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Sample records for automated two-dimensional protein

  1. Towards Automated Screening of Two-dimensional Crystals

    OpenAIRE

    Cheng, Anchi; Leung, Albert; Fellmann, Denis; Quispe, Joel; Suloway, Christian; Pulokas, James; Carragher, Bridget; Potter, Clinton S.

    2007-01-01

    Screening trials to determine the presence of two-dimensional (2D) protein crystals suitable for three-dimensional structure determination using electron crystallography is a very labor-intensive process. Methods compatible with fully automated screening have been developed for the process of crystal production by dialysis and for producing negatively stained grids of the resulting trials. Further automation via robotic handling of the EM grids, and semi-automated transmission electron micros...

  2. Two-dimensional polyacrylamide gel electrophoresis of intracellular proteins

    International Nuclear Information System (INIS)

    Since two-dimensional electrophoresis was established by O'Farrell for analysis of intracellular proteins of Escherichia coli, it has been applied to separation of proteins of animal cells and tissues, and especially to identification of stress proteins. Using this technique, proteins are separated by isoelectric focusing containing 8 m urea in the first dimension and by SDS-PAGE in the second dimension. The gels are stained with Coomassie Blue R-250 dye, followed by silver staining. In the case of radio-labeled proteins, the gels are dried and then autoradiographed. In order to identify a specific protein separated by two-dimensional electrophoresis, a technique determining the N-terminal amino acid sequence of the protein has been developed recently. After the proteins in the gel were electrotransferred to a polyvinylidene difluoride membrane, the membrane was stained for protein with Commassie Blue and a stained membrane fragment was applied to a protein sequencer. Our recent studies demonstrated that fish cells newly synthesized various proteins in response to heat shock, cold nd osmotic stresses. For example, when cellular proteins extracted from cold-treated rainbow trout cells were subjected to two-dimensional gel electrophoresis, the 70 kDa protein was found to be synthesized during the cold-treatment. N-Terminal sequence analysis showed that the cold-inducible protein was a homolog of mammalian valosin-containing protein and yeast cell division cycle gene product CDC48p. Furthermore, the sequence data were useful for preparing PCR primers and a rabbit antibody against a synthetic peptide to analyze a role for the protein in the function of trout cells and mechanisms for regulation

  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. Two dimensional (2-D) electrophoresis and silver staining of proteins in SDS gels

    International Nuclear Information System (INIS)

    Two dimensional electrophoresis is a powerful way to analyze protein samples. It separates molecules by charge, then by size in a polyacrylamide or agarose gel. Combining these two techniques allows visualization of up to 1000 peptides on a single gel. Silver staining of proteins provides a rapid and ultra-sensitive method for the detection of nanogram amounts of proteins. The procedures for two dimensional electrophoresis and silver staining of proteins in gels are described

  5. 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...

  6. 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.

  7. Detergents and Chaotropes for Protein Solubilization before Two-Dimensional Electrophoresis.

    OpenAIRE

    Rabilloud, Thierry; Luche, Sylvie; Santoni, Véronique; Chevallet, Mireille

    2006-01-01

    Because of the outstanding separating capabilities of two-dimensional electrophoresis for complete proteins, it would be advantageous to be able to apply it to all types of proteins. Unfortunately, severe solubility problems hamper the analysis of many classes of proteins, but especially membrane proteins. These problems arise mainly in the extraction and isoelectric focusing steps, and solutions are sought to improve protein solubility under the conditions prevailing during isoelectric focus...

  8. Detergents and chaotropes for protein solubilization before two-dimensional electrophoresis.

    OpenAIRE

    Rabilloud, Thierry

    2009-01-01

    Because of the outstanding ability of two-dimensional electrophoresis to separate complex mixtures of intact proteins, it would be advantageous to apply it to all types of proteins, including hydrophobic and membrane proteins. Unfortunately, poor solubility hampers the analysis of these molecules. As these problems arise mainly in the extraction and isoelectric focusing steps, the solution is to improve protein solubility under the conditions prevailing during isoelectric focusing. This chapt...

  9. Identification of the major membrane and core proteins of vaccinia virus by two-dimensional electrophoresis.

    OpenAIRE

    Jensen, O N; Houthaeve, T; Shevchenko, A.; Cudmore, S; Ashford, T; MANN, M; Griffiths, G; Krijnse Locker, J

    1996-01-01

    Vaccinia virus assembly has been well studied at the ultrastructural level, but little is known about the molecular events that occur during that process. Towards this goal, we have identified the major membrane and core proteins of the intracellular mature virus (IMV). Pure IMV preparations were subjected to Nonidet P-40 (NP-40) and dithiothreitol (DTT) treatment to separate the core proteins from the membrane proteins. These proteins were subsequently separated by two-dimensional (2D) gel e...

  10. Two-dimensional electrophoresis of plant proteins with phastsystem using nonequilibrium pH gradient separation.

    Science.gov (United States)

    Ferullo, J M; Nespoulous, L

    1991-10-01

    We have adapted a two-dimensional electrophoretic technique described by P. Z. O'Farrell et al. (Cell 12, 1133-1142, 1977) to Phastsystem, resolving both acidic and basic proteins by using nonequilibrium pH gradient electrophoresis in the first dimension and sodium dodecyl sulfate polyacrylamide gel electrophoresis in the second dimension. Protein separation was optimized for the analysis of plant proteins. The use of the Phastsystem apparatus reduced times of preparation and separation, allowing the rapid screening of plant proteins on a large scale of isoelectric points. This technique was used for the immunodetection and characterization of two stress-induced proteins in irradiated tomato leaves. PMID:1789413

  11. Evaluation of nonionic and zwitterionic detergents as membrane protein solubilizers in two-dimensional electrophoresis.

    OpenAIRE

    Luche, Sylvie; Santoni, Véronique; Rabilloud, Thierry

    2003-01-01

    The solubilizing power of various nonionic and zwitterionic detergents as membrane protein solubilizers for two-dimensional electrophoresis was investigated. Human red blood cell ghosts and Arabidopsis thaliana leaf membrane proteins were used as model systems. Efficient detergents could be found in each class, i.e. with oligooxyethylene, sugar or sulfobetaine polar heads. Among the commercially available nonionic detergents, dodecyl maltoside and decaethylene glycol mono hexadecyl ether prov...

  12. 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.

  13. 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...... chromatograms. Instead of evaluating the chromatograms individually and determining the content of single compounds or groups of compounds, the raw data of all the samples are analyzed simultaneously. Instrument variation negatively impacts this approach to analysis. It is important to remove non...

  14. 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.

  15. Two-dimensional polyacylamide gel electrophoresis of envelope proteins of Escherichia coli.

    Science.gov (United States)

    Johnson, W C; Silhavy, T J; Boos, W

    1975-03-01

    A method of separating envelope proteins by two-dimensional polyacrylamide gel electrophoresis is described. Escherichia coli envelopes (inner and outer membranes) were prepared by French pressing and washed by repeated centrifugation. Membrane proteins were solubilized with guanidine thiocyanate and were dialyzed against urea prior to two-dimensional electrophoretic analysis. The slab gel apparatus and conditions were similar to the technique developed by Metz and Bogorad (1974) for the separation of ribosomal proteins. This separation occurs in 8 M urea for the first dimension and in 0.2% sodium dodecyl sulfate for the second dimension. The technique separates about 70 different membrane proteins in a highly reproducible fashion according to both intrinsic charge and molecular weight. Some examples of alterations in the membrane protein pattern are demonstrated. These alterations are caused by a mutation affecting a sugar transport system and by growth in the presence of D-fucose, inducer of the transport system. A further example of membrane protein changes introduced by growth at the nonpermissive temperature of a temperature-sensitive cell division mutant is shown. Finally, it is demonstrated that the major outer membrane component of Escherichia coli K-12 contains more than four proteins of similar molecular weight. PMID:803821

  16. Two-dimensional electrophoresis analysis of proteins extracted from Alexandrium sp. LC3

    Science.gov (United States)

    Li, Hao; Miao, Jinlai; Cui, Fengxia; Li, Guangyou

    2007-10-01

    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 14kDa-31kDa and 43kDa-66kDa, and more proteins were detected between 14kDa and 31kDa. With the improved protein preparation, the two-dimensional electrophoresis patterns indicated that the relative molecular weights of the proteins were between 14kDa and 100kDa, and most of them ranged from 14kDa to 31kDa. 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 (pH3 5.6), and about 320 protein spots could be visualized on the 2-DE map by staining. Within pH3 10 and pH3 5.6 strips, the protein samples of Alexandrium sp. LC3 could be separated well.

  17. 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.

  18. Application of two-dimensional electrophoresis in the research of retinal proteins of diabetic rat.

    Science.gov (United States)

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

    2007-02-01

    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. PMID:17349213

  19. 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.

  20. 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.

  1. Two-dimensional gel electrophoresis of selenized yeast and autoradiography of 75Se-containing proteins

    International Nuclear Information System (INIS)

    Two-dimensional high-resolution gel electrophoresis (2DE) has been applied to the fractionation of 75Se-containing proteins in yeast, grown in 75Se-containing medium, and autoradiography was used for detection of the 75Se-containing proteins. Gel filtration and ultrafiltration were used to check whether the selenium side-chains were stable in the presence of the chemicals used for lysis and 2DE. The mass distribution of the selenium-containing proteins was estimated by use of gel filtration and the results were compared with the distribution obtained by 2DE. A 2DE map of selenium-containing proteins in yeast is presented, and compared with a total protein map of yeast. (orig.)

  2. 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.

  3. Protein analysis on two-dimensional polyacrylamide gels in the femtogram range: use of a new sulfur-labeling reagent

    International Nuclear Information System (INIS)

    An ultrasensitive staining procedure for two-dimensional polyacrylamide gels of protein homogenates has been developed. It combines the use of ultrathin gels and the labeling of proteins by a 35S-labeling reagent

  4. Two-dimensional electrophoretic analysis of human leukocyte proteins from patients with rheumatoid arthritis

    Energy Technology Data Exchange (ETDEWEB)

    Willard, K.E. (Argonne National Lab., IL); Thorsrud, A.K.; Munthe, E.; Jellum, E.

    1982-04-01

    Human leukocyte proteins from more than 150 patients with rheumatoid arthritis, together with age- and sex-matched controls, were analyzed by use of the ISO-DALT technique of two-dimensional polyacrylamide gel electrophoresis. Patients with ankylosing spondylitis, polymyalgia rheumatica, psoriatic arthritis, calcium tendinitis, post-infectious arthritis, and asymmetrical seronegative arthritis were also included as positive controls. Synthesis of several proteins, referred to by number as members of the Rheuma set, is shown to increase in the leukocyte preparations from patients with classical rheumatoid arthritis. Several of these proteins are specific to monocytes or granulocytes; others are of unknown cellular origin, but appear to be unique to rheumatoid arthritis. The Rheuma proteins appear to be indicators of disease activity, because their increased synthesis can be correlated with sedimentation rate and other clinical indices of rheumatoid disease activity.

  5. 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.

  6. 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.

  7. NMRKIN: Simulating line shapes from two-dimensional spectra of proteins upon ligand binding

    International Nuclear Information System (INIS)

    The analysis of the shape of signals in NMR spectra is a powerful tool to study exchange and reaction kinetics. Line shapes in two-dimensional spectra of proteins recorded for titrations with ligands provide information about binding rates observed at individual residues. Here we describe a fast method to simulate a series of line shapes derived from two-dimensional spectra of a protein during a ligand titration. This procedure, which takes the mutual effects of two dimensions into account, has been implemented in MATLAB as an add-on to NMRLab (Guenther et al., 2000). In addition, more complex kinetic models, including sequential and parallel reactions, were simulated to demonstrate common features of more complex line shapes which could be encountered in protein-ligand interactions. As an example of this method, we describe its application to line shapes obtained for a titration of the p85 N-SH2 domain of PI3-kinase with a peptide derived from polyomavirus middle T antigen (MT)

  8. 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.

  9. 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

  10. 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.)

  11. 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.

  12. Two-dimensional nitrosylated protein fingerprinting by using poly (methyl methacrylate) microchips.

    Science.gov (United States)

    Wang, Siyang; Njoroge, Samuel K; Battle, Katrina; Zhang, Cheng; Hollins, Bryant C; Soper, Steven A; Feng, June

    2012-09-21

    S-nitrosylation (also referred to as nitrosation), a reversible post translational modification (PTM) of cysteine, plays an important role in cellular functions and cell signalling pathways. Nitrosylated proteins are considered as biomarkers of aging and Alzheimer's disease (AD). Microfluidics has been widely used for development of novel tools for separation of protein mixtures. Here we demonstrate two-dimensional micro-electrophoresis (2D μ-CE) separations of nitrosylated proteins from the human colon epithelial adenocarcinoma cells (HT-29) and AD transgenic mice brain tissues. Sodium dodecyl sulphate micro-capillary gel electrophoresis (SDS μ-CGE) and microemulsion electrokinetic chromatography (MEEKC) were used for the first and second dimensional separations, respectively. The effective separation lengths for both dimensions were 10 mm, and electrokinetic injection was used with field strength at 200 V cm(-1). After 80 s separation in the first CGE dimension, fractions were successfully transferred to a second MEEKC dimension for a short 10 s separation. We first demonstrate this 2D μ-CE separation by resolving five standard proteins with molecular weight (MW) ranging from 20 to 64 kDa. We also present a high peak capacity 3D landscape image of nitrosylated proteins from HT-29 cells before and following menadione (MQ) treatment to induce oxidative stress. Additionally, to illustrate the potential of the 2D μ-CE separation method for rapid profiling of oxidative stress-induced biomarkers implicated in AD disease, the nitrosylated protein fingerprints from 11-month-old AD transgenic mice brain and their age matched controls were also generated. To our knowledge, this is the first report on 2D profiling of nitrosylated proteins in biological samples on a microchip. The characteristics of this biomarker profiling will potentially serve as the screening for early detection of AD. PMID:22766561

  13. 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. PMID:26263918

  14. 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 inf...

  15. Characterization of wheat gliadin proteins by combined two-dimensional gel electrophoresis and tandem mass spectrometry.

    Science.gov (United States)

    Mamone, Gianfranco; Addeo, Francesco; Chianese, Lina; Di Luccia, Aldo; De Martino, Alessandra; Nappo, Annunziata; Formisano, Annarita; De Vivo, Pasqualina; Ferranti, Pasquale

    2005-07-01

    A proteomics-based approach was used for characterizing wheat gliadins from an Italian common wheat (Triticum aestivum) cultivar. A two-dimensional gel electrophoresis (2-DE) map of roughly 40 spots was obtained by submitting the 70% alcohol-soluble crude protein extract to isoelectric focusing on immobilized pH gradient strips across two pH gradient ranges, i.e., 3-10 or pH 6-11, and to sodium dodecyl sulfate-polyacrylamide electrophoresis in the second dimension. The chymotryptic digest of each spot was characterized by matrix-assisted laser desorption/ionization-time of flight mass spectrometry and nano electrospray ionization-tandem mass spectrometry (MS/MS) analysis, providing a "peptide map" for each digest. The measured masses were subsequently sought in databases for sequences. For accurate identification of the parent protein, it was necessary to determine de novo sequences by MS/MS experiments on the peptides. By partial mass fingerprinting, we identified protein molecules such as alpha/beta-, gamma-, omega-gliadin, and high molecular weight-glutenin. The single spots along the 2-DE map were discriminated on the basis of their amino acid sequence traits. alpha-Gliadin, the most represented wheat protein in databases, was highly conserved as the relative N-terminal sequence of the components from the 2-DE map contained only a few silent amino acid substitutions. The other closely related gliadins were identified by sequencing internal peptide chains. The results gave insight into the complex nature of gliadin heterogeneity. This approach has provided us with sound reference data for differentiating gliadins amongst wheat varieties. PMID:15952231

  16. Electrophoretic analysis of proteins from Mycoplasma hominis strains detected by SDS-PAGE, two-dimensional gel electrophoresis and immunoblotting

    DEFF Research Database (Denmark)

    Andersen, H; Birkelund, Svend; Christiansen, Gunna; Freundt, A

    1987-01-01

    The proteins of 14 strains of Mycoplasma hominis were compared by SDS-PAGE in gradient gels, by two-dimensional (2D) gel electrophoresis of extracts of 35S-labelled cells and by immunoblot analysis of cell proteins. The strains examined included the M. hominis type strain PG21 and 13 others...

  17. 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...

  18. 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...

  19. 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

    2016-05-19

    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 ((C98)RhuA) are essentially defect-free and undergo substantial, but fully correlated, changes in molecular arrangement, yielding coherently dynamic 2D molecular lattices. (C98)RhuA lattices display a Poisson's ratio of -1-the lowest thermodynamically possible value for an isotropic material-making them auxetic. PMID:27135928

  20. 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.

  1. 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.

  2. Simplification and improvement of protein detection in two-dimensional electrophoresis gels with SERVA HPE™ lightning red.

    Science.gov (United States)

    Griebel, Anja; Obermaier, Christian; Westermeier, Reiner; Moche, Martin; Büttner, Knut

    2013-07-01

    A new fluorescent amino-reactive dye has been tested for both labelling proteins prior to electrophoretic separations and between the two steps of two-dimensional electrophoresis. A series of experiments showed, that the labelling of lysines with this dye is compatible with all standard additives used for sample preparation, including reducing substances and carrier ampholytes. Using this dye for pre-labelling considerably simplifies the electrophoresis and detection workflow and provides highly sensitive and quantitative visualisation of proteins. PMID:23786184

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

    OpenAIRE

    Zheng Xiaojuan; Zhang Xin; Zhou Jiyong; Wu Yongping; Jiang Xuetao; Shi Lixue; Yin Wei; Wang Junhua

    2009-01-01

    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 viru...

  4. 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

  5. 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.; Roepstorff, P.; Svensson, Birte

    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...... 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...

  6. 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

  7. 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-PAGE to......-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...

  8. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Goldman, D.; Giri, P.R.; O' Brien, J.O.

    1987-05-01

    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.

  10. Two-dimensional gel electrophoretic detection of protein carbonyls derivatized with biotin-hydrazide.

    Science.gov (United States)

    Wu, Jinzi; Luo, Xiaoting; Jing, Siqun; Yan, Liang-Jun

    2016-04-15

    Protein carbonyls are protein oxidation products that are often used to measure the magnitude of protein oxidative damage induced by reactive oxygen or reactive nitrogen species. Protein carbonyls have been found to be elevated during aging and in age-related diseases such as stroke, diabetes, and neurodegenerative diseases. In the present article, we provide detailed protocols for detection of mitochondrial protein carbonyls labeled with biotin-hydrazide followed by 2-dimensional isoelectric focusing (IEF)/SDS-PAGE and Western blotting probed with horse-radish peroxidase-conjugated streptavidin. The presented procedures can also be modified for detection of carbonylation of non-mitochondrial proteins. PMID:26590475

  11. 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

  12. Uniform and selective deuteration in two-dimensional NMR of proteins

    International Nuclear Information System (INIS)

    This paper reports on the practicality of isotopic labeling, particularly deuteration, that has received considerable impetus from advances in molecular biology, which have allowed ready production of NMR quantities of labeled proteins. Protein expression in Escherichia coli allows use of the considerable metabolic genetics known for the organism in shaping the biosynthetic process to meet the labeling demands of the NMR experiments. In addition to deuteration's common use in spectral assignment problems, it also offers considerable potential for enhancing the quality of the nuclear Overhauser effect (NOE) distance and dihedral angle constraints used for solution structural analysis of proteins. Recent reviews emphasize the sample preparation and spectral benefits of protein deuteration

  13. 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...

  14. 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.

  15. Identification of Glioblastoma Phosphotyrosine-Containing Proteins with Two-Dimensional Western Blotting and Tandem Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Tianyao Guo

    2015-01-01

    Full Text Available To investigate the presence of, and the potential biological roles of, protein tyrosine phosphorylation in the glioblastoma pathogenesis, two-dimensional gel electrophoresis- (2DGE- based Western blotting coupled with liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS analysis was used to detect and identify the phosphotyrosine immunoreaction-positive proteins in a glioblastoma tissue. MS/MS and Mascot analyses were used to determine the phosphotyrosine sites of each phosphopeptide. Protein domain and motif analysis and systems pathway analysis were used to determine the protein domains/motifs that contained phosphotyrosine residue and signal pathway networks to clarify the potential biological functions of protein tyrosine phosphorylation. A total of 24 phosphotyrosine-containing proteins were identified. Each phosphotyrosine-containing protein contained at least one tyrosine kinase phosphorylation motif and a certain structural and functional domains. Those phosphotyrosine-containing proteins were involved in the multiple signal pathway systems such as oxidative stress, stress response, and cell migration. Those data show 2DGE-based Western blotting, MS/MS, and bioinformatics are a set of effective approaches to detect and identify glioblastoma tyrosine-phosphorylated proteome and to effectively rationalize the biological roles of tyrosine phosphorylation in the glioblastoma biological systems. It provides novel insights regarding tyrosine phosphorylation and its potential role in the molecular mechanism of a glioblastoma.

  16. 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....

  17. 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 and...

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

    DEFF Research Database (Denmark)

    Torp, J.; Andersen, Brian

    1982-01-01

    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...

  19. Automated dual two-dimensional liquid chromatography approach for fast acquisition of three-dimensional data using combinations of zwitterionic polymethacrylate and silica-based monolithic columns.

    Science.gov (United States)

    Hájek, Tomáš; Jandera, Pavel; Staňková, Magda; Česla, Petr

    2016-05-13

    A monolithic sulfobetaine polymethacrylate micro-column BIGDMA-MEDSA designed in our laboratory, shows dual retention mechanism: In acetonitrile-rich mobile phase, hydrophilic interactions control the retention (HILIC system), whereas in more aqueous mobile phases the column shows essentially reversed-phase behavior with major role of hydrophobic interactions. The zwitterionic polymethacrylate micro-column can be used in the first dimension of two-dimensional LC in alternating reversed-phase (RP) and HILIC modes, coupled with an alkyl-bonded core-shell or silica-based monolithic column in the second dimension, for HILIC×RP and RP×RP comprehensive two-dimensional separations. During the HILIC×RP period, a gradient of decreasing acetonitrile gradient is used for separation in the first dimension, so that at the end of the gradient the polymeric monolithic micro-column is equilibrated with a highly aqueous mobile phase and is ready for repeated sample injection, this time for separation under reversed-phase gradient conditions with increasing concentration of acetonitrile in the first dimension. The fast repeating reversed-phase gradients on a short silica-monolithic or core-shell column in the second dimension can be optimized independently of the actual running first-dimension gradient program. As the alternating HILIC and RP separations on the first-dimension zwitterionic methacrylate column are based on complementary retention mechanisms, the instrumental setup essentially represents two coupled two-dimensional systems. It is first time that such an automated dual LCxLC approach is reported. The novel system allows obtaining three-dimensional data in a relatively short time and can be applied not only to multidimensional gradient separations of flavones and related polyphenolic compounds. PMID:27083260

  20. Isolation and Purification of Water Soluble Proteins from Ginger Root (Zingiber officinale) by Two Dimensional Liquid Chromatography

    Science.gov (United States)

    Sandovall, A.O.; Andrews, K.; Wahab, A.; Choudhary, M.I.; Ahmed, A.

    2014-01-01

    The RI-INBRE Centralized Core Facility was established in 2003 and participates annually in Undergraduate Summer Research Program. It provides students hands on research experience in key technologies in biomedical sciences. We present here the isolation and purification of water soluble proteins from ginger, a rhizome of the plant, Zingiber officinale. It is an important ingredient of species used in traditional South Asian cuisines. In Indian, Pakistani and Chinese folk medicine, ginger is used for gastro-intestinal disorders, nausea, vomiting, inflammatory diseases, muscle and joint pain. Limited studies have been reported on the bioactive proteins from ginger extract. The water soluble proteins were extracted from ginger root and successfully purified to homogeneity by using two-dimensional liquid chromatography (FPLC/RP-HPLC) approach. The ginger root was washed with distilled water; skin removed and then emulsified using an electric blender. Sample was stirred for four days at 4°C with and without protease inhibitor. Purification of a 42kDa protein was achieved by employing gel filtration, ion-exchange and reversed phase HPLC. The homogeneity of the protein was confirmed by SDS-PAGE gel electrophoresis and MALDI-TOF mass spectrometry. Future work will be conducted on the protein characterization using mass spectrometry and Edman protein sequencing. Supported by grant 5P20GM103430 from the National Institute of General Medical Sciences, NIH, USA.

  1. 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.; Jacobsen, Susanne; Søndergaard, Ib

    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...... electrophoresis. The gels were scanned, compared using ImageMaster(R) software and the data sets were analyzed by principal component analysis (PCA) using THE UNSCRAMBLER software. Afterwards MATLAB was used to make a cluster analysis of the varieties based on PCA. The analysis of the gels showed, that the...... separately. When the results were combined from the two years five varieties could be differentiated. The results from the PCA confirmed the finding of the unique spots and cluster analysis was made in order to illustrate the results. The combination of the results from 2-D electrophoresis and other grain...

  2. 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

  3. 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)

  4. 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...

  5. [Development of online conventional array-based two-dimensional liquid chromatographic system for proteins separation in human plasma].

    Science.gov (United States)

    Huang, Zhi; Hong, Guangfeng; Gao, Mingxia; Zhang, Xiangmin

    2014-04-01

    Human plasma is one of the proteins-containing samples most difficult to characterize on account of the wide dynamic concentration range of its intact proteins. Herein, we developed a high-throughput conventional array-based two-dimensional liquid chromatographic system for proteins separation in human plasma in online mode. In the system, a conventional strong-anion exchange chromatographic column was used as the first separation dimension and eight parallel conventional reversed-phase liquid chromatographic columns were integrated as the second separation dimension. The fractions from the first dimension were sequentially transferred into the corresponding reversed-phase liquid chromatographic precolumns for retention and enrichment using a 10-port electrically actuated multi-position valve. The second dimensional solvent flow was directly and identically split into 8 channels. The fractions were concurrently back-flushed from the precolumns into the 8 conventional RP columns and were separated simultaneously. An 8-channel fraction collector was refitted to collect the reversed-phase liquid chromatographic fractions for further investigation. Bicinchoninic acid (BCA) dyein solution was conveniently used for high-abundance protein location. Two separation dimensions were relatively independent parts, as well as each channel of the second dimensional array separation. Therefore, the new system could improve the separation throughput and total peak capacity. The system was successfully applied for the separation of human plasma intact proteins. The results indicated the established system is an effective method for removing high abundance proteins in plasma and in-depth research in plasma proteomics. PMID:25069321

  6. Two-dimensional parallel array technology as a new approach to automated combinatorial solid-phase organic synthesis

    Science.gov (United States)

    Brennan; Biddison; Frauendorf; Schwarcz; Keen; Ecker; Davis; Tinder; Swayze

    1998-01-01

    An automated, 96-well parallel array synthesizer for solid-phase organic synthesis has been designed and constructed. The instrument employs a unique reagent array delivery format, in which each reagent utilized has a dedicated plumbing system. An inert atmosphere is maintained during all phases of a synthesis, and temperature can be controlled via a thermal transfer plate which holds the injection molded reaction block. The reaction plate assembly slides in the X-axis direction, while eight nozzle blocks holding the reagent lines slide in the Y-axis direction, allowing for the extremely rapid delivery of any of 64 reagents to 96 wells. In addition, there are six banks of fixed nozzle blocks, which deliver the same reagent or solvent to eight wells at once, for a total of 72 possible reagents. The instrument is controlled by software which allows the straightforward programming of the synthesis of a larger number of compounds. This is accomplished by supplying a general synthetic procedure in the form of a command file, which calls upon certain reagents to be added to specific wells via lookup in a sequence file. The bottle position, flow rate, and concentration of each reagent is stored in a separate reagent table file. To demonstrate the utility of the parallel array synthesizer, a small combinatorial library of hydroxamic acids was prepared in high throughput mode for biological screening. Approximately 1300 compounds were prepared on a 10 μmole scale (3-5 mg) in a few weeks. The resulting crude compounds were generally >80% pure, and were utilized directly for high throughput screening in antibacterial assays. Several active wells were found, and the activity was verified by solution-phase synthesis of analytically pure material, indicating that the system described herein is an efficient means for the parallel synthesis of compounds for lead discovery. Copyright 1998 John Wiley & Sons, Inc. PMID:10099494

  7. Two-Dimensional Differential Gel Electrophoresis to Identify Protein Biomarkers in Amniotic Fluid of Edwards Syndrome (Trisomy 18 Pregnancies.

    Directory of Open Access Journals (Sweden)

    Te-Yao Hsu

    Full Text Available Edwards syndrome (ES is a severe chromosomal abnormality with a prevalence of about 0.8 in 10,000 infants born alive. The aims of this study were to identify candidate proteins associated with ES pregnancies from amniotic fluid supernatant (AFS using proteomics, and to explore the role of biological networks in the pathophysiology of ES.AFS from six second trimester pregnancies with ES fetuses and six normal cases were included in this study. Fluorescence-based two-dimensional difference gel electrophoresis (2D-DIGE and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF/MS were used for comparative proteomic analysis. The identified proteins were further validated by Western blotting and the role of biological networks was analyzed.Twelve protein spots were differentially expressed by more than 1.5-fold in the AFS of the ES pregnancies. MALDI-TOF/MS identified one up-regulated protein: apolipoprotein A1 (ApoA1, and four under-regulated proteins: vitamin D binding protein (VDBP, alpha-1-antitrypsin (A1AT, insulin-like growth factor-binding protein 1 (IGFBP-1, and transthyretin (TTR. Western blot and densitometric analysis of ApoA1, A1AT, IGFBP-1, and TTR confirmed the alteration of these proteins in the amniotic fluid samples. Biological network analysis revealed that the proteins of the ES AFS were involved mainly in lipid and hormone metabolism, immune response, and cardiovascular disease.These five proteins may be involved in the pathogenesis of ES. Further studies are needed to explore.

  8. Heuristic-based tabu search algorithm for folding two-dimensional AB off-lattice model proteins.

    Science.gov (United States)

    Liu, Jingfa; Sun, Yuanyuan; Li, Gang; Song, Beibei; Huang, Weibo

    2013-12-01

    The protein structure prediction problem is a classical NP hard problem in bioinformatics. The lack of an effective global optimization method is the key obstacle in solving this problem. As one of the global optimization algorithms, tabu search (TS) algorithm has been successfully applied in many optimization problems. We define the new neighborhood conformation, tabu object and acceptance criteria of current conformation based on the original TS algorithm and put forward an improved TS algorithm. By integrating the heuristic initialization mechanism, the heuristic conformation updating mechanism, and the gradient method into the improved TS algorithm, a heuristic-based tabu search (HTS) algorithm is presented for predicting the two-dimensional (2D) protein folding structure in AB off-lattice model which consists of hydrophobic (A) and hydrophilic (B) monomers. The tabu search minimization leads to the basins of local minima, near which a local search mechanism is then proposed to further search for lower-energy conformations. To test the performance of the proposed algorithm, experiments are performed on four Fibonacci sequences and two real protein sequences. The experimental results show that the proposed algorithm has found the lowest-energy conformations so far for three shorter Fibonacci sequences and renewed the results for the longest one, as well as two real protein sequences, demonstrating that the HTS algorithm is quite promising in finding the ground states for AB off-lattice model proteins. PMID:24077543

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Ultra-fast two-dimensional microchip electrophoresis using SDS micro-CGE and microemulsion electrokinetic chromatography for protein separations.

    Science.gov (United States)

    Osiri, John K; Shadpour, Hamed; Soper, Steven A

    2010-09-01

    A poly(methyl methacrylate) microfluidic chip was used to perform a two-dimensional (2-D) separation of a complex protein mixture in short development times. The separation was performed by combining sodium dodecyl sulfate micro-capillary gel electrophoresis (SDS micro-CGE) with microemulsion electrokinetic chromatography (micro-MEEKC), which were used for the first and second dimensions, respectively. Fluorescently labeled Escherichia coli cytosolic proteins were profiled by this 2-D approach with the results compared to a similar 2-D separation using SDS micro-CGE x micro-MEKC (micelle electrokinetic chromatography). The relatively short column lengths (effective length = 10 mm) for both dimensions were used to achieve separations requiring only 220 s of development time. High spot production rates (131 +/- 11 spots min(-1)) and reasonable peak capacities (481 +/- 18) were generated despite the fact that short columns were used. In addition, the use of mu-MEEKC in the second dimension was found to produce higher peak capacities compared to micro-MEKC (481 +/- 18 for micro-MEEKC and 332 +/- 17 for micro-MEKC) due to the higher plate numbers associated with micro-MEEKC. PMID:20614109

  14. 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 ...

  15. 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

  16. 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

  17. Major proteins in normal human lymphocyte subpopulations separated by fluorescence-activated cell sorting and analyzed by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Madsen, P S; Hokland, M; Ellegaard, J; Hokland, P; Ratz, G P; Celis, A

    1988-01-01

    We have compared the overall patterns of protein synthesis of normal human lymphocyte subpopulations taken from five volunteers using high resolution two-dimensional gel electrophoresis. The lymphocytes were isolated using density gradient centrifugation, labeled with subtype-specific MoAbs, and ...

  18. Comparison of protein patterns after two-dimensional gel electrophoresis from leaves of in vitro cultures and seedlings of Rubus chamaemorus L.

    Directory of Open Access Journals (Sweden)

    Barbara Thiem

    2014-02-01

    Full Text Available Proteins from leaves of Rubus chamaemorus propagated in vitro were subjected to miniaturized 2-D electrophoresis. The 2-DE patterns of proteins showed qualitative differences between plants propagated in vitro and control seedlings. More proteins of a high molecular weight were observed in leaves of plants from in vitro culture. A two-dimensional map of proteins from leaves provides detailed data concerning both polymorphism and protein patterns of this species. This makes it possible to start constructing a protein map of R. chamaemorus. The reasons for qualitative differences are discussed.

  19. Sequencing of proteins from two-dimensional gels by using in situ digestion and transfer of peptides to polyvinylidene difluoride membranes: application to proteins associated with sensitization in Aplysia.

    OpenAIRE

    Kennedy, T. E.; Gawinowicz, M A; Barzilai, A; Kandel, E R; Sweatt, J D

    1988-01-01

    We have developed a method for obtaining partial internal amino acid sequence data from proteins isolated directly from preparative two-dimensional polyacrylamide gels. Proteins from a crude cell homogenate are separated using preparative two-dimensional polyacrylamide gel electrophoresis. Then, the gel is stained with Coomassie blue and the protein spots of interest are cut out. The in situ protein is digested with Staphylococcus aureus V8 protease in a second polyacrylamide gel and the pept...

  20. 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...

  1. Approaches to automated protein crystal harvesting

    International Nuclear Information System (INIS)

    Approaches to automated and robot-assisted harvesting of protein crystals are critically reviewed. While no true turn-key solutions for automation of protein crystal harvesting are currently available, systems incorporating advanced robotics and micro-electromechanical systems represent exciting developments with the potential to revolutionize the way in which protein crystals are harvested

  2. Two-dimensional analysis of human lymphocyte proteins. III. Preliminary report on a marker for the early detection and diagnosis of infectious mononucleosis

    Energy Technology Data Exchange (ETDEWEB)

    Willard, K.E.

    1982-04-01

    Two-dimensional gel electrophoretic patterns of human peripheral blood leukocytes from 12 patients with infectious mononucleosis were prepared by use of the ISO-DALT system. Before the two-dimensional separation, the leukocytes were purified by Ficoll-Paque gradient centrifugation and labeled overnight with (/sup 35/S) methionine. Quantitative increases in two proteins were detected in the patterns of infected leukocytes from the patients as compared with controls. Fluorescence-activated cell sorting of leukocytes from normal human peripheral blood before subsequent two-dimensional gel analysis revealed that the dramatic increase in one of these proteins (Inmono:2) could be due to shifts in the population ratios of lymphocytes, monocytes, and granulocytes. In contrast, the appearance in the infected leukocytes of a second protein, Inmono:1, could not be accounted for by cell-population shifts. Increased amounts of these two proteins have been found in every patient studied who had clinically detectable infectious mononucleosis. In addition, a patient who displayed symptoms of infectious mononucleosis but who did not have a positive result in the MONOSPOT test (Ortho) until three weeks after our analysis also demonstrated increased relative amounts of these proteins in his leukocyte pattern.

  3. Two-dimensional analysis of human lymphocyte proteins. III. Preliminary report on a marker for the early detection and diagnosis of infectious mononucleosis

    International Nuclear Information System (INIS)

    Two-dimensional gel electrophoretic patterns of human peripheral blood leukocytes from 12 patients with infectious mononucleosis were prepared by use of the ISO-DALT system. Before the two-dimensional separation, the leukocytes were purified by Ficoll-Paque gradient centrifugation and labeled overnight with [35S] methionine. Quantitative increases in two proteins were detected in the patterns of infected leukocytes from the patients as compared with controls. Fluorescence-activated cell sorting of leukocytes from normal human peripheral blood before subsequent two-dimensional gel analysis revealed that the dramatic increase in one of these proteins (Inmono:2) could be due to shifts in the population ratios of lymphocytes, monocytes, and granulocytes. In contrast, the appearance in the infected leukocytes of a second protein, Inmono:1, could not be accounted for by cell-population shifts. Increased amounts of these two proteins have been found in every patient studied who had clinically detectable infectious mononucleosis. In addition, a patient who displayed symptoms of infectious mononucleosis but who did not have a positive result in the MONOSPOT test (Ortho) until three weeks after our analysis also demonstrated increased relative amounts of these proteins in his leukocyte pattern

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. New apparatus for direct counting of β particles from two-dimensional gels and an application to changes in protein synthesis due to cell density

    International Nuclear Information System (INIS)

    A new method is described for scanning two-dimensional gels by the direct counting of β particles instead of autoradiography. The methodology is described; results are compared with autoradiographic results; and data are presented demonstrating changed patterns of protein synthesis accompanying changes in cell density. The method is rapid and permits identification of differences in protein abundance of approximately 10% for a substantial fraction of the more prominent proteins. A modulation effect of more than 5 standard deviations, accompanying contact inhibition of cell growth, is shown to occur for an appreciable number of these proteins. The method promises to be applicable to a variety of biochemical and genetic experiments designed to delineate changes in protein synthesis accompanying changes in genome, molecular environment, history, and state of differentiation of the cell populations studied. 13 refs., 8 figs., 4 tabs

  9. The human keratinocyte two-dimensional gel protein database (update 1995): mapping components of signal transduction pathways

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Gromov, P;

    1995-01-01

    identified (protein name, organelle components, etc.) using a procedure 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, (v...

  10. Effects of interferon gamma on Chlamydia trachomatis serovar A and L2 protein expression investigated by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A; Christiansen, Gunna; Birkelund, Svend

    1999-01-01

    Chlamydia trachomatis is an obligate intracellular bacterium causing human ocular and genital disease. The lymphokine interferon gamma (IFN-gamma) is an important immune effector exerting antimicrobial effects towards several intracellular parasites, the chlamydia included. IFN-gamma has been......]methionine and two-dimensional gel electrophoresis with immobilized pH gradients in order to investigate changes in the protein expression of C. trachomatis serovar A and L2 caused by treatment with IFN-gamma. In contrast to what was observed in C. trachomatis L2, our results showed that, in C. trachomatis A...

  11. 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.

  12. General model for lipid-mediated two-dimensional array formation of membrane proteins: Application to bacteriorhodopsin

    DEFF Research Database (Denmark)

    Sabra, Mads Christian; Uitdehaag, J.C.M.; Watts, A

    1998-01-01

    Based on experimental evidence for 2D array formation of bacteriorhodopsin, we propose a general model for lipid-mediated 2D array formation of membrane proteins in lipid bilayers. The model includes two different lipid Species; "annular" lipids and "neutral" lipids, and one protein species. The ...

  13. 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.

  14. Evaluation of protein extraction methods suitable for two-dimensional gel electrophoresis of the soybean cyst nematode (Heterodera glycines)

    Science.gov (United States)

    Soybean cyst nematode (Heterodera glycines, SCN) is the most destructive pathogen of soybean (Glycine max (L.) Merr.) worldwide. In this study, three different protein extraction methods including phenol/ammonium acetate (phenol method), thiourea/urea solublization (lysis method) and trichloroaceti...

  15. Monitoring development of chemoresistance to cyclin-dependent kinases inhibition by two-dimensional liquid phase protein fractionation

    Czech Academy of Sciences Publication Activity Database

    Skalníková, Helena; Halada, Petr; Hajdúch, M.; Vydra, D.; Dzubak, P.; Dziechciarková, M.; Strnad, M.; Kovářová, Hana

    Oxford: Worcester College, 2006, s. 1. [Third Annual European Symposium on Protein Fractionation and Biomarker Discovery . Oxford (GB), 12.09.2006-13.09.2006] R&D Projects: GA ČR GA301/05/0418 Institutional research plan: CEZ:AV0Z50450515; CEZ:AV0Z50200510 Keywords : cyclin-dependent kinases Subject RIV: EB - Genetics ; Molecular Biology

  16. 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...

  17. High-resolution two-dimensional polyacrylamide gel electrophoresis reveals a glucose-response protein of 65 kDa in pancreatic islet cells

    International Nuclear Information System (INIS)

    High-resolution two-dimensional PAGE was used to search for glucose-response proteins in isolated pancreatic islets that were labeled with [35S]methionine at ambient glucose concentrations of 0-18 mM. A 65-kDa protein, isoelectric focusing point of approximately 6.6-7.0, was discovered that showed at least a 20-fold stimulation of radiolabeling when glucose in the labeling medium was increased from 3 to 18 mM, in contrast to a 2.5-fold enhancement of label incorporation into total islet proteins. This 65-kDa protein is evident after 30 min of labeling with 18 mM glucose and is preferentially synthesized compared to its nearest neighbors after both 30 and 60 min of labeling. Glucose induction of the 65-kDa protein was virtually blocked by D-mannoheptulose. Glucose induction of this 65-kDa protein is in practically all aspects comparable to glucose induction of insulin and glucokinase in pancreatic beta cells. A working hypothesis is developed proposing that glucose-response proteins or glucospondins are pivotal constituents of pancreatic islet cells and that their discovery and exploration promise new insights into normal and pathological islet cell function

  18. 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.

  19. Increased Depth and Breadth of Plasma Protein Quantitation via Two-Dimensional Liquid Chromatography/Multiple Reaction Monitoring-Mass Spectrometry with Labeled Peptide Standards.

    Science.gov (United States)

    Percy, Andrew J; Yang, Juncong; Chambers, Andrew G; Borchers, Christoph H

    2016-01-01

    Absolute quantitative strategies are emerging as a powerful and preferable means of deriving concentrations in biological samples for systems biology applications. Method development is driven by the need to establish new-and validate current-protein biomarkers of high-to-low abundance for clinical utility. In this chapter, we describe a methodology involving two-dimensional (2D) reversed-phase liquid chromatography (RPLC), operated under alkaline and acidic pH conditions, combined with multiple reaction monitoring (MRM)-mass spectrometry (MS) (also called selected reaction monitoring (SRM)-MS) and a complex mixture of stable isotope-labeled standard (SIS) peptides, to quantify a broad and diverse panel of 253 proteins in human blood plasma. The quantitation range spans 8 orders of magnitude-from 15 mg/mL (for vitamin D-binding protein) to 450 pg/mL (for protein S100-B)-and includes 31 low-abundance proteins (defined as being application of our recently developed software tool-Qualis-SIS-for protein quantitation (via regression analysis of standard curves) and quality assessment of the resulting data. Overall, this chapter provides the blueprint for the replication of this quantitative proteomic method by proteomic scientists of all skill levels. PMID:26867735

  20. 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

  1. 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.

  2. 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.

  3. 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

  4. Characterization of pH titration shifts for all the nonlabile proton resonances in a protein by two-dimensional NMR: The case of mouse epidermal growth factor

    International Nuclear Information System (INIS)

    The pH titration shifts for all the nonlabile proton resonances in a 53-residue protein (mouse epidermal growth factor) were measured in the p2H range 1.5-9 with two-dimensional (2D) 1H NMR. The 2D NMR pH titration experiment made it possible to determine the pK values for all the ionizable group which were titrated in the pH range 1.5-9 in the protein. The pK values of the nine ionizable groups (α-amino group, four Asp, two Glu, one His, and α-carboxyl group) were found to be near their normal values. The 2D titration experiment also provided a detailed description of the pH-dependent behavior of the proton chemical shifts and enabled us to characterize the pH-dependent changes of protein conformation. Analysis of the pH-dependent shifts of ca. 200 proton resonances offered evidence of conformational changes in slightly basic pH solution: The deprotonation of the N-terminal α-amino group induced a widespread conformational change over the β-sheet structure in the protein, while the effects of deprotonation of the His22 imidazole group were relatively localized. The authors found that the 2D NMR pH titration experiment is a powerful tool for investigating the structural and dynamic properties of proteins

  5. 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.

  6. 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)

  7. Analysis of Secreted Proteins from Undifilum cinereum by Two Dimensional Gel Electrophoresis and Liquid Chromatography-Mass Spectrometry/Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Deanna Baucom

    2012-01-01

    Full Text Available The locoweed plant (Astragalus is a widely distributed toxic plant in many rangeland regions around the world. It is well known that locoweed plants can produce the alkaloid swainsonine which inhibits α-mannosidases and causing neurological poisonings problems through the consumption of locoweed. Locoweed poisoned grazing animal’s exhibit symptoms of locoism. Locoism was caused by locoweed is one of the most destructive disease of rangeland. Recent studies shown that swainsonine was produced by endophytic Undifilum cinereum which was isolated from Astragalus locoweed (Astragalus mollissimus and Astragalus lentiginosus sp. and responsible for locoism in grazing animals. The toxicosis effect of U. oxytropis fungi on rats is indistinguishable from locoweed toxicosis on rats. The mechanisms of swainsonine underlying U. cinereum and locoweed are poorly understood. To gain a better understanding of the swainsonine biosynthesis in U. cinereum and to facilitate management of locoweed poisoning problems, two-dimensional gel electrophoresis (2-DE was performed. The 2-DE is a promising tool to study the protein expression profiling and metabolic pathway. To researchers knowledge the present study was the first proteomic reference map using immobilized pH gradients of U. cinereum. To identify proteins in U. cinereum, proteins extracted from mycelial were separated by 2-DE and IEF, digestion and Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS with an LTQ ion trap mass spectrometer (Thermo Scientific, Waltham, MA. Samples were analyzed by LC-MS/MS and identified using MASCOT MS/MS search in protein databases.

  8. 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

  9. 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; Holm, A; Christiansen, Gunna; Birkelund, Svend

    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 imp...... and future data accessible for interlaboratory comparison, we constructed a 2-D PAGE database on the World Wide Web....... mapping of [35S]methionine/cysteine-labeled HeLa cell proteins with the 2-D PAGE (IPG)-system, using matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) and N-terminal sequencing for protein identification. To date 21 proteins have been identified and mapped. In order to make these...

  10. 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

  11. Automated Alphabet Reduction for Protein Datasets

    Directory of Open Access Journals (Sweden)

    Valencia Alfonso

    2009-01-01

    Full Text Available Abstract Background We investigate automated and generic alphabet reduction techniques for protein structure prediction datasets. Reducing alphabet cardinality without losing key biochemical information opens the door to potentially faster machine learning, data mining and optimization applications in structural bioinformatics. Furthermore, reduced but informative alphabets often result in, e.g., more compact and human-friendly classification/clustering rules. In this paper we propose a robust and sophisticated alphabet reduction protocol based on mutual information and state-of-the-art optimization techniques. Results We applied this protocol to the prediction of two protein structural features: contact number and relative solvent accessibility. For both features we generated alphabets of two, three, four and five letters. The five-letter alphabets gave prediction accuracies statistically similar to that obtained using the full amino acid alphabet. Moreover, the automatically designed alphabets were compared against other reduced alphabets taken from the literature or human-designed, outperforming them. The differences between our alphabets and the alphabets taken from the literature were quantitatively analyzed. All the above process had been performed using a primary sequence representation of proteins. As a final experiment, we extrapolated the obtained five-letter alphabet to reduce a, much richer, protein representation based on evolutionary information for the prediction of the same two features. Again, the performance gap between the full representation and the reduced representation was small, showing that the results of our automated alphabet reduction protocol, even if they were obtained using a simple representation, are also able to capture the crucial information needed for state-of-the-art protein representations. Conclusion Our automated alphabet reduction protocol generates competent reduced alphabets tailored specifically for a

  12. 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

  13. 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; Rogowska-Wrzesinska, Adelina

    2011-01-01

    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...... metal-catalyzed oxidation, 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...

  14. 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

    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...... 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 of the...

  15. Two-dimensional hydrogen atom

    International Nuclear Information System (INIS)

    In the region of continuous spectrum the expansions of the parabolic basis of a two-dimensional hydrogen atom on the polar basis and the inverse expansion have been found. The connection between these expansions and the corresponding expansions in the discrete spectrum is also analysed. The group-theoretical meaning of the two-dimensional Coulomb scattering phase is established

  16. Two-Dimensional NMR Lineshape Analysis.

    Science.gov (United States)

    Waudby, Christopher A; Ramos, Andres; Cabrita, Lisa D; Christodoulou, John

    2016-01-01

    NMR titration experiments are a rich source of structural, mechanistic, thermodynamic and kinetic information on biomolecular interactions, which can be extracted through the quantitative analysis of resonance lineshapes. However, applications of such analyses are frequently limited by peak overlap inherent to complex biomolecular systems. Moreover, systematic errors may arise due to the analysis of two-dimensional data using theoretical frameworks developed for one-dimensional experiments. Here we introduce a more accurate and convenient method for the analysis of such data, based on the direct quantum mechanical simulation and fitting of entire two-dimensional experiments, which we implement in a new software tool, TITAN (TITration ANalysis). We expect the approach, which we demonstrate for a variety of protein-protein and protein-ligand interactions, to be particularly useful in providing information on multi-step or multi-component interactions. PMID:27109776

  17. Detection of phosphorylated forms of Moloney murine leukemia virus major capsid protein p30 by immunoprecipitation and two-dimensional gel electrophoresis.

    OpenAIRE

    Ikuta, K.; Luftig, R B

    1988-01-01

    We detected phosphorylation of the major Moloney murine leukemia virus (M-MuLV) capsid polypeptide, p30, by using 32Pi-labeled virions. This was observed both on two-dimensional polyacrylamide gels directly or on one-dimensional gels of viral lysates that had been immunoprecipitated with monospecific goat anti-p30 serum. The phosphorylation event had been difficult to detect because pp12 the major virion phosphoprotein incorporates almost all of the 32P label added to infected cells (Y. Yoshi...

  18. Two-dimensional NMR spectrometry

    International Nuclear Information System (INIS)

    This article is the second in a two-part series. In part one (ANALYTICAL CHEMISTRY, May 15) the authors discussed one-dimensional nuclear magnetic resonance (NMR) spectra and some relatively advanced nuclear spin gymnastics experiments that provide a capability for selective sensitivity enhancements. In this article and overview and some applications of two-dimensional NMR experiments are presented. These powerful experiments are important complements to the one-dimensional experiments. As in the more sophisticated one-dimensional experiments, the two-dimensional experiments involve three distinct time periods: a preparation period, t0; an evolution period, t1; and a detection period, t2

  19. Two-dimensional analysis of metabolically and cell surface radiolabeled proteins of some human lymphoid and myeloid leukemia cell lines. II

    International Nuclear Information System (INIS)

    Cell surface glycoproteins, radiolabelled by the sodium metaperiodate/tritiated borohydride technique, and cell phosphoproteins, metabolically radiolabelled with 32P-orthophosphate were analyzed by two-dimensional electrophoretic analysis in some myeloid and lymphoid leukemia cell lines. Some markedly expressed major glycoproteins were predominant in some of the cell lines (such as 95k and 100k glycoproteins with marked charge heterogeneity in non-T, non-B acute lymphoblastic leukemia cell lines NALM 6 and NALM 16), but markedly quantitatively reduced in other examined cell lines, such as lymphoblastoid cell line UHKT 34/2. 32P-orthophosphate radiolabelled phosphoprotein two-dimensional patterns of the examined lymphoid leukemia cell lines were essentially similar, with some minor differences, in examined lymphoid and myeloid leukemia cell lines, such as marked expression of a series of large phosphoproteins in the molecular weight range 80-100k in lymphoid cell lines and almost complete absence of these phosphoproteins on the examined myeloid leukemia cell lines. Another configuration of acidic phosphoproteins (30-35k) exhibited individual cell line variability and differences between both individual myeloid leukemia cell lines and between the lymphoid and myeloid cell lines examined. (author) 2 figs., 15 refs

  20. 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; Magi, B; Marzocchi, B; Comanducci, M; Christiansen, Gunna; Birkelund, Svend; Cevenini, R; Vetrou, E; Ratti, G; Pallini, V

    1996-01-01

    (OMP2), the DnaK-like, GroEL-like, and macrophage infectivity potentiator (MIP)-like proteins, the plasmid-encoded pgp3 protein, two ribosomal proteins (S1 and L7/L12), and the protein-elongation factor EF-Tu. Other proteins, for which gene assignment was not possible, have been identified by three...

  1. Detection of phosphorylated forms of moloney murine leukemia virus major capsid protein p30 by immunoprecipitation and two-dimensional gel electrophoresis

    International Nuclear Information System (INIS)

    The authors detected phosphorylation of the major Moloney murine leukemia virus (M-MuLV) capsid polypeptide, p30, by using 32P/sub i/-labeled virions. This was observed both on two-dimensional polyacrylamide gels directly or on one-dimensional gels of viral lysates that had been immunoprecipitated with monospecific goat anti-p30 serum. The phosphorylation event had been difficult to detect because pp12 the major virion phosphoprotein incorporates almost all of the 32P label added to infected cells. When immunoprecipitates from M-MuLV lysates labeled with 32P/sub i/ were compared with those labeled with [35S]methionine, it was calculated that the degree of phosphorylation at the p30 domain of Pr65/sup gag/ was only 0.22 to 0.54% relative to phosphorylation at the p12 domain. Two-dimensional gel electrophoresis of the 32P-labeled p30 immunoprecipitates showed that there were three phosphorylated p30 forms with isoelectric points (pIs) of 5.7, 5.8, and 6.0. These forms were generally more acidic than the [35S] methionine-labeled p30 forms, which had pIs of 6.0, 6.1, 6.3 (the major constituent with > 80% of the label), and 6.6. The predominant phosphoamino acid of the major phosphorylated p30 form (pI 5.8) was phosphoserine. Further, tryptic peptide analysis of this p30 form showed that only one peptide was predominantly phosphorylated. Based on a comparison of specific labeling of p30 tryptic peptides with [14C]sesrine, [35S]methionine, and 32P/sub i/, we tentatively assigned the phosphorylation site to a 2.4-kilodalton NH2-terminal peptide containing triple tandem serines spanning the region from amino acids 4 to 24

  2. Detection of phosphorylated forms of moloney murine leukemia virus major capsid protein p30 by immunoprecipitation and two-dimensional gel electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Ikuta, K.; Luftig, R.B.

    1988-01-01

    The authors detected phosphorylation of the major Moloney murine leukemia virus (M-MuLV) capsid polypeptide, p30, by using /sup 32/P/sub i/-labeled virions. This was observed both on two-dimensional polyacrylamide gels directly or on one-dimensional gels of viral lysates that had been immunoprecipitated with monospecific goat anti-p30 serum. The phosphorylation event had been difficult to detect because pp12 the major virion phosphoprotein incorporates almost all of the /sup 32/P label added to infected cells. When immunoprecipitates from M-MuLV lysates labeled with /sup 32/P/sub i/ were compared with those labeled with (/sup 35/S)methionine, it was calculated that the degree of phosphorylation at the p30 domain of Pr65/sup gag/ was only 0.22 to 0.54% relative to phosphorylation at the p12 domain. Two-dimensional gel electrophoresis of the /sup 32/P-labeled p30 immunoprecipitates showed that there were three phosphorylated p30 forms with isoelectric points (pIs) of 5.7, 5.8, and 6.0. These forms were generally more acidic than the (/sup 35/S) methionine-labeled p30 forms, which had pIs of 6.0, 6.1, 6.3 (the major constituent with > 80% of the label), and 6.6. The predominant phosphoamino acid of the major phosphorylated p30 form (pI 5.8) was phosphoserine. Further, tryptic peptide analysis of this p30 form showed that only one peptide was predominantly phosphorylated. Based on a comparison of specific labeling of p30 tryptic peptides with (/sup 14/C)sesrine, (/sup 35/S)methionine, and /sup 32/P/sub i/, we tentatively assigned the phosphorylation site to a 2.4-kilodalton NH/sub 2/-terminal peptide containing triple tandem serines spanning the region from amino acids 4 to 24.

  3. 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 ...

  4. 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

    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...

  5. 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.

  6. Two-dimensional critical phenomena

    International Nuclear Information System (INIS)

    Two dimensional critical systems are studied using transformation to free fields and conformal invariance methods. The relations between the two approaches are also studied. The analytical results obtained generally depend on universality hypotheses or on renormalization group trajectories which are not established rigorously, so numerical verifications, mainly using the transfer matrix approach, are presented. The exact determination of critical exponents; the partition functions of critical models on toruses; and results as the critical point is approached are discussed

  7. 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

  8. 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.

  9. Two dimensional superfluidity and melting

    International Nuclear Information System (INIS)

    The author reviews the equilibrium theory of superfluidity and XY magnetism, due in large part to the seminal work of Kosterlitz and Thouless. A dynamic generalization of this theory, with application to third sound in helium films is discussed. The statistical mechanics of two-dimensional melting on both smooth and periodic substrates, is discussed. The dynamic version of the theory is sketched. A theory of melting dynamics is particularly important in interpreting of the experiments on melting and crystallization described earlier. Finally the theory as it applies to anisotropic media including layered materials like smectics, cholesterics, and Rayleigh-Benard convection cells, is discussed. (Auth.)

  10. 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 ...

  11. 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.

  12. 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

  13. 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...

  14. Post-polymerization photografting on methacrylate-based monoliths for separation of intact proteins and protein digests with comprehensive two-dimensional liquid chromatography hyphenated with high-resolution mass spectrometry.

    Science.gov (United States)

    Vonk, Rudy J; Wouters, Sam; Barcaru, Andrei; Vivó-Truyols, Gabriel; Eeltink, Sebastiaan; de Koning, Leo J; Schoenmakers, Peter J

    2015-05-01

    Post-polymerization photografting is a versatile tool to alter the surface chemistry of organic-based monoliths so as to obtain desired stationary phase properties. In this study, 2-acrylamido-2-methyl-1-propanesulfonic acid was grafted to a hydrophobic poly(butyl methacrylate-co-ethylene glycol dimethacrylate) monolith to create a strong cation exchange stationary phase. Both single-step and two-step photografting were addressed, and the effects of grafting conditions were assessed. An experimental design has been applied in an attempt to optimize three of the key parameters of the two-step photografting chemistry, i.e. the grafting time of the initiator, the monomer concentration and the monomer irradiation time. The photografted columns were implemented in a comprehensive two-dimensional column liquid chromatography ( (t) LC ×  (t) LC) workflow and applied for the separation of intact proteins and peptides. A baseline separation of 11 intact proteins was obtained within 20 min by implementing a gradient across a limited RP composition window in the second dimension. (t) LC ×  (t) LC with UV detection was used for the separation of cytochrome c digest, bovine serum insulin digest and a digest of a complex protein mixture. A semi-quantitative estimation of the occupation of separation space, the orthogonality, of the (t) LC ×  (t) LC system yielded 75%. The (t) LC ×  (t) LC setup was hyphenated to a high-resolution Fourier transform ion cyclotron resonance mass spectrometer instrument to identify the bovine serum insulin tryptic peptides and to demonstrate the compatibility with MS analysis. PMID:25801383

  15. 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

    ) vaccinia virus expression of full length cDNAs. These are listed both in alphabetical order and with increasing SSP number, together with their M(r), pI, cellular localization and credit to the investigator(s) that aided in the identification. Furthermore, we list 239 microsequenced proteins recorded in...

  16. 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)...

  17. 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

  18. 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.

  19. Identification of Proteins Modulated in the Date Palm Stem Infested with Red Palm Weevil (Rhynchophorus ferrugineus Oliv. Using Two Dimensional Differential Gel Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Khawaja Ghulam Rasool

    2015-08-01

    Full Text Available A state of the art proteomic methodology using Matrix Assisted Laser Desorption/Ionization-Time of Flight (MALDI TOF has been employed to characterize peptides modulated in the date palm stem subsequent to infestation with red palm weevil (RPW. Our analyses revealed 32 differentially expressed peptides associated with RPW infestation in date palm stem. To identify RPW infestation associated peptides (I, artificially wounded plants (W were used as additional control beside uninfested plants, a conventional control (C. A constant unique pattern of differential expression in infested (I, wounded (W stem samples compared to control (C was observed. The upregulated proteins showed relative fold intensity in order of I > W and downregulated spots trend as W > I, a quite interesting pattern. This study also reveals that artificially wounding of date palm stem affects almost the same proteins as infestation; however, relative intensity is quite lower than in infested samples both in up and downregulated spots. All 32 differentially expressed spots were subjected to MALDI-TOF analysis for their identification and we were able to match 21 proteins in the already existing databases. Relatively significant modulated expression pattern of a number of peptides in infested plants predicts the possibility of developing a quick and reliable molecular methodology for detecting plants infested with date palm.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Critical two dimensional statistical systems

    International Nuclear Information System (INIS)

    A systematic review of the recent achievements in conformal invariant two-dimensional field theories would already require a volume size. In this paper, the authors discuss some finite size effects at criticality because they reveal important features, as noted by Cardy. The computation of the partition function in a finite geometry -a torus enables one to understand the spectrum of the theory. The later is compendium of the critical dimensions of the various operators. The simple examples, namely bosonic or fermionic free fields (respective the Gaussian and the Ising model) will serve as a pedagog introduction, although the corresponding computations are not without some subtleties. The authors then proceed to considerations related to module invariance. The foe forthcoming analysis is of course based on the fundamental work by Belavin, Polyakov and Zamolodchikov (quoted as BPZ) and its subsequent development by a number of authors including Dotsenko Fateev, Friedan Qui and Shenker, Cardy and many others. it also relied on the mathematics of infinite Lie algebras (also known as current algebras) elaborated by Kac, Feigin and Fuchs, Rocha-Caridi... The whole subject is to a large extent similar to the one of string theories

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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)

  10. Two-dimensional function photonic crystals

    CERN Document Server

    Wu, Xiang-Yao; Liu, Xiao-Jing; Liang, Yu

    2016-01-01

    In this paper, we have firstly proposed two-dimensional function photonic crystals, which the dielectric constants of medium columns are the functions of space coordinates $\\vec{r}$, it is different from the two-dimensional conventional photonic crystals constituting by the medium columns of dielectric constants are constants. We find the band gaps of two-dimensional function photonic crystals are different from the two-dimensional conventional photonic crystals, and when the functions form of dielectric constants are different, the band gaps structure should be changed, which can be designed into the appropriate band gaps structures by the two-dimensional function photonic crystals.

  11. Automated protein-DNA interaction screening of Drosophila regulatory elements

    OpenAIRE

    Hens, Korneel; Feuz, Jean-Daniel; Isakova, Alina; Iagovitina, Antonina; Massouras, Andreas; Bryois, Julien; Callaerts, Patrick; Celniker, Susan E.; Deplancke, Bart

    2011-01-01

    Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation in the context of gene regulatory networks, we need convenient tools to identify the proteins that bind to them. Here, we present the development and validation of a highly automated protein-DNA interaction detection method, enabling the high-throughput yeast one-hybrid-based screening of DNA elements ver...

  12. 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...

  13. Automated Protein Assay Using Flow Injection Analysis

    Science.gov (United States)

    Wolfe, Carrie A. C.; Oates, Matthew R.; Hage, David S.

    1998-08-01

    The technique of flow injection analysis (FIA) is a common instrumental method used in detecting a variety of chemical and biological agents. This paper describes an undergraduate laboratory that uses FIA to perform a bicinchoninic acid (BCA) colorimetric assay for quantitating protein samples. The method requires less than 2 min per sample injection and gives a response over a broad range of protein concentrations. This method can be used in instrumental analysis labs to illustrate the principles and use of FIA, or as a means for introducing students to common methods employed in the analysis of biological agents.

  14. 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)

  15. 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

  16. Redox options in two-dimensional electrophoresis.

    Science.gov (United States)

    Wait, R; Begum, S; Brambilla, D; Carabelli, A M; Conserva, F; Rocco Guerini, A; Eberini, I; Ballerio, R; Gemeiner, M; Miller, I; Gianazza, E

    2005-05-01

    Two-dimensional electrophoresis is usually run on fully reduced samples. Under these conditions even covalently bound oligomers are dissociated and individual polypeptide chains may be fully unfolded by both, urea and SDS, which maximizes the number of resolved components and allows their pI and M(r) to be most accurately evaluated. However, various electrophoretic protocols for protein structure investigation require a combination of steps under varying redox conditions. We review here some of the applications of these procedures. We also present some original data about a few related samples -- serum from four species: Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus -- which we run under fully unreduced and fully reduced conditions as well as with reduction between first and second dimension. We demonstrate that in many cases the unreduced proteins migrate with a better resolution than reduced proteins, mostly in the crowded 'alpha-globulin' area of pI 4.5-6 and M(r) 50-70 kDa. PMID:15744479

  17. Protein Expression Profiling of Coccidioides posadasii by Two-Dimensional Differential In-Gel Electrophoresis and Evaluation of a Newly Recognized Peroxisomal Matrix Protein as a Recombinant Vaccine Candidate

    OpenAIRE

    Orsborn, Kris I.; Shubitz, Lisa F.; Peng, Tao; Kellner, Ellen M.; Orbach, Marc J; Haynes, Paul A.; Galgiani, John N.

    2006-01-01

    Coccidioides posadasii and Coccidioides immitis are dimorphic, soil-dwelling pathogenic ascomycetes endemic to the southwestern United States. Infection can result from inhalation of a very few arthroconidia, but following natural infection, long-lived immunity is the norm. Previous work in the field has shown that spherule-derived vaccines afford more protection than those from mycelia. We have used two-dimensional differential in-gel electrophoresis coupled with nano-high-performance liquid...

  18. 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…

  19. 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...

  20. Basics and recent advances of two dimensional- polyacrylamide gel electrophoresis

    OpenAIRE

    Magdeldin, Sameh; Enany, Shymaa; Yoshida, Yutaka; Xu, Bo; Zhang, Ying; Zureena, Zam; Lokamani, Ilambarthi; Yaoita, Eishin; Yamamoto, Tadashi

    2014-01-01

    Gel- based proteomics is one of the most versatile methods for fractionating protein complexes. Among these methods, two dimensional- polyacrylamide gel electrophoresis (2-DE) represents a mainstay orthogonal approach, which is popularly used to simultaneously fractionate, identify, and quantify proteins when coupled with mass spectrometric identification or other immunological tests. Although 2-DE was first introduced more than three decades ago, several challenges and limitations to its uti...

  1. Automated Analysis of Fluorescence Microscopy Images to Identify Protein-Protein Interactions

    OpenAIRE

    Morrell-Falvey, J. L.; Qi, H.; Doktycz, M. J.; Venkatraman, S.

    2006-01-01

    The identification of protein interactions is important for elucidating biological networks. One obstacle in comprehensive interaction studies is the analyses of large datasets, particularly those containing images. Development of an automated system to analyze an image-based protein interaction dataset is needed. Such an analysis system is described here, to automatically extract features from fluorescence microscopy images obtained from a bacterial protein interaction assay. These features ...

  2. 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.

  3. 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.

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

    International Nuclear Information System (INIS)

    A novel automated approach for the sequence specific NMR assignments of 1HN, 13Cα, 13Cβ, 13C'/1Hα and 15N 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 1HN and 15N chemical shifts with those of 13Cα, 13Cβ and 13C'/1Hα. The information derived from such correlations is used to create a 'masterlist' consisting of all possible sets of 1HNi, 15Ni, 13Cαi, 13Cβi, 13C'i/1Hαi, 13Cαi-1, 13Cβi-1 and 13C'i-1/ 1Hαi-1 chemical shifts. On the basis of an extensive statistical analysis of 13Cα and 13Cβ 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 masterlist and also to translate the protein primary sequence into an array called ppsarray. The program then uses the masterlist 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 assigarray, with the two-digit code assigned earlier. The assigarray is then mapped onto the ppsarray for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18-42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the masterlist

  5. 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.

  6. Automated two-dimensional interface for capillary gas chromatography

    Science.gov (United States)

    Strunk, Michael R.; Bechtold, William E.

    1996-02-20

    A multidimensional gas chromatograph (GC) system having wide bore capillary and narrow bore capillary GC columns in series and having a novel system interface. Heart cuts from a high flow rate sample, separated by a wide bore GC column, are collected and directed to a narrow bore GC column with carrier gas injected at a lower flow compatible with a mass spectrometer. A bimodal six-way valve is connected with the wide bore GC column outlet and a bimodal four-way valve is connected with the narrow bore GC column inlet. A trapping and retaining circuit with a cold trap is connected with the six-way valve and a transfer circuit interconnects the two valves. The six-way valve is manipulated between first and second mode positions to collect analyte, and the four-way valve is manipulated between third and fourth mode positions to allow carrier gas to sweep analyte from a deactivated cold trap, through the transfer circuit, and then to the narrow bore GC capillary column for separation and subsequent analysis by a mass spectrometer. Rotary valves have substantially the same bore width as their associated columns to minimize flow irregularities and resulting sample peak deterioration. The rotary valves are heated separately from the GC columns to avoid temperature lag and resulting sample deterioration.

  7. 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

  8. Towards two-dimensional search engines

    OpenAIRE

    Ermann, Leonardo; Chepelianskii, Alexei D; Shepelyansky, Dima L.

    2011-01-01

    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 that paves the way for development of two-dimensional search engines of new type. Statistical properties of inf...

  9. 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...

  10. 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.

  11. 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

  12. 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.

  13. Isoforms of a cuticular protein from larvae of the meal beetle, Tenebrio molitor, studied by mass spectrometry in combination with Edman degradation and two-dimensional polyacrylamide gel electrophor

    DEFF Research Database (Denmark)

    Haebel, Sophie; Jensen, Charlotte; Andersen, Svend Olav; Roepstorff, Peter

    Allelic variants, electroelution, gel electrophoresis, insect cuticle proteins, mass spectrometry, protein sequencing.......Allelic variants, electroelution, gel electrophoresis, insect cuticle proteins, mass spectrometry, protein sequencing....

  14. 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

  15. 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)

  16. 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.

  17. Toward two-dimensional search engines

    Science.gov (United States)

    Ermann, L.; Chepelianskii, A. D.; Shepelyansky, D. L.

    2012-07-01

    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.

  18. Towards two-dimensional search engines

    CERN Document Server

    Ermann, Leonardo; Shepelyansky, Dima L

    2011-01-01

    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 that paves the way for development of two-dimensional search engines of new type. Information flow properties on PageRank-CheiRank plane are analyzed for networks of British, French and Italian Universities, Wikipedia, Linux Kernel, gene regulation and other networks. Methods of spam links control are also analyzed.

  19. Two-dimensional sensitivity calculation code: SENSETWO

    International Nuclear Information System (INIS)

    A SENSETWO code for the calculation of cross section sensitivities with a two-dimensional model has been developed, on the basis of first order perturbation theory. It uses forward neutron and/or gamma-ray fluxes and adjoint fluxes obtained by two-dimensional discrete ordinates code TWOTRAN-II. The data and informations of cross sections, geometry, nuclide density, response functions, etc. are transmitted to SENSETWO by the dump magnetic tape made in TWOTRAN calculations. The required input for SENSETWO calculations is thus very simple. The SENSETWO yields as printed output the cross section sensitivities for each coarse mesh zone and for each energy group, as well as the plotted output of sensitivity profiles specified by the input. A special feature of the code is that it also calculates the reaction rate with the response function used as the adjoint source in TWOTRAN adjoint calculation and the calculated forward flux from the TWOTRAN forward calculation. (author)

  20. 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, ...

  1. Two-Dimensional Modeling of Thermoelectric Cells

    OpenAIRE

    Oliveira, Klaudio S. M.; Cardoso, Rodrigo P.; Hermes, Christian J. L.

    2014-01-01

    The present paper is aimed at putting forward a two-dimensional model for thermoelectric cells. The energy conservation equation was formulated in order to account for the Fourier, the Thomson and the Joule effects on the temperature distribution. The electric field was also solved to come out with the current and voltage distributions. The governing equations were discretized by means of the finite-volume method, whereas the TDMA algorithm was adopted for solving the sets of linear equations...

  2. Two dimensional invisibility cloaking via transformation optics

    OpenAIRE

    Liu, Hongyu; Ting ZHOU

    2010-01-01

    We investigate two-dimensional invisibility cloaking via transformation optics approach. The cloaking media possess much more singular parameters than those having been considered for three-dimensional cloaking in literature. Finite energy solutions for these cloaking devices are studied in appropriate weighted Sobolev spaces. We derive some crucial properties of the singularly weighted Sobolev spaces. The invisibility cloaking is then justified by decoupling the underlying singular PDEs into...

  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. Two-dimensional structured illumination microscopy.

    Science.gov (United States)

    Schropp, M; Uhl, R

    2014-10-01

    In widefield fluorescence microscopy, images from all but very flat samples suffer from fluorescence emission from layers above or below the focal plane of the objective lens. Structured illumination microscopy provides an elegant approach to eliminate this unwanted image contribution. To this end a line grid is projected onto the sample and phase images are taken at different positions of the line grid. Using suitable algorithms 'quasi-confocal images' can be derived from a given number of such phase-images. Here, we present an alternative structured illumination microscopy approach, which employs two-dimensional patterns instead of a one-dimensional one. While in one-dimensional structured illumination microscopy the patterns are shifted orthogonally to the pattern orientation, in our two-dimensional approach it is shifted at a single, pattern-dependent angle, yet it already achieves an isotropic power spectral density with this unidirectional shift, which otherwise would require a combination of pattern-shift and -rotation. Moreover, our two-dimensional approach also yields a better signal-to-noise ratio in the evaluated image. PMID:25113075

  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. P174-T Affinity Protein Purification by Automation Using a Magtration Robotic System

    OpenAIRE

    Patel, S.; Duan, X.; TerBush, D.; Yang, Q.; Obata, K.

    2007-01-01

    Affinity purification is a powerful tool for protein enrichment in proteomics studies. We here present a fully automated system for purification of His-tag proteins and IgG using Ni2+/Co2+ and Protein A magnetic beads, respectively. Reagents for His-tag protein or IgG purification are pre-dispensed in a sealed cartridge for automated runs on a Magtration 12GC robot. The automated purification is based on Magtration technology to perform magnetic bead separation similar to a filtration process...

  7. 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

  8. 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

  9. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    International Nuclear Information System (INIS)

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of 14C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. Two-dimensional hydrogen atom. Elliptic basis

    International Nuclear Information System (INIS)

    The paper is devoted to analysis of a two-dimensional hydrogen atom in elliptic coordinates. By the method of separation of variables the problem is redUced to the solution of Ince equation in the complex plane under certain boundary conditions. It is shown that solutions obtained in the limits R→0 and R→ infinity (R is a parameter defining the eliptic coordinates) change into the polar and parabolic bases, respectively. An explicit form of the elliptic basis is given for lowest quantum states

  15. Two dimensional thick center vortex model

    International Nuclear Information System (INIS)

    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

  16. Bubbles in sheared two-dimensional foams

    OpenAIRE

    Quilliet, C.; Idiart, M. A. P.; Dollet, B.; Berthier, L.; Yekini, A.

    2005-01-01

    Oscillatory shear on two-dimensional monodisperse liquid foams was performed. We show that the effect of the oscillatory shear is to cause the migration of bubbles which size is greater than that of a typical bubble of the foam. These so-called flaws move towards the periphery of the foam in a non random motion, thus realizing size segregation in a system which is by construction gravity insensitive. We also show that elongated cavities in the foam could be relaxed towards a more isotropic fo...

  17. Can Two-Dimensional Boron Superconduct?

    Science.gov (United States)

    Penev, Evgeni S; Kutana, Alex; Yakobson, Boris I

    2016-04-13

    Two-dimensional boron is expected to exhibit various structural polymorphs, all being metallic. Additionally, its small atomic mass suggests strong electron-phonon coupling, which in turn can enable superconducting behavior. Here we perform first-principles analysis of electronic structure, phonon spectra, and electron-phonon coupling of selected 2D boron polymorphs and show that the most stable structures predicted to feasibly form on a metal substrate should also exhibit intrinsic phonon-mediated superconductivity, with estimated critical temperature in the range of Tc ≈ 10-20 K. PMID:27003635

  18. 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)

  19. Thermodynamics of two-dimensional Josephson junctions

    International Nuclear Information System (INIS)

    We derive the effective free energy of a two-dimensional Josephson junction in the presence of an external current and predict that the junction has a phase transition at a temperature TJ below the bulk transition temperature Tc. In the range TJ c is reduced by thermal fluctuations; for a junction of size L, Ic ∝ Lb(T) where b(T) J c vanishes at L → ∞) while 0 J. Our results may account for the absence of an observable supercurrent at temperatures below Tc in YBa2Cu3Ox-and Bi2Sr2CaCu2O8-based junctions. (orig.)

  20. Program For Two-Dimensional Thermoplastic Deformation

    Science.gov (United States)

    Orient, George E.

    1993-01-01

    SOLAS contains number of utility programs for use with finite-element simulations. Designed to handle two-dimensional problems of quasi-static thermoplastic deformation. Includes optional postprocessing software, independent of solution codes, generating unified element-by-element list of quantitative results of computation, plus file containing signed equivalent stresses, equivalent strains, and multiaxiality factor parameter. Signs of equivalent quantities expressed either with respect to maximum principal quantities or with respect to directions defined by user. Written in UNIX shell script and FORTRAN 77.

  1. 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.

  2. 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...

  3. Two dimensional shielding benchmark analysis for sodium

    International Nuclear Information System (INIS)

    Results of the analysis of a shielding benchmark experiment on 'fast reactor source' neutron transport through 1.8 metres of sodium is presented in this paper. The two dimensional discrete ordinates code DOT and DLC 37 coupled neutron-gamma multigroup cross sections were used in the analyses. These calculations are compared with measurements on: (i) neutron spectral distribution given by activation detector response, and (ii) gamma ray doses. The agreement is found to be within ± 30 per cent in the fast spectrum region, and within a factor 3.5 in thermal region. For gammas these calculations overpredict the dose rate by a factor of four. (author)

  4. 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. ...

  5. 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

  6. Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    OpenAIRE

    Mandal Nakul; Heegaard Steffen; Prause Jan; Honoré Bent; Vorum Henrik

    2009-01-01

    Abstract The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional differe...

  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

    207 known proteins in alphabetical order), "basal cell markers", "differentiation markers", "proteins highly up-regulated in psoriatic skin", "microsequenced proteins" and "human autoantigens". For reference, we have also included 2-D gel (isoelectric focusing) patterns of cultured normal and...

  8. 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.

  9. 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

  10. 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 $E......^{\\TF}(\\lambda)$ 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....

  11. Two dimensional NMR studies of polysaccharides

    International Nuclear Information System (INIS)

    Polysaccharides are very important components in the immune response system. Capsular polysaccharides and lipopolysaccharides occupy cell surface sites of bacteria, play key roles in recognition and some have been used to develop vaccines. Consequently, the ability to determine chemical structures of these systems is vital to an understanding of their immunogenic action. The authors have been utilizing recently developed two-dimensional homonuclear and heteronuclear correlation spectroscopy for unambiguous assignment and structure determination of a number of polysaccharides. In particular, the 1H-detected heteronuclear correlation experiments are essential to the rapid and sensitive determination of these structures. Linkage sites are determined by independent polarization transfer experiments and multiple quantum correlation experiments. These methods permit the complete structure determination on very small amounts of the polysaccharides. They present the results of a number of structural determinations and discuss the limits of these experiments in terms of their applications to polysaccharides

  12. 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.

  13. 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.

  14. Parallel Two-Dimensional Quicksort Algorithm (PTSA

    Directory of Open Access Journals (Sweden)

    Hamed A. Rjoub

    2008-01-01

    Full Text Available In this research, a Parallel Two-Dimensional Sorting Algorithm (PTSA is presented that has better performance than the classical Quicksort, to sort a data vector of size n = r (rows× c(columns. PTSA algorithm divides the input vector into n/r sub-vectors, which represents tow-dimensional vector of Slave Processor Elements (VPE , the maximum number of VPE for parallel sorting is equal to r×c, VPE just the read,and write operations. The number of Master Processors (MP which do the sort operation is equal to c, The time needed for PTSA algorithm is reduced by θ(n/r log n/r with respect to the time needed by Quicksort θ (n log n to sort the same vector. Simulation results show that the efficiency of sorting using PTSA algorithm is increased and the complexity is reduced significantly compared with classical Quicksort.

  15. Two-dimensional swimming behavior of bacteria

    Science.gov (United States)

    Li, Ye; Zhai, He; Sanchez, Sandra; Kearns, Daniel; Wu, Yilin

    Many bacteria swim by flagella motility which is essential for bacterial dispersal, chemotaxis, and pathogenesis. Here we combined single-cell tracking, theoretical analysis, and computational modeling to investigate two-dimensional swimming behavior of a well-characterized flagellated bacterium Bacillus subtilis at the single-cell level. We quantified the 2D motion pattern of B. subtilis in confined space and studied how cells interact with each other. Our findings shed light on bacterial colonization in confined environments, and will serve as the ground for building more accurate models to understand bacterial collective motion. Mailing address: Room 306 Science Centre North Block, The Chinese University of Hong Kong, Shatin, N.T. Hong Kong SAR. Phone: +852-3943-6354. Fax: +852-2603-5204. E-mail: ylwu@phy.cuhk.edu.hk.

  16. Evaporation of two dimensional black holes

    CERN Document Server

    Hawking, Stephen William

    1992-01-01

    Callan, Giddings, Harvey and Strominger have proposed an interesting two dimensional model theory that allows one to consider black hole evaporation in the semi-classical approximation. They originally hoped the black hole would evaporate completely without a singularity. However, it has been shown that the semi-classical equations will give a singularity where the dilaton field reaches a certain critical value. Initially, it seems this singularity will be hidden inside a black hole. However, 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 semi-classical approximation breaks down when the dilaton field approaches the critical value.

  17. Geometrical aspects of solvable two dimensional models

    International Nuclear Information System (INIS)

    It was noted that there is a connection between the non-linear two-dimensional (2D) models and the scalar curvature r, i.e., when r = -2 the equations of motion of the Liouville and sine-Gordon models were obtained. Further, solutions of various classical nonlinear 2D models can be obtained from the condition that the appropriate curvature two form Ω = 0, which suggests that these models are closely related. This relation is explored further in the classical version by obtaining the equations of motion from the evolution equations, the infinite number of conserved quantities, and the common central charge. The Poisson brackets of the solvable 2D models are specified by the Virasoro algebra. 21 refs

  18. 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.

  19. 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

  20. Renormalization of two-dimensional XQCD

    CERN Document Server

    Fukaya, Hidenori

    2015-01-01

    Recently, Kaplan proposed an interesting extension of QCD named Extended QCD or XQCD with bosonic auxiliary fields [1]. While its partition function is kept exactly the same as that of QCD, XQCD naturally contains properties of low-energy hadrons. We apply this extension to the two-dimensional QCD in the large $N_c$ limit ('t Hooft model) [2]. In this solvable model, it is possible to directly examine the hadronic picture of the 2d XQCD and analyze its renormalization group flow to understand how the auxiliary degrees of freedom behave in the low energy region. We confirm that the additional scalar fields can become dynamical acquiring the kinetic term, and its parity-odd part becomes dominant in the low energy region. This renomalization of XQCD provides an "extension" of the renormalization scheme of QCD, inserting different field variables from those in the original theory, without any changes in physical observables.

  1. Two dimensional generalizations of the Newcomb equation

    International Nuclear Information System (INIS)

    The Bineau reduction to scalar form of the equation governing ideal, zero frequency linearized displacements from a hydromagnetic equilibrium possessing a continuous symmetry is performed in 'universal coordinates', applicable to both the toroidal and helical cases. The resulting generalized Newcomb equation (GNE) has in general a more complicated form than the corresponding one dimensional equation obtained by Newcomb in the case of circular cylindrical symmetry, but in this cylindrical case , the equation can be transformed to that of Newcomb. In the two dimensional case there is a transformation which leaves the form of the GNE invariant and simplifies the Frobenius expansion about a rational surface, especially in the limit of zero pressure gradient. The Frobenius expansions about a mode rational surface is developed and the connection with Hamiltonian transformation theory is shown. 17 refs

  2. 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.

  3. Extending models for two-dimensional constraints

    DEFF Research Database (Denmark)

    Forchhammer, Søren

    2009-01-01

    Random fields in two dimensions may be specified on 2 times 2 elements such that the probabilities of finite configurations and the entropy may be calculated explicitly. The Pickard random field is one example where probability of a new (non-boundary) element is conditioned on three previous...... models of two-dimensional constraints and as examples we apply it to the hard-square constraint and the no isolated bits (n.i.b) constraint. The iterative scaling can ensure that the entropy of the extension is optimized and that the entropy is increased compared to the initial model defined on 2 times 2...... elements. Application to a simple stationary model with hidden states is also outlined. For the n.i.b constraint, the initial model is based on elements defined by blocks of (1 times 2) binary symbols....

  4. Equivalency of two-dimensional algebras

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Gildemar Carneiro dos; Pomponet Filho, Balbino Jose S. [Universidade Federal da Bahia (UFBA), BA (Brazil). Inst. de Fisica

    2011-07-01

    Full text: Let us consider a vector z = xi + yj over the field of real numbers, whose basis (i,j) satisfy a given algebra. Any property of this algebra will be reflected in any function of z, so we can state that the knowledge of the properties of an algebra leads to more general conclusions than the knowledge of the properties of a function. However structural properties of an algebra do not change when this algebra suffers a linear transformation, though the structural constants defining this algebra do change. We say that two algebras are equivalent to each other whenever they are related by a linear transformation. In this case, we have found that some relations between the structural constants are sufficient to recognize whether or not an algebra is equivalent to another. In spite that the basis transform linearly, the structural constants change like a third order tensor, but some combinations of these tensors result in a linear transformation, allowing to write the entries of the transformation matrix as function of the structural constants. Eventually, a systematic way to find the transformation matrix between these equivalent algebras is obtained. In this sense, we have performed the thorough classification of associative commutative two-dimensional algebras, and find that even non-division algebra may be helpful in solving non-linear dynamic systems. The Mandelbrot set was used to have a pictorial view of each algebra, since equivalent algebras result in the same pattern. Presently we have succeeded in classifying some non-associative two-dimensional algebras, a task more difficult than for associative one. (author)

  5. 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)。

  6. 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...

  7. 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.

  8. Automated system for high-throughput protein production using the dialysis cell-free method.

    Science.gov (United States)

    Aoki, Masaaki; Matsuda, Takayoshi; Tomo, Yasuko; Miyata, Yukako; Inoue, Makoto; Kigawa, Takanori; Yokoyama, Shigeyuki

    2009-12-01

    High-throughput protein production systems have become an important issue, because protein production is one of the bottleneck steps in large-scale structural and functional analyses of proteins. We have developed a dialysis reactor and a fully automated system for protein production using the dialysis cell-free synthesis method, which we previously established to produce protein samples on a milligram scale in a high-throughput manner. The dialysis reactor was designed to be suitable for an automated system and has six dialysis cups attached to a flat dialysis membrane. The automated system is based on a Tecan Freedom EVO 200 workstation in a three-arm configuration, and is equipped with shaking incubators, a vacuum module, a robotic centrifuge, a plate heat sealer, and a custom-made tilting carrier for collection of reaction solutions from the flat-bottom cups with dialysis membranes. The consecutive process, from the dialysis cell-free protein synthesis to the partial purification by immobilized metal affinity chromatography on a 96-well filtration plate, was performed within ca. 14h, including 8h of cell-free protein synthesis. The proteins were eluted stepwise in a high concentration using EDTA by centrifugation, while the resin in the filtration plate was washed on the vacuum manifold. The system was validated to be able to simultaneously and automatically produce up to 96 proteins in yields of several milligrams with high well-to-well reliability, sufficient for structural and functional analyses of proteins. The protein samples produced by the automated system have been utilized for NMR screening to judge the protein foldedness and for structure determinations using heteronuclear multi-dimensional NMR spectroscopy. The automated high-throughput protein production system represents an important breakthrough in the structural and functional studies of proteins and has already contributed a massive amount of results in the structural genomics project at the

  9. 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.

  10. Two-dimensional gel electrophoresis in platelet proteomics research.

    Science.gov (United States)

    García, Angel

    2007-01-01

    Proteomics technology allows a comprehensive and efficient analysis of the proteome and has become an indispensable tool in biomedical research. Since the late 80s, advances on mass spectrometry (MS) instrumentation and techniques have revolutionized the way proteins can be analyzed. Such analysis would only be possible with a proper sample preparation and separation ahead of the MS step. Different gel and nongel-based methods are available for protein separation. This chapter will focus on the use of two-dimensional gel electrophoresis (2-DE) in proteomics and its application to platelet research. 2-DE separates proteins according to their isoelectric point (pI) and size (molecular weight) and allows the detection of thousands of proteins at a time. Platelets are enucleated cells that play a critical function in the control of bleeding and wound healing. As platelets do not have a nucleus, proteomics offers a powerful alternative approach to provide data on protein expression in these cells, helping to address their biology. This chapter presents a protocol for an efficient sample preparation, protein separation by 2-DE, and protein digestion ahead of the MS analysis. The experimental approach, already successfully applied to the study of the platelet proteome, includes recommendations for an efficient platelet preparation for proteomics studies. PMID:18287684

  11. Analysis of Two-Dimensional Electrophoresis Gel Images

    DEFF Research Database (Denmark)

    Pedersen, Lars

    2002-01-01

    This thesis describes and proposes solutions to some of the currently most important problems in pattern recognition and image analysis of two-dimensional gel electrophoresis (2DGE) images. 2DGE is the leading technique to separate individual proteins in biological samples with many biological and...... methods based on image analysis techniques in order to significantly accelerate this key technology. The methods described and developed fall into three categories: image segmentation, point pattern matching, and a unified approach simultaneously segmentation the image and matching the spots. The main...... 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...

  12. 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

    recovered from the gels (based on quantitations of polypeptides labeled with a mixture of 16 14C-amino acids), protein name (including credit to investigators that aided identification), antibody against protein, cellular localization, (nuclear, 40S hnRNP, 20S snRNP U5, proteasomes, endoplasmic reticulum...... particular, the 2-D gel protein database may become increasingly important in view of the concerted effort to map and sequence the entire human genome. Udgivelsesdato: 1990-Dec...

  13. Two-dimensional SDS-PAGE fractionation of biological samples for biomarker discovery

    OpenAIRE

    Rabilloud, Thierry; Triboulet, Sarah

    2013-01-01

    Two-dimensional electrophoresis is still a very valuable tool in proteomics, due to its reproducibility and its ability to analyze complete proteins. However, due to its sensitivity to dynamic range issues, its most suitable use in the frame of biomarker discovery is not on very complex fluids such as plasma, but rather on more proximal, simpler fluids such as CSF, urine, or secretome samples. Here, we describe the complete workflow for the analysis of such dilute samples by two-dimensional e...

  14. Epitaxial Growth of Two-Dimensional Stanene

    Science.gov (United States)

    Jia, Jinfeng

    Ultrathin semiconductors present various novel electronic properties. The first experimental realized two-dimensional (2D) material is graphene. Searching 2D materials with heavy elements bring the attention to Si, Ge and Sn. 2D buckled Si-based silicene was realized by molecular beam epitaxy (MBE) growth. Ge-based germanene was realized by mechanical exfoliation. Sn-based stanene has its unique properties. Stanene and its derivatives can be 2D topological insulators (TI) with a very large band gap as proposed by first-principles calculations, or can support enhanced thermoelectric performance, topological superconductivity and the near-room-temperature quantum anomalous Hall (QAH) effect. For the first time, in this work, we report a successful fabrication of 2D stanene by MBE. The atomic and electronic structures were determined by scanning tunneling microscopy (STM) and angle-resolved photoemission spectroscopy (ARPES) in combination with first-principles calculations. This work will stimulate the experimental study and exploring the future application of stanene. In cooperation with Fengfeng Zhu, Wei-jiong Chen, Yong Xu, Chun-lei Gao, Dan-dan Guan, Canhua Liu, Dong Qian, Shou-Cheng Zhang.

  15. 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 ...

  16. Internal representation of two-dimensional shape.

    Science.gov (United States)

    Makioka, S; Inui, T; Yamashita, H

    1996-01-01

    The psychological space of shapes has been studied in many experiments. However, how shapes are represented in the brain has not been a major issue in psychological literature. Here, the characteristics of internal representation and how it was formed have been considered and an attempt has been made to explain the results of experiments in a unified manner. First, the data of similarity of alphabetic characters and random-dot patterns were reexamined. Multivariate analysis suggested that those patterns were represented by the combination of global features. Second, three-layer neural networks were trained to perform categorization or identity transformation of the same sets of patterns as used in psychological experiments, and activation patterns of the hidden units were analyzed. When the network learned categorization of the patterns, its internal representation was not similar to the representation suggested by psychological experiments. But a network which learned identity transformation of the patterns could acquire such an internal representation. The transformation performed by this kind of network is similar to principal-component analysis in that it projects the input image onto a lower-dimensional space. From these results it is proposed that two-dimensional shapes are represented in human brain by a process like principal-component analysis. This idea is compatible with the findings in neurophysiological studies about higher visual areas. PMID:8938008

  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. 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

  19. Two-dimensional cyanates: stabilization through hydrogenation.

    Science.gov (United States)

    Tsetseris, Leonidas

    2016-06-01

    According to first-principles calculations, it should be possible to grow two-dimensional (2D) forms of copper thio-cyanate (CuSCN) and copper seleno-cyanate (CuSeCN) since their energies are only marginally higher than those of their most stable three-dimensional (3D) wurtzite structures. Here we show using the same theoretical approach that chemisorption reactions of hydrogen molecules with the above-mentioned 2D CuSCN and CuSeCN systems enhance their stability as they decrease the energy difference with respect to the corresponding hydrogenated forms of the wurtzite crystals. Hydrogenation causes a sizeable decrease in the energy band gap by 0.56 eV and 0.65 eV for hydrogenated 2D-CuSCN (CuSCNH2) and 2D-CuSeCN (CuSeCNH2), respectively. Finally, we describe the stability of hydrogen vacancies in CuSCNH2 and CuSeCNH2 and show that the presence of isolated single H vacancies or di-vacancies does not affect significantly the electronic properties of the host systems close to the valence and conduction band edges. PMID:27183226

  20. Turbulent equipartitions in two dimensional drift convection

    International Nuclear Information System (INIS)

    Unlike the thermodynamic equipartition of energy in conservative systems, turbulent equipartitions (TEP) describe strongly non-equilibrium systems such as turbulent plasmas. In turbulent systems, energy is no longer a good invariant, but one can utilize the conservation of other quantities, such as adiabatic invariants, frozen-in magnetic flux, entropy, or combination thereof, in order to derive new, turbulent quasi-equilibria. These TEP equilibria assume various forms, but in general they sustain spatially inhomogeneous distributions of the usual thermodynamic quantities such as density or temperature. This mechanism explains the effects of particle and energy pinch in tokamaks. The analysis of the relaxed states caused by turbulent mixing is based on the existence of Lagrangian invariants (quantities constant along fluid-particle or other orbits). A turbulent equipartition corresponds to the spatially uniform distribution of relevant Lagrangian invariants. The existence of such turbulent equilibria is demonstrated in the simple model of two dimensional electrostatically turbulent plasma in an inhomogeneous magnetic field. The turbulence is prescribed, and the turbulent transport is assumed to be much stronger than the classical collisional transport. The simplicity of the model makes it possible to derive the equations describing the relaxation to the TEP state in several limits

  1. 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

  2. Two-dimensional magnetic colloids under shear.

    Science.gov (United States)

    Mohorič, Tomaž; Dobnikar, Jure; Horbach, Jürgen

    2016-04-01

    Complex rheological properties of soft disordered solids, such as colloidal gels or glasses, inspire a range of novel applications. However, the microscopic mechanisms of their response to mechanical loading are not well understood. Here, we elucidate some aspects of these mechanisms by studying a versatile model system, i.e. two-dimensional superparamagnetic colloids in a precessing magnetic field, whose structure can be tuned from a hexagonal crystal to a disordered gel network by varying the external field opening angle θ. We perform Langevin dynamics simulations subjecting these structures to a constant shear rate and observe three qualitatively different types of material response. In hexagonal crystals (θ = 0°), at a sufficiently low shear rate, plastic flow occurs via successive stress drops at which the stress releases due to the formation of dislocation defects. The gel network at θ = 48°, on the contrary, via bond rearrangement and transient shear banding evolves into a homogeneously stretched network at large strains. The latter structure remains metastable after switching off of the shear. At θ = 50°, the external shear makes the system unstable against phase separation and causes a failure of the network structure leading to the formation of hexagonal close packed clusters interconnected by particle chains. At a microcopic level, our simulations provide insight into some of the mechanisms by which strain localization as well as material failure occur in a simple gel-like network. Furthermore, we demonstrate that new stretched network structures can be generated by the application of shear. PMID:26877059

  3. Foundation of The Two dimensional Quantum Theory of Gravity

    OpenAIRE

    Ghaboussi, F.

    1997-01-01

    The two dimensional substructure of general relativity and gravity, and the two dimensional geometry of quantum effect by black hole are disclosed. Then the canonical quantization of the two dimensional theory of gravity is performed. It is shown that the resulting uncertainty relations can explain black hole quantum effects. A quantum gravitational length is also derived which can clarify the origin of Planck length.

  4. 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...

  5. Gaia: automated quality assessment of protein structure models

    OpenAIRE

    Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V.

    2011-01-01

    Motivation: Increasing use of structural modeling for understanding structure–function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures.

  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. 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...

  9. 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

  10. Two-dimensional vibrational-electronic spectroscopy

    International Nuclear Information System (INIS)

    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 (νCN) and either a ligand-to-metal charge transfer transition ([FeIII(CN)6]3− dissolved in formamide) or a metal-to-metal charge transfer (MMCT) transition ([(CN)5FeIICNRuIII(NH3)5]− 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 νCN 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 wide range of complex molecular, material, and biological systems

  11. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995.

    OpenAIRE

    Appel, Ron David; Sanchez, Jean-Charles; Bairoch, Amos Marc; Golaz, Olivier Georges; Ravier, Florence; Pasquali, Christian; Hughes, Graham; Hochstrasser, Denis

    1996-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (Saccharomyces cerevisiae) and Escherichia coli origin, as well as virtual entries for each of the protein sequences in the SWISS-PROT database.

  12. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis.

    OpenAIRE

    Appel, Ron David; Sanchez, Jean-Charles; Bairoch, Amos Marc; Golaz, Olivier Georges; Ravier, Florence; Pasquali, Christian; Hughes, Graham; Hochstrasser, Denis

    1994-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of Geneva in collaboration with the Department of Medical Biochemistry of Geneva University. The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition.

  13. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Appel, R D; Sanchez, J C; Bairoch, A; Golaz, O; Ravier, F; Pasquali, C; Hughes, G J; Hochstrasser, D F

    1994-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), created and maintained at the University Hospital of Geneva in collaboration with the Department of Medical Biochemistry of Geneva University. The proteins have been identified on various 2-D PAGE reference maps by microsequencing, immunoblotting, gel comparison and amino acid composition. Images PMID:7937063

  14. The SWISS-2DPAGE database of two-dimensional polyacrylamide gel electrophoresis, its status in 1995.

    Science.gov (United States)

    Appel, R D; Sanchez, J C; Bairoch, A; Golaz, O; Ravier, F; Pasquali, C; Hughes, G J; Hochstrasser, D F

    1996-01-01

    SWISS-2DPAGE is a database of proteins identified on two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The current release contains 343 entries of human, yeast (Saccharomyces cerevisiae) and Escherichia coli origin, as well as virtual entries for each of the protein sequences in the SWISS-PROT database. PMID:8594575

  15. The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation

    OpenAIRE

    Stevens Fred J; Johnson Seth; Desai Valmik; Zavaljevski Nela; Yu Chenggang; Reifman Jaques

    2008-01-01

    Abstract Background Automated protein function prediction methods are needed to keep pace with high-throughput sequencing. With the existence of many programs and databases for inferring different protein functions, a pipeline that properly integrates these resources will benefit from the advantages of each method. However, integrated systems usually do not provide mechanisms to generate customized databases to predict particular protein functions. Here, we describe a tool termed PIPA (Pipeli...

  16. Automated Hydrophobic Interaction Chromatography Column Selection for Use in Protein Purification

    OpenAIRE

    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.

  17. 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

  18. 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。

  19. 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

  20. Two Dimensional Array Imaging with Beam Steered Data

    OpenAIRE

    Patole, Sujeet; Torlak, Murat

    2013-01-01

    This paper discusses different approaches used for millimeter wave imaging of two-dimensional objects. Imaging of a two dimensional object requires reflected wave data to be collected across two distinct dimensions. In this paper, we propose a reconstruction method that uses narrowband waveforms along with two dimensional beam steering. The beam is steered in azimuthal and elevation direction, which forms the two distinct dimensions required for the reconstruction. The Reconstruction techniqu...

  1. Two-Dimensional Black Holes and Planar General Relativity

    OpenAIRE

    Lemos, Jose' P. S.

    1994-01-01

    The Einstein-Hilbert action with a cosmological term is used to derive a new action in 1+1 spacetime dimensions. It is shown that the two-dimensional theory is equivalent to planar symmetry in General Relativity. The two-dimensional theory admits black holes and free dilatons, and has a structure similar to two-dimensional string theories. Since by construction these solutions also solve Einstein's equations, such a theory can bring two-dimensional results into the four-dimensional real world...

  2. 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.

  3. 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

  4. 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

  5. A Novel Approach to Sequence Validating Protein Expression Clones with Automated Decision Making

    OpenAIRE

    Mohr Stephanie E; Zuo Dongmei; Hu Yanhui; Rolfs Andreas; Taycher Elena; Williamson Janice; LaBaer Joshua

    2007-01-01

    Abstract Background Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens ...

  6. 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....

  7. The classical solutions of two-dimensional gravity

    CERN Document Server

    Schmidt, H J

    1999-01-01

    The solutions of two-dimensional gravity following from a non-linear Lagrangian L = f(R) are classified, and their symmetry and singularity properties are described. Then a conformal transformation is applied to rewrite these solutions as analogous solutions of two-dimensional Einstein-dilaton gravity and vice versa.

  8. 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…

  9. 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

  10. Dynamics of vortex interactions in two-dimensional flows

    DEFF Research Database (Denmark)

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

    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...

  11. 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.

  12. Two-dimensional simulation of the polarization switching in ferroelectrics

    International Nuclear Information System (INIS)

    The main switching properties in ferroelectrics are simulated within the framework of the extended Ishibashi dipole-lattice model including the dipole-dipole interaction in a two-dimensional case. The mechanism of the polarization reversal is modeled in the two-dimensional case. The results of the modeling are in a good agreement with experimental data for the set of materials.

  13. 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.

  14. Automated protein backbone assignment using the projection-decomposition approach

    International Nuclear Information System (INIS)

    Spectral projection experiments by NMR in conjunction with decomposition analysis have been previously introduced for the backbone assignment of proteins; various pulse sequences as well as the behaviour with low signal-to-noise or chemical shift degeneracy have been illustrated. As a guide for routine applications of this combined tool, we provide here a systematic analysis on different types of proteins using welldefined run-time parameters. As a second result of this study, the backbone assignment module SHABBA was extensively rewritten and improved. Calculations on ubiquitin yielded again fully correct and nearly complete backbone and CHβ assignments. For the 128 residue long azurin, missing assignments mostly affect Hα and Hβ. Among the remaining backbone (plus Cβ) nuclei 97.5% could be assigned with 1.0% differences to a reference. Finally, the new SHABBA algorithm was applied to projections recorded for a yeast histone protein domain at room temperature, where the protein is subject to partial unfolding: this leads to unobservable resonances (about a dozen missing signals in a normal 15N-HSQC) and extensive degeneracy among the resonances. From the clearly observable residues, 97.5% of the backbone and CHβresonances could be assigned, of which only 0.8 % showed differences to published shifts. An additional study on the protein MMP20, which exhibits spectral difficulties to an even larger extent, explores the limitations of the approach.

  15. The Protein Maker: an automated system for high-throughput parallel purification

    International Nuclear Information System (INIS)

    The Protein Maker instrument addresses a critical bottleneck in structural genomics by allowing automated purification and buffer testing of multiple protein targets in parallel with a single instrument. Here, the use of this instrument to (i) purify multiple influenza-virus proteins in parallel for crystallization trials and (ii) identify optimal lysis-buffer conditions prior to large-scale protein purification is described. The Protein Maker is an automated purification system developed by Emerald BioSystems for high-throughput parallel purification of proteins and antibodies. This instrument allows multiple load, wash and elution buffers to be used in parallel along independent lines for up to 24 individual samples. To demonstrate its utility, its use in the purification of five recombinant PB2 C-terminal domains from various subtypes of the influenza A virus is described. Three of these constructs crystallized and one diffracted X-rays to sufficient resolution for structure determination and deposition in the Protein Data Bank. Methods for screening lysis buffers for a cytochrome P450 from a pathogenic fungus prior to upscaling expression and purification are also described. The Protein Maker has become a valuable asset within the Seattle Structural Genomics Center for Infectious Disease (SSGCID) and hence is a potentially valuable tool for a variety of high-throughput protein-purification applications

  16. 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.

  17. 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...

  18. 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...

  19. 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.

  20. 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.

  1. 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

  2. Highly automated protein backbone resonance assignment within a few hours: the strategy and software package

    International Nuclear Information System (INIS)

    Sequential resonance assignment represents an essential step towards the investigation of protein structure, dynamics, and interaction surfaces. Although the experimental sensitivity has significantly increased in recent years, with the availability of high field magnets and cryogenically cooled probes, resonance assignment, even of small globular proteins, still generally requires several days of data collection and analysis using standard protocols. Here we introduce the BATCH strategy for fast and highly automated backbone resonance assignment of 13C, 15N-labelled proteins. BATCH makes use of the fast data acquisition and analysis tools BEST, ASCOM, COBRA, and HADAMAC, recently developed in our laboratory. An improved Hadamard encoding scheme, presented here, further increases the performance of the HADAMAC experiment. A new software platform, interfaced to the NMRView software package, has been developed that enables highly automated NMR data processing and analysis, sequential resonance assignment, and 13C chemical shift extraction. We demonstrate for four small globular proteins that sequential resonance assignment can be routinely obtained within a few hours, or less, in a highly automated and robust way

  3. 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.

  4. 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

  5. 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)

  6. 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.

  7. A Justification of Two-Dimensional Nonlinear Viscoelastic Shells Model

    OpenAIRE

    Fushan Li

    2012-01-01

    By applying formal asymptotic analysis and Laplace transformation, we obtain two-dimensional nonlinear viscoelastic shells model satisfied by the leading term of asymptotic expansion of the solution to the three-dimensional equations.

  8. Foliations with unbounded deviation on the two-dimensional torus

    OpenAIRE

    Panov, Dmitri

    2002-01-01

    There exists a smooth foliation with 3 singular points on the two-dimensional torus such that any lifting of a leaf of this foliation on the universal covering of the torus is a dense subset of the covering.

  9. 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.

  10. 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.

  11. 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.

  12. 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...

  13. Two-dimensional quantum conformal group, strings and lattices

    International Nuclear Information System (INIS)

    The two-dimensional conformal group plays an important role in two-dimensional quantum field theory. The Virasoro algebra commutation relations are given. Local currents and affine Kac-Moody algebras, the simplest class of infinite Lie algebras, are discussed. In relation to these topics, the theory of Integral Lattices plays a role. Applications of conformal groups in the theories of extended supergravity and superstrings are reviewed. 47 refs.,

  14. 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.

  15. 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.

  16. 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.

  17. 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 ...

  18. Monte Carlo simulation of a two-dimensional magnetic foam

    International Nuclear Information System (INIS)

    A two-dimensional Ising-like model with spin 1 and long-range interactions is studied numerically through a Monte Carlo simulation. The goal of the simulation is to describe pattern formations and critical temperature of two-dimensional magnetic structures. Three sets of parameters are considered, that give rise to stripes, labyrinths or cellular domain structures. We determine for each configuration the transition ordering temperatures, the relaxation of the energy, the hysteresis cycle, and the average size of the domains

  19. 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.

  20. 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...

  1. 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)

  2. Automated Selected Reaction Monitoring Software for Accurate Label-Free Protein Quantification

    OpenAIRE

    Teleman, Johan; Karlsson, Christofer; Waldemarson, Sofia; Hansson, Karin; James, Peter; Malmström, Johan; Levander, Fredrik

    2012-01-01

    Selected reaction monitoring (SRM) is a mass spectrometry method with documented ability to quantify proteins accurately and reproducibly using labeled reference peptides. However, the use of labeled reference peptides becomes impractical if large numbers of peptides are targeted and when high flexibility is desired when selecting peptides. We have developed a label-free quantitative SRM workflow that relies on a new automated algorithm, Anubis, for accurate peak detection. Anubis efficiently...

  3. 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

  4. Fast acoustic tweezers for the two-dimensional manipulation of individual particles in microfluidic channels

    CERN Document Server

    Tran, S B Q; Thibault, Pierre; 10.1063/1.4751348

    2012-01-01

    This paper presents a microfluidic device that implements standing surface acoustic waves in order to handle single cells, droplets, and generally particles. The particles are moved in a very controlled manner by the two-dimensional drifting of a standing wave array, using a slight frequency modulation of two ultrasound emitters around their resonance. These acoustic tweezers allow any type of motion at velocities up to few 10mm/s, while the device transparency is adapted for optical studies. The possibility of automation provides a critical step in the development of lab-on-a-chip cell sorters and it should find applications in biology, chemistry, and engineering domains.

  5. Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Honoré Bent

    2010-01-01

    Full Text Available Abstract The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE and mass spectrometry (MS. Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.

  6. Ocular Proteomics with Emphasis on Two-Dimensional Gel Electrophoresis and Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Mandal Nakul

    2009-12-01

    Full Text Available Abstract The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE and mass spectrometry (MS. Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.

  7. A fully automated plasma protein precipitation sample preparation method for LC-MS/MS bioanalysis.

    Science.gov (United States)

    Ma, Ji; Shi, Jianxia; Le, Hoa; Cho, Robert; Huang, Judy Chi-jou; Miao, Shichang; Wong, Bradley K

    2008-02-01

    This report describes the development and validation of a robust robotic system that fully integrates all peripheral devices needed for the automated preparation of plasma samples by protein precipitation. The liquid handling system consisted of a Tecan Freedom EVO 200 liquid handling platform equipped with an 8-channel liquid handling arm, two robotic plate-handling arms, and two plate shakers. Important additional components integrated into the platform were a robotic temperature-controlled centrifuge, a plate sealer, and a plate seal piercing station. These enabled unattended operation starting from a stock solution of the test compound, a set of test plasma samples and associated reagents. The stock solution of the test compound was used to prepare plasma calibration and quality control samples. Once calibration and quality control samples were prepared, precipitation of plasma proteins was achieved by addition of three volumes of acetonitrile. Integration of the peripheral devices allowed automated sequential completion of the centrifugation, plate sealing, piercing and supernatant transferral steps. The method produced a sealed, injection-ready 96-well plate of plasma extracts. Accuracy and precision of the automated system were satisfactory for the intended use: intra-day and the inter-day precision were excellent (C.V.<5%), while the intra-day and inter-day accuracies were acceptable (relative error<8%). The flexibility of the platform was sufficient to accommodate pharmacokinetic studies of different numbers of animals and time points. To the best of our knowledge, this represents the first complete automation of the protein precipitation method for plasma sample analysis. PMID:18226589

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. Scaling fields in the two-dimensional abelian sandpile model

    CERN Document Server

    Mahieu, S

    2001-01-01

    We consider the isotropic two-dimensional abelian sandpile model from a perspective based on two-dimensional (conformal) field theory. We compute lattice correlation functions for various cluster variables (at and off criticality), from which we infer the field-theoretic description in the scaling limit. We find a perfect agreement with the predictions of a c=-2 conformal field theory and its massive perturbation, thereby providing direct evidence for conformal invariance and more generally for a description in terms of a local field theory. The question of the height 2 variable is also addressed, with however no definite conclusion yet.

  13. Langley's two-dimensional research facilities: Capabilities and plans

    Science.gov (United States)

    Ray, E. J.

    1979-01-01

    The current capabilities and the forthcoming plans for Langley's two-dimensional research facilities are described. The characteristics of the Langley facilities are discussed in terms of Reynolds number, Mach number, and angle-of-attack capabilities. Comments are made with regard to the approaches which have been investigated to alleviate typical problem areas such as wall boundary effects. Because of the need for increased Reynolds number capability at high subsonic speeds, a considerable portion of the paper deals with a description of the 20 by 60 cm two-dimensional test section of the Langley 0.3 meter transonic cryogenic tunnel which is currently in the calibration and shakedown phase.

  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. Chiral anomaly, fermionic determinant and two dimensional models

    International Nuclear Information System (INIS)

    The chiral anomaly in random pair dimension is analysed. This anomaly is perturbatively calculated by dimensional regularization method. A new method for non-perturbative Jacobian calculation of a general chiral transformation, 1.e., finite and non-Abelian, is developed. This method is used for non-perturbative chiral anomaly calculation, as an alternative to bosonization of two-dimensional theories for massless fermions and to study the phenomenum of fermion number fractionalization. The fermionic determinant from two-dimensional quantum chromodynamics is also studied, and calculated, exactly, as in decoupling gauge as with out reference to a particular gauge. (M.C.K.)

  16. 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.

  17. 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

  18. 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...

  19. Densis. Densimetric representation of two-dimensional matrices

    International Nuclear Information System (INIS)

    Densis is a Fortran V program which allows off-line control of a Calcomp digital plotter, to represent a two-dimensional matrix of numerical elements in the form of a variable shading intensity map in two colours. Each matrix element is associated to a square of a grid which is traced over by lines whose number is a function of the element value according to a selected scale. Program features, subroutine structure and running instructions, are described. Some typical results, for gamma-gamma coincidence experimental data and a sampled two-dimensional function, are indicated. (author)

  20. 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.

  1. HoxPred: automated classification of Hox proteins using combinations of generalised profiles

    Directory of Open Access Journals (Sweden)

    Leyns Luc

    2007-07-01

    Full Text Available Abstract Background Correct identification of individual Hox proteins is an essential basis for their study in diverse research fields. Common methods to classify Hox proteins focus on the homeodomain that characterise homeobox transcription factors. Classification is hampered by the high conservation of this short domain. Phylogenetic tree reconstruction is a widely used but time-consuming classification method. Results We have developed an automated procedure, HoxPred, that classifies Hox proteins in their groups of homology. The method relies on a discriminant analysis that classifies Hox proteins according to their scores for a combination of protein generalised profiles. 54 generalised profiles dedicated to each Hox homology group were produced de novo from a curated dataset of vertebrate Hox proteins. Several classification methods were investigated to select the most accurate discriminant functions. These functions were then incorporated into the HoxPred program. Conclusion HoxPred shows a mean accuracy of 97%. Predictions on the recently-sequenced stickleback fish proteome identified 44 Hox proteins, including HoxC1a only found so far in zebrafish. Using the Uniprot databank, we demonstrate that HoxPred can efficiently contribute to large-scale automatic annotation of Hox proteins into their paralogous groups. As orthologous group predictions show a higher risk of misclassification, they should be corroborated by additional supporting evidence. HoxPred is accessible via SOAP and Web interface http://cege.vub.ac.be/hoxpred/. Complete datasets, results and source code are available at the same site.

  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. 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%The analysis of protein differences in cerebrospinal fluid of tuberculous meningitis and cryptococcus meningitis by two-dimensional electrophoresis

    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

  4. 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.

  5. 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

  6. Identification of Frankia Strains by Two-Dimensional Polyacrylamide Gel Electrophoresis

    OpenAIRE

    Benson, David R.; Buchholz, S. E.; Hanna, D. G.

    1984-01-01

    Fifteen Frankia strains from five different plant species were analyzed by two-dimensional polyacryl-amide gel electrophoresis to determine their relatedness by comparing the polypeptide patterns obtained. Three major subgroups (A, C, and D) were found in the Alnus-Comptonia-Myrica cross-inoculation group. An isolate from Purshia tridentata had a unique protein pattern and represents a distinct group of frankiae. Members of group A were isolated from root nodules of Alnus incana subsp. rugosa...

  7. Two-dimensional phos-tag zymograms for tracing phosphoproteins by activity in-gel staining

    OpenAIRE

    Meisrimler, Claudia-Nicole; Schwendke, Alexandra; Lüthje, Sabine

    2015-01-01

    Protein phosphorylation is one of the most common post-translational modifications regulating many cellular processes. The phos-tag technology was combined with two-dimensional zymograms, which consisted of non-reducing IEF PAGE or NEPHGE in the first dimension and high resolution clear native electrophoresis (hrCNE) in the second dimension. The combination of these electrophoresis methods was mild enough to accomplish in-gel activity staining for Fe(III)-reductases by NADH/Fe(III)-citrate/fe...

  8. 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...

  9. New Approach for Segmentation and Quantification of Two-Dimensional Gel Electrophoresis Images

    DEFF Research Database (Denmark)

    Anjo, Antonio dos; Laurell Blom Møller, Anders; Ersbøll, Bjarne Kjær; Finnie, Christine; Shahbazkia, Hamid R.

    2011-01-01

    Motivation: Detection of protein spots in two-dimensional gel electrophoresis images (2-DE) is a very complex task and current approaches addressing this problem still suffer from significant shortcomings. When quantifying a spot, most of the current software applications include a lot of....... Results: Five sections from different gels are used to test the performance of the presented method concerning the detection of protein spots, and three gel sections are used to test the quantification of sixty protein spots. Comparisons with a state-of-the-art commercial software and an academic state...

  10. 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...

  11. Algebraic analysis of a model of two-dimensional gravity

    CERN Document Server

    Frolov, A M; Kuzmin, S V

    2009-01-01

    An algebraic analysis of the Hamiltonian formulation of the model two-dimensional gravity is performed. The crucial fact is an exact coincidence of the Poisson brackets algebra of the secondary constraints of this Hamiltonian formulation with the SO(2,1)-algebra. The eigenvectors of the canonical Hamiltonian $H_{c}$ are obtained and explicitly written in closed form.

  12. On elliptic basis of a two-dimensional hydrogen atom

    International Nuclear Information System (INIS)

    An explicit form is found the elliptic basis of a two-dimensional hydrogen atom and elliptic separation constant at large and small values of the product Rsub(ω) (ω=√-2E and R is a free parameter entering into the definition of elliptic coordinates)

  13. 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.

  14. 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.

  15. 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

  16. Graphene and Boron Nitride: Members of Two Dimensional Material Family

    OpenAIRE

    Riaz, Ibtsam

    2012-01-01

    Name of University: University of ManchesterCandidate full name: Ibtsam RiazDegree Title: Doctor of Philosophy in the Faculty of Engineering and Physical sciencesThesis Title: Graphene and Boron Nitride: Members of Two Dimensional Material FamilyDate: 18-JAN-2012

  17. 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

  18. 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...

  19. Simple two-dimensional separation platform for peptide analysis

    Czech Academy of Sciences Publication Activity Database

    Duša, Filip; Šesták, Jozef; Moravcová, Dana; Planeta, Josef; Kahle, Vladislav

    2013. s. 830-830. [International Symposium on High Performance Liquid Phase Separations and Related Techniques /39./. 16.06.2013-20.06.2013, Amsterdam] R&D Projects: GA MV VG20112015021; GA MV VG20102015023 Institutional support: RVO:68081715 Keywords : two-dimensional * decoupler * peptides Subject RIV: CB - Analytical Chemistry, Separation

  20. Two-dimensional hazard estimation for longevity analysis

    DEFF Research Database (Denmark)

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

    2004-01-01

    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 i...

  1. 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)

  2. 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.

  3. Thickness identification of two-dimensional materials by optical imaging.

    Science.gov (United States)

    Wang, Ying Ying; Gao, Ren Xi; Ni, Zhen Hua; He, Hui; Guo, Shu Peng; Yang, Huan Ping; Cong, Chun Xiao; Yu, Ting

    2012-12-14

    Two-dimensional materials, e.g. graphene and molybdenum disulfide (MoS(2)), have attracted great interest in recent years. Identification of the thickness of two-dimensional materials will improve our understanding of their thickness-dependent properties, and also help with scientific research and applications. In this paper, we propose to use optical imaging as a simple, quantitative and universal way to identify the thickness of two-dimensional materials, i.e. mechanically exfoliated graphene, nitrogen-doped chemical vapor deposition grown graphene, graphene oxide and mechanically exfoliated MoS(2). The contrast value can easily be obtained by reading the red (R), green (G) and blue (B) values at each pixel of the optical images of the sample and substrate, and this value increases linearly with sample thickness, in agreement with our calculation based on the Fresnel equation. This method is fast, easily performed and no expensive equipment is needed, which will be an important factor for large-scale sample production. The identification of the thickness of two-dimensional materials will greatly help in fundamental research and future applications. PMID:23154446

  4. Thickness identification of two-dimensional materials by optical imaging

    International Nuclear Information System (INIS)

    Two-dimensional materials, e.g. graphene and molybdenum disulfide (MoS2), have attracted great interest in recent years. Identification of the thickness of two-dimensional materials will improve our understanding of their thickness-dependent properties, and also help with scientific research and applications. In this paper, we propose to use optical imaging as a simple, quantitative and universal way to identify the thickness of two-dimensional materials, i.e. mechanically exfoliated graphene, nitrogen-doped chemical vapor deposition grown graphene, graphene oxide and mechanically exfoliated MoS2. The contrast value can easily be obtained by reading the red (R), green (G) and blue (B) values at each pixel of the optical images of the sample and substrate, and this value increases linearly with sample thickness, in agreement with our calculation based on the Fresnel equation. This method is fast, easily performed and no expensive equipment is needed, which will be an important factor for large-scale sample production. The identification of the thickness of two-dimensional materials will greatly help in fundamental research and future applications. (paper)

  5. Dynamic two-dimensional beam-pattern steering technique

    Science.gov (United States)

    Zhou, Shaomin; Yeh, Pochi; Liu, Hua-Kuang

    1993-01-01

    A dynamic two-dimensional laser-beam-pattern steering technique using photorefractive holograms in conjunction with electrically addressed spatial light modulators is proposed and investigated. The experimental results demonstrate the dynamic steering of random combinations of basis beam patterns. The proposed method has the advantages of random beam-pattern combination, good beam intensity uniformity, and higher diffraction efficiency compared with conventional methods.

  6. 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.

  7. 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...

  8. The encoding complexity of two dimensional range minimum data structures

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Brodnik, Andrej; Davoodi, Pooya

    2013-01-01

    In the two-dimensional range minimum query problem an input matrix A of dimension m ×n, m ≤ n, has to be preprocessed into a data structure such that given a query rectangle within the matrix, the position of a minimum element within the query range can be reported. We consider the space complexi...

  9. 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

  10. 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.

  11. Adiabatic single scan two-dimensional NMR spectrocopy.

    Science.gov (United States)

    Pelupessy, Philippe

    2003-10-01

    New excitation schemes, based on the use adiabatic pulses, for single scan two-dimensional NMR experiments (Frydman et al., Proc. Nat. Acad. Sci. 2002, 99, 15 858-15 862) are introduced. The advantages are discussed. Applications in homo- and heteronuclear experiments are presented. PMID:14519020

  12. The Fresnel coefficients of a two-dimensional atomic crystal

    CERN Document Server

    Merano, Michele

    2016-01-01

    I deduce the Fresnel coefficients valid for a generic two dimensional crystal. In general the optical properties of an atomically thin monolayer are interpreted by modelling it as a homogeneous medium with an effective thickness. The comparison with experimental results, published in literature, shows that the Fresnel coefficients are better suited to this end than the above mentioned model.

  13. 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.

  14. Spontaneous emission in two-dimensional photonic crystal microcavities

    DEFF Research Database (Denmark)

    Søndergaard, Thomas

    2000-01-01

    The properties of the radiation field in a two-dimensional photonic crystal with and without a microcavity introduced are investigated through the concept of the position-dependent photon density of states. The position-dependent rate of spontaneous radiative decay for a two-level atom with random...

  15. Two-dimensional nonlinear gauge theories from Hamiltonian BRST cohomology

    Energy Technology Data Exchange (ETDEWEB)

    Bizdadea, C.; Saliu, L.; Saliu, S.O. [Craiova Univ. (Romania)

    2001-03-01

    Consistent couplings among a set of scalar and vector fields in two dimensions are derived along a Hamiltonian BRST deformation procedure based on cohomological techniques. The resulting interactions deform both the gauge transformations and their algebra, and lead to a two-dimensional nonlinear gauge theory. (orig.)

  16. Nonlinear excitations in two-dimensional molecular structures with impurities

    DEFF Research Database (Denmark)

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

    1995-01-01

    We study the nonlinear dynamics of electronic excitations interacting with acoustic phonons in two-dimensional molecular structures with impurities. We show that the problem is reduced to the nonlinear Schrodinger equation with a varying coefficient. The latter represents the influence of the imp...

  17. 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.

  18. 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.

  19. Improvement of an automated protein crystal exchange system PAM for high-throughput data collection

    International Nuclear Information System (INIS)

    A special liquid-nitrogen Dewar with double capacity for the sample-exchange robot has been created at AR-NE3A at the Photon Factory, allowing continuous fully automated data collection. In this work, this new system is described and the stability of its calibration is discussed. Photon Factory Automated Mounting system (PAM) protein crystal exchange systems are available at the following Photon Factory macromolecular beamlines: BL-1A, BL-5A, BL-17A, AR-NW12A and AR-NE3A. The beamline AR-NE3A has been constructed for high-throughput macromolecular crystallography and is dedicated to structure-based drug design. The PAM liquid-nitrogen Dewar can store a maximum of three SSRL cassettes. Therefore, users have to interrupt their experiments and replace the cassettes when using four or more of them during their beam time. As a result of investigation, four or more cassettes were used in AR-NE3A alone. For continuous automated data collection, the size of the liquid-nitrogen Dewar for the AR-NE3A PAM was increased, doubling the capacity. In order to check the calibration with the new Dewar and the cassette stand, calibration experiments were repeatedly performed. Compared with the current system, the parameters of the novel system are shown to be stable

  20. 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

  1. A novel approach to sequence validating protein expression clones with automated decision making

    Directory of Open Access Journals (Sweden)

    Mohr Stephanie E

    2007-06-01

    Full Text Available Abstract Background Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation. Results We have developed an Automated Clone Evaluation (ACE system – the first comprehensive, multi-platform, web-based plasmid sequence verification software package. ACE automates the clone verification process by defining each clone sequence as a list of multidimensional discrepancy objects, each describing a difference between the clone and its expected sequence including the resulting polypeptide consequences. To evaluate clones automatically, this list can be compared against user acceptance criteria that specify the allowable number of discrepancies of each type. This strategy allows users to re-evaluate the same set of clones against different acceptance criteria as needed for use in other experiments. ACE manages the entire sequence validation process including contig management, identifying and annotating discrepancies, determining if discrepancies correspond to polymorphisms and clone finishing. Designed to manage thousands of clones simultaneously, ACE maintains a relational database to store information about clones at various completion stages, project processing parameters and acceptance criteria. In a direct comparison, the automated analysis by ACE took less time and was more accurate than a manual analysis of a 93 gene clone set. Conclusion ACE was designed to facilitate high throughput clone sequence

  2. Transport regulation of two-dimensional receptor-ligand association.

    Science.gov (United States)

    Ju, Lining; Qian, Jin; Zhu, Cheng

    2015-04-01

    The impact of flow disturbances on platelet adhesion is complex and incompletely understood. At the molecular scale, platelet glycoprotein Ibα (GPIbα) must associate with the von Willebrand factor A1 domain (VWF-A1) with a rapid on-rate under high hemodynamic forces, as occurs in arterial thrombosis, where various transport mechanisms are at work. Here, we theoretically modeled the coupled transport-reaction process of the two-dimensional (2D) receptor-ligand association kinetics in a biomembrane force probe to explicitly account for the effects of molecular length, confinement stiffness, medium viscosity, surface curvature, and separation distance. We experimentally verified the theoretical approach by visualizing association and dissociation of individual VWF-A1-GPIbα bonds in a real-time thermal fluctuation assay. The apparent on-rate, reciprocal of the average time intervals between sequential bonds, decreased with the increasing gap distance between A1- and GPIbα-bearing surfaces with an 80-nm threshold (beyond which bond formation became prohibitive) identified as the combined contour length of the receptor and ligand molecules. The biomembrane force probe spring constant and diffusivity of the protein-bearing beads also significantly influenced the apparent on-rate, in accordance with the proposed transport mechanisms. The global agreement between the experimental data and the model predictions supports the hypothesis that receptor-ligand association behaves distinctly in the transport- and reaction-limited scenarios. To our knowledge, our results represent the first detailed quantification of physical regulation of the 2D on-rate that allows platelets to sense and respond to local changes in their hemodynamic environment. In addition, they provide an approach for determining the intrinsic kinetic parameters that employs simultaneous experimental measurements and theoretical modeling of bond association in a single assay. The 2D intrinsic forward rate

  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 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

  6. 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.

  7. 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.

  8. 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.

  9. Object tracking based on two-dimensional PCA

    Science.gov (United States)

    Xu, Fuyuan; Gu, Guohua; Kong, Xiaofang; Wang, Pengcheng; Ren, Kan

    2016-04-01

    In this paper, we present a novel object tracking method based on two-dimensional PCA. The low quality of images and the changes of the object appearance are very challenging for the object tracking. The representation of the training features is usually used to solve these challenges. Two-dimensional PCA (2DPCA) based on the image covariance matrix is constructed directly using the original image matrices. An appearance model is presented and its likelihood estimation has been established based on 2DPCA representation in this paper. Compared with the state-of-the-art methods, our method has higher reliability and real-time property. The performances of the proposed tracking method are quantitatively and qualitatively shown in experiments.

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

    International Nuclear Information System (INIS)

    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 HfO2, 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

  11. 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)

  12. Dynamics of decaying two-dimensional magnetohydrodynamic turbulence

    International Nuclear Information System (INIS)

    High-resolution numerical studies of decaying two-dimensional magnetohydrodynamic turbulence using up to 7682 modes in general periodic systems reveal the following properties: I) the evolution proceeds in a quasi-selfsimilar way with constant kinetic to magnetic energy ratio and constant micro- and macro-scale Reynolds numbers; II) the energy dissipation rate is independent of the values of the dissipation coefficients η, μ; III) the inertial-range energy spectra follow a Kolmogorov law, Ek=Cε2/3k-5/3 with C=3.7±0.3. Small-scale fluctuations are concentrated in the region of weak large-scale magnetic fields. The resulting strong intermittency is analogous to the behavior recently observed in two-dimensional hydrodynamic turbulence (see, for instance, J. Fluid Mech. (1988) 194, 333), with the magnetic field intensity taking the role vorticity plays in hydrodynamic systems. (orig.)

  13. 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...

  14. Two-dimensional simulations of correlation reflectometry in fusion plasmas

    International Nuclear Information System (INIS)

    A two-dimensional wave propagation code, developed specifically to simulate correlation reflectometry in large-scale fusion plasmas, is described. The code makes use of separate computational methods in the vacuum, underdense and reflection regions of the plasma in order to obtain the high computational efficiency necessary for correlation analysis. Simulations of TFTR plasma with internal transport barriers are presented and compared with one-dimensional full-wave simulations. It is shown that the two-dimensional simulations are remarkably similar to the results of the one-dimensional full-wave analysis for a wide range of turbulent correlation lengths. Implications for the interpretation of correlation reflectometer measurements in fusion plasma are discussed. (author). Letter-to-the-editor

  15. Two-dimensional radiative transfer. I. Planar geometry

    International Nuclear Information System (INIS)

    Differential-equation methods for solving the transfer equation in two-dimensional planar geometries are developed. One method, which uses a Hermitian integration formula on ray segments through grid points, proves to be extremely well suited to velocity-dependent problems. An efficient elimination scheme is developed for which the computing time scales linearly with the number of angles and frequencies; we are thus able to treat problems with large velocity amplitudes accurately.A very accurate and efficient method for performing a formal solution is also presented. A discussion is given of several examples of periodic media and freestanding slabs, both in static cases and with velocity fields. For the freestanding slabs, two-dimensional transport effects are significant near boundaries, but no important effects were found in any of the periodic cases that we have studied

  16. F2D: A two dimensional compressible gas flow code

    International Nuclear Information System (INIS)

    The F2D computer code is a general-purpose, two-dimensional, fully compressible thermal-fluids code that models most phenomena found in experimental environments with coupled fluid flow and heat transfer. The code solves momentum, continuity, gas energy, and structure energy equations, simultaneously utilizing a predictor-corrector solution algorithm. The F2D code applied to a particle-bed reactor operating at 5 MW/L with a flow-control cold frit, revealed a skew in the temperature contours caused by two-dimensional flow effects. A thermal-fluid stability analysis of particle-bed and NERVA type reactors reveals similar behavior for the stability threshold

  17. 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.

  18. 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.

  19. 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

  20. Improved Absolute Approximation Ratios for Two-Dimensional Packing Problems

    Science.gov (United States)

    Harren, Rolf; van Stee, Rob

    We consider the two-dimensional bin packing and strip packing problem, where a list of rectangles has to be packed into a minimal number of rectangular bins or a strip of minimal height, respectively. All packings have to be non-overlapping and orthogonal, i.e., axis-parallel. Our algorithm for strip packing has an absolute approximation ratio of 1.9396 and is the first algorithm to break the approximation ratio of 2 which was established more than a decade ago. Moreover, we present a polynomial time approximation scheme (mathcal{PTAS}) for strip packing where rotations by 90 degrees are permitted and an algorithm for two-dimensional bin packing with an absolute worst-case ratio of 2, which is optimal provided mathcal{P} not= mathcal{NP}.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Universal Approach to Cosmological Singularities in Two Dimensional Dilaton Gravity

    OpenAIRE

    Martin, G. N.; Mazzitelli, F. D.

    1994-01-01

    We show that in a large class of two dimensional models with conformal matter fields, the semiclassical cosmological solutions have a weak coupling singularity if the classical matter content is below a certain threshold. This threshold and the approach to the singularity are model-independent. When the matter fields are not conformally invariant, the singularity persists if the quantum state is the vacuum near the singularity, and could dissappear for other quantum states.

  7. 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

  8. 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...

  9. 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.

  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. Robust Two-Dimensional FIR Filter Design for Broadband Beamformers

    OpenAIRE

    Nordebo, Sven

    1995-01-01

    With conventional least squares or Chebyshev approximation methods in the design of a fixed, broadband, delay{and{sum beamformer, the filter weight values may become excessively large. This anomaly is due to large, unspecified regions of the corresponding two{dimensional FIR filter frequency plane. With large filter weight values, the frequency response of the resulting beamformer may be severely degraded due to inaccuracies in sensor positions and/or sensor frequency response. For an adaptiv...

  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. On Two-Dimensional Quaternion Wigner-Ville Distribution

    OpenAIRE

    Mawardi Bahri

    2014-01-01

    In this paper, 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-Vi...

  15. 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 $l \\geq 1$.

  16. Orientational order of the two-dimensional hard disk system

    OpenAIRE

    Jaster, Andreas

    1998-01-01

    We report Monte Carlo results for the two-dimensional hard disk system. Simulations were performed in the NVT ensemble with up to 65536 disks, using a new updating scheme. We analyze the bond orientational order parameter and correlation length in the isotropic phase and the scaling behaviour of the bond orientational order parameter in the transition region. The data are consistent with predictions of the Kosterlitz-Thouless-Halperin-Nelson-Young theory, while a first-order phase transition ...

  17. Stochastic 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 can be calculated theoretically for a certain range of parameters. The theoretical value agrees well with numerical simulations

  18. 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.

  19. Two-dimensional readout in a liquid xenon ionisation chamber

    International Nuclear Information System (INIS)

    A two-dimensional readout with metal strips deposited on both sides of a glass plate is investigated aiming to assess the possibility of its use in a liquid xenon ionisation chamber for positron emission tomography. Here, we present results obtained with an α-source. It is shown that position resolution of ≤1 mm, fwhm, can be achieved for free charge depositions equivalent to those due to γ-rays with energy from 220 down to 110 keV

  20. 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 ...

  1. 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.

  2. 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.

  3. 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.

  4. Anisotropic electronic conduction in stacked two-dimensional titanium carbide

    OpenAIRE

    Tao Hu; Hui Zhang; Jiemin Wang; Zhaojin Li; Minmin Hu; Jun Tan; Pengxiang Hou; Feng Li; Xiaohui Wang

    2015-01-01

    Stacked two-dimensional titanium carbide is an emerging conductive material for electrochemical energy storage which requires an understanding of the intrinsic electronic conduction. Here we report the electronic conduction properties of stacked Ti3C2 T 2 (T = OH, O, F) with two distinct stacking sequences (Bernal and simple hexagonal). On the basis of first-principles calculations and energy band theory analysis, both stacking sequences give rise to metallic conduction with Ti 3d electrons c...

  5. 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...

  6. 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...

  7. Nonlinear Transport in a Two Dimensional Holographic Superconductor

    OpenAIRE

    Zeng, Hua Bi; Tian, Yu; 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 th...

  8. 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.

  9. Dielectric-barrier discharges in two-dimensional lattice potentials

    OpenAIRE

    Sinclair, Josiah; Walhout, Matthew

    2011-01-01

    We use a pin-grid electrode to introduce a corrugated electrical potential into a planar dielectric-barrier discharge (DBD) system, so that the amplitude of the applied electric field has the profile of a two-dimensional square lattice. The lattice potential provides a template for the spatial distribution of plasma filaments in the system and has pronounced effects on the patterns that can form. The positions at which filaments become localized within the lattice unit cell vary with the widt...

  10. 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.

  11. 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.

  12. Two-Dimensional Charge Transport in Disordered Organic Semiconductors

    OpenAIRE

    Brondijk, J. J.; Roelofs, WSC Christian; Mathijssen, SGJ Simon; Shehu, A; Cramer, T.; Biscarini, F Fabio; Blom, PWM Paul; Leeuw, van der, R.

    2012-01-01

    We analyze the effect of carrier confinement on the charge-transport properties of organic field-effect transistors. Confinement is achieved experimentally by the use of semiconductors of which the active layer is only one molecule thick. The two-dimensional confinement of charge carriers provides access to a previously unexplored charge-transport regime and is reflected by a reduced temperature dependence of the transfer curves of organic monolayer transistors.

  13. Band Gap Engineering of Two-Dimensional Nitrogene

    OpenAIRE

    Lee, Jason; Wang, Wei-Liang; Yao, Dao-Xin

    2016-01-01

    Recently, two-dimensional honeycomb monolayers of pnictogen have been predicted. In particular, the honeycomb monolayer of nitrogen has been studied, and we call it nitrogene. In this paper, we investigate the band structure of nitrogene under various conditions: stacking of monolayers, biaxial tensile strain, and perpendicular electric field. The band gap of nitrogene is found to decrease with increasing number of layers. The perpendicular electric field can also decrease the energy gap, and...

  14. 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....

  15. 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.

  16. 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 ...

  17. Colloquium: Transport in strongly correlated two dimensional electron fluids

    Science.gov (United States)

    Spivak, B.; Kravchenko, S. V.; Kivelson, S. A.; Gao, X. P. A.

    2010-04-01

    An overview of the measured transport properties of the two dimensional electron fluids in high mobility semiconductor devices with low electron densities is presented as well as some of the theories that have been proposed to account for them. Many features of the observations are not easily reconciled with a description based on the well understood physics of weakly interacting quasiparticles in a disordered medium. Rather, they reflect new physics associated with strong correlation effects, which warrant further study.

  18. 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.

  19. Fresnel coefficients of a two-dimensional atomic crystal

    OpenAIRE

    Merano, Michele

    2015-01-01

    In general the experiments on the linear optical properties of a single-layer two-dimensional atomic crystal are interpreted by modeling it as a homogeneous slab with an effective thickness. Here I fit the most remarkable experiments in graphene optics by using the Fresnel coefficients, fixing both the surface susceptibility and the surface conductivity of graphene. It is shown that the Fresnel coefficients and the slab model are not equivalent. Experiments indicate that the Fresnel coefficie...

  20. TOPICAL REVIEW: Nonlinear two-dimensional vibrational spectroscopy of peptides

    Science.gov (United States)

    Woutersen, Sander; Hamm, Peter

    2002-10-01

    In this overview, we discuss theoretical and experimental aspects of nonlinear two-dimensional infrared (2D-IR) spectroscopy. With this technique both peptide conformation and conformational flexibility can be probed. The quantitative relation between the experimental 2D-IR spectrum and the peptide conformation is discussed, and examples of how the conformation of a peptide and the timescale of its fluctuations are derived from its (time-resolved) 2D spectrum are presented.

  1. Kolmogorov's law for two-dimensional electron-magnetohydrodynamic turbulence

    OpenAIRE

    Celani, A.; Prandi, R.; Boffetta, G

    1997-01-01

    The analogue of the Kolmogorov's four-fifths law is derived for two-dimensional, homogeneous, isotropic EMHD turbulence in the energy cascade inertial range. Direct numerical simulations for the freely decaying case show that this relation holds true for different values of the adimensional electron inertial length scale, $d_e$. The energy spectrum is found to be close to the expected Kolmogorov spectrum.

  2. 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...

  3. Compressibility sum rule for the two-dimensional electron gas.

    Science.gov (United States)

    Das, M P; Golden, K I; Green, F

    2001-07-01

    The authors establish formulas for the isothermal compressibility and long-wavelength static density-density response function of a weakly correlated two-dimensional electron gas in the 1pressure calculation in the latter domain is based on the Totsuji classical cluster-expansion formula for the correlation energy [H. Totsuji, J. Phys. Soc. Jpn. 40, 857 (1976); Phys. Rev. A 19, 889 (1979)]. PMID:11461304

  4. Numerical Computation of Two Dimensional Wind Accretion of Isothermal Gas

    OpenAIRE

    Shima, Eiji; Matsuda, Takuya; Anzer, Ulrich; Borner, Gerhard; Boffin, Henri M. J.

    1998-01-01

    A new numerical algorithm for calculating isothermal wind accretion flows has been developed and is applied here to the analysis of the hydrodynamics of two-dimensional plane symmetric accretion flows in wind-fed sources. Polar coordinates are used to ensure fine resolution near the object. It is found that a thin accretion column is formed which shows wave-like oscillations. Small accretion disks are formed temporarily around the object. Mass accretion rate and angular momentum accretion rat...

  5. Scaling relations in two-dimensional relativistic hydrodynamic turbulence

    Science.gov (United States)

    Westernacher-Schneider, John Ryan; Lehner, Luis; Oz, Yaron

    2015-12-01

    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 black hole/black brane spacetimes with anti-de Sitter asymptotics should exhibit similar scaling relations.

  6. Two-dimensional multi-fluid tokamak transport code

    International Nuclear Information System (INIS)

    A code is presented which describes the time evolution of axisymmetric plasmas of arbitrary cross section in toroidal geometries. Assuming that flux surface shapes change more slowly than plasma parameters, transport can be regarded as proceeding through a sequence of magnetohydrodynamic equilibria. This assumption suggests an algorithm which involves iteration between one-dimensional transport calculations and two-dimensional equilibrium calculations. Numerical results pertaining to the accuracy of the code and the validity of the algorithm are presented

  7. Anisotropic mass density by two-dimensional acoustic metamaterials

    OpenAIRE

    Torrent Martí, Daniel; Sánchez-Dehesa Moreno-Cid, José

    2008-01-01

    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 prop...

  8. Acoustic resonances in two dimensional radial sonic crystals shells

    OpenAIRE

    Torrent, Daniel; Sánchez-Dehesa, José

    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 ...

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

    OpenAIRE

    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...

  10. Two-dimensional hexagonal smectic structure formed by topological defects

    Science.gov (United States)

    Dolganov, P. V.; Shuravin, N. S.; Fukuda, Atsuo

    2016-03-01

    A two-dimensional hexagonal smectic structure formed by point topological defects and intersecting defect walls was discovered. This unique structure was predicted theoretically about 30 years ago but not observed. For a long time the hexagonal structure was a challenge for experimentalists. A different type of self-organization in smectic films was found and used to form the hexagonal structure. Methods applied for building the hexagonal phase can be used for the formation of complicated liquid-crystal structures.

  11. 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...

  12. 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...

  13. 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...

  14. Exact analytic flux distributions for two-dimensional solar concentrators.

    Science.gov (United States)

    Fraidenraich, Naum; Henrique de Oliveira Pedrosa Filho, Manoel; Vilela, Olga C; Gordon, Jeffrey M

    2013-07-01

    A new approach for representing and evaluating the flux density distribution on the absorbers of two-dimensional imaging solar concentrators is presented. The formalism accommodates any realistic solar radiance and concentrator optical error distribution. The solutions obviate the need for raytracing, and are physically transparent. Examples illustrating the method's versatility are presented for parabolic trough mirrors with both planar and tubular absorbers, Fresnel reflectors with tubular absorbers, and V-trough mirrors with planar absorbers. PMID:23842256

  15. 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.

  16. 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.

  17. 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.)

  18. GEPOIS: a two dimensional nonuniform mesh Poisson solver

    International Nuclear Information System (INIS)

    A computer code is described which solves Poisson's equation for the electric potential over a two dimensional cylindrical (r,z) nonuniform mesh which can contain internal electrodes. Poisson's equation is solved over a given region subject to a specified charge distribution with either Neumann or Dirichlet perimeter boundary conditions and with Dirichlet boundary conditions on internal surfaces. The static electric field is also computed over the region with special care given to normal electric field components at boundary surfaces

  19. 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...

  20. 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.

  1. 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.

  2. 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.

  3. Constraints and hidden symmetry in two-dimensional gravity

    International Nuclear Information System (INIS)

    We study the hidden symmetry of Polyakov two-dimensional gravity by means of first-class constraints. These are obtained from the combination of Fourier mode expansions of the usual (second-class) constraints of the theory. We show that, more than the usual SL(2,R), there is a hidden Virasoro symmetry in the theory. The results of the above analysis are also confirmed from the point of view of a geometrical symplectic treatment

  4. 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...

  5. 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 of...... angle-dependent response of a single split ring resonator, revealing the importance of cross coupling between electric dipoles and magnetic dipoles for quantifying the pseudochiral response under oblique incidence of split ring lattices....

  6. A study on correlation effects in two dimensional topological insulators

    OpenAIRE

    Tada, Y; Peters, R; Oshikawa, M.; Koga, A.; Kawakami, N.; Fujimoto, S.

    2012-01-01

    We investigate correlation effects in two dimensional topological insulators (TI). In the first part, we discuss finite size effects for interacting systems of different sizes in a ribbon geometry. For large systems, there are two pairs of well separated massless modes on both edges. For these systems, we analyze the finite size effects using a standard bosonization approach. For small systems, where the edge states are massive Dirac fermions, we use the inhomogeneous dynamical mean field the...

  7. Two-Dimensional Immobilized Metal Affinity Electrophoresis for Capturing a Phosphoprotein

    OpenAIRE

    Gupta, Shalini; Lasanthi, G.D.; Jayathilaka, P.; Huang, Jin-Sheng; Lee, Bao-Shiang

    2010-01-01

    A two-dimensional immobilized metal affinity electrophoresis method is described here. In this method, ferric ions are immobilized in the second-dimensional polyacrylamide gel to extract the phosphoprotein β-casein from a mixture containing proteins with a broad range of pI and MW. Native 7.5–15% gradient tris-glycine gel with SDS tris-glycine gel running buffer are used so that proteins can be separated according to their molecular mass in the second dimension.

  8. 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].

  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. 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.

  11. 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.

  12. 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

  13. Assay of mouse-cell clones for retrovirus p30 protein by use of an automated solid-state radioimmunoassay

    International Nuclear Information System (INIS)

    A solid-state radioimmunoassay system has been developed that is useful for automated analysis of samples in microtiter plates. Assays for interspecies and type-specific antigenic determinants of the C-type retrovirus protein, p30, have been used to identify clones of cells producing this protein. This method allows testing of at least 1000 clones a day, making it useful for studies of frequencies of virus protein induction, defective virus production, and formation of recombinant viruses

  14. Exploring the potential of two-dimensional electronic spectroscopy

    International Nuclear Information System (INIS)

    During the last decade multi-dimensional ultrafast spectroscopies have shown great potential by opening an increasingly broad experimental window into the structure and dynamics of atomic and molecular systems on femtosecond and picosecond timescales. The versatility and significance of two-dimensional electronic spectroscopy relies on the gain of additional information obtained by spreading the spectra into two frequency dimensions. The present work summarizes part of our efforts in the field of two-dimensional electronic spectroscopy. The progress thereby ran parallel on two tracks: on the one hand, improvements in the instrumentation have led to a broader applicability of the method. By implementing a compact, easy to align, and passively phasestabilized setup for recording two-dimensional electronic spectra in three different phase-matching directions, it has become possible to study not only single-quantum but also double-quantum coherences. On the other hand, the existing methods have been applied to study the electronic and vibronic dynamics of molecular systems of varying complexity. An electronic two-level system whose electronic transition is coupled to a low-frequency vibrational mode has served as a starting point in our investigations. The vibronic wave packet that is induced by excitation with a femtosecond laser pulse manifests itself in oscillating line-shapes in the two-dimensional spectra. In a second step, the line-shape dynamics of a monomer-dimer system in equilibrium have been investigated. It was found that exciton delocalization effects in the dimer strongly influence the timescale of spectral diffusion. The degree of complexity reached its maximum in the investigation of pathways and timescales of energy transfer in double-wall cylindrical J-aggregates. Exciton dynamics in these molecular nanotubes have been characterized by temporal, energetic, and spatial properties. In addition, the double-exciton manifold of C8S3 aggregates has been

  15. Automating gene library synthesis by structure-based combinatorial protein engineering: examples from plant sesquiterpene synthases.

    Science.gov (United States)

    Dokarry, Melissa; Laurendon, Caroline; O'Maille, Paul E

    2012-01-01

    Structure-based combinatorial protein engineering (SCOPE) is a homology-independent recombination method to create multiple crossover gene libraries by assembling defined combinations of structural elements ranging from single mutations to domains of protein structure. SCOPE was originally inspired by DNA shuffling, which mimics recombination during meiosis, where mutations from parental genes are "shuffled" to create novel combinations in the resulting progeny. DNA shuffling utilizes sequence identity between parental genes to mediate template-switching events (the annealing and extension of one parental gene fragment on another) in PCR reassembly reactions to generate crossovers and hence recombination between parental genes. In light of the conservation of protein structure and degeneracy of sequence, SCOPE was developed to enable the "shuffling" of distantly related genes with no requirement for sequence identity. The central principle involves the use of oligonucleotides to encode for crossover regions to choreograph template-switching events during PCR assembly of gene fragments to create chimeric genes. This approach was initially developed to create libraries of hybrid DNA polymerases from distantly related parents, and later developed to create a combinatorial mutant library of sesquiterpene synthases to explore the catalytic landscapes underlying the functional divergence of related enzymes. This chapter presents a simplified protocol of SCOPE that can be integrated with different mutagenesis techniques and is suitable for automation by liquid-handling robots. Two examples are presented to illustrate the application of SCOPE to create gene libraries using plant sesquiterpene synthases as the model system. In the first example, we outline how to create an active-site library as a series of complex mixtures of diverse mutants. In the second example, we outline how to create a focused library as an array of individual clones to distil minimal combinations of

  16. The NASA Ames Research Center one- and two-dimensional stratospheric models. Part 2: The two-dimensional model

    Science.gov (United States)

    Whitten, R. C.; Borucki, W. J.; Watson, V. R.; Shimazaki, T.; Woodward, H. T.; Riegel, C. A.; Capone, L. A.; Becker, T.

    1977-01-01

    The two-dimensional model of stratospheric constituents is presented in detail. The derivation of pertinent transport parameters and the numerical solution of the species continuity equations, including a technique for treating the stiff differential equations that represent the chemical kinetic terms, and appropriate methods for simulating the diurnal variations of the solar zenith angle and species concentrations are discussed. Predicted distributions of tracer constituents (ozone, carbon 14, nitric acid) are compared with observed distributions.

  17. 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.

  18. The Stanford Automated Mounter: Enabling High-Throughput Protein Crystal Screening at SSRL

    International Nuclear Information System (INIS)

    The macromolecular crystallography experiment lends itself perfectly to high-throughput technologies. The initial steps including the expression, purification, and crystallization of protein crystals, along with some of the later steps involving data processing and structure determination have all been automated to the point where some of the last remaining bottlenecks in the process have been crystal mounting, crystal screening, and data collection. At the Stanford Synchrotron Radiation Laboratory, a National User Facility that provides extremely brilliant X-ray photon beams for use in materials science, environmental science, and structural biology research, the incorporation of advanced robotics has enabled crystals to be screened in a true high-throughput fashion, thus dramatically accelerating the final steps. Up to 288 frozen crystals can be mounted by the beamline robot (the Stanford Auto-Mounting System) and screened for diffraction quality in a matter of hours without intervention. The best quality crystals can then be remounted for the collection of complete X-ray diffraction data sets. Furthermore, the entire screening and data collection experiment can be controlled from the experimenter's home laboratory by means of advanced software tools that enable network-based control of the highly automated beamlines.

  19. 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.

  20. 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.

  1. 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

  2. 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)

  3. 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.

  4. 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.

  5. 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

  6. Interbasis expansions in a two-dimensional hydrogen atom

    International Nuclear Information System (INIS)

    It is shown that the expansion coefficients of parabolic sub-bases of a two-dimensional hydrogen atom over polar subbases are expressed in terms of a generalized hypergeometric function 3F2 at the argument x=1. Exapansions of an elliptic basis over the polar and parabolic ones are studied as well. The limits R → 0 and R → infinity (R is a parameter of the definition of elictic coordinates) are traced in elliptic-basis expansions, and formulas are found for the expansion coefficients of the elliptic basis in terms of the elliptic separation constant

  7. Symmetry Reduction of the Two-Dimensional Ricci Flow Equation

    OpenAIRE

    Mehdi Nadjafikhah; Mehdi Jafari

    2013-01-01

    This paper is devoted to obtain the one-dimensional group invariant solutions of the two-dimensional Ricci flow ((2D) Rf) equation. By classifying the orbits of the adjoint representation of the symmetry group on its Lie algebra, the optimal system of one-dimensional subalgebras of the ((2D) Rf) equation is obtained. For each class, we will find the reduced equation by the method of similarity reduction. By solving these reduced equations, we will obtain new sets of group invariant solutions...

  8. Aharonov-Bohm detection of two-dimensional magnetostatic cloaks

    Science.gov (United States)

    Valagiannopoulos, Constantinos A.; Askarpour, Amir Nader; Alù, Andrea

    2015-12-01

    Two-dimensional magnetostatic cloaks, even when perfectly designed to mitigate the magnetic field disturbance of a scatterer, may be still detectable with Aharonov-Bohm (AB) measurements, and therefore may affect quantum interactions and experiments with elongated objects. We explore a multilayered cylindrical cloak whose permeability profile is tailored to nullify the magnetic-flux perturbation of the system, neutralizing its effect on AB measurements, and simultaneously optimally suppress the overall scattering. In this way, our improved magnetostatic cloak combines substantial mitigation of the magnetostatic scattering response with zero detectability by AB experiments.

  9. 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.

  10. Stochastic 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 numerically. 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 the authors can calculate theoretically for a certain range of parameters. A scaling law derived using percollation theory is also compared to the numerical results. 1 ref

  11. 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

  12. Mass Transport Velocity in a Two-dimensional Wave Tank

    Directory of Open Access Journals (Sweden)

    M. S. Parvin

    2014-12-01

    Full Text Available Waves occurred on the surface of water in two-dimensional wave tank are studied. Deriving vorticity equation from incompressible Navier-Stokes equation, the boundary condition on the free surface, water bottom and flap surface are discussed. Using separation of variable method, velocity potential takes the general form in terms of eigen function. To obtain the values of horizontal and vertical velocity components, the boundary conditions on the water bottom and the flap surface are used and then mass transport velocity has been derived. Finally, time average of horizontal velocity component at mean water level is generalized.

  13. 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.

  14. Strings and two-dimensional QCD for finite N

    International Nuclear Information System (INIS)

    The string theory description of SU(N) Yang-Mills on an arbitrary two-dimensional manifold, previously developed for the large N asymptotic expansion, is extended to include finite values of N. The theory is considered from two points of view, first using a canonical Hamiltonian formulation, second using a global description of the partition function. In both formalisms, the effect on the string theory of taking a finite value of N is described by a local projection operator which has a simple description in terms of the symmetric group Sn. ((orig.))

  15. Solving time-dependent two-dimensional eddy current problems

    Science.gov (United States)

    Lee, Min Eig; Hariharan, S. I.; Ida, Nathan

    1990-01-01

    Transient eddy current calculations are presented for an EM wave-scattering and field-penetrating case in which a two-dimensional transverse magnetic field is incident on a good (i.e., not perfect) and infinitely long conductor. The problem thus posed is of initial boundary-value interface type, where the boundary of the conductor constitutes the interface. A potential function is used for time-domain modeling of the situation, and finite difference-time domain techniques are used to march the potential function explicitly in time. Attention is given to the case of LF radiation conditions.

  16. 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

  17. Qualification of the two-dimensional transport code Paragon

    International Nuclear Information System (INIS)

    PARAGON is a new two-dimensional transport based on collision probability/coupled interface currents methods and written entirely in FORTRAN 90/95. The qualification of PARAGON has been completed and the results are very good. This qualification included a number of critical experiments. Comparisons to the Monte Carlo code MCNP for a wide variety of PWR assembly lattice types were also performed. In addition, PARAGON-based core simulator models have been compared against PWR plant start up and operational data for a large number of plants. Some results of these calculations and also comparisons against models developed with a licensed Westinghouse lattice code, PHOENIX-P, will be presented

  18. 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.

  19. 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.

  20. Minimal quantization of two-dimensional models with chiral anomalies

    International Nuclear Information System (INIS)

    Two-dimensional gauge models with chiral anomalies - ''left-handed'' QED and the chiral Schwinger model, are quantized consistently in the frames of the minimal quantization method. The choice of the cone time as a physical time for system of quantization is motivated. The well-known mass spectrum is found but with a fixed value of the regularization parameter a=2. Such a unique solution is obtained due to the strong requirement of consistency of the minimal quantization that reflects in the physically motivated choice of the time axis

  1. 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.

  2. 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.

  3. On surface properties of two-dimensional percolation clusters

    OpenAIRE

    de Queiroz, S. L. A.

    1995-01-01

    The two-dimensional site percolation problem is studied by transfer-matrix methods on finite-width strips with free boundary conditions. The relationship between correlation-length amplitudes and critical indices, predicted by conformal invariance, allows a very precise determination of the surface decay-of-correlations exponent, $\\eta_s = 0.6664 \\pm 0.0008$, consistent with the analytical value $\\eta_s = 2/3$. It is found that a special transition does not occur in the case, corroborating ea...

  4. Nonlinear conductivity of two-dimensional Coulomb glasses

    OpenAIRE

    Caravaca, M.; Somoza, A. M.; Ortuño, M.

    2011-01-01

    We have studied the nonlinear conductivity of two-dimensional Coulomb glasses. We have used a Monte Carlo algorithm to simulate the dynamic of the system under an applied electric field $E$. We found that in the nonlinear regime the site occupancy in the Coulomb gap follows a Fermi-Dirac distribution with an effective temperature $T_{\\rm eff}$, higher than the phonon bath temperature $T$. The value of the effective temperature is compatible with that obtained for slow modes from the generaliz...

  5. Optimum high temperature strength of two-dimensional nanocomposites

    Directory of Open Access Journals (Sweden)

    M. A. Monclús

    2013-11-01

    Full Text Available High-temperature nanoindentation was used to reveal nano-layer size effects on the hardness of two-dimensional metallic nanocomposites. We report the existence of a critical layer thickness at which strength achieves optimal thermal stability. Transmission electron microscopy and theoretical bicrystal calculations show that this optimum arises due to a transition from thermally activated glide within the layers to dislocation transmission across the layers. We demonstrate experimentally that the atomic-scale properties of the interfaces profoundly affect this critical transition. The strong implications are that interfaces can be tuned to achieve an optimum in high temperature strength in layered nanocomposite structures.

  6. Optimum high temperature strength of two-dimensional nanocomposites

    International Nuclear Information System (INIS)

    High-temperature nanoindentation was used to reveal nano-layer size effects on the hardness of two-dimensional metallic nanocomposites. We report the existence of a critical layer thickness at which strength achieves optimal thermal stability. Transmission electron microscopy and theoretical bicrystal calculations show that this optimum arises due to a transition from thermally activated glide within the layers to dislocation transmission across the layers. We demonstrate experimentally that the atomic-scale properties of the interfaces profoundly affect this critical transition. The strong implications are that interfaces can be tuned to achieve an optimum in high temperature strength in layered nanocomposite structures

  7. Optimum high temperature strength of two-dimensional nanocomposites

    Energy Technology Data Exchange (ETDEWEB)

    Monclús, M. A.; Molina-Aldareguía, J. M., E-mail: jon.molina@imdea.org [IMDEA Materials Institute, C/Eric Kandel 2, 28906 Getafe, Madrid (Spain); Zheng, S. J.; Mayeur, J. R.; Beyerlein, I. J.; Mara, N. A. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Polcar, T. [Czech Technical University in Prague, Technická 2, Prague 6 (Czech Republic); Llorca, J. [IMDEA Materials Institute, C/Eric Kandel 2, 28906 Getafe, Madrid (Spain); Department of Materials Science, Polytechnic University of Madrid, E. T. S. de Ingenieros de Caminos, 28040 Madrid (Spain)

    2013-11-01

    High-temperature nanoindentation was used to reveal nano-layer size effects on the hardness of two-dimensional metallic nanocomposites. We report the existence of a critical layer thickness at which strength achieves optimal thermal stability. Transmission electron microscopy and theoretical bicrystal calculations show that this optimum arises due to a transition from thermally activated glide within the layers to dislocation transmission across the layers. We demonstrate experimentally that the atomic-scale properties of the interfaces profoundly affect this critical transition. The strong implications are that interfaces can be tuned to achieve an optimum in high temperature strength in layered nanocomposite structures.

  8. 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

  9. 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.

  10. Dynamic Multiscaling in Two-dimensional Fluid Turbulence

    CERN Document Server

    Ray, Samriddhi Sankar; Perlekar, Prasad; Pandit, Rahul

    2011-01-01

    We obtain, by extensive direct numerical simulations, time-dependent and equal-time structure functions for the vorticity, in both quasi-Lagrangian and Eulerian frames, for the direct-cascade regime in two-dimensional fluid turbulence with air-drag-induced friction. We show that different ways of extracting time scales from these time-dependent structure functions lead to different dynamic-multiscaling exponents, which are related to equal-time multiscaling exponents by different classes of bridge relations; for a representative value of the friction we verify that, given our error bars, these bridge relations hold.

  11. On bosonization ambiguities of two dimensional quantum electrodynamics

    International Nuclear Information System (INIS)

    We study bosonization ambiguities in two dimensional quantum electrodynamics in the presence and in the absence of topologically charged gauge fields. The computation of fermionic correlation functions gives us a mechanism to fix the ambiguities in nontrivial topologies, provided that we do not allow changes of sector as we evaluate functional integrals. This removes an infinite arbitrariness from the theory. In the case of trivial topologies, we find upper and lower bounds for the Jackiw-Rajaraman parameter, corresponding to the limiting cases of regularizations which preserve gauge or chiral symmetry. (author). 19 refs

  12. 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

  13. 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.

  14. Two-dimensional electrodynamics and the global structure of space

    Energy Technology Data Exchange (ETDEWEB)

    McHale, G.; Jaroszkiewicz, G.A.

    1986-08-01

    Two-dimensional electrodynamics based on the spacetime S/sup 1/ x R is formulated using Fourier series and Dirac's constraint theory. The role of the background electric field F as a dynamical variable is established. The background field is shown to be unstable against a class of charged pair creation processes involving the global topology of S/sup 1/ provided (F)> 1/2e, where e is the unit of electric charge. The results do not require any discussion of the Coulomb Green function or of the role of charges on spatial boundaries.

  15. Two-dimensional electrodynamics and the global structure of space

    International Nuclear Information System (INIS)

    Two-dimensional electrodynamics based on the spacetime S1 x R is formulated using Fourier series and Dirac's constraint theory. The role of the background electric field F as a dynamical variable is established. The background field is shown to be unstable against a class of charged pair creation processes involving the global topology of S1 provided (F)> 1/2e, where e is the unit of electric charge. The results do not require any discussion of the Coulomb Green function or of the role of charges on spatial boundaries. (author)

  16. Transport in two dimensional electronic micro-emulsions

    International Nuclear Information System (INIS)

    In two dimensional electron systems with Coulomb or dipolar interactions, a direct transition, whether first or second order, from a liquid to a crystalline state is forbidden. As a result, between these phases there must be other (micro-emulsion) phases which can be viewed as a meso-scale mixture of the liquid and crystalline phases. We investigate the transport properties of these new electronic phases and present arguments that they are responsible for the various transport anomalies that have been seen in experiments on the strongly correlated 2DEG in high mobility semiconductor devices with low electron densities

  17. Two-Dimensional Scandium Carbide Monolayer and its Nanotubes

    OpenAIRE

    Wang, Jing; Ma, Hong-Man; Liu, Ying(College of Nuclear Science and Technology, Beijing Normal University, 100875, Beijing, China)

    2015-01-01

    A two-dimensional scandium carbide monolayer with a Sc3C10 primitive cell (Sc3C10 sheet) has been identified using first-principles density functional theory. In the Sc3C10 sheet, there is a similar basic structure to the one in the Volleyballene Sc20C60, the Sc8C10 subunit, in which two connected carbon pentagons are surrounded by one scandium octagon. The hybridization between Sc d orbitals and C s-p orbitals is crucial for stabilizing the Sc3C10 sheet. Ab initio molecular dynamics simulati...

  18. Interacting bosons in two-dimensional flat band systems

    Science.gov (United States)

    Pudleiner, Petra; Mielke, Andreas

    2015-08-01

    The Hubbard model of bosons on two dimensional lattices with a lowest flat band is discussed. In these systems there is a critical density, where the ground state is known exactly and can be represented as a charge density wave. Above this critical filling, depending on the lattice structure and the interaction strength, the additional particles are either delocalised and condensate in the ground state, or they form pairs. Pairs occur at strong interactions, e.g., on the chequerboard lattice. The general mechanism behind this phenomenon is discussed.

  19. Fresnel coefficients of a two-dimensional atomic crystal

    Science.gov (United States)

    Merano, Michele

    2016-01-01

    In general the experiments on the linear optical properties of a single-layer two-dimensional atomic crystal are interpreted by modeling it as a homogeneous slab with an effective thickness. Here I fit the most remarkable experiments in graphene optics by using the Fresnel coefficients, fixing both the surface susceptibility and the surface conductivity of graphene. It is shown that the Fresnel coefficients and the slab model are not equivalent. Experiments indicate that the Fresnel coefficients are able to simulate the overall experiments here analyzed, while the slab model fails to predict absorption and the phase of the reflected light.

  20. Approximation algorithms for maximum two-dimensional pattern matching

    Energy Technology Data Exchange (ETDEWEB)

    Arikati, S.R. [Memphis Univ., TN (United States); Dessmark, A.; Lingas, A. [Lund Univ. (Sweden); Marathe, M.

    1996-07-01

    We introduce the following optimization version of the classical pattern matching problem (referred to as the maximum pattern matching problem). Given a two-dimensional rectangular text and a 2- dimensional rectangular pattern find the maximum number of non- overlapping occurrences of the pattern in the text. Unlike the classical 2-dimensional pattern matching problem, the maximum pattern matching problem is NP - complete. We devise polynomial time approximation algorithms and approximation schemes for this problem. We also briefly discuss how the approximation algorithms can be extended to include a number of other variants of the problem.