XY model, in superfluid films and in two-dimensional crystals. The Thouless-Kosterlitz iterated mean field theory of the dipole gas. The renormalization group treatment of the XY model, superfluid films and two-dimensional crystal. (author)

  19. Two-Dimensional Materials for Sensing: Graphene and Beyond

    Directory of Open Access Journals (Sweden)

    Seba Sara Varghese

    2015-09-01

    Full Text Available Two-dimensional materials have attracted great scientific attention due to their unusual and fascinating properties for use in electronics, spintronics, photovoltaics, medicine, composites, etc. Graphene, transition metal dichalcogenides such as MoS2, phosphorene, etc., which belong to the family of two-dimensional materials, have shown great promise for gas sensing applications due to their high surface-to-volume ratio, low noise and sensitivity of electronic properties to the changes in the surroundings. Two-dimensional nanostructured semiconducting metal oxide based gas sensors have also been recognized as successful gas detection devices. This review aims to provide the latest advancements in the field of gas sensors based on various two-dimensional materials with the main focus on sensor performance metrics such as sensitivity, specificity, detection limit, response time, and reversibility. Both experimental and theoretical studies on the gas sensing properties of graphene and other two-dimensional materials beyond graphene are also discussed. The article concludes with the current challenges and future prospects for two-dimensional materials in gas sensor applications.

  20. The AUDANA algorithm for automated protein 3D structure determination from NMR NOE data.

    Science.gov (United States)

    Lee, Woonghee; Petit, Chad M; Cornilescu, Gabriel; Stark, Jaime L; Markley, John L

    2016-06-01

    We introduce AUDANA (Automated Database-Assisted NOE Assignment), an algorithm for determining three-dimensional structures of proteins from NMR data that automates the assignment of 3D-NOE spectra, generates distance constraints, and conducts iterative high temperature molecular dynamics and simulated annealing. The protein sequence, chemical shift assignments, and NOE spectra are the only required inputs. Distance constraints generated automatically from ambiguously assigned NOE peaks are validated during the structure calculation against information from an enlarged version of the freely available PACSY database that incorporates information on protein structures deposited in the Protein Data Bank (PDB). This approach yields robust sets of distance constraints and 3D structures. We evaluated the performance of AUDANA with input data for 14 proteins ranging in size from 6 to 25 kDa that had 27-98 % sequence identity to proteins in the database. In all cases, the automatically calculated 3D structures passed stringent validation tests. Structures were determined with and without database support. In 9/14 cases, database support improved the agreement with manually determined structures in the PDB and in 11/14 cases, database support lowered the r.m.s.d. of the family of 20 structural models. PMID:27169728

  1. 用于双向凝胶电泳分析的奶牛乳清蛋白样品制备方法的比较%Comparison of Bovine Whey Protein Preparation Methods for Two-Dimensional Gel Electrophoresis Analysis

    Institute of Scientific and Technical Information of China (English)

    边艳杰; 李庆章; 张岚; 郭洪波; 吕英

    2011-01-01

    为建立适用于双向凝胶电泳分析的奶牛乳清蛋白的制备方法,分别比较了直接裂解法、三氯乙酸-丙酮法,Trizol法和2-D clean up kit法对奶牛乳清蛋白提取效率和双向凝胶电泳图谱的影响.用2-D Quant Kit试剂盒测定蛋白浓度,分别用十二烷基磺酸钠.聚丙烯酰胺凝胶电泳和双向凝胶电泳进行奶牛乳清蛋白的分离.蛋白定量结果表明,2-D clean up kit法产率最高,直接裂解法、三氯乙酸一丙酮法次之,trizol法产率最低;十二烷基磺酸钠-聚丙烯酰胺凝胶电泳结果表明,2-D clean up kit法提取的蛋白质量最高;双向电泳图谱分析表明,2-D clean up kit法得到的蛋白图谱与另外3种方法相比,检测到的蛋白点最多,图谱背景清晰,分辨率最高.结果提示,2-D clean-up法相对最适合于双向凝胶电泳分析奶牛乳清蛋白样品的制备,尤其对一些低丰度高分子量蛋白的分离效果较为明显.%Bovine whey contains many kinds of high-abundance proteins and varied interferential impurity, so it' s hard to obtain satisfied protein images of bovine whey in two dimensional electrophoresis (2-DE). Protein extraction from bovine whey is a key step to achieve high-resolution protein separation in 2-DE. Four routine total protein extraction methods were compared in order to determine an optimal one in 2-DE analysis for bovine whey. Bovine whey protein were extracted by direct schizolysis, TCA-acetone, trizol precipitation and 2-D clean up kit. The concentration of total protein was measured by 2-D quant kit, bovine whey protein were separated using SDS-PAGE and 2-DE. The data showed that use of 2-D clean up kit gave maximum protein yield, and the use of trizol gave the lowest. The result of SDSPAGE showed that use of 2-D clean up kit generated the highest-quality protein among these four methods. The result of 2-DE gels showed that 238 protein spots were detected on the 2-DE gel using 2-D clean up kit, and the gel

  2. Optical modulators with two-dimensional layered materials

    CERN Document Server

    Sun, Zhipei; Wang, Feng

    2016-01-01

    Light modulation is an essential operation in photonics and optoelectronics. With existing and emerging technologies increasingly demanding compact, efficient, fast and broadband optical modulators, high-performance light modulation solutions are becoming indispensable. The recent realization that two-dimensional layered materials could modulate light with superior performance has prompted intense research and significant advances, paving the way for realistic applications. In this review, we cover the state-of-the-art of optical modulators based on two-dimensional layered materials including graphene, transition metal dichalcogenides and black phosphorus. We discuss recent advances employing hybrid structures, such as two-dimensional heterostructures, plasmonic structures, and silicon/fibre integrated structures. We also take a look at future perspectives and discuss the potential of yet relatively unexplored mechanisms such as magneto-optic and acousto-optic modulation.

  3. Young's modulus of a solid two-dimensional Langmuir monolayer

    Science.gov (United States)

    Bercegol, H.; Meunier, J.

    1992-03-01

    LANGMUIR monolayers-films of amphiphilic molecules at the surface of water-exhibit many phases1,2. Some of these behave like two-dimensional solids on experimental timescales, but previous measurements of the shear modulus of these 'solid' monolayers3-5 have yielded a value too small to be compatible with a two-dimensional crystal. The interpretation of these is complicated, however, by the likelihood of inhomogeneities in the films, which are probably assemblies of microscopic crystalline domains. Here we describe measurements of the Young's modulus of an isolated "solid' domain of NBD-stearic acid monolayers. We obtain a value large enough to be compatible with the modulus of a two-dimensional crystal6-8. This suggests that Langmuir monolayers should provide model systems for studies of melting in two dimensions6-8.

  4. Control Operator for the Two-Dimensional Energized Wave Equation

    Directory of Open Access Journals (Sweden)

    Sunday Augustus REJU

    2006-07-01

    Full Text Available This paper studies the analytical model for the construction of the two-dimensional Energized wave equation. The control operator is given in term of space and time t independent variables. The integral quadratic objective cost functional is subject to the constraint of two-dimensional Energized diffusion, Heat and a source. The operator that shall be obtained extends the Conjugate Gradient method (ECGM as developed by Hestenes et al (1952, [1]. The new operator enables the computation of the penalty cost, optimal controls and state trajectories of the two-dimensional energized wave equation when apply to the Conjugate Gradient methods in (Waziri & Reju, LEJPT & LJS, Issues 9, 2006, [2-4] to appear in this series.

  5. Singular analysis of two-dimensional bifurcation system

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Bifurcation properties of two-dimensional bifurcation system are studied in this paper.Universal unfolding and transition sets of the bifurcation equations are obtained.The whole parametric plane is divided into several different persistent regions according to the type of motion,and the different qualitative bifurcation diagrams in different persistent regions are given.The bifurcation properties of the two-dimensional bifurcation system are compared with its reduced one-dimensional system.It is found that the system which is reduced to one dimension has lost many bifurcation properties.

  6. Critical Behaviour of a Two-Dimensional Random Antiferromagnet

    DEFF Research Database (Denmark)

    Als-Nielsen, Jens Aage; Birgeneau, R. J.; Guggenheim, H. J.;

    1976-01-01

    A neutron scattering study of the order parameter, correlation length and staggered susceptibility of the two-dimensional random antiferromagnet Rb2Mn0.5Ni0.5F4 is reported. The system is found to exhibit a well-defined phase transition with critical exponents identical to those of the isomorphou...... pure materials K2NiF4 and K2MnF4. Thus, in these systems, which have the asymptotic critical behaviour of the two-dimensional Ising model, randomness has no measurable effect on the phase-transition behaviour....

  7. Molecular dynamics simulation of a two-dimensional system

    Directory of Open Access Journals (Sweden)

    S. M. Huseini

    2001-06-01

    Full Text Available   The study of a two-dimensional (2-D system started nearly half a century ago when Peierls and Landau showed the lack of long range translational order in a two-dimensional solid. In 1968, Mermin proved that despite the absence of long range translational order. Two-dimensional solids can still exhibit a different kind of long range bond orientation. During the last decade, fascinating theories were put forward to explain the role of topological defects in the melting of two-dimensional solids, starting with Kosterlitz and Thouless. Recent surge of interest in melting is also due to the theoretical ideas of Halperin, Nelson and Young. They have suggested that the transition may be fundamentally different from that observed in ordinary three-dimensional systems. Computer simulations suggest that the transition is of the usual first-order type observed in a three-dimensional system. A large body of experimental and simulation research into the two-dimensional melting followed the announcement of the KTHNY theory. In spite of all this effort, the question as to the nature of two dimensional melting remains unresolved. Recent experimental work supporting the existence of continuous melting transitions in some two-dimentsional systems indicates the need for further theoretical and computational work to lead to an understanding of the experimental results.   In this paper we intend to summarze and clarify the current situation with regard to research in the two-dimensional melting with an emphasis on computer simulations. The paper begins with an overview of the current status of relevant theoretical, experimental and simulation research, then a two-dimensional simulation of an ionic salt system is studied in detail. This simulation has been done by using the molecular dynamics method. The most important parameters that have been determined are ,The trnsition temperature, the total energy of the system, the mean square displacement and the bond

  8. Spectral analysis of two-dimensional Bose-Hubbard models

    Science.gov (United States)

    Fischer, David; Hoffmann, Darius; Wimberger, Sandro

    2016-04-01

    One-dimensional Bose-Hubbard models are well known to obey a transition from regular to quantum-chaotic spectral statistics. We are extending this concept to relatively simple two-dimensional many-body models. Also in two dimensions a transition from regular to chaotic spectral statistics is found and discussed. In particular, we analyze the dependence of the spectral properties on the bond number of the two-dimensional lattices and the applied boundary conditions. For maximal connectivity, the systems behave most regularly in agreement with the applicability of mean-field approaches in the limit of many nearest-neighbor couplings at each site.

  9. Two-dimensional SCFTs from D3-branes

    Science.gov (United States)

    Benini, Francesco; Bobev, Nikolay; Crichigno, P. Marcos

    2016-07-01

    We find a large class of two-dimensional N = (0, 2) SCFTs obtained by compactifying four-dimensional N = 1 quiver gauge theories on a Riemann surface. We study these theories using anomalies and c-extremization. The gravitational duals to these fixed points are new AdS3 solutions of IIB supergravity which we exhibit explicitly. Along the way we uncover a universal relation between the conformal anomaly coefficients of fourdimensional and two-dimensional SCFTs connected by an RG flow across dimensions. We also observe an interesting novel phenomenon in which the superconformal R-symmetry mixes with baryonic symmetries along the RG flow.

  10. Chaotic dynamics in two-dimensional noninvertible maps

    CERN Document Server

    Mira, Christian; Cathala, Jean-Claude; Gardini, Laura

    1996-01-01

    This book is essentially devoted to complex properties (Phase plane structure and bifurcations) of two-dimensional noninvertible maps, i.e. maps having either a non-unique inverse, or no real inverse, according to the plane point. They constitute models of sets of discrete dynamical systems encountered in Engineering (Control, Signal Processing, Electronics), Physics, Economics, Life Sciences. Compared to the studies made in the one-dimensional case, the two-dimensional situation remained a long time in an underdeveloped state. It is only since these last years that the interest for this resea

  11. Quantum Communication Through a Two-Dimensional Spin Network

    Institute of Scientific and Technical Information of China (English)

    王兆明; 顾永建

    2012-01-01

    We investigate the state or entanglement transfer through a two-dimensional spin network. We show that for state transfer, better fidelity can be gained along the diagonal direction but for entanglement transfer, when the initial entanglement is created along the boundary, the concurrence is more inclined to propagate along the boundary. This behavior is produced by quantum mechanical interference and the communication quality depends on the precise size of the network. For some number of sites, the fidelity in a two-dimensional channel is higher than one-dimensional case. This is an important result for realizing quantum communication through high dimension spin chain networks.

  12. Spin dynamics in a two-dimensional quantum gas

    DEFF Research Database (Denmark)

    Pedersen, Poul Lindholm; Gajdacz, Miroslav; Deuretzbacher, Frank;

    2014-01-01

    We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions with superimp......We have investigated spin dynamics in a two-dimensional quantum gas. Through spin-changing collisions, two clouds with opposite spin orientations are spontaneously created in a Bose-Einstein condensate. After ballistic expansion, both clouds acquire ring-shaped density distributions...... with nonlocal Einstein-Podolsky-Rosen entanglement....

  13. Quasinormal frequencies of asymptotically flat two-dimensional black holes

    CERN Document Server

    Lopez-Ortega, A

    2011-01-01

    We discuss whether the minimally coupled massless Klein-Gordon and Dirac fields have well defined quasinormal modes in single horizon, asymptotically flat two-dimensional black holes. To get the result we solve the equations of motion in the massless limit and we also calculate the effective potentials of Schrodinger type equations. Furthermore we calculate exactly the quasinormal frequencies of the Dirac field propagating in the two-dimensional uncharged Witten black hole. We compare our results on its quasinormal frequencies with other already published.

  14. Equilibrium state of a trapped two-dimensional Bose gas

    International Nuclear Information System (INIS)

    We study experimentally and numerically the equilibrium density profiles of a trapped two-dimensional 87Rb Bose gas and investigate the equation of state of the homogeneous system using the local density approximation. We find a clear discrepancy between in situ measurements and quantum Monte Carlo simulations, which we attribute to a nonlinear variation of the optical density of the atomic cloud with its spatial density. However, good agreement between experiment and theory is recovered for the density profiles measured after time of flight, taking advantage of their self-similarity in a two-dimensional expansion.

  15. TreePM Method for Two-Dimensional Cosmological Simulations

    Indian Academy of Sciences (India)

    Suryadeep Ray

    2004-09-01

    We describe the two-dimensional TreePM method in this paper. The 2d TreePM code is an accurate and efficient technique to carry out large two-dimensional N-body simulations in cosmology. This hybrid code combines the 2d Barnes and Hut Tree method and the 2d Particle–Mesh method. We describe the splitting of force between the PM and the Tree parts. We also estimate error in force for a realistic configuration. Finally, we discuss some tests of the code.

  16. Dynamics of vortex interactions in two-dimensional flows

    DEFF Research Database (Denmark)

    Juul Rasmussen, J.; Nielsen, A.H.; Naulin, V.

    2002-01-01

    The dynamics and interaction of like-signed vortex structures in two dimensional flows are investigated by means of direct numerical solutions of the two-dimensional Navier-Stokes equations. Two vortices with distributed vorticity merge when their distance relative to their radius, d/R-0l. is below...... a critical value, a(c). Using the Weiss-field, a(c) is estimated for vortex patches. Introducing an effective radius for vortices with distributed vorticity, we find that 3.3 spiral vorticity filaments in the merging process...

  17. 双向凝胶电泳联合 MALDI-TOF/TOF MS 技术探寻狼疮性肾炎的血清标志物%Exploring Serum Protein Biomarkers of Lupus Nephritis by Using Two-Dimensional Gel Electrophoresis Com-bined with Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    许嵘; 朱加明; 龚劭敏; 卢泽军; 张慧; 刘少鹏; 丁小强; 钟一红

    2015-01-01

    发病机制。%Objective:To explore the potential serum biomarkers of patients with lupus nephritis(LN)by using two-dimensional electrophoresis combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF/TOF MS),so as to lay the foundation for illuminating pathogenesis.Methods:A total of 40 LN patients were divided into two groups,the active LN group and the inactive LN group,with 20 in each.In addition,20 IgA nephritis patients and 20 healthy volunteers were enrolled as IgAN group and healthy control group.Two-dimensional gel electrophoresis was used to separate and analyze the serum proteins,and MALDI-TOF/TOF MS was applied to the identification of the differentially expressed pro-teins.Results:A total of fifty differentially expressed proteins were identified.Compared with that in healthy control group,23 differentially expressed proteins were discovered in active LN group and inactive LN group,among which,8 proteins were up-regulated and 1 5 proteins were down-regulated.And 1 8 differentially expressed proteins,compared with IgA nephritis group, were found in active LN group and inactive LN group,including 13 up-regulated proteins and 5 down-regulated proteins.Fur-thermore,the number of up-regulated and down-regulated proteins in active LN group,compared with those in inactive LN group,were 4 and 5,respectively.Among the 50 identified differentially expressed proteins,the expression of serum amyloid protein A(SAA )in active LN group was higher than that in the other groups while the expression of complement component C4A in active LN group was lower than that in the other groups.And the expression of chain B (solution structure of double super helix model)in the inactive LN group was higher than that in the other groups.Compared with that in healthy control group,the expression of vitamin D-binding protein isoform 1 precursor,chain A(crystal structure of uncomplexed vitamin D-binding protein)and chain B (a covalent dimer of transthyretin that affects the

  18. On some classes of two-dimensional local models in discrete two-dimensional monatomic FPU lattice with cubic and quartic potential

    Institute of Scientific and Technical Information of China (English)

    Xu Quan; Tian Qiang

    2009-01-01

    This paper discusses the two-dimensional discrete monatomic Fermi-Pasta-Ulam lattice, by using the method of multiple-scale and the quasi-discreteness approach. By taking into account the interaction between the atoms in the lattice and their nearest neighbours, it obtains some classes of two-dimensional local models as follows: two-dimensional bright and dark discrete soliton trains, two-dimensional bright and dark line discrete breathers, and two-dimensional bright and dark discrete breather.

  19. Mapping two-dimensional polar active fluids to two-dimensional soap and one-dimensional sandblasting.

    Science.gov (United States)

    Chen, Leiming; Lee, Chiu Fan; Toner, John

    2016-01-01

    Active fluids and growing interfaces are two well-studied but very different non-equilibrium systems. Each exhibits non-equilibrium behaviour distinct from that of their equilibrium counterparts. Here we demonstrate a surprising connection between these two: the ordered phase of incompressible polar active fluids in two spatial dimensions without momentum conservation, and growing one-dimensional interfaces (that is, the 1+1-dimensional Kardar-Parisi-Zhang equation), in fact belong to the same universality class. This universality class also includes two equilibrium systems: two-dimensional smectic liquid crystals, and a peculiar kind of constrained two-dimensional ferromagnet. We use these connections to show that two-dimensional incompressible flocks are robust against fluctuations, and exhibit universal long-ranged, anisotropic spatio-temporal correlations of those fluctuations. We also thereby determine the exact values of the anisotropy exponent ζ and the roughness exponents χx,y that characterize these correlations. PMID:27452107

  20. Mapping two-dimensional polar active fluids to two-dimensional soap and one-dimensional sandblasting

    Science.gov (United States)

    Chen, Leiming; Lee, Chiu Fan; Toner, John

    2016-07-01

    Active fluids and growing interfaces are two well-studied but very different non-equilibrium systems. Each exhibits non-equilibrium behaviour distinct from that of their equilibrium counterparts. Here we demonstrate a surprising connection between these two: the ordered phase of incompressible polar active fluids in two spatial dimensions without momentum conservation, and growing one-dimensional interfaces (that is, the 1+1-dimensional Kardar-Parisi-Zhang equation), in fact belong to the same universality class. This universality class also includes two equilibrium systems: two-dimensional smectic liquid crystals, and a peculiar kind of constrained two-dimensional ferromagnet. We use these connections to show that two-dimensional incompressible flocks are robust against fluctuations, and exhibit universal long-ranged, anisotropic spatio-temporal correlations of those fluctuations. We also thereby determine the exact values of the anisotropy exponent ζ and the roughness exponents χx,y that characterize these correlations.

  1. 双向电泳技术在副干酪乳杆菌盐胁迫应激反应研究中的应用%Proteomic Analysis of Protein Induction in Lactobacillus paracasei by Salt Stress Using Two-Dimensional Electrophoresis

    Institute of Scientific and Technical Information of China (English)

    乌日娜; 岳喜庆; 武俊瑞

    2015-01-01

    对耐盐副干酪乳杆菌在盐胁迫下的应激反应进行研究,比较其在含有6 g/dL NaCl和未含有NaCl的培养基中生长至对数生长中期的蛋白质组双向电泳图谱差异。结果表明:有20个蛋白质点表达发生明显变化,经过基质辅助激光解吸/电离飞行时间质谱鉴定,其中热休克蛋白质GroEL和DnaK在盐胁迫下表达上调,参与脂肪酸合成的3-氧酰基-(酰载体蛋白)合酶Fab G表达下调,可能与该菌应对盐胁迫密切相关。%Lactobacillus paracasei LN-1 with salt tolerance property was isolated from traditional fermented food,suancai,which was made in the northeast of China. In order to understand the mechanism involved,proteomics analysis was undertaken to reveal the response of the strain during growth in medium with or without NaCl using two-dimensional electrophoresis (2-DE). Out of 20 protein spots that showed differential changes in expression,seven spots were identified by matrix assisted laser desorption and ionization time-of-flight mass spectrometry (MALDI-TOF/MS). Further analysis showed that chaperone protein (GroEL and DnaK) and fatty acid biosynthesis enemy(Fab G) possibly play important role in Lactobacillus paracasei LN-1 to resist to salt stress.

  2. Total Protein Analysis by Two-dimensional Electrophoresis in Cysticerci of Taenia solium and Taenia asiatica%猪带绦虫囊尾蚴与亚洲带绦虫囊尾蚴蛋白双向电泳图谱分析

    Institute of Scientific and Technical Information of China (English)

    方文; 肖靓靓; 包怀恩; 牟荣

    2011-01-01

    Two 20-day-old three-way crossed hybrid pigs were infected with 80 000 Taenia solium or T. Asiatica eggs, respectively. Immature cysticerci of the two species in liver were collected at 40 days after infection. The total proteins were separated by two-dimensional electrophoresis, and differentially expressed proteins were analyzed by Image-Master 2D Plantinum 6.0 software. The results showed that there were (236±12) and (231 ±14) protein spots in 2D electrophoresis gel images of T. Solium and T. Asiatica, respectively, with 3 proteins up-regulated and 7 proteins down-lated in T- scutum rt-Tir^rrus iiy 2-fold or more compared with those in T. Asioiica cystirercua-%将2头20日龄三元杂交乳猪分别感染猪带绦虫虫卵和亚洲带绦虫虫卵,8×104个/头.感染后40 d分别收集寄生在肝脏的未成熟猪带绦虫囊尾蚴(简称猪囊尾蚴)和亚洲带绦虫囊尾蚴,制备囊尾蚴蛋白,并进行蛋白双向电泳分析,用ImageMaster 2D Plantinum 6.0软件分析差异表达蛋白.结果显示,感染后40 d肝脏寄生的未成熟猪囊尾蚴和亚洲带绦虫囊尾蚴蛋白的双向电泳凝胶上分别有(236±12)和(231±14)个蛋白斑点,差异表达2倍以上的蛋白共10个,其中猪囊尾蚴表达上调的蛋白3个,下调的蛋白7个.

  3. ARC: Automated Resource Classifier for agglomerative functional classification of prokaryotic proteins using annotation texts

    Indian Academy of Sciences (India)

    Muthiah Gnanamani; Naveen Kumar; Srinivasan Ramachandran

    2007-08-01

    Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general, automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters ($\\mathcal{C}$), Cell division ($\\mathcal{D}$), Information ($\\mathcal{I}$), Translocation ($\\mathcal{L}$), Metabolism ($\\mathcal{M}$), Stress($\\mathcal{R}$), Signal and communication($\\mathcal{S}$) and 2 ancillary classes: Others ($\\mathcal{O}$) and Hypothetical ($\\mathcal{H}$). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps, this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

  4. Two-dimensional electronic spectroscopy for the quantum-optics enthusiast

    OpenAIRE

    Branczyk, Agata M.; Turner, Daniel B.; Scholes, Gregory D.

    2013-01-01

    Recent interest in the role of quantum mechanics in the primary events of photosynthetic energy transfer has led to a convergence of nonlinear optical spectroscopy and quantum optics on the topic of energy-transfer dynamics in pigment-protein complexes. The convergence of these two communities has unveiled a mismatch between the background and terminology of the respective fields. To make connections, we provide a pedagogical guide to understanding the basics of two-dimensional electronic spe...

  5. Localization of Tight Closure in Two-Dimensional Rings

    Indian Academy of Sciences (India)

    Kamran Divaani-Aazar; Massoud Tousi

    2005-02-01

    It is shown that tight closure commutes with localization in any two-dimensional ring of prime characteristic if either is a Nagata ring or possesses a weak test element. Moreover, it is proved that tight closure commutes with localization at height one prime ideals in any ring of prime characteristic.

  6. Graphene: A Promising Two-Dimensional Support for Heterogeneous Catalysts

    OpenAIRE

    Fan, Xiaobin

    2015-01-01

    Graphene has many advantages that make it an attractive two-dimensional (2D) support for heterogeneous catalysts. It not only allows the high loading of targeted catalytic species but also facilitates the mass transfer during the reaction processes. These advantages, along with its unique physical and chemical properties, endow graphene great potential as catalyst support in heterogeneous catalysis.

  7. Jump processes related to the two-dimensional Dirac equation

    International Nuclear Information System (INIS)

    The purpose of this lecture is to present for real time a probabilistic representation for the solution of the two dimensional Dirac equation in terms of pure jump processes, even in the presence of an external electromagnetic field. (orig./HSI)

  8. Dynamical phase transitions in the two-dimensional ANNNI model

    Energy Technology Data Exchange (ETDEWEB)

    Barber, M.N.; Derrida, B.

    1988-06-01

    We study the phase diagram of the two-dimensional anisotropic next-nearest neighbor Ising (ANNNI) model by comparing the time evolution of two distinct spin configurations submitted to the same thermal noise. We clearly se several dynamical transitions between ferromagnetic, paramagnetic, antiphase, and floating phases. These dynamical transitions seem to occur rather close to the transition lines determined previously in the literature.

  9. Solution of a model for two-dimensional intradiffusion

    CERN Document Server

    Erochenkova, G

    2002-01-01

    A system of partial differential equations corresponding to two-dimensional intradiffusion (Wicke) model for a weakly nonlinear isotherm of sorption is solved by reducing it to the Burgers' equation. Some limiting cases interesting from the physical point of view are considered in details.

  10. Two-dimensional position sensitive Si(Li) detector

    International Nuclear Information System (INIS)

    Circular, large-area two-dimensional Si(Li) position sensitive detectors have been fabricated. The detectors employ a thin lithium-diffused n+ resisitive layer for one contact and a boron implanted p+ resistive layer for the second contact. A position resolution of the order of 100 μm is indicated

  11. Dynamical Behaviors in a Two-dimensional Map

    Institute of Scientific and Technical Information of China (English)

    Yu Chang; Xu-dong Li

    2003-01-01

    We consider the dynamics of a two-dimensional map proposed by Maynard Smith as a population model. The existence of chaos in the sense of Marotto's theorem is first proved, and the bifurcations of periodic points are studied by analytic methods. The numerical simulations not only show the consistence with the theoretical analysis but also exhibi the complex dynamical behaviors.

  12. Forensic potential of comprehensive two-dimensional gas chromatography

    NARCIS (Netherlands)

    A. Sampat; M. Lopatka; M. Sjerps; G. Vivo-Truyols; P. Schoenmakers; A. van Asten

    2016-01-01

    In this study, the application of comprehensive two-dimensional (2D) gas chromatography (GC × GC) in forensic science is reviewed. The peer-reviewed publications on the forensic use of GC × GC and 2D gas chromatography with mass spectrometric detection (GC × GC-MS) have been studied in detail, not o

  13. Two-Dimensional Electronic Spectroscopy of a Model Dimer System

    Directory of Open Access Journals (Sweden)

    Prokhorenko V.I.

    2013-03-01

    Full Text Available Two-dimensional spectra of a dimer were measured to determine the timescale for electronic decoherence at room temperature. Anti-correlated beats in the crosspeaks were observed only during the period corresponding to the measured homogeneous lifetime.

  14. Coherent addition of two dimensional array of fiber lasers

    CERN Document Server

    Fridman, Moti; Davidson, Nir; Friesem, Asher A; Luria, Elena; Krupkin, Vladimir

    2008-01-01

    Configurations for efficient free space coherent addition of four separate fiber lasers arranged in two dimensional array are presented. They include compact and robust interferometric combiners that can be inserted either inside or outside the cavity of the combined lasers system. The results reveal that over 85% combining efficiency can be obtained.

  15. Adapting Grids For Computing Two-Dimensional Flows

    Science.gov (United States)

    Davies, Carol B.; Venkatapathy, Ethiraj

    1992-01-01

    SAGE2D is two-dimensional implementation of Self Adaptive Grid Evolution computer program that intelligently redistributes initial grid points on basis of initial flow-field solution. Grids modified according to initial computed flows enabling recomputation at greater accuracy. Written in FORTRAN 77.

  16. Easy interpretation of optical two-dimensional correlation spectra

    NARCIS (Netherlands)

    Lazonder, K.; Pshenichnikov, M.S.; Wiersma, D.A.

    2006-01-01

    We demonstrate that the value of the underlying frequency-frequency correlation function can be retrieved from a two-dimensional optical correlation spectrum through a simple relationship. The proposed method yields both intuitive clues and a quantitative measure of the dynamics of the system. The t

  17. Instability of two-dimensional heterotic stringy black holes

    CERN Document Server

    Azreg-Ainou, M

    1999-01-01

    We solve the eigenvalue problem of general relativity for the case of charged black holes in two-dimensional heterotic string theory, derived by McGuigan et al. For the case of $m^{2}>q^{2}$, we find a physically acceptable time-dependent growing mode; thus the black hole is unstable. The extremal case $m^{2}=q^{2}$ is stable.

  18. Describing two-dimensional vortical flows the typhoon case

    CERN Document Server

    Spineanu, F

    2005-01-01

    We present results of a numerical study of the differential equation governing the stationary states of the two-dimensional planetary atmosphere and magnetized plasma (within the Charney Hasegawa Mima model). The most strinking result is that the equation appears to be able to reproduce the main features of the flow structure of a typhoon.

  19. Specification of a Two-Dimensional Test Case

    DEFF Research Database (Denmark)

    Nielsen, Peter Vilhelm

    This paper describes the geometry and other boundary conditions for a test case which can be used to test different two-dimensional CFD codes in the lEA Annex 20 work. The given supply opening is large compared with practical openings. Therefore, this geometry will reduce the need for a high number...

  20. Two-dimensional probe absorption in coupled quantum dots

    Science.gov (United States)

    Liu, Ningwu; Zhang, Yan; Kang, Chengxian; Wang, Zhiping; Yu, Benli

    2016-07-01

    We investigate the two-dimensional (2D) probe absorption in coupled quantum dots. It is found that, due to the position-dependent quantum interference effect, the 2D optical absorption spectrum can be easily controlled via adjusting the system parameters. Thus, our scheme may provide some technological applications in solid-state quantum communication.

  1. Field analysis of two-dimensional focusing grating

    NARCIS (Netherlands)

    Borsboom, P.P.; Frankena, H.J.

    1995-01-01

    The method that we have developed [P-P. Borsboom, Ph.D. dissertation (Delft University of Technology, Delft, The Netherlands); P-P. Borsboom and H. J. Frankena, J. Opt. Soc. Am. A 12, 1134–1141 (1995)] is successfully applied to a two-dimensional focusing grating coupler. The field in the focal regi

  2. Bounds on the capacity of constrained two-dimensional codes

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Justesen, Jørn

    2000-01-01

    Bounds on the capacity of constrained two-dimensional (2-D) codes are presented. The bounds of Calkin and Wilf apply to first-order symmetric constraints. The bounds are generalized in a weaker form to higher order and nonsymmetric constraints. Results are given for constraints specified by run...

  3. Optical properties of two-dimensional magnetoelectric point scattering lattices

    DEFF Research Database (Denmark)

    Hansen, Per Lunnemann; Sersic, Ivana; Koenderink, A. Femius

    2013-01-01

    We explore the electrodynamic coupling between a plane wave and an infinite two-dimensional periodic lattice of magnetoelectric point scatterers, deriving a semianalytical theory with consistent treatment of radiation damping, retardation, and energy conservation. We apply the theory to arrays...

  4. Two-dimensional effects in nonlinear Kronig-Penney models

    DEFF Research Database (Denmark)

    Gaididei, Yuri Borisovich; Christiansen, Peter Leth; Rasmussen, Kim;

    1997-01-01

    An analysis of two-dimensional (2D) effects in the nonlinear Kronig-Penney model is presented. We establish an effective one-dimensional description of the 2D effects, resulting in a set of pseudodifferential equations. The stationary states of the 2D system and their stability is studied...

  5. Vibrations of Thin Piezoelectric Shallow Shells: Two-Dimensional Approximation

    Indian Academy of Sciences (India)

    N Sabu

    2003-08-01

    In this paper we consider the eigenvalue problem for piezoelectric shallow shells and we show that, as the thickness of the shell goes to zero, the eigensolutions of the three-dimensional piezoelectric shells converge to the eigensolutions of a two-dimensional eigenvalue problem.

  6. Topology optimization of two-dimensional elastic wave barriers

    DEFF Research Database (Denmark)

    Van Hoorickx, C.; Sigmund, Ole; Schevenels, M.;

    2016-01-01

    Topology optimization is a method that optimally distributes material in a given design domain. In this paper, topology optimization is used to design two-dimensional wave barriers embedded in an elastic halfspace. First, harmonic vibration sources are considered, and stiffened material is inserted...

  7. Surface hopping modeling of two-dimensional spectra

    NARCIS (Netherlands)

    Tempelaar, Roel; Vegte, Cornelis P. van der; Knoester, Jasper; Jansen, Thomas L.C.

    2013-01-01

    Recently, two-dimensional (2D) electronic spectroscopy has become an important tool to unravel the excited state properties of complex molecular assemblies, such as biological light harvesting systems. In this work, we propose a method for simulating 2D electronic spectra based on a surface hopping

  8. Torque magnetometry studies of two-dimensional electron systems

    NARCIS (Netherlands)

    Schaapman, Maaike Ruth

    2004-01-01

    This thesis describes a study of the magnetization two-dimensional electron gases (2DEGs). To detect the typically small magnetization, a sensitive magnetometer with optical angular detection was developed. The magnetometer uses a quadrant detector to measure the rotation of the sample. By mounting

  9. Observation of two-dimensional nonlocal gap solitons

    DEFF Research Database (Denmark)

    Rasmussen, Per Dalgaard; Bennett, Francis H.; Neshev, Dragomir N.;

    2009-01-01

    We demonstrate, both theoretically and experimentally, the existence of nonlocal gap solitons in twodimensional periodic photonic structures with defocusing thermal nonlinearity. We employ liquid-infiltrated photonic crystal fibers and show how the system geometry can modify the effective response...... of a nonlocal medium and the properties of two-dimensional gap solitons. © 2009 Optical Society of America...

  10. Magnetic order in two-dimensional nanoparticle assemblies

    NARCIS (Netherlands)

    Georgescu, M

    2008-01-01

    This thesis involves a fundamental study of two-dimensional arrays of magnetic nanoparticles using non-contact Atomic Force Microscopy, Magnetic Force Microscopy, and Atomic Force Spectroscopy. The goal is to acquire a better understanding of the interactions between magnetic nanoparticles and the r

  11. Operator splitting for two-dimensional incompressible fluid equations

    CERN Document Server

    Holden, Helge; Karper, Trygve K

    2011-01-01

    We analyze splitting algorithms for a class of two-dimensional fluid equations, which includes the incompressible Navier-Stokes equations and the surface quasi-geostrophic equation. Our main result is that the Godunov and Strang splitting methods converge with the expected rates provided the initial data are sufficiently regular.

  12. Topological states of matter in two-dimensional fermionic systems

    NARCIS (Netherlands)

    Beugeling, W.

    2012-01-01

    Topological states of matter in two-dimensional systems are characterised by the different properties of the edges and the bulk of the system: The edges conduct electrical current while the bulk is insulating. The first well-known example is the quantum Hall effect, which is induced by a perpendicul

  13. The analysis of protein differences in cerebrospinal fluid of tuberculous meningitis and cryptococcus meningitis by two-dimensional electrophoresis%应用双向电泳分析结核性脑膜炎与隐球菌性脑膜炎脑脊液的蛋白差异

    Institute of Scientific and Technical Information of China (English)

    黄绍梅; 杨瑜; 邱薇; 吴睿彦; 谢贝; 刘志辉; 陈志成

    2016-01-01

    Objective To screen the diagnostic markers between tuberculous meningitis and cryptococcus meningitis by analyzing the protein differences in cerebrospinal fluid (CSF).Methods The proteins in CSF of 4 cases of tuberculous meningitis and 4 cases of cryptococcal meningitis were separated by two-dimensional gel electrophoresis (2-DE).The differential proteins expression was descriptively analyzed according to the protein isoelectric point PI,molecular weight,matching rate,gray value by PDQuest8.0 software.Results 111 and 114 protein spots were captured from CSF of tuberculose meningitis and cryptococcus meningitis.The molecular weight of proteins ranged from 10 to 130 kDa.The isoelectric point (PI) was from 4.4 to 6.7.The matching rate of two groups was 95%.There were 24 differential proteins between two groups,of which 3 proteins were expressed only in tuberculous meningitis and 2 proteins expressed only in cryptococcal meningitis.19 matching protein point were two-fold differential expression.Conclusion 2-DE profiles with high resolution and reproducibility of CSF for tuberculous meningitis and cryptococcus meningitis are established,and some differences in protein expression exist between the two.%目的 比较分析结核性脑膜炎(TBM)与隐球菌性脑膜炎脑脊液的差异蛋白质,筛选二者的鉴别诊断标志物.方法 采用双向凝胶电泳技术对4例TBM和4例隐球菌性脑膜炎脑脊液蛋白进行电泳分离,以PDQuest8.0软件根据蛋白的等电点PI、分子量、匹配率、灰度值等进行差异蛋白描述性分析.结果 结核性、隐球菌性两组脑脊液分别检测到蛋白点数为111和114,蛋白点分子量均分布为10~130 kDa,等电点PI为4.4~6.7间.两组脑脊液蛋白图谱匹配率为95%,产生24个差异蛋白点,其中3个蛋白点只在TBM中表达,2个蛋白点只在隐球菌性脑膜炎中表达,19个匹配蛋白点存在2倍差异表达.结论 双向电泳技术可得到分辨率和重复率较高

  14. PPLook: an automated data mining tool for protein-protein interaction

    Directory of Open Access Journals (Sweden)

    Xia Li

    2010-06-01

    Full Text Available Abstract Background Extracting and visualizing of protein-protein interaction (PPI from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results. Results We developed a PPI search system, termed PPLook, which automatically extracts and visualizes protein-protein interaction (PPI from text. Given a query protein name, PPLook can search a dataset for other proteins interacting with it by using a keywords dictionary pattern-matching algorithm, and display the topological parameters, such as the number of nodes, edges, and connected components. The visualization component of PPLook enables us to view the interaction relationship among the proteins in a three-dimensional space based on the OpenGL graphics interface technology. PPLook can also provide the functions of selecting protein semantic class, counting the number of semantic class proteins which interact with query protein, counting the literature number of articles appearing the interaction relationship about the query protein. Moreover, PPLook provides heterogeneous search and a user-friendly graphical interface. Conclusions PPLook is an effective tool for biologists and biosystem developers who need to access PPI information from the literature. PPLook is freely available for non-commercial users at http://meta.usc.edu/softs/PPLook.

  15. Mass Spectrometry-Based Monitoring of Millisecond Protein-Ligand Binding Dynamics Using an Automated Microfluidic Platform

    Energy Technology Data Exchange (ETDEWEB)

    Cong, Yongzheng; Katipamula, Shanta; Trader, Cameron D.; Orton, Daniel J.; Geng, Tao; Baker, Erin Shammel; Kelly, Ryan T.

    2016-03-24

    Characterizing protein-ligand binding dynamics is crucial for understanding protein function and developing new therapeutic agents. We have developed a novel microfluidic platform that features rapid mixing of protein and ligand solutions, variable incubation times, and on-chip electrospray ionization to perform label-free, solution-based monitoring of protein-ligand binding dynamics. This platform offers many advantages including automated processing, rapid mixing, and low sample consumption.

  16. Two-dimensional polyacrylamide gel analysis of Plodia interpunctella granulosis virus

    Energy Technology Data Exchange (ETDEWEB)

    Russell, D.L.; Consigli, R.A.

    1986-10-01

    The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure.

  17. Two-Dimensional Polyacrylamide Gel Analysis of Plodia interpunctella Granulosis Virus.

    Science.gov (United States)

    Russell, D L; Consigli, R A

    1986-10-01

    The structural polypeptides of purified Plodia interpunctella granulosis virus were analyzed by three different two-dimensional gel systems. Isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of 53 acidic polypeptides in the enveloped nucleocapsid of the virus ranging in molecular weight from 97,300 to 8,000. Nine of these polypeptides were shown to be glycoproteins by the technique of radiolabeled lectin blotting. Separation of the granulin in this system allowed resolution of five species, all of which have identical tryptic peptide maps. This matrix protein was demonstrated to be a phosphoglycoprotein by radiolabeled lectin blotting and acid phosphatase dephosphorylation. Nonequilibrium pH gel electrophoresis followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed resolution of the major basic protein of the virus, VP12, from a more acidic protein of the same molecular weight. Tryptic peptide analysis demonstrated that these two proteins were indeed different and acid urea gels followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis allowed localization of the acidic protein to the envelope and the basic protein to the nucleocapsid of the virus. Finally, probing of the separated envelope nucleocapsid proteins in both the isoelectric focusing and nonequilibrium pH gel electrophoresis two-dimensional systems after transfer to nitrocellulose with iodinated, purified viral proteins allowed further insight into reactions which may be important in the maintenance of the virion structure.

  18. Brewster Angle Microscope Investigations of Two Dimensional Phase Transitions

    Science.gov (United States)

    Schuman, Adam William

    The liquid-liquid interface is investigated by microscopic and thermodynamic means to image and measure interfacial properties when the system undergoes a two-dimensional (2D) phase transition of a Gibbs monolayer by varying the sample temperature. An in-house Brewster angle microscope (BAM) is constructed to visualize the interface during this transition while a quasi-elastic light scattering technique is used to determine the interfacial tension. These results complement x-ray investigations of the same systems. Evidence of interfacial micro-separated structure, microphases, comes from observations across a hexane-water interface with the inclusion of a long-chain fluorinated alcohol surfactant into the bulk hexane. Microphases take the form of spatially modulated structure to the density of the surfactant as it spans laterally across the interface. The surfactant monolayer exhibits microphase morphology over a range of a couple degrees as the temperature of the system is scanned through the 2D gas-solid phase transition. Microphase structure was observed for heating and cooling the hexane-water system and structural comparisons are given when the temperature step and quench depth of the cooling process is varied. A complete sequence of morphological structure was observed from 2D gas to cluster to labyrinthine stripe to a 2D solid mosaic pattern. Two characteristic length scales emerge giving rise to speculation of an elastic contribution to the standard repulsive and attractive competitive forces stabilizing the microphase. The benefit of BAM to laterally image very thin films across the surface of an interface on the micrometer length scale nicely complements x-ray reflectivity methods that average structural data transverse to the liquid interface on a molecular scale. To properly analyze x-ray reflectivity data, the interface is required to be laterally homogeneous. BAM can sufficiently characterize the interface for this purpose as is done for a Langmuir

  19. Automation of NMR measurements and data evaluation for systematically screening interactions of small molecules with target proteins

    International Nuclear Information System (INIS)

    In this technical note we describe the setup and application of automated sample preparation and usage of flow-through NMR equipment for the characterization of ligand binding on proteins. In addition, we focus on the perspectives of automated analysis of 2D HSQC spectra to identify changes in patterns indicative for ligand binding or changes of sample conditions. In this context we discuss a combination of statistical and non-statistical data analysis

  20. Automated hydrophobic interaction chromatography column selection for use in protein purification.

    Science.gov (United States)

    Murphy, Patrick J M; Stone, Orrin J; Anderson, Michelle E

    2011-01-01

    In contrast to other chromatographic methods for purifying proteins (e.g. gel filtration, affinity, and ion exchange), hydrophobic interaction chromatography (HIC) commonly requires experimental determination (referred to as screening or "scouting") in order to select the most suitable chromatographic medium for purifying a given protein (1). The method presented here describes an automated approach to scouting for an optimal HIC media to be used in protein purification. HIC separates proteins and other biomolecules from a crude lysate based on differences in hydrophobicity. Similar to affinity chromatography (AC) and ion exchange chromatography (IEX), HIC is capable of concentrating the protein of interest as it progresses through the chromatographic process. Proteins best suited for purification by HIC include those with hydrophobic surface regions and able to withstand exposure to salt concentrations in excess of 2 M ammonium sulfate ((NH(4;))(2;)SO(4;)). HIC is often chosen as a purification method for proteins lacking an affinity tag, and thus unsuitable for AC, and when IEX fails to provide adequate purification. Hydrophobic moieties on the protein surface temporarily bind to a nonpolar ligand coupled to an inert, immobile matrix. The interaction between protein and ligand are highly dependent on the salt concentration of the buffer flowing through the chromatography column, with high ionic concentrations strengthening the protein-ligand interaction and making the protein immobile (i.e. bound inside the column) (2). As salt concentrations decrease, the protein-ligand interaction dissipates, the protein again becomes mobile and elutes from the column. Several HIC media are commercially available in pre-packed columns, each containing one of several hydrophobic ligands (e.g. S-butyl, butyl, octyl, and phenyl) cross-linked at varying densities to agarose beads of a specific diameter (3). Automated column scouting allows for an efficient approach for determining

  1. 日本血吸虫虫卵、童虫和雌雄成虫膜蛋白的双向电泳%Analysis of membrane proteins from egg, schistosomulum, adult male and female worm of Schistosoma japonicum by two dimensional electrophoresis

    Institute of Scientific and Technical Information of China (English)

    程国锋; 冯新港; 林矫矫; 石耀军; 陆柯; 周元聪; 蔡幼民

    2005-01-01

    Membrane proteins were extracted from eggs, schistosomulum, adult male and female worms of Schistosoma japonicum in order to analyze the differently expressed profile by two dimensional electrophoresis. Schistosomulum and adult worms were obtained from rabbits infected with 1 500 cercariaes on 14 and 42 days after challenge, respectively. Adult male and female worms on 42 days were manually detached and stored into liquid nitrogen until use. Eggs were collected by PercollTM from the liver of rabbits. ProteoPrep Membrane Extraction KitTM was employed to extracted membrane proteins by reducing and alkylating with TBP and iodoacetamide from 200mg of eggs, schistosomulums, adult male worm and female worms, respectively. Immobilized pH gradient strips with a linear pH range of 3-10(130mm) were rehydrated together with membrane proteins (30μg) in 250μl solution containing 7mol urea, 2mol thiourea, 2% SB3-10, 4% CHAPS, 40mmol Tris, 30mmol DTT, then separated on 12.5% SDS polyacrylamide gel for the second dimensional electrophoresis. Gels were stained with silver, scanned by Labscan, and analyzed using ImageMasterTM Analysis software. The 2D maps of egg, schistosomulum, adult female worm and male worm were showed 78±3, 67±3, 108±4 and 122±4 spots respectively. There were 35±1 spots which showed specific expression in female worm as compared with male worm, but 45±2 spots were in male worms. Most differently expressed spots between male and female worms were located in the area of 40-70kD and pI 4-7. The large number of unique spots from sehistosomulum was located in the area of alkalescence. The 2D map of for adult male worms uniquely showed 5 spots as compared with that of schistosomulum and female worm. The female worm showed 4 unique spots as compared with that of schistosomulum, egg and male worm. The unique spots between male and female worms were identified by the database of SWISS 2D-PAGE according to the molecular weight and isoelectronic point

  2. Screening of differentially expressed proteins in serum from subjects with Keshan disease by two-dimensional electrophoresis and mass and mass spectrometry%双向电泳-质谱技术筛选克山病血清差异蛋白

    Institute of Scientific and Technical Information of China (English)

    何淑兰; 谭武红; 王静; 王盼; 相有章

    2013-01-01

    目的 比较克山病患者与健康者血清蛋白表达谱,探讨克山病发病机制,寻找与克山病发生相关差异蛋白.方法 从克山病病区选择8例慢型克山病,病区对照以及非病区对照各8例,应用双向凝胶电泳技术分离克山病患者同健康者的差异蛋白点,基质辅助激光解吸电离-飞行时间质谱鉴定差异蛋白.结果 凝胶图像分析显示9个差异蛋白质点,经质谱鉴定确定8种蛋白.3种蛋白在克山病组较非病区健康组上调,其功能主要与脂类代谢,免疫调节,凋亡抑制有关.3种蛋白下调,主要与细胞内铁离子平衡密切相关.克山病组较病区健康组2种蛋白表达上调,主要与蛋白酶抑制等功能有关.结论 该研究发现触珠蛋白、血清白蛋白和α1-抗胰蛋白酶、转铁蛋白、α2-HS糖蛋白可作为克山病的诊断与预后的候选生物学指标,具有重要意义.%Objective To screen differentially expressed proteins in serum in patients with Keshan disease (KD),peripheral blood protein expression spectrum between subjects with Keshan disease and health controls were compared.Methods Differentially expressed protein spots were screened by two-dimensional gel electrophoresis (2-DE) between Keshan disease and health control subjects,and constitutive protein were identified by matrix assisted laser adsorption/ionization-time of flight mass spectrometry (MALDI-TOF-MS).Results 9 differentially expressed protein spots were showed in 2-DE images and 8 differentially expressed proteins were identified by MALDI-TOF-MS.In them,3 up-regulated proteins,mainly related to lipid metabolism,apoptosis resistance,immunological regulation and 3 down-regulated proteins,involved to cellular iron ion homeostasis; 2 up-regulated proteins in serum in patients with KD versus controls from KD areas were detected,mainly associated with protease inhibition.Conclusions Haptoglobin,serum albumin,alpha-1-antitrypsin,transferring and αt2-heremans

  3. Automated data extraction from in situ protein stable isotope probing studies

    Energy Technology Data Exchange (ETDEWEB)

    Slysz, Gordon W.; Steinke, Laurey A.; Ward, David M.; Klatt, Christian G.; Clauss, Therese RW; Purvine, Samuel O.; Payne, Samuel H.; Anderson, Gordon A.; Smith, Richard D.; Lipton, Mary S.

    2014-01-27

    Protein stable isotope probing (protein-SIP) has strong potential for revealing key metabolizing taxa in complex microbial communities. While most protein-SIP work to date has been performed under controlled laboratory conditions to allow extensive isotope labeling of the target organism, a key application will be in situ studies of microbial communities under conditions that result in small degrees of partial labeling. One hurdle restricting large scale in situ protein-SIP studies is the lack of algorithms and software for automated data processing of the massive data sets resulting from such studies. In response, we developed Stable Isotope Probing Protein Extraction Resources software (SIPPER) and applied it for large scale extraction and visualization of data from short term (3 h) protein-SIP experiments performed in situ on Yellowstone phototrophic bacterial mats. Several metrics incorporated into the software allow it to support exhaustive analysis of the complex composite isotopic envelope observed as a result of low amounts of partial label incorporation. SIPPER also enables the detection of labeled molecular species without the need for any prior identification.

  4. Two-dimensional phase changes of nitric oxide adsorbed on lamellar halides. Two-dimensional triple points

    International Nuclear Information System (INIS)

    Adsorption isotherms of nitric oxide on the cleavage face of fourteen lamellar halides (NiCl2, CoCl2, FeCl2, NiBr2, CoBr2, FeBr2, MgBr2, CdCl2, Col2, CdBr2, MnI2, CdI2, CaI2 and PbI2) have been determined. Adsorbents having a uniform surface have been prepared by sublimation in a rapid current of dry nitrogen. The isotherms show vertical steps corresponding to two-dimensional phase transitions. Except for CaI2, a crystalline monomolecular layer β constituted of dimers oriented perpendicularly to the surface of the substrate, is formed. At low temperatures this phase is formed directly during a two-dimensional condensation. Above the temperature of a two-dimensional triple point, a crystalline layer α, where the dimers lie flat on the surface, appears as an intermediate phase. The variations of the two-dimensional triple point temperature and of the free energy of the β phase with the nature and the crystal parameter of the adsorbent are explained

  5. Automation of C-terminal sequence analysis of 2D-PAGE separated proteins

    Directory of Open Access Journals (Sweden)

    P.P. Moerman

    2014-06-01

    Full Text Available Experimental assignment of the protein termini remains essential to define the functional protein structure. Here, we report on the improvement of a proteomic C-terminal sequence analysis method. The approach aims to discriminate the C-terminal peptide in a CNBr-digest where Met-Xxx peptide bonds are cleaved in internal peptides ending at a homoserine lactone (hsl-derivative. pH-dependent partial opening of the lactone ring results in the formation of doublets for all internal peptides. C-terminal peptides are distinguished as singlet peaks by MALDI-TOF MS and MS/MS is then used for their identification. We present a fully automated protocol established on a robotic liquid-handling station.

  6. Optimization of extraction method of the water-soluble proteins of barley and malt and construction of two-dimensional electrophoretic map%大麦和麦芽水溶性蛋白提取方案的优化及双向电泳图谱的建立

    Institute of Scientific and Technical Information of China (English)

    夏先锋; 朴永哲; 沈海萍; 翟明昌; 成建国; 赵长新

    2012-01-01

    To develop an efficient and high resolution 2-DE procedure for barley and malt research, in this study, the method of extraction and sample preparation for two dimensional gel electrophoresis (2-DE) were optimized using high quality barley cultivars Gairdner and by changing the type and amount of extraction reagents as well as extraction time. By using the optimized method, protein extraction and sample preparation methods could be achieved. The protein sample of barley was obtained after grinding, buffer-phenol extraction, ethanol washing, and was freeze-dried. Protein spots were separated by 2-DE technique, stained with silver nitrate, recorded and detected by PDQuest software. The results showed that over 700 spots of barley and about 500 spots of malt were separated by 2-DE. The established of those methods may provide powerful tools for developmental proteomics and quality improvement of barley in the future.%为了建立一套适用于大麦和麦芽的双向电泳分析方法,得到更加清晰、全面的双向电泳图谱。以高产优质大麦品种Gairdner为材料,对提取方法以及提取过程中所用的试剂的种类、用量和处理时间等进行比较分析和优化,运用蛋白定量法测定提取样品的蛋白质含量,摸索出一套完整的用于双向电泳分析的大麦蛋白提取和样品制备方法。大麦或麦芽经研磨,缓冲液-苯酚提取,醇洗,冻干后得到的蛋白质样品,双向电泳分离,硝酸银染色,PDQuest分析,图谱结果显示大麦检测到700个蛋白质点,麦芽检测到500个蛋白质点。这一方法的构建可作为大麦蛋白质组研究的重要工具,为今后大麦蛋白质组学以及对大麦品质改良的研究奠定了一定的基础。

  7. Hidden symmetries in the two-dimensional isotropic antiferromagnet

    CERN Document Server

    Leonel, S A; Oliveira, W; Silva, G L; Xavier, L M V

    2013-01-01

    We discuss the two-dimensional isotropic antiferromagnet in the framework of gauge invariance. Gauge invariance is one of the most subtle useful concepts in theoretical physics, since it allows one to describe the time evolution of complex physical systesm in arbitrary sequences of reference frames. All theories of the fundamental interactions rely on gauge invariance. In Dirac's approach, the two-dimensional isotropic antiferromagnet is subject to second class constraints, which are independent of the Hamiltonian symmetries and can be used to eliminate certain canonical variables from the theory. We have used the symplectic embedding formalism developed by a few of us to make the system under study gauge-invariant. After carrying out the embedding and Dirac analysis, we systematically show how second class constraints can generate hidden symmetries. We obtain the invariant second-order Lagrangian and the gauge-invariant model Hamiltonian. Finally, for a particular choice of factor ordering, we derive the fun...

  8. Analysis of one dimensional and two dimensional fuzzy controllers

    Institute of Scientific and Technical Information of China (English)

    Ban Xiaojun; Gao Xiaozhi; Huang Xianlin; Wu Tianbao

    2006-01-01

    The analytical structures and the corresponding mathematical properties of the one dimensional and two dimensional fuzzy controllers are first investigated in detail.The nature of these two kinds of fuzzy controllers is next probed from the perspective of control engineering. For the one dimensional fuzzy controller, it is concluded that this controller is a combination of a saturation element and a nonlinear proportional controller, and the system that employs the one dimensional fuzzy controller is the combination of an open-loop control system and a closedloop control system. For the latter case, it is concluded that it is a hybrid controller, which comprises the saturation part, zero-output part, nonlinear derivative part, nonlinear proportional part, as well as nonlinear proportional-derivative part, and the two dimensional fuzzy controller-based control system is a loop-varying system with varying number of control loops.

  9. Boron nitride as two dimensional dielectric: Reliability and dielectric breakdown

    Energy Technology Data Exchange (ETDEWEB)

    Ji, Yanfeng; Pan, Chengbin; Hui, Fei; Shi, Yuanyuan; Lanza, Mario, E-mail: mlanza@suda.edu.cn [Institute of Functional Nano and Soft Materials, Collaborative Innovation Center of Suzhou Nano Science and Technology, Soochow University, 199 Ren-Ai Road, Suzhou 215123 (China); Zhang, Meiyun; Long, Shibing [Key Laboratory of Microelectronics Devices & Integrated Technology, Institute of Microelectronics, Chinese Academy of Sciences, Beijing 100029 (China); Lian, Xiaojuan; Miao, Feng [National Laboratory of Solid State Microstructures, School of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093 (China); Larcher, Luca [DISMI, Università di Modena e Reggio Emilia, 42122 Reggio Emilia (Italy); Wu, Ernest [IBM Research Division, Essex Junction, Vermont 05452 (United States)

    2016-01-04

    Boron Nitride (BN) is a two dimensional insulator with excellent chemical, thermal, mechanical, and optical properties, which make it especially attractive for logic device applications. Nevertheless, its insulating properties and reliability as a dielectric material have never been analyzed in-depth. Here, we present the first thorough characterization of BN as dielectric film using nanoscale and device level experiments complementing with theoretical study. Our results reveal that BN is extremely stable against voltage stress, and it does not show the reliability problems related to conventional dielectrics like HfO{sub 2}, such as charge trapping and detrapping, stress induced leakage current, and untimely dielectric breakdown. Moreover, we observe a unique layer-by-layer dielectric breakdown, both at the nanoscale and device level. These findings may be of interest for many materials scientists and could open a new pathway towards two dimensional logic device applications.

  10. Entanglement Entropy in Two-Dimensional String Theory.

    Science.gov (United States)

    Hartnoll, Sean A; Mazenc, Edward A

    2015-09-18

    To understand an emergent spacetime is to understand the emergence of locality. Entanglement entropy is a powerful diagnostic of locality, because locality leads to a large amount of short distance entanglement. Two-dimensional string theory is among the very simplest instances of an emergent spatial dimension. We compute the entanglement entropy in the large-N matrix quantum mechanics dual to two-dimensional string theory in the semiclassical limit of weak string coupling. We isolate a logarithmically large, but finite, contribution that corresponds to the short distance entanglement of the tachyon field in the emergent spacetime. From the spacetime point of view, the entanglement is regulated by a nonperturbative "graininess" of space. PMID:26430982

  11. Two Dimensional Lattice Boltzmann Method for Cavity Flow Simulation

    Directory of Open Access Journals (Sweden)

    Panjit MUSIK

    2004-01-01

    Full Text Available This paper presents a simulation of incompressible viscous flow within a two-dimensional square cavity. The objective is to develop a method originated from Lattice Gas (cellular Automata (LGA, which utilises discrete lattice as well as discrete time and can be parallelised easily. Lattice Boltzmann Method (LBM, known as discrete Lattice kinetics which provide an alternative for solving the Navier–Stokes equations and are generally used for fluid simulation, is chosen for the study. A specific two-dimensional nine-velocity square Lattice model (D2Q9 Model is used in the simulation with the velocity at the top of the cavity kept fixed. LBM is an efficient method for reproducing the dynamics of cavity flow and the results which are comparable to those of previous work.

  12. Folding two dimensional crystals by swift heavy ion irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ochedowski, Oliver; Bukowska, Hanna [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Freire Soler, Victor M. [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Departament de Fisica Aplicada i Optica, Universitat de Barcelona, E08028 Barcelona (Spain); Brökers, Lara [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany); Ban-d' Etat, Brigitte; Lebius, Henning [CIMAP (CEA-CNRS-ENSICAEN-UCBN), 14070 Caen Cedex 5 (France); Schleberger, Marika, E-mail: marika.schleberger@uni-due.de [Fakultät für Physik and CENIDE, Universität Duisburg-Essen, D-47048 Duisburg (Germany)

    2014-12-01

    Ion irradiation of graphene, the showcase model of two dimensional crystals, has been successfully applied to induce various modifications in the graphene crystal. One of these modifications is the formation of origami like foldings in graphene which are created by swift heavy ion irradiation under glancing incidence angle. These foldings can be applied to locally alter the physical properties of graphene like mechanical strength or chemical reactivity. In this work we show that the formation of foldings in two dimensional crystals is not restricted to graphene but can be applied for other materials like MoS{sub 2} and hexagonal BN as well. Further we show that chemical vapour deposited graphene forms foldings after swift heavy ion irradiation while chemical vapour deposited MoS{sub 2} does not.

  13. Enstrophy inertial range dynamics in generalized two-dimensional turbulence

    Science.gov (United States)

    Iwayama, Takahiro; Watanabe, Takeshi

    2016-07-01

    We show that the transition to a k-1 spectrum in the enstrophy inertial range of generalized two-dimensional turbulence can be derived analytically using the eddy damped quasinormal Markovianized (EDQNM) closure. The governing equation for the generalized two-dimensional fluid system includes a nonlinear term with a real parameter α . This parameter controls the relationship between the stream function and generalized vorticity and the nonlocality of the dynamics. An asymptotic analysis accounting for the overwhelming dominance of nonlocal triads allows the k-1 spectrum to be derived based upon a scaling analysis. We thereby provide a detailed analytical explanation for the scaling transition that occurs in the enstrophy inertial range at α =2 in terms of the spectral dynamics of the EDQNM closure, which extends and enhances the usual phenomenological explanations.

  14. Extension of modified power method to two-dimensional problems

    Science.gov (United States)

    Zhang, Peng; Lee, Hyunsuk; Lee, Deokjung

    2016-09-01

    In this study, the generalized modified power method was extended to two-dimensional problems. A direct application of the method to two-dimensional problems was shown to be unstable when the number of requested eigenmodes is larger than a certain problem dependent number. The root cause of this instability has been identified as the degeneracy of the transfer matrix. In order to resolve this instability, the number of sub-regions for the transfer matrix was increased to be larger than the number of requested eigenmodes; and a new transfer matrix was introduced accordingly which can be calculated by the least square method. The stability of the new method has been successfully demonstrated with a neutron diffusion eigenvalue problem and the 2D C5G7 benchmark problem.

  15. On Dirichlet eigenvectors for neutral two-dimensional Markov chains

    CERN Document Server

    Champagnat, Nicolas; Miclo, Laurent

    2012-01-01

    We consider a general class of discrete, two-dimensional Markov chains modeling the dynamics of a population with two types, without mutation or immigration, and neutral in the sense that type has no influence on each individual's birth or death parameters. We prove that all the eigenvectors of the corresponding transition matrix or infinitesimal generator \\Pi\\ can be expressed as the product of "universal" polynomials of two variables, depending on each type's size but not on the specific transitions of the dynamics, and functions depending only on the total population size. These eigenvectors appear to be Dirichlet eigenvectors for \\Pi\\ on the complement of triangular subdomains, and as a consequence the corresponding eigenvalues are ordered in a specific way. As an application, we study the quasistationary behavior of finite, nearly neutral, two-dimensional Markov chains, absorbed in the sense that 0 is an absorbing state for each component of the process.

  16. Two-Dimensional Computational Model for Wave Rotor Flow Dynamics

    Science.gov (United States)

    Welch, Gerard E.

    1996-01-01

    A two-dimensional (theta,z) Navier-Stokes solver for multi-port wave rotor flow simulation is described. The finite-volume form of the unsteady thin-layer Navier-Stokes equations are integrated in time on multi-block grids that represent the stationary inlet and outlet ports and the moving rotor passages of the wave rotor. Computed results are compared with three-port wave rotor experimental data. The model is applied to predict the performance of a planned four-port wave rotor experiment. Two-dimensional flow features that reduce machine performance and influence rotor blade and duct wall thermal loads are identified. The performance impact of rounding the inlet port wall, to inhibit separation during passage gradual opening, is assessed.

  17. Transport behavior of water molecules through two-dimensional nanopores

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chongqin; Li, Hui; Meng, Sheng, E-mail: smeng@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  18. Two-dimensional three-regions rewetting modelling using ANSYS

    International Nuclear Information System (INIS)

    Modelling rewetting processes is a challenging problem. One-dimensional modelling is an over simplification whereas a mechanistic unsteady three-dimensional modelling presents obvious difficulties. However, two-dimensional simulation using commercial software has been found to give reasonable results. This paper describes two-dimensional modelling studies of the rewetting of a hot plate by a moving liquid film using the ANSYS code. The entire plate is divided into three regions - namely the wet region, the dry region and the transition region between the wet and dry regions. In the transition zone, the wetting phenomenon of intermittent contact of water with metal at high temperature is modelled by imposing a time averaged (over the period of cycle) heat transfer coefficient in the transition region. The parameters studied are the intermittent contact frequency, heat transfer coefficient, and the length of intermittent contact region. The results are in plausible agreement with the experimental data. (author)

  19. Phase separation under two-dimensional Poiseuille flow.

    Science.gov (United States)

    Kiwata, H

    2001-05-01

    The spinodal decomposition of a two-dimensional binary fluid under Poiseuille flow is studied by numerical simulation. We investigated time dependence of domain sizes in directions parallel and perpendicular to the flow. In an effective region of the flow, the power-law growth of a characteristic length in the direction parallel to the flow changes from the diffusive regime with the growth exponent alpha=1/3 to a new regime. The scaling invariance of the growth in the perpendicular direction is destroyed after the diffusive regime. A recurrent prevalence of thick and thin domains which determines log-time periodic oscillations has not been observed in our model. The growth exponents in the infinite system under two-dimensional Poiseuille flow are obtained by the renormalization group.

  20. Entanglement Entropy in Two-Dimensional String Theory.

    Science.gov (United States)

    Hartnoll, Sean A; Mazenc, Edward A

    2015-09-18

    To understand an emergent spacetime is to understand the emergence of locality. Entanglement entropy is a powerful diagnostic of locality, because locality leads to a large amount of short distance entanglement. Two-dimensional string theory is among the very simplest instances of an emergent spatial dimension. We compute the entanglement entropy in the large-N matrix quantum mechanics dual to two-dimensional string theory in the semiclassical limit of weak string coupling. We isolate a logarithmically large, but finite, contribution that corresponds to the short distance entanglement of the tachyon field in the emergent spacetime. From the spacetime point of view, the entanglement is regulated by a nonperturbative "graininess" of space.

  1. Statistical mechanics of two-dimensional and geophysical flows

    CERN Document Server

    Bouchet, Freddy

    2011-01-01

    The theoretical study of the self-organization of two-dimensional and geophysical turbulent flows is addressed based on statistical mechanics methods. This review is a self-contained presentation of classical and recent works on this subject; from the statistical mechanics basis of the theory up to applications to Jupiter's troposphere and ocean vortices and jets. Emphasize has been placed on examples with available analytical treatment in order to favor better understanding of the physics and dynamics. The equilibrium microcanonical measure is built from the Liouville theorem. On this theoretical basis, we predict the output of the long time evolution of complex turbulent flows as statistical equilibria. This is applied to make quantitative models of two-dimensional turbulence, the Great Red Spot and other Jovian vortices, ocean jets like the Gulf-Stream, and ocean vortices. We also present recent results for non-equilibrium situations, for the studies of either the relaxation towards equilibrium or non-equi...

  2. Topological states in two-dimensional hexagon lattice bilayers

    Science.gov (United States)

    Zhang, Ming-Ming; Xu, Lei; Zhang, Jun

    2016-10-01

    We investigate the topological states of the two-dimensional hexagon lattice bilayer. The system exhibits a quantum valley Hall (QVH) state when the interlayer interaction t⊥ is smaller than the nearest neighbor hopping energy t, and then translates to a trivial band insulator state when t⊥ / t > 1. Interestingly, the system is found to be a single-edge QVH state with t⊥ / t = 1. The topological phase transition also can be presented via changing bias voltage and sublattice potential in the system. The QVH states have different edge modes carrying valley current but no net charge current. The bias voltage and external electric field can be tuned easily in experiments, so the present results will provide potential application in valleytronics based on the two-dimensional hexagon lattice.

  3. Two-dimensional hazard estimation for longevity analysis

    DEFF Research Database (Denmark)

    Fledelius, Peter; Guillen, M.; Nielsen, J.P.;

    2004-01-01

    for prediction purposes. However, we suggest that life insurance companies use the estimation technique and the cross-validation for bandwidth selection when analyzing their portfolio mortality. The non-parametric approach may give valuable information prior to developing more sophisticated prediction models......We investigate developments in Danish mortality based on data from 1974-1998 working in a two-dimensional model with chronological time and age as the two dimensions. The analyses are done with non-parametric kernel hazard estimation techniques. The only assumption is that the mortality surface...... the two-dimensional mortality surface. Furthermore we look at aggregated synthetic population metrics as 'population life expectancy' and 'population survival probability'. For Danish women these metrics indicate decreasing mortality with respect to chronological time. The metrics can not directly be used...

  4. CORPORATE VALUATION USING TWO-DIMENSIONAL MONTE CARLO SIMULATION

    Directory of Open Access Journals (Sweden)

    Toth Reka

    2010-12-01

    Full Text Available In this paper, we have presented a corporate valuation model. The model combine several valuation methods in order to get more accurate results. To determine the corporate asset value we have used the Gordon-like two-stage asset valuation model based on the calculation of the free cash flow to the firm. We have used the free cash flow to the firm to determine the corporate market value, which was calculated with use of the Black-Scholes option pricing model in frame of the two-dimensional Monte Carlo simulation method. The combined model and the use of the two-dimensional simulation model provides a better opportunity for the corporate value estimation.

  5. The interaction of nonlinear waves in two-dimensional lattice

    Institute of Scientific and Technical Information of China (English)

    Yang Xiao-Xia; Duan Wen-Shan; Li Sheng-Chang; Han Jiu-Ning

    2008-01-01

    This paper investigates the collision between two nonlinear waves with arbitrary angle in two-dimensional nonlinear lattice. By using the extended Poincaré-Lighthill-Kuo perturbation method, it obtains two Korteweg-de Vries equations for nonlinear waves in both the ε and η directions,respectively, and derives the analytical phase shifts after the collision of two nonlinear waves. Finally, the solution of u(v) up to O(ε3) order is given.

  6. Ultrafast Charge Transfer Visualized by Two-Dimensional Electronic Spectroscopy

    OpenAIRE

    Mančal T.; Milota F.; Hauer J; Christensson N.; Bixner O.; Lukeš V.; Kauffmann H. F.

    2013-01-01

    Two-dimensional electronic spectroscopy (2D-ES) is used to investigate ultrafast excited-state dynamics in a lutetium bisphthalocyanine dimer. Following optical excitation, a chain of electron and hole transfer steps gives rise to characteristic cross-peak dynamics in the electronic 2D spectra. The combination of density matrix propagation and quantum chemical calculations results in a molecular view of the charge transfer dynamics and highlights the role of the counter-ion in providing an en...

  7. Condition of Prequantization to Two-Dimensional Manifolds with Boundary

    Institute of Scientific and Technical Information of China (English)

    SHAO Ming-Xue; ZHU Zhong-Yuan

    2001-01-01

    The Weil's integrality condition of prequantization is generalized to two-dimensional phase space with boundaries. It is shown that in the prequantization condition a term related to the symplectic potential on the boundary appears. The necessity of the generalized condition is proved by analyzing the isolated singularities of the Hermitian bundle while the sufficiency of the condition is proved via geometric construction on the space of equivalence class.

  8. Stochastic and collisional diffusion in two-dimensional periodic flows

    International Nuclear Information System (INIS)

    The global effective diffusion coefficient D* for a two-dimensional system of convective rolls with a time dependent perturbation added, is calculated. The perturbation produces a background diffusion coefficient D, which is calculated analytically using the Menlikov-Arnold integral. This intrinsic diffusion coefficient is then enhanced by the unperturbed flow, to produce the global effective diffusion coefficient D*, which we can calculate theoretically for a certain range of parameters. The theoretical value agrees well with numerical simulations. 23 refs., 4 figs

  9. Ostwald ripening of faceted two-dimensional islands

    OpenAIRE

    Kaganer, V. M.; Braun, W; Sabelfeld, K. K.

    2007-01-01

    We study Ostwald ripening of two-dimensional adatom and advacancy islands on a crystal surface by means of kinetic Monte Carlo simulations. At large bond energies the islands are square-shaped, which qualitatively changes the coarsening kinetics. The Gibbs--Thomson chemical potential is violated: the coarsening proceeds through a sequence of `magic' sizes corresponding to square or rectangular islands. The coarsening becomes attachment-limited, but Wagner's asymptotic law is reached after a v...

  10. General Properties of Two-dimensional Conformal Transformation in Electrostatics

    OpenAIRE

    Zeng, Yong; Liu, Jinjie; Werner, Douglas H.

    2010-01-01

    Electrostatic properties of two-dimensional nanosystems can be described by their geometry resonances. In this paper we prove that these modes as well as the corresponding eigenvalues are invariant under any conformal transformation. This invariance further leads to a new way to studying the transformed structures. Namely, transforming a geometry is equivalent to modifying the strengths of these invariant eigenmodes excited by the external excitations.

  11. Level crossings in complex two-dimensional potentials

    Indian Academy of Sciences (India)

    Qing-Hai Wang

    2009-08-01

    Two-dimensional $\\mathcal{PT}$-symmetric quantum-mechanical systems with the complex cubic potential 12 = 2 + 2 + 2 and the complex Hénon–Heiles potential HH = 2 + 2 + (2 − 3/3) are investigated. Using numerical and perturbative methods, energy spectra are obtained to high levels. Although both potentials respect the $\\mathcal{PT}$ symmetry, the complex energy eigenvalues appear when level crossing happens between same parity eigenstates.

  12. Transformation Optics scheme for two-dimensional materials

    CERN Document Server

    Kumar, Anshuman; Reid, M T Homer; Fang, Nicholas

    2014-01-01

    Two dimensional optical materials, such as graphene can be characterized by a surface conductivity. So far, the transformation optics schemes have focused on three dimensional properties such as permittivity $\\epsilon$ and permeability $\\mu$. In this paper, we use a scheme for transforming surface currents to highlight that the surface conductivity transforms in a way different from $\\epsilon$ and $\\mu$. We use this surface conductivity transformation to demonstrate an example problem of reducing scattering of plasmon mode from sharp protrusions in graphene.

  13. Scaling Relations in Two-Dimensional Relativistic Hydrodynamic Turbulence

    CERN Document Server

    Westernacher-Schneider, John Ryan; Oz, Yaron

    2015-01-01

    We derive exact scaling relations for two-dimensional relativistic hydrodynamic turbulence in the inertial range of scales. We consider both the energy cascade towards large scales and the enstrophy cascade towards small scales. We illustrate these relations by numerical simulations of turbulent weakly compressible flows. Intriguingly, the fluid-gravity correspondence implies that the gravitational field in spacetimes with anti-de Sitter asymptotics should exhibit similar scaling relations.

  14. Quantum Hamilton-Jacobi Approach to Two Dimensional Singular Oscillator

    Institute of Scientific and Technical Information of China (English)

    (O)zlem Yesiltas; Bengü Demircio(g)lu

    2008-01-01

    We obtain the solutions of two-dimensional singular oscillator which is known as the quantum Calogero-Sutherland model both in cartesian and parabolic coordinates within the framework of quantum Hamilton Jacobi formalism. Solvability conditions and eigenfunctions are obtained by using the singularity structures of quantum momentum functions under some conditions. New potentials are generated by using the first two states of singular oscillator for parabolic coordinates.

  15. Harmonic generation in a two dimensional nonlinear quasicrystal

    OpenAIRE

    Broderick, Neil; Peacock, Anna; Gallo, Katia; Lewen, Ruth; Bratfalean, Radu

    2004-01-01

    Second harmonic generation in a two dimensional nonlinear quasi-crystal is demonstrated for the first time. Temperature and wavelength tuning of the crystal reveal the uniformity of the pattern while angle tuning reveals the dense nature of the crystal's Fourier spectrum. These results compare well with theoretical predictions showing the excellent uniformity of the crystal and suggest that more complicated ``nonlinear holograms'' should be possible.

  16. On Critical Point for Two Dimensional Holomorphics Systems

    CERN Document Server

    Valenzuela, Francisco

    2011-01-01

    Let $f:M\\rightarrow M$ be a biholomorphisms on two--dimensional a complex manifold, and let $X\\subseteq M$ be a compact $f$--invariant set such that $f|X$ is asymptotically dissipative and without sinks periodic points. We introduce a solely dynamical obstruction to dominated splitting, namely critical point. Critical point is a dynamical object and capture many of the dynamical properties of their one--dimensional counterpart.

  17. Complex dynamical invariants for two-dimensional complex potentials

    Indian Academy of Sciences (India)

    J S Virdi; F Chand; C N Kumar; S C Mishra

    2012-08-01

    Complex dynamical invariants are searched out for two-dimensional complex potentials using rationalization method within the framework of an extended complex phase space characterized by $x = x_{1} + ip_{3}. y = x_{2} + ip_{4}, p_{x} = p_{1} + ix_{3}, p_{y} = p_{2} + ix_{4}$. It is found that the cubic oscillator and shifted harmonic oscillator admit quadratic complex invariants. THe obtained invariants may be useful for studying non-Hermitian Hamiltonian systems.

  18. Two-dimensional hydrogen negative ion in a magnetic field

    Institute of Scientific and Technical Information of China (English)

    Xie Wen-Fang

    2004-01-01

    Making use of the adiabatic hyperspherical approach, we report a calculation for the energy spectrum of the ground and low-excited states of a two-dimensional hydrogen negative ion H- in a magnetic field. The results show that the ground and low-excited states of H- in low-dimensional space are more stable than those in three-dimensional space and there may exist more bound states.

  19. A UNIVERSAL VARIATIONAL FORMULATION FOR TWO DIMENSIONAL FLUID MECHANICS

    Institute of Scientific and Technical Information of China (English)

    何吉欢

    2001-01-01

    A universal variational formulation for two dimensional fluid mechanics is obtained, which is subject to the so-called parameter-constrained equations (the relationship between parameters in two governing equations). By eliminating the constraints, the generalized variational principle (GVPs) can be readily derived from the formulation. The formulation can be applied to any conditions in case the governing equations can be converted into conservative forms. Some illustrative examples are given to testify the effectiveness and simplicity of the method.

  20. Two-Dimensional Laser-Speckle Surface-Strain Gauge

    Science.gov (United States)

    Barranger, John P.; Lant, Christian

    1992-01-01

    Extension of Yamaguchi's laser-speckle surface-strain-gauge method yields data on two-dimensional surface strains in times as short as fractions of second. Laser beams probe rough spot on surface of specimen before and after processing. Changes in speckle pattern of laser light reflected from spot indicative of changes in surface strains during processing. Used to monitor strains and changes in strains induced by hot-forming and subsequent cooling of steel.

  1. Optical second harmonic generation probe of two-dimensional ferroelectricity

    CERN Document Server

    Aktsipetrov, O A; Murzina, T V; Blinov, L M; Fridkin, V M; Palto, S P

    1999-01-01

    Optical second harmonic generation (SHG) is used as a noninvasive probe of two-dimensional (2D) ferroelectricity in Langmuir-Blodgett (LB) films of copolymer vinylidene fluoride with trifluorethylene. The surface 2D ferroelectric-paraelectric phase transition in the topmost layer of LB films and a thickness independent (almost 2D) transition in the bulk of these films are observed in temperature studies of SHG.

  2. Two-dimensional Chiral Anomaly in Differential Regularization

    CERN Document Server

    Chen, W F

    1999-01-01

    The two-dimensional chiral anomaly is calculated using differential regularization. It is shown that the anomaly emerges naturally in the vector and axial Ward identities on the same footing as the four-dimensional case. The vector gauge symmetry can be achieved by an appropriate choice of the mass scales without introducing the seagull term. The necessity of a short-distance expansion in the Fourier transform into momentum space is emphasized.

  3. Two dimensional transition metal dichalcogenides grown by chemical vapor deposition

    OpenAIRE

    Tsang, Ka-yi; 曾家懿

    2014-01-01

    An atomically thin film of semiconducting transition metal dichalcogenides (TMDCs) is emerging as a class of key materials in chemistry and physics due to their remarkable chemical and electronic properties. The TMDCs are layered materials with weak out-of-plane van der Waals (vdW) interaction and strong in-plane covalent bonding enabling scalable exfoliation into two-dimensional (2D) layers of atomic thickness. The growth techniques to prepare these 2D TMDC materials in high yield and large ...

  4. Waiting Time Dynamics in Two-Dimensional Infrared Spectroscopy

    OpenAIRE

    Jansen, Thomas L. C.; Knoester, Jasper

    2009-01-01

    We review recent work on the waiting time dynamics of coherent two-dimensional infrared (2DIR) spectroscopy. This dynamics can reveal chemical and physical processes that take place on the femto- and picosecond time scale, which is faster than the time scale that may be probed by, for example, nuclear magnetic resonance spectroscopy. A large number of chemically relevant processes take place on this time scale. Such processes range from forming and breaking hydrogen bonds and proton transfer ...

  5. SU(1,2) invariance in two-dimensional oscillator

    CERN Document Server

    Krivonos, Sergey

    2016-01-01

    Performing the Hamiltonian analysis we explicitly established the canonical equivalence of the deformed oscillator, constructed in arXiv:1607.03756[hep-th], with the ordinary one. As an immediate consequence, we proved that the SU(1,2) symmetry is the dynamical symmetry of the ordinary two-dimensional oscillator. The characteristic feature of this SU(1,2) symmetry is a non-polynomial structure of its generators written it terms of the oscillator variables.

  6. USERS' TWO-DIMENSIONAL INTEREST AND ITS STORAGE METHOD

    Institute of Scientific and Technical Information of China (English)

    Xu Baowen; Zhang Weifeng

    2002-01-01

    The users' interest can be mined from the web cache and can be used widely. The interest can be specialized by the two-tuple (term, weight) in the simple interest model, in which the association relations are not mined, and then the interest cannot be associated in expressing the users' interest. Based on analyzing the WWW cache model, this letter brings forward a twodimensional interest model and gives the interrelated methods on how to store the two-dimensional interest model effectively.

  7. Smoothed universal correlations in the two-dimensional Anderson model

    OpenAIRE

    Uski, V.; Mehlig, B.; R.A. Romer; Schreiber, M.

    1998-01-01

    We report on calculations of smoothed spectral correlations in the two-dimensional Anderson model for weak disorder. As pointed out in (M. Wilkinson, J. Phys. A: Math. Gen. 21, 1173 (1988)), an analysis of the smoothing dependence of the correlation functions provides a sensitive means of establishing consistency with random matrix theory. We use a semiclassical approach to describe these fluctuations and offer a detailed comparison between numerical and analytical calculations for an exhaust...

  8. Nonlocal bottleneck effect in two-dimensional turbulence

    OpenAIRE

    Biskamp, D.; Celani, A; E. Schwarz

    1998-01-01

    The bottleneck pileup in the energy spectrum is investigated for several two-dimensional (2D) turbulence systems by numerical simulation using high-order diffusion terms to amplify the effect, which is weak for normal diffusion. For 2D magnetohydrodynamic (MHD) turbulence, 2D electron MHD (EMHD) turbulence and 2D thermal convection, which all exhibit direct energy cascades, a nonlocal behavior is found resulting in a logarithmic enhancement of the spectrum.

  9. Flows of granular material in two-dimensional channels

    OpenAIRE

    Bain, Oliver; Billingham, John; Houston, Paul; Lowndes, Ian

    2015-01-01

    Secondary cone-type crushing machines are an important part of the aggregate production process. These devices process roughly crushed material into aggregate of greater consistency and homogeneity. We apply a continuum model for granular materials (`A Constitutive Law For Dense Granular Flows', Nature 441, p727-730, 2006) to flows of granular material in representative two-dimensional channels, applying a cyclic applied crushing stress in lieu of a moving boundary. Using finite element metho...

  10. Heat diffusion in a two-dimensional thermal fuse model

    OpenAIRE

    Tørå, Glenn; Hansen, Alex

    2009-01-01

    We present numerical studies of electrical breakdown in disordered materials using a two-dimensional thermal fuse model with heat diffusion. A conducting fuse is heated locally by a Joule heating term. Heat diffuses to neighbouring fuses by a diffusion term. When the temperature reaches a given threshold, the fuse breaks and turns into an insulator. The time dynamics is governed by the time scales related to the two terms, in the presence of quenched disorder in the conductances of the fuses....

  11. Colloidal interactions in two-dimensional nematic emulsions

    Indian Academy of Sciences (India)

    N M Silvestre; P Patrício; M M Telo Da Gama

    2005-06-01

    We review theoretical and experimental work on colloidal interactions in two-dimensional (2D) nematic emulsions. We pay particular attention to the effects of (i) the nematic elastic constants, (ii) the size of the colloids, and (iii) the boundary conditions at the particles and the container. We consider the interactions between colloids and fluid (deformable) interfaces and the shape of fluid colloids in smectic-C films.

  12. Acoustic transparency in two-dimensional sonic crystals

    International Nuclear Information System (INIS)

    Acoustic transparency is studied in two-dimensional sonic crystals consisting of hexagonal distributions of cylinders with continuously varying properties. The transparency condition is achieved by selectively closing the acoustic bandgaps, which are governed by the structure factor of the cylindrical scatterers. It is shown here that cylindrical scatterers with the proposed continuously varying properties are physically realizable by using metafluids based on sonic crystals. The feasibility of this proposal is analyzed by a numerical experiment based on multiple scattering theory.

  13. Acoustic transparency in two-dimensional sonic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Sanchez-Dehesa, Jose; Torrent, Daniel [Wave Phenomena Group, Department of Electronic Engineering, Polytechnic University of Valencia, C/ Camino de Vera s/n, E-46022 Valencia (Spain); Cai Liangwu [Department of Mechanical and Nuclear Engineering, Kansas State University, Manhattan, KS 66506 (United States)], E-mail: jsdehesa@upvnet.upv.es

    2009-01-15

    Acoustic transparency is studied in two-dimensional sonic crystals consisting of hexagonal distributions of cylinders with continuously varying properties. The transparency condition is achieved by selectively closing the acoustic bandgaps, which are governed by the structure factor of the cylindrical scatterers. It is shown here that cylindrical scatterers with the proposed continuously varying properties are physically realizable by using metafluids based on sonic crystals. The feasibility of this proposal is analyzed by a numerical experiment based on multiple scattering theory.

  14. Quantum entanglement in a two-dimensional ion trap

    Institute of Scientific and Technical Information of China (English)

    王成志; 方卯发

    2003-01-01

    In this paper, we investigate the quantum entanglement in a two-dimensional ion trap system. We discuss the quantum entanglement between the ion and phonons by using reduced entropy, and that between two degrees of freedom of the vibrational motion along x and y directions by using quantum relative entropy. We discuss also the influence of initial state of the system on the quantum entanglement and the relation between two entanglements in the trapped ion system.

  15. Acoustic Bloch oscillations in a two-dimensional phononic crystal.

    Science.gov (United States)

    He, Zhaojian; Peng, Shasha; Cai, Feiyan; Ke, Manzhu; Liu, Zhengyou

    2007-11-01

    We report the observation of acoustic Bloch oscillations at megahertz frequency in a two-dimensional phononic crystal. By creating periodically arrayed cavities with a decreasing gradient in width along one direction in the phononic crystal, acoustic Wannier-Stark ladders are created in the frequency domain. The oscillatory motion of an incident Gaussian pulse inside the sample is demonstrated by both simulation and experiment.

  16. Graphene – A Two-Dimensional Dirac Material

    OpenAIRE

    Liu, Danny; Wicklund, Johan

    2014-01-01

    Graphene is a two-dimensional material, whose popularity has soared in both condensedmatter physics and material science the past decade. Due to its unique properties, graphene can be used in a vast array of new and interesting applications that could fundamentally change the material industry. This report reviews the current research and literature in order to trace the historical development of graphene. Then, in order to better understand the material, the unique properties of graphene are...

  17. Electric and magnetic fields from two-dimensional anisotropic bisyncytia.

    OpenAIRE

    Sepulveda, N G; Wikswo, J.P.

    1987-01-01

    Cardiac tissue can be considered macroscopically as a bidomain, anisotropic conductor in which simple depolarization wavefronts produce complex current distributions. Since such distributions may be difficult to measure using electrical techniques, we have developed a mathematical model to determine the feasibility of magnetic localization of these currents. By applying the finite element method to an idealized two-dimensional bisyncytium with anisotropic conductivities, we have calculated th...

  18. Virial theorem for Onsager vortices in two-dimensional hydrodynamics

    OpenAIRE

    Chavanis, Pierre-Henri

    2012-01-01

    We derive the virial theorem appropriate to two-dimensional point vortices at statistical equilibrium in the microcanonical and canonical ensembles. In an unbounded domain, it relates the angular velocity to the angular momentum and the temperature. Our expression is valid for an arbitrary number of point vortices of possibly different species. In the single-species case, and in the mean field approximation, it reduces to the relation empirically obtained by J.H. Williamson [J. Plasma Physics...

  19. Excitons and Two-dimensional Screening: Critical Screening Lengths

    OpenAIRE

    Tanguy, Christian

    2001-01-01

    A beautiful and intriguing relationship has recently been proposed to express the critical screening lengths associated with the apparition of new bound states for the two-dimensional statically screened Coulomb potential. Semiclassical quantum theory show that this relationship is unfortunately not strictly exact. These results are confirmed by a variational calculation, which provides upper bounds for the critical screening lengths in the case $l \\geq 1$.

  20. Perturbative treatment of nuclear rotations: Two-dimensional case

    International Nuclear Information System (INIS)

    A full quantum mechanical treatment is applied to a residual (symmetry restoring) hamiltonian in a deformed basis, in a simple case (two-dimensional rotor). Intrinsic excitation energies, moments of inertia and matrix elements between members of a rotational band are calculated. The results reproduce the exact values to the required order of an expansion in powers of Omega-1, where Omega is the degeneracy of the system. The lowest order is correctly given by the usual semiclassical approximations. (orig.)

  1. THE DEGENERACY PROBLEM OF TWO-DIMENSIONAL LINEAR RECURRING ARRAYS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The degeneracy degree and degeneracy position sets of a wo-dimensional linear recurrence relation set are characterized. The fact that a linear recurring array is essentially a doubly periodic array is shown. By using the Grbner base theory, a calculation formula for degeneracy degree is given and the existence of a special degeneracy position set is proved. In the present paper, the degeneracy problem of the two-dimensional linear recurring arrays is completely solved.

  2. On Two-Dimensional Quaternion Wigner-Ville Distribution

    Directory of Open Access Journals (Sweden)

    Mawardi Bahri

    2014-01-01

    Full Text Available We present the two-dimensional quaternion Wigner-Ville distribution (QWVD. The transform is constructed by substituting the Fourier transform kernel with the quaternion Fourier transform (QFT kernel in the classical Wigner-Ville distribution definition. Based on the properties of quaternions and the QFT kernel we obtain three types of the QWVD. We discuss some useful properties of various definitions for the QWVD, which are extensions of the classical Wigner-Ville distribution properties.

  3. Two-dimensional model of elastically coupled molecular motors

    Institute of Scientific and Technical Information of China (English)

    Zhang Hong-Wei; Wen Shu-Tang; Chen Gai-Rong; Li Yu-Xiao; Cao Zhong-Xing; Li Wei

    2012-01-01

    A flashing ratchet model of a two-headed molecular motor in a two-dimensional potential is proposed to simulate the hand-over-hand motion of kinesins.Extensive Langevin simulations of the model are performed.We discuss the dependences of motion and efficiency on the model parameters,including the external force and the temperature.A good qualitative agreement with the expected behavior is observed.

  4. Fabrication of Two-Dimensional Organic Photonic Crystal Microcavity

    Institute of Scientific and Technical Information of China (English)

    JIANG Ping; HU Xiao-Yong; YANG Hong; GONG Qi-Huang

    2006-01-01

    @@ A two-dimensional polystyrene photonic crystal microcavity is fabricated by the method of focused ion beam etching. The scanning electron microscopy and the transmittance spectrum are used to characterize the properties of the photonic crystal microcavity. The quality factor and the transmittance of the photonic crystal microcavity is more than 530 and 90%, respectively. The measured results are in agreement with the theoretical predictions.

  5. Vortex dynamics for two-dimensional XY models

    OpenAIRE

    Kim, Beom Jun; Minnhagen, Petter; Olsson, Peter

    1998-01-01

    Two-dimensional XY models with resistively shunted junction (RSJ) dynamics and time dependent Ginzburg-Landau (TDGL) dynamics are simulated and it is verified that the vortex response is well described by the Minnhagen phenomenology for both types of dynamics. Evidence is presented supporting that the dynamical critical exponent $z$ in the low-temperature phase is given by the scaling prediction (expressed in terms of the Coulomb gas temperature $T^{CG}$ and the vortex renormalization given b...

  6. Interior design of a two-dimensional semiclassic black hole

    CERN Document Server

    Levanony, Dana; 10.1103/PhysRevD.80.084008

    2009-01-01

    We look into the inner structure of a two-dimensional dilatonic evaporating black hole. We establish and employ the homogenous approximation for the black-hole interior. The field equations admit two types of singularities, and their local asymptotic structure is investigated. One of these singularities is found to develop, as a spacelike singularity, inside the black hole. We then study the internal structure of the evaporating black hole from the horizon to the singularity.

  7. Two-Dimensional Software Defect Models with Test Execution History

    OpenAIRE

    Tomotaka Ishii; Tadashi Dohi

    2012-01-01

    In general, the software-testing time may be measured by two kinds of time scales: calendar time and test execution time. In this paper, we develop two-dimensional software reliability models with two-time measures and incorporate both of them to assess the software reliability with higher accuracy. Since the resulting software defect models are based on the familiar nonhomogeneous Poisson processes with two time scales, which are the natural extensions of one-dimensional software defect mode...

  8. Comparison of automated method and improved AOAC Kjeldahl method for determination of protein in meat and meat products.

    Science.gov (United States)

    McGill, D L

    1981-01-01

    The Kjel-Foss automated method for protein determination meat and meat products was compared with the improved AOAC Kjeldahl method. Meat samples were separated into 3 categories based on fat content and analyzed in duplicate by both methods. No significant difference was found in a paired comparison of the 2 methods in each of the 3 meat categories, using Student's t-test at the 99% confidence level. A number of additional meat samples analyzed 6-9 times by the automated method showed an overall average range of 0.55% protein and average standard deviation of 0.20. The Kjel-Foss automated method was applicable for total protein determination in a wide variety of meat and meat products.

  9. Experimental realization of two-dimensional boron sheets

    Science.gov (United States)

    Feng, Baojie; Zhang, Jin; Zhong, Qing; Li, Wenbin; Li, Shuai; Li, Hui; Cheng, Peng; Meng, Sheng; Chen, Lan; Wu, Kehui

    2016-06-01

    A variety of two-dimensional materials have been reported in recent years, yet single-element systems such as graphene and black phosphorus have remained rare. Boron analogues have been predicted, as boron atoms possess a short covalent radius and the flexibility to adopt sp2 hybridization, features that favour the formation of two-dimensional allotropes, and one example of such a borophene material has been reported recently. Here, we present a parallel experimental work showing that two-dimensional boron sheets can be grown epitaxially on a Ag(111) substrate. Two types of boron sheet, a β12 sheet and a χ3 sheet, both exhibiting a triangular lattice but with different arrangements of periodic holes, are observed by scanning tunnelling microscopy. Density functional theory simulations agree well with experiments, and indicate that both sheets are planar without obvious vertical undulations. The boron sheets are quite inert to oxidization and interact only weakly with their substrate. We envisage that such boron sheets may find applications in electronic devices in the future.

  10. Experimental realization of two-dimensional boron sheets.

    Science.gov (United States)

    Feng, Baojie; Zhang, Jin; Zhong, Qing; Li, Wenbin; Li, Shuai; Li, Hui; Cheng, Peng; Meng, Sheng; Chen, Lan; Wu, Kehui

    2016-06-01

    A variety of two-dimensional materials have been reported in recent years, yet single-element systems such as graphene and black phosphorus have remained rare. Boron analogues have been predicted, as boron atoms possess a short covalent radius and the flexibility to adopt sp(2) hybridization, features that favour the formation of two-dimensional allotropes, and one example of such a borophene material has been reported recently. Here, we present a parallel experimental work showing that two-dimensional boron sheets can be grown epitaxially on a Ag(111) substrate. Two types of boron sheet, a β12 sheet and a χ3 sheet, both exhibiting a triangular lattice but with different arrangements of periodic holes, are observed by scanning tunnelling microscopy. Density functional theory simulations agree well with experiments, and indicate that both sheets are planar without obvious vertical undulations. The boron sheets are quite inert to oxidization and interact only weakly with their substrate. We envisage that such boron sheets may find applications in electronic devices in the future. PMID:27219700

  11. Two-dimensional entropy model for video shot partitioning

    Institute of Scientific and Technical Information of China (English)

    ZHU SongHao; LIU YunCai

    2009-01-01

    A shot presents a contiguous action recorded by an uninterrupted camera operation and frames within a shot keep spatio-temporal coherence. Segmenting a serial video stream file into meaningful shots is the first pass for the task of video analysis, content-based video understanding. In this paper, a novel scheme based on improved two-dimensional entropy is proposed to complete the partition of video shots. Firstly, shot transition candidates are detected using a two-pass algorithm: a coarse searching pass and a fine searching pass. Secondly, with the character of two-dimensional entropy of the image, correctly detected transition candidates are further classified into different transition types whereas those falsely detected shot breaks are distinguished and removed. Finally, the boundary of gradual transition can be precisely located by merging the characters of two-dimensional entropy of the image into the gradual transition. A large number of video sequences are used to test our system performance and promising results are obtained.

  12. Two-dimensional map for impact oscillator with drift

    Science.gov (United States)

    Pavlovskaia, Ekaterina; Wiercigroch, Marian; Grebogi, Celso

    2004-09-01

    An impact oscillator with drift is considered. The model accounts for viscoelastic impacts and is capable of mimicking the dynamics of progressive motion, which is important in many applications. To simplify the analysis of this system, a transformation decoupling the original coordinates is introduced. As a result, the bounded oscillations are separated from the drift motion. To study the bounded dynamics, a two-dimensional analytical map is developed and analyzed. In general, the dynamic state of the system is fully described by four variables: time τ , relative displacement p and velocity y of the mass, and relative displacement q of the slider top. However, this number can be reduced to two if the beginning of the progression phase is being monitored. The lower and upper bounds of the map domain are approximated. A graphical method of iteration of the two-dimensional map, similar to the cobweb method used in the one-dimensional case, is proposed. The results of numerical iterations of this two-dimensional map are presented, and a comparison is given between bifurcation diagrams calculated for this map and for the original system of differential equations.

  13. Two-dimensional electrophoresis analysis of proteomics based on image feature and mathematical morphology

    Institute of Scientific and Technical Information of China (English)

    SHEN; Peng; FAN; Xiaohui; ZENG; Zhen

    2005-01-01

    In this paper, a novel method to automatically detect protein spots on a two-dimensional (2-D) electrophoresis gel image is proposed to implement proteomics analysis of complex analyte.On the basis of the identifying spots results based on color variation and spot size features, morphological feature is introduced as a new criterion to distinguish protein spots from non-protein spots.Image-sharpening, edge-detecting and morphological feature extraction methods were consequently combined to detect protein spots on a 2-D electrophoresis gel image subject to strong disturbance.The proposed method was applied to detect the protein spots of proteomic gel images from E.coli cell, human kidney tissue and human serum.The results demonstrated that this method is more accurate and reliable than previous methods such as PDQuest 7.2 and ImageMaster 5.0 software for detecting protein spots on gel images with strong interferences.

  14. Primary establishment of human uterine muscle proteomic profiling by two-dimensional electrophoresis and mass spectrometry

    Institute of Scientific and Technical Information of China (English)

    Lin Hai-yuan; Lang Jing-he; Liu Zhu-feng; Zhu Lan; Leng Jin-hua; Sun Da-wei; Wang Xiao-rong

    2008-01-01

    Objective:To establish the protein profiling of human uterine muscle by two-dimensional electrophoresis.Methods:Five patients who underwent trans-abdominal hysterectomy due to cervical carcinoma in situ were in-cluded in this study.Postoperative uterine muscles were normal histologically.The total protein extracts from uter-ine muscle were separated using two-dimensional electrophoresis(2DE).Protein spots were stained by silver and de-tected by image analysis software.Matrix-assisted laser desorption/ionization time of flight mass spectrometry(MALDI-TOF-MS)and peptide mass fingerprint(PMF)were used to identify the selected protein spots.Results:Well-resolved,reproducible 2DE maps of human uterine muscle were obtained.Average protein spots were 468±52 and matching rate was 82.76%.Five protein spots were successfully identified by mass spectrome-try.Conclusions:2DE coupled with MALDI-TOF-MS and PMF is a useful approach for establishing human uterine muscle proteomic profiling.This data will be useful for establishing human uterine muscle proteome database.

  15. Quantification of proteome changes in bovine muscle from two-dimensional electrophoresis data

    Directory of Open Access Journals (Sweden)

    Daniel Franco

    2015-09-01

    Full Text Available Proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress were assessed on the basis of two-dimensional electrophoresis (2-DE data. In this study, the bootstrap resampling statistical technique and a new measure of relative change of the volume of 2-DE protein spots are shown to be more efficient than commonly used statistics to reliably quantify changes in protein abundance in stress response. The data are supplied in this article and are related to “Tackling proteome changes in the longissimus thoracis bovine muscle in response to pre-slaughter stress” by Franco et al. [1].

  16. An Investigation of Two-Dimensional CAD Generated Models with Body Decoupled Cartesian Grids for DSMC

    Energy Technology Data Exchange (ETDEWEB)

    OTAHAL,THOMAS J.; GALLIS,MICHAIL A.; BARTEL,TIMOTHY J.

    2000-06-27

    This paper presents an investigation of a technique for using two-dimensional bodies composed of simple polygons with a body decoupled uniform Cmtesian grid in the Direct Simulation Monte Carlo method (DSMC). The method employs an automated grid pre-processing scheme beginning form a CAD geometry definition file, and is based on polygon triangulation using a trapezoid algorithm. A particle-body intersection time comparison is presented between the Icarus DSMC code using a body-fitted structured grid and using a structured body-decoupled Cartesian grid with both linear and logarithmic search techniques. A comparison of neutral flow over a cylinder is presented using the structured body fitted grid and the Cartesian body de-coupled grid.

  17. The analysis of carbohydrates in milk powder by a new "heart-cutting" two-dimensional liquid chromatography method.

    Science.gov (United States)

    Ma, Jing; Hou, Xiaofang; Zhang, Bing; Wang, Yunan; He, Langchong

    2014-03-01

    In this study, a new"heart-cutting" two-dimensional liquid chromatography method for the simultaneous determination of carbohydrate contents in milk powder was presented. In this two dimensional liquid chromatography system, a Venusil XBP-C4 analysis column was used in the first dimension ((1)D) as a pre-separation column, a ZORBAX carbohydrates analysis column was used in the second dimension ((2)D) as a final-analysis column. The whole process was completed in less than 35min without a particular sample preparation procedure. The capability of the new two dimensional HPLC method was demonstrated in the determination of carbohydrates in various brands of milk powder samples. A conventional one dimensional chromatography method was also proposed. The two proposed methods were both validated in terms of linearity, limits of detection, accuracy and precision. The comparison between the results obtained with the two methods showed that the new and completely automated two dimensional liquid chromatography method is more suitable for milk powder sample because of its online cleanup effect involved.

  18. The characters of nonlinear vibration in the two-dimensional discrete monoatomic lattice

    Institute of Scientific and Technical Information of China (English)

    XU Quan; TIAN Qiang

    2005-01-01

    The two-dimensional discrete monoatomic lattice is analyzed. Taking nearest-neighbor interaction into account, the characters of the nonlinear vibration in two-dimensional discrete monoatomic lattice are described by the two-dimensional cubic nonlinear Schrodinger equation. Considering the quartic nonlinear potential, the two-dimensional discrete-soliton trains and the solutions perturbed by the neck mode are presented.

  19. Fast automated protein NMR data collection and assignment by ADAPT-NMR on Bruker spectrometers

    Science.gov (United States)

    Lee, Woonghee; Hu, Kaifeng; Tonelli, Marco; Bahrami, Arash; Neuhardt, Elizabeth; Glass, Karen C.; Markley, John L.

    2013-11-01

    ADAPT-NMR (Assignment-directed Data collection Algorithm utilizing a Probabilistic Toolkit in NMR) supports automated NMR data collection and backbone and side chain assignment for [U-13C, U-15N]-labeled proteins. Given the sequence of the protein and data for the orthogonal 2D 1H-15N and 1H-13C planes, the algorithm automatically directs the collection of tilted plane data from a variety of triple-resonance experiments so as to follow an efficient pathway toward the probabilistic assignment of 1H, 13C, and 15N signals to specific atoms in the covalent structure of the protein. Data collection and assignment calculations continue until the addition of new data no longer improves the assignment score. ADAPT-NMR was first implemented on Varian (Agilent) spectrometers [A. Bahrami, M. Tonelli, S.C. Sahu, K.K. Singarapu, H.R. Eghbalnia, J.L. Markley, PLoS One 7 (2012) e33173]. Because of broader interest in the approach, we present here a version of ADAPT-NMR for Bruker spectrometers. We have developed two AU console programs (ADAPT_ORTHO_run and ADAPT_NMR_run) that run under TOPSPIN Versions 3.0 and higher. To illustrate the performance of the algorithm on a Bruker spectrometer, we tested one protein, chlorella ubiquitin (76 amino acid residues), that had been used with the Varian version: the Bruker and Varian versions achieved the same level of assignment completeness (98% in 20 h). As a more rigorous evaluation of the Bruker version, we tested a larger protein, BRPF1 bromodomain (114 amino acid residues), which yielded an automated assignment completeness of 86% in 55 h. Both experiments were carried out on a 500 MHz Bruker AVANCE III spectrometer equipped with a z-gradient 5 mm TCI probe. ADAPT-NMR is available at http://pine.nmrfam.wisc.edu/ADAPT-NMR in the form of pulse programs, the two AU programs, and instructions for installation and use.

  20. PASS2: an automated database of protein alignments organised as structural superfamilies

    Directory of Open Access Journals (Sweden)

    Sowdhamini Ramanathan

    2004-04-01

    Full Text Available Abstract Background The functional selection and three-dimensional structural constraints of proteins in nature often relates to the retention of significant sequence similarity between proteins of similar fold and function despite poor sequence identity. Organization of structure-based sequence alignments for distantly related proteins, provides a map of the conserved and critical regions of the protein universe that is useful for the analysis of folding principles, for the evolutionary unification of protein families and for maximizing the information return from experimental structure determination. The Protein Alignment organised as Structural Superfamily (PASS2 database represents continuously updated, structural alignments for evolutionary related, sequentially distant proteins. Description An automated and updated version of PASS2 is, in direct correspondence with SCOP 1.63, consisting of sequences having identity below 40% among themselves. Protein domains have been grouped into 628 multi-member superfamilies and 566 single member superfamilies. Structure-based sequence alignments for the superfamilies have been obtained using COMPARER, while initial equivalencies have been derived from a preliminary superposition using LSQMAN or STAMP 4.0. The final sequence alignments have been annotated for structural features using JOY4.0. The database is supplemented with sequence relatives belonging to different genomes, conserved spatially interacting and structural motifs, probabilistic hidden markov models of superfamilies based on the alignments and useful links to other databases. Probabilistic models and sensitive position specific profiles obtained from reliable superfamily alignments aid annotation of remote homologues and are useful tools in structural and functional genomics. PASS2 presents the phylogeny of its members both based on sequence and structural dissimilarities. Clustering of members allows us to understand diversification of

  1. Ultrafast Charge Transfer Visualized by Two-Dimensional Electronic Spectroscopy

    Directory of Open Access Journals (Sweden)

    Mančal T.

    2013-03-01

    Full Text Available Two-dimensional electronic spectroscopy (2D-ES is used to investigate ultrafast excited-state dynamics in a lutetium bisphthalocyanine dimer. Following optical excitation, a chain of electron and hole transfer steps gives rise to characteristic cross-peak dynamics in the electronic 2D spectra. The combination of density matrix propagation and quantum chemical calculations results in a molecular view of the charge transfer dynamics and highlights the role of the counter-ion in providing an energetic perturbation which promotes charge transfer across the complex.

  2. Holes in a two-dimensional quantum antiferromagnet

    International Nuclear Information System (INIS)

    A brief review is presented on the studies of the hole motion in a two-dimensional quantum antiferromagnetic. An extended introduction is given to cover the background of the problem. The quantum Bogoliubov-de Gennes formalism which treats the local distortion of the spin configuration and the quantum renormalization process on an equal footing, is outlined. The latest development on the central issue, whether a hole can freely propagate on an antiferromagnetic background, is overviewed. (author). 108 refs, 11 figs, 1 tab

  3. Quasi-two-dimensional Turing patterns in an imposed gradient

    Science.gov (United States)

    Lengyel, István; Kádár, Sándor; Epstein, Irving R.

    1992-11-01

    In experiments on quasi-two-dimensional Turing structures, patterns form perpendicular to a concentration gradient imposed by the boundary conditions. Using linear stability analysis, with the ClO2-I2-MA (malonic acid) reaction as an example, we obtain conditions on the position along the gradient direction and possible three dimensionality of the structures. Experiments on the effects of MA and starch concentrations on the position of the structures support the theory. Simulations taking into account the starch indicator yield Turing patterns even with equal diffusion coefficients for the activator and inhibitor species.

  4. Bubble breakup in two-dimensional Stokes flow

    International Nuclear Information System (INIS)

    A new class of exact solutions is reported for an evolving bubble in a two-dimensional slow viscous flow. It is observed that for an expanding bubble the interface grows smoother with time, whereas the contracting-bubble solutions display a tendency to form sharp corners (''near cusps'') for small values of surface tension. In the latter case, we also obtain analytic solutions that describe bubble breakup: For a large class of initial shapes, the interface will eventually develop a thin ''neck'' whose width goes to zero before the bubble is completely removed from the liquid

  5. Inverse radiative transfer problems in two-dimensional heterogeneous media

    International Nuclear Information System (INIS)

    The analysis of inverse problems in participating media where emission, absorption and scattering take place has several relevant applications in engineering and medicine. Some of the techniques developed for the solution of inverse problems have as a first step the solution of the direct problem. In this work the discrete ordinates method has been used for the solution of the linearized Boltzmann equation in two dimensional cartesian geometry. The Levenberg - Marquardt method has been used for the solution of the inverse problem of internal source and absorption and scattering coefficient estimation. (author)

  6. Symmetry and topology of two-dimensional noncentrosymmetric superconductors

    Science.gov (United States)

    Samokhin, K. V.

    2015-11-01

    We present a detailed study of the gap symmetry and the quasiparticle wave function topology in two-dimensional superconductors without inversion center. The strong spin-orbit coupling of electrons with the crystal lattice makes it necessary to describe superconductivity in terms of one or more nondegenerate bands characterized by helicity. We develop a topological classification of the superconducting states using the integer-valued Maurer-Cartan invariants and the Bogoliubov Wilson loops, and also calculate the spectrum of fermionic boundary modes.

  7. Smoothed Particle Hydrodynamics Method for Two-dimensional Stefan Problem

    CERN Document Server

    Tarwidi, Dede

    2016-01-01

    Smoothed particle hydrodynamics (SPH) is developed for modelling of melting and solidification. Enthalpy method is used to solve heat conduction equations which involved moving interface between phases. At first, we study the melting of floating ice in the water for two-dimensional system. The ice objects are assumed as solid particles floating in fluid particles. The fluid and solid motion are governed by Navier-Stokes equation and basic rigid dynamics equation, respectively. We also propose a strategy to separate solid particles due to melting and solidification. Numerical results are obtained and plotted for several initial conditions.

  8. Optofluidic two-dimensional grating volume refractive index sensor.

    Science.gov (United States)

    Sarkar, Anirban; Shivakiran Bhaktha, B N; Khastgir, Sugata Pratik

    2016-09-10

    We present an optofluidic reservoir with a two-dimensional grating for a lab-on-a-chip volume refractive index sensor. The observed diffraction pattern from the device resembles the analytically obtained fringe pattern. The change in the diffraction pattern has been monitored in the far-field for fluids with different refractive indices. Reliable measurements of refractive index variations, with an accuracy of 6×10-3 refractive index units, for different fluids establishes the optofluidic device as a potential on-chip tool for monitoring dynamic refractive index changes. PMID:27661360

  9. Two-Dimensional Change Detection Methods Remote Sensing Applications

    CERN Document Server

    Ilsever, Murat

    2012-01-01

    Change detection using remotely sensed images has many applications, such as urban monitoring, land-cover change analysis, and disaster management. This work investigates two-dimensional change detection methods. The existing methods in the literature are grouped into four categories: pixel-based, transformation-based, texture analysis-based, and structure-based. In addition to testing existing methods, four new change detection methods are introduced: fuzzy logic-based, shadow detection-based, local feature-based, and bipartite graph matching-based. The latter two methods form the basis for a

  10. Numerical model for two-dimensional hydrodynamics and energy transport

    International Nuclear Information System (INIS)

    The theoretical basis and computational procedure of the VECTRA computer program are presented. VECTRA (Vorticity-Energy Code for TRansport Analysis) is designed for applying numerical simulation to a broad range of intake/discharge flows in conjunction with power plant hydrological evaluation. The code computational procedure is based on finite-difference approximation of the vorticity-stream function partial differential equations which govern steady flow momentum transport of two-dimensional, incompressible, viscous fluids in conjunction with the transport of heat and other constituents

  11. Quasi-integrability and two-dimensional QCD

    International Nuclear Information System (INIS)

    The notion of integrability in two-dimensional QCD is discussed. We show that in spite of an infinite number of conserved charges, particle production is not entirely suppressed. This phenomenon, which we call quasi-integrability, is explained in terms of quantum corrections to the combined algebra of higher-conserved and spectrum-generating currents. We predict the qualitative form of particle production probabilities and verify that they are in agreement with numerical data. We also discuss four-dimensional self-dual Yang-Mills theory in the light of our results. (author). 25 refs, 4 figs, 1 tab

  12. Two-dimensional carbon fundamental properties, synthesis, characterization, and applications

    CERN Document Server

    Yihong, Wu; Ting, Yu

    2013-01-01

    After a brief introduction to the fundamental properties of graphene, this book focuses on synthesis, characterization and application of various types of two-dimensional (2D) nanocarbons ranging from single/few layer graphene to carbon nanowalls and graphene oxides. Three major synthesis techniques are covered: epitaxial growth of graphene on SiC, chemical synthesis of graphene on metal, and chemical vapor deposition of vertically aligned carbon nanosheets or nanowalls. One chapter is dedicated to characterization of 2D nanocarbon using Raman spectroscopy. It provides extensive coverage for a

  13. Mean flow generation in rotating anelastic two-dimensional convection

    CERN Document Server

    Currie, Laura K

    2016-01-01

    We investigate the processes that lead to the generation of mean flows in two-dimensional anelastic convection. The simple model consists of a plane layer that is rotating about an axis inclined to gravity. The results are two-fold: firstly we numerically investigate the onset of convection in three-dimensions, paying particular attention to the role of stratification and highlight a curious symmetry. Secondly, we investigate the mechanisms that drive both zonal and meridional flows in two dimensions. We find that, in general, non-trivial Reynolds stresses can lead to systematic flows and, using statistical measures, we quantify the role of stratification in modifying the coherence of these flows.

  14. Graphene and Two-Dimensional Materials for Optoelectronic Applications

    Directory of Open Access Journals (Sweden)

    Andreas Bablich

    2016-03-01

    Full Text Available This article reviews optoelectronic devices based on graphene and related two-dimensional (2D materials. The review includes basic considerations of process technology, including demonstrations of 2D heterostructure growth, and comments on the scalability and manufacturability of the growth methods. We then assess the potential of graphene-based transparent conducting electrodes. A major part of the review describes photodetectors based on lateral graphene p-n junctions and Schottky diodes. Finally, the progress in vertical devices made from 2D/3D heterojunctions, as well as all-2D heterostructures is discussed.

  15. Band alignment of two-dimensional lateral heterostructures

    CERN Document Server

    Zhang, Junfeng; Xie, Weiyu; Zhang, S B

    2016-01-01

    Band alignment in two-dimensional (2D) lateral heterostructures is fundamentally different from three-dimensional (3D), as Schottky barrier height is at the Schottky-Mott limit and band offset is at the Anderson limit, regardless interfacial conditions. This robustness arises because, in the asymptotic limit, effect of interfacial dipole vanishes. First-principles calculations of graphene/h-BN and MoS2/WS2 show that 2D junction width W is typically an order of magnitude longer than 3D. Therefore, heterostructures with dimension less than W can also be made, leading to tunable band alignment.

  16. Topological phases in two-dimensional materials: a review

    Science.gov (United States)

    Ren, Yafei; Qiao, Zhenhua; Niu, Qian

    2016-06-01

    Topological phases with insulating bulk and gapless surface or edge modes have attracted intensive attention because of their fundamental physics implications and potential applications in dissipationless electronics and spintronics. In this review, we mainly focus on recent progress in the engineering of topologically nontrivial phases (such as {{{Z}}2} topological insulators, quantum anomalous Hall effects, quantum valley Hall effects etc) in two-dimensional systems, including quantum wells, atomic crystal layers of elements from group III to group VII, and the transition metal compounds.

  17. Particle Diffusion in a Quasi-Two-Dimensional Bacterial Bath

    Science.gov (United States)

    Wu, Xiao-Lun; Libchaber, Albert

    2000-03-01

    We study the effect of bacterial motion on micron-scale beads in a freely suspended soap film. Given the sizes of bacteria and beads, the geometry of the experiment is quasi-two-dimensional. Large positional fluctuations are observed for beads as large as 10 μm in diameter, and the measured mean-square displacements indicate superdiffusion in short times and normal diffusion in long times. Though the phenomenon is similar to Brownian motions of small particles, its physical origin is different and can be attributed to the collective dynamics of bacteria.

  18. Functionalization of Two-Dimensional Transition-Metal Dichalcogenides.

    Science.gov (United States)

    Chen, Xin; McDonald, Aidan R

    2016-07-01

    Two-dimensional (2D) layered transition-metal dichalcogenides (TMDs) are a fascinating class of nanomaterials that have the potential for application in catalysis, electronics, photonics, energy storage, and sensing. TMDs are rather inert, and thus pose problems for chemical derivatization. However, to further modify the properties of TMDs and fully harness their capabilities, routes towards their chemical functionalization must be identified. Herein, recent efforts toward the chemical (bond-forming) functionalization of 2D TMDs are critically reviewed. Recent successes are highlighted, along with areas where further detailed analyses and experimentation are required. This burgeoning field is very much in its infancy but has already provided several important breakthroughs. PMID:26848815

  19. Numerical Simulation of Two-dimensional Nonlinear Sloshing Problems

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Numerical simulation of a two-dimensional nonlinearsloshing problem is preceded by the finite element method. Two theories are used. One is fully nonlinear theory; the other is time domain second order theory. A liquid sloshing in a rectangular container subjected to a horizontal excitation is simulated using these two theories. Numerical results are obtained and comparisons are made. It is found that a good agreement is obtained for the case of small amplitude oscillation. For the situation of large amplitude excitation, although the differences between using the two theories are obvious the second order solution can still exhibit typical nonlinear features of nonlinear wave.

  20. Finite Element Analysis to Two-Dimensional Nonlinear Sloshing Problems

    Institute of Scientific and Technical Information of China (English)

    严承华; 王赤忠; 程尔升

    2001-01-01

    A two-dimensional nonlinear sloshing problem is analyzed by means of the fully nonlinear theory and time domainsecond order theory of water waves. Liquid sloshing in a rectangular container subjected to a horizontal excitation is sim-ulated by the finite element method. Comparisons between the two theories are made based on their numerical results. Itis found that good agreement is obtained for the case of small amplitude oscillation and obvious differences occur forlarge amplitude excitation. Even though, the second order solution can still exhibit typical nonlinear features ofnonlinear wave and can be used instead of the fully nonlinear theory.

  1. Analysis of Positioning Error for Two-Dimensional Location System

    Directory of Open Access Journals (Sweden)

    Yi Jiang

    2013-01-01

    Full Text Available This paper investigates the positioning error using different positioning techniques for two-dimensional location system. Based on the measurement models of TOA with/without the time synchronization and TDOA techniques, the performance comparison analysis between TOA with/without the time synchronization and TDOA is presented respectively. The performance of TOA with the time synchronization and TDOA is influenced by the specific distribution of the reference nodes. Hence, it is hard to determine which one is better. The performance of TDOA is always superior to TOA without the time synchronization using the same reference nodes. These conclusions are finally illustrated by the simulation results presented in two scenarios.

  2. Wake-induced bending of two-dimensional plasma crystals

    CERN Document Server

    Röcker, T B; Zhdanov, S K; Couëdel, L; Morfill, G E

    2014-01-01

    It is shown that the wake-mediated interactions between microparticles in a two-dimensional plasma crystal affect the shape of the monolayer, making it non-flat. The equilibrium shape is calculated for various distributions of the particle number density in the monolayer. For typical experimental conditions, the levitation height of particles in the center of the crystal can be noticeably smaller than at the periphery. It is suggested that the effect of wake-induced bending can be utilized in experiments, to deduce important characteristics of the interparticle interaction.

  3. Wake-induced bending of two-dimensional plasma crystals

    Energy Technology Data Exchange (ETDEWEB)

    Röcker, T. B., E-mail: tbr@mpe.mpg.de; Ivlev, A. V., E-mail: ivlev@mpe.mpg.de; Zhdanov, S. K.; Morfill, G. E. [Max Planck Institute for Extraterrestrial Physics, 85741 Garching (Germany); Couëdel, L. [CNRS, Aix-Marseille-Université, Laboratoire de Physique des Interactions Ioniques et Moléculaires, UMR 7345, 13397 Marseille Cedex 20 (France)

    2014-07-15

    It is shown that the wake-mediated interactions between microparticles in a two-dimensional plasma crystal affect the shape of the monolayer, making it non-flat. The equilibrium shape is calculated for various distributions of the particle number density in the monolayer. For typical experimental conditions, the levitation height of particles in the center of the crystal can be noticeably smaller than at the periphery. It is suggested that the effect of wake-induced bending can be utilized in experiments, to deduce important characteristics of the interparticle interaction.

  4. AN APPROACH IN MODELING TWO-DIMENSIONAL PARTIALLY CAVITATING FLOW

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    An approach of modeling viscosity, unsteady partially cavitating flows around lifting bodies is presented. By employing an one-fluid Navier-Stokers solver, the algorithm is proved to be able to handle two-dimensional laminar cavitating flows at moderate Reynolds number. Based on the state equation of water-vapor mixture, the constructive relations of densities and pressures are established. To numerically simulate the cavity wall, different pseudo transition of density models are presumed. The finite-volume method is adopted and the algorithm can be extended to three-dimensional cavitating flows.

  5. Numerical Study of Two-Dimensional Focusing Waves

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Two-dimensional focusing waves are generated and investigated by numerical method. The numerical model is developed by introducing the wave maker boundary on the high-order spectral (HOS) method proposed by Dommermuth and Yue in 1987 and verified by theoretical and experimental data. Some cases of focusing waves considering different parameters such as assumed focusing amplitudes, frequency bandwidth, central frequency and frequency spectrum are generated. Characteristics of the focusing wave including surface elevations, the maximum crest, shift of focusing points and frequency spectra are discussed. The results show that the focusing wave characteristics are strongly affected by focusing amplitudes, frequency bandwidth, central frequency and frequency spectrum.

  6. Two-dimensional, homogeneous, isotropic fluid turbulence with polymer additives

    CERN Document Server

    Gupta, Anupam; Pandit, Rahul

    2012-01-01

    We present the most extensive direct numerical simulations, attempted so far, of statistically steady, homogeneous, isotropic turbulence in two-dimensional fluid films with air-drag-induced friction and with polymer additives. Our study reveals that the polymers (a) reduce the total fluid energy, enstrophy, and palinstrophy, (b) modify the fluid energy spectrum both in inverse- and forward-cascade regimes, (c) reduce small-scale intermittency, (d) suppress regions of large vorticity and strain rate, and (e) stretch in strain-dominated regions. We compare our results with earlier experimental studies; and we propose new experiments.

  7. Anisotropic mass density by two-dimensional acoustic metamaterials

    International Nuclear Information System (INIS)

    We show that specially designed two-dimensional arrangements of full elastic cylinders embedded in a nonviscous fluid or gas define (in the homogenization limit) a new class of acoustic metamaterials characterized by a dynamical effective mass density that is anisotropic. Here, analytic expressions for the dynamical mass density and the effective sound velocity tensors are derived in the long wavelength limit. Both show an explicit dependence on the lattice filling fraction, the elastic properties of cylinders relative to the background, their positions in the unit cell, and their multiple scattering interactions. Several examples of these metamaterials are reported and discussed

  8. Drift modes of a quasi-two-dimensional current sheet

    Energy Technology Data Exchange (ETDEWEB)

    Artemyev, A. V.; Malova, Kh. V.; Popov, V. Yu.; Zelenyi, L. M. [Russian Academy of Sciences, Space Research Institute (Russian Federation)

    2012-03-15

    Stability of a plasma configuration consisting of a thin one-dimensional current sheet embedded into a two-dimensional background current sheet is studied. Drift modes developing in plasma as unstable waves along the current direction are considered. Dispersion relations for kink and sausage perturbation modes are obtained depending on the ratio of parameters of thin and background current sheets. It is shown that the existence of the background sheet results in a decrease in the instability growth rates and a significant increase in the perturbation wavelengths. The role of drift modes in the excitation of oscillations observed in the current sheet of the Earth's magnetotail is discussed.

  9. Superconductivity in the two-dimensional generalized Hubbard model

    Science.gov (United States)

    Lima, L. S.

    2016-08-01

    We have used the Green's functions method at finite temperature and the Kubo's formalism, to calculate the electron conductivity σ(ω) in the generalized two-dimensional Hubbard model. We have obtained a behavior superconductor for the system to T > T0. The AC conductivity falls to zero in ω =ω0 , where ω0 depends on Δ, which is the gap of the system. The behavior gotten is according of with the behavior of the superconductors of high Tc where there is a changes abruptly from a Mott's insulator state to superconductor.

  10. Creating arbitrary arrays of two-dimensional topological defects

    Science.gov (United States)

    Murray, Bryce S.; Pelcovits, Robert A.; Rosenblatt, Charles

    2014-11-01

    An atomic force microscope was used to scribe a polyimide-coated substrate with complex patterns that serve as an alignment template for a nematic liquid crystal. By employing a sufficiently large density of scribe lines, two-dimensional topological defect arrays of arbitrary defect strength were patterned on the substrate. When used as the master surface of a liquid crystal cell, in which the opposing slave surface is treated for planar degenerate alignment, the liquid crystal adopts the pattern's alignment with a disclination line emanating at the defect core on one surface and terminating at the other surface.

  11. Two-dimensional conformal field theory and the butterfly effect

    CERN Document Server

    Roberts, Daniel A

    2014-01-01

    We study chaotic dynamics in two-dimensional conformal field theory through out-of-time order thermal correlators of the form $\\langle W(t)VW(t)V\\rangle$. We reproduce bulk calculations similar to those of [1], by studying the large $c$ Virasoro identity block. The contribution of this block to the above correlation function begins to decrease exponentially after a delay of $\\sim t_* - \\frac{\\beta}{2\\pi}\\log \\beta^2E_w E_v$, where $t_*$ is the scrambling time $\\frac{\\beta}{2\\pi}\\log c$, and $E_w,E_v$ are the energy scales of the $W,V$ operators.

  12. Periodic trajectories for two-dimensional nonintegrable Hamiltonians

    International Nuclear Information System (INIS)

    I want to report on some calculations of classical periodic trajectories in a two-dimensional nonintegrable potential. After a brief introduction, I will present some details of the theory. The main part of this report will be devoted to showing pictures of the various families of trajectories and to discussing the topology (in E-τ space) and branching behavior of these families. Then I will demonstrate the connection between periodic trajectories and ''nearby'' nonperiodic trajectories, which nicely illustrates the relationship of this work to chaos. Finally, I will discuss very briefly how periodic trajectories can be used to calculate tori. 12 refs., 40 figs

  13. Fabrication of a Two-Dimensional Organic Photonic Crystal

    Institute of Scientific and Technical Information of China (English)

    HU Xiao-Yong; LI Yan; GONG Qi-Huang; CHENG Bing-Ying; ZHANG Dao-Zhong

    2005-01-01

    @@ A high-quality two-dimensional polystyrene photonic crystal is fabricated by the method of focused ion beam etching. The scanning electron microscopy (SEM) and the transmittance spectrum are used to characterize the properties of the photonic crystal. The measured transmittance spectrum is in agreement with the theoretical one. The influences of the disorders caused by the random perturbations in the diameter or the position of the air holes on the photonic band structure are analysed. It is found that the phtonic bandgap can tolerate less than 10% degree of disorder.

  14. Homogenization of Two-Dimensional Phononic Crystals at Low Frequencies

    Institute of Scientific and Technical Information of China (English)

    NI Qing; CHENG Jian-Chun

    2005-01-01

    @@ Effective velocities of elastic waves propagating in two-dimensional phononic crystal at low frequencies are analysed theoretically, and exact analytical formulas for effective velocities of elastic waves are derived according to the method presented by Krokhin et al. [Phys. Rev. Lett. 91 (2003) 264302]. Numerical calculations for phononic crystals consisted of array of Pb cylinders embedded in epoxy show that the composites have distinct anisotropy at low filling fraction. The anisotropy increases as the filling fraction increases, while as the filling fraction closes to the limitation, the anisotropy decreases.

  15. A Direct Two-Dimensional Pressure Formulation in Molecular Dynamics

    CERN Document Server

    YD, Sumith

    2016-01-01

    Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.

  16. Two-dimensional chiral topological superconductivity in Shiba lattices

    Science.gov (United States)

    Li, Jian; Neupert, Titus; Wang, Zhijun; MacDonald, A. H.; Yazdani, A.; Bernevig, B. Andrei

    2016-07-01

    The chiral p-wave superconductor is the archetypal example of a state of matter that supports non-Abelian anyons, a highly desired type of exotic quasiparticle. With this, it is foundational for the distant goal of building a topological quantum computer. While some candidate materials for bulk chiral superconductors exist, they are subject of an ongoing debate about their actual paring state. Here we propose an alternative route to chiral superconductivity, consisting of the surface of an ordinary superconductor decorated with a two-dimensional lattice of magnetic impurities. We furthermore identify a promising experimental platform to realize this proposal.

  17. Seabed disposal project two-dimensional axisymmetric penetrometer simulations

    International Nuclear Information System (INIS)

    Preliminary two-dimensional, one-constituent hole closure analyses of an experimental apparatus and the flow of in situ ocean sediments following a penetrometer explacement have been performed. Boundary conditions associated with the experimental apparatus were found to greatly affect cavity response. Difficulties were encountered in modelling penetrometer-sediment interfaces and in obtaining smooth stress histories. The use of a different computer code in later analyses led to more realistic penetrometer-sediment interface models and to improved success in obtaining stress histories. These results along with some recommendations for future work are presented

  18. Two-Dimensionally Confined Topological Edge States in Photonic Crystals

    CERN Document Server

    Barik, Sabyasachi; DeGottardi, Wade; Waks, Edo; Hafezi, Mohammad

    2016-01-01

    We present an all-dielectric photonic crystal structure that supports two-dimensionally confined helical topological edge states. The topological properties of the system are controlled by the crystal parameters. An interface between two regions of differing band topologies gives rise to topological edge states confined in a dielectric slab that propagate around sharp corners without backscattering. Three dimensional finite-difference time-domain calculations show these edges to be confined in the out-of-plane direction by total internal reflection. Such nanoscale photonic crystal architectures could enable strong interactions between photonic edge states and quantum emitters.

  19. Quantum computation with two-dimensional graphene quantum dots

    Institute of Scientific and Technical Information of China (English)

    Li Jie-Sen; Li Zhi-Bing; Yao Dao-Xin

    2012-01-01

    We study an array of graphene nano sheets that form a two-dimensional S =1/2 Kagome spin lattice used for quantum computation.The edge states of the graphene nano sheets axe used to form quantum dots to confine electrons and perform the computation.We propose two schemes of bang-bang control to combat decoherence and realize gate operations on this array of quantum dots.It is shown that both schemes contain a great amount of information for quantum computation.The corresponding gate operations are also proposed.

  20. A class of two dimensional models with extended structure solutions

    Energy Technology Data Exchange (ETDEWEB)

    Piette, B.; Zakrzewski, W.J. (Durham Univ. (United Kingdom). Dept. of Mathematical Sciences); Tchrakian, D.H. (Saint Patrick' s Coll., Maynooth (Ireland). Dept. of Mathematical Physics Dublin Inst. for Advanced Studies (Ireland). School of Theoretical Physics)

    1992-06-01

    We study some properties of a class of two-dimensional models which have infinite dimensional groups of symmetry which includes both the Euclidean and Minkowskian groups. We show that all solutions of these models are self-dual and correspond to mappings of the 2 dimensional plane into itself which locally preserve the area. When treated as candidates of soliton-like structures we see that the structures are localised. In most cases the energy density of these structures has a power-like tail; in some cases, e.g. the modified sine-Gordon model the localisation is exponential. (orig.).

  1. Automated classification of immunostaining patterns in breast tissue from the human protein Atlas

    Directory of Open Access Journals (Sweden)

    Issac Niwas Swamidoss

    2013-01-01

    Full Text Available Background: The Human Protein Atlas (HPA is an effort to map the location of all human proteins (http://www.proteinatlas.org/. It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. Materials and Methods: The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM features, complex wavelet co-occurrence matrix (CWCM features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM and linear discriminant analysis (LDA classifier. Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. Results: We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Conclusions: Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for

  2. Extracting information from two-dimensional electrophoresis gels by partial least squares regression

    DEFF Research Database (Denmark)

    Jessen, Flemming; Lametsch, R.; Bendixen, E.;

    2002-01-01

    Two-dimensional gel electrophoresis (2-DE) produces large amounts of data and extraction of relevant information from these data demands a cautious and time consuming process of spot pattern matching between gels. The classical approach of data analysis is to detect protein markers that appear...... or disappear depending on the experimental conditions. Such biomarkers are found by comparing the relative volumes of individual spots in the individual gels. Multivariate statistical analysis and modelling of 2-DE data for comparison and classification is an alternative approach utilising the combination...... of all proteins/spots in the gels. In the present study it is demonstrated how information can be extracted by multivariate data analysis. The strategy is based on partial least squares regression followed by variable selection to find proteins that individually or in combination with other proteins vary...

  3. Online comprehensive two-dimensional ion chromatography × capillary electrophoresis.

    Science.gov (United States)

    Ranjbar, Leila; Gaudry, Adam J; Breadmore, Michael C; Shellie, Robert A

    2015-09-01

    A comprehensively coupled online two-dimensional ion chromatography-capillary electrophoresis (IC × CE) system for quantitative analysis of inorganic anions and organic acids in water is introduced. The system employs an in-house built sequential injection-capillary electrophoresis instrument and a nonfocusing modulation interface comprising a tee-piece and a six-port two-position injection valve that allows comprehensive sampling of the IC effluent. High field strength (+2 kV/cm) enables rapid second-dimension separations in which each peak eluted from the first-dimension separation column is analyzed at least three times in the second dimension. The IC × CE approach has been successfully used to resolve a suite of haloacetic acids, dalapon, and common inorganic anions. Two-dimensional peak capacity for IC × CE was 498 with a peak production rate of 9 peaks/min. Linear calibration curves were obtained for all analytes from 5 to 225 ng/mL (except dibromoacetic acid (10-225 ng/mL) and tribromoacetic acid (25-225 ng/mL)). The developed approach was used to analyze a spiked tap water sample, with good measured recoveries (69-119%).

  4. Comprehensive two-dimensional liquid chromatographic analysis of poloxamers.

    Science.gov (United States)

    Malik, Muhammad Imran; Lee, Sanghoon; Chang, Taihyun

    2016-04-15

    Poloxamers are low molar mass triblock copolymers of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO), having number of applications as non-ionic surfactants. Comprehensive one and two-dimensional liquid chromatographic (LC) analysis of these materials is proposed in this study. The separation of oligomers of both types (PEO and PPO) is demonstrated for several commercial poloxamers. This is accomplished at the critical conditions for one of the block while interaction for the other block. Reversed phase LC at CAP of PEO allowed for oligomeric separation of triblock copolymers with regard to PPO block whereas normal phase LC at CAP of PPO renders oligomeric separation with respect to PEO block. The oligomeric separation with regard to PEO and PPO are coupled online (comprehensive 2D-LC) to reveal two-dimensional contour plots by unconventional 2D IC×IC (interaction chromatography) coupling. The study provides chemical composition mapping of both PEO and PPO, equivalent to combined molar mass and chemical composition mapping for several commercial poloxamers.

  5. Nonclassical Symmetry Analysis of Heated Two-Dimensional Flow Problems

    Science.gov (United States)

    Naeem, Imran; Naz, Rehana; Khan, Muhammad Danish

    2015-12-01

    This article analyses the nonclassical symmetries and group invariant solution of boundary layer equations for two-dimensional heated flows. First, we derive the nonclassical symmetry determining equations with the aid of the computer package SADE. We solve these equations directly to obtain nonclassical symmetries. We follow standard procedure of computing nonclassical symmetries and consider two different scenarios, ξ1≠0 and ξ1=0, ξ2≠0. Several nonclassical symmetries are reported for both scenarios. Furthermore, numerous group invariant solutions for nonclassical symmetries are derived. The similarity variables associated with each nonclassical symmetry are computed. The similarity variables reduce the system of partial differential equations (PDEs) to a system of ordinary differential equations (ODEs) in terms of similarity variables. The reduced system of ODEs are solved to obtain group invariant solution for governing boundary layer equations for two-dimensional heated flow problems. We successfully formulate a physical problem of heat transfer analysis for fluid flow over a linearly stretching porous plat and, with suitable boundary conditions, we solve this problem.

  6. Two-dimensional echocardiographic assessment of dextrocardia: a segmental approach.

    Science.gov (United States)

    Huhta, J C; Hagler, D J; Seward, J B; Tajik, A J; Julsrud, P R; Ritter, D G

    1982-12-01

    Two-dimensional echocardiography was used in the prospective evaluation of 40 patients with the clinical diagnosis of dextrocardia. A segmental analysis of the situs, connections, ventricular anatomy, and chamber positions was utilized for a complete diagnostic assessment. An adequate examination was possible in 33 of these patients; the findings were confirmed by cardiac catheterization and angiography in 31 patients and at operation in 26. Use of the location of the liver and the drainage of the hepatic veins and inferior vena cava allowed atrial visceral situs to be defined in 33 patients (solitus 21, inversus 9, and ambiguous 3). Pulmonary venous connections were correctly identified in 27. In 33 patients, atrioventricular (AV) and ventriculoarterial connections and ventricular anatomy were correctly predicted. Twenty patients had 2 separate well-developed ventricles. Ventriculoarterial connections were determined correctly in all 20 patients: concordant in 5, discordant in 6, double-outlet right ventricle in 5, and single-outlet right ventricle (pulmonary atresia) in 4. In 16 patients a ventricular septal defect was correctly identified. In the remainder the ventricular septum was intact. Thirteen patients had univentricular heart: 8 had 2 AV valves (double-inlet ventricle) 3 had common AV inlet, and 2 had atresia of 1 AV connection. Two-dimensional echocardiography allowed the accurate assessment of complex congenital heart defects associated with dextrocardia. Utilizing a segmental approach, one can correctly predict atrial-visceral situs, ventricular morphology and situs, and AV and ventriculoarterial connections.

  7. Two-dimensional fluorescence spectroscopy of laser-produced plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Harilal, Sivanandan S.; LaHaye, Nicole L.; Phillips, Mark C.

    2016-08-01

    We use a two-dimensional laser-induced fluorescence spectroscopy technique to measure the coupled absorption and emission properties of atomic species in plasmas produced via laser ablation of solid aluminum targets at atmospheric pressure. Emission spectra from the Al I 394.4 nm and Al I 396.15 nm transitions are measured while a frequency-doubled, continuous-wave, Ti:Sapphire laser is tuned across the Al I 396.15 nm transition. The resulting two-dimensional spectra show the energy coupling between the two transitions via increased emission intensity for both transitions during resonant absorption of the continuous-wave laser at one transition. Time-delayed and gated detection of the emission spectrum is used to isolate the resonantly-excited fluorescence emission from the thermally-excited emission from the plasma. In addition, the tunable continuous-wave laser measures the absorption spectrum of the Al transition with ultra-high resolution after the plasma has cooled, resulting in narrower spectral linewidths than observed in emission spectra. Our results highlight that fluorescence spectroscopy employing continuous-wave laser re-excitation after pulsed laser ablation combines benefits of both traditional emission and absorption spectroscopic methods.

  8. Electronic transport in two-dimensional high dielectric constant nanosystems.

    Science.gov (United States)

    Ortuño, M; Somoza, A M; Vinokur, V M; Baturina, T I

    2015-01-01

    There has been remarkable recent progress in engineering high-dielectric constant two dimensional (2D) materials, which are being actively pursued for applications in nanoelectronics in capacitor and memory devices, energy storage, and high-frequency modulation in communication devices. Yet many of the unique properties of these systems are poorly understood and remain unexplored. Here we report a numerical study of hopping conductivity of the lateral network of capacitors, which models two-dimensional insulators, and demonstrate that 2D long-range Coulomb interactions lead to peculiar size effects. We find that the characteristic energy governing electronic transport scales logarithmically with either system size or electrostatic screening length depending on which one is shorter. Our results are relevant well beyond their immediate context, explaining, for example, recent experimental observations of logarithmic size dependence of electric conductivity of thin superconducting films in the critical vicinity of superconductor-insulator transition where a giant dielectric constant develops. Our findings mark a radical departure from the orthodox view of conductivity in 2D systems as a local characteristic of materials and establish its macroscopic global character as a generic property of high-dielectric constant 2D nanomaterials. PMID:25860804

  9. Quantum creep in a highly crystalline two-dimensional superconductor

    Science.gov (United States)

    Saito, Yu; Kasahara, Yuichi; Ye, Jianting; Iwasa, Yoshihiro; Nojima, Tsutomu

    Conventional studies on quantum phase transitions, especially on superconductor-insulator or superconductor-metal-insulator transitions have been performed in deposited metallic thin films such as Bismuth or MoGe. Although the techniques of thin films deposition have been considerably improved, unintentional disorder such as impurities and deficiencies, generating the pinning centers, seems to still exist in such systems. The mechanical exfoliated highly crystalline two-dimensional material can be a good candidate to realize a less-disordered 2D superconductor with extremely weak pinning, combined with transfer method or ionic-liquid gating. We report on the quantum metal, namely, magnetic-field-induced metallic state observed in an ion-gated two-dimensional superconductor based on an ultra-highly crystalline layered band insulator, ZrNCl. We found that the superconducting state is extremely fragile against external magnetic fields; that is, zero resistance state immediately disappears, once an external magnetic field switches on. This is because the present system is relatively clean and the pinning potential is extremely weak, which cause quantum tunneling and flux flow of vortices, resulting in metallic ground state.

  10. Two Dimensional Connectivity for Vehicular Ad-Hoc Networks

    CERN Document Server

    Farivar, Masoud; Ashtiani, Farid

    2008-01-01

    In this paper, we focus on two-dimensional connectivity in sparse vehicular ad hoc networks (VANETs). In this respect, we find thresholds for the arrival rates of vehicles at entrances of a block of streets such that the connectivity is guaranteed for any desired probability. To this end, we exploit a mobility model recently proposed for sparse VANETs, based on BCMP open queuing networks and solve the related traffic equations to find the traffic characteristics of each street and use the results to compute the exact probability of connectivity along these streets. Then, we use the results from percolation theory and the proposed fast algorithms for evaluation of bond percolation problem in a random graph corresponding to the block of the streets. We then find sufficiently accurate two dimensional connectivity-related parameters, such as the average number of intersections connected to each other and the size of the largest set of inter-connected intersections. We have also proposed lower bounds for the case ...

  11. On Space Efficient Two Dimensional Range Minimum Data Structures

    DEFF Research Database (Denmark)

    Davoodi, Pooya; Brodal, Gerth Stølting; Rao, S. Srinivasa

    2010-01-01

    , the lower bound is tight up to a constant factor. In two dimensions, we complement the lower bound with an indexing data structure of size O(N/c) bits additional space which can be preprocessed in O(N) time and achieves O(clog2 c) query time. For c = O(1), this is the first O(1) query time algorithm using......The two dimensional range minimum query problem is to preprocess a static two dimensional m by n array A of size N = m · n, such that subsequent queries, asking for the position of the minimum element in a rectangular range within A, can be answered efficiently. We study the trade-off between...... optimal O(N) bits additional space. For the case where queries can not probe A, we give a data structure of size O(N· min {m,logn}) bits with O(1) query time, assuming m ≤ n. This leaves a gap to the lower bound of Ω(Nlogm) bits for this version of the problem....

  12. On Space Efficient Two Dimensional Range Minimum Data Structures

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Davoodi, Pooya; Rao, S. Srinivasa

    2012-01-01

    of the problem, the lower bound is tight up to a constant factor. In two dimensions, we complement the lower bound with an indexing data structure of size O(N/c) bits which can be preprocessed in O(N) time to support O(clog 2 c) query time. For c=O(1), this is the first O(1) query time algorithm using a data......The two dimensional range minimum query problem is to preprocess a static m by n matrix (two dimensional array) A of size N=m⋅n, such that subsequent queries, asking for the position of the minimum element in a rectangular range within A, can be answered efficiently. We study the trade-off between...... the space and query time of the problem. We show that every algorithm enabled to access A during the query and using a data structure of size O(N/c) bits requires Ω(c) query time, for any c where 1≤c≤N. This lower bound holds for arrays of any dimension. In particular, for the one dimensional version...

  13. Two Dimensional Intermodulation Distortion Scanning of Superconducting Filter Resonators

    Science.gov (United States)

    Bischak, Michael; Remillard, Stephen

    2015-03-01

    Nonlinear superconducting conductivity produces distortion that has usually been measured globally across the entire sample. In order to fully understand the origin of non linearity, local methods must be used to examine specific points in the sample. The nonlinear Ohm's law, V =IZ(I) includes the current dependence in the impedance. The method in this work raster scans a magnetic loop probe across a sample. In order to address limited resolution, we reduced the size of the magnetic loop probe. Using the electromagnetic field solver, sonnet, two dimensional current simulations of superconducting microwave filters composed of Tl2Ba2CaCu2O8 or of YBa2Cu3O7 reveal microwave current which is bunched up at the corners and sides of the sample. Two dimensional images of third order intermodulation distortion made with the magnetic probe at the same corners and edges reveal elevated distortion in the same places. Using the magnetic probe, third order intermodulation was seen to come from the same corners and edges where the current is bunched. This research was funded by the National Science Foundation under grant number DMR-1206149.

  14. Configuration of Shock Waves in Two-Dimensional Overexpanded Jets

    Institute of Scientific and Technical Information of China (English)

    Masashi Kashitani; Yutaka Yamaguchi; Yoshiaki Miyazato; Mitsuharu Masuda; Kazuyasu Matsuo

    2003-01-01

    An experimental and analytical study has been carried out to obtain the clear understanding of a shock wave transition associated with a steady two-dimensional overexpanded flow. Two-dimensional inviscid theory with respect to a shock wave reflection is used in the present study on the characteristic of shock waves. The results obtained from the flow analysis are compared with those obtained from flow visualizations. It is shown that in the region of regular reflection, the angle of an incident shock wave becomes lower than that calculated by two shock theory with an increment in the ratio pe/pb of the nozzle exit pressure pe to the back pressure pb. It is indicated that the configuration of shock waves in overexpanded jets is influenced by the divergent angle at the nozzle exit. Also it is shown from the flow visualization that a series of shock waves move into the nozzle inside with a decrease in pressure ratio pe/pb, even if the pe/pb is under overexpanded conditions.

  15. New two-dimensional response matrix iterative sweeping techniques

    International Nuclear Information System (INIS)

    Four closely related two-dimensional iterative sweeping techniques for solving response matrix equations have been developed and specifically applied to the within-group inner iteration strategy of the nodal transport option of the Argonne National Laboratory DIF3D production code. This option is used for multidimensional neutron transport calculations with a standard fission source outer/inner iteration strategy and fission source extrapolation (FSE) as a possible outer iteration acceleration technique. The inner iterations using a red/black (R/B) checkerborad strategy solve for the nodal surface quantities defined by response matrix equations. To counteract anomalous behavior in the fine-mesh limit, DP1 weights and positive ordinates are used to approximate the exponential integral functions. The new sweeping methods (specialized here for x-y geometry) employ a strategy similar to that used in the Bettis SN code TPT. For the new two-dimensional iterative techniques, this encompasses an upsweep/downsweep through the spatial mesh calculating the nodal surface quantities

  16. Two-dimensional visualization of cluster beams by microchannel plates

    CERN Document Server

    Khoukaz, Alfons; Grieser, Silke; Hergemöller, Ann-Katrin; Köhler, Esperanza; Täschner, Alexander

    2013-01-01

    An advanced technique for a two-dimensional real time visualization of cluster beams in vacuum as well as of the overlap volume of cluster beams with particle accelerator beams is presented. The detection system consists of an array of microchannel plates (MCP) in combination with a phosphor screen which is read out by a CCD camera. This setup together with the ionization of a cluster beam by an electron or ion beam allows for spatial resolved investigations of the cluster beam position, size, and intensity. Moreover, since electrically uncharged clusters remain undetected, the operation in an internal beam experiment opens the way to monitor the overlap region and thus the position and size of an accelerator beam crossing an originally electrically neutral cluster jet. The observed intensity distribution of the recorded image is directly proportional to the convolution of the spatial ion beam and cluster beam intensities and is by this a direct measure of the two-dimensional luminosity distribution. This inf...

  17. Emergent friction in two-dimensional Frenkel-Kontorova models

    Science.gov (United States)

    Norell, Jesper; Fasolino, Annalisa; de Wijn, Astrid S.

    2016-08-01

    Simple models for friction are typically one-dimensional, but real interfaces are two-dimensional. We investigate the effects of the second dimension on static and dynamic friction by using the Frenkel-Kontorova (FK) model. We study the two most straightforward extensions of the FK model to two dimensions and simulate both the static and dynamic properties. We show that the behavior of the static friction is robust and remains similar in two dimensions for physically reasonable parameter values. The dynamic friction, however, is strongly influenced by the second dimension and the accompanying additional dynamics and parameters introduced into the models. We discuss our results in terms of the thermal equilibration and phonon dispersion relations of the lattices, establishing a physically realistic and suitable two-dimensional extension of the FK model. We find that the presence of additional dissipation channels can increase the friction and produces significantly different temperature dependence when compared to the one-dimensional case. We also briefly study the anisotropy of the dynamic friction and show highly nontrivial effects, including that the friction anisotropy can lead to motion in different directions depending on the value of the initial velocity.

  18. Two-dimensional nuclear magnetic resonance of quadrupolar systems

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shuanhu

    1997-09-17

    This dissertation describes two-dimensional nuclear magnetic resonance theory and experiments which have been developed to study quadruples in the solid state. The technique of multiple-quantum magic-angle spinning (MQMAS) is extensively reviewed and expanded upon in this thesis. Specifically, MQMAS is first compared with another technique, dynamic-angle spinning (DAS). The similarity between the two techniques allows us to extend much of the DAS work to the MQMAS case. Application of MQMAS to a series of aluminum containing materials is then presented. The superior resolution enhancement through MQMAS is exploited to detect the five- and six-coordinated aluminum in many aluminosilicate glasses. Combining the MQMAS method with other experiments, such as HETCOR, greatly expands the possibility of the use of MQMAS to study a large range of problems and is demonstrated in Chapter 5. Finally, the technique switching-angle spinning (SAS) is applied to quadrupolar nuclei to fully characterize a quadrupolar spin system in which all of the 8 NMR parameters are accurately determined. This dissertation is meant to demonstrate that with the combination of two-dimensional NMR concepts and new advanced spinning technologies, a series of multiple-dimensional NMR techniques can be designed to allow a detailed study of quadrupolar nuclei in the solid state.

  19. SCAPS, a two-dimensional ion detector for mass spectrometer

    Science.gov (United States)

    Yurimoto, Hisayoshi

    2014-05-01

    Faraday Cup (FC) and electron multiplier (EM) are of the most popular ion detector for mass spectrometer. FC is used for high-count-rate ion measurements and EM can detect from single ion. However, FC is difficult to detect lower intensities less than kilo-cps, and EM loses ion counts higher than Mega-cps. Thus, FC and EM are used complementary each other, but they both belong to zero-dimensional detector. On the other hand, micro channel plate (MCP) is a popular ion signal amplifier with two-dimensional capability, but additional detection system must be attached to detect the amplified signals. Two-dimensional readout for the MCP signals, however, have not achieve the level of FC and EM systems. A stacked CMOS active pixel sensor (SCAPS) has been developed to detect two-dimensional ion variations for a spatial area using semiconductor technology [1-8]. The SCAPS is an integrated type multi-detector, which is different from EM and FC, and is composed of more than 500×500 pixels (micro-detectors) for imaging of cm-area with a pixel of less than 20 µm in square. The SCAPS can be detected from single ion to 100 kilo-count ions per one pixel. Thus, SCAPS can be accumulated up to several giga-count ions for total pixels, i.e. for total imaging area. The SCAPS has been applied to stigmatic ion optics of secondary ion mass spectrometer, as a detector of isotope microscope [9]. The isotope microscope has capabilities of quantitative isotope images of hundred-micrometer area on a sample with sub-micrometer resolution and permil precision, and of two-dimensional mass spectrum on cm-scale of mass dispersion plane of a sector magnet with ten-micrometer resolution. The performance has been applied to two-dimensional isotope spatial distribution for mainly hydrogen, carbon, nitrogen and oxygen of natural (extra-terrestrial and terrestrial) samples and samples simulated natural processes [e.g. 10-17]. References: [1] Matsumoto, K., et al. (1993) IEEE Trans. Electron Dev. 40

  20. Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue

    OpenAIRE

    Timo Gaiser; Lissa Berroa-Garcia; Ralf Kemmerling; Aparajita Dutta; Thomas Ried; Kerstin Heselmeyer-Haddad

    2010-01-01

    Background: The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes withi...

  1. Generalized two-dimensional correlation spectroscopy-- Theory and applications in analytical field

    Institute of Scientific and Technical Information of China (English)

    DOU; Xiaoming; YUAN; Bo; ZHAO; Haiying; YIN; Guangzhong; Y

    2004-01-01

    Since the theory of generalized two-dimensional (2-D) correlation spectroscopy was proposed, it has been keenly concerned in scientific research and its analytical method has been widely applied in various analytical fields. The mathematical process to construct generalized 2-D correlation spectroscopy and the physical meaning of 2-D correlation spectral map are described, and three examples in the fields of chemical analysis and molecular biology are provided, such as the component analysis of organic solvent, the analysis of biological molecules in the solvent with different pH values and structural analysis of protein. The theory and analytical method of generalized 2-D correlation spectroscopy are also detailedly commented.

  2. Two-dimensional electronic spectroscopy for the quantum-optics enthusiast

    CERN Document Server

    Branczyk, Agata M; Scholes, Gregory D

    2013-01-01

    Recent interest in the role of quantum mechanics in the primary events of photosynthetic energy transfer has led to a convergence of nonlinear optical spectroscopy and quantum optics on the topic of energy-transfer dynamics in pigment-protein complexes. The convergence of these two communities has unveiled a mismatch between the background and terminology of the respective fields. To make connections, we provide a pedagogical guide to understanding the basics of two-dimensional electronic spectra aimed at researchers with a background in quantum optics.

  3. Automated clustering of ensembles of alternative models in protein structure databases.

    Science.gov (United States)

    Domingues, Francisco S; Rahnenführer, Jörg; Lengauer, Thomas

    2004-06-01

    Experimentally determined protein structures have been classified in different public databases according to their structural and evolutionary relationships. Frequently, alternative structural models, determined using X-ray crystallography or NMR spectroscopy, are available for a protein. These models can present significant structural dissimilarity. Currently there is no classification available for these alternative structures. In order to classify them, we developed STRuster, an automated method for clustering ensembles of structural models according to their backbone structure. The method is based on the calculation of carbon alpha (Calpha) distance matrices. Two filters are applied in the calculation of the dissimilarity measure in order to identify both large and small (but significant) backbone conformational changes. The resulting dissimilarity value is used for hierarchical clustering and partitioning around medoids (PAM). Hierarchical clustering reflects the hierarchy of similarities between all pairs of models, while PAM groups the models into the 'optimal' number of clusters. The method has been applied to cluster the structures in each SCOP species level and can be easily applied to any other sets of conformers. The results are available at: http://bioinf.mpi-sb.mpg.de/projects/struster/. PMID:15319469

  4. Airfoil model in Two-Dimensional Low-Turbulence Tunnel

    Science.gov (United States)

    1939-01-01

    Airfoil model with pressure taps inside the test section of the Two-Dimensional Low-Turbulence Tunnel. The Two-Dimensional Low-Turbulence Tunnel was originally called the Refrigeration or 'Ice' tunnel because it was intended to support research on aircraft icing. The tunnel was built of wood, lined with sheet steel, and heavily insulated on the outside. Refrigeration equipment was installed to generate icing conditions inside the test section. The NACA sent out a questionnaire to airline operators, asking them to detail the specific kinds of icing problems they encountered in flight. The replies became the basis for a comprehensive research program begun in 1938 when the tunnel commenced operation. Research quickly focused on the concept of using exhaust heat to prevent ice from forming on the wing's leading edge. This project was led by Lewis Rodert, who later would win the Collier Trophy for his work on deicing. By 1940, aircraft icing research had shifted to the new Ames Research Laboratory, and the Ice tunnel was refitted with screens and honeycomb. Researchers were trying to eliminate all turbulence in the test section. From TN 1283: 'The Langley two-dimensional low-turbulence pressure tunnel is a single-return closed-throat tunnel.... The tunnel is constructed of heavy steel plate so that the pressure of the air may be varied from approximately full vacuum to 10 atmospheres absolute, thereby giving a wide range of air densities. Reciprocating compressors with a capacity of 1200 cubic feet of free air per minute provide compressed air. Since the tunnel shell has a volume of about 83,000 cubic feet, a compression rate of approximately one atmosphere per hour is obtained. ... The test section is rectangular in shape, 3 feet wide, 7 1/2 feet high, and 7 1/2 feet long. ... The over-all size of the wind-tunnel shell is about 146 feet long and 58 feet wide with a maximum diameter of 26 feet. The test section and entrance and exit cones are surrounded by a 22-foot

  5. Nonlinear optical response of a two-dimensional atomic crystal.

    Science.gov (United States)

    Merano, Michele

    2016-01-01

    The theory of Bloembergen and Pershan for the light waves at the boundary of nonlinear media is extended to a nonlinear two-dimensional (2D) atomic crystal, i.e., a single planar atomic lattice, placed between linear bulk media. The crystal is treated as a zero-thickness interface, a real 2D system. Harmonic waves emanate from it. Generalization of the laws of reflection and refraction give the direction and the intensity of the harmonic waves. As a particular case that contains all the essential physical features, second-order harmonic generation is considered. The theory, due to its simplicity that stems from the special character of a single planar atomic lattice, is able to elucidate and explain the rich experimental details of harmonic generation from a 2D atomic crystal.

  6. Persistent Photoconductivity in A Magnetic Two Dimensional Electron Gas

    Science.gov (United States)

    Ray, O.; Smorchkova, I. P.; Samarth, N.

    1998-03-01

    Magnetic two-dimensional electron gases (2DEGs) based on modulation-doped (Zn,Cd,Mn)Se/ZnSe heterostructures are of current interest because of their novel transport properties (PRL 78, 3571 (1997)). Here, we examine the phenomenon of persistent photoconductivity (PPC) in these structures, with the aim of understanding the nature of defects and their role in limiting the 2DEG mobility. We have observed significant PPC at high temperatures in modulation doped magnetic 2DEGs. The clear presence of a deep trap responsible for the observed PPC is established through temperature-dependent photoconductivity, photoluminescence, deep level transient fourier spectroscopy and photo induced current transient spectroscopy. An analysis of these experiments will be presented, summarizing the specific characteristics and possible origins of this deep level.

  7. Transport of Bose-Einstein condensates through two dimensional cavities

    International Nuclear Information System (INIS)

    The recent experimental advances in manipulating ultra-cold atoms make it feasible to study coherent transport of Bose-Einstein condensates (BEC) through various mesoscopic structures. In this work the quasi-stationary propagation of BEC matter waves through two dimensional cavities is investigated using numerical simulations within the mean-field approach of the Gross-Pitaevskii equation. The focus is on the interplay between interference effects and the interaction term in the non-linear wave equation. One sees that the transport properties show a complicated behaviour with multi-stability, hysteresis and dynamical instabilities for non-vanishing interaction. Furthermore, the prominent weak localization effect, which is a robust interference effect emerging after taking a configuration average, is reduced and partially inverted for non-vanishing interaction.

  8. Two-dimensional heterostructures: fabrication, characterization, and application.

    Science.gov (United States)

    Wang, Hong; Liu, Fucai; Fu, Wei; Fang, Zheyu; Zhou, Wu; Liu, Zheng

    2014-11-01

    Two-dimensional (2D) materials such as graphene, hexagonal boron nitrides (hBN), and transition metal dichalcogenides (TMDs, e.g., MoS2) have attracted considerable attention in the past few years because of their novel properties and versatile potential applications. These 2D layers can be integrated into a monolayer (lateral 2D heterostructure) or a multilayer stack (vertical 2D heterostructure). The resulting artificial 2D structures provide access to new properties and applications beyond their component 2D atomic crystals and hence, they are emerging as a new exciting field of research. In this article, we review recent progress on the fabrication, characterization, and applications of various 2D heterostructures. PMID:25219598

  9. Optical Spectroscopy of Two Dimensional Graphene and Boron Nitride

    Science.gov (United States)

    Ju, Long

    This dissertation describes the use of optical spectroscopy in studying the physical properties of two dimensional nano materials like graphene and hexagonal boron nitride. Compared to bulk materials, atomically thin two dimensional materials have a unique character that is the strong dependence of physical properties on external control. Both electronic band structure and chemical potential can be tuned in situ by electric field-which is a powerful knob in experiment. Therefore the optical study at atomic thickness scale can greatly benefit from modern micro-fabrication technique and electric control of the material properties. As will be shown in this dissertation, such control of both gemometric and physical properties enables new possibilities of optical spectroscopic measurement as well as opto-electronic studies. Other experimental techniques like electric transport and scanning tunneling microscopy and spectroscopy are also combined with optical spectroscopy to reveal the physics that is beyond the reach of each individual technique. There are three major themes in the dissertation. The first one is focused on the study of plasmon excitation of Dirac electrons in monolayer graphene. Unlike plasmons in ordinary two dimensional electron gas, plasmons of 2D electrons as in graphene obey unusual scaling laws. We fabricate graphene micro-ribbon arrays with photolithography technique and use optical absorption spectroscopy to study its absorption spectrum. The experimental result demonstrates the extraordinarily strong light-plasmon coupling and its novel dependence on both charge doping and geometric dimensions. This work provides a first glance at the fundamental properties of graphene plasmons and forms the basis of an emerging subfield of graphene research and applications such as graphene terahertz metamaterials. The second part describes the opto-electronic response of heterostructures composed of graphene and hexagonal boron nitride. We found that there is

  10. Phonon-polariton in two-dimensional piezoelectric phononic crystals

    Energy Technology Data Exchange (ETDEWEB)

    Yang Mingyi; Wu Liangchieh [Department of Mechanical Engineering, National Taiwan University, Taipei, Taiwan 10617 (China); Tseng Jiunyi [Materials and Chemical Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan 31040 (China)], E-mail: jytseng@itri.org.tw

    2008-06-23

    The phonon-polariton behaviors of two-dimensional piezoelectric phononic crystals (PPCs) were studied using the plane wave expansion method. The governing equations combine Maxwell's equations and Newton's equations of motion. A mode-repulsion can be formed by strong coupling between electromagnetic (EM) waves and elastic waves in the vicinity of the center of the first Brillouin zone for PPC that comprises piezoelectric material and with opposite polarization in different periodically organized areas. Take a 2D ZnO PPC as a numerical example, it was decoupled into two independent groups. One refers to the mixed mode of the in-plane elastic waves and the transverse-magnetic (TM) mode EM waves. The other group refers to the mixed mode of the out-of-plane elastic waves and the transverse-electric (TE) mode EM waves. Coupling repulsion is also observed in these two groups.

  11. Elastic interactions between two-dimensional geometric defects.

    Science.gov (United States)

    Moshe, Michael; Sharon, Eran; Kupferman, Raz

    2015-12-01

    In this paper, we introduce a methodology applicable to a wide range of localized two-dimensional sources of stress. This methodology is based on a geometric formulation of elasticity. Localized sources of stress are viewed as singular defects-point charges of the curvature associated with a reference metric. The stress field in the presence of defects can be solved using a scalar stress function that generalizes the classical Airy stress function to the case of materials with nontrivial geometry. This approach allows the calculation of interaction energies between various types of defects. We apply our methodology to two physical systems: shear-induced failure of amorphous materials and the mechanical interaction between contracting cells. PMID:26764699

  12. Renormalization of two-dimensional R2-gravity

    International Nuclear Information System (INIS)

    Two Dimensional Gravity with R2-term is quantized around the R2-Liouville solution in the semiclassical way. Renormalization, regularization (infra-red, ultra-violet) and a topological term (∂(arphi∂arphi) ) are carefully treated. All (1-loop) divergences are renormalized by the cosmological constant (μ) and the R2-coupling-constant (β) for the case β>0. The quantum meaning of the topological term is clarified. The renormalization group beta-functions of the couplings β and μ are obtained. It is found that the theory is conformal (i.e. the beta-functions=0) for w=(β/A).(16π.48π/(26-cm))≥1 (where A is a fixed area) exactly when the coupling constant ξ of the topological term takes the value of 1. As for 0m<26 and μ is asymptotically non-free. (orig.)

  13. Two-dimensional wave propagation in layered periodic media

    KAUST Repository

    Quezada de Luna, Manuel

    2014-09-16

    We study two-dimensional wave propagation in materials whose properties vary periodically in one direction only. High order homogenization is carried out to derive a dispersive effective medium approximation. One-dimensional materials with constant impedance exhibit no effective dispersion. We show that a new kind of effective dispersion may arise in two dimensions, even in materials with constant impedance. This dispersion is a macroscopic effect of microscopic diffraction caused by spatial variation in the sound speed. We analyze this dispersive effect by using highorder homogenization to derive an anisotropic, dispersive effective medium. We generalize to two dimensions a homogenization approach that has been used previously for one-dimensional problems. Pseudospectral solutions of the effective medium equations agree to high accuracy with finite volume direct numerical simulations of the variable-coeffi cient equations.

  14. Flat Chern band in a two-dimensional organometallic framework.

    Science.gov (United States)

    Liu, Zheng; Wang, Zheng-Fei; Mei, Jia-Wei; Wu, Yong-Shi; Liu, Feng

    2013-03-01

    By combining exotic band dispersion with nontrivial band topology, an interesting type of band structure, namely, the flat Chern band, has recently been proposed to spawn high-temperature fractional quantum Hall states. Despite the proposal of several theoretical lattice models, however, it remains doubtful whether such a "romance of flatland" could exist in a real material. Here, we present a first-principles design of a two-dimensional indium-phenylene organometallic framework that realizes a nearly flat Chern band right around the Fermi level by combining lattice geometry, spin-orbit coupling, and ferromagnetism. An effective four-band model is constructed to reproduce the first-principles results. Our design, in addition, provides a general strategy to synthesize topologically nontrivial materials by virtue of organic chemistry and nanotechnology.

  15. Anomaly matching condition in two-dimensional systems

    CERN Document Server

    Dubinkin, O; Gubankova, E

    2016-01-01

    Based on Son-Yamamoto relation obtained for transverse part of triangle axial anomaly in ${\\rm QCD}_4$, we derive its analog in two-dimensional system. It connects the transverse part of mixed vector-axial current two-point function with diagonal vector and axial current two-point functions. Being fully non-perturbative, this relation may be regarded as anomaly matching for conductivities or certain transport coefficients depending on the system. We consider the holographic RG flows in holographic Yang-Mills-Chern-Simons theory via the Hamilton-Jacobi equation with respect to the radial coordinate. Within this holographic model it is found that the RG flows for the following relations are diagonal: Son-Yamamoto relation and the left-right polarization operator. Thus the Son-Yamamoto relation holds at wide range of energy scales.

  16. A spectroelectrochemical cell for ultrafast two-dimensional infrared spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    El Khoury, Youssef; Van Wilderen, Luuk J. G. W.; Vogt, Tim; Winter, Ernst; Bredenbeck, Jens, E-mail: bredenbeck@biophysik.uni-frankfurt.org, E-mail: bredenbeck@biophysik.uni-frankfurt.de [Institut für Biophysik, Johann Wolfgang Goethe-Universität, Max-von-Laue-Strasse 1, 60438 Frankfurt (Germany)

    2015-08-15

    A spectroelectrochemical cell has been designed to combine electrochemistry and ultrafast two-dimensional infrared (2D-IR) spectroscopy, which is a powerful tool to extract structure and dynamics information on the femtosecond to picosecond time scale. Our design is based on a gold mirror with the dual role of performing electrochemistry and reflecting IR light. To provide the high optical surface quality required for laser spectroscopy, the gold surface is made by electron beam evaporation on a glass substrate. Electrochemical cycling facilitates in situ collection of ultrafast dynamics of redox-active molecules by means of 2D-IR. The IR beams are operated in reflection mode so that they travel twice through the sample, i.e., the signal size is doubled. This methodology is optimal for small sample volumes and successfully tested with the ferricyanide/ferrocyanide redox system of which the corresponding electrochemically induced 2D-IR difference spectrum is reported.

  17. Dispersionless Toda hierarchy and two-dimensional string theory

    Science.gov (United States)

    Takasaki, Kanehisa

    1995-05-01

    The dispersionless Toda hierarchy turns out to lie in the heart of a recently proposed Landau-Ginzburg formulation of two-dimensional string theory at self-dual compactification radius. The dynamics of massless tachyons with discrete momenta is shown to be encoded into the structure of a special solution of this integrable hierarchy. This solution is obtained by solving a Riemann-Hilbert problem. Equivalence to the tachyon dynamics is proven by deriving recursion relations of tachyon correlation functions in the machinery of the dispersionless Toda hierarchy. Fundamental ingredients of the Landau-Ginzburg formulation, such as Landau-Ginzburg potentials and tachyon Landau-Ginzburg fields, are translated into the language of the Lax formalism. Furthermore, a wedge algebra is pointed out to exist behind the Riemann-Hilbert problem, and speculations on its possible role as generators of “extra” states and fields are presented.

  18. Nonlinear transport in a two dimensional holographic superconductor

    Science.gov (United States)

    Zeng, Hua Bi; Tian, Yu; Fan, Zhe Yong; Chen, Chiang-Mei

    2016-06-01

    The problem of nonlinear transport in a two-dimensional superconductor with an applied oscillating electric field is solved by the holographic method. The complex conductivity can be computed from the dynamics of the current for both the near- and nonequilibrium regimes. The limit of weak electric field corresponds to the near-equilibrium superconducting regime, where the charge response is linear and the conductivity develops a gap determined by the condensate. A larger electric field drives the system into a superconducting nonequilibrium steady state, where the nonlinear conductivity is quadratic with respect to the electric field. Increasing the amplitude of the applied electric field results in a far-from-equilibrium nonsuperconducting steady state with a universal linear conductivity of one. In the lower temperature regime we also find chaotic behavior of the superconducting gap, which results in a nonmonotonic field-dependent nonlinear conductivity.

  19. Two-Dimensional Massless Light Front Fields and Solvable Models

    Science.gov (United States)

    Martinovic̆, L'ubomír; Grangé, Pierre

    2016-07-01

    Quantum field theory formulated in terms of light front (LF) variables has a few attractive as well as some puzzling features. The latter hindered a wider acceptance of LF methods. In two space-time dimensions, it has been a long-standing puzzle how to correctly quantize massless fields, in particular fermions. Here we show that two-dimensional massless LF fields (scalar and fermion) can be recovered in a simple way as limits of the corresponding massive fields and thereby quantized without any loss of physical information. Bosonization of the fermion field then follows in a straightforward manner and the solvable models can be studied directly in the LF theory. We sketch the LF operator solution of the Thirring-Wess model and also point out the closeness of the massless LF fields to those of conformal field theory.

  20. Dynamics across the morphological transition in two-dimensional aggregates

    Science.gov (United States)

    Bandi, Mahesh; Das, Tamoghna

    2015-03-01

    Microscopic dynamics of two-dimensional aggregates have been studied by analysing simulated particle trajectories generated by molecular dynamics. Tuning the competition between the short-range attraction and long-range repulsion in a particulate system at fixed temperature and density results in a continuous non-compact to compact morphological transition. The finite-size aggregates, obtained by very slow cooling, show long-time sub-diffusive behaviour irrespective of their morphologies. By analysing the relative displacement fluctuations of particles with respect to their nearest neighbours, non-compact aggregates can be attributed to bonding between particles while caging is found to be responsible for compact clusters. These dynamical mechanisms are further illustrated by the self-displacement fluctuation of particles which show a continuous change from power-law to exponential behaviour across the non-compact to compact transition. This work was supported by the OIST Graduate University with subsidy funding from the Cabinet Office, Government of Japan.

  1. Cooperation in two-dimensional mixed-games

    International Nuclear Information System (INIS)

    Evolutionary game theory is a common framework to study the evolution of cooperation, where it is usually assumed that the same game is played in all interactions. Here, we investigate a model where the game that is played by two individuals is uniformly drawn from a sample of two different games. Using the master equation approach we show that the random mixture of two games is equivalent to play the average game when (i) the strategies are statistically independent of the game distribution and (ii) the transition rates are linear functions of the payoffs. We also use Monte-Carlo simulations in a two-dimensional lattice and mean-field techniques to investigate the scenario when the two above conditions do not hold. We find that even outside of such conditions, several quantities characterizing the mixed-games are still the same as the ones obtained in the average game when the two games are not very different. (paper)

  2. Cooperation in two-dimensional mixed-games

    Science.gov (United States)

    Amaral, Marco A.; Wardil, Lucas; da Silva, Jafferson K. L.

    2015-11-01

    Evolutionary game theory is a common framework to study the evolution of cooperation, where it is usually assumed that the same game is played in all interactions. Here, we investigate a model where the game that is played by two individuals is uniformly drawn from a sample of two different games. Using the master equation approach we show that the random mixture of two games is equivalent to play the average game when (i) the strategies are statistically independent of the game distribution and (ii) the transition rates are linear functions of the payoffs. We also use Monte-Carlo simulations in a two-dimensional lattice and mean-field techniques to investigate the scenario when the two above conditions do not hold. We find that even outside of such conditions, several quantities characterizing the mixed-games are still the same as the ones obtained in the average game when the two games are not very different.

  3. Two-dimensional static deformation of an anisotropic medium

    Indian Academy of Sciences (India)

    Kuldip Singh; Dinesh Kumar Madan; Anita Goel; Nat Ram Garg

    2005-08-01

    The problem of two-dimensional static deformation of a monoclinic elastic medium has been studied using the eigenvalue method, following a Fourier transform. We have obtained expressions for displacements and stresses for the medium in the transformed domain. As an application of the above theory, the particular case of a normal line-load acting inside an orthotropic elastic half-space has been considered in detail and closed form expressions for the displacements and stresses are obtained. Further, the results for the displacements for a transversely isotropic as well as for an isotropic medium have also been derived in the closed form. The use of matrix notation is straightforward and avoids unwieldy mathematical expressions. To examine the effect of anisotropy, variations of dimensionless displacements for an orthotropic, transversely isotropic and isotropic elastic medium have been compared numerically and it is found that anisotropy affects the deformation significantly.

  4. Self-organized defect strings in two-dimensional crystals.

    Science.gov (United States)

    Lechner, Wolfgang; Polster, David; Maret, Georg; Keim, Peter; Dellago, Christoph

    2013-12-01

    Using experiments with single-particle resolution and computer simulations we study the collective behavior of multiple vacancies injected into two-dimensional crystals. We find that the defects assemble into linear strings, terminated by dislocations with antiparallel Burgers vectors. We show that these defect strings propagate through the crystal in a succession of rapid one-dimensional gliding and rare rotations. While the rotation rate decreases exponentially with the number of defects in the string, the diffusion constant is constant for large strings. By monitoring the separation of the dislocations at the end points, we measure their effective interactions with high precision beyond their spontaneous formation and annihilation, and we explain the double-well form of the dislocation interaction in terms of continuum elasticity theory.

  5. Random diffusion and cooperation in continuous two-dimensional space.

    Science.gov (United States)

    Antonioni, Alberto; Tomassini, Marco; Buesser, Pierre

    2014-03-01

    This work presents a systematic study of population games of the Prisoner's Dilemma, Hawk-Dove, and Stag Hunt types in two-dimensional Euclidean space under two-person, one-shot game-theoretic interactions, and in the presence of agent random mobility. The goal is to investigate whether cooperation can evolve and be stable when agents can move randomly in continuous space. When the agents all have the same constant velocity cooperation may evolve if the agents update their strategies imitating the most successful neighbor. If a fitness difference proportional is used instead, cooperation does not improve with respect to the static random geometric graph case. When viscosity effects set-in and agent velocity becomes a quickly decreasing function of the number of neighbors they have, one observes the formation of monomorphic stable clusters of cooperators or defectors in the Prisoner's Dilemma. However, cooperation does not spread in the population as in the constant velocity case. PMID:24316109

  6. Stopping power of two-dimensional spin quantum electron gases

    Science.gov (United States)

    Zhang, Ya; Jiang, Wei; Yi, Lin

    2015-04-01

    Quantum effects can contribute significantly to the electronic stopping powers in the interactions between the fast moving beams and the degenerate electron gases. From the Pauli equation, the spin quantum hydrodynamic (SQHD) model is derived and used to calculate the stopping power and the induced electron density for protons moving above a two-dimensional (2D) electron gas with considering spin effect under an external in-plane magnetic field. In our calculation, the stopping power is not only modulated by the spin direction, but also varied with the strength of the spin effect. It is demonstrated that the spin effect can obviously enhance or reduce the stopping power of a 2D electron gas within a laboratory magnetic field condition (several tens of Tesla), thus a negative stopping power appears at some specific proton velocity, which implies the protons drain energy from the Pauli gas, showing another significant example of the low-dimensional physics.

  7. Stopping power of two-dimensional spin quantum electron gases

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ya [School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China); Jiang, Wei, E-mail: weijiang@hust.edu.cn [School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China); Centre for mathematical Plasma-Astrophysics, Department of Mathematics, Katholieke Universiteit Leuven, B-3001 Leuven (Belgium); Yi, Lin [School of Physics, Huazhong University of Science and Technology, Wuhan 430074 (China)

    2015-04-15

    Quantum effects can contribute significantly to the electronic stopping powers in the interactions between the fast moving beams and the degenerate electron gases. From the Pauli equation, the spin quantum hydrodynamic (SQHD) model is derived and used to calculate the stopping power and the induced electron density for protons moving above a two-dimensional (2D) electron gas with considering spin effect under an external in-plane magnetic field. In our calculation, the stopping power is not only modulated by the spin direction, but also varied with the strength of the spin effect. It is demonstrated that the spin effect can obviously enhance or reduce the stopping power of a 2D electron gas within a laboratory magnetic field condition (several tens of Tesla), thus a negative stopping power appears at some specific proton velocity, which implies the protons drain energy from the Pauli gas, showing another significant example of the low-dimensional physics.

  8. Exit time distribution in spherically symmetric two-dimensional domains

    CERN Document Server

    Rupprecht, J -F; Grebenkov, D S; Voituriez, R

    2014-01-01

    The distribution of exit times is computed for a Brownian particle in spherically symmetric two- dimensional domains (disks, angular sectors, annuli) and in rectangles that contain an exit on their boundary. The governing partial differential equation of Helmholtz type with mixed Dirichlet- Neumann boundary conditions is solved analytically. We propose both an exact solution relying on a matrix inversion, and an approximate explicit solution. The approximate solution is shown to be exact for an exit of vanishing size and to be accurate even for large exits. For angular sectors, we also derive exact explicit formulas for the moments of the exit time. For annuli and rectangles, the approximate expression of the mean exit time is shown to be very accurate even for large exits. The analysis is also extended to biased diffusion. Since the Helmholtz equation with mixed boundary conditions is encountered in microfluidics, heat propagation, quantum billiards, and acoustics, the developed method can find numerous appl...

  9. Structure and computation of two-dimensional incompressible extended MHD

    CERN Document Server

    Grasso, D; Abdelhamid, H M; Morrison, P J

    2016-01-01

    A comprehensive study of a reduced version of Lust's equations, the extended magnetohydrodynamic (XMHD) model obtained from the two-fluid theory for electrons and ions with the enforcement of quasineutrality, is given. Starting from the Hamiltonian structure of the fully three-dimensional theory, a Hamiltonian two-dimensional incompressible four-field model is derived. In this way energy conservation along with four families of Casimir invariants are naturally obtained. The construction facilitates various limits leading to the Hamiltonian forms of Hall, inertial, and ideal MHD, with their conserved energies and Casimir invariants. Basic linear theory of the four-field model is treated, and the growth rate for collisionless reconnection is obtained. Results from nonlinear simulations of collisionless tearing are presented and interpreted using, in particular normal fields, a product of the Hamiltonian theory that gives rise to simplified equations of motion.

  10. Oscillation of Two-Dimensional Neutral Delay Dynamic Systems

    Directory of Open Access Journals (Sweden)

    Xinli Zhang

    2013-01-01

    Full Text Available We consider a class of nonlinear two-dimensional dynamic systems of the neutral type (x(t-a(tx(τ1(tΔ=p(tf1(y(t, yΔ(t=-q(tf2(x(τ2(t. We obtain sufficient conditions for all solutions of the system to be oscillatory. Our oscillation results when a(t=0 improve the oscillation results for dynamic systems on time scales that have been established by Fu and Lin (2010, since our results do not restrict to the case where f(u=u. Also, as a special case when =ℝ, our results do not require an to be a positive real sequence. Some examples are given to illustrate the main results.

  11. Synchronization of Coupled Oscillators on a Two-Dimensional Plane.

    Science.gov (United States)

    Guo, Dameng; Fu, Yong Qing; Zheng, Bo

    2016-08-01

    The effect of the transfer rate of signal molecules on coupled chemical oscillators arranged on a two-dimensional plane was systematically investigated in this paper. A microreactor equipped with a surface acoustic wave (SAW) mixer was applied to adjust the transfer rate of the signal molecules in the microreactor. The SAW mixer with adjustable input powers provided a simple means to generate different mixing rates in the microreactor. A robust synchronization of the oscillators was found at an input radio frequency power of 20 dBm, with which the chemical waves were initiated at a fixed site of the oscillator system. With increasing input power, the frequency of the chemical waves was increased, which agreed well with the prediction given by the time-delayed phase oscillator model. Results from the finite element simulation agreed well with the experimental results. PMID:27124217

  12. Superfluid response of two-dimensional parahydrogen clusters in confinement

    Energy Technology Data Exchange (ETDEWEB)

    Idowu, Saheed; Boninsegni, Massimo [Department of Physics, University of Alberta, Edmonton, Alberta T6G 2E7 (Canada)

    2015-04-07

    We study by computer simulations the effect of confinement on the superfluid properties of small two-dimensional (2D) parahydrogen clusters. For clusters of fewer than twenty molecules, the superfluid response in the low temperature limit is found to remain comparable in magnitude to that of free clusters, within a rather wide range of depth and size of the confining well. The resilience of the superfluid response is attributable to the “supersolid” character of these clusters. We investigate the possibility of establishing a bulk 2D superfluid “cluster crystal” phase of p-H{sub 2}, in which a global superfluid response would arise from tunnelling of molecules across adjacent unit cells. The computed energetics suggests that for clusters of about ten molecules, such a phase may be thermodynamically stable against the formation of the equilibrium insulating crystal, for values of the cluster crystal lattice constant possibly allowing tunnelling across adjacent unit cells.

  13. Acoustic resonances in two dimensional radial sonic crystals shells

    CERN Document Server

    Torrent, Daniel

    2010-01-01

    Radial sonic crystals (RSC) are fluidlike structures infinitely periodic along the radial direction. They have been recently introduced and are only possible thanks to the anisotropy of specially designed acoustic metamaterials [see Phys. Rev. Lett. {\\bf 103} 064301 (2009)]. We present here a comprehensive analysis of two-dimensional RSC shells, which consist of a cavity defect centered at the origin of the crystal and a finite thickness crystal shell surrounded by a fluidlike background. We develop analytic expressions demonstrating that, like for other type of crystals (photonic or phononic) with defects, these shells contain Fabry-Perot like resonances and strongly localized modes. The results are completely general and can be extended to three dimensional acoustic structures and to their photonic counterparts, the radial photonic crystals.

  14. Acoustic resonances in two-dimensional radial sonic crystal shells

    Science.gov (United States)

    Torrent, Daniel; Sánchez-Dehesa, José

    2010-07-01

    Radial sonic crystals (RSC) are fluidlike structures infinitely periodic along the radial direction that verify the Bloch theorem and are possible only if certain specially designed acoustic metamaterials with mass density anisotropy can be engineered (see Torrent and Sánchez-Dehesa 2009 Phys. Rev. Lett. 103 064301). A comprehensive analysis of two-dimensional (2D) RSC shells is reported here. A given shell is in fact a circular slab with a central cavity. These finite crystal structures contain Fabry-Perot-like resonances and modes strongly localized at the central cavity. Semi-analytical expressions are developed to obtain the quality factors of the different resonances, their symmetry features and their excitation properties. The results reported here are completely general and can be extended to equivalent 3D spherical shells and to their photonic counterparts.

  15. Extension of the approximate two-dimensional electron gas formulation

    Science.gov (United States)

    Pierret, R. F.

    1985-07-01

    The functional two-dimensional electron gas (2DEG) formalism employed in the analysis of modulation-doped field-effect transistors is extended to properly account for the bulk charge and to more accurately model sub- and near-threshold behavior. The implemented changes basically transform the functional formulation from an above-threshold formalism for lightly doped structures to one of additional utility which automatically approaches expected limits under widely divergent conditions. Sample computations of the surface carrier concentration, relevant energy level positionings, and the semiconductor depletion width as a function of surface potential and doping are also presented and examined. These computations exhibit the general utility of the extended theory and provide an indirect evaluation of the standard two-level 2DEG theory.

  16. Coherent two-dimensional spectroscopy of a Fano model

    CERN Document Server

    Poulsen, Felipe; Pullerits, Tõnu; Hansen, Thorsten

    2016-01-01

    The Fano lineshape arises from the interference of two excitation pathways to reach a continuum. Its generality has resulted in a tremendous success in explaining the lineshapes of many one-dimensional spectroscopies - absorption, emission, scattering, conductance, photofragmentation - applied to very varied systems - atoms, molecules, semiconductors and metals. Unravelling a spectroscopy into a second dimension reveals the relationship between states in addition to decongesting the spectra. Femtosecond-resolved two-dimensional electronic spectroscopy (2DES) is a four-wave mixing technique that measures the time-evolution of the populations, and coherences of excited states. It has been applied extensively to the dynamics of photosynthetic units, and more recently to materials with extended band-structures. In this letter, we solve the full time-dependent third-order response, measured in 2DES, of a Fano model and give the new system parameters that become accessible.

  17. Entropic Barriers for Two-Dimensional Quantum Memories

    Science.gov (United States)

    Brown, Benjamin J.; Al-Shimary, Abbas; Pachos, Jiannis K.

    2014-03-01

    Comprehensive no-go theorems show that information encoded over local two-dimensional topologically ordered systems cannot support macroscopic energy barriers, and hence will not maintain stable quantum information at finite temperatures for macroscopic time scales. However, it is still well motivated to study low-dimensional quantum memories due to their experimental amenability. Here we introduce a grid of defect lines to Kitaev's quantum double model where different anyonic excitations carry different masses. This setting produces a complex energy landscape which entropically suppresses the diffusion of excitations that cause logical errors. We show numerically that entropically suppressed errors give rise to superexponential inverse temperature scaling and polynomial system size scaling for small system sizes over a low-temperature regime. Curiously, these entropic effects are not present below a certain low temperature. We show that we can vary the system to modify this bound and potentially extend the described effects to zero temperature.

  18. Spin from defects in two-dimensional quantum field theory

    CERN Document Server

    Novak, Sebastian

    2015-01-01

    We build two-dimensional quantum field theories on spin surfaces starting from theories on oriented surfaces with networks of topological defect lines and junctions. The construction uses a combinatorial description of the spin structure in terms of a triangulation equipped with extra data. The amplitude for the spin surfaces is defined to be the amplitude for the underlying oriented surface together with a defect network dual to the triangulation. Independence of the triangulation and of the other choices follows if the line defect and junctions are obtained from a Delta-separable Frobenius algebra with involutive Nakayama automorphism in the monoidal category of topological defects. For rational conformal field theory we can give a more explicit description of the defect category, and we work out two examples related to free fermions in detail: the Ising model and the so(n) WZW model at level 1.

  19. Two-dimensional optical scanner with monolithically integrated glass microlens

    Science.gov (United States)

    Yoo, Sunghyun; Jin, Joo-Young; Ha, Joon-Geun; Ji, Chang-Hyeon; Kim, Yong-Kweon

    2014-05-01

    A miniaturized two-dimensional forward optical scanner with a monolithically integrated glass microlens was developed for microendoscopic imaging applications. The fabricated device measures 2.26 × 1.97 × 0.62 mm3 in size and a through-silicon microlens with a diameter of 400 µm and numerical aperture of 0.37 has been successfully integrated within the silicon layer. An XY stage structure with lens shuttle and comb actuators was designed, and proprietary glass isolation blocks were utilized in mechanical and electric isolation of X- and Y-axis actuators. Resonant frequencies of the stage in X and Y directions were 3.238 and 2.198 kHz and quality factors were 168 and 69.1, respectively, at atmospheric pressure. Optical scanning test has been performed and scan angles of ±4.7° and ±4.9° were achieved for X and Y directions, respectively.

  20. Two-dimensional curvature functionals with superquadratic growth

    CERN Document Server

    Kuwert, Ernst; Li, Yuxiang

    2011-01-01

    For two-dimensional, immersed closed surfaces $f:\\Sigma \\to \\R^n$, we study the curvature functionals $\\mathcal{E}^p(f)$ and $\\mathcal{W}^p(f)$ with integrands $(1+|A|^2)^{p/2}$ and $(1+|H|^2)^{p/2}$, respectively. Here $A$ is the second fundamental form, $H$ is the mean curvature and we assume $p > 2$. Our main result asserts that $W^{2,p}$ critical points are smooth in both cases. We also prove a compactness theorem for $\\mathcal{W}^p$-bounded sequences. In the case of $\\mathcal{E}^p$ this is just Langer's theorem \\cite{langer85}, while for $\\mathcal{W}^p$ we have to impose a bound for the Willmore energy strictly below $8\\pi$ as an additional condition. Finally, we establish versions of the Palais-Smale condition for both functionals.

  1. Two dimensional radiated power diagnostics on Alcator C-Moda)

    Science.gov (United States)

    Reinke, M. L.; Hutchinson, I. H.

    2008-10-01

    The radiated power diagnostics for the Alcator C-Mod tokamak have been upgraded to measure two dimensional structure of the photon emissivity profile in order to investigate poloidal asymmetries in the core radiation. Commonly utilized unbiased absolute extreme ultraviolet (AXUV) diode arrays view the plasma along five different horizontal planes. The layout of the diagnostic set is shown and the results from calibrations and recent experiments are discussed. Data showing a significant, 30%-40%, inboard/outboard emissivity asymmetry during ELM-free H-mode are presented. The ability to use AXUV diode arrays to measure absolute radiated power is explored by comparing diode and resistive bolometer-based emissivity profiles for highly radiative L-mode plasmas seeded with argon. Emissivity profiles match in the core but disagree radially outward resulting in an underprediction of Prad of nearly 50% by the diodes compared to Prad determined using resistive bolometers.

  2. Enstrophy cascades in two-dimensional dense granular flows

    Science.gov (United States)

    Saitoh, Kuniyasu; Mizuno, Hideyuki

    2016-08-01

    Employing two-dimensional molecular dynamics simulations of dense granular materials under simple shear deformations, we investigate vortex structures of particle rearrangements. Introducing vorticity fields as a measure of local spinning motions of the particles, we observe their heterogeneous distributions, where statistics of vorticity fields exhibit the highly non-Gaussian behavior and typical domain sizes of vorticity fields significantly increase if the system is yielding under quasistatic deformations. In such dense granular flows, a power-law decay of vorticity spectra can be observed at mesoscopic scale, implying anomalous local structures of kinetic energy dissipation. We explain the power-law decay, or enstrophy cascades in dense granular materials, by a dimensional analysis, where the dependence of vorticity spectra not only on the wave number, but also on the shear rate, is well explained. From our dimensional analyses, the scaling of granular temperature and rotational kinetic energy is also predicted.

  3. Two dimensional tunable photonic crystals and n doped semiconductor materials

    International Nuclear Information System (INIS)

    In this paper, we theoretically investigate the effect of the doping concentration on the properties of two dimensional semiconductor photonic band structures. We consider two structures; type I(II) that is composed of n doped semiconductor (air) rods arranged into a square lattice of air (n doped semiconductor). We consider three different shapes of rods. Our numerical method is based on the frequency dependent plane wave expansion method. The numerical results show that the photonic band gaps in type II are more sensitive to the changes in the doping concentration than those of type I. In addition, the width of the gap of type II is less sensitive to the shape of the rods than that of type I. Moreover, the cutoff frequency can be strongly tuned by the doping concentrations. Our structures could be of technical use in optical electronics for semiconductor applications

  4. Jamming patterns in a two-dimensional hopper

    Indian Academy of Sciences (India)

    Kiwing To

    2005-06-01

    We report experimental studies of jamming phenomenon of monodisperse metal disks falling through a two-dimensional hopper when the hopper opening is larger than three times the size of the disks. For each jamming event, the configuration of the arch formed at the hopper opening is studied. The cumulative distribution functions () for hoppers of opening size d are measured. (Here is the horizontal component of the arch vector, which is defined as the displacement vector from the center of the first disk to the center of the last disk in the arch.) We found that the distribution of () can be collasped into a master curve () = ()() that decays exponentially for > 4. The scaling factor () is a decreasing function of d and is approximately proportional to the jamming probability.

  5. Extended quantum jump description of vibronic two-dimensional spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Albert, Julian; Falge, Mirjam; Keß, Martin; Wehner, Johannes G.; Engel, Volker [Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Campus Nord, Emil-Fischer-St. 42, 97074 Würzburg (Germany); Zhang, Pan-Pan; Eisfeld, Alexander [Max-Planck-Institute for the Physics of Complex Systems, Noethnitzer St. 38, D-01187 Dresden (Germany)

    2015-06-07

    We calculate two-dimensional (2D) vibronic spectra for a model system involving two electronic molecular states. The influence of a bath is simulated using a quantum-jump approach. We use a method introduced by Makarov and Metiu [J. Chem. Phys. 111, 10126 (1999)] which includes an explicit treatment of dephasing. In this way it is possible to characterize the influence of dissipation and dephasing on the 2D-spectra, using a wave function based method. The latter scales with the number of stochastic runs and the number of system eigenstates included in the expansion of the wave-packets to be propagated with the stochastic method and provides an efficient method for the calculation of the 2D-spectra.

  6. Extended quantum jump description of vibronic two-dimensional spectroscopy.

    Science.gov (United States)

    Albert, Julian; Falge, Mirjam; Keß, Martin; Wehner, Johannes G; Zhang, Pan-Pan; Eisfeld, Alexander; Engel, Volker

    2015-06-01

    We calculate two-dimensional (2D) vibronic spectra for a model system involving two electronic molecular states. The influence of a bath is simulated using a quantum-jump approach. We use a method introduced by Makarov and Metiu [J. Chem. Phys. 111, 10126 (1999)] which includes an explicit treatment of dephasing. In this way it is possible to characterize the influence of dissipation and dephasing on the 2D-spectra, using a wave function based method. The latter scales with the number of stochastic runs and the number of system eigenstates included in the expansion of the wave-packets to be propagated with the stochastic method and provides an efficient method for the calculation of the 2D-spectra. PMID:26049460

  7. Attractive Coulomb interaction of two-dimensional Rydberg excitons

    Science.gov (United States)

    Shahnazaryan, V.; Shelykh, I. A.; Kyriienko, O.

    2016-06-01

    We analyze theoretically the Coulomb scattering processes of highly excited excitons in the direct-band-gap semiconductor quantum wells. We find that contrary to the interaction of ground-state excitons, the electron and hole exchange interaction between excited excitons has an attractive character both for s - and p -type two-dimensional (2D) excitons. Moreover, we show that similar to the three-dimensional highly excited excitons, the direct interaction of 2D Rydberg excitons exhibits van der Waals-type long-range interaction. The results predict the linear growth of the absolute value of exchange interaction strength with an exciton principal quantum number and point the way towards enhancement of optical nonlinearity in 2D excitonic systems.

  8. Nonlinear Transport in a Two Dimensional Holographic Superconductor

    CERN Document Server

    Zeng, Hua Bi; Fan, Zhe Yong; Chen, Chiang-Mei

    2016-01-01

    The problem of nonlinear transport in a two dimensional superconductor with an applied oscillating electric field is solved by the holographic method. The complex conductivity can be computed from the dynamics of the current for both near- and non-equilibrium regimes. The limit of weak electric field corresponds to the near equilibrium superconducting regime, where the charge response is linear and the conductivity develops a gap determined by the condensate. A larger electric field drives the system into a superconducting non-equilibrium steady state, where the nonlinear conductivity is quadratic with respect to the electric field. Keeping increasing the amplitude of applied electric field results in a far-from-equilibrium non-superconducting steady state with a universal linear conductivity of one. In lower temperature regime we also find chaotic behavior of superconducting gap, which results in a non-monotonic field dependent nonlinear conductivity.

  9. Dynamic metastability in the two-dimensional Potts ferromagnet.

    Science.gov (United States)

    Ibáñez Berganza, Miguel; Petri, Alberto; Coletti, Pietro

    2014-05-01

    We investigate the nonequilibrium dynamics of the two-dimensional (2D) Potts model on the square lattice after a quench below the discontinuous transition point. By means of numerical simulations of systems with q=12, 24, and 48, we observe the onset of a stationary regime below the temperature-driven transition, in a temperature interval decreasing with the system size and increasing with q. These results obtained dynamically agree with those obtained from the analytical continuation of the free energy [J. L. Meunier and A. Morel, Eur. Phys. J. B 13, 341 (2000)], from which metastability in the 2D Potts model results to be a finite-size effect. PMID:25353747

  10. Acoustic metamaterials for new two-dimensional sonic devices

    International Nuclear Information System (INIS)

    It has been shown that two-dimensional arrays of rigid or fluidlike cylinders in a fluid or a gas define, in the limit of large wavelengths, a class of acoustic metamaterials whose effective parameters (sound velocity and density) can be tailored up to a certain limit. This work goes a step further by considering arrays of solid cylinders in which the elastic properties of cylinders are taken into account. We have also treated mixtures of two different elastic cylinders. It is shown that both effects broaden the range of acoustic parameters available for designing metamaterials. For example, it is predicted that metamaterials with perfect matching of impedance with air are now possible by using aerogel and rigid cylinders equally distributed in a square lattice. As a potential application of the proposed metamaterial, we present a gradient index lens for airborne sound (i.e. a sonic Wood lens) whose functionality is demonstrated by multiple scattering simulations

  11. Acoustic resonances in two-dimensional radial sonic crystal shells

    International Nuclear Information System (INIS)

    Radial sonic crystals (RSC) are fluidlike structures infinitely periodic along the radial direction that verify the Bloch theorem and are possible only if certain specially designed acoustic metamaterials with mass density anisotropy can be engineered (see Torrent and Sanchez-Dehesa 2009 Phys. Rev. Lett. 103 064301). A comprehensive analysis of two-dimensional (2D) RSC shells is reported here. A given shell is in fact a circular slab with a central cavity. These finite crystal structures contain Fabry-Perot-like resonances and modes strongly localized at the central cavity. Semi-analytical expressions are developed to obtain the quality factors of the different resonances, their symmetry features and their excitation properties. The results reported here are completely general and can be extended to equivalent 3D spherical shells and to their photonic counterparts.

  12. Self-organized defect strings in two-dimensional crystals.

    Science.gov (United States)

    Lechner, Wolfgang; Polster, David; Maret, Georg; Keim, Peter; Dellago, Christoph

    2013-12-01

    Using experiments with single-particle resolution and computer simulations we study the collective behavior of multiple vacancies injected into two-dimensional crystals. We find that the defects assemble into linear strings, terminated by dislocations with antiparallel Burgers vectors. We show that these defect strings propagate through the crystal in a succession of rapid one-dimensional gliding and rare rotations. While the rotation rate decreases exponentially with the number of defects in the string, the diffusion constant is constant for large strings. By monitoring the separation of the dislocations at the end points, we measure their effective interactions with high precision beyond their spontaneous formation and annihilation, and we explain the double-well form of the dislocation interaction in terms of continuum elasticity theory. PMID:24483371

  13. Irreversibility of the two-dimensional enstrophy cascade

    CERN Document Server

    Piretto,; Boffetta, G

    2016-01-01

    We study the time irreversibility of the direct cascade in two-dimensional turbulence by looking at the time derivative of the square vorticity along Lagrangian trajectories, a quantity which we call metenstrophy. By means of extensive numerical simulations we measure the time irreversibility from the asymmetry of the PDF of the metenstrophy and we find that it increases with the Reynolds number of the cascade, similarly to what found in three-dimensional turbulence. A detailed analysis of the different contributions to the enstrophy budget reveals a remarkable difference with respect to what observed for the direct cascade, in particular the role of the statistics of the forcing to determine the degree of irreversibility.

  14. Statistical features of freely decaying two-dimensional hydrodynamic turbulence

    CERN Document Server

    Kudryavtsev, A N; Sereshchenko, E V

    2013-01-01

    Statistical characteristics of freely decaying two-dimensional hydrodynamic turbulence at high Reynolds numbers are numerically studied. In particular, numerical experiments (with resolution up to $8192\\times 8192$) provide a Kraichnan-type turbulence spectrum $E_k\\sim k^{-3}$. By means of spatial filtration, it is found that the main contribution to the spectrum comes from the sharp vorticity gradients in the form of quasi-shocks. Such quasi-singularities are responsible for a strong angular dependence of the spectrum owing to well-localized (in terms of the angle) jets with minor and/or large overlapping. In each jet, the spectrum decreases as $k^{-3}$. The behavior of the third-order structure function accurately agrees with Kraichnan direct cascade concept corresponding to a constant enstrophy flux. It is shown that the power law exponents $\\zeta_n$ for higher structure functions grow more slowly than the linear dependence of $n$, which testifies to turbulence intermittency.

  15. Entanglement in a two-dimensional string theory

    CERN Document Server

    Donnelly, William

    2016-01-01

    What is the meaning of entanglement in a theory of extended objects such as strings? To address this question we consider entanglement entropy in the Gross-Taylor model, the string theory dual to two-dimensional Yang-Mills theory at large $N$. The string diagrams that contribute to the entanglement entropy describe open strings with endpoints anchored to the entangling surface, as first argued by Susskind. We develop a canonical theory of these open strings, and describe how closed strings are divided into open strings at the level of the Hilbert space, giving a precise state-counting interpretation to the entropy, including its leading $O(N^2)$ piece. In the process we reinterpret the sphere partition function as a thermal ensemble of of open strings whose endpoints are anchored to an object at the entangling surface that we call an E-brane.

  16. Two-dimensional Numerical Modeling Research on Continent Subduction Dynamics

    Institute of Scientific and Technical Information of China (English)

    WANG Zhimin; XU Bei; ZHOU Yaoqi; XU Hehua; HUANG Shaoying

    2004-01-01

    Continent subduction is one of the hot research problems in geoscience. New models presented here have been set up and two-dimensional numerical modeling research on the possibility of continental subduction has been made with the finite element software, ANSYS, based on documentary evidence and reasonable assumptions that the subduction of oceanic crust has occurred, the subduction of continental crust can take place and the process can be simplified to a discontinuous plane strain theory model. The modeling results show that it is completely possible for continental crust to be subducted to a depth of 120 km under certain circumstances and conditions. At the same time, the simulations of continental subduction under a single dynamical factor have also been made, including the pull force of the subducted oceanic lithosphere, the drag force connected with mantle convection and the push force of the mid-ocean ridge. These experiments show that the drag force connected with mantle convection is critical for continent subduction.

  17. Soliton nanoantennas in two-dimensional arrays of quantum dots

    CERN Document Server

    Gligorić, G; Hadžievski, Lj; Slepyan, G Ya; Malomed, B A

    2015-01-01

    We consider two-dimensional (2D) arrays of self-organized semiconductor quantum dots (QDs) strongly interacting with electromagnetic field in the regime of Rabi oscillations. The QD array built of two-level states is modelled by two coupled systems of discrete nonlinear Schr\\"{o}dinger equations. Localized modes in the form of single-peaked fundamental and vortical stationary Rabi solitons and self-trapped breathers have been found. The results for the stability, mobility and radiative properties of the Rabi modes suggest a concept of a self-assembled 2D \\textit{% soliton-based nano-antenna}, which should be stable against imperfections In particular, we discuss the implementation of such a nano-antenna in the form of surface plasmon solitons in graphene, and illustrate possibilities to control their operation by means of optical tools.

  18. Failure of the Regge approach in two dimensional quantum gravity

    CERN Document Server

    Bock, W; Wolfgang Bock; Jeroen C Vink

    1994-01-01

    Regge's method for regularizing euclidean quantum gravity is applied to two dimensional gravity. We use two different strategies to simulate the Regge path integral at a fixed value of the total area: A standard Metropolis simulation combined with a histogramming method and a direct simulation using a Hybrid Monte Carlo algorithm. Using topologies with genus zero and two and a scale invariant integration measure, we show that the Regge method does not reproduce the value of the string susceptibility of the continuum model. We show that the string susceptibility depends strongly on the choice of the measure in the path integral. We argue that the failure of the Regge approach is due to spurious contributions of reparametrization degrees of freedom to the path integral.

  19. Two-Dimensional Organic-Inorganic Hybrid Perovskite Photonic Films.

    Science.gov (United States)

    Meng, Ke; Gao, Shanshan; Wu, Longlong; Wang, Geng; Liu, Xin; Chen, Gang; Liu, Zhou; Chen, Gang

    2016-07-13

    Organic-inorganic hybrid perovskites have created enormous expectations for low-cost and high-performance optoelectronic devices. In prospect, future advancements may derive from reaping novel electrical and optical properties beyond pristine perovskites through microscopic structure design and engineering. Herein, we report the successful preparation of two-dimensional inverse-opal perovskite (IOP) photonic films, featuring unique nanostructures and vivid colors. Further compositional and structural managements promise optical property and energy level tunability of the IOP films. They are further functionalized in solar cells, resulting in colorful devices with respectable power conversion efficiency. Such concept has not been previously applied for perovskite-based solar cells, which could open a route for more versatile optoelectronic devices. PMID:27267266

  20. Approaches to verification of two-dimensional water quality models

    Energy Technology Data Exchange (ETDEWEB)

    Butkus, S.R. (Tennessee Valley Authority, Chattanooga, TN (USA). Water Quality Dept.)

    1990-11-01

    The verification of a water quality model is the one procedure most needed by decision making evaluating a model predictions, but is often not adequate or done at all. The results of a properly conducted verification provide the decision makers with an estimate of the uncertainty associated with model predictions. Several statistical tests are available for quantifying of the performance of a model. Six methods of verification were evaluated using an application of the BETTER two-dimensional water quality model for Chickamauga reservoir. Model predictions for ten state variables were compared to observed conditions from 1989. Spatial distributions of the verification measures showed the model predictions were generally adequate, except at a few specific locations in the reservoir. The most useful statistics were the mean standard error of the residuals. Quantifiable measures of model performance should be calculated during calibration and verification of future applications of the BETTER model. 25 refs., 5 figs., 7 tabs.