Sample records for agar diffusion method

  1. Improved agar diffusion method for detecting residual antimicrobial agents.

    PubMed

    Tsai, C E; Kondo, F

    2001-03-01

    The improved agar diffusion method for determination of residual antimicrobial agents was investigated, and the sensitivities of various combinations of test organisms and assay media were determined using 7 organisms, 5 media, and 31 antimicrobial agents. Bacillus stearothermophilus and synthetic assay medium (SAM) showed the greatest sensitivity for screening penicillins (penicillin G and ampicillin). The combination of Bacillus subtilis and minimum medium (MM) was the most sensitive for tetracyclines (oxytetracycline and chlortetracycline), B. stearothermophilus and SAM or Micrococcus luteus and Mueller-Hinton agar (MHA) for detecting tylosin and erythromycin, B. subtilis and MHA for aminoglycosides (streptomycin, kanamycin, gentamicin, and dihydrostreptomycin), B. stearothermophilus and SAM for polyethers (salinomycin and lasalocid), and B. subtilis and MM or Clostridium perfringens and GAM for polypeptides (thiopeptin, enramycin, virginiamycin, and bacitracin). However, gram-negative bacterium Escherichia coli ATCC 27166 and MM were better for screening for colistin and polymixin-B. For detecting the synthetic drugs tested, the best combination was B. subtilis and MM for sulfonamides, E. coli 27166 and MM for quinolones (oxolinic acid and nalidixic acid), B. subtilis and MM for furans (furazolidone), and the bioluminescent bacterium Photobacterium phosphoreum and luminescence assay medium for chloramphenicol and oxolinic acid. The results showed that the use of four assay plates, B. stearothermophilus and SAM, B. subtilis and MM, M. luteus and MHA, and E. coli 27166 and MM, was superior to the currently available techniques for screening for residual antimicrobial agents in edible animal tissues. PMID:11252480

  2. Antimicrobial susceptibility of Neisseria gonorrhoeae isolates determined by the agar dilution, disk diffusion and Etest methods: comparison of results using GC agar and chocolate agar

    Microsoft Academic Search

    Chun-Hsing Liao; Chih-Cheng Lai; Meng-Shuian Hsu; Fang-Yeh Chu; Mei-Yu Wu; Yu-Tsung Huang; Po-Ren Hsueh

    2010-01-01

    Although the use of GC agar for determining Neisseria gonorrhoeae antimicrobial susceptibilities is suggested by Clinical and Laboratory Standard Institute (CLSI) guidelines, chocolate agar is still used in some regions owing to its low cost and availability. To determine the differences in susceptibilities determined using GC and chocolate agars, 163 non-duplicate N. gonorrhoeae isolates were tested. Minimum inhibitory concentrations (MICs)

  3. Comparison of the Cobas-Bact five-hour susceptibility testing system with the NCCLS agar diffusion and dilution methods

    Microsoft Academic Search

    J. Wrist I; W. Heizmann; U. Hardegger; B. Manncke

    1988-01-01

    The results of susceptibility tests performed by the Cobas-Bact system were compared with those of the NCCLS agar diffusion (Kirby-Bauer) and NCCLS agar dilution methods. A total of 998 clinical isolates were tested against 10 to 18 antimicrobial agents. Essential agreement (comprising full agreement and minor discrepancies) varied from 90.5 % to 99.2 % on comparison of Cobas-Bact with Kirby-Bauer

  4. Comparison of disc diffusion & E test methods with agar dilution for antimicrobial susceptibility testing of Haemophilus influenzae

    Microsoft Academic Search

    Anand Manoharan; Rekha Pai; V. Shankar; Kurien Thomas; M. K. Lalitha

    2003-01-01

    Methods: A total of 46 isolates of H. influenzae from various invasive sites were included as test strains. Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method for ampicillin, chloramphenicol, trimethoprim-sulphamethoxazole (TMP-SMZ) and cefotaxime. Minimum Inhibitory Concentration (MIC) determination was performed by E test and agar dilution for the same set of antimicrobials. All tests were performed on Haemophilus

  5. Tentative Inhibition Zone Criteria (Bauer-Kirby Agar Disk Diffusion Method) for Rifampin against Staphylococci

    Microsoft Academic Search

    Walter H. Traub; Marlene Spohr; Dierk Bauer

    1987-01-01

    Two of 359 (0.6%) clinical isolates of Staphylococcus aureus and 12 of 218 (5.5%) clinical isolates of coagulase-negative staphylococci were resistant or of intermediate susceptibility against rifampin as based on minimal inhibitory concentration (MIC) breakpoints obtained with the agar dilution method: MIC ?2 ?g\\/ml = resistant; MIC 0.25–1 ?g\\/ml = intermediate susceptible; MIC ?0.125 ?g\\/ml= susceptible. The following inhibition zone

  6. [Study of antibiotic sensitivity of microorganisms by the method of diffusion in agar layers].

    PubMed

    Serov, G D; Sizov, A A

    1998-03-01

    The proposed method for assessing microorganism sensitivity in solid and semisolid liquid nutrient media provides more accurate results and permits isolation of resistant forms of bacteria and studies of antibiotic interactions. Bacteriological study of latent growth zones of bacteria, although rather long, makes the results more reliable. The method can be used for assessing the microflora sensitivity in patients without resorting to isolation of pure cultures and in biotechnology for isolation of new antibiotics. PMID:9575733

  7. The antibacterial activity of sodium hypochlorite and chlorhexidine against Enterococcus faecalis: A review on agar diffusion and direct contact methods.

    PubMed

    Luddin, Norhayati; Ahmed, Hany Mohamed Aly

    2013-01-01

    Complete debridement and disinfection of the root canal system are fundamental requirements for successful endodontic treatment. Despite the morphological challenges of the internal root anatomy, root canal irrigants play an important role in the optimization of the root canal preparation, which is essentially a chemo-mechanical procedure. Enterococcus faecalis is one of the most resistant microorganisms that dominants the microbial ecosystem of persistent periradicular lesions in retreatment cases. For that reason, many in vitro and in vivo studies evaluated and compared the antibacterial activity of sodium hypochlorite and chlorhexidine at varying concentrations using different experimental models against this microorganism. However, many controversies with regard to the ideal irrigant and concentration do in fact exist. Hence, this review aims to discuss the antibacterial activity of these two main root canal irrigants against Enterococcus faecalis using the agar diffusion and direct contact methods and the possible modulating factors responsible for inconsistent findings among different studies. In addition, the disinfection potential of both chemical agents on gutta percha and Resilon cones are also discussed. The source of this review was conducted through an electronic literature search using PubMed database from December 1997 until December 2011, which analyze the related laboratory investigations of both irrigants, published in major endodontic journals. PMID:23349569

  8. CAS agar diffusion assay for the measurement of siderophores in biological fluids

    Microsoft Academic Search

    Sung Heui Shin; Yong Lim; Shee Eun Lee; Nam Woong Yang; Joon Haeng Rhee

    2001-01-01

    We developed a simple and universal method, by modifying the universal CAS (Chrome azurol S) assay, measuring siderophores in various biological fluids. We named the assay as CAS agar diffusion (CASAD) assay. CAS plate devoid of nutrients was prepared by using Bacto-agar (1.5%, w\\/v) as a matrix. Holes with 5-mm-diameter were punched on the CAS agar plate. Each hole was

  9. Agar Underlay Method for Recovery of Sublethally Heat-Injured Bacteria

    PubMed Central

    Kang, D. H.; Siragusa, G. R.

    1999-01-01

    A method of recovering sublethally heat-injured bacteria was developed. The procedure (termed the agar underlay method) uses a nonselective agar underlaid with a selective medium. In a two-chambered petri dish, the Lutri plate (LP), a nonselective agar is inoculated with a population of sublethally heat-injured bacteria. After a 2-h repair incubation period, selective agar is added to the bottom chamber of the LP and incubated. By diffusing through the nonselective top agar, selective agents from the underlay medium impart selectivity to the system. By the agar underlay method, recovery rates of the heat-injured food-borne pathogens Escherichia coli O157:H7 and Salmonella typhimurium were not different (P > 0.05) from recovery rates determined with nonselective media. Sublethally heat-injured cells (60°C for 1.5 min in buffer or 80°C for 30 s on meat surfaces) grew and produced a typical colony morphology and color reaction when the agar underlay procedure was used with the appropriate respective selective agars. Unlike agar overlay methods for injury repair, the agar underlay procedure allows the typical selective-medium colony morphology to develop and allows colonies to be more easily picked for further characterization. Higher recovery rates of heat-injured fecal enterococci from bovine fecal samples and total coliforms from animal waste lagoons were obtained by the agar underlay method with selective agars than by direct plating on the respective selective media. PMID:10583985

  10. Performance of the EUCAST disk diffusion method, the CLSI agar screen method, and the Vitek 2 automated antimicrobial susceptibility testing system for detection of clinical isolates of Enterococci with low- and medium-level VanB-type vancomycin resistance: a multicenter study.

    PubMed

    Hegstad, Kristin; Giske, Christian G; Haldorsen, Bjørg; Matuschek, Erika; Schønning, Kristian; Leegaard, Truls M; Kahlmeter, Gunnar; Sundsfjord, Arnfinn

    2014-05-01

    Different antimicrobial susceptibility testing methods to detect low-level vancomycin resistance in enterococci were evaluated in a Scandinavian multicenter study (n=28). A phenotypically and genotypically well-characterized diverse collection of Enterococcus faecalis (n=12) and Enterococcus faecium (n=18) strains with and without nonsusceptibility to vancomycin was examined blindly in Danish (n=5), Norwegian (n=13), and Swedish (n=10) laboratories using the EUCAST disk diffusion method (n=28) and the CLSI agar screen (n=18) or the Vitek 2 system (bioMérieux) (n=5). The EUCAST disk diffusion method (very major error [VME] rate, 7.0%; sensitivity, 0.93; major error [ME] rate, 2.4%; specificity, 0.98) and CLSI agar screen (VME rate, 6.6%; sensitivity, 0.93; ME rate, 5.6%; specificity, 0.94) performed significantly better (P=0.02) than the Vitek 2 system (VME rate, 13%; sensitivity, 0.87; ME rate, 0%; specificity, 1). The performance of the EUCAST disk diffusion method was challenged by differences in vancomycin inhibition zone sizes as well as the experience of the personnel in interpreting fuzzy zone edges as an indication of vancomycin resistance. Laboratories using Oxoid agar (P<0.0001) or Merck Mueller-Hinton (MH) agar (P=0.027) for the disk diffusion assay performed significantly better than did laboratories using BBL MH II medium. Laboratories using Difco brain heart infusion (BHI) agar for the CLSI agar screen performed significantly better (P=0.017) than did those using Oxoid BHI agar. In conclusion, both the EUCAST disk diffusion and CLSI agar screening methods performed acceptably (sensitivity, 0.93; specificity, 0.94 to 0.98) in the detection of VanB-type vancomycin-resistant enterococci with low-level resistance. Importantly, use of the CLSI agar screen requires careful monitoring of the vancomycin concentration in the plates. Moreover, disk diffusion methodology requires that personnel be trained in interpreting zone edges. PMID:24599985

  11. Performance of the EUCAST Disk Diffusion Method, the CLSI Agar Screen Method, and the Vitek 2 Automated Antimicrobial Susceptibility Testing System for Detection of Clinical Isolates of Enterococci with Low- and Medium-Level VanB-Type Vancomycin Resistance: a Multicenter Study

    PubMed Central

    Giske, Christian G.; Haldorsen, Bjørg; Matuschek, Erika; Schønning, Kristian; Leegaard, Truls M.; Kahlmeter, Gunnar

    2014-01-01

    Different antimicrobial susceptibility testing methods to detect low-level vancomycin resistance in enterococci were evaluated in a Scandinavian multicenter study (n = 28). A phenotypically and genotypically well-characterized diverse collection of Enterococcus faecalis (n = 12) and Enterococcus faecium (n = 18) strains with and without nonsusceptibility to vancomycin was examined blindly in Danish (n = 5), Norwegian (n = 13), and Swedish (n = 10) laboratories using the EUCAST disk diffusion method (n = 28) and the CLSI agar screen (n = 18) or the Vitek 2 system (bioMérieux) (n = 5). The EUCAST disk diffusion method (very major error [VME] rate, 7.0%; sensitivity, 0.93; major error [ME] rate, 2.4%; specificity, 0.98) and CLSI agar screen (VME rate, 6.6%; sensitivity, 0.93; ME rate, 5.6%; specificity, 0.94) performed significantly better (P = 0.02) than the Vitek 2 system (VME rate, 13%; sensitivity, 0.87; ME rate, 0%; specificity, 1). The performance of the EUCAST disk diffusion method was challenged by differences in vancomycin inhibition zone sizes as well as the experience of the personnel in interpreting fuzzy zone edges as an indication of vancomycin resistance. Laboratories using Oxoid agar (P < 0.0001) or Merck Mueller-Hinton (MH) agar (P = 0.027) for the disk diffusion assay performed significantly better than did laboratories using BBL MH II medium. Laboratories using Difco brain heart infusion (BHI) agar for the CLSI agar screen performed significantly better (P = 0.017) than did those using Oxoid BHI agar. In conclusion, both the EUCAST disk diffusion and CLSI agar screening methods performed acceptably (sensitivity, 0.93; specificity, 0.94 to 0.98) in the detection of VanB-type vancomycin-resistant enterococci with low-level resistance. Importantly, use of the CLSI agar screen requires careful monitoring of the vancomycin concentration in the plates. Moreover, disk diffusion methodology requires that personnel be trained in interpreting zone edges. PMID:24599985

  12. Photopyroelectric method using a thermal wave resonator cavity for detection of phase transitions in agar

    Microsoft Academic Search

    R. Medina-Esquivel; J. M. Yanez-Limon; Juan J. Alvarado-Gil

    2005-01-01

    In this work, the Photopyroelectric (PPE) technique using a Thermal Wave Resonator Cavity (TWRC) is used to measure the thermal diffusivity of agar. We, determine the liquid to gel phase transition temperature as a function of agar concentration, detecting a shift in that temperature. As agar concentration decreases, the phase transition temperatures get lower. The thermal diffusivity of agar as

  13. Eine verbesserte Methode zur quantitativen Hochspannungselektrophorese in Agar-Agar-Schichten

    Microsoft Academic Search

    K. Dose; S. Risi

    1964-01-01

    Es wurde ein Schnellverfahren zur quantitativen Hochspannungselektrophorese in Agar-Schichten ausgearbeitet. Nach der elektrophoretischen Trennung werden die Agar-Agar-Schichten zu transparenten Filmen getrocknet und die einzelnen Fraktionen in situ spektroskopisch analysiert. Als Anwendungsbeispiele werden die Trennung und analytische Bestimmung von Nucleinsäurebausteinen gezeigt.

  14. CAS agar diffusion assay for the measurement of siderophores in biological fluids.

    PubMed

    Shin, S H; Lim, Y; Lee, S E; Yang, N W; Rhee, J H

    2001-02-01

    We developed a simple and universal method, by modifying the universal CAS (Chrome azurol S) assay, measuring siderophores in various biological fluids. We named the assay as CAS agar diffusion (CASAD) assay. CAS plate devoid of nutrients was prepared by using Bacto-agar (1.5%, w/v) as a matrix. Holes with 5-mm-diameter were punched on the CAS agar plate. Each hole was added by 35 microl of the test fluids containing Desferal that was twofold serially diluted. After incubating at 37 degrees C or room temperature for 4-8 h, the size of orange haloes formed around the holes was measured. The size of orange haloes correlated well with the concentration of Desferal in all the biological fluids tested in this study. CASAD assay showed consistent results in wide pH range from 5 to 9. Addition of iron to the test fluids containing Desferal decreased the size of orange haloes in a dose-dependent manner, which suggests that the CASAD assay detects only iron non-bound siderophore. These results suggest that CASAD assay would serve as a simple, stable, and highly reproducible test for screening and quantitative siderophore analysis in biological fluids. PMID:11166103

  15. Antimicrobial Susceptibility Testing of Bacillus anthracis: Comparison of Results Obtained by Using the National Committee for Clinical Laboratory Standards Broth Microdilution Reference and Etest Agar Gradient Diffusion Methods

    Microsoft Academic Search

    M. Jasmine Mohammed; Chung K. Marston; Tanja Popovic; Robbin S. Weyant; Fred C. Tenover

    We determined the patterns of antimicrobial susceptibility of 65 isolates of Bacillus anthracis (50 historical and 15 recent U.S. clinical isolates) to nine antimicrobial agents using the National Committee for Clinical Laboratory Standards (NCCLS) broth microdilution reference method. The results for the 50 historical B. anthracis isolates obtained by the broth microdilution method were compared to those generated by the

  16. Susceptibility of a polycaprolactone-based root canal filling material to degradation using an agar-well diffusion assay

    PubMed Central

    Hiraishi, Noriko; Sadek, Fernanda T.; King, Nigel M.; Ferrari, Marco; Pashley, David H.; Tay, Franklin R

    2013-01-01

    Purpose Cholesterol esterase is both a component of salivary hydrolases as well as an inflammatory cell-derived enzyme and has been shown to cause biodegradation of methacrylate-based resin composites. This study examined whether Resilon, a polycaprolactone-based thermoplastic root filling material is susceptible to biodegradation by cholesterol esterase using agar-well diffusion assay of serially-diluted aqueous Resilon emulsions that were dispersed in agar. Materials and methods Emulsions of Resilon and polycaprolactone were prepared and dispersed in agar on culture plates. Two different concentrations of a cholesterol esterase (0.3 and 1.2 U/mL) were prepared and fed to wells prepared in the agar plates using an agar-well diffusion assay for examination the degradation of polymeric materials. Results Degradation of the emulsified Resilon was manifested as the formation of clear zones of different sizes around the agar wells. No clear zones were observed in agar wells that contain sterile distilled water as the negative control. Clinical significance Although dispersion Resilon into an emulsion is not the way in which this material is employed as a root filling material, the potential for Resilon to be degraded by cholesterol esterase is of potential concern as one cannot limit the degradation of extruded Resilon from a root apex by monocyte-derived macrophages to just the anatomical root apex. As the present study employed a high concentration of cholesterol esterase, further studies should be directed to examining the degradation of Resilon using macrophage cell cultures. PMID:18578181

  17. Laboratory 1: Bacterial Abundance Method 1: SERIAL DILUTION-AGAR PLATING TO QUANTITATE VIABLE CELLS

    E-print Network

    Vallino, Joseph J.

    Laboratory 1: Bacterial Abundance Method 1: SERIAL DILUTION- AGAR PLATING TO QUANTITATE VIABLE) and spread with an ethanol-flamed glass rod. Cool glass rod on agar plat before spreading. Incubate the five

  18. Activity staining method of chitinase on chitin agar plate through polyacrylamide gel electrophoresis

    Microsoft Academic Search

    Vipul Gohel; Pranav Vyas; H. S. Chhatpar

    2005-01-01

    A method for detection of chitinase activity on chitin agar plate after polyacrylamide gel electrophoresis is described. Different staining dyes such as calcofluor white M2R, fluorescein isothiocyanate, rhodamine B, ruthenium red and congo red were separately incorporated in chitin agar plates. After running polyacrylamide gel electrophoresis, the gel was transferred onto chitin agar plate containing different dyes for the activity

  19. A colony-forming assay for human tumour xenografts using agar in diffusion chambers.

    PubMed Central

    Smith, I. E.; Courtenay, V. D.; Gordon, M. Y.

    1976-01-01

    A technique for growing colonies from single-cell suspensions of human tumour xenografts using agar in diffusion chambers is described. Modified Millipore diffusion chambers containing tumour cells in semi-solid agar-medium were implanted into the peritoneal cavity of pre-irradiated mice and provided standard culture conditions for the study of colony-forming cells. All 11 xenograft tumours so far studied produced colonies. The incubation period for colony growth ranged from 12 to 28 days and the plating efficiency ranged from 0-3% to 16% for different tumours, but both parameters were constant for each individual tumour. The reproducibility of the system provides a colony-forming assay which can be used to study the effects of irradiation and cytotoxic drugs on human tumour clonogenic cells and may therefore have some advantages over similar assays based on experimental animal tumours. Images Fig. 1(b) Fig. 1(c) Fig. 1(a) PMID:999782

  20. Combination cellulose plate (non-agar solid support) and agar plate method improves isolation of fungi from soil.

    PubMed

    Nonaka, Kenichi; Todaka, Nemuri; ?mura, Satoshi; Masuma, Rokuro

    2014-11-01

    This is the first report describing the improved isolation of common filamentous fungi via a method combining cellulose plate and agar plate system. A cellulose plate is a porous plate made of nanofibrous crystaline cellulose. Isolating fungi from soils using these types of media separately resulted in the number of fungal colonies appearing on cellulose plates being lower than that on agar plates. However, the number of actual fungal species isolated using cellulose plates alone was more or less the same as that found using agar plates. Significantly, the diversity of isolates using a combination of the two media was greater than using each media individually. As a result, numerous new or rare fungal species with potential, including previously proposed new species, were isolated successfully in this way. All fungal colonies, including the Penicillium species, that appeared on the cellulose plate penetrated in potato dextrose were either white or yellow. Cultivation on cellulose plates with added copper ion overcomes the change in coloration, the colonies appearing as they do following cultivation on potato dextrose agar. PMID:24849537

  1. Interlaboratory variability of disc diffusion and agar dilution susceptibility tests with cefamandole and cephalothin

    Microsoft Academic Search

    A. L. Barry; F. D. Schoenknecht; S. Shadomy; J. C. Sherris; C. Thornsberry; J. A. Washington; R. B. Kramer

    1978-01-01

    Reproducibility of antimicrobic susceptibility tests was estimated by examining control data accumulated during a multicenter\\u000a study for evaluating cefamandole and cephalothin. The precision of agar dilution minimal inhibitory concentrations was compared\\u000a with the standardized Bauer-Kirby disc method. Regression lines were established for each antimicrobic and were used to calculate\\u000a the range of minimal inhibitory concentration values that corresponded to the

  2. Use of agar diffusion assay to evaluate bactericidal activity of formulations of alkaline salts of fatty acids against bacteria associated with poultry processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The agar diffusion assay was used to examine antibacterial activity of alkaline salts of fatty acids (FA). Wells in agar media seeded with bacteria were filled with FA-potassium hydroxide (KOH) solutions, plates were incubated, and zones of inhibition were measured. The relationship between bacteric...

  3. Double-layer agar cell cultures as a method of studying cell growth factors

    SciTech Connect

    Cherepantseva, E.A.; Shevlyagin, V.Ya.; Al'tshtein, A.D.

    1986-12-01

    This paper describes the development of a method of double-layer agar cell cultures which can be conveniently used to study the ability of some donor cells to produce tumor growth factors for other recipient or test cells. The donor and recipient cells are placed in different layers of agar, separated by an intermediate layer. Under a microscope, the two cell layers can be distinguished and assessed in relation to colony formation. Hamster cells were used in the experiments. The role of proliferation in manifestation of the donor properties of the cells was assessed, using donor cells seeded in different amounts of agar and also cells irradiated with gamma-rays and which had lost their ability to divide. The cells were compared and results are presented.

  4. Agar plate method for rapid screening of rhizobium for tolerance to acid-aluminum stress

    SciTech Connect

    Ayanaba, A.; Asanuma, S.; Munns, D.N.

    1983-01-01

    An agar plate method has been developed for the rapid, preliminary screening of large numbers of rhizobia for tolerance to acidity and aluminum (acid-Al). Media containing pH indicators are used, and distinguish true tolerance from cases where growth depends on a previous pH shift. Strains which were highly tolerant or sensitive to acid Al on agar behaved similarly in defined liquid media. Strains that formed dry, pinpoint colonies were more sensitive to acid-Al than those that formed large, gummy colonies.

  5. MODIFIED AGAR MEDIUM FOR DETECTING ENVIRONMENTAL SALMONELLAE BY THE MOST-PROBABLE-NUMBER METHOD

    EPA Science Inventory

    Salmonellae in the environment remain a potential source of disease. Low numbers of salmonellae have been detected and enumerated from environmental samples by most probable number methods that require careful colony selection from plated agar medium. A modified xylose lysine bri...

  6. Correlation of Neo-Sensitabs Tablet Diffusion Assay Results on Three Different Agar Media with CLSI Broth Microdilution M27-A2 and Disk Diffusion M44-A Results for Testing Susceptibilities of Candida spp. and Cryptococcus neoformans to Amphotericin B, Caspofungin, Fluconazole, Itraconazole, and Voriconazole

    Microsoft Academic Search

    A. Espinel-Ingroff; E. Canton; D. Gibbs; A. Wang

    2007-01-01

    We compared the Neo-Sensitabs tablet assay to both reference M27-A2 broth microdilution and M44-A disk diffusion methods for testing susceptibilities of 110 isolates of Candida spp. and Cryptococcus neoformans to amphotericin B, caspofungin, fluconazole, itraconazole, and voriconazole. Neo-Sensitabs assay inhibition zone diameters in millimeters on three agars (Mueller-Hinton agar supplemented with 2% dextrose and 0.5 g\\/ml methylene blue (MGM), Shadomy

  7. Structure of Agar-Agar

    Microsoft Academic Search

    E. G. V. Percival; J. Munro; J. C. Somerville

    1937-01-01

    WE now communicate some preliminary results of the investigation on methylated agar prepared from the acetate previously described in NATURE1. By the simultaneous deacetylation and methylation of acetylated agar in chloroform; CH3CO = 38.5 per cent), an apparently homogeneous methylated agar was obtained - 78° in chloroform; OCH3 = 31 per cent), the methoxyl content of which remained constant despite

  8. AgarTrap: a simplified Agrobacterium-mediated transformation method for sporelings of the liverwort Marchantia polymorpha L.

    PubMed

    Tsuboyama, Shoko; Kodama, Yutaka

    2014-01-01

    The liverwort Marchantia polymorpha L. is being developed as an emerging model plant, and several transformation techniques were recently reported. Examples are biolistic- and Agrobacterium-mediated transformation methods. Here, we report a simplified method for Agrobacterium-mediated transformation of sporelings, and it is termed Agar-utilized Transformation with Pouring Solutions (AgarTrap). The procedure of the AgarTrap was carried out by simply exchanging appropriate solutions in a Petri dish, and completed within a week, successfully yielding sufficient numbers of independent transformants for molecular analysis (e.g. characterization of gene/protein function) in a single experiment. The AgarTrap method will promote future molecular biological study in M. polymorpha. PMID:24259681

  9. COMPARISON OF MENTEROCOCCUS AGAR AND THE U.S. ENVIRONMENTAL PROTECTION AGENCY-RECOMENDED ENTEROCOCCI METHODS, ME AND MEI AGAR

    EPA Science Inventory

    To maintain waters that are "fishable and swimmable", mandated by the Clean Water Act, the U.S. Environmental Protection Agency (EPA) is developing a list of approved methods for use in enumerating enterococci and E. coli in ambient waters. As part of this effort, we compared mEn...

  10. INTERLABORATORY EVALUATION OF MI AGAR AND THE US ENVIRONMENTAL PROTECTION AGENCY-APPROVED MEMBRANE FILTER METHOD FOR THE RECOVERY OF TOTAL COLIFORMS AND ESCHERICHIA COLI FROM DRINKING WATER

    EPA Science Inventory

    A new membrane filter (MF) medium, MI agar, recently validated for use in recovering chlorine-damaged total coloiforms (TC) and Escherichia coli from drinking water, was compared to the US Environmental Protection Agency (EPA)-approved MF method(mEndo agar and nutrient agar suppl...

  11. Application of thin agar layer method for recovery of injured Salmonella typhimurium

    Microsoft Academic Search

    Dong-Hyun Kang; Daniel Y. C Fung

    2000-01-01

    Xylose lysine decarboxylase (XLD) medium, a selective plating medium, can inhibit heat-injured Salmonella typhimurium from growing, whereas tryptic soy agar (TSA), a nonselective medium, does not. To facilitate recovery of heat-injured S. typhimurium cells while providing selectivity of isolation of S. typhimurium from other bacteria in the sample, a thin agar layer (TAL) procedure was developed by overlaying 14 ml

  12. Susceptibilities of genital mycoplasmas to the newer quinolones as determined by the agar dilution method.

    PubMed

    Kenny, G E; Hooton, T M; Roberts, M C; Cartwright, F D; Hoyt, J

    1989-01-01

    The increasing resistance of genital mycoplasmas to tetracycline poses a problem because tetracycline is one of the few antimicrobial agents active against Mycoplasma hominis, Ureaplasma urealyticum, chlamydiae, gonococci, and other agents of genitourinary-tract disease. Since the quinolones are a promising group of antimicrobial agents, the susceptibilities of M. hominis and U. urealyticum to the newer 6-fluoroquinolones were determined by the agar dilution method. Ciprofloxacin, difloxacin, and ofloxacin had good activity against M. hominis, with the MIC for 50% of isolates tested (MIC50) being 1 microgram/ml. Fleroxacin, lomefloxacin, pefloxacin, and rosoxacin had MIC50s of 2 micrograms/ml. Enoxacin, norfloxacin, and amifloxacin had MIC50s of 8 to 16 micrograms/ml, and cinoxacin and nalidixic acid were inactive (MIC50, greater than or equal to 256 micrograms/ml). Overall, the activities of 6-fluoroquinolones for ureaplasmas were similar to those for M. hominis, with MICs being the same or twofold greater. The most active 6-fluoroquinolones against ureaplasmas were difloxacin, ofloxacin, and pefloxacin, with MIC50s of 1 to 2 micrograms/ml. Ciprofloxacin was unusual in that the MIC50 for M. hominis was 1 microgram/ml, whereas the MIC50 for ureaplasmas was 8 micrograms/ml. Since the MIC50s for the most active quinolones approximate achievable concentrations in blood and urine, quinolones have promise in treating mycoplasmal infections. PMID:2712541

  13. An agar-agar chamber for study of electromagnetic waves in an inhomogeneous medium

    Microsoft Academic Search

    K. Iizuka

    1971-01-01

    A medium for the propagation of electromagnetic waves whose dielectric constant or loss tangent has a prescribed profile was fabricated by using a large quantity of agar-agar in simulation chambers. The dielectric constant of the agar-agar could be changed continuously by means of a controlled diffusion of ethyl alcohol. The loss tangent of the same medium could be changed continuously

  14. Serological Typing of Ureaplasma urealyticum Isolates from Urethritis Patients by an Agar Growth Inhibition Method

    PubMed Central

    Shepard, Maurice C.; Lunceford, Carl D.

    1978-01-01

    An agar growth inhibition method for serotyping Ureaplasma urealyticum is described, and the results of applying this method to serotyping 338 strains of the organism are presented. The serotyped strains consisted of cloned isolates from male patients with primary and recurrent nongonococcal urethritis (NGU), isolates from symptomatic patients with other genitourinary tract infections and disorders, and isolates from asymptomatic carriers of U. urealyticum in the genitourinary tract (controls). Among 122 male patients with NGU, serotype 4 was associated most frequently (52%) with this disease at Camp Lejeune, N.C. Seventeen percent of the isolates were type 2. The remaining isolates consisted of types 1, 3, 6, and 8 and accounted for 6 to 9% each of the serotypes isolated from the NGU group. Types 5 and 7 were not isolated. Among 91 symptomatic patients with other genitourinary tract infections and disorders, U. urealyticum type 4 also was associated most frequently (37%) with these disorders. The remaining isolates, represented by types 1, 2, 3, 6, 7, and 8, accounted for 9 to 15% each of the types isolated from this group. Type 5 was not isolated. Among 125 symptomfree carriers of U. urealyticum in the genitourinary tract, type 8 was recovered most frequently (30%), whereas type 4 was isolated next most frequently (24%). The remaining isolates consisted of types 1, 2, 3, 5, and 6 and accounted for 2 to 15% each in this asymptomatic control group. Type 7 was not isolated. Of the present eight serotypes of U. urealyticum studied in this investigation, type 4 was associated most frequently with disease (NGU) and certain other disorders of the genitourinary tract at Camp Lejeune. A previously unknown association of U. urealyticum with frequently abacteriuric, unexplained pyuria (with or without urethral pruritis and dysuria) is reported, suggesting the existence of asymptomatic Ureaplasma urethritis. Images PMID:730828

  15. Improved Method for the Determination of Antimicrobial Activity of Essential Oils in Agar Medium

    Microsoft Academic Search

    Adnane Remmal; Touria Bouchikhi; Khadija Rhayour; Mohamed Ettayebi; Abdelrhafour Tantaoui-Elaraki

    1993-01-01

    The influence of the number of bacterial cells inoculated and the emulsifying agent used to disperse essential oils (EO) into the culture media on the measurement of the antibacterial activity of EO in an agar medium was determined. The results showed that EO (oregano, thyme and clove) were most effective as antimicrobial agents when the bacterial load was low. Minimum

  16. Agar diffusion, agar dilution, Etest®, and agar screening test in the detection of methicillin resistance in staphylococci ? ? Part of this paper was presented at the 101 st General Meeting of the American Society for Microbiology (Orlando, Fl, 2001)

    Microsoft Academic Search

    Fabiana Rowe; Silvana Vargas Superti; Rosane Machado Scheibe; C??cero Gomes Dias

    2002-01-01

    Methicillin resistant Staphylococcus is an important worldwide problem. Resistance is verified in strains harboring the mecA gene and laboratory methods used to detect resistance are object of constant investigation. In the present study, 99 clinical isolates of staphylococci (41 S. aureus, 33 S. epidermidis, 12 S. saprophyticus and 13 members of other species) were submitted to different phenotypic methods and

  17. Performance of an Agar Dilution Method and a Vitek 2 Card for Detection of Inducible Clindamycin Resistance in Staphylococcus spp.?

    PubMed Central

    Lavallée, Christian; Rouleau, Danielle; Gaudreau, Christiane; Roger, Michel; Tsimiklis, Catherine; Locas, Marie-Claude; Gagnon, Simon; Delorme, Jocelyn; Labbé, Annie-Claude

    2010-01-01

    The D-zone test detects inducible clindamycin resistance in Staphylococcus spp. Two other methods not described by the Clinical and Laboratory Standards Institute (CLSI) are available to test for this resistance mechanism: an agar dilution method and new Vitek 2 cards. This study evaluated the performance of both methods in detecting inducible clindamycin resistance. Nonduplicate clinical strains of Staphylococcus spp. (111 Staphylococcus aureus and 52 coagulase-negative staphylococcus strains), intermediate or resistant to erythromycin but susceptible to clindamycin, were obtained from three hospitals in Montreal, Quebec, Canada. Molecular analysis to detect resistance genes was conducted on all strains. A Mueller-Hinton agar containing 1 mg of erythromycin and 0.5 mg of clindamycin/liter was used for the dilution method, and two inocula were tested: 104 and 105 CFU per spot. Plates were read at 24 and 48 h. The Vitek 2 AST-P580 card was used according to the manufacturer's recommendations. The results were compared to those of the D-zone test. The D-zone test was positive in 134 of 163 (82%) strains. With the 104 CFU inoculum, the sensitivities were 84 and 99% at 24 and 48 h, respectively. The 105 CFU inoculum increased the sensitivities at 24 and 48 h to 91 and 100%, respectively. The specificity was 100% for the 104 CFU inoculum at 24 h and 97% for the other combinations. The sensitivity and specificity for the Vitek 2 card were 93 and 100%, respectively. The performance of both the agar dilution method and the Vitek 2 card was good, but these methods were not as sensitive as the D-zone test at 24 h. PMID:20164285

  18. Effect of sodium hydroxide pretreatment on the relaxation spectrum of concentrated agar-agar gels

    Microsoft Academic Search

    M. Watase; K. Nishinari

    1981-01-01

    Summary Stress relaxation and ultrasonic absorption measurements were made for agar-agar pretreated by various concentrations of sodium hydroxide, in order to clarify the dominating factors in its rheological properties. Stress relaxation measurements were made up to 30 hours. Relaxation spectra were obtained by the reduced variable method. Gels prepared from agar-agar pretreated by concentrated sodium hydroxide show a larger relaxation

  19. Abstract--Hybrid diffusion imaging (HYDI) is a new diffusion MRI method for characterizing complex diffusion.

    E-print Network

    Bucci, David J.

    Abstract-- Hybrid diffusion imaging (HYDI) is a new diffusion MRI method for characterizing complex diffusion. Diffusion-weighted measurements are obtained on multiple `shells' of constant diffusion weighting. This diffusion encoding approach is amenable to multiple types of diffusion imaging analysis. The inner shells

  20. Electro-osmosis in gels: Application to Agar-Agar

    Microsoft Academic Search

    Fabien Cherblanc; Jérôme Boscus; Jean-Claude Bénet

    2008-01-01

    Widely used in food- and bio-engineering as a reference material, Agar-Agar gel is the focus of an experimental investigation concerning the electro-osmosis phenomenon. After presenting the experimental methods, one trial is discussed in detail. A fair reproducibility of results is obtained, and the averaged electro-osmotic permeability is provided. This value lies in the range generally measured on various kind of

  1. Nonlinear methods for solving the diffusion equation

    E-print Network

    Shober, Robert Anthony

    1976-01-01

    This thesis is concerned with methods for the transient solution of the neutron diffusion equations in one or two energy groups. Initially, nonlinear methods for solving the static diffusion equations using the finite ...

  2. MYPGP-agar; BHIT-agar; Colombia agar with 10% sheep blood; and ordinary blood agar with

    E-print Network

    Paris-Sud XI, Université de

    MYPGP-agar; BHIT-agar; Colombia agar with 10% sheep blood; and ordinary blood agar with 5% horse blood. The results revealed that more spores will ger- minate when they are incubated in air/CO2 mix- tures. In 5% CO2, both J-agar and MYPGP-agar yield significantly more colonies per plate com- pared

  3. Validation of a modified Kirby-Bauer disk diffusion method for metronidazole susceptibility testing of Helicobacter pylori

    Microsoft Academic Search

    Peter D. Midolo; John Turnidge; John R. Lambert; Jan M. Bell

    1995-01-01

    Triple antimicrobial therapy that includes metronidazole has been recommended as a first-line therapy for Helicobacter pylori because it has the highest eradication rates. However, resistance in H. pylori to metronidazole has been reported worldwide and its presence may reduce the efficacy of triple therapy. Various methods for testing H. pylori against metronidazole have been used including agar dilution, disk diffusion

  4. Periodic crystallisation of magnesium hydroxide in agar-agar gel. Influence of temperature

    Microsoft Academic Search

    S. Ambrose; F. D. Gnanam; P. Ramasamy

    1983-01-01

    The influence of temperature on periodic crystallisation of magnesium hydroxide in agar-agar gel has been studied. The increase\\u000a in velocity constant with temperature is attributed to the increase in the diffusion constant with temperature. The activation\\u000a energy for diffusion of aqueous ammonia is calculated from the temperature — velocity constant correlation. The solubility\\u000a of Mg(OH)2 decreases with temperature. The decrease

  5. Mathematical Methods for Diffusion MRI Processing

    PubMed Central

    Lenglet, C.; Campbell, J.S.W.; Descoteaux, M.; Haro, G.; Savadjiev, P.; Wassermann, D.; Anwander, A.; Deriche, R.; Pike, G.B.; Sapiro, G.; Siddiqi, K.; Thompson, P.

    2009-01-01

    In this article, we review recent mathematical models and computational methods for the processing of diffusion Magnetic Resonance Images, including state-of-the-art reconstruction of diffusion models, cerebral white matter connectivity analysis, and segmentation techniques. We focus on Diffusion Tensor Images (DTI) and Q-Ball Images (QBI). PMID:19063977

  6. Bacteria holding times for fecal coliform by mFC agar method and total coliform and Escherichia coli by Colilert®-18 Quanti-Tray® method

    USGS Publications Warehouse

    Aulenbach, Brent T.

    2010-01-01

    Bacteria holding-time experiments of up to 62 h were performed on five surface-water samples from four urban stream sites in the vicinity of Atlanta, GA, USA that had relatively high densities of coliform bacteria (Escherichia coli densities were all well above the US Environmental Protection Agency criterion of 126 colonies (100 ml)???1 for recreational waters). Holding-time experiments were done for fecal coliform using the membrane filtration modified fecal coliform (mFC) agar method and for total coliform and E. coli using the Colilert®-18 Quanti-Tray® method. The precisions of these analytical methods were quantified. Precisions determined for fecal coliform indicated that the upper bound of the ideal range of counts could reasonably be extended upward and would improve precision. For the Colilert®-18 method, analytical precisions were similar to the theoretical precisions for this method. Fecal and total coliform densities did not change significantly with holding times up to about 27 h. Limited information indicated that fecal coliform densities might be stable for holding times of up to 62 h, whereas total coliform densities might not be stable for holding times greater than about 27 h. E. coli densities were stable for holding times of up to 18 h—a shorter period than indicated from a previous studies. These results should be applicable to non-regulatory monitoring sampling designs for similar urban surface-water sample types.

  7. Hydrogel composition based on carboxymethylcellulose and agar-agar

    Microsoft Academic Search

    D. T. Satybaldyeva; M. Yu. Mukhamedzhanova; A. A. Sarymsakov; Yu. T. Tashpulatov

    1998-01-01

    The results are given of a study of the rheological properties of concentrated solutions of CNC and agar-agar and the influence of their quantitative ratio on the anomalous flow behavior of their solutions. A hypothesis is put forward of the formation of intermolecular associates from CMC and agar-agar which leads to the formation of a stronger structural network of solutions

  8. A comparison of gel diffusion, fluorescent antibody and virus isolation methods in experimental and natural cases of infectious bursal disease.

    PubMed Central

    Ide, P R

    1975-01-01

    In studies with chicks inoculated with the Sk-1 strain of infectious bursal agent the bursa of Fabricius was found to be the tissue of choice for virus isolation as well as for use in the fluorescent antibody test and the agar gel diffusion test. In separate experiments positive results were obtained until postinoculation days 3 or 4 by the agar gel diffusion test, 5 or 6 by the fluorescent antibody test and 14 by the virus isolation method, respectively. Bursas from chickens involved in seven natural outbreaks of infectious bursal disease were then examined by these three methods. Virus was isolated from six outbreaks and infectious bursal agent antigen was demonstrated in three by the agar gel diffusion test method and seven (three by direct examination and four after one passage in chicks) by the fluorescent antibody test method. Passage in chicks was required when nonspecific fluorescence complicated the interpretation of fluorescent antibody test results. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. PMID:164991

  9. Ability of three DNA-based assays to identify presumptive Escherichia coli colonies isolated from water by the culture-based mFC agar method.

    PubMed

    Maheux, Andrée F; Bérubé, Eve; Boudreau, Dominique K; Cantin, Philippe; Boissinot, Maurice; Bissonnette, Luc; Rodrigue, Lynda; Bergeron, Michel G

    2011-04-01

    We tested the ability of three PCR assays, targeting uidA and tuf genes to correctly identify Escherichia coli colonies isolated from water and we compared them to two ?-glucuronidase-based culture methods (Colilert(®) and Readycult(®)), in terms of specificity and sensitivity. E. coli isolates recovered on mFC agar were first tested for the presence of the uidA positive colonies were presumed to be E. coli. For further characterization, uidA-negative colonies were subsequently identified using the Vitek 2 automated system. Colilert(®) and Readycult(®) detected 436 and 442 of 468 colonies identified as E. coli on mFC corresponding to sensitivities of 93.2 and 94.4%, respectively. None of the 59 non-E. coli isolates was detected by both methods for a specificity of 100%. Two (2) uidA and 1 tuf PCR assays were also tested. The uidA PCR assays yielded positive signals for 447 (95.5%) and 434 (92.7%) of 468 E. coli isolates tested respectively, whereas the tuf PCR assay showed a sensitivity of 100%. None of the 59 non-E. coli isolates was detected by both uidA PCR assays (100% specificity), whereas tuf PCR false-positive signals were obtained with Escherichia fergusonii and Escherichia albertii. However, since these 2 species are principally found in the feces of mammals and birds, their detection indicates a fecal contamination. Consequently, using a 1-h tuf rtPCR assay to confirm the identity of E. coli colonies on mFC agar is as specific, more sensitive, and potentially more cost-efficient than culture methods based on ?-glucuronidase detection. PMID:21420142

  10. Extraction of agar from Gelidium sesquipedale (Rhodopyta) and surface characterization of agar based films.

    PubMed

    Guerrero, P; Etxabide, A; Leceta, I; Peñalba, M; de la Caba, K

    2014-01-01

    The chemical structure of the agar obtained from Gelidium sesquipedale (Rhodophyta) has been determined by (13)C nuclear magnetic resonance ((13)C NMR) and Fourier transform infrared spectroscopy (FTIR). Agar (AG) films with different amounts of soy protein isolate (SPI) were prepared using a thermo-moulding method, and transparent and hydrophobic films were obtained and characterized. FTIR analysis provided a detailed description of the binding groups present in the films, such as carboxylic, hydroxyl and sulfonate groups, while the surface composition was examined using X-ray photoelectron spectroscopy (XPS). The changes observed by FTIR and XPS spectra suggested interactions between functional groups of agar and SPI. This is a novel approach to the characterization of agar-based films and provides knowledge about the compatibility of agar and soy protein for further investigation of the functional properties of biodegradable films based on these biopolymers. PMID:24274535

  11. Preparation of an agar-silver nanoparticles (A-AgNp) film for increasing the shelf-life of fruits.

    PubMed

    Gudadhe, Janhavi A; Yadav, Alka; Gade, Aniket; Marcato, Priscyla D; Durán, Nelson; Rai, Mahendra

    2014-12-01

    Preparation of protective coating possessing antimicrobial properties is present day need as they increase the shelf life of fruits and vegetables. In the present study, preparation of agar-silver nanoparticle film for increasing the shelf life of fruits is reported. Silver nanoparticles (Ag-NPs) biosynthesised using an extract of Ocimum sanctum leaves, were mixed with agar-agar to prepare an agar-silver nanoparticles (A-AgNp) film. This film was surface-coated over the fruits, Citrus aurantifolium (Thornless lime) and Pyrus malus (Apple), and evaluated for the determination of antimicrobial activity of A-AgNp films using disc diffusion method, weight loss and shelf life of fruits. This study demonstrates that these A-AgNp films possess antimicrobial activity and also increase the shelf life of fruits. PMID:25429496

  12. Virtual source method for diffuse optical imaging.

    PubMed

    Erkol, Hakan; Unlu, Mehmet Burcin

    2013-07-10

    The Green's function for diffusive wave propagation can be obtained by utilizing the representation theorems of the convolution type and the correlation type. In this work, the Green's function is retrieved by making use of the Robin boundary condition and the representation theorems for diffusive media. The diffusive Green's function between two detectors for photon flux is calculated by combining detector readings due to point light sources and utilizing virtual light sources at the detector positions in optical tomography. Two dimensional simulations for a circular region with eight sources and eight detectors located on the boundary are performed using a finite element method to demonstrate the feasibility of virtual sources. The most important potential application would be the replacement of noisy measurements with synthetic measurements that are provided by the virtual sources. This becomes an important issue in small animal and human studies. In addition, the same method may also be used to reduce the imaging time. PMID:23852209

  13. Clustering method for estimating principal diffusion directions.

    PubMed

    Nazem-Zadeh, Mohammad-Reza; Jafari-Khouzani, Kourosh; Davoodi-Bojd, Esmaeil; Jiang, Quan; Soltanian-Zadeh, Hamid

    2011-08-01

    Diffusion tensor magnetic resonance imaging (DTMRI) is a non-invasive tool for the investigation of white matter structure within the brain. However, the traditional tensor model is unable to characterize anisotropies of orders higher than two in heterogeneous areas containing more than one fiber population. To resolve this issue, high angular resolution diffusion imaging (HARDI) with a large number of diffusion encoding gradients is used along with reconstruction methods such as Q-ball. Using HARDI data, the fiber orientation distribution function (ODF) on the unit sphere is calculated and used to extract the principal diffusion directions (PDDs). Fast and accurate estimation of PDDs is a prerequisite for tracking algorithms that deal with fiber crossings. In this paper, the PDDs are defined as the directions around which the ODF data is concentrated. Estimates of the PDDs based on this definition are less sensitive to noise in comparison with the previous approaches. A clustering approach to estimate the PDDs is proposed which is an extension of fuzzy c-means clustering developed for orientation of points on a sphere. MDL (Minimum description length) principle is proposed to estimate the number of PDDs. Using both simulated and real diffusion data, the proposed method has been evaluated and compared with some previous protocols. Experimental results show that the proposed clustering algorithm is more accurate, more resistant to noise, and faster than some of techniques currently being utilized. PMID:21642005

  14. Clustering method for estimating principal diffusion directions

    PubMed Central

    Nazem-Zadeh, Mohammad-Reza; Jafari-Khouzani, Kourosh; Davoodi-Bojd, Esmaeil; Jiang, Quan; Soltanian-Zadeh, Hamid

    2012-01-01

    Diffusion tensor magnetic resonance imaging (DTMRI) is a non-invasive tool for the investigation of white matter structure within the brain. However, the traditional tensor model is unable to characterize anisotropies of orders higher than two in heterogeneous areas containing more than one fiber population. To resolve this issue, high angular resolution diffusion imaging (HARDI) with a large number of diffusion encoding gradients is used along with reconstruction methods such as Q-ball. Using HARDI data, the fiber orientation distribution function (ODF) on the unit sphere is calculated and used to extract the principal diffusion directions (PDDs). Fast and accurate estimation of PDDs is a prerequisite for tracking algorithms that deal with fiber crossings. In this paper, the PDDs are defined as the directions around which the ODF data is concentrated. Estimates of the PDDs based on this definition are less sensitive to noise in comparison with the previous approaches. A clustering approach to estimate the PDDs is proposed which is an extension of fuzzy c-means clustering developed for orientation of points on a sphere. MDL (Minimum description length) principle is proposed to estimate the number of PDDs. Using both simulated and real diffusion data, the proposed method has been evaluated and compared with some previous protocols. Experimental results show that the proposed clustering algorithm is more accurate, more resistant to noise, and faster than some of techniques currently being utilized. PMID:21642005

  15. Comparison of direct and modified direct complement-fixation and agar-gel precipitin methods in detecting chlamydial antibody in wild birds.

    PubMed

    Grimes, J E; Page, L A

    1978-01-01

    Detection of chlamydial antibody in serums of wild birds was compared for the following methods: direct complement-fixation (DCF), modified DCF (MDCF), and agar-gel precipitin (AGP). The birds species used were great-tailed grackles (Cassidix mexicanus), common grackles (Quiscalus quiscula), brown-headed cowbirds (Molothrus ater), bronzed cowbirds (Tangavius aeneus), and mourning doves (Zenaida macroura). The birds were either inoculated with an isolate of Chlamydia psittaci obtained originally from turkeys or kept as uninoculated cagemates. DCF detected antibody in most inoculated common grackles, mourning doves, and brown-headed cowbirds. It was unreliable, however, for great-tailed grackles and bronzed cowbirds inoculated intramuscularly. MDCF method detected antibody in all inoculated birds except 1 mourning dove, and gave higher titers than did DCF. AGP detected antibody in all inoculated brown-headed cowbirds and all mourning doves, 1 inoculated and 1 exposed great-tailed grackle, and none of the other 2 species. Chlamydiae were apparently transmitted to the uninoculated great-tailed and common grackles and mourning doves, for antibody was detected by all 3 methods in these species kept as uninoculated cagemates. PMID:100098

  16. Troubleshooting in the Analysis of Hexachlorocyclohexane Isomers in Agar-Agar Culture Media

    Microsoft Academic Search

    M. Barriada-Pereira; M. J. González-Castro; S. Muniategui-Lorenzo; P. López-MahÍa; D. Prada-RodrÍguez; E. Fernández-Fernández

    2007-01-01

    A method to determine hexachlorocyclohexane isomers (HCHs) in agar-agar culture media was developed in order to study the bioremediation potential of these compounds. Spiked culture medium samples (0.5 g) were finely chopped and then extracted with 20 ml of hexane:ethyl acetate (80:20) in an ultrasonic bath during 30 min and analyzed by gas chromatography and electron capture detection (GC-ECD). Analytical

  17. Comparison of Neo-Sensitabs Tablet Diffusion Assay with CLSI Broth Microdilution M38-A and Disk Diffusion Methods for Testing Susceptibility of Filamentous Fungi with Amphotericin B, Caspofungin, Itraconazole, Posaconazole, and Voriconazole

    Microsoft Academic Search

    A. Espinel-Ingroff; E. Canton

    2008-01-01

    We compared the Neo-Sensitabs tablet assay to both reference M38-A broth microdilution and disk diffusion methods for testing the susceptibility of 183 filamentous isolates to amphotericin B, caspofungin, itraconazole, posaconazole, and voriconazole. Neo-Sensitabs and disk assay inhibition zone diameters, in millimeters, were obtained on nonsupplemented Mueller-Hinton agar at 16 to 48 h. The reproducibility of zone diameters (i.e., the percentage

  18. A comparison of a new centrifuge sugar flotation technique with the agar method for the extraction of immature Culicoides (Diptera: Ceratopogonidae) life stages from salt marsh soils.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two sampling techniques, agar extraction (AE) and centrifuge sugar flotation extraction (CSFE) were compared to determine their relative efficacy to recover immature stages of Culicoides spp from salt marsh substrates. Three types of samples (seeded with known numbers of larvae, homogenized field s...

  19. Statistical evaluation of a quality control method for isolation of pathogenic Vibrio species on selected thiosulfate-citrate-bile salts-sucrose agars.

    PubMed Central

    West, P A; Russek, E; Brayton, P R; Colwell, R R

    1982-01-01

    The recovery of Vibrio cholerae, Vibrio fluvialis, Vibrio parahaemolyticus, and Vibrio vulnificus, employing eight strains of each species, was studied by using four brands of thiosulfate-citrate-bile salts-sucrose (TCBS) agar prepared according to manufacturers' instructions and following a standardized procedure. A standardized broth inoculum of each strain was placed on duplicate plates of each brand of TCBS agar and also on tryptic soy agar (Difco Laboratories) containing 1% (wt/vol) NaCl, the latter serving as the control. Plates were inoculated in a sequence designed to compensate for bias associated with multiplication of the bacteria during the inoculation procedure. Colony counts and quality of growth were recorded after incubation for 18 h at 35 degrees C. The comparison procedure was repeated four times at weekly intervals. Data were analyzed by using an analysis of variance model. The recovery and quality of growth of each species varied significantly on the different brands of TCBS agar. Significant variability was also identified for some components of the inoculation procedure. Modifications of the inoculation procedure are suggested to minimize sources of variance. A simplified statistical procedure, based on the t test, is described for media quality control for laboratories routinely isolating pathogenic Vibrio spp. PMID:6761362

  20. 48 CFR 401.371 - AGAR Advisories.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 4 2012-10-01 2012-10-01 false AGAR Advisories. 401.371 Section 401.371 ...SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of...

  1. 48 CFR 401.371 - AGAR Advisories.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 4 2013-10-01 2013-10-01 false AGAR Advisories. 401.371 Section 401.371 ...SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of...

  2. 48 CFR 401.371 - AGAR Advisories.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 4 2014-10-01 2014-10-01 false AGAR Advisories. 401.371 Section 401.371 ...SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of...

  3. 48 CFR 401.371 - AGAR Advisories.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 4 2011-10-01 2011-10-01 false AGAR Advisories. 401.371 Section 401.371 ...SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of...

  4. Molecular Diffusion Coefficients: Experimental Determination and Demonstration.

    ERIC Educational Resources Information Center

    Fate, Gwendolyn; Lynn, David G.

    1990-01-01

    Presented are laboratory methods which allow the demonstration and determination of the diffusion coefficients of compounds ranging in size from water to small proteins. Included are the procedures involving the use of a spectrometer, UV cell, triterated agar, and oxygen diffusion. Results including quantification are described. (CW)

  5. New methods in Diffusion Weighted and Diffusion Tensor Imaging

    PubMed Central

    Bammer, Roland; Holdsworth, Samantha J.; Veldhuis, Wouter B.; Skare, Stefan T.

    2009-01-01

    Synopsis Considerable strides have been made by countless individual researchers in diffusion-weighted imaging (DWI) to push DWI from an experimental tool – limited to a few institutions with specialized instrumentation – to a powerful tool used routinely for diagnostic imaging. Despite its current success, the field of DWI constantly evolves and progress has been made on several fronts, awaiting adoption by vendors and clinical users to bring in the next generation of DWI. These developments are primarily comprised of improved robustness against patient and physiologic motion, increased spatial resolution, new biophysical and tissue models, and new clinical applications for DWI. This article aims to provide a succinct overview of some of these new developments and a description of some of the major challenges associated with DWI. Trying to understand some of these challenges is helpful not only to the technically savvy MRI user, but also to radiologists who are interested in the potential strengths and weaknesses of these techniques, what is in the “diffusion pipeline”, and in how to interpret artifacts on DWI scans. PMID:19406353

  6. Abilities of the mCP Agar Method and CRENAME Alpha Toxin-Specific Real-Time PCR Assay To Detect Clostridium perfringens Spores in Drinking Water

    PubMed Central

    Maheux, Andrée F.; Bérubé, Ève; Boudreau, Dominique K.; Villéger, Romain; Cantin, Philippe; Boissinot, Maurice; Bissonnette, Luc

    2013-01-01

    We first determined the analytical specificity and ubiquity (i.e., the ability to detect all or most strains) of a Clostridium perfringens-specific real-time PCR (rtPCR) assay based on the cpa gene (cpa rtPCR) by using a bacterial strain panel composed of C. perfringens and non-C. perfringens Clostridium strains. All non-C. perfringens Clostridium strains tested negative, whereas all C. perfringens strains tested positive with the cpa rtPCR, for an analytical specificity and ubiquity of 100%. The cpa rtPCR assay was then used to confirm the identity of 116 putative C. perfringens isolates recovered after filtration of water samples and culture on mCP agar. Colonies presenting discordant results between the phenotype on mCP agar and cpa rtPCR were identified by sequencing the 16S rRNA and cpa genes. Four mCP?/rtPCR+ colonies were identified as C. perfringens, whereas 3 mCP+/rtPCR? colonies were identified as non-C. perfringens. The cpa rtPCR was negative with all 51 non-C. perfringens strains and positive with 64 of 65 C. perfringens strains. Finally, we compared mCP agar and a CRENAME (concentration and recovery of microbial particles, extraction of nucleic acids, and molecular enrichment) procedure plus cpa rtPCR (CRENAME + cpa rtPCR) for their abilities to detect C. perfringens spores in drinking water. CRENAME + cpa rtPCR detected as few as one C. perfringens CFU per 100 ml of drinking water sample in less than 5 h, whereas mCP agar took at least 25 h to deliver results. CRENAME + cpa rtPCR also allows the simultaneous and sensitive detection of Escherichia coli and C. perfringens from the same potable water sample. In itself, it could be used to assess the public health risk posed by drinking water potentially contaminated with pathogens more resistant to disinfection. PMID:24077714

  7. Immobilization of pectin degrading enzyme from Bacillus licheniformis KIBGE IB-21 using agar-agar as a support.

    PubMed

    Rehman, Haneef Ur; Aman, Afsheen; Zohra, Raheela Rahmat; Qader, Shah Ali Ul

    2014-02-15

    Pectinase from Bacillus licheniformis KIBGE IB-21 was immobilized in agar-agar matrix using entrapment technique. Effect of different concentrations of agar-agar on pectinase immobilization was investigated and it was found that maximum immobilization was achieved at 3.0% agar-agar with 80% enzyme activity. After immobilization, the optimum temperature of enzyme increased from 45 to 50 °C and reaction time from 5 to 10 minutes as compared to free enzyme. Due to the limited diffusion of high molecular weight substrate, K(m) of immobilized enzyme slightly increased from 1.017 to 1.055 mg ml(-1), while Vmax decreased from 23,800 to 19,392 ?M min(-1) as compared to free enzyme. After 120 h entrapped pectinase retained their activity up to 82% and 71% at 30 °C and 40 °C, respectively. The entrapped pectinase showed activity until 10th cycle and maintain 69.21% activity even after third cycle. PMID:24507327

  8. Range Image Segmentation by an Effective Jump-Diffusion Method

    E-print Network

    Zhu, Song Chun

    Range Image Segmentation by an Effective Jump-Diffusion Method Feng Han, Zhuowen Tu, and Song-Chun Zhu Abstract--This paper presents an effective jump-diffusion method for segmenting a range image accuracy and speed. Then, the algorithm is applied to three data sets of range images under the same

  9. Syneresis and delayed detachment in agar plates

    NASA Astrophysics Data System (ADS)

    Divoux, Thibaut; Mao, Bosi; Snabre, Patrick

    Biogels made of crosslinked polymers such as proteins or polysaccharides behave as porous soft solids and store large amount of solvent. These gels undergo spontaneous aging, called syneresis that consists in the shrinkage of the gel matrix and the progressive expulsion of the solvent. As a result, a biogel originally casted in a container often lose contact with the container sidewalls, and the detachment time is a priori difficult to anticipate since it may occur over variable time spans (from hours to days). Here we report on the syneresis phenomena in agar plates that consist in Petri dishes filled with a gel mainly composed of agar. Direct observations and speckle pattern correlation analysis allow us to rationalize the delayed detachment of the gel from the sidewall of the Petri dish. The detachment time $t^*$ is surprisingly not controlled by the mass loss as one would intuitively expect. Instead, $t^*$ is strongly correlated to the gel minimum thickness $e_{min}$ measured along the sidewall of the plate, and increases as a robust function of $e_{min}$ independently of the prior mass-loss history. Time-resolved correlation spectroscopy atypically applied to such weakly diffusive media gives access to the local thinning rate of the gel. This technique also allows us to detect the gel micro-displacements that are triggered by the water evaporation prior to the detachment, and even to anticipate the latter from a few hours. Our work provides observables to predict the detachment time of agar gels in dishes, and highlights the relevance of speckle pattern correlation analysis for the quantitative investigation of the syneresis dynamics in biopolymer gels.

  10. A hermite finite element method for convection-diffusion equations

    NASA Astrophysics Data System (ADS)

    Ruas, V.; Trales, P.

    2013-10-01

    This work addresses a technique to solve convection-diffusion problems based on Hermite interpolation. More specifically we extend to the case of these equations a Hermite finite element method providing flux continuity across interelement boundaries, shown to be a well-adapted tool for simulating purely diffusive phenomena [6]. The method can be viewed as a non trivial improved version of the lowest order Raviart-Thomas mixed method [4] and its extension to convection-diffusion problems proposed by Douglas and Roberts [2]. Convergence results are proven to hold, and comparative numerical results illustrate the good performance of the new method.

  11. Comparison of radon diffusion coefficients measured by transient-diffusion and steady-state laboratory methods

    SciTech Connect

    Kalwarf, D.R.; Nielson, K.K.; Rich, D.C.; Rogers, V.C.

    1982-11-01

    A method was developed and used to determine radon diffusion coefficients in compacted soils by transient-diffusion measurements. A relative standard deviation of 12% was observed in repeated measurements with a dry soil by the transient-diffusion method, and a 40% uncertainty was determined for moistures exceeding 50% of saturation. Excellent agreement was also obtained between values of the diffusion coefficient for radon in air, as measured by the transient-diffusion method, and those in the published literature. Good agreement was also obtained with diffusion coefficients measured by a steady-state method on the same soils. The agreement was best at low moistures, averaging less than ten percent difference, but differences of up to a factor of two were observed at high moistures. The comparison of the transient-diffusion and steady-state methods at low moistures provides an excellent verification of the theoretical validity and technical accuracy of these approaches, which are based on completely independent experimental conditions, measurement methods and mathematical interpretations.

  12. Comparing in vitro activity of tigecycline by using the disk diffusion test, the manual microdilution method, and the VITEK 2 automated system.

    PubMed

    Leal Castro, A L; Buitrago Gutierrez, G; Ovalle, V; Cortes, J A; Alvarez, C A

    2010-01-01

    Tigecycline is a broad spectrum antibiotic having activity against multiresistant isolates. In vitro susceptibility testing is difficult to perform with the use of traditional microbiological techniques. The aim of this study was to evaluate the disk diffusion test with three different Mueller-Hinton agar brands, and the Vitek 2 automated system in comparison with the standard broth microdilution method against 200 gram-negative isolates (Escherichia coil, Klebsiella pneumoniae, Enterobacter cloacae, Serratia marcescens and Acinetobacter baumannii). Among Enterobacteriaceae, the Becton Dickinson agar had the lowest rate of minor (32.5%) and major errors (3.8%). No very major errors were found. For A. baumanni, the rate of minor and major errors was lower. A high rate of agreement (94%) was found between the broth microdilution method and the Vitek 2 system. Our results show that there are important differences between agars used for the disk diffusion test, and that Vitek 2 is a valid tool for susceptibility testing in clinical laboratories. PMID:21180392

  13. A Method for Identifying Diffusive Trajectories with Stochastic Models

    NASA Astrophysics Data System (ADS)

    O'Malley, D.; Vesselinov, V. V.; Cushman, J. H.

    2014-09-01

    Single particle tracking is a tool that is being increasingly used to study diffusive or dispersive processes in many branches of natural science. Often the ability to collect these trajectories experimentally or produce them numerically outpaces the ability to understand them theoretically. On the other hand many stochastic models have been developed and continue to be developed capable of capturing complex diffusive behavior such as heavy tails, long-range correlations, nonstationarity, and combinations of these things. We describe a computational method for connecting particle trajectory data with stochastic models of diffusion. Several tests are performed to demonstrate the efficacy of the method, and the method is applied to polymer diffusion, RNA diffusion in E. coli, and RAFOS dispersion in the Gulf of Mexico.

  14. A design and analysis method for centrifugal compressor vaned diffusers

    Microsoft Academic Search

    Xiaoyan Huang; Qinghuan Wang

    1989-01-01

    In order to develop a CAD computer code system for centrifugal compressor, a numerical technique for design and flow analysis of vaned diffusers has been introduced. The design of diffusers has been performed by a streamline extension method. The velocity and pressure distributions at design and off-design operating modes have been calculated by a time-dependent finite difference scheme and have

  15. Variational methods in steady state diffusion problems

    SciTech Connect

    Lee, C.E.; Fan, W.C.P.; Bratton, R.L.

    1983-01-01

    Classical variational techniques are used to obtain accurate solutions to the multigroup multiregion one dimensional steady state neutron diffusion equation. Analytic solutions are constructed for benchmark verification. Functionals with cubic trial functions and conservational lagrangian constraints are exhibited and compared with nonconservational functionals with respect to neutron balance and to relative flux and current at interfaces. Excellent agreement of the conservational functionals using cubic trial functions is obtained in comparison with analytic solutions.

  16. Influence of agar on in vitro cultures: I. Physicochemical properties of agar and agar gelled media

    Microsoft Academic Search

    Margherita Beruto; Dario Beruto; Pierre Debergh

    1999-01-01

    Summary  The success of in vitro culture is related to several factors. Beside factors associated with the plant material or the medium\\u000a composition, the physicochemical characteristics of gelled media can play an important role. In this paper, the latter aspect\\u000a has been considered and the nature of agar powders has been investigated. Moreover, the process of gel formation for three\\u000a different

  17. Ultrasonic backscatter coefficients for weakly scattering, agar spheres in agar phantoms

    E-print Network

    Illinois at Urbana-Champaign, University of

    Ultrasonic backscatter coefficients for weakly scattering, agar spheres in agar phantoms Michael R and experimental backscatter coefficient BSC results. The phantoms consisted of agar spheres of various diameters nominally between 90 and 212 m , containing ultrafiltered milk, suspended in an agar background. BSC

  18. Quantifying Biomolecule Diffusivity Using an Optimal Bayesian Method

    PubMed Central

    Voisinne, Guillaume; Alexandrou, Antigoni; Masson, Jean-Baptiste

    2010-01-01

    Abstract We propose a Bayesian method to extract the diffusivity of biomolecules evolving freely or inside membrane microdomains. This approach assumes a model of motion for the particle considered, namely free Brownian motion or confined diffusion. In each framework, a systematic Bayesian scheme is provided for estimating the diffusivity. We show that this method reaches the best performances theoretically achievable. Its efficiency overcomes that of widely used methods based on the analysis of the mean-square displacement. The approach presented here also gives direct access to the uncertainty on the estimation of the diffusivity and predicts the number of steps of the trajectory necessary to achieve any desired precision. Its robustness with respect to noise on the position of the biomolecule is also investigated. PMID:20159156

  19. A hybrid transport-diffusion method for 2D transport problems with diffusive subdomains

    NASA Astrophysics Data System (ADS)

    Stehle, Nicholas D.; Anistratov, Dmitriy Y.; Adams, Marvin L.

    2014-08-01

    In this paper we present a computational method based on the Simple Corner Balance (SCB) scheme for solving 2D transport problems in diffusive media. It utilizes decomposition of spatial domain into transport and diffusive subregions. This methodology uses the low-order equations of the Second-Moment (SM) method for the first two angular moments of the transport solution. These low-order SM equations are solved globally. The high-order transport solution is computed only in transport subregions. The transport boundary conditions at interfaces with neighbouring diffusion subregions are formulated using asymptotic analysis of SCB. We apply the quasidiffusion (Eddington) tensor to evaluate transport effects in the problem domain and determine spatial ranges of diffusive subregions. Numerical results are presented. They demonstrate the accuracy of the developed methodology for the SCB scheme.

  20. [The detection of salmonellas using Rambach agar].

    PubMed

    Weber, A; Wachowitz, R

    1994-02-01

    Selective enrichment in Rappaport-Vassiliadis medium of 1595 animal fed samples and of 82 feedstuff and carcass meal was streaked simultaneously onto water-blue-metachrome-yellow-lactose-agar acc. to Gassner, onto brilliant-green-phenol-red-lactose-agar acc. to Kauffmann and onto Rambach agar. Salmonellae were isolated in 34 cases with Rambach agar (sensitivity 94.4%), in 33 cases with water-blue-metachrome-yellow-lactose-agar acc. to Gassner (sensitivity 91.7%) and in 31 cases with brilliant-green-phenol-red-lactose-agar acc. to Kauffmann (sensitivity 86.1%). The high specificity (99.87%) recommends the use of Rambach agar for isolation of Salmonellae from selective enrichment. PMID:7993335

  1. Adaptive streamline diffusion methods for compressible flow using conservation variables

    Microsoft Academic Search

    Peter Hansbo; Claes Johnson

    1991-01-01

    A streamline diffusion (SD) finite element method based on conservation variables is applied to compressible flow. Adaptive algorithms based on a posteriori error estimates for the SD method in the case of convection-dominated problems are described. Computational results for adaptive SD methods applied to the nonstationary Euler equations for a 2D compressible flow are presented.

  2. A Fractional Lie Group Method For Anomalous Diffusion Equations

    E-print Network

    Guo-cheng Wu

    2010-09-21

    Lie group method provides an efficient tool to solve a differential equation. This paper suggests a fractional partner for fractional partial differential equations using a fractional characteristic method. A space-time fractional diffusion equation is used as an example to illustrate the effectiveness of the Lie group method.

  3. Oxygen self-diffusion ``fast-paths'' in titanite single crystals and a general method for deconvolving self-diffusion

    E-print Network

    Watson, E. Bruce

    Oxygen self-diffusion ``fast-paths'' in titanite single crystals and a general method for deconvolving self-diffusion profiles with ``tails'' X.Y. Zhang a,b,*, E.B. Watson a , D.J. Cherniak that might affect lattice diffusion, there may be extended line- or planar defects along which fast diffusion

  4. Efficient Stochastic Galerkin Methods For Random Diffusion ...

    E-print Network

    2008-09-16

    Further extensions along this line include using piecewise basis functions to deal with discontinuity in ... variables. The resulting deterministic equations from a Galerkin method are a set of ...... A stochastic collocation method for elliptic partial differential ... High-order collocation methods for differential equations with random ...

  5. The method for detecting diffusion ring diameter in Hemagglutinin measuring

    NASA Astrophysics Data System (ADS)

    Jing, Wenbo; Liu, Xue; Duan, Jin; Wang, Xiao-man

    2014-11-01

    The diffuser ring diameter measurement is the most critical in hemagglutinin Measuring. The traditional methods, such as a vernier caliper or high-definition scanned images are subjective and low for the measurement data reliability. Propose high-resolution diffusion ring image for drop-resolution processing, adaptive Canny operator and local detection method to extract complete and clear diffusion ring boundaries, and finally make use of polynomial interpolation algorithm to make diffusion ring outer boundary pixel coordinates achieve sub-pixel accuracy and the least-squares fitting circle algorithm to calculate the precise center of the circle and the diameter of the diffuser ring. Experimental results show that the method detection time is only 63.61ms, which is a faster speed; diffuser ring diameter estimation error can achieve 0.55 pixel, high stability in experimental data. This method is adapted to the various types of influenza vaccine hemagglutinin content measurements, and has important value in the influenza vaccine quality detection.

  6. On matrix diffusion: formulations, solution methods and qualitative effects

    Microsoft Academic Search

    Jesús Carrera; Xavier Sánchez-Vila; Inmaculada Benet; Agustín Medina; Germán Galarza; Jordi Guimerà

    1998-01-01

    Matrix diffusion has become widely recognized as an important transport mechanism. Unfortunately, accounting for matrix diffusion\\u000a complicates solute-transport simulations. This problem has led to simplified formulations, partly motivated by the solution\\u000a method. As a result, some confusion has been generated about how to properly pose the problem. One of the objectives of this\\u000a work is to find some unity among

  7. Multifrequency-Gray Method for Radiation Diffusion with Compton Scattering

    Microsoft Academic Search

    Alan M. Winslow

    1995-01-01

    We describe an improved multifrequency-gray method for time-dependent nonequilibrium flux-limited radiation diffusion in a high temperature system, using a two-temperature model for electrons and ions and including energy exchange between photons and electrons by Compton scattering. Our gray equation has a nonsymmetric finite difference matrix that allows us to represent negative gray diffusion coefficients, which occur in the presence of

  8. Comparing parameter estimation methods for service-based diffusion models

    Microsoft Academic Search

    Daniel Arthur

    This paper compares methods for parameter estimation of diffusion models when seeking to extend these to service industry contexts from the traditional product focus. In the marketing science and economics literature, parameter estimation is dominated by econometric methods. This presents certain limitations as well as advantages compared to calibration in system dynamics modelling, which emphasises estimation of parameters by direct

  9. Adsorptive removal of methylene blue by agar: effects of NaCl and ethanol

    PubMed Central

    2012-01-01

    Adsorption of methylene blue (MB) on agar was investigated as a function of temperature (308-328 K), different concentrations of NaCl and HCl and various weight percentages of binary mixtures of ethanol with water. It was observed that the maximum experimental adsorption capacity, qm, exp, in water is up to 50 mg g-1 and decreases with increase in weight percentage of ethanol and NaCl and HCl concentration compared to that of water. Analysis of data using ARIAN model showed that MB adsorbs as monomer and dimer on the surface of agar. Binding constants of MB to agar were calculated using the Temkin isotherm. The process is exothermic in water and other solutions. The mean adsorption energy (E) value indicated binding of MB to agar is chemical adsorption. Kinetics of this interaction obeys from the pseudo-second-order model and diffusion of the MB molecules into the agar is the main rate-controlling step. PMID:22339759

  10. The Validation of Complete Fourier Direct MR Method for Diffusion MRI via Biological and Numerical Phantoms

    PubMed Central

    Özcan, Alpay; Quirk, James D.; Wang, Yong; Wang, Qing; Sun, Peng; Spees, William M.; Song, Sheng–Kwei

    2012-01-01

    The equations of the Complete Fourier Direct (CFD) MR model are explicitly derived for diffusion weighted NMR experiments. The CFD–MR theory is validated by comparing a biological phantom constructed from nerve bundles and agar gel with its numerical implementation. The displacement integral distribution function estimated from the experimental data is in high agreement with the numerical phantom. CFD–MR’s ability to estimate accurately and fully spin diffusion properties demonstrated here, provides the experimental validation of the theoretical CFD–MR model. PMID:22255156

  11. A Diffusion Synthetic Acceleration Method for Block Adaptive Mesh Refinement.

    SciTech Connect

    Ward, R. C. (Robert C.); Baker, R. S. (Randall S.); Morel, J. E. (Jim E.)

    2005-01-01

    A prototype two-dimensional Diffusion Synthetic Acceleration (DSA) method on a Block-based Adaptive Mesh Refinement (BAMR) transport mesh has been developed. The Block-Adaptive Mesh Refinement Diffusion Synthetic Acceleration (BAMR-DSA) method was tested in the PARallel TIme-Dependent SN (PARTISN) deterministic transport code. The BAMR-DSA equations are derived by differencing the DSA equation using a vertex-centered diffusion discretization that is diamond-like and may be characterized as 'partially' consistent. The derivation of a diffusion discretization that is fully consistent with diamond transport differencing on BAMR mesh does not appear to be possible. However, despite being partially consistent, the BAMR-DSA method is effective for many applications. The BAMR-DSA solver was implemented and tested in two dimensions for rectangular (XY) and cylindrical (RZ) geometries. Testing results confirm that a partially consistent BAMR-DSA method will introduce instabilities for extreme cases, e.g., scattering ratios approaching 1.0 with optically thick cells, but for most realistic problems the BAMR-DSA method provides effective acceleration. The initial use of a full matrix to store and LU-Decomposition to solve the BAMR-DSA equations has been extended to include Compressed Sparse Row (CSR) storage and a Conjugate Gradient (CG) solver. The CSR and CG methods provide significantly more efficient and faster storage and solution methods.

  12. Preparation of hydroxypropyl agars and their properties.

    PubMed

    Zhang, Xiaodong; Liu, Xin; Cao, Mingzhao; Xia, Kai; Zhang, Yuqiao

    2015-09-20

    A series of hydroxypropyl agars (HPAs) with different hydroxypropyl molar substitution (MS) were prepared and their physicochemical properties were characterized. After hydroxypropylation, the dissolving temperature, the gelling temperature, the gel melting temperature, the gel strength, and the thermal stability of agar all decreased except that its hygroscopicity increased. The gel skeleton structures of raw agar and HPAs were all of the porous network structures, but the pores of gel skeleton structure of HPAs became smaller and denser. PMID:26050892

  13. Coagulase-Negative Staphylococci: Comparison of Phenotypic and Genotypic Oxacillin Susceptibility Tests and Evaluation of the Agar Screening Test by Using Different Concentrations of Oxacillin

    PubMed Central

    Ferreira, Rosana B. R.; Iorio, Natalia L. P.; Malvar, Karoline L.; Nunes, Ana Paula F.; Fonseca, Leila S.; Bastos, Carla C. R.; Santos, Kátia R. N.

    2003-01-01

    This study evaluated the oxacillin susceptibilities of 152 coagulase-negative staphylococcal (CoNS) strains of 12 species by disk diffusion; agar dilution; E-test; the slide latex agglutination test (Slidex MRSA Detection test; bioMérieux S/A, Paris, France); the agar screening test with 1, 2, 4, or 6 ?g of oxacillin per ml and incubation for 24 or 48 h; and detection of the mecA gene by PCR. The results revealed that the agar screening test with 4 ?g of oxacillin per ml and incubation for 48 h was superior to any single phenotype-based susceptibility assay, presenting a sensitivity and a specificity of 100% each. For the different methods evaluated, the sensitivities and specificities were as follows: for disk diffusion, 94.2 and 91.8%, respectively; for the agar dilution test 100 and 73.5%, respectively; for E-test, 100 and 71.4%, respectively; and for the slide latex agglutination test, 97.1 and 98%, respectively. A good correlation was observed between oxacillin susceptibility testing results and PCR results for Staphylococcus epidermidis, S. haemolyticus, S. hominis subsp. hominis, and all mecA-positive strains. However, at least 60% of the mecA-negative isolates of the species S. saprophyticus, S. cohnii subsp. urealyticum, S. lugdunensis, and S. sciuri were erroneously classified as oxacillin resistant by the agar dilution test. Conversely, the slide latex agglutination test presented a high sensitivity (97.1%) and a high specificity (98%) for all CoNS species. Our results demonstrated the accuracy of the agar screening test with 4 ?g of oxacillin per ml and incubation for 48 h and the slide latex agglutination test for the appropriate detection of the oxacillin susceptibilities of CoNS isolates. Both assays are technically simple and can be easier to perform in routine laboratories than PCR. PMID:12904363

  14. Stochastic operator-splitting method for reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Choi, TaiJung; Maurya, Mano Ram; Tartakovsky, Daniel M.; Subramaniam, Shankar

    2012-11-01

    Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.

  15. A maximum entropy mean field method for driven diffusive systems

    Microsoft Academic Search

    N. C. Pesheva; Yitzhak Shnidman; R. K. P. Zia

    1993-01-01

    We introduce a method of generating systematic mean field (MF) approximations for the nonequilibrium steady state of ferromagnetic Ising driven diffusive systems (DDS), based on the maximum entropy principle due to Jaynes. In the phase coexistence region, MF approximations to the master equation do not provide a closed system of equations in the MF variables. This can be traced to

  16. An adaptive SUPG method for evolutionary convection-diffusion equations

    E-print Network

    John, Volker

    An adaptive SUPG method for evolutionary convection-diffusion equations Javier de Frutos a,1 and coarsening. The main idea consists in considering the SUPG solution of the evolutionary problem as the SUPG] will be applied, which has proved to be robust in the SUPG norm. The effectivity of this error estimator

  17. "VIRTUAL SOURCE" METHODS FOR DIFFUSIVE FIELDS: APPLICATIONS OF INTERFEROMETRY AND

    E-print Network

    Snieder, Roel

    "VIRTUAL SOURCE" METHODS FOR DIFFUSIVE FIELDS: APPLICATIONS OF INTERFEROMETRY AND SYNTHETIC. Young Professor and Head, Department of Geophysics ii #12;ABSTRACT The phrase virtual source refers, a receiver is converted to a "virtual source". In the synthetic aperture technique, a large "virtual source

  18. Chronological Life Span Method Serial Dilutions and Pin Stamps Materials: Sterile 96-well plates, YPD liquid medium, YPD-G418 agar plates (~20 ml, cured on bench

    E-print Network

    Aris, John P.

    Chronological Life Span Method ­ Serial Dilutions and Pin Stamps Materials: Sterile 96-well plates reservoir, multichannel pipetter. 1. Use a 96-well plate for dilutions and pin stamping. Use 6 wells.2 X 10-4 4. Use pin stamp to `stamp' diluted samples onto YPD-G418 plates. Dip pin stamp in 100

  19. Recovery of Sublethally Injured Bacteria Using Selective Agar Overlays.

    ERIC Educational Resources Information Center

    McKillip, John L.

    2001-01-01

    This experiment subjects bacteria in a food sample and an environmental sample to conditions of sublethal stress in order to assess the effectiveness of the agar overlay method to recover sublethally injured cells compared to direct plating onto the appropriate selective medium. (SAH)

  20. Method of making gas diffusion layers for electrochemical cells

    DOEpatents

    Frisk, Joseph William (Oakdale, MN); Boand, Wayne Meredith (Lino Lakes, MN); Larson, James Michael (Saint Paul, MN)

    2002-01-01

    A method is provided for making a gas diffusion layer for an electrochemical cell comprising the steps of: a) combining carbon particles and one or more surfactants in a typically aqueous vehicle to make a preliminary composition, typically by high shear mixing; b) adding one or more highly fluorinated polymers to said preliminary composition by low shear mixing to make a coating composition; and c) applying the coating composition to an electrically conductive porous substrate, typically by a low shear coating method.

  1. Numerical crosswind smear in the streamline diffusion method

    Microsoft Academic Search

    Bill Semper

    1994-01-01

    The streamline diffusion method is a popular method for approximating convection dominated transport equations. The solution to such equations may develop boundary or internal layers in the crosswind direction (orthogonal to the flow direction), and this results in numerical crosswind layers. It is known that the size of these layers is O(h(sup 1\\/2)) or perhaps O(h(sup 3\\/4)) (h being the

  2. Some basic mathematical methods of diffusion theory. [emphasis on atmospheric applications

    NASA Technical Reports Server (NTRS)

    Giere, A. C.

    1977-01-01

    An introductory treatment of the fundamentals of diffusion theory is presented, starting with molecular diffusion and leading up to the statistical methods of turbulent diffusion. A multilayer diffusion model, designed to permit concentration and dosage calculations downwind of toxic clouds from rocket vehicles, is described. The concepts and equations of diffusion are developed on an elementary level, with emphasis on atmospheric applications.

  3. Growth kinetics of three species of Tetrahymena on solid agar

    SciTech Connect

    Dobra, K.W.; McArdle, E.W.; Ehret, C.F.

    1980-01-01

    A nutrient-agar method without liquid overlay has been developed for cultivation of ciliates. Three species of Tetrahymena-T. pyriformis strain W, T. rostrata strain UNI, and T. vorax strain V/sub 2/S, representing the 3 main groups of Tetrahymena species, were used; however the method should apply to other ciliates. Growth on the surface of the agar was facilitated by an optimal surface-to-volume ratio yielding a high density of ciliates and short generation times. At the highest density achieved, the cells became irregularly hexagonal and formed a monolayer tissue on the agar. Ciliates grown on agar were like those in liquid culture, typical oral ciliature, food-vacuole formation, and typical cortical patterns being retained. Advantages of this method include high cell density, easy recovery, and optimal O/sub 2/ supply. The organisms can also be cultivated on the surface of sterile cellulose-nitrate filters, facilitating in situ fixation and staining as well as transfer into different media by transfer of filters with cells, without prior centrifugation and resuspension.

  4. A High-Order Kernel Method for Diffusion and Reaction-Diffusion Equations on Surfaces

    E-print Network

    Fuselier, Edward J

    2012-01-01

    In this paper we present a high-order kernel method for numerically solving diffusion and reaction-diffusion partial differential equations (PDEs) on smooth, closed surfaces embedded in $\\mathbb{R}^d$. For two-dimensional surfaces embedded in $\\mathbb{R}^3$, these types of problems have received growing interest in biology, chemistry, and computer graphics to model such things as diffusion of chemicals on biological cells or membranes, pattern formations in biology, nonlinear chemical oscillators in excitable media, and texture mappings. Our kernel method is based on radial basis functions (RBFs) and uses a semi-discrete approach (or the method-of-lines) in which the surface derivative operators that appear in the PDEs are approximated using collocation. The method only requires nodes at "scattered" locations on the surface and the corresponding normal vectors to the surface. Additionally, it does not rely on any surface-based metrics and avoids any intrinsic coordinate systems, and thus does not suffer from ...

  5. Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

    PubMed Central

    Bauler, Patricia; Huber, Gary A.; McCammon, J. Andrew

    2012-01-01

    Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems. PMID:22559470

  6. Studies on irradiation of agar–agar in the solid state: On the changes of melting point of the agar–agar hydrogel and setting point of the agar–agar hydrosol produced by irradiation

    Microsoft Academic Search

    Mizuho Nisizawa

    1975-01-01

    The effects of radiation on the formation of the cross-links of the agar-agar hydrogel were studied by measuring the melting point and setting point, and by calculating the heats of reaction for the cross-linking processes at different radiation doses, times after irradiation and concentrations of added substances (sugar and starch). The empirical equations for the melting point and the setting

  7. In Vitro Activity of Fosfomycin against a Collection of Clinical Pseudomonas aeruginosa Isolates from 16 Spanish Hospitals: Establishing the Validity of Standard Broth Microdilution as Susceptibility Testing Method

    PubMed Central

    Díez-Aguilar, María; del Campo, Rosa; García-Castillo, María; Zamora, Javier; Cantón, Rafael

    2013-01-01

    The broth microdilution method for fosfomycin and Pseudomonas aeruginosa was assessed and compared with the approved agar dilution method in 206 genetically unrelated P. aeruginosa clinical isolates. Essential agreement between the two methods was 84%, and categorical agreement was 89.3%. Additionally, Etest and disk diffusion assays were performed. Results validate broth microdilution as a reliable susceptibility testing method for fosfomycin against P. aeruginosa. Conversely, unacceptable concordance was established between Etest and disk diffusion results with agar dilution results. PMID:23939889

  8. High-order accurate, low numerical diffusion methods for aerodynamics

    NASA Astrophysics Data System (ADS)

    Ekaterinaris, John A.

    2005-04-01

    In recent years numerical methods have been widely used to effectively resolve complex flow features of aerodynamics flows with meshes that are reasonable for today's computers. High-order numerical methods were used mainly in direct numerical simulations and aeroacoustics. For many aeronautical applications, accurate computation of vortex-dominated flows is important because the vorticity in the flow field and the wake of swept wings at an incidence and rotor blades largely determines the distribution of loading. The main deficiency of widely available, second-order accurate methods for the accurate computation of these flows is the numerical diffusion of vorticity to unacceptable levels. Application of high-order accurate, low-diffusion numerical methods can significantly alleviate this deficiency of traditional second order methods. Furthermore, higher-order space discretizations have the potential to improve detached eddy simulation predictions of separated flows with significant unsteadiness. Recently developed high-order accurate finite-difference, finite-volume, and finite-element methods are reviewed. These methods can be used as an attractive alternative of traditional low-order central and upwind computational fluid dynamics methods for improved predictions of vortical and other complex, separated, unsteady flows. The main features of these methods are summarized, from a practical user's point of view, their applicability and relative strength is indicated, and examples from recent applications are presented to illustrate their performance on selected problems.

  9. Measurement of gas diffusion through soils: comparison of laboratory methods.

    PubMed

    Allaire, Suzanne E; Lafond, Jonathan A; Cabral, Alexandre R; Lange, Sébastien F

    2008-11-01

    Gas movement through soils is important for ecosystems and engineering in many ways such as for microbial and plant respiration, passive methane oxidation in landfill covers and oxidation of mine residues. Diffusion is one of the most important gas movement processes and the determination of the diffusion coefficient is a crucial step in any study. Five laboratory methods used for measuring the relative gas diffusion coefficient (D(s)/D(o)) were compared using a loamy sand, a porous media commonly found in agricultural fields and in several engineered structures, such as in landfill final covers. In the absence of macropores, all methods gave rather similar values of D(s)/D(o). Methods allowing the study of microscale variability indicated that the presence of macropores highly influenced gas movement, thus the value of D(s)/D(o), which, near a macropore may be one order of magnitude higher than in regions without macropores. Repacked columns do not allow the study of heterogeneity in D(s)/D(o). Natural spatial variability in D(s)/D(o) due to water distribution and preferential pathways can only be studied in large systems, but these systems are difficult to handle. Advantages and disadvantages of each method are discussed. PMID:18974902

  10. Diffusely reflecting paints including polytetrafluoroethylene and method of manufacture

    NASA Technical Reports Server (NTRS)

    Schutt, J. B.; Shai, M. C. (inventors)

    1985-01-01

    The invention pertains to a high diffuse, reflective paint comprising an alcohol soluble binder, polytetrafluoroethylene (TFE) and an alcohol for coating a substrate and forming an optical reference with a superior Lambertian characteristic. A method for making the paint by first mixing the biner and alcohol, and thereafter by mixing in outgassed TFE is described. A wetting agent may be employed to aid the mixing process.

  11. Columbia Anaerobe 5% Sheep Blood Agar

    Microsoft Academic Search

    Columbia Agars; EP ISO; Columbia Agar Base; Fildes Enrichment

    1 , using Columbia Agar Base, formulated reducible anaerobic media designed to improve recovery of anaerobes with minimal difficulty. The reducing agents used were cysteine, palladium chloride and dithiothreitol. The presence of \\

  12. DRYING OF WATER GELS: DETERMINATION OF THE CHARACTERISTIC CURVE OF AGAR-AGAR

    Microsoft Academic Search

    O. Iglesias; A. Garcia; M. Roques; J. L. Bueno

    1993-01-01

    Agar-agar is a polysaccharide extracted as a hydrocolloid from red seaweed, whose gels are homogeneous, stable and transparent. The characterization of ternary equilibrium and mass transfer kinetics in the agar-water-air system is essential for designing operations in the extractive process as well as for ascertaining the behaviour of these gels and sols during evaporation. humectation and swelling.In this work, the

  13. A comparison of agar dilution, identification of beta-lactamases and disc diffusion methods for assessing the sensitivity to ticarcillin-clavulanic acid.

    PubMed

    Joly, B; Chanal, M; Sirot, D; Cluzel, M; Sirot, J; Cluzel, R

    1986-05-01

    The in-vitro antibacterial activity of Timentin has been evaluated with a view to proposing valid criteria for sensitivity and resistance. Minimal inhibitory concentrations (MIC) were determined for 284 strains including Enterobacteriaceae, Pseudomonas aeruginosa, Acinetobacter spp., staphylococci and enterococci. The same strains were also used for the determination of inhibition zones around discs containing 75 micrograms ticarcillin and 10 micrograms clavulanic acid, and a straight regression line was drawn correlating MIC with inhibition zones. The bacterial population was subsequently grouped according to the diameters of inhibition zones of the antibiogram for 2427 strains of Enterobacteriaceae classified by phenotypes. The comparison of MICs of Timentin and ticarcillin for these strains shows that for penicillinase-producing strains, the Timentin MIC is lower than for ticarcillin whereas cephalosporinase-producing strains have equal MICs for the two. Finally strains that produce many different beta-lactamases are not affected by the presence of clavulanic acid. These results should make it possible to propose provisional zone diameters for determining sensitivity and resistance to Timentin. PMID:3522530

  14. Preparation and characterization of agar/clay nanocomposite films: the effect of clay type.

    PubMed

    Rhim, Jong-Whan; Lee, Soo-Bin; Hong, Seok-In

    2011-04-01

    Agar-based nanocomposite films with different types of nanoclays, such as Cloisite Na+, Cloisite 30B, and Cloisite 20A, were prepared using a solvent casting method, and their tensile, water vapor barrier, and antimicrobial properties were tested. Tensile strength (TS), elongation at break (E), and water vapor permeability (WVP) of control agar film were 29.7±1.7 MPa, 45.3±9.6%, and (2.22±0.19)×10(-9) g·m/m2·s·Pa, respectively. All the film properties tested, including transmittance, tensile properties, WVP, and X-ray diffraction patterns, indicated that Cloisite Na+ was the most compatible with agar matrix. TS of the nanocomposite films prepared with 5% Cloisite Na+ increased by 18%, while WVP of the nanocomposite films decreased by 24% through nanoclay compounding. Among the agar/clay nanocomposite films tested, only agar/Cloisite 30B nanocomposite film showed a bacteriostatic function against?Listeria monocytogenes. PMID:21535851

  15. Physicochemical and morphological properties of plasticized poly(vinyl alcohol)-agar biodegradable films.

    PubMed

    Madera-Santana, T J; Freile-Pelegrín, Y; Azamar-Barrios, J A

    2014-08-01

    The effects of the addition of glycerol (GLY) on the physicochemical and morphological properties of poly(vinyl alcohol) (PVA)-agar films were reported. PVA-agar films were prepared by solution cast method, and the addition of GLY in PVA-agar films altered the optical properties, resulting in a decrease in opacity values and in the color difference (?E) of the films. Structural characterization using Fourier transformation infrared (FTIR) spectroscopy and X-ray diffraction (XRD) indicated that the presence of GLY altered the intensity of the bands (from 1200 to 800cm(-1)) and crystallinity. The characterization of the thermal properties indicated that an increase in the agar content produces a decrease in the melting temperature and augments the heat of fusion. Similar tendencies were observed in plasticized films, but at different magnification. The formulation that demonstrated the lowest mechanical properties contained 25wt.% agar, whereas the formulation that contained 75wt.% agar demonstrated a significant improvement. The water vapor transmission rate (WVTR) and surface morphology analysis demonstrated that the structure of PVA-agar films is reorganized upon GLY addition. The physicochemical properties of PVA-agar films using GLY as a plasticizer provide information for the application of this formulation as packaging material for specific food applications. PMID:24875313

  16. A diffusive information preservation method for small Knudsen number flows

    SciTech Connect

    Fei, Fei; Fan, Jing, E-mail: jfan@imech.ac.cn

    2013-06-15

    The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker–Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ? 10{sup ?3}–10{sup ?4} have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.

  17. Antimicrobial susceptibility testing of Helicobacter pylori comparison of E-test, broth microdilution, and disk diffusion for ampicillin, clarithromycin, and metronidazole

    Microsoft Academic Search

    Charles Y. Hachem; Jill E. Clarridge; Rita Reddy; Robert Flamm; Dolores G. Evans; S. Ken Tanaka; David Y. Graham

    1996-01-01

    The optimal method for the determination of the minimum inhibitory concentration (MIC) of antimicrobials against Helicobacter pylori has not been established. The epsilometer agar diffusion gradient test (E-Test; AB Biodisk, Solna, Sweden) was compared with broth microdilution, the reference method, and disk diffusion for the antimicrobial susceptibility testing of 122 clinical isolates of H. pylori to ampicillin, clarithromycin, and metronidazole.

  18. New method of echo detection for diffuse reflection laser ranging

    NASA Astrophysics Data System (ADS)

    Wang, Kun-peng; Zhang, Yan; Wang, Xing-qi; Quan, Lin; Zhao, Peng

    2015-03-01

    The echo received from diffuse reflection laser ranging (DRLR) system for space debris and satellite without corner reflector is too weak to detect available echo-photon robustly. A new method based on image saliency feature for echophoton detection was proposed, which used the concept of image saliency in computer vision field to describe echophoton distribution feature. The O-C residue distribution information was used to generate O-C residue image, and then saliency feature recognition, Piecewise Hough detection and polynomial fitting were adopt orderly to obtain available echo signal. The actual experiment results show the effectiveness and robustness of the algorithm.

  19. Standard Test Method for Measured Speed of Oil Diffusion Pumps

    E-print Network

    American Society for Testing and Materials. Philadelphia

    1982-01-01

    1.1 This test method covers the determination of the measured speed (volumetric flow rate) of oil diffusion pumps. 1.2 The values stated in inch-pound units are to be regarded as the standard. The metric equivalents of inch-pound units may be approximate. 1.3 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  20. Biased anisotropic diffusion method for PET image segmentation

    NASA Astrophysics Data System (ADS)

    Lin, Hong-Dun; Wang, Han-Yuan; Hu, Yu-Chang; Lin, Kang-Ping; Yu, Chin-Lung; Wu, Liang-Chi; Liu, Ren-Shyan

    2001-05-01

    In the context of functional positron emission tomographic (PET) images analysis, the segmentation method can not only entails the separation of the image into regions of similar attribute but also presents clearer understanding about the features embedded in the original image to improve the quantitative analysis. However, for completely recording, clinical instruments often collect subject signal as well as signals from background environment, which are regarded as noises of various levels. High noise often makes the original PET image unrecognizable and difficult to analyze. Thus, manual or semiautomatic methods have been utilized to overcome the difficulty of high noise image segmentation. Furthermore, the success of image segmentation is one of the important key factors in the accompanying automated system, and there has been no general segmentation method that can be applied to the high noise PET images of different feature characteristics. However, the PET image is high noisy causing by the imaging procedure, and the image quality of PET image is affected inherently. To improve this issue, a novel nonlinear anisotropic diffusion technique based on the diffusion theorem with multi-scale and edge detection scheme to inhibit the noise level and hold the boundary characteristics of the high noise PET image was provided in this paper.

  1. Diffuse optical methods for assessing breast cancer chemotherapy

    NASA Astrophysics Data System (ADS)

    Tromberg, Bruce J.

    2014-03-01

    In his talk, "Diffuse Optical Methods for Assessing Breast Cancer Chemotherapy," SPIE Fellow Bruce Tromberg (Beckman Laser Institute and Medical Clinic) describes a method combining frequency domain photon migration, essentially a method of tracking photon motion in tissue, with a NIR spectroscopy technique using 850nm LEDs. The result is a scatter corrected absorption spectra. The technique takes advantage of elevated blood and water levels and decreased lipid levels in the presence of tumors to provide a more accurate mapping of the breast, allowing more effective treatment. Tromberg's team recently completed their first full mapping of the breast and have taken the instrument from a standalone unit to a portable one suitable for travel. In addition to providing feedback to enhance breast cancer treatment, Tromberg expects that this technique will be applicable in treating other forms of cancer as well.

  2. Room-temperature phosphorescence of pyrene in agar-agar solid matrix doped with lead acetate

    Microsoft Academic Search

    G. V. Melnikov; A. N. Salnikov; A. V. Spivack

    2001-01-01

    Luminescence analysis, involving electronic recombination of the pyrene molecules, introduced into agar-agar solid-matrix was carried out. For the first time, room temperature phosphorescence (RTP) of pyrene, activated with lead acetate, was observed. It was established that increased lead acetate concentration resulted in weakened luminosity of pyrene excimers and emergence of phosphorescence.

  3. On matrix diffusion: formulations, solution methods and qualitative effects

    NASA Astrophysics Data System (ADS)

    Carrera, Jesús; Sánchez-Vila, Xavier; Benet, Inmaculada; Medina, Agustín; Galarza, Germán; Guimerà, Jordi

    Matrix diffusion has become widely recognized as an important transport mechanism. Unfortunately, accounting for matrix diffusion complicates solute-transport simulations. This problem has led to simplified formulations, partly motivated by the solution method. As a result, some confusion has been generated about how to properly pose the problem. One of the objectives of this work is to find some unity among existing formulations and solution methods. In doing so, some asymptotic properties of matrix diffusion are derived. Specifically, early-time behavior (short tests) depends only on ?m2RmDm / Lm2, whereas late-time behavior (long tracer tests) depends only on ?mRm, and not on matrix diffusion coefficient or block size and shape. The latter is always true for mean arrival time. These properties help in: (a) analyzing the qualitative behavior of matrix diffusion; (b) explaining one paradox of solute transport through fractured rocks (the apparent dependence of porosity on travel time); (c) discriminating between matrix diffusion and other problems (such as kinetic sorption or heterogeneity); and (d) describing identifiability problems and ways to overcome them. RésuméLa diffusion matricielle est un phénomène reconnu maintenant comme un mécanisme de transport important. Malheureusement, la prise en compte de la diffusion matricielle complique la simulation du transport de soluté. Ce problème a conduit à des formulations simplifiées, en partie à cause de la méthode de résolution. Il s'en est suivi une certaine confusion sur la façon de poser correctement le problème. L'un des objectifs de ce travail est de trouver une certaine unité parmi les formulations et les méthodes de résolution. C'est ainsi que certaines propriétés asymptotiques de la diffusion matricielle ont été dérivées. En particulier, le comportement à l'origine (expériences de traçage courtes) dépend uniquement du terme ?m2RmDm / Lm2, alors que le comportement à long terme (traçages de longue durée) ne dépend que de ?mRm, et non pas du coefficient de diffusion matricielle ou de la forme et de la taille des blocs. Ceci est toujours vrai pour le temps moyen d'arrivée. Ces propriétés permettent: (a) d'analyser le comportement de la diffusion matricielle; (b) d'expliquer un paradoxe du transport de soluté dans les roches fracturées (la dépendance apparente entre la porosité et le temps de transit); (c) de faire la distinction entre la diffusion matricielle et d'autres problèmes, tels que la sorption cinétique ou l'hétérogénéité et (d) de décrire les problèmes d'identification et les façons de les résoudre. Resumen La difusión en la matriz está reconocida en la actualidad como un importante mecanismo de transporte de solutos. Desgraciadamente, tener en cuenta este proceso complica las simulaciones de transporte. Esto ha llevado a una serie de formulaciones simplificadas, motivadas en parte por el propio método de solución. Como resultado, se ha producido cierta confusión respecto a cuál es la manera adecuada de formular el problema. Uno de los objetivos de este trabajo es encontrar una cierta unidad entre las formulaciones existentes y los métodos de solución, lo que conduce a algunas propiedades asintóticas de la difusión en la matriz; específicamente, se comprueba que el comportamiento para tiempos cortos depende únicamente del parámetro ?m2RmDm / Lm2, mientras que el de tiempos largos depende sólo de ?mRm, y no del coeficiente de difusión en la matriz o del tamaño o forma del bloque. Esto último también es cierto, en todos los casos, respecto al tiempo medio de llegada (definido como el valor esperado de la distribución de tiempos de llegada). Estas propiedades son útiles para: (a) analizar el comportamiento cualitativo de la difusión en la matriz; (b) explicar una de las paradojas del transporte de solutos en medios fracturados, la aparente dependencia entre porosidad y tiempo de llegada; (c) discriminar entre difusión en la matriz y otros problemas, como las reacciones con cinética

  4. A novel agar formulation for isolation and direct enumeration of Vibrio vulnificus from oyster tissue.

    PubMed

    Griffitt, Kimberly J; Grimes, D Jay

    2013-08-01

    A new selective and differential medium, Vibrio vulnificus X-Gal (VVX), was developed for direct enumeration of V. vulnificus (Vv) from oyster samples. This agar utilizes cellobiose and lactose as carbon sources, and the antibiotics colistin and polymyxin B as selective agents. Hydrolysis of 5-bromo-4-chloro-3-indolyl- beta-d-galactopyranoside (x-gal), used in the agar as a lactose analog, produces an insoluble blue dye that makes lactose positive colonies easily distinguishable from any non-lactose fermenting bacteria. Various bacterial species were spot plated onto thiosulfate-citrate-bile salts-sucrose agar (TCBS), and CHROMagar Vibrio, two vibrio-specific selective agars, non-selective agar, and VVX to compare selectivity of VVX to other widely used media. A V. vulnificus pure culture was serially diluted on VVX and non-selective agar to determine the VVX percent recovery. Water and oyster samples were spread plated on VVX agar and allowed to incubate for 16-18 h at 33 °C. Blue and white colonies from VVX agar were picked and screened by end point PCR for the Vv hemolysin vvhA. VVX agar showed a significant improvement over TCBS and CHROMagar at preventing non-target growth. There was an 87.5% recovery compared to non-selective plating and a 98% positivity rate of blue colonies picked from oyster tissue plating. The findings suggest that this new agar is a fast, distinctive, and accurate method for enumeration of V. vulnificus from the environment. PMID:23660708

  5. Comparison of agar versus broth dilution techniques for determining antibiotic susceptibilities of Ureaplasma urealyticum.

    PubMed

    Waites, K B; Figarola, T A; Schmid, T; Crabb, D M; Duffy, L B; Simecka, J W

    1991-01-01

    We determined minimal inhibitory concentrations (MIC) for tetracycline and erythromycin for 72 clinical isolates using broth and agar dilution methods. Erythromycin MIC ranges were less than 0.125-8 micrograms/ml and 1-64 micrograms/ml in broth and agar, respectively. The erythromycin MIC50 and MIC90 as determined by broth were two dilutions (fourfold) lower than those for agar. Tetracycline MIC ranges in broth and agar were less than 0.125-greater than 64 and 0.25-greater than 64 micrograms/ml, respectively. The tetracycline broth MIC50 was one dilution lower than that for agar. The tetracycline broth MIC90 was 64 micrograms/ml and that for agar was greater than 64 micrograms/ml. Of the strains tested, 98.6% using broth were susceptible or moderately susceptible to erythromycin as compared with 75% using agar, representing a significant difference (p less than 0.001). For tetracycline, 80.6% of strains were susceptible or moderately susceptible using broth and 73.6% using agar. MICs were determined by agar dilution after 72 and 96 hr of incubation in 32 strains. There was an increase in the erythromycin MIC by one dilution in 16 strains and two dilutions in one strain with the longer incubation. The tetracycline MIC increased by one dilution in nine strains between readings. Broth MICs were reproducible with one dilution for both drugs in 10 of 12 strains tested twice. Agar MICs were reproducible within a maximum of two dilutions (fourfold). Different interpretations of susceptibility versus resistance may be made depending on which assay is utilized, thus influencing conclusions regarding spectrum of activity of investigational drugs as well as treatment options. The technique employed should always be considered whenever apparently differing drug susceptibility patterns are reported. PMID:1889178

  6. Extrapolation techniques applied to matrix methods in neutron diffusion problems

    NASA Technical Reports Server (NTRS)

    Mccready, Robert R

    1956-01-01

    A general matrix method is developed for the solution of characteristic-value problems of the type arising in many physical applications. The scheme employed is essentially that of Gauss and Seidel with appropriate modifications needed to make it applicable to characteristic-value problems. An iterative procedure produces a sequence of estimates to the answer; and extrapolation techniques, based upon previous behavior of iterants, are utilized in speeding convergence. Theoretically sound limits are placed on the magnitude of the extrapolation that may be tolerated. This matrix method is applied to the problem of finding criticality and neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron-diffusion equations is treated. Results for this example are indicated.

  7. Compact finite volume methods for the diffusion equation

    NASA Technical Reports Server (NTRS)

    Rose, Milton E.

    1989-01-01

    An approach to treating initial-boundary value problems by finite volume methods is described, in which the parallel between differential and difference arguments is closely maintained. By using intrinsic geometrical properties of the volume elements, it is possible to describe discrete versions of the div, curl, and grad operators which lead, using summation-by-parts techniques, to familiar energy equations as well as the div curl = 0 and curl grad = 0 identities. For the diffusion equation, these operators describe compact schemes whose convergence is assured by the energy equations and which yield both the potential and the flux vector with second order accuracy. A simplified potential form is especially useful for obtaining numerical results by multigrid and alternating direction implicit (ADI) methods. The treatment of general curvilinear coordinates is shown to result from a specialization of these general results.

  8. Detection of Agar, by Analysis of Sugar Markers, Associated with Bacillus Anthracis Spores, After Culture

    SciTech Connect

    Wunschel, David S.; Colburn, Heather A.; Fox, Alvin; Fox, Karen F.; Harley, William M.; Wahl, Jon H.; Wahl, Karen L.

    2008-08-01

    Detection of small quantities of agar associated with spores of Bacillus anthracis could provide key information regarding its source or growth characteristics. Agar, widely used in growth of bacteria on solid surfaces, consists primarily of repeating polysaccharide units of 3,6-anhydro-L-galactose (AGal) and galactose (Gal) with sulfated and O-methylated galactoses present as minor constituents. Two variants of the alditol acetate procedure were evaluated for detection of potential agar markers associated with spores. The first method employed a reductive hydrolysis step, to stabilize labile anhydrogalactose, by converting to anhydrogalactitol. The second eliminated the reductive hydrolysis step simplifying the procedure. Anhydrogalactitol, derived from agar, was detected using both derivatization methods followed by gas chromatography-mass spectrometry (GC-MS) analysis. However, challenges with artefactual background (reductive hydrolysis) or marker destruction (hydrolysis) lead to the search for alternative sugar markers. A minor agar component, 6-O-methyl galactose (6-O-M gal), was readily detected in agar-grown but not broth-grown bacteria. Detection was optimized by the use of gas chromatography-tandem mass spectrometry (GC-MS-MS). With appropriate choice of sugar marker and analytical procedure, detection of sugar markers for agar has considerable potential in microbial forensics.

  9. Electro-osmosis in gel -Application to Agar-Agar Fabien Cherblanc, Jer^ome Boscus, Jean-Claude Benet

    E-print Network

    Paris-Sud XI, Université de

    Electro-osmosis in gel - Application to Agar-Agar Fabien Cherblanc, J´er^ome Boscus, Jean-Claude B-engineering as a reference material, Agar-Agar gel is the focus of an experimental investigation concerning the electro-osmosis from liquid phase transport phenomena that take place in porous media (osmosis, electro-osmosis

  10. Migration of chemotactic bacteria in soft agar: role of gel concentration

    E-print Network

    O. A. Croze; G. P. Ferguson; M. E. Cates; W. C. K. Poon

    2011-08-06

    We study the migration of chemotactic wild-type Escherichia coli populations in semisolid (soft) agar in the concentration range C = 0.15-0.5% (w/v). For C migrate as broad circular bands rather than sharp rings. These are growth/diffusion waves arising because of suppression of chemotaxis by the agar and have not been previously reported experimentally to our knowledge. For C = 0.4-0.5%, expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The migration front speed is weakly dependent on agar concentration at C < 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel transport parameter expressions accounting for perturbations of the chemotactic response by collisions with the agar. The model makes it possible to fit the observed front speed decay in the range C = 0.15-0.35%, and its solutions qualitatively reproduce the observed transition from chemotactic to growth/diffusion bands. We discuss the implications of our results for the study of bacteria in porous media and for the design of improved bacteriological chemotaxis assays.

  11. Direct disk diffusion test using European Clinical Antimicrobial Susceptibility Testing breakpoints provides reliable results compared with the standard method.

    PubMed

    Stokkou, Sofia; Geginat, Gernot; Schlüter, Dirk; Tammer, Ina

    2015-03-01

    Sepsis represents a life-threatening infection requiring the immediate start of antibacterial treatment to reduce morbidity. Thus, laboratories use direct antimicrobial susceptibility testing (AST) to rapidly generate preliminary results from positive blood cultures. As the direct AST has not yet been published to be evaluated with EUCAST breakpoints, the purpose of the study was to investigate the reliability of the direct agar diffusion test to correctly produce AST results from positive monobacterial blood cultures compared with the VITEK2-based definitive AST, when current EUCAST breakpoints were used. A total of 428 isolates from unselected monobacterial routine blood cultures and 110 challenge strains were included. Direct agar diffusion-based and standard VITEK2-based AST of 2803 bacterium-drug combinations yielded a total clinical category agreement of 95.47% with 1.28% very major errors and 3.42% combined major and minor errors. On the species level, very major errors were observed in the species-drug combinations Enterococcus spp.-high-level gentamicin (10.87%) and Staphylococcus spp.-rifampicin (5%), only. No very major errors occurred with Enterobacteriaceae and Pseudomonas aeruginosa. In most species-drug combinations, the direct agar diffusion test using EUCAST breakpoints precisely predicted the result of the definitive antibiotic susceptibility test and, thus, it can be used to optimize empiric antibiotic therapy until definitive results are available. PMID:25883798

  12. Direct disk diffusion test using European Clinical Antimicrobial Susceptibility Testing breakpoints provides reliable results compared with the standard method

    PubMed Central

    Stokkou, Sofia; Geginat, Gernot; Schlüter, Dirk

    2015-01-01

    Sepsis represents a life-threatening infection requiring the immediate start of antibacterial treatment to reduce morbidity. Thus, laboratories use direct antimicrobial susceptibility testing (AST) to rapidly generate preliminary results from positive blood cultures. As the direct AST has not yet been published to be evaluated with EUCAST breakpoints, the purpose of the study was to investigate the reliability of the direct agar diffusion test to correctly produce AST results from positive monobacterial blood cultures compared with the VITEK2-based definitive AST, when current EUCAST breakpoints were used. A total of 428 isolates from unselected monobacterial routine blood cultures and 110 challenge strains were included. Direct agar diffusion-based and standard VITEK2-based AST of 2803 bacterium–drug combinations yielded a total clinical category agreement of 95.47% with 1.28% very major errors and 3.42% combined major and minor errors. On the species level, very major errors were observed in the species–drug combinations Enterococcus spp.–high-level gentamicin (10.87%) and Staphylococcus spp.–rifampicin (5%), only. No very major errors occurred with Enterobacteriaceae and Pseudomonas aeruginosa. In most species–drug combinations, the direct agar diffusion test using EUCAST breakpoints precisely predicted the result of the definitive antibiotic susceptibility test and, thus, it can be used to optimize empiric antibiotic therapy until definitive results are available. PMID:25883798

  13. Use of agar agar stabilized milled zero-valent iron particles for in situ groundwater remediation

    NASA Astrophysics Data System (ADS)

    Schmid, Doris; Velimirovi?, Milica; Wagner, Stephan; Mici? Batka, Vesna; von der Kammer, Frank; Hofmann, Thilo

    2015-04-01

    A major obstacle for use of nanoscale zero-valent iron (nZVI) particles as a nontoxic material for effective in situ degradation of chlorinated aliphatic hydrocarbons (CAHs) is the high production cost. For that reason, submicro-scale milled zero-valent iron particles were recently developed (milled ZVI, UVR-FIA, Germany) by grinding macroscopic raw materials of elementary iron as a cheaper alternative to products produced by solid-state reduction. However, milled ZVI particles tend to aggregate and due to the rather large particle size (d50= 11.9 µm) also rapidly sediment. To prevent aggregation and consequently sedimentation of milled ZVI particles and therefore improve the mobility after in situ application, the use of a stabilizer is considered in literature as a most promising option. In this study, milled ZVI particles (1 g L-1 of particle concentration) were stabilized by environmentally friendly polymer agar agar (>0.5 g L-1), which had a positive impact on the milled ZVI stability. Sedimentation rate was significantly decreased by increasing the suspension viscosity. Column transport experiments were performed for bare and agar agar stabilized milled ZVI particles in commercially available fine grained quartz sand (DORSILIT® Nr.8, Gebrüder Dorfner GmbH Co, Germany) and different porous media collected from brownfields. The experiments were carried out under field relevant injection conditions of 100 m d-1. The maximal travel distance (LT) of less than 10 cm was determined for non-stabilized suspension in fine grained quartz sand, while agar agar (1 g L-1) stabilized milled ZVI suspension revealed LT of 12 m. Similar results were observed for porous media from brownfields showing that mobility of agar agar stabilized particle suspensions was significantly improved compared to bare particles. Based on the mobility data, agar agar stabilized milled zero-valent iron particles could be used for in situ application. Finally, lab-scale batch degradation experiments were performed to determine the impact of agar agar on the reactivity of milled ZVI and investigate the apparent corrosion rate of particles by quantifying the hydrogen gas generated by anaerobic corrosion of milled ZVI. The results indicate that agar agar had a positive impact on the milled ZVI stability and mobility, however adverse impact on the reactivity towards trichloroethene (TCE) was observed compared to the non-stabilized material. On the other hand, this study shows that the apparent corrosion rate of non-stabilized and agar agar stabilized milled ZVI particles is in the same order of magnitude. These data indicate that the dechlorination pathway of TCE by agar agar stabilized milled ZVI particles is possibly impacted by blocking of the reactive sites and not hydrogen revealed during particles corrosion. Finally, calculated longevity of the particles based on the apparent corrosion rate is significantly prolonged compared to the longevity of the nZVI particles reported in previous studies. This research receives funding from the European Union's Seventh Framework Programme FP7/2007-2013 under grant agreement n°309517.

  14. Luminescent DNA- and agar-based membranes.

    PubMed

    Leones, R; Fernandes, M; Ferreira, R A S; Cesarino, I; Lima, J F; Carlos, L D; Bermudez, V de Zea; Magon, C J; Donoso, J P; Silva, M M; Pawlicka, A

    2014-09-01

    Luminescent materials containing europium ions are investigated for different optical applications. They can be obtained using bio-macromolecules, which are promising alternatives to synthetic polymers based on the decreasing oil resources. This paper describes studies of the DNA- and Agar-europium triflate luminescent membranes and its potential technological applications are expanded to electroluminescent devices. Polarized optical microscopy demonstrated that the samples are birefringent with submicrometer anisotropy. The X-ray diffraction analysis revealed predominantly amorphous nature of the samples and the atomic force microscopy images showed a roughness of the membranes of 409.0 and 136.1 nm for the samples of DNA10Eu and Agar1.11Eu, respectively. The electron paramagnetic resonance spectra of the DNA(n)Eu membranes with the principal lines at g ? 2.0 and g ? 4.8 confirmed uniform distribution of rare earth ions in a disordered matrix. Moreover, these strong and narrow resonance lines for the samples of DNA(n)Eu when compared to the Agar(n)Eu suggested a presence of paramagnetic radicals arising from the DNA matrix. The emission spectra suggested that the Eu3+ ions occupy a single local environment in both matrices and the excitation spectra monitored around the Eu emission lines pointed out that the Eu3+ ions in the Agar host were mainly excited via the broad band component rather than by direct intra-4f(6) excitation, whereas the opposite case occurred for the DNA-based sample. PMID:25924317

  15. A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability

    PubMed Central

    Tanaka, Tomohiro; Kawasaki, Kosei; Daimon, Serina; Kitagawa, Wataru; Yamamoto, Kyosuke; Tamaki, Hideyuki; Tanaka, Michiko; Nakatsu, Cindy H.

    2014-01-01

    Microbiologists have been using agar growth medium for over 120 years. It revolutionized microbiology in the 1890s when microbiologists were seeking effective methods to isolate microorganisms, which led to the successful cultivation of microorganisms as single clones. But there has been a disparity between total cell counts and cultivable cell counts on plates, often referred to as the “great plate count anomaly,” that has long been a phenomenon that still remains unsolved. Here, we report that a common practice microbiologists have employed to prepare agar medium has a hidden pitfall: when phosphate was autoclaved together with agar to prepare solid growth media (PT medium), total colony counts were remarkably lower than those grown on agar plates in which phosphate and agar were separately autoclaved and mixed right before solidification (PS medium). We used a pure culture of Gemmatimonas aurantiaca T-27T and three representative sources of environmental samples, soil, sediment, and water, as inocula and compared colony counts between PT and PS agar plates. There were higher numbers of CFU on PS medium than on PT medium using G. aurantiaca or any of the environmental samples. Chemical analysis of PT agar plates suggested that hydrogen peroxide was contributing to growth inhibition. Comparison of 454 pyrosequences of the environmental samples to the isolates revealed that taxa grown on PS medium were more reflective of the original community structure than those grown on PT medium. Moreover, more hitherto-uncultivated microbes grew on PS than on PT medium. PMID:25281372

  16. A Genetic Algorithm Method for Multi-spot Diffuse Infrared Wireless Communications

    E-print Network

    Haddadi, Hamed

    A Genetic Algorithm Method for Multi-spot Diffuse Infrared Wireless Communications M Nikkar SNR in multi-spot diffuse infrared communication systems is proposed. The technique aims to adjust on the SNR that can be achieved by spot-diffuse system such as LSMS[1] in a mobile scenario. In practice

  17. The measurement of grain boundary diffusion by the method of autoradiography

    Microsoft Academic Search

    T. J. Renouf

    1970-01-01

    The method of autoradiography is used in the quantitative measurement of grain boundary diffusion. The autoradiographic image is examined using the Joyce-Loebl isodensitracer to produce an accurate two-dimensional density map of the grain boundary region sufficient in detail to allow a more extensive analysis of grain boundary diffusion. Tracer diffusion of the very high, medium and very low energy isotopes

  18. Highly stable Ag nanoparticles in agar-agar matrix as inorganic–organic hybrid

    Microsoft Academic Search

    Elayaraja Muthuswamy; S. Sree Ramadevi; H. N. Vasan; Cécile Garcia; Laure Noé; Marc Verelst

    2007-01-01

    A novel synthesis of inorganic–organic hybrid films containing well dispersed and almost uniform size Ag nanoparticles in\\u000a agar-agar matrix has been reported. The films are found to be highly stable for more than a year. The colloidal particles\\u000a of Ag can be obtained in large quantities in the form of a film or in the gel form when dispersed in

  19. Self Diffusion and Binary Maxwell–Stefan Diffusion in Simple Fluids with the Green–Kubo Method

    Microsoft Academic Search

    G. A. Fernández; J. Vrabec; H. Hasse

    2004-01-01

    Self-diffusion coefficients and binary Maxwell–Stefan diffusion coefficients were determined by equilibrium molecular dynamics simulations with the Green–Kubo method. The study covers five pure fluids: neon, argon, krypton, xenon, and methane and three binary mixtures: argon+krypton, argon+xenon, and krypton+xenon. The fluids are modeled by spherical Lennard-Jones pair-potentials, with parameters which were determined solely on the basis of vapor-liquid equilibrium data. The

  20. Exact solutions for time-fractional diffusion-wave equations by decomposition method

    Microsoft Academic Search

    Santanu Saha Ray

    2007-01-01

    The time-fractional diffusion-wave equation is considered. The time-fractional diffusion equation is obtained from the standard diffusion equation by replacing the first-order time derivative with a fractional derivative of order ? ? (0,2]. The fractional derivative is described in the Caputo sense. This paper presents the analytical solutions of the fractional diffusion equations by an Adomian decomposition method. By using initial

  1. Operator splitting implicit integration factor methods for stiff reaction–diffusion–advection systems

    Microsoft Academic Search

    Su Zhao; Jeremy Ovadia; Xinfeng Liu; Yong-Tao Zhang; Qing Nie

    2011-01-01

    For reaction–diffusion–advection equations, the stiffness from the reaction and diffusion terms often requires very restricted time step size, while the nonlinear advection term may lead to a sharp gradient in localized spatial regions. It is challenging to design numerical methods that can efficiently handle both difficulties. For reaction–diffusion systems with both stiff reaction and diffusion terms, implicit integration factor (IIF)

  2. A novel method for effective diffusion coefficient measurement in gas diffusion media of polymer electrolyte fuel cells

    NASA Astrophysics Data System (ADS)

    Yang, Linlin; Sun, Hai; Fu, Xudong; Wang, Suli; Jiang, Luhua; Sun, Gongquan

    2014-07-01

    A novel method for measuring effective diffusion coefficient of porous materials is developed. The oxygen concentration gradient is established by an air-breathing proton exchange membrane fuel cell (PEMFC). The porous sample is set in a sample holder located in the cathode plate of the PEMFC. At a given oxygen flux, the effective diffusion coefficients are related to the difference of oxygen concentration across the samples, which can be correlated with the differences of the output voltage of the PEMFC with and without inserting the sample in the cathode plate. Compared to the conventional electrical conductivity method, this method is more reliable for measuring non-wetting samples.

  3. Method for manufacturing nuclear radiation detector with deep diffused junction

    Microsoft Academic Search

    Hall

    1977-01-01

    Germanium radiation detectors are manufactured by diffusing lithium into high purity p-type germanium. The diffusion is most readily accomplished from a lithium-lead-bismuth alloy at approximately 430°C and is monitored by a quartz half cell containing a standard composition of this alloy. Detectors having n-type cores may be constructed by converting high purity p-type germanium to n-type by a lithium diffusion

  4. Automatic surface inoculation of agar trays.

    NASA Technical Reports Server (NTRS)

    Wilkins, J. R.; Mills, S. M.; Boykin, E. H.

    1972-01-01

    Description of a machine and technique for the automatic inoculation of a plastic tray containing agar media with a culture, using either a conventional inoculation loop or a cotton swab. The design of the machine is simple, it is easy to use, and it relieves the operator from the manual task of streaking cultures. The described technique makes possible the visualization of the overall qualitative and, to some extent, quantitative relationships of various bacterial types in a sample tested.

  5. AEROSOL SIZE MEASUREMENT BY ELECTRICAL MOBILITY AND DIFFUSION ANALYSIS - A COMPARISON OF METHODS

    EPA Science Inventory

    The principle of the electrical aerosol analyzer method is reviewed and the diffusion battery method is described in detail. An appendix explains the basis of the calculations used. The diffusion battery method is complicated by counting losses of very small particles, inherent t...

  6. Polymeric hydrogen diffusion barrier, high-pressure storage tank so equipped, method of fabricating a storage tank and method of preventing hydrogen diffusion

    DOEpatents

    Lessing, Paul A.

    2004-09-07

    An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.

  7. Polymeric hydrogen diffusion barrier, high-pressure storage tank so equipped, method of fabricating a storage tank and method of preventing hydrogen diffusion

    DOEpatents

    Lessing, Paul A. (Idaho Falls, ID)

    2008-07-22

    An electrochemically active hydrogen diffusion barrier which comprises an anode layer, a cathode layer, and an intermediate electrolyte layer, which is conductive to protons and substantially impermeable to hydrogen. A catalytic metal present in or adjacent to the anode layer catalyzes an electrochemical reaction that converts any hydrogen that diffuses through the electrolyte layer to protons and electrons. The protons and electrons are transported to the cathode layer and reacted to form hydrogen. The hydrogen diffusion barrier is applied to a polymeric substrate used in a storage tank to store hydrogen under high pressure. A storage tank equipped with the electrochemically active hydrogen diffusion barrier, a method of fabricating the storage tank, and a method of preventing hydrogen from diffusing out of a storage tank are also disclosed.

  8. Antimicrobial activity of highly stable silver nanoparticles embedded in agar–agar matrix as a thin film

    Microsoft Academic Search

    S. Ghosh; R. Kaushik; K. Nagalakshmi; S. L. Hoti; G. A. Menezes; B. N. Harish; H. N. Vasan

    2010-01-01

    Highly stable silver nanoparticles (Ag NPs) in agar–agar (Ag\\/agar) as inorganic–organic hybrid were obtained as free-standing film by in situ reduction of silver nitrate by ethanol. The antimicrobial activity of Ag\\/agar film on Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Candida albicans (C. albicans) was evaluated in a nutrient broth and also in saline solution. In particular, films

  9. Continuous degradation of maltose: improvement in stability and catalytic properties of maltase (?-glucosidase) through immobilization using agar-agar gel as a support.

    PubMed

    Nawaz, Muhammad Asif; Karim, Asad; Aman, Afsheen; Marchetti, Roberta; Qader, Shah Ali Ul; Molinaro, Antonio

    2015-04-01

    Maltose degrading enzyme was immobilized within agar-agar support via entrapment method due to its industrial utilization. The maximum immobilization efficiency (82.77%) was achieved using 4.0% agar-agar keeping the diameter of bead up to 3.0 mm. The matrix entrapment showed maximum catalytic activity at pH 7.0 and temperature 65 °C. Substrate saturation kinetics showed that the K m of immobilized enzyme increased from 1.717 to 2.117 mM ml(-1) where as Vmax decreased from 8,411 to 7,450 U ml(-1 )min(-1) as compared to free enzyme. The immobilization significantly increased the stability of maltase against various temperatures and immobilized maltase retain 100% of its original activity after 2 h at 50 °C, whereas the free maltase only showed 60% residual activity under same condition. The reusability of entrapped maltase showed activity up to 12 cycles and retained 50% of activity even after 5th cycle. Storage stability of agar entrapped maltase retain 73% of its initial activity even after 2 months when stored at 30 °C while free enzyme showed only 37% activity at same storage conditions. PMID:25326060

  10. Xanthan gum: an economical partial substitute for agar in microbial culture media.

    PubMed

    Babbar, Shashi B; Jain, Ruchi

    2006-04-01

    Xanthan gum, microbial desiccation-resistant polysaccharide prepared commercially by aerobic submerged fermentation from Xanthomonas campestris, has been successfully used alone and in combination with agar for microbial culture media. As illustrative examples, eight bacteria and eight fungi were grown on media solidified with either agar (A, 1.5%), xanthan gum (X, 1%), or combinations of both (0.9% X + 0.1% A, 0.8% X + 0.2% A, 0.7% X + 0.3% A, 0.6% X + 0.4% A). All fungi and bacteria exhibited normal growth and differentiation in all these treatments. Rather, growth of most of the fungi was better on xanthan (alone) and xanthan + agar media than agar medium. As the media gelled with xanthan gum alone flow, it was not possible to incubate Petri plates in inverted position. Moreover, because of the softness, streaking of bacteria was difficult on such media. However, these problems could be overcome by partially replacing xanthan gum with 0.3% agar. Bacterial enumeration studies carried out for Serratia sp. and Pseudomonas sp. by serial dilution and pour-plate method on agar (1.5%), 0.7%/0.6% X + 0.3%/0.4% A yielded similar counts. Selective media, succinate medium for Pseudomonas sp., and MacConkey broth medium for Escherichia coli gelled with 0.7%/0.6% X + 0.3%/0.4% A did not support growth of other bacteria when inoculated along with the above-mentioned bacteria. Likewise, differential medium, CRMA (Congo red mannitol agar) gelled with xanthan-agar combination could differentiate between Agrobacterium tumefaciens and Rhizobium sp. PMID:16550465

  11. Bordetellae and Charcoal Horse Blood Agar: Inactivation of Antibiotics in Agar during Prolonged Incubation for Susceptibility Testing

    Microsoft Academic Search

    Jörg E. Hoppe; Anton Haug; Konrad Botzenhart

    1988-01-01

    We examined the degree of inactivation of 22 antibiotics caused by prolonged incubation at 36 °C of agar plates during agar dilution susceptibility testing of Bordetellae. Fresh antibiotic-containing plates of charcoal horse blood agar and plates which had been held at 36 °C for 2 or 3 days prior to inoculation were inoculated with strains of Bordetella pertussis and Bordetella

  12. A Level Set Method for Anisotropic Geometric Diffusion in 3D Image Processing

    E-print Network

    Preusser, Tobias

    A Level Set Method for Anisotropic Geometric Diffusion in 3D Image Processing Tobias Preußer and Martin Rumpf Abstract--A new morphological multiscale method in 3D image process- ing is presented which combines the image processing methodology based on nonlinear diffusion equations and the theory

  13. A discontinuous residual-free bubble method for advection-diffusion problems

    E-print Network

    Sangalli, Giancarlo

    -diffusion, finite element method, stabilization, SUPG, residual-free bub- bles, multiscale. AMS Subject in the eight- ies [12,18,19]. Their Streamline-Upwind Petrov-Galerkin (SUPG) method adds diffusion only;consistency of the variational formulation. The SUPG technique performs better than the naive artificial

  14. A diffusion accelerated Sn transport method for radiation transport on a general quadrilateral mesh

    Microsoft Academic Search

    R. E. Alcouffe

    1989-01-01

    We present the development of a diffusion accelerated Sn transport method for the solution of temperature coupled radiation flow problems on a spatial mesh of arbitrary quadrilaterals in R-Z geometry. The diffusion acceleration equation is derived from the diamond-like transport spatial discretization. The effectiveness of the DSA method is shown on an example calculation and also computation times are indicated.

  15. An electrochemical method for accelerated testing of chloride diffusivity in concrete

    Microsoft Academic Search

    T. Zhang; O. E. Gjoerv

    1994-01-01

    In the present paper an electrochemical method for accelerated testing of chloride diffusivity in concrete is presented. The method is based on a theoretical relationship between chloride diffusivity and observed steady-state rate of chloride migration through the concrete. The concentration of the chloride source solution has a significant influence on the rate of chloride migration and, therefore, a correction factor

  16. A numerical method for a system of singularly perturbed reaction-diffusion equations.1

    E-print Network

    A numerical method for a system of singularly perturbed reaction-diffusion equations.1 S. Matthews points of the do- main independently of the singular perturbation parameters is constructed and analysed-diffusion, singular perturbation, parameter- uniform. 1 Introduction In this paper we examine a numerical method

  17. EULERIAN-LAGRANGIAN LOCALIZED ADJOINT METHODS FOR A NONLINEAR ADVECTION-DIFFUSION EQUATION

    E-print Network

    Russell, Thomas F.

    EULERIAN-LAGRANGIAN LOCALIZED ADJOINT METHODS FOR A NONLINEAR ADVECTION-DIFFUSION EQUATION Helge K the characteristics has been used e#11;ectively in [1, 5, 7, 8, 9, 10, 16, 17, 18] under the term modi#12;ed method

  18. Diffusion

    NSDL National Science Digital Library

    Christopher Thomas (None; )

    2006-11-09

    Diffusion is the movement of particles from an area of high concentration to an area of low concentration. The molecules move until equilibrium is reached. If a perfume is sprayed on one side of the room, the perfume molecules will eventually spread out all over the room until there are equal concentrations of the molecules throughout the space.

  19. COMPARISON OF THE RECOVERIES OF ESCHERICHIA COLI AND TOTAL COLIFORMS FROM DRINKING WATER BY THE MI AGAR METHOD AND THE U.S. ENVIRONMENTAL PROTECTION AGENCY-APPROVED MEMBRANE FILTER METHOD

    EPA Science Inventory

    Drinking water regulations under the Final Coliform Rule require that total coliform-positive drinking water samples be examined for the presence of Escherichia coli or fecal coliforms. The current U.S. Environmental Protection Agency-approved membrane filter (MF) method for E. c...

  20. Application of the clustering method in molecular dynamics simulation of the diffusion coefficient

    Microsoft Academic Search

    Qingzhi Liu; Yangdong Hu

    2008-01-01

    Using molecular dynamics (MD) simulation, the diffusion of oxygen, methane, ammonia and carbon dioxide in water was simulated\\u000a in the canonical NVT ensemble, and the diffusion coefficient was analyzed by the clustering method. By comparing to the conventional\\u000a method (using the Einstein model) and the differentiation-interval variation method, we found that the results obtained by\\u000a the clustering method used in

  1. The Local Discontinuous Galerkin Method for Time-Dependent Convection-Diffusion Systems

    Microsoft Academic Search

    Bernardo Cockburn; Chi-Wang Shu

    1998-01-01

    this paper, we study the Local Discontinuous Galerkin methods fornonlinear, time-dependent convection-diffusion systems. These methods are an extensionof the Runge-Kutta Discontinuous Galerkin methods for purely hyperbolicsystems to convection-diffusion systems and share with those methods their highparallelizability, their high-order formal accuracy, and their easy handling of complicatedgeometries, for convection dominated problems. It is proven that for scalarequations, the Local...

  2. Diffusion NMR Methods Applied to Xenon Gas for Materials Study

    E-print Network

    R. W. Mair; M. S. Rosen; R. Wang; D. G. Cory; R. L. Walsworth

    2002-11-09

    We report initial NMR studies of i) xenon gas diffusion in model heterogeneous porous media, and ii) continuous flow laser-polarized xenon gas. Both areas utilize the Pulsed Gradient Spin Echo techniques in the gas-phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients - a brief overview of this area is provided in the introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t), (an indicator of mean squared displacement) to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. The Pade approximation is used to interpolate D(t) data between the short and long time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20 - 200 mm/s). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm/s due to the high diffusivity of gases compared to liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data: namely, flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack.

  3. Examination of three methods for studying ion diffusion in cement pastes, mortars and concrete

    Microsoft Academic Search

    N. R. Buenfeld; J. B. Newman

    1987-01-01

    Three laboratory techniques for studying ion diffusion in hydrated cement pastes, mortars and concrete are described and compared.\\u000a In the first method, concentration profiles are produced by analysing material sampled at various distances from the surface\\u000a exposed to the selected ion, after various periods of exposure. The second technique employs a diffusion cell and calculation\\u000a of an effective diffusion coefficient

  4. Grid-free simulation of diffusion using random walk methods

    NASA Technical Reports Server (NTRS)

    Ghoniem, A. F.; Sherman, F. S.

    1985-01-01

    The simulation of the diffusion of a continuum field by the random walk (RW) displacement of a set of particles is considered. Elements of the gradients of the diffusive concentration are transported by computational particles. It is demonstrated that, by the use of concentration gradients in the RW process, statistical errors are reduced and each realization of the numerical solution is a representation of the exact solution. The algorithm is grid-free, and the computational elements move to follow the gradients; hence, the algorithm is self-adaptive, and uniform resolution is achieved for all times.

  5. A comparison of blood agar supplemented with NAD with plain blood agar and chocolated blood agar in the isolation of Streptococcus pneumoniae and Haemophilus influenzae from sputum

    Microsoft Academic Search

    K. J. NYE; D. FALLON; B. GEE; S. MESSER; R. E. WARREN; N. ANDREWS

    1999-01-01

    Streptococcus pneumoniae grows well and generally exhibits typical morphology on Columbia blood agar, whereas Haemophilus influenzae requires a more complex medium to meet its growth requirements - usually chocolated blood agar - on which S. pneumoniae is less easily recognisable. Therefore, a single medium that produces typical morphology of S. pneumoniae and facilitates the growth of H. influenzae would have

  6. Diffusion

    NSDL National Science Digital Library

    Since the advent of the internet, a number of artists and related organizations have become interested in utilizing the web to promulgate new forms of artistic creation and their subsequent dissemination. Supported by the Arts Council of England, these Diffusion eBooks are essentially pdf files that readers can download, print out and make into booklets. As the site suggests, "the Diffusion format challenges conventions of interactivity-blending the physical and the virtual and breaking the dominance of mouse and screen as the primary forms of human computer interaction...the format's aim is to take the reader away from the screen and computer and engage them in the process of production." There are a number of creative booklets available here for visitors, complete with instruction on how to assemble them for the desired effect. For anyone with even a remote interest in the possibilities afforded by this rather curious new form of expression, this website is worth a look.

  7. OPTIMIZED SCHWARZ WAVEFORM RELAXATION METHODS FOR ADVECTION REACTION DIFFUSION PROBLEMS

    Microsoft Academic Search

    M. J. GANDER; L. HALPERN

    2006-01-01

    We study in this paper a new class of waveformrelaxation algorithm s for large sys- tems of ordinary differential equations arising from discretizations of partial differential equations of advection reaction diffusion type. We show that the transmission conditions between the subsys- tems have a tremendous influence on the convergence speed of the waveform relaxation algorithms, and we identify transmission conditions

  8. TIME SAMPLING OF DIFFUSION SYSTEMS USING SEMIGROUP DECOMPOSITION METHODS

    E-print Network

    Moura, José

    - versified fields of science and technology. In Bi- ology examples range from cell (e.g. ion currents) (Smith diffusion model as in the case of distributed collector solar fields (Silva et al., 2003). The classical. Lemos has been done under the project AMBIDISC, contract POSI/SRI/36328/2000. fusion models are a basic

  9. Criteria for the assessment of susceptibility to ceftazidime using the disc diffusion procedure

    Microsoft Academic Search

    H. Grimm

    1983-01-01

    Summary Using regression analyses, we have determined criteria for the assessment of ceftazidime using the agar diffusion test with a 10 µg disc. With the ICS procedure, inhibition zones of =15 mm on Mueller-Hinton agar, =17 mm on Iso-sensitest agar and =18 mm on DST agar indicate susceptibility (MIC =16 mg\\/l). Using the Kirby-Bauer procedure, Mueller-Hinton agar and the same

  10. A fully implicit method for 3D quasi-steady state magnetic advection-diffusion.

    SciTech Connect

    Siefert, Christopher; Robinson, Allen Conrad

    2009-09-01

    We describe the implementation of a prototype fully implicit method for solving three-dimensional quasi-steady state magnetic advection-diffusion problems. This method allows us to solve the magnetic advection diffusion equations in an Eulerian frame with a fixed, user-prescribed velocity field. We have verified the correctness of method and implementation on two standard verification problems, the Solberg-White magnetic shear problem and the Perry-Jones-White rotating cylinder problem.

  11. A Stabilized Finite Element Method for AdvectionDiffusion Equations on Surfaces

    E-print Network

    method, transport equations, advection­diffusion equation, SUPG stabilization AMS Subject Classifications is sufficiently fine. The paper introduces a stabilized finite element formulation based on the SUPG technique, advection-diffusion equation, SUPG stabilization AMS subject classifications. 58J32, 65N12, 65N30, 76D45, 76

  12. On the Choice of Parameters in Stabilization Methods for ConvectionDiffusion Equations

    E-print Network

    John, Volker

    ­diffusion equations is the streamline upwind/Petrov­Galerkin(SUPG) method. Unfortunately, in the convection­dominated regime, the SUPG solution often con- tains spurious oscillations along sharp layers. A possible remedy is to introduce an additional artificial diffusion term in the SUPG discretization. We call such ap- proaches

  13. A stochastic variational multiscale method for diffusion in heterogeneous random media

    E-print Network

    Zabaras, Nicholas J.

    A stochastic variational multiscale method for diffusion in heterogeneous random media for numerical solution of stochastic elliptic equations that arise while mod- elling diffusion in heterogeneous-scale solution. The coarse-scale solution is then obtained by solving a modi- fied coarse formulation that takes

  14. AgarTrap-mediated genetic transformation using intact gemmae/gemmalings of the liverwort Marchantia polymorpha L.

    PubMed

    Tsuboyama-Tanaka, Shoko; Kodama, Yutaka

    2015-03-01

    The dioecious liverwort, Marchantia polymorpha L., is an emerging model plant. Various molecular biological techniques have been optimized for M. polymorpha for the past several years, and recently we reported a simplified Agrobacterium-mediated transformation method using sporelings (immature thalli from spores) of M. polymorpha. This method, termed AgarTrap (Agar-utilized Transformation with Pouring Solutions), completed by exchanging appropriate solutions on a single Petri dish to produce a sufficient number of independent transgenic sporelings. However, because spores are produced by crosses between males and females, the genetic backgrounds of resulting transgenic sporelings are not uniform. To easily produce transgenic liverworts with a uniform genetic background using AgarTrap, we developed an AgarTrap-mediated transformation method using intact gemmae/gemmalings produced by asexual reproduction. Using AgarTrap with male and female gemmae/gemmalings produced a sufficient number of independent transgenic gemmalings with uniform genetic backgrounds. The optimized transformation efficiencies were approximately 30 and 50 % in males and females, respectively. As with AgarTrap using sporelings, AgarTrap using intact gemmae/gemmalings will be useful in promoting studies of the molecular biology of M. polymorpha. PMID:25663453

  15. Characterization of bionanocomposite films prepared with agar and paper-mulberry pulp nanocellulose.

    PubMed

    Reddy, Jeevan Prasad; Rhim, Jong-Whan

    2014-09-22

    Crystallized nanocellulose (CNC) was separated from paper-mulberry (Broussonetia kazinoki Siebold) bast pulp by sulfuric acid hydrolysis method and they were blended with agar to prepare bionanocomposite films. The effect of CNC content (1, 3, 5 and 10 wt% based on agar) on the mechanical, water vapor permeability (WVP), and thermal properties of the nanocomposites were studied. Changes of the cellulose fibers in structure, morphology, crystallinity, and thermal properties of the films were evaluated using FT-IR, TEM, SEM, XRD, and TGA analysis methods. The CNC was composed of fibrous and spherical or elliptic granules of nano-cellulose with sizes of 50-60 nm. Properties of agar film such as mechanical and water vapor barrier properties were improved significantly (p<0.05) by blending with the CNC. The tensile modulus and tensile strength of agar film increased by 40% and 25%, respectively, in the composite film with 5 wt% of CNC, and the WVP of agar film decreased by 25% after formation of nanocomposite with 3 wt% of CNC. The CNC obtained from the paper-mulberry bast pulp can be used as a reinforcing agent for the preparation of bio-nanocomposites, and they have a high potential for the development of completely biodegradable food packaging materials. PMID:24906782

  16. Diffusion NMR methods applied to xenon gas for materials study.

    PubMed

    Mair, R W; Rosen, M S; Wang, R; Cory, D G; Walsworth, R L

    2002-12-01

    We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. PMID:12807139

  17. Automatic Surface Inoculation of Agar Trays1

    PubMed Central

    Wilkins, Judd R.; Mills, Stacey M.; Boykin, Elizabeth H.

    1972-01-01

    A machine is described which automatically inoculates a plastic tray containing agar media with a culture by use of either a conventional inoculating loop or a cotton swab. Isolated colonies were obtained with an inoculating loop when a heavy inoculum (109 cells/ml) was used or with a cotton swab when a light inoculum (ca. 104 cells/ml) was used. Trays containing combinations of differential or selective media were used to (i) separate mixtures of gram-positive and gram-negative bacteria, (ii) facilitate isolation of organisms from clinical specimens, and (iii) compare colony growth characteristics of pure cultures. The design of the machine is simple, it is easy to use, and it relieves the operator from the manual task of streaking cultures. Images PMID:16349943

  18. The presence of embedded bacterial pure cultures in agar plates stimulate the culturability of soil bacteria

    Microsoft Academic Search

    Mette Burmølle; Kaare Johnsen; Waleed Abu Al-Soud; Lars Hestbjerg Hansen; Søren Johannes Sørensen

    2009-01-01

    Traditional methods for bacterial cultivation recover only a small fraction of bacteria from all sorts of natural environments, and attempts have been made to improve the bacterial culturability. Here we describe the development of a cultivation method, based on the embedment of pure bacterial cultures in between two layers of agar. Plates containing either embedded Pseudomonas putida or Arthrobacter globiformis

  19. Preliminary Evaluation of a Semisolid Agar Antifungal Susceptibility Test for Yeasts and Molds

    Microsoft Academic Search

    HARRIET PROVINE; SUSAN HADLEY

    2000-01-01

    This report presents a semisolid agar antifungal susceptibility (SAAS) method for the rapid susceptibility screening of yeasts and molds. The reproducibility and accuracy of the SAAS method were assessed by com- paring the MICs of amphotericin B and fluconazole obtained for 10 candidate quality control (QC) American Type Culture Collection yeast strains in >15 replicates with those found by six

  20. A Local Incident Flux Response Expansion Transport Method for Coupling to the Diffusion Method in Cylindrical Geometry

    SciTech Connect

    Dingkang Zhang; Farzad Rahnema; Abderrafi M. Ougouag

    2013-09-01

    A local incident flux response expansion transport method is developed to generate transport solutions for coupling to diffusion theory codes regardless of their solution method (e.g., fine mesh, nodal, response based, finite element, etc.) for reactor core calculations in both two-dimensional (2-D) and three-dimensional (3-D) cylindrical geometries. In this approach, a Monte Carlo method is first used to precompute the local transport solution (i.e., response function library) for each unique transport coarse node, in which diffusion theory is not valid due to strong transport effects. The response function library is then used to iteratively determine the albedo coefficients on the diffusion-transport interfaces, which are then used as the coupling parameters within the diffusion code. This interface coupling technique allows a seamless integration of the transport and diffusion methods. The new method retains the detailed heterogeneity of the transport nodes and naturally constructs any local solution within them by a simple superposition of local responses to all incoming fluxes from the contiguous coarse nodes. A new technique is also developed for coupling to fine-mesh diffusion methods/codes. The local transport method/module is tested in 2-D and 3-D pebble-bed reactor benchmark problems consisting of an inner reflector, an annular fuel region, and a controlled outer reflector. It is found that the results predicted by the transport module agree very well with the reference fluxes calculated directly by MCNP in both benchmark problems.

  1. A comparison between protein crystals grown with vapor diffusion methods in microgravity and protein crystals using a gel liquid-liquid diffusion ground-based method

    NASA Technical Reports Server (NTRS)

    Miller, Teresa Y.; He, Xiao-Min; Carter, Daniel C.

    1992-01-01

    Crystals of human serum albumin have been successfully grown in a variety of gels using crystallization conditions otherwise equivalent to those utilized in the popular hanging-drop vapor-equilibrium method. Preliminary comparisons of gel grown crystals with crystals grown by the vapor diffusion method via both ground-based and microgravity methods indicate that crystals superior in size and quality may be grown by limiting solutal convection. Preliminary X-ray diffraction statistics are presented.

  2. Growth of Microorganisms from Supragingival Dental Plaque on Saliva Agar

    Microsoft Academic Search

    M. H. De Jong; J. S. Van Der Hoeven; J. H. Van Os

    1986-01-01

    The role of saliva in supporting the growth of dental plaque has scarcely been investigated. We have studied the growth and recovery of micro-organisms from dental plaque samples on saliva-agar plates, prepared from filter-sterilized wax-stimulated whole saliva. Under optimal conditions, the mean recovery of plaque samples on saliva agar was about 50% (range, 22-77) of the recovery on blood agar.

  3. Cell Growth on Soft Agar Plates Buffers Needed

    E-print Network

    Pike, Linda J.

    Cell Growth on Soft Agar Plates Buffers Needed: 2x DME (for 250 ml of 2x) 6.7 g Powdered DME 1.85 g (for 200 ml) 40 ml calf serum (use OLD Gibco serum) 4 ml glutamine 160 ml 2x DME 1.2% agar, sterilized 0.6% agar, sterilized Procedure: 1. Trypsinize cells and stop trypsinization by addition of serum

  4. 21 CFR 866.4600 - Ouchterlony agar plate.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ...AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a)...

  5. 21 CFR 866.4600 - Ouchterlony agar plate.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a)...

  6. Comparative study of methods used to estimate ionic diffusion coefficients using migration tests

    SciTech Connect

    Narsilio, G.A. [Department of Civil and Environmental Engineering, School of Engineering, University of Melbourne, Victoria 3010 (Australia)], E-mail: narsilio@unimelb.edu.au; Li, R. [Department of Civil and Environmental Engineering, School of Engineering, University of Melbourne, Victoria 3010 (Australia); Institute of Geotechnical Engineering, Southeast University (SEU), Nanjing, Jiangsu (China)], E-mail: lirenmin@seu.edu.cn; Pivonka, P. [Department of Civil and Environmental Engineering, School of Engineering, University of Melbourne, Victoria 3010 (Australia)], E-mail: ppivonka@unimelb.edu.au; Smith, D.W. [Department of Civil and Environmental Engineering, School of Engineering, University of Melbourne, Victoria 3010 (Australia)], E-mail: david.smith@unimelb.edu.au

    2007-08-15

    Ionic diffusion coefficients are estimated rapidly using electromigration tests. In this paper, electromigration tests are accurately simulated by numerically solving the Nernst-Planck (NP) equation (coupled with the electroneutrality condition (EN)) using the finite element method. Numerical simulations are validated against experimental data obtained elsewhere [E. Samson, J. Marchand, K.A. Snyder, Calculation of ionic diffusion coefficients on the basis of migration test results, Materials and Structures/Materiaux et Constructions 36 (257) (2003) 156-165., H. Friedmann, O. Amiri, A. Ait-Mokhtar, A direct method for determining chloride diffusion coefficient by using migration test, Cement and Concrete Research 34 (11) (2004) 1967-1973.]. It is shown that migration due to the non-linear electric potential completely overwhelms diffusion due to concentration gradients. The effects of different applied voltage differences and chloride source concentrations on estimations of chloride diffusion coefficients are explored. We show that the pore fluid within concrete and mortar specimens generally differs from the curing solution, lowering the apparent diffusion coefficient, primarily due to interactions of chloride ions with other ions in the pore fluid. We show that the variation of source chloride concentration strongly affects the estimation of diffusion coefficients in non-steady-state tests; however this effect vanishes under steady-state conditions. Most importantly, a comparison of diffusion coefficients obtained from sophisticated analyses (i.e., NP-EN) and a variety of commonly used simplifying methods to estimate chloride diffusion coefficients allows us to identify those methods and experimental conditions where both approaches deliver good estimates for chloride diffusion coefficients. Finally, we demonstrate why simultaneous use and monitoring of current density and fluxes are recommended for both the non-steady and steady-state migration tests.

  7. A robust and efficient method for steady state patterns in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

    2012-06-01

    An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton's method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton's method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton's method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space.

  8. A comparison of the point kinetics equations with the QUANDRY analytic nodal diffusion method 

    E-print Network

    Velasquez, Arthur

    1993-01-01

    The point kinetics equations were incorporated into QUANDRY, a nuclear reactor analysis computer program which uses the analytic nodal method to solve the neutron diffusion equation. Both the point kinetics equations, solved using the IMSL MATH...

  9. Novel exponentially fitted triangular finite element method for an advection-diffusion problem with boundary layers

    SciTech Connect

    Wang, Song [Curtin Univ. of Technology, Perth (Australia)] [Curtin Univ. of Technology, Perth (Australia)

    1997-07-01

    Using a linear model for the incompressible Navier-Stokes equations, a singularly perturbed advection-diffusion problem can be solved by a set of piecewise exponentially basis functions fitted to a triangular finite element method.

  10. Evaluation of method of preparation of passive diffusion tubes for measurement of ambient nitrogen dioxide 

    E-print Network

    Hamilton, Richard P; Heal, Mathew R

    2004-01-01

    This study was carried out in response to suggestions that the measurement of NO2 by Palmes-type passive diffusion tubes (PDT) is affected by the method of preparation of the triethanolamine (TEA) absorbent coating on the ...

  11. Stability and Convergence of a Finite Volume Method for a Reaction Diffusion System in

    E-print Network

    Pierre, Charles

    Stability and Convergence of a Finite Volume Method for a Reaction Diffusion System in Electro, at a macroscopic scale : H = Hi = He = m , V, i, e : H R Fibrous structure of the muscular tissue = anisotropy

  12. Synthesis of agar microparticles using temperature-controlled microfluidic devices for Cordyceps militaris cultivation.

    PubMed

    Lin, Yung-Sheng; Yang, Chih-Hui; Lu, Kang; Huang, Keng-Shiang; Zheng, Ying-Zhen

    2011-11-01

    A temperature-controlled microfluidic approach was developed for fabricating monodispersed agar beads with the potential to be a brand-new strategy for cultivating Cordyceps militaris. The proposed microfluidic system features a circulating water bath with precise temperature control (temperature deviation ?T<0.1°C). This device holds the promise of allowing us to develop a temperature-controlled system, characterized as simple, low cost, and easy to set up and use. The size-controllable agar beads were achieved by utilizing microfluidic emulsification in the cross-junction channel under temperature-controlled conditions. The flow conditions of the dispersed/continuous phases were adjusted to generate various sizes of agar beads. Our results show that the microparticles produced are as small as 176 ??m with a 95% particle size distribution within 5? ?m. The prepared agar microparticles performed well as a substrate for the cultivation of C. militaris. The proposed method could also be applied for encapsulating biomaterials, enzymes, drugs, catalysts, and nanoparticles into agar beads for biomedical applications. PMID:22012813

  13. Note on coefficient matrices from stochastic Galerkin methods for random diffusion equations

    SciTech Connect

    Zhou Tao, E-mail: tzhou@lsec.cc.ac.c [Institute of Computational Mathematics, The Chinese Academy of Sciences, Beijing 100190 (China); Tang Tao, E-mail: ttang@hkbu.edu.h [Department of Mathematics, Hong Kong Baptist University, Kowloon Tong (Hong Kong)

    2010-11-01

    In a recent work by Xiu and Shen [D. Xiu, J. Shen, Efficient stochastic Galerkin methods for random diffusion equations, J. Comput. Phys. 228 (2009) 266-281], the Galerkin methods are used to solve stochastic diffusion equations in random media, where some properties for the coefficient matrix of the resulting system are provided. They also posed an open question on the properties of the coefficient matrix. In this work, we will provide some results related to the open question.

  14. An efficient wavelet analysis method to film-pore diffusion model arising in mathematical chemistry.

    PubMed

    Hariharan, G

    2014-04-01

    In this paper, we have established an efficient Legendre wavelet based approximation method to solve film-pore diffusion model arising in engineering. Film-pore diffusion model is widely used to determine study the kinetics of adsorption systems. The use of Legendre wavelet based approximation method is found to be accurate, simple, fast, flexible, convenient, and computationally attractive. It is shown that film-pore diffusion model satisfactorily describe kinetics of methylene blue adsorption onto the three low-cost adsorbents, Guava, teak and gulmohar plant leaf powders, used in this study. PMID:24562792

  15. An electrochemical method for accelerated testing of chloride diffusivity in concrete

    SciTech Connect

    Zhang, T.; Gjoerv, O.E. (Norwegian Inst. of Tech., Trondheim (Norway). Div. of Building Materials)

    1994-01-01

    In the present paper an electrochemical method for accelerated testing of chloride diffusivity in concrete is presented. The method is based on a theoretical relationship between chloride diffusivity and observed steady-state rate of chloride migration through the concrete. The concentration of the chloride source solution has a significant influence on the rate of chloride migration and, therefore, a correction factor for ionic interaction in the relationship is introduced. It is shown that the relationship can be used for calculation of chloride diffusivity under various testing conditions. Some experimental results are also presented.

  16. Cosmic-ray diffusion modeling: Solutions using variational methods

    NASA Astrophysics Data System (ADS)

    Tautz, R. C.; Lerche, I.

    2013-05-01

    The diffusion of energetic particles in turbulent magnetic fields is usually described via the two-point, two-time velocity correlation function. A variational principle is used to determine the characteristic function that results from the Fourier-transformed correlation function. Both for a linear approximation and for the wave vector set to zero, explicit solutions are derived that depend on the Fokker-Planck coefficient of pitch-angle scattering. It is shown that, for an isotropic form of the Fokker-Planck coefficient, the characteristic function is divergent, which can be remedied only by using a Fokker-Planck coefficient that is finite at all pitch angles.

  17. Evaluation of the direct and diffusion methods for the determination of fluoride content in table salt

    PubMed Central

    Martínez-Mier, E. Angeles; Soto-Rojas, Armando E.; Buckley, Christine M.; Margineda, Jorge; Zero, Domenick T.

    2010-01-01

    Objective The aim of this study was to assess methods currently used for analyzing fluoridated salt in order to identify the most useful method for this type of analysis. Basic research design Seventy-five fluoridated salt samples were obtained. Samples were analyzed for fluoride content, with and without pretreatment, using direct and diffusion methods. Element analysis was also conducted in selected samples. Fluoride was added to ultra pure NaCl and non-fluoridated commercial salt samples and Ca and Mg were added to fluoride samples in order to assess fluoride recoveries using modifications to the methods. Results Larger amounts of fluoride were found and recovered using diffusion than direct methods (96%–100% for diffusion vs. 67%–90% for direct). Statistically significant differences were obtained between direct and diffusion methods using different ion strength adjusters. Pretreatment methods reduced the amount of recovered fluoride. Determination of fluoride content was influenced both by the presence of NaCl and other ions in the salt. Conclusion Direct and diffusion techniques for analysis of fluoridated salt are suitable methods for fluoride analysis. The choice of method should depend on the purpose of the analysis. PMID:20088217

  18. Fabrication and characterization of oxygen - diffused titanium using spectroscopy method.

    PubMed

    Lubas, M; Sitarz, M; Jasinski, J J; Jelen, P; Klita, L; Podsiad, P; Jasinski, J

    2014-12-10

    A thin native oxide film that forms on the titanium surface makes contact with the bone tissue has been considered to be of great importance to successful osseointegration. The study investigated oxygen-diffused grade 2 titanium obtained by introducing oxygen into the titanium crystal lattice using thermal treatment in fluidized bed performed at 610°C and 640°C in 6, 8, 12h. The thermal treatment at different temperatures and different times led to the formation of a TiO2 rutile film on the titanium surface and a concentration gradient of oxygen into titanium (XRD/GID analyses and GDOS results). Moreover Raman spectroscopy results showed that the TiO2 film on the surface titanium was composed of two oxides (TiO2), i.e. anatase and rutile, for the analyzed variants of heat treatment. The aim of the present study was to establish the optimum conditions for obtaining oxygen-diffused TiO2 film. The results obtained in the study demonstrated that the use of a fluidized bed for titanium oxidation processes allows for obtaining uniform oxide layers with good adhesion to the substrate, thus improving the titanium surface to suit biomedical applications. PMID:25008161

  19. Coagulase-Negative Staphylococci: Comparison of Phenotypic and Genotypic Oxacillin Susceptibility Tests and Evaluation of the Agar Screening Test by Using Different Concentrations of Oxacillin

    Microsoft Academic Search

    Rosana B. R. Ferreira; Natalia L. P. Iorio; Karoline L. Malvar; Ana Paula; F. Nunes; Leila S. Fonseca; Carla C. R. Bastos; Katia R. N. Santos

    2003-01-01

    This study evaluated the oxacillin susceptibilities of 152 coagulase-negative staphylococcal (CoNS) strains of 12 species by disk diffusion; agar dilution; E-test; the slide latex agglutination test (Slidex MRSA Detection test; bioMerieux S\\/A, Paris, France); the agar screening test with 1, 2, 4, or 6 g of oxacillin per ml and incubation for 24 or 48 h; and detection of the

  20. Operator Splitting Implicit Integration Factor Methods for Stiff Reaction-Diffusion-Advection Systems.

    PubMed

    Zhao, Su; Ovadia, Jeremy; Liu, Xinfeng; Zhang, Yong-Tao; Nie, Qing

    2011-07-01

    For reaction-diffusion-advection equations, the stiffness from the reaction and diffusion terms often requires very restricted time step size, while the nonlinear advection term may lead to a sharp gradient in localized spatial regions. It is challenging to design numerical methods that can efficiently handle both difficulties. For reaction-diffusion systems with both stiff reaction and diffusion terms, implicit integration factor (IIF) method and its higher dimensional analog compact IIF (cIIF) serve as an efficient class of time-stepping methods, and their second order version is linearly unconditionally stable. For nonlinear hyperbolic equations, weighted essentially non-oscillatory (WENO) methods are a class of schemes with a uniformly high-order of accuracy in smooth regions of the solution, which can also resolve the sharp gradient in an accurate and essentially non-oscillatory fashion. In this paper, we couple IIF/cIIF with WENO methods using the operator splitting approach to solve reaction-diffusion-advection equations. In particular, we apply the IIF/cIIF method to the stiff reaction and diffusion terms and the WENO method to the advection term in two different splitting sequences. Calculation of local truncation error and direct numerical simulations for both splitting approaches show the second order accuracy of the splitting method, and linear stability analysis and direct comparison with other approaches reveals excellent efficiency and stability properties. Applications of the splitting approach to two biological systems demonstrate that the overall method is accurate and efficient, and the splitting sequence consisting of two reaction-diffusion steps is more desirable than the one consisting of two advection steps, because CWC exhibits better accuracy and stability. PMID:21666863

  1. Operator splitting implicit integration factor methods for stiff reaction-diffusion-advection systems

    NASA Astrophysics Data System (ADS)

    Zhao, Su; Ovadia, Jeremy; Liu, Xinfeng; Zhang, Yong-Tao; Nie, Qing

    2011-07-01

    For reaction-diffusion-advection equations, the stiffness from the reaction and diffusion terms often requires very restricted time step size, while the nonlinear advection term may lead to a sharp gradient in localized spatial regions. It is challenging to design numerical methods that can efficiently handle both difficulties. For reaction-diffusion systems with both stiff reaction and diffusion terms, implicit integration factor (IIF) method and its higher dimensional analog compact IIF (cIIF) serve as an efficient class of time-stepping methods, and their second order version is linearly unconditionally stable. For nonlinear hyperbolic equations, weighted essentially non-oscillatory (WENO) methods are a class of schemes with a uniformly high order of accuracy in smooth regions of the solution, which can also resolve the sharp gradient in an accurate and essentially non-oscillatory fashion. In this paper, we couple IIF/cIIF with WENO methods using the operator splitting approach to solve reaction-diffusion-advection equations. In particular, we apply the IIF/cIIF method to the stiff reaction and diffusion terms and the WENO method to the advection term in two different splitting sequences. Calculation of local truncation error and direct numerical simulations for both splitting approaches show the second order accuracy of the splitting method, and linear stability analysis and direct comparison with other approaches reveals excellent efficiency and stability properties. Applications of the splitting approach to two biological systems demonstrate that the overall method is accurate and efficient, and the splitting sequence consisting of two reaction-diffusion steps is more desirable than the one consisting of two advection steps, because CWC exhibits better accuracy and stability.

  2. Do current lattice Boltzmann methods for diffusion and diffusion-type equations respect maximum principles and the non-negative constraint?

    E-print Network

    S. Karimi; K. B. Nakshatrala

    2015-04-10

    The lattice Boltzmann method (LBM) has established itself as a valid numerical method in computational fluid dynamics. Recently, multiple-relaxation-time LBM has been proposed to simulate anisotropic advection-diffusion processes. The governing differential equations of advective-diffusive systems are known to satisfy maximum principles, comparison principles, the non-negative constraint, and the decay property. In this paper, it will be shown that current single- and multiple-relaxation-time lattice Boltzmann methods fail to preserve these mathematical properties for transient diffusion-type equations. It will also be shown that the discretization of Dirichlet boundary conditions will affect the performance of lattice Boltzmann methods in meeting these mathematical principles. A new way of discretizing the Dirichlet boundary conditions is also proposed. Several benchmark problems have been solved to illustrate the performance of lattice Boltzmann methods and the effect of discretization of boundary conditions with respect to the aforementioned mathematical properties for transient diffusion and advection-diffusion equations.

  3. A MINIMUM-RESIDUAL FINITE ELEMENT METHOD FOR THE CONVECTION-DIFFUSION EQUATION

    E-print Network

    Evans, John A.

    -Galerkin (SUPG) method [4]. The method can be in- terpreted as adding a sufficient amount of artificial viscosity-diffusion" norm [5]. SUPG is also an example of a residual-based stabilization, where the stabilization mechanism) functions are allowed to differ. Specifically, the SUPG method can be interpreted as a modification

  4. Disaster Risk Assessment Based on Variable Fuzzy Sets and Improved Information Diffusion Method

    Microsoft Academic Search

    Qiong Li; Jianzhong Zhou; Donghan Liu; Gang Tang; Qiang Zou

    2012-01-01

    The predictive analysis of natural disasters and their consequences is challenging because of uncertainties and incomplete data. The present article studies the use of variable fuzzy sets (VFS) and the improved information diffusion method (IIDM) to construct a composite method. The proposed method aims to integrate multiple factors and quantification of uncertainties within a consistent system for catastrophic risk assessment.

  5. Eigenfunction methods in magnetospheric radial-diffusion theory

    NASA Technical Reports Server (NTRS)

    Schulz, Michael

    1986-01-01

    Complete sets of orthonormal basis functions constructed according to a generalization of the quantum-mechanical WKB approximation can be used to generate a nearly-diagonal matrix representation of the radial-transport operator for ring-current ions in the presence of radial diffusion and charge exchange. The resulting eigenfunctions (constructed by weighting the basis functions in proportion to the respective components of the eigenvectors of the matrix representation) and eigenvalues provide a spatial and temporal description of the evolving phase-space density during and following a magnetospheric disturbance (e.g., a magnetic storm). A linear superposition of the basis functions can also be used to eliminate any discrepancy between the steady-state solution of the transport equation and the appropriate WKB approximation of this steady-state solution.

  6. Laboratory diagnosis of Acanthamoeba keratitis using buffered charcoal-yeast extract agar

    Microsoft Academic Search

    Rebecca L. Penland; Kirk R. Wilhelmus

    1998-01-01

    PURPOSE: To evaluate the use of buffered charcoal-yeast extract agar for the isolation of Acanthamoeba from clinical specimens.METHODS: We retrospectively reviewed laboratory records of patients with ocular acanthamebic infection from October 1993 to September 1997 to compare the recovery of Acanthamoeba from clinical specimens inoculated onto various media. We then compared the experimental recovery of 10 corneal isolates of Acanthamoeba

  7. Development of hyperspectral imaging technique for salmonella enteritidis and typhimurium on agar plates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Salmonella is a common cause of foodborne disease resulting from the consumption of contaminated food products. Although a direct plating method is widely used for presumptive positive screening of pathogenic Salmonella colonies on agar plates, it is labor-intensive, time-consuming and also prone to...

  8. Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species

    Microsoft Academic Search

    Mine Yücesoy; Serhat Marol

    2003-01-01

    BACKGROUND: The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. METHODS: A total number of 270 yeast strains including 169 Candida albicans, 33 C.

  9. A New Method for the Calculation of Diffusion Coefficients with Monte Carlo

    NASA Astrophysics Data System (ADS)

    Dorval, Eric

    2014-06-01

    This paper presents a new Monte Carlo-based method for the calculation of diffusion coefficients. One distinctive feature of this method is that it does not resort to the computation of transport cross sections directly, although their functional form is retained. Instead, a special type of tally derived from a deterministic estimate of Fick's Law is used for tallying the total cross section, which is then combined with a set of other standard Monte Carlo tallies. Some properties of this method are presented by means of numerical examples for a multi-group 1-D implementation. Calculated diffusion coefficients are in general good agreement with values obtained by other methods.

  10. Diffusion-synthetic acceleration methods for the discrete-ordinates equations

    SciTech Connect

    Larsen, E.W.

    1983-01-01

    The diffusion-synthetic acceleration (DSA) method is an iterative procedure for obtaining numerical solutions of discrete-ordinates problems. The DSA method is operationally more complicated than the standard source-iteration (SI) method, but if encoded properly it converges much more rapidly, especially for problems with diffusion-like regions. In this article we describe the basic ideas beind the DSA method and give a (roughly chronological) review of its long development. We conclude with a discussion which covers additional topics, including some remaining open problems and the status of current efforts aimed at solving these problems.

  11. Method of applying a cerium diffusion coating to a metallic alloy

    DOEpatents

    Jablonski, Paul D. (Salem, OR); Alman, David E. (Benton, OR)

    2009-06-30

    A method of applying a cerium diffusion coating to a preferred nickel base alloy substrate has been discovered. A cerium oxide paste containing a halide activator is applied to the polished substrate and then dried. The workpiece is heated in a non-oxidizing atmosphere to diffuse cerium into the substrate. After cooling, any remaining cerium oxide is removed. The resulting cerium diffusion coating on the nickel base substrate demonstrates improved resistance to oxidation. Cerium coated alloys are particularly useful as components in a solid oxide fuel cell (SOFC).

  12. Microscopic derivation of causal diffusion equation using the projection operator method.

    PubMed

    Koide, T

    2005-08-01

    We derive a coarse-grained equation of motion of a number density by applying the projection operator method to a non-relativistic model. The derived equation is an integrodifferential equation and contains the memory effect. The equation is consistent with causality and the sum rule associated with the number conservation in the low momentum limit, in contrast to usual acausal diffusion equations given by using the Fick's law. After employing the Markov approximation, we find that the equation has the similar form to the causal diffusion equation. Our result suggests that current-current correlations are not necessarily adequate as the definition of diffusion constants. PMID:16196672

  13. A hybrid transport-diffusion Monte Carlo method for frequency-dependent radiative-transfer simulations

    SciTech Connect

    Densmore, Jeffery D., E-mail: jdd@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States); Thompson, Kelly G., E-mail: kgt@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States); Urbatsch, Todd J., E-mail: tmonster@lanl.gov [Computational Physics and Methods Group, Los Alamos National Laboratory, P.O. Box 1663, MS D409, Los Alamos, NM 87545 (United States)

    2012-08-15

    Discrete Diffusion Monte Carlo (DDMC) is a technique for increasing the efficiency of Implicit Monte Carlo radiative-transfer simulations in optically thick media. In DDMC, particles take discrete steps between spatial cells according to a discretized diffusion equation. Each discrete step replaces many smaller Monte Carlo steps, thus improving the efficiency of the simulation. In this paper, we present an extension of DDMC for frequency-dependent radiative transfer. We base our new DDMC method on a frequency-integrated diffusion equation for frequencies below a specified threshold, as optical thickness is typically a decreasing function of frequency. Above this threshold we employ standard Monte Carlo, which results in a hybrid transport-diffusion scheme. With a set of frequency-dependent test problems, we confirm the accuracy and increased efficiency of our new DDMC method.

  14. First-Order Hyperbolic System Method for Time-Dependent Advection-Diffusion Problems

    NASA Technical Reports Server (NTRS)

    Mazaheri, Alireza; Nishikawa, Hiroaki

    2014-01-01

    A time-dependent extension of the first-order hyperbolic system method for advection-diffusion problems is introduced. Diffusive/viscous terms are written and discretized as a hyperbolic system, which recovers the original equation in the steady state. The resulting scheme offers advantages over traditional schemes: a dramatic simplification in the discretization, high-order accuracy in the solution gradients, and orders-of-magnitude convergence acceleration. The hyperbolic advection-diffusion system is discretized by the second-order upwind residual-distribution scheme in a unified manner, and the system of implicit-residual-equations is solved by Newton's method over every physical time step. The numerical results are presented for linear and nonlinear advection-diffusion problems, demonstrating solutions and gradients produced to the same order of accuracy, with rapid convergence over each physical time step, typically less than five Newton iterations.

  15. A new method of optimal design for a two-dimensional diffuser by using dynamic programming

    NASA Technical Reports Server (NTRS)

    Gu, Chuangang; Zhang, Moujin; Chen, XI; Miao, Yongmiao

    1991-01-01

    A new method for predicting the optimal velocity distribution on the wall of a two dimensional diffuser is presented. The method uses dynamic programming to solve the optimal control problem with inequality constraints of state variables. The physical model of optimization is designed to prevent the separation of the boundary layer while approaching the maximum pressure ratio in a diffuser of a specified length. The computational results are in fair agreement with the experimental ones. Optimal velocity distribution on a diffuser wall is said to occur when the flow decelerates quickly at first and then smoothly, while the flow is near separation, but always protected from it. The optimal velocity distribution can be used to design the contour of the diffuser.

  16. Application of an agar-agar chamber for the study of electromagnetic waves in an inhomogeneous medium

    Microsoft Academic Search

    K. Iizuka

    1972-01-01

    A detailed description of techniques developed to control and measure the inhomogeneity of the electrical properties of agar-agar has been reported previously. Various physical problems occur when one attempts to reproduce on a larger scale tests which had been successful on the smaller scale. The actual application of these techniques to the construction of the medium on a large scale

  17. Method of fluxless brazing and diffusion bonding of aluminum containing components

    NASA Technical Reports Server (NTRS)

    Featherston, A. B.; Okelly, K. P. (inventors)

    1976-01-01

    A method of diffusion bonding and fluxless brazing of aluminum containing components is reported. The aluminum surfaces are freed of any aluminum oxide coating and are coated with a polymeric sealer which can be thermally removed leaving essentially no residue. The polymeric sealer is being removed in a substantially oxygen free environment, and the aluminum components are then being brazed or diffusion bonded without the use of a flux to remove oxide coating.

  18. Diffusion Reflection: A Novel Method for Detection of Oral Cancer.

    PubMed

    Fixler, D; Ankri, R; Kaplan, I; Novikov, I; Hirshberg, A

    2014-04-01

    Intraoperative detection of residual disease in oral cancer may reduce the high rate of recurrences. The aim of the present study was to evaluate the detection sensitivity of diffusion reflection (DR) measurements of bioconjugated gold nanorods (GNRs) to cancerous sites in a rat model of oral squamous cell carcinoma. We used hyperspectral spectroscopy and DR measurements of GNRs bioconjugated to slide specimens of rat tongues where squamous carcinoma was induced by 4NQO (4-nitroquinoline-N-oxide). Wistar-derived male rats were used: 6 were sacrificed at wk 32 to 37 following 4NQO administration (experimental rats), as were 2 control rats at wk 32 and 36. The detection results were compared with histopathology: 19 sites of cancerous changes were identified microscopically (11 invasive cancer and 8 carcinoma in situ [CIS]). The GNRs attached selectively to areas of carcinomatous changes with an intensity exceeding 17 intensity units at 780 nm (overall specificity, 97%; overall sensitivity, 87%) when the hyperspectral spectroscopy system was used. The resulting DR slopes of the reflected intensity showed an increase of >80% in areas of invasive cancer and an increase of >30% in the CIS sites. The resulting intensity units of the hyperspectral spectroscopy system in the invasive cancer significantly exceed those of the CIS (t test, p = .0002; Mann-Whitney, p = .0024). The results demonstrate a great potential of the direct DR scanning as a new and simple tool for detecting residual disease intraoperatively. PMID:24695671

  19. A combined reconstruction-classification method for diffuse optical tomography.

    PubMed

    Hiltunen, P; Prince, S J D; Arridge, S

    2009-11-01

    We present a combined classification and reconstruction algorithm for diffuse optical tomography (DOT). DOT is a nonlinear ill-posed inverse problem. Therefore, some regularization is needed. We present a mixture of Gaussians prior, which regularizes the DOT reconstruction step. During each iteration, the parameters of a mixture model are estimated. These associate each reconstructed pixel with one of several classes based on the current estimate of the optical parameters. This classification is exploited to form a new prior distribution to regularize the reconstruction step and update the optical parameters. The algorithm can be described as an iteration between an optimization scheme with zeroth-order variable mean and variance Tikhonov regularization and an expectation-maximization scheme for estimation of the model parameters. We describe the algorithm in a general Bayesian framework. Results from simulated test cases and phantom measurements show that the algorithm enhances the contrast of the reconstructed images with good spatial accuracy. The probabilistic classifications of each image contain only a few misclassified pixels. PMID:19820265

  20. Advanced computational methods for nodal diffusion, Monte Carlo, and S[sub N] problems

    SciTech Connect

    Martin, W.R.

    1993-01-01

    This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. A alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.

  1. Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.

    SciTech Connect

    Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl

    2011-09-01

    Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.

  2. A fractional step [theta]-method for convection-diffusion problems

    NASA Astrophysics Data System (ADS)

    Chrispell, J. C.; Ervin, V. J.; Jenkins, E. W.

    2007-09-01

    In this article, we analyze the fractional step [theta]-method for the time-dependent convection-diffusion equation. In our implementation, we completely separate the convection operator from the diffusion operator, and stabilize the convective problem using a Streamline Upwinded Petrov-Galerkin (SUPG) method. We establish a priori error estimates and show that the optimal value of [theta] yields a scheme that is second-order in time. Numerical computations are presented which demonstrate the method and support the theoretical results.

  3. A First-Passage Kinetic Monte Carlo method for reaction–drift–diffusion processes

    SciTech Connect

    Mauro, Ava J., E-mail: avamauro@bu.edu [Department of Mathematics and Statistics, Boston University, 111 Cummington Mall, Boston, MA 02215 (United States); Sigurdsson, Jon Karl; Shrake, Justin [Department of Mathematics, University of California, Santa Barbara (United States)] [Department of Mathematics, University of California, Santa Barbara (United States); Atzberger, Paul J., E-mail: atzberg@math.ucsb.edu [6712 South Hall, Department of Mathematics, University of California, Santa Barbara, CA 93106 (United States); Isaacson, Samuel A., E-mail: isaacson@math.bu.edu [Department of Mathematics and Statistics, Boston University, 111 Cummington Mall, Boston, MA 02215 (United States)

    2014-02-15

    Stochastic reaction–diffusion models are now a popular tool for studying physical systems in which both the explicit diffusion of molecules and noise in the chemical reaction process play important roles. The Smoluchowski diffusion-limited reaction model (SDLR) is one of several that have been used to study biological systems. Exact realizations of the underlying stochastic processes described by the SDLR model can be generated by the recently proposed First-Passage Kinetic Monte Carlo (FPKMC) method. This exactness relies on sampling analytical solutions to one and two-body diffusion equations in simplified protective domains. In this work we extend the FPKMC to allow for drift arising from fixed, background potentials. As the corresponding Fokker–Planck equations that describe the motion of each molecule can no longer be solved analytically, we develop a hybrid method that discretizes the protective domains. The discretization is chosen so that the drift–diffusion of each molecule within its protective domain is approximated by a continuous-time random walk on a lattice. New lattices are defined dynamically as the protective domains are updated, hence we will refer to our method as Dynamic Lattice FPKMC or DL-FPKMC. We focus primarily on the one-dimensional case in this manuscript, and demonstrate the numerical convergence and accuracy of our method in this case for both smooth and discontinuous potentials. We also present applications of our method, which illustrate the impact of drift on reaction kinetics.

  4. a Mean-Field Method for Driven Diffusive Systems Based on Maximum Entropy Principle

    Microsoft Academic Search

    Nina Christova Pesheva

    1989-01-01

    Here, we propose a method for generating a hierarchy of mean-field approximations to study the properties of the driven diffusive Ising model at nonequilibrium steady state. In addition, the present study offers a demonstration of the practical application of the information theoretic methods to a simple interaction nonequilibrium system. The application of maximum entropy principle to the system, which is

  5. Surface preparation for determining diffusion length by the surface photovoltage method

    Microsoft Academic Search

    1985-01-01

    A method of treating the surface of a sample of n-type silicon material in preparation for measurements for determining the minority carrier diffusion length of the material by the surface photovoltage method comprises applying a strong oxidizing agent to an appropriately prepared surface of a semiconductor material such as silicon. The oxidizing agent is taken from the group consisting of

  6. Stability of the SUPG Finite Element Method for Transient Advection-Diffusion Problems

    E-print Network

    Bochev, Pavel

    Stability of the SUPG Finite Element Method for Transient Advection-Diffusion Problems Pavel B coupled with SUPG discretization in space leads to addi- tional terms that provide consistency and improve of the SUPG method. While consistent with a straightforward finite element stability analysis, this contention

  7. Effect of underwater local cavity welding method conditions on diffusible hydrogen content in deposited metal

    Microsoft Academic Search

    Dariusz Fydrych; Grzegorz Rogalski

    2011-01-01

    One of the methods with great potential for applications in underwater repairs is local cavity welding. In local cavity method, cooling conditions and diffusible hydrogen amount in weld metal are nearly the same as those existed during welding in the air. This paper presents the results of literature survey and preliminary tests of the effect of local cavity welding conditions

  8. Method of hepatitis diagnostics of changes in human skin diffuse reflectivity

    Microsoft Academic Search

    M. L. Kirsh; A. M. Sokol; V. S. Lomanets; O. R. Gayka

    1999-01-01

    The results on the study of influence of bilirubinum concentration in a human blood on the spectrum of a diffuse reflectivity of his skin are represented. On this basis, the method for hepatitis diagnostics has been developed, and the laboratory device implementing this method has been designed. Bibtex entry for this abstract Preferred format for this abstract (see Preferences) Find

  9. Method of hepatitis diagnostics of changes in human skin diffuse reflectivity

    NASA Astrophysics Data System (ADS)

    Kirsh, M. L.; Sokol, A. M.; Lomanets, V. S.; Gayka, O. R.

    1999-11-01

    The results on the study of influence of bilirubinum concentration in a human blood on the spectrum of a diffuse reflectivity of his skin are represented. On this basis, the method for hepatitis diagnostics has been developed, and the laboratory device implementing this method has been designed.

  10. CONVERGENCE ANALYSIS OF A MULTIGRID METHOD FOR CONVECTION{DIFFUSION EQUATIONS

    E-print Network

    CONVERGENCE ANALYSIS OF A MULTIGRID METHOD FOR CONVECTION{DIFFUSION EQUATIONS ARNOLD REUSKEN #3 modi#12;- cations have been proposed in the literature, such as \\robust" smoothers (smoothers which try techniques. For an explanation of these methods we refer to [9, 27, 3, 7, 13, 14, 16, 17, 21, 30]. These modi

  11. As a Bacterial Culture Medium, Citrated Sheep Blood Agar Is a Practical Alternative to Citrated Human Blood Agar in Laboratories of Developing Countries

    Microsoft Academic Search

    F. M. Russell; S. S. N. Biribo; G. Selvaraj; F. Oppedisano; S. Warren; A. Seduadua; E. K. Mulholland; J. R. Carapetis

    2006-01-01

    Human blood agar (HuBA) is widely used in developing countries for the isolation of bacteria from clinical specimens. This study compared citrated sheep blood agar (CSBA) and HuBA with defibrinated horse blood agar and defibrinated sheep blood agar (DSBA) for the isolation and antibiotic susceptibility testing of reference and clinical strains of Streptococcus pneumoniae, Streptococcus pyogenes, and Staphylococcus aureus. Reference

  12. Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture.

    PubMed

    Angolini, Célio Fernando F; Vendramini, Pedro Henrique; Araújo, Francisca D S; Araújo, Welington L; Augusti, Rodinei; Eberlin, Marcos N; de Oliveira, Luciana Gonzaga

    2015-07-01

    Herein we describe a new protocol that allows direct mass spectrometry imaging (IMS) of agar cultures. A simple sample dehydration leads to a thin solid agar, which enables the direct use of spray-based ambient mass spectrometry techniques. To demonstrate its applicability, metal scavengers siderophores were imaged directly from agar culture of S. wadayamensis, and well resolved and intense images were obtained using both desorption electrospray ionization (DESI) and easy ambient sonic-spray ionization (EASI) with well-defined selective spatial distributions for the free and the metal-bound molecules, providing clues for their roles in cellular metabolism. PMID:26067682

  13. Diffusive shock acceleration in oblique MHD shocks comparison with Monte Carlo methods and observations

    E-print Network

    Kang, H; Kang, Hyesung

    1996-01-01

    We report simulations of diffusive particle acceleration in oblique magnetohydrodynamical (MHD) shocks. These calculations are based on extension to oblique shocks of a numerical model for ``thermal leakage'' injection of particles at low energy into the cosmic-ray population. That technique, incorporated into a fully dynamical diffusion-convection formalism, was recently introduced for parallel shocks by Kang \\& Jones (1995). Here, we have compared results of time dependent numerical simulations using our technique with Monte Carlo simulations by Ellison, Baring \\& Jones 1995 and with {\\it in situ} observations from the Ulysses spacecraft of oblique interplanetary shocks discussed by Baring \\etal (1995). Through the success of these comparisons we have demonstrated that our {diffusion-convection} method and injection techniques provide a practical tool to capture essential physics of the injection process and particle acceleration at oblique MHD shocks. In addition to the diffusion-convection simulat...

  14. Fast finite difference methods for space-fractional diffusion equations with fractional derivative boundary conditions

    NASA Astrophysics Data System (ADS)

    Jia, Jinhong; Wang, Hong

    2015-07-01

    Numerical methods for space-fractional diffusion equations often generate dense or even full stiffness matrices. Traditionally, these methods were solved via Gaussian type direct solvers, which requires O (N3) of computational work per time step and O (N2) of memory to store where N is the number of spatial grid points in the discretization. In this paper we develop a preconditioned fast Krylov subspace iterative method for the efficient and faithful solution of finite difference methods (both steady-state and time-dependent) space-fractional diffusion equations with fractional derivative boundary conditions in one space dimension. The method requires O (N) of memory and O (Nlog ? N) of operations per iteration. Due to the application of effective preconditioners, significantly reduced numbers of iterations were achieved that further reduces the computational cost of the fast method. Numerical results are presented to show the utility of the method.

  15. Practical method of diffusion-welding steel plate in air

    NASA Technical Reports Server (NTRS)

    Holko, K. H.; Moore, T. J.

    1971-01-01

    Method is ideal for critical service requirements where parent metal properties are equaled in notch toughness, stress rupture and other characteristics. Welding technique variations may be used on a variety of materials, such as carbon steels, alloy steels, stainless steels, ceramics, and reactive and refractory materials.

  16. Comparison of the thermogravimetric analysis (TGA) and Franz cell methods to assess dermal diffusion of volatile chemicals

    Microsoft Academic Search

    Matias Rauma; Gunnar Johanson

    2009-01-01

    Recent work in our laboratory shows that it is possible to measure the minute weight changes of skin during exposure to chemical vapor using the thermogravimetric analysis (TGA) method. Further, the TGA weight curves can be analyzed with a two-compartment diffusion model, yielding two sets of diffusion and skin:air partition coefficients. In this study, the dermal diffusion of six chemical

  17. Determination of diffusion coefficients in polypyrrole thin films using a current pulse relaxation method

    NASA Technical Reports Server (NTRS)

    Penner, Reginald M.; Vandyke, Leon S.; Martin, Charles R.

    1987-01-01

    The current pulse E sub oc relaxation method and its application to the determination of diffusion coefficients in electrochemically synthesized polypyrrole thin films is described. Diffusion coefficients for such films in Et4NBF4 and MeCN are determined for a series of submicron film thicknesses. Measurement of the double-layer capacitance, C sub dl, and the resistance, R sub u, of polypyrrole thin films as a function of potential obtained with the galvanostatic pulse method is reported. Measurements of the electrolyte concentration in reduced polypyrrole films are also presented to aid in the interpretation of the data.

  18. Accepted Manuscript Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric

    E-print Network

    Taylor, Lee

    agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota) József Geml, Frank Kauff, Christian Brochmann circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae dispersals in the lichenised agaric genus1 Lichenomphalia (Hygrophoraceae, Basidiomycota)2 3 4 József Geml1

  19. An adaptive pseudo-spectral method for reaction diffusion problems

    NASA Technical Reports Server (NTRS)

    Bayliss, A.; Matkowsky, B. J.; Gottlieb, D.; Minkoff, M.

    1989-01-01

    The spectral interpolation error was considered for both the Chebyshev pseudo-spectral and Galerkin approximations. A family of functionals I sub r (u), with the property that the maximum norm of the error is bounded by I sub r (u)/J sub r, where r is an integer and J is the degree of the polynomial approximation, was developed. These functionals are used in the adaptive procedure whereby the problem is dynamically transformed to minimize I sub r (u). The number of collocation points is then chosen to maintain a prescribed error bound. The method is illustrated by various examples from combustion problems in one and two dimensions.

  20. An adaptive pseudo-spectral method for reaction diffusion problems

    NASA Technical Reports Server (NTRS)

    Bayliss, A.; Gottlieb, D.; Matkowsky, B. J.; Minkoff, M.

    1987-01-01

    The spectral interpolation error was considered for both the Chebyshev pseudo-spectral and Galerkin approximations. A family of functionals I sub r (u), with the property that the maximum norm of the error is bounded by I sub r (u)/J sub r, where r is an integer and J is the degree of the polynomial approximation, was developed. These functionals are used in the adaptive procedure whereby the problem is dynamically transformed to minimize I sub r (u). The number of collocation points is then chosen to maintain a prescribed error bound. The method is illustrated by various examples from combustion problems in one and two dimensions.

  1. 21 CFR 866.4600 - Ouchterlony agar plate.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a)...

  2. 21 CFR 866.4600 - Ouchterlony agar plate.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a)...

  3. 21 CFR 866.4600 - Ouchterlony agar plate.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents § 866.4600 Ouchterlony agar plate. (a)...

  4. On the Solutions of the Generalized Reaction-Diffusion Model for Bacterial Colony

    Microsoft Academic Search

    A. M. A. El-Sayed; S. Z. Rida; A. A. M. Arafa

    2010-01-01

    In this paper, the Adomian’s decomposition method has been developed to yield approximate solution of the reaction-diffusion\\u000a model of fractional order which describe the evolution of the bacterium Bacillus subtilis, which grows on the surface of thin\\u000a agar plates. The fractional derivatives are described in the Caputo sense. The method introduces a promising tool for solving\\u000a many linear and nonlinear

  5. High-order compact boundary value method for the solution of unsteady convection-diffusion problems

    Microsoft Academic Search

    Mehdi Dehghan; Akbar Mohebbi

    2008-01-01

    In this paper, we propose a new class of high-order accurate methods for solving the two-dimensional unsteady convection–diffusion equation. These techniques are based on the method of lines approach. We apply a compact finite difference approximation of fourth order for discretizing spatial derivatives and a boundary value method of fourth order for the time integration of the resulted linear system

  6. Preparation of poly(?-lactide-co-glycolide) nanoparticles by modified spontaneous emulsification solvent diffusion method

    Microsoft Academic Search

    Hideki Murakami; Masao Kobayashi; Hirofumi Takeuchi; Yoshiaki Kawashima

    1999-01-01

    Purpose: The objectives of this study were to establish a new preparation method for poly(DL-lactide-co-glycolide) (PLGA) nanoparticles by modifying the spontaneous emulsification solvent diffusion (SESD) method and to elucidate the mechanism of nanoparticle formation on the basis of the phase separation principle of PLGA and poly(vinyl alcohol) (PVA) in the preparation system. Methods: PLGA nanoparticles were prepared by the modified-SESD

  7. Blood Agar and Mycobacterium tuberculosis: the End of a Dogma

    Microsoft Academic Search

    M. Drancourt; P. Carrieri; M.-J. Gevaudan; D. Raoult

    2003-01-01

    Incidental blood agar-based recovery of Mycobacterium tuberculosis led us to further investigate this routine medium for primary isolation and culture of M. tuberculosis. Fifteen respiratory tract and eight lymph node Ziehl-Neelsen-positive specimens were inoculated in parallel into tubes containing egg-based medium and 5% sheep blood agar. Colonies appeared sooner on this medium than on the egg-based medium, but this difference

  8. A rare event sampling method for diffusion Monte Carlo using smart darting

    NASA Astrophysics Data System (ADS)

    Roberts, K.; Sebsebie, R.; Curotto, E.

    2012-02-01

    We identify a set of multidimensional potential energy surfaces sufficiently complex to cause both the classical parallel tempering and the guided or unguided diffusion Monte Carlo methods to converge too inefficiently for practical applications. The mathematical model is constructed as a linear combination of decoupled Double Wells [(DDW)n]. We show that the set (DDW)n provides a serious test for new methods aimed at addressing rare event sampling in stochastic simulations. Unlike the typical numerical tests used in these cases, the thermodynamics and the quantum dynamics for (DDW)n can be solved deterministically. We use the potential energy set (DDW)n to explore and identify methods that can enhance the diffusion Monte Carlo algorithm. We demonstrate that the smart darting method succeeds at reducing quasiergodicity for n ? 100 using just 1 × 106 moves in classical simulations (DDW)n. Finally, we prove that smart darting, when incorporated into the regular or the guided diffusion Monte Carlo algorithm, drastically improves its convergence. The new method promises to significantly extend the range of systems computationally tractable by the diffusion Monte Carlo algorithm.

  9. Stability and error analysis of nodal expansion method for convection-diffusion equation

    SciTech Connect

    Deng, Z. [Inst. of Nuclear and New Energy Technology, Tsinghua Univ., Beijing10084 (China); Rizwan-Uddin [Univ. of Illinois at Urbana-Champaign, 216 Talbot Lab., 104 S. Wright St., Urbana, IL 61801 (United States); Li, F.; Sun, Y. [Inst. of Nuclear and New Energy Technology, Tsinghua Univ., Beijing10084 (China)

    2012-07-01

    The development, and stability and error analyses of nodal expansion method (NEM) for one dimensional steady-state convection diffusion equation is presented. Following the traditional procedure to develop NEM, the discrete formulation of the convection-diffusion equation, which is similar to the standard finite difference scheme, is derived. The method of discrete perturbation analysis is applied to this discrete form to study the stability of the NEM. The scheme based on the NEM is found to be stable for local Peclet number less than 4.644. A maximum principle is proved for the NEM scheme, followed by an error analysis carried out by applying the Maximum principle together with a carefully constructed comparison function. The scheme for the convection diffusion equation is of second-order. Numerical experiments are carried and the results agree with the conclusions of the stability and error analyses. (authors)

  10. A Domain Decomposition Method for Time Fractional Reaction-Diffusion Equation

    PubMed Central

    Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie

    2014-01-01

    The computational complexity of one-dimensional time fractional reaction-diffusion equation is O(N2M) compared with O(NM) for classical integer reaction-diffusion equation. Parallel computing is used to overcome this challenge. Domain decomposition method (DDM) embodies large potential for parallelization of the numerical solution for fractional equations and serves as a basis for distributed, parallel computations. A domain decomposition algorithm for time fractional reaction-diffusion equation with implicit finite difference method is proposed. The domain decomposition algorithm keeps the same parallelism but needs much fewer iterations, compared with Jacobi iteration in each time step. Numerical experiments are used to verify the efficiency of the obtained algorithm. PMID:24778594

  11. Enhanced degradation of caffeine by immobilized cells of Pseudomonas sp. in agar–agar matrix using statistical approach

    Microsoft Academic Search

    Sathyanarayana N. Gummadi; K. B. Ganesh; Devarai Santhosh

    2009-01-01

    Previously, we isolated caffeine degrading Pseudomonas strain from soil of coffee plantation area, which could utilize caffeine as sole carbon and nitrogen source and could tolerate caffeine up to 20g\\/L. In this study, caffeine degradation by immobilized cells of this strain was investigated. Various matrices were considered and agar–agar was chosen based on degradation rate (0.08g\\/(Lh)), bead stability and reusability.

  12. Stability of the SUPG finite element method for transient advection–diffusion problems

    Microsoft Academic Search

    Pavel B. Bochev; Max D. Gunzburger; John N. Shadid

    2004-01-01

    Implicit time integration coupled with SUPG discretization in space leads to additional terms that provide consistency and improve the phase accuracy for convection dominated flows. Recently, it has been suggested that for small Courant numbers these terms may dominate the streamline diffusion term, ostensibly causing destabilization of the SUPG method. While consistent with a straightforward finite element stability analysis, this

  13. Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column

    DOEpatents

    Rutherford, William M. (Dayton, OH)

    1988-05-24

    A thermal diffusion counterflow method and apparatus for separating isotopes in solution in which the solution is confined in a long, narrow, vertical slit which tapers from bottom to top. The variation in the width of the slit permits maintenance of a stable concentration distribution with relatively long columns, thus permitting isotopic separation superior to that obtainable in the prior art.

  14. Exploring technology diffusion and classification of business methods: Using the patent citation network

    Microsoft Academic Search

    Shann-Bin Chang; Kuei-Kuei Lai; Shu-Min Chang

    2009-01-01

    Among the many technology forecasting indicators, patents and patent citations are useful and important indicators. The more frequently a certain patent is cited by subsequent patents, the more the related technology can be said to be diffused, implying that the technology is more widely applied and thus more valuable. This paper analyzes the business methods technology which retrieves patents from

  15. An adaptive finite element method with crosswind diffusion for low Mach, steady, laminar combustion

    Microsoft Academic Search

    Erik Burman; Alexandre Ern; Vincent Giovangigli

    2003-01-01

    We investigate adaptive finite element methods for low Mach, steady, laminar combustion. The finite element discretization of the flame equations involves least squares control of streamline derivatives and pressure–velocity coupling as well as a new shock capturing term based on nonlinear crosswind diffusion yielding a suitable discrete maximum principle for the discrete solution. A posteriori error estimates derived from the

  16. A numerical method for a system of singularly perturbed reaction–diffusion equations

    Microsoft Academic Search

    S. Matthews; E. O'Riordan; G. I. Shishkin

    2002-01-01

    A Dirichlet problem for a system of two coupled singularly perturbed reaction–diffusion ordinary differential equations is examined. A numerical method whose solutions converge pointwise at all points of the domain independently of the singular perturbation parameters is constructed and analysed. Numerical results are presented, which illustrate the theoretical results.

  17. Calculation of effective diffusion coefficient in even approximations of the surface pseudo source method

    SciTech Connect

    Kovalishin, A. A., E-mail: kaa@adis.vver.kiae.ru; Laletin, N. I. [Russian Research Centre Kurchatov Institute (Russian Federation)

    2011-12-15

    The preference of even approximations of the surface pseudo source method for calculation of the diffusion coefficient is substantiated. The homogenization limit for the G{sub 0} approximation in the case of the cell size tending to zero is analytically proved.

  18. a Particle Method for a Lotka-Volterra System with Nonlinear Cross and Self-Diffusion

    NASA Astrophysics Data System (ADS)

    Greco, A. M.; Sammartino, M.

    2008-04-01

    In this paper we apply a particle method to a system of two non linearly coupled reaction-diffusion equations. Time discretization is based on the Peaceman-Rachford operator splitting scheme. Numerical simulations show pattern formation and the possibility of survival of the dominated species due to segregation.

  19. MRI Phantoms – Are There Alternatives to Agar?

    PubMed Central

    Hellerbach, Alexandra; Schuster, Verena; Jansen, Andreas; Sommer, Jens

    2013-01-01

    The suitability of different gelling agents as MRI phantoms was evaluated in terms of homogeneity, gel stability and reproducibility. Time and effort for preparation were also taken into account. The relaxation times of various gel compositions were estimated. Carbomer-980 and Carbopol-974P were determined to be promising novel phantom materials. These gelling agents are readily available, inexpensive and easy to handle given that thermal treatment is not required. Furthermore, the viscoelasticity of their polymer network is pH-dependent. With such characteristics, it was even possible to embed sensitive objects and retrieve them after testing. This was demonstrated with a fiber phantom for Diffusion Weighted MRI applications. Since Carbomer-980 and Carbopol-974P are non-hazardous, they are also suitable for multimodal setups (e.g., MRI as well as ultrasonic imaging). PMID:23940563

  20. Analysis of Preconditioning and Relaxation Operators for the Discontinuous Galerkin Method Applied to Diffusion

    NASA Technical Reports Server (NTRS)

    Atkins, H. L.; Shu, Chi-Wang

    2001-01-01

    The explicit stability constraint of the discontinuous Galerkin method applied to the diffusion operator decreases dramatically as the order of the method is increased. Block Jacobi and block Gauss-Seidel preconditioner operators are examined for their effectiveness at accelerating convergence. A Fourier analysis for methods of order 2 through 6 reveals that both preconditioner operators bound the eigenvalues of the discrete spatial operator. Additionally, in one dimension, the eigenvalues are grouped into two or three regions that are invariant with order of the method. Local relaxation methods are constructed that rapidly damp high frequencies for arbitrarily large time step.

  1. A new in-situ method to determine the apparent gas diffusion coefficient of soils

    NASA Astrophysics Data System (ADS)

    Laemmel, Thomas; Paulus, Sinikka; Schack-Kirchner, Helmer; Maier, Martin

    2015-04-01

    Soil aeration is an important factor for the biological activity in the soil and soil respiration. Generally, gas exchange between soil and atmosphere is assumed to be governed by diffusion and Fick's Law is used to describe the fluxes in the soil. The "apparent soil gas diffusion coefficient" represents the proportional factor between the flux and the gas concentration gradient in the soil and reflects the ability of the soil to "transport passively" gases through the soil. One common way to determine this coefficient is to take core samples in the field and determine it in the lab. Unfortunately this method is destructive and needs laborious field work and can only reflect a small fraction of the whole soil. As a consequence insecurity about the resulting effective diffusivity on the profile scale must remain. We developed a new in-situ method using new gas sampling device, tracer gas and inverse soil gas modelling. The gas sampling device contains several sampling depths and can be easily installed into vertical holes of an auger, which allows for fast installation of the system. At the lower end of the device inert tracer gas is injected continuously. The tracer gas diffuses into the surrounding soil. The resulting distribution of the tracer gas concentrations is used to deduce the diffusivity profile of the soil. For Finite Element Modeling of the gas sampling device/soil system the program COMSOL is used. We will present the results of a field campaign comparing the new in-situ method with lab measurements on soil cores. The new sampling pole has several interesting advantages: it can be used in-situ and over a long time; so it allows following modifications of diffusion coefficients in interaction with rain but also vegetation cycle and wind.

  2. Large eddy simulation of turbulent diffusion of scalar and temperature using immersed boundary method

    NASA Astrophysics Data System (ADS)

    Tabuchi, Go; Senshuu, Masanobu; Asakura, Keisuke; Nakayama, Akihiko

    2011-11-01

    The turbulent diffusion of passive scalar and temperature in quiescent and in turbulent flows has been computed by Large-eddy simulation method. The boundary-following curvilinear coordinates are used but the immersed boundary technique (IBM) is used to represent obstacles, such as buildings in atmosphere. The general boundary condition is better applied on the boundary-fitted coordinates but noslip conditions on discrete obstacles are better represented by the IBM. Examples of buoyant jet and diffusion of contaminant over topography will be shown. The work was conducted as a cooperative work with Japan Aerospace Exploration Agency and Kobe University and financial sipport of JAXA is acknowledged.

  3. Diffuse attenuation coefficient of downwelling irradiance: An evaluation of remote sensing methods

    Microsoft Academic Search

    Zhong-Ping Lee; Miroslaw Darecki; Kendall L. Carder; Curtiss O. Davis; Dariusz Stramski; W. Joseph Rhea

    2005-01-01

    The propagation of downwelling irradiance at wavelength ? from surface to a depth (z) in the ocean is governed by the diffuse attenuation coefficient, $\\\\bar{K}_{d}$(?). There are two standard methods for the derivation of $\\\\bar{K}_{d}$(?) in remote sensing, which both are based on empirical relationships involving the blue-to-green ratio of ocean color. Recently, a semianalytical method to derive $\\\\bar{K}_{d}$(?) from

  4. Preparation of PLGA nanoparticles containing estrogen by emulsification–diffusion method

    Microsoft Academic Search

    Hye-Young Kwon; Jun-Young Lee; Sung-Wook Choi; Yangsoo Jang; Jung-Hyun Kim

    2001-01-01

    Nano-sized poly (d,l lactide-co-glycolide) (PLGA) particles, widely used as a biodegradable polymeric carrier, containing estrogen were prepared employing emulsification–diffusion method. Estrogen was chosen as a model drug. The preparation method consists of emulsifying a solution of polymer and drug in the aqueous phase containing stabilizer, previously saturated, followed by adding excess water. Influence of process variables on the mean particle

  5. A new method for determining binary diffusion coefficients in dilute condensable vapors

    Microsoft Academic Search

    C. C. M. Luijten; K. J. Bosschaart; M. E. H. Van Dongen

    1997-01-01

    A new method for determining binary diffusion coefficients in dilute condensable vapors is outlined. The method is based on condensational droplet growth. It can be used in a large range of pressures and temperatures, even below the freezing point of the condensing vapor. Results are obtained for the mixtures water-nitrogen and water-helium in the pressure range 11–44 bar. The product

  6. Solution of the time-dependent diffusion equation using a conservation variational method 

    E-print Network

    Wilson, Bruce Carl

    1981-01-01

    -dependent diffusion equation; ~3C r, t v D(r, t) vC(r, t) - z(r, t) C(r, t) + S(r, t) Bt where C(r, t) 1s the atomic concentration of the d1ffusing isotope at posit1on r and t1me t, D(r, t) is the diffusion coefficient of the isotope, x(r, t) is the radioactive...(r, t) is the source term for the diffus1ng 1sotope, and D(r) is the spatially dependent d1ffusion coefficient of the isotope. The solution of equat1on (I) for C(r, t) is usually approximated by f1nite difference methods which y1eld numer1cal...

  7. Simulation of gaseous diffusion in partially saturated porous media under variable gravity with lattice Boltzmann methods

    NASA Technical Reports Server (NTRS)

    Chau, Jessica Furrer; Or, Dani; Sukop, Michael C.; Steinberg, S. L. (Principal Investigator)

    2005-01-01

    Liquid distributions in unsaturated porous media under different gravitational accelerations and corresponding macroscopic gaseous diffusion coefficients were investigated to enhance understanding of plant growth conditions in microgravity. We used a single-component, multiphase lattice Boltzmann code to simulate liquid configurations in two-dimensional porous media at varying water contents for different gravity conditions and measured gas diffusion through the media using a multicomponent lattice Boltzmann code. The relative diffusion coefficients (D rel) for simulations with and without gravity as functions of air-filled porosity were in good agreement with measured data and established models. We found significant differences in liquid configuration in porous media, leading to reductions in D rel of up to 25% under zero gravity. The study highlights potential applications of the lattice Boltzmann method for rapid and cost-effective evaluation of alternative plant growth media designs under variable gravity.

  8. An Advanced Integrated Diffusion/Transport Method for the Design, Analysis and Optimization of the Very-High-Temperature Reactors

    SciTech Connect

    Farzad Rahnema; Dingkang Zhang; Abderrafi Ougouag; Frederick Gleicher

    2011-04-04

    The main objective of this research is to develop an integrated diffusion/transport (IDT) method to substantially improve the accuracy of nodal diffusion methods for the design and analysis of Very High Temperature Reactors (VHTR). Because of the presence of control rods in the reflector regions in the Pebble Bed Reactor (PBR-VHTR), traditional nodal diffusion methods do not accurately model these regions, within which diffusion theory breaks down in the vicinity of high neutron absorption and steep flux gradients. The IDT method uses a local transport solver based on a new incident flux response expansion method in the controlled nodes. Diffusion theory is used in the rest of the core. This approach improves the accuracy of the core solution by generating transport solutions of controlled nodes while maintaining computational efficiency by using diffusion solutions in nodes where such a treatment is sufficient. The transport method is initially developed and coupled to the reformulated 3-D nodal diffusion model in the CYNOD code for PBR core design and fuel cycle analysis. This method is also extended to the prismatic VHTR. The new method accurately captures transport effects in highly heterogeneous regions with steep flux gradients. The calculations of these nodes with transport theory avoid errors associated with spatial homogenization commonly used in diffusion methods in reactor core simulators

  9. Flow cytometric analysis of E. coli on agar plates: implications for recombinant protein production.

    PubMed

    Wyre, Chris; Overton, Tim W

    2014-07-01

    Recombinant protein production in bacterial hosts is a commercially important process in the pharmaceutical industry. Optimisation of such processes is of critical importance for process productivity and reproducibility. Here, flow cytometry methods were developed to assess characteristics of bacteria during two process steps that are infrequently studied: agar plate culture and liquid culture set-up. During storage on agar plates, three discrete populations of varying green fluorescence intensity were observed along with a progressive shift of cells from the high green fluorescence population to an intermediate green fluorescence population, observed to be due formation of amyloid inclusion bodies. The dynamics of cellular fluorescence and scatter properties upon setup of liquid cultures were also assessed. These methods have the potential to improve the development of fermentation set-up, a currently little-understood area. PMID:24652548

  10. GPU-accelerated 3D neutron diffusion code based on finite difference method

    SciTech Connect

    Xu, Q.; Yu, G.; Wang, K. [Dept. of Engineering Physics, Tsinghua Univ. (China)

    2012-07-01

    Finite difference method, as a traditional numerical solution to neutron diffusion equation, although considered simpler and more precise than the coarse mesh nodal methods, has a bottle neck to be widely applied caused by the huge memory and unendurable computation time it requires. In recent years, the concept of General-Purpose computation on GPUs has provided us with a powerful computational engine for scientific research. In this study, a GPU-Accelerated multi-group 3D neutron diffusion code based on finite difference method was developed. First, a clean-sheet neutron diffusion code (3DFD-CPU) was written in C++ on the CPU architecture, and later ported to GPUs under NVIDIA's CUDA platform (3DFD-GPU). The IAEA 3D PWR benchmark problem was calculated in the numerical test, where three different codes, including the original CPU-based sequential code, the HYPRE (High Performance Pre-conditioners)-based diffusion code and CITATION, were used as counterpoints to test the efficiency and accuracy of the GPU-based program. The results demonstrate both high efficiency and adequate accuracy of the GPU implementation for neutron diffusion equation. A speedup factor of about 46 times was obtained, using NVIDIA's Geforce GTX470 GPU card against a 2.50 GHz Intel Quad Q9300 CPU processor. Compared with the HYPRE-based code performing in parallel on an 8-core tower server, the speedup of about 2 still could be observed. More encouragingly, without any mathematical acceleration technology, the GPU implementation ran about 5 times faster than CITATION which was speeded up by using the SOR method and Chebyshev extrapolation technique. (authors)

  11. A diffusion-based truncated projection artifact reduction method for iterative digital breast tomosynthesis reconstruction

    NASA Astrophysics Data System (ADS)

    Lu, Yao; Chan, Heang-Ping; Wei, Jun; Hadjiiski, Lubomir M.

    2013-02-01

    Digital breast tomosynthesis (DBT) has strong promise to improve sensitivity for detecting breast cancer. DBT reconstruction estimates the breast tissue attenuation using projection views (PVs) acquired in a limited angular range. Because of the limited field of view (FOV) of the detector, the PVs may not completely cover the breast in the x-ray source motion direction at large projection angles. The voxels in the imaged volume cannot be updated when they are outside the FOV, thus causing a discontinuity in intensity across the FOV boundaries in the reconstructed slices, which we refer to as the truncated projection artifact (TPA). Most existing TPA reduction methods were developed for the filtered backprojection method in the context of computed tomography. In this study, we developed a new diffusion-based method to reduce TPAs during DBT reconstruction using the simultaneous algebraic reconstruction technique (SART). Our TPA reduction method compensates for the discontinuity in background intensity outside the FOV of the current PV after each PV updating in SART. The difference in voxel values across the FOV boundary is smoothly diffused to the region beyond the FOV of the current PV. Diffusion-based background intensity estimation is performed iteratively to avoid structured artifacts. The method is applicable to TPA in both the forward and backward directions of the PVs and for any number of iterations during reconstruction. The effectiveness of the new method was evaluated by comparing the visual quality of the reconstructed slices and the measured discontinuities across the TPA with and without artifact correction at various iterations. The results demonstrated that the diffusion-based intensity compensation method reduced the TPA while preserving the detailed tissue structures. The visibility of breast lesions obscured by the TPA was improved after artifact reduction.

  12. Quantitative evaluation of registration methods for atlas-based diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Wu, Xue; Eggebrecht, Adam T.; Culver, Joseph P.; Zhan, Yuxuan; Basevi, Hector; Dehghani, Hamid

    2013-06-01

    In Diffuse Optical Tomography (DOT), an atlas-based model can be used as an alternative to a subject-specific anatomical model for recovery of brain activity. The main step of the generation of atlas-based subject model is the registration of atlas model to the subject head. The accuracy of the DOT then relies on the accuracy of registration method. In this work, 11 registration methods are quantitatively evaluated. The registration method with EEG 10/20 systems with 19 landmarks and non-iterative point to point algorithm provides approximately 1.4 mm surface error and is considered as the most efficient registration method.

  13. Error estimates for a finite element method for the drift-diffusion semiconductor device equations

    SciTech Connect

    Chen, Z.; Cockburn, B. (Univ. of Minnesota, Minneapolis, MN (United States))

    1994-08-01

    In this paper, optimal error estimates are obtained for a method for numerically solving the so-called unipolar model (a one-dimensional simplified version of the drift-diffusion semi-conductor device equations). The numerical method combines a mixed finite element method using a continuous piecewise-linear approximation of the electric field with an explicit upwinding finite element method using a piecewise-constant approximation of the electron concentration. For initial and boundary data ensuring that the electron concentration is smooth, the L[sup [infinity

  14. A Monte Carlo synthetic-acceleration method for solving the thermal radiation diffusion equation

    SciTech Connect

    Evans, Thomas M., E-mail: evanstm@ornl.gov [Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37831 (United States); Mosher, Scott W., E-mail: moshersw@ornl.gov [Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37831 (United States); Slattery, Stuart R., E-mail: sslattery@wisc.edu [University of Wisconsin–Madison, 1500 Engineering Dr., Madison, WI 53716 (United States); Hamilton, Steven P., E-mail: hamiltonsp@ornl.gov [Oak Ridge National Laboratory, 1 Bethel Valley Rd., Oak Ridge, TN 37831 (United States)

    2014-02-01

    We present a novel synthetic-acceleration-based Monte Carlo method for solving the equilibrium thermal radiation diffusion equation in three spatial dimensions. The algorithm performance is compared against traditional solution techniques using a Marshak benchmark problem and a more complex multiple material problem. Our results show that our Monte Carlo method is an effective solver for sparse matrix systems. For solutions converged to the same tolerance, it performs competitively with deterministic methods including preconditioned conjugate gradient and GMRES. We also discuss various aspects of preconditioning the method and its general applicability to broader classes of problems.

  15. Hyperspectral imaging for detecting pathogens grown on agar plates

    NASA Astrophysics Data System (ADS)

    Yoon, Seung Chul; Lawrence, Kurt C.; Siragusa, Gregory R.; Line, John E.; Park, Bosoon; Windham, William R.

    2007-09-01

    This paper is concerned with the development of a hyperspectral imaging technique for detecting and identifying one of the most common foodborne pathogens, Campylobacter. Direct plating using agars is an effective tool for laboratory tests and analyses of microorganisms. The morphology (size, growth pattern, color, etc.) of colonies grown on agar plates has been widely used to tentatively differentiate organisms. However, it is sometimes difficult to differentiate target organisms like Campylobacters from other contaminants grown together on the same agar plates. A hyperspectral imaging system operating at the visible and near infrared (VNIR) spectral region from 400 nm to 900 nm was set up to measure spectral signatures of 17 different Campylobacter and non-Campylobacter subspecies. Protocols for culturing, imaging samples and for calibrating measured data were developed. The VNIR spectral library of all 17 organisms commonly encountered in poultry was established from calibrated hyperspectral images. A classification algorithm was developed to locate and identify Campylobacters, non-Campylobacter contaminants, and background agars with 99.29% accuracy. This research has a potential to be expanded to detect other pathogens grown on agar media.

  16. Application of Electrode Methods in Studies of Nitric Oxide Metabolism and Diffusion Kinetics

    PubMed Central

    Liu, Xiaoping; Zweier, Jay L.

    2012-01-01

    Nitric oxide (NO) has many important physiological roles in the body. Since NO electrodes can directly measure NO concentration in the nM range and in real time, NO electrode methods have been generally used in laboratories for measuring NO concentration in vivo and in vitro. This review focuses on the application of electrode methods in studies of NO diffusion and metabolic kinetics. We have described the physical and chemical properties that need to be considered in the preparation of NO stock solution, discussed the effect of several interfering factors on the measured curves of NO concentration that need to be eliminated in the experimental setup for NO measurements, and provided an overview of the application of NO electrode methods in measuring NO diffusion and metabolic kinetics in solution and in biological systems. This overview covers NO metabolism by oxygen (O2), superoxide, heme proteins, cells and tissues. Important conclusions and physiological implication of these studies are discussed. PMID:23730264

  17. Diffuse surface calibration method to improve accuracy and dynamic range of aerosol elastic light scattering measurements

    NASA Astrophysics Data System (ADS)

    Crosland, B. M.; Johnson, M. R.; Thomson, K. A.

    2013-03-01

    A new method to calibrate detectors for elastic light scattering (ELS) measurement based on diffuse scattering from a Lambertian surface is presented. The method produces a calibration signal that is approximately seven orders of magnitude larger than a propane gas Rayleigh scattering calibration. The method also allows for calibration of detectors such as photodiodes, which are not sensitive enough to detect Rayleigh scattering for calibration but possess characteristics desirable for the measurement of soot ELS. Since the method is only suitable for backward scattering calibrations, transfer of calibration data from a backward- to a forward-oriented detector is accomplished with a secondary laser and integrating sphere. In demonstration experiments, calibration constants for photomultiplier tube (PMT) detectors obtained using both Rayleigh scattering and diffuse surface scattering agreed within experimental uncertainties as did measurements of in-flame scattering coefficients obtained with PMTs and photodiodes. However, achievable uncertainties with the diffuse-surface calibration approach were significantly reduced. More importantly, by enabling the use of photodiode detectors in ELS measurements, the new method facilitates operation at higher photon fluxes resulting in improved signal-to-noise ratios, reduced influence of photon shot noise, and the ability to achieve higher dynamic range in transient measurements.

  18. Krylov implicit integration factor WENO methods for semilinear and fully nonlinear advection-diffusion-reaction equations

    NASA Astrophysics Data System (ADS)

    Jiang, Tian; Zhang, Yong-Tao

    2013-11-01

    Implicit integration factor (IIF) methods are originally a class of efficient “exactly linear part” time discretization methods for solving time-dependent partial differential equations (PDEs) with linear high order terms and stiff lower order nonlinear terms. For complex systems (e.g. advection-diffusion-reaction (ADR) systems), the highest order derivative term can be nonlinear, and nonlinear nonstiff terms and nonlinear stiff terms are often mixed together. High order weighted essentially non-oscillatory (WENO) methods are often used to discretize the hyperbolic part in ADR systems. There are two open problems on IIF methods for solving ADR systems: (1) how to obtain higher than the second order global time discretization accuracy; (2) how to design IIF methods for solving fully nonlinear PDEs, i.e., the highest order terms are nonlinear. In this paper, we solve these two problems by developing new Krylov IIF-WENO methods to deal with both semilinear and fully nonlinear advection-diffusion-reaction equations. The methods can be designed for arbitrary order of accuracy. The stiffness of the system is resolved well and the methods are stable by using time step sizes which are just determined by the nonstiff hyperbolic part of the system. Large time step size computations are obtained. We analyze the stability and truncation errors of the schemes. Numerical examples of both scalar equations and systems in two and three spatial dimensions are shown to demonstrate the accuracy, efficiency and robustness of the methods.

  19. Photothermal characterization of the gelation process in Gelidium robustum Agar

    NASA Astrophysics Data System (ADS)

    Freile-Pelegrín, Y.; Bante, J.; Alvarado-Gil, J. J.; Yánez-Limón, J. M.

    2005-06-01

    Agar is a hydrophilic colloid formed by polysaccharides, whose ability to form reversible gels simply by cooling hot aqueous solutions is the most important property and can be regarded as the prototype and model for all gelling systems. In this paper the evolution of the gelation process of agar obtained from algae of the species Gelidium robustum, using the photopyroelectric technique is reported. It is shown that thermal effusivity increase when the agar is cooled, reaching a maximum value around 37°C. The increase in thermal effusivity can be related to the increasing of the bondings in the gel as temperature decreases, reaching the maximum at the gelation point. The decrease of the thermal effusivity at lower temperature could be due to the syneresis process involving a gradual release of water after gelation.

  20. A unifying theoretical and algorithmic framework for least squares methods of estimation in diffusion tensor imaging

    NASA Astrophysics Data System (ADS)

    Koay, Cheng Guan; Chang, Lin-Ching; Carew, John D.; Pierpaoli, Carlo; Basser, Peter J.

    2006-09-01

    A unifying theoretical and algorithmic framework for diffusion tensor estimation is presented. Theoretical connections among the least squares (LS) methods, (linear least squares (LLS), weighted linear least squares (WLLS), nonlinear least squares (NLS) and their constrained counterparts), are established through their respective objective functions, and higher order derivatives of these objective functions, i.e., Hessian matrices. These theoretical connections provide new insights in designing efficient algorithms for NLS and constrained NLS (CNLS) estimation. Here, we propose novel algorithms of full Newton-type for the NLS and CNLS estimations, which are evaluated with Monte Carlo simulations and compared with the commonly used Levenberg-Marquardt method. The proposed methods have a lower percent of relative error in estimating the trace and lower reduced ?2 value than those of the Levenberg-Marquardt method. These results also demonstrate that the accuracy of an estimate, particularly in a nonlinear estimation problem, is greatly affected by the Hessian matrix. In other words, the accuracy of a nonlinear estimation is algorithm-dependent. Further, this study shows that the noise variance in diffusion weighted signals is orientation dependent when signal-to-noise ratio (SNR) is low (?5). A new experimental design is, therefore, proposed to properly account for the directional dependence in diffusion weighted signal variance.

  1. A variational meshfree method for solving time-discrete diffusion equations

    NASA Astrophysics Data System (ADS)

    Krottje, Johannes K.

    2006-08-01

    A meshfree method is developed for solving time-discrete diffusion equations that arise in models in brain research. Important criteria for a suitable method are flexibility with respect to domain geometry and the ability to work with very small moving sources requiring easy refinement possibilities. One part of the work concerns a meshfree discretization of the modified Helmholtz equation based on the related minimization problem and a local least-squares function approximation. In a second part, a node choosing algorithm is presented that moves around randomly distributed nodes for optimizing the node distribution and varying the node density as needed. The method is illustrated by two numerical tests.

  2. Orthogonal spline collocation method for the two-dimensional fractional sub-diffusion equation

    NASA Astrophysics Data System (ADS)

    Yang, Xuehua; Zhang, Haixiang; Xu, Da

    2014-01-01

    The aim of this paper is to develop a novel numerical techniques for the solution of the two-dimensional fractional sub-diffusion equation. The proposed technique is based on orthogonal spline collocation (OSC) method in space and a finite difference method (FDM) in time. Stability and convergence of the proposed method are rigorously discussed and theoretically proven. We present the results of numerical experiments in one and two space variables, which confirm the predicted convergence rates and exhibit optimal accuracy in various norms.

  3. Comparative study of bio-ethanol production from mahula ( Madhuca latifolia L.) flowers by Saccharomyces cerevisiae cells immobilized in agar agar and Ca-alginate matrices

    Microsoft Academic Search

    Shuvashish Behera; Shaktimay Kar; Rama Chandra Mohanty; Ramesh Chandra Ray

    2010-01-01

    Batch fermentation of mahula (Madhuca latifolia L., a tree commonly found in tropical rain forest) flowers was carried out using immobilized cells (in agar agar and calcium alginate) and free cells of Saccharomyces cerevisiae. The ethanol yields were 151.2, 154.5 and 149.1gkg?1 flowers using immobilized (in agar agar and calcium alginate) and free cells, respectively. Cell entrapment in calcium alginate

  4. Evaluation of a new chromogenic agar medium for Alicyclobacillus acidoterrestris.

    PubMed

    Uchida, Masafumi; Teramura, Hajime; Kashida, Mitsuaki; Kodaka, Hidemasa

    2013-01-01

    Spoilage of fruit juices by a thermoacidophilic spore-forming bacterium, Alicyclobacillus acidoterrestris, is a big problem for fruit juice industries worldwide. We have developed a novel chromogenic selective agar medium (EAATSM) for the isolation and enumeration of A. acidoterrestris. A. acidoterrestris strains appeared as blue colonies on the EAATSM. Other Alicyclobacillus strains appeared as white colonies or were inhibited. A study comparing EAATSM and YSG agar was carried out using artificially contaminated samples of 50 fruit juice products. The correlation coefficient between EAATSM and YSG was 0.991. PMID:23796641

  5. GELRITE as an Agar Substitute in Bacteriological Media

    PubMed Central

    Shungu, Daniel; Valiant, Mary; Tutlane, Vicki; Weinberg, Ellen; Weissberger, Barbara; Koupal, Larry; Gadebusch, Hans; Stapley, Edward

    1983-01-01

    GELRITE gellan gum (formerly known as PS-60 and S-60) is a new naturally derived, highly purified polysaccharide which displays several interesting properties, including selfgelling. The suitability of GELRITE as an agar substitute was tested by evaluating the performance of several media selected from among those most commonly used in the isolation, identification, and enumeration of microorganisms in clinical laboratories. Fifty different bacterial species previously implicated in human infections served as test strains. On the basis of the various parameters considered, namely, colony characteristics, biochemical reactions, hemolytic patterns, and plating efficiency, media gelled by agar and by GELRITE compared quite favorably. Images PMID:16346398

  6. Charcoal-Yeast Extract Agar: Primary Isolation Mediumfor Legionella pneumophila

    Microsoft Academic Search

    JAMES C. FEELEY; ROBERT J. GIBSON; GEORGE W. GORMAN; NANCY C. LANGFORD; J. KAMILE RASHEED; DON C. MACKEL; WILLIAM B. BAINE

    1979-01-01

    Charcoal-yeast extract agar isa new bacteriological mediumthatsupports excellent growth oftheLegionella pneumophila. Itresults frommodifications madeinan existing L.pneumophila medium,F-Gagar.Yeastextract, instead of an acidhydrolysate ofcasein, servesastheprotein source.Beefextractives and starch are notadded. Activated charcoal (Norit A or Norit SG)isincluded at 0.20%(wt\\/vol). Comparison ofcharcoal-yeast extract andF-Gagars showedthat a greater numberofcolony-forming units ofL.pneumophila was recovered from astandardized tissue inoculum on charcoal-yeast extract agar(4.35 x 106colony- forning

  7. Surface preparation for determining diffusion length by the surface photovoltage method

    SciTech Connect

    Goodman, A.M.

    1985-03-26

    A method of treating the surface of a sample of n-type silicon material in preparation for measurements for determining the minority carrier diffusion length of the material by the surface photovoltage method comprises applying a strong oxidizing agent to an appropriately prepared surface of a semiconductor material such as silicon. The oxidizing agent is taken from the group consisting of potassium permanganate (KMnO/sub 4/), potassium dichromate (K/sub 2/Cr/sub 2/O/sub 7/), and ammonium dichromate ((NH/sub 4/)/sub 2/Cr/sub 2/O/sub 7/). The surface preparation assures a consistently large surface photovoltage that is stable during the surface photovoltage measurement for minority carrier diffusion length.

  8. Determination of O-isopropyl methylphosphonic acid in living microorganism-agar matrixes using ion chromatography conductivity detection.

    SciTech Connect

    Nassar, Alaa F. (BCO); Lucas, Samuel V. (BCO); Thomas, Susan A. (BATTELLE (PACIFIC NW LAB))

    1999-01-01

    A direct an anion exchange, ion chromatography (IC)-based method for the detection of the chemical warfare agent surrogate O-isopropyl methylphosphonic acid (IMPA) in agar medium has been developed. This is the first report of the systematic development and validation of an IC-based method for the analysis of the chemical warfare agent degradation product, IMPA, in Petri dishes containing the agar medium with 10, 100 and 1000 mg/mL IMPA. Samples were prepared by dilution of the agar medium with deionized water followed by sonication and then filtration before the analysis by IC/conductivity detection. Using this method, the amount of IMPA in the Petri dishes was measured. Excellent separation efficiency and freedom from interference due to common anions such as phosphate and sulfate was obtained in the developed methods. Retention time precision is less than 1.0% relative standard deviation (%RSD) and the detection limit is 0.1 mg/mL. Three calibration curves were performed over the range 1-100 mg/mL using blank agar matrices spiked with five IMPA concentrations; with correlation coefficients (R{sup 2}) of 0.993, 0.991, and 0.992 for the calibration standard without dilution of agar matrix, at 4-times dilution and at 40-times dilution, respectively. Using three different samples at three IMPA spike levels, analysis accuracy was assessed by spiking the actual agar samples with IMPA. Average recoveries were 76, 79, and 84% for 10, 100, and 1000 mg/mL, respectively.

  9. Thermal Diffusivity of a Hard Boiled Candy Obtained by Photothermal Beam Deflection and Standard Photopyroelectric Method

    Microsoft Academic Search

    Jan Paul Favier; Dorin Dadarlat; Jürgen Gibkes; Cornelius Van Den Berg; Dane Bicanic

    1998-01-01

    Two different photothermal techniques, the photopyroelectric (PPE) detection and photothermal beam deflection (PTBD) method, were used for the thermal characterisation of a glassy sugar system, commercially available hard boiled candy. Thermal diffusivities (at room temperature) obtained are comparable (i.e., 14.7 x 10 and 12.0 x 10 ms for PPE and PTBD respectively).In addition, the PPE technique was also used to

  10. Preparation of PLGA nanoparticles using TPGS in the spontaneous emulsification solvent diffusion method

    Microsoft Academic Search

    Farnaz Esmaeili; Fatemeh Atyabi; Rassoul Dinarvand

    2007-01-01

    D-alpha-tocopheryl poly (ethylene glycol) 1000 succinate (TPGS) is a widely used form of vitamin E that has been used as a solubilizer, an emulsifier and as a vehicle for drug delivery formulations. In this study, poly lactide-co-glycolide (PLGA) nanoparticles were prepared by spontaneous emulsification solvent diffusion (SESD) method. TPGS as an emulsifier and further as a matrix material blended with

  11. The optimized order 2 method : Application to convection-diffusion problems

    Microsoft Academic Search

    C. Japhet; F. Nataf; F. Rogier

    2001-01-01

    We present an iterative, non-overlapping domain decomposition method for solving the convection–diffusion equation. A reformulation of the problem leads to an equivalent problem, where the unknowns are on the boundary of the subdomains [F. Nataf, F. Rogier, E. de Sturler, in: A. Sequeira (Ed.), Navier–Stokes Equations on Related Nonlinear Analysis, Plenum Press, New York, 1995, pp. 307–377]. The solving of

  12. 3D modeling for solving forward model of no-contact fluorescence diffuse optical tomography method

    Microsoft Academic Search

    F. Nouizi; R. Chabrier; M. Torregrossa; P. Poulet

    2009-01-01

    This paper presents detailed computational aspects of a new 3D modeling for solving the direct problem in a no-contact time-resolved Fluorescent Diffuse Optical Tomography (FDOT) method that rely on near-infrared scattered and fluorescent photons to image the optical properties and distribution of fluorescent probes in small laboratory animals. An optical scanner allowing performing in-vivo measurements in no-contact scheme was built

  13. Improvements to the Diffusion Synthetic Acceleration method in neutron transport with highly anisotropic scattering

    SciTech Connect

    Colombo, V. [Universita degli Studi di Bologna (Italy); Coppa, G.G.M.; Melisurgo, V.; Ravetto, P. [Politecnico di Torino (Italy)

    1995-12-31

    Some modifications of the Diffusion Synthetic Acceleration (DSA) technique are proposed to face its loss of effectiveness when dealing with highly anisotropic scattering. A model case convergence analysis of the proposed techniques is performed; an extensive set of comparisons with results obtained by means of already assessed DSA modification techniques is reported for various scattering cross-section configurations. The importance of non asymptotic convergence velocity as a theoretical means to characterize and optimize different acceleration methods is also discussed.

  14. Effect of Culture Medium on the Disk Diffusion Method for Determining Antifungal Susceptibilities of Dermatophytes

    PubMed Central

    Fernández-Torres, Belkys; Carrillo-Muñoz, Alfonso; Inza, Isabel; Guarro, Josep

    2006-01-01

    We have evaluated a disk diffusion method to determine the activities of five drugs against 50 strains of dermatophytes and to assess the influence of the culture medium (antibiotic medium 3, high-resolution medium, and RPMI) on the inhibition zone diameters (IZD). There were no differences among the medium/drug combinations, except for itraconazole-RPMI, which showed the narrowest IZD. PMID:16723589

  15. Preparation of a stable silica membrane by a counter diffusion chemical vapor deposition method

    Microsoft Academic Search

    Mikihiro Nomura; Kenta Ono; Suraj Gopalakrishnan; Takashi Sugawara; Shin-Ichi Nakao

    2005-01-01

    A stable silica membrane having excellent H2\\/N2 permeance ratio (over 1000) was prepared by the counter diffusion chemical vapor deposition method using tetramethyl orthosilicate (TMOS) and O2 as reactants at 873K. TMOS and O2 were provided in the opposing geometry of the substrates, and silica layer was deposited in the substrate pores. Apparent activation energies through the silica membranes increased

  16. High accuracy non-equidistant method for singular perturbation reaction-diffusion problem

    Microsoft Academic Search

    Xin Cai; Dan-lin Cai; Rui-qian Wu; Kang-he Xie

    2009-01-01

    Singular perturbation reaction-diffusion problem with Dirichlet boundary condition is considered. It is a multi-scale problem.\\u000a Presence of small parameter leads to boundary layer phenomena in both sides of the region. A non-equidistant finite difference\\u000a method is presented according to the property of boundary layer. The region is divided into an inner boundary layer region\\u000a and an outer boundary layer region

  17. Pollinia-borne chemicals that induce early postpollination effects in Dendrobium flowers move rapidly into agar blocks and include ACC and compounds with auxin activity.

    PubMed

    Promyou, Surassawadee; Ketsa, Saichol; van Doorn, Wouter G

    2014-11-15

    The early visible effects of pollination in orchids are likely due to pollinia-borne chemicals. In Dendrobium we tested whether such compounds were water soluble and would diffuse in solid-aqueous phase, and determined both 1-aminocyclopropane-1-carboxylic acid (ACC) concentrations and auxin activity. Following pollination, the flower peduncle showed epinastic movement, followed by yellowing of the flower lip, flower senescence and ovary growth. Placing pollinia on agar blocks for 3, 6, 9 or 12h, prior to transferring them to the stigma, increased the time to these early postpollination effects or prevented them. Placing agar blocks that had been used for contact with the pollinia on the stigma also induced the early postpollination effects. The concentrations of ACC, the direct precursor of ethylene, in pollinia was lower the longer the pollinia had been in contact with the agar blocks, whilst the ACC content in the agar blocks increased with the period of contact. The auxin activity of the agar blocks also increased with the time of contact with pollinia. It is concluded that chemicals in the pollinia are responsible for the early visible postpollination effects, and that these (a) rapidly diffuse in aqueous media, and (b) comprise at least ACC and compounds with auxin activity. The idea is discussed that ACC plus auxin is adequate for the production of the early postpollination effects. PMID:25240156

  18. Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

    NASA Astrophysics Data System (ADS)

    Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean-François; Brommer, Peter; Mousseau, Normand

    2015-06-01

    We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion paths and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. This study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.

  19. Evaluation of Methods to Correct for IR Loss in Eppley PSP Diffuse Measurements

    SciTech Connect

    Vignola, F.; Long, Charles N.; Reda, I.

    2007-09-13

    The IR loss in diffuse measurements made by thermopile pyranometers is examined. Diffuse measurements are used for the study of IR losses to minimize the effects of beam irradiance and therefore much of the cosine response error influences. Specifically, diffuse measurements of an Eppley PSP pyranometer are compared to those made with a Schenk Star pyranometer. Eppley B&W and Star type pyranometers suffer minimal IR loss because the reference and receiving junctions of the thermopile are at the same thermal level. The difference between diffuse values can be attributed to calibration and cosine response errors as well as IR loss. Therefore it is necessary to separate out the various sources of error and examination of the differences over various times of the year can help, at least for systematic errors. Several methods of correcting for IR loss will be examined. First subtracting out the average nighttime offset during the day will be tested. Next an extrapolation between early morning and late evening offsets will be tested. This should help eliminate the IR offset in both the morning and evening, but underestimate the IR losses during the rest of the day. Correlations of the remaining IR losses with temperature, relative humidity, and irradiance will be evaluated. In addition, the IR losses will be studied both for clear days and for totally overcast periods. Pyrgeometer measurements will also be compared to the estimated IR losses. The above measurements and comparisons will help quantify the magnitude and variation of the IR losses.

  20. Contribution to an effective design method for stationary reaction-diffusion patterns

    NASA Astrophysics Data System (ADS)

    Szalai, István; Horváth, Judit; De Kepper, Patrick

    2015-06-01

    The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.

  1. Method and apparatus for determining minority carrier diffusion length in semiconductors

    DOEpatents

    Goldstein, Bernard (Princeton, NJ); Dresner, Joseph (Princeton, NJ); Szostak, Daniel J. (Mercerville, NJ)

    1983-07-12

    Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon which has a significantly small minority carrier diffusion length using the constant-magnitude surface-photovoltage (SPV) method. An unmodulated illumination provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV. A vibrating Kelvin method-type probe electrode couples the SPV to a measurement system. The operating optical wavelength of an adjustable monochromator to compensate for the wavelength dependent sensitivity of a photodetector is selected to measure the illumination intensity (photon flux) on the silicon. Measurements of the relative photon flux for a plurality of wavelengths are plotted against the reciprocal of the optical absorption coefficient of the material. A linear plot of the data points is extrapolated to zero intensity. The negative intercept value on the reciprocal optical coefficient axis of the extrapolated linear plot is the diffusion length of the minority carriers.

  2. Computing quasi-linear diffusion coefficients using the delta-f particle-in-cell method

    SciTech Connect

    Austin, T. M.; Smithe, D. N.; Ranjbar, V. [Tech-X Corporation, 5621 Arapahoe Ave., Suite A, Boulder, CO 80303 (United States)

    2009-11-26

    Linear wave codes AORSA and TORIC couple to the bounce-averaged nonlinear Fokker-Planck code CQL3D through quasi-linear diffusion coefficients. Both linear wave codes rely on the quasi-local approximation that includes only first-order parallel and perpendicular gradient variations of cyclotron frequency and ignores field line curvature along with temperature and density gradient effects. The delta-f particle-in-cell (DFPIC) method has been successfully used for simulating ion-cyclotron fast wave behavior. This method also permits particle behavior such as multiple pass resonance, banana orbits, and superadiabaticity. We present new work on generating quasi-linear diffusion coefficients using the DFPIC method that will permit the electromagnetic particle-in-cell (EMPIC) code, VORPAL, to couple to CQL3D and to compare to AORSA and TORIC. A new multiple weight delta-f approach will be presented that converts velocity derivatives to action derivatives and yields a full tensor quasi-linear diffusion coefficient.

  3. Plaque Formation in Agar by Single Antibody-Producing Cells

    Microsoft Academic Search

    Niels K. Jerne; Albert A. Nordin

    1963-01-01

    Distinct plaques, each of which is due to the release of hemolysin by a single antibody-forming cell, are revealed by complement after incubation, in an agar layer, of a mixture of sheep red cells and lymphoid cells from a rabbit immunized with sheep red cells.

  4. Maintenance of Leptospira Species in Leptospira Vanaporn Wuthiekanun Agar

    PubMed Central

    Wuthiekanun, Vanaporn; Amornchai, Premjit; Langla, Sayan; Oyuchua, Malinee; Day, Nicholas P. J.

    2014-01-01

    The maintenance of Leptospira species in liquid or semisolid medium is time-consuming and at risk of contamination due to the needs of routine subculture and dark field microscopy. Using Leptospira Vanaporn Wuthiekanun (LVW) agar, we maintained 100 pathogenic Leptospira isolates for 12 months without the need for subculture and confirmed the viability of all isolates by the naked eye. PMID:25253789

  5. Direct Cloning of Human Ovarian Carcinoma Cells in Agar1

    Microsoft Academic Search

    Anne W. Hamburger; Sydney E. Salmon; Mary B. Kim; Jeff M. Trent; Barbara J. Soehnlen

    We have recently developed an in vitro assay for human tumor stem cells that permits cloning of human ovarian adenocarcinoma cells in soft agar. Tumor colonies grew from both effusions and biopsies from 85% of 31 ovarian cancer patients. The cloning efficiency did not vary with the histology of the tumor. Growth was induced with medium conditioned by the adherent

  6. Hyperspectral Imaging for Detecting Pathogens Grown on Agar Plates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This paper is concerned with the development of a hyperspectral imaging technique for detecting and identifying one of the most common foodborne pathogens, Campylobacter. Direct plating using agars is an effective tool for laboratory tests and analyses of microorganisms. The morphology (size, growth...

  7. Agar Ingestion Combined with Phototherapy in Jaundiced Newborn Infants

    Microsoft Academic Search

    Finn Ebbesen; Jørn Møller

    1977-01-01

    49 jaundiced, nonimmunized newborn infants with a birth weight of more than 2,000 g were given phototherapy with white light for more than 36 h. The average period of treatment was 61 h. 24 infants received 250 mg agar at the beginning of each meal at 3-hour intervals during phototherapy. 25 infants received phototherapy only. Serum bilirubin levels were decreased

  8. Diffusive Shock Acceleration in Oblique MHD Shocks: Comparison with Monte Carlo Methods and Observations

    E-print Network

    Hyesung Kang; T. W. Jones

    1996-07-10

    We report simulations of diffusive particle acceleration in oblique magnetohydrodynamical (MHD) shocks. These calculations are based on extension to oblique shocks of a numerical model for ``thermal leakage'' injection of particles at low energy into the cosmic-ray population. That technique, incorporated into a fully dynamical diffusion-convection formalism, was recently introduced for parallel shocks by Kang \\& Jones (1995). Here, we have compared results of time dependent numerical simulations using our technique with Monte Carlo simulations by Ellison, Baring \\& Jones 1995 and with {\\it in situ} observations from the Ulysses spacecraft of oblique interplanetary shocks discussed by Baring \\etal (1995). Through the success of these comparisons we have demonstrated that our {diffusion-convection} method and injection techniques provide a practical tool to capture essential physics of the injection process and particle acceleration at oblique MHD shocks. In addition to the diffusion-convection simulations, we have included time dependent two-fluid simulations for a couple of the shocks to demonstrate the basic validity of that formalism in the oblique shock context. Using simple models for the two-fluid closure parameters based on test-particle considerations, we find good agreement with the dynamical properties of the more detailed diffusion-convection results. We emphasize, however, that such two-fluid results can be sensitive to the properties of these closure parameters when the flows are not truly steady. Furthermore, we emphasize through example how the validity of the two-fluid formalism does not necessarily mean that {\\it steady-state} two-fluid models provide a reliable tool for predicting the efficiency of particle acceleration in real shocks.

  9. Hierarchical clustering method for improved prostate cancer imaging in diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Kavuri, Venkaiah C.; Liu, Hanli

    2013-03-01

    We investigate the feasibility of trans-rectal near infrared (NIR) based diffuse optical tomography (DOT) for early detection of prostate cancer using a transrectal ultrasound (TRUS) compatible imaging probe. For this purpose, we designed a TRUS-compatible, NIR-based image system (780nm), in which the photo diodes were placed on the trans-rectal probe. DC signals were recorded and used for estimating the absorption coefficient. We validated the system using laboratory phantoms. For further improvement, we also developed a hierarchical clustering method (HCM) to improve the accuracy of image reconstruction with limited prior information. We demonstrated the method using computer simulations laboratory phantom experiments.

  10. Finite analytic numerical method for transient heat diffusion in layered composite materials

    NASA Astrophysics Data System (ADS)

    Ramos, Fernando M.; Giovannini, Andre

    1992-12-01

    The finite analytic (FA) method, which has been recently developed and used in fluid flow and heat transfer problems, is presented and extended to the solution of the problem of transient heat conduction in a one-dimensional multilayered composite slab. The basic idea of the FA method is to incorporate a local analytic solution of the governing equation in the numerical solution of the boundary-value problem. In this study, the local analytic solutions are obtained by the standard integral-transformation technique and the associated eigenvalue problem is solved by the Galerkin method. Some numerical examples are computed to demonstrate the applicability of the FA method in dealing with heat diffusion in a composite material. It is shown that the FA method is accurate and provides reductions in computational costs.

  11. Fixed and pulsed gradient diffusion methods in low-field core analysis.

    PubMed

    Leu, Gabriela; Fordham, Edmund J; Hürlimann, Martin D; Frulla, Phil

    2005-02-01

    We review diffusion-weighted relaxation protocols for two-dimensional diffusion/relaxation time (D, T(2)) distributions and their application to fluid-saturated sedimentary rocks at low fields typical of oil-well logging tools (< or = 2 MHz for 1H). Fixed field gradient (FFG) protocols may be implemented in logging tools and in the laboratory; there, pulsed field gradient (PFG) protocols are also available. In either category, direct or stimulated echoes may be used for the diffusion evolution periods. We compare the results of several variant FFG and PFG protocols obtained on liquids and two contrasting sedimentary rocks. For liquids and rocks of negligible internal gradients (g(int)), results are comparable, as expected, for all the studied protocols. For rocks of strong g(int), protocol-dependent artifacts are seen in the joint (D, T2) distributions, consistent with the effects of the internal fields. For laboratory petrophysics, the PFG methods offer several advantages: (a) significantly improved signal-to-noise ratio and acquisition times for repetitions over many samples; (b) freedom from heteronuclear contamination when fluorinated liquids are used in core holders; and (c) a palette of variants--one comparable with the FFG--for the study of rocks of significant g(int). Given suitable hardware, both PFG and FFG methods can be implemented in the same bench-top apparatus, providing a versatile test bed for application in a petrophysical laboratory. PMID:15833632

  12. A balancing domain decomposition method by constraints for advection-diffusion problems

    SciTech Connect

    Tu, Xuemin; Li, Jing

    2008-12-10

    The balancing domain decomposition methods by constraints are extended to solving nonsymmetric, positive definite linear systems resulting from the finite element discretization of advection-diffusion equations. A pre-conditioned GMRES iteration is used to solve a Schur complement system of equations for the subdomain interface variables. In the preconditioning step of each iteration, a partially sub-assembled finite element problem is solved. A convergence rate estimate for the GMRES iteration is established, under the condition that the diameters of subdomains are small enough. It is independent of the number of subdomains and grows only slowly with the subdomain problem size. Numerical experiments for several two-dimensional advection-diffusion problems illustrate the fast convergence of the proposed algorithm.

  13. Dating of iron gall ink using the dissolution-diffusion method.

    PubMed

    Li, Biao; Xie, Peng

    2015-03-01

    In many criminal and civil cases, some questioned documents are written with iron gall ink. Determining the date when an iron gall ink entry was written can be important to assess the authenticity of a document. A dissolution-diffusion method was successfully employed to draw aging curves of iron gall ink entries stored in controlled conditions over 40 months. Calibration curves were created to indicate the relationship between the average dissolution-diffusion rate of ink components and the age of ink entries stored under natural aging conditions. As preliminary findings of this study, the mixed solution of dimethyl formamide (DMF) and anhydrous ethanol was suitable to dissolve the dye of iron gall ink strokes made at different time. It was also determined that brands of iron gall inks, types of paper, and thickness of iron gall ink strokes had varying impacts on estimating the dates of iron gall ink strokes. PMID:25677356

  14. GPU-Accelerated Finite Element Method for Modelling Light Transport in Diffuse Optical Tomography

    PubMed Central

    Schweiger, Martin

    2011-01-01

    We introduce a GPU-accelerated finite element forward solver for the computation of light transport in scattering media. The forward model is the computationally most expensive component of iterative methods for image reconstruction in diffuse optical tomography, and performance optimisation of the forward solver is therefore crucial for improving the efficiency of the solution of the inverse problem. The GPU forward solver uses a CUDA implementation that evaluates on the graphics hardware the sparse linear system arising in the finite element formulation of the diffusion equation. We present solutions for both time-domain and frequency-domain problems. A comparison with a CPU-based implementation shows significant performance gains of the graphics accelerated solution, with improvements of approximately a factor of 10 for double-precision computations, and factors beyond 20 for single-precision computations. The gains are also shown to be dependent on the mesh complexity, where the largest gains are achieved for high mesh resolutions. PMID:22013431

  15. Direct estimation of diffuse gaseous emissions from coal fires: current methods and future directions

    USGS Publications Warehouse

    Engle, Mark A.; Olea, Ricardo A.; O'Keefe, Jennifer M. K.; Hower, James C.; Geboy, Nicholas J.

    2013-01-01

    Coal fires occur in nature spontaneously, contribute to increases in greenhouse gases, and emit atmospheric toxicants. Increasing interest in quantifying coal fire emissions has resulted in the adaptation and development of specialized approaches and adoption of numerical modeling techniques. Overview of these methods for direct estimation of diffuse gas emissions from coal fires is presented in this paper. Here we take advantage of stochastic Gaussian simulation to interpolate CO2 fluxes measured using a dynamic closed chamber at the Ruth Mullins coal fire in Perry County, Kentucky. This approach allows for preparing a map of diffuse gas emissions, one of the two primary ways that gases emanate from coal fires, and establishing the reliability of the study both locally and for the entire fire. Future research directions include continuous and automated sampling to improve quantification of gaseous coal fire emissions.

  16. Discretizing the Gent-McWilliams velocity and isopycnal diffusion with a discontinuous Galerkin finite element method

    NASA Astrophysics Data System (ADS)

    Pestiaux, A.; Kärnä, T.; Melchior, S.; Lambrechts, J.; Remacle, J. F.; Deleersnijder, E.; Fichefet, T.

    2012-04-01

    The discretization of the Gent-McWilliams velocity and isopycnal diffusion with a discontinuous Galerkin finite element method is presented. Both processes are implemented in an ocean model thanks to a tensor related to the mesoscale eddies. The antisymmetric part of this tensor is computed from the Gent-McWilliams velocity and is subsequently included in the tracer advection equation. This velocity can be constructed to be divergence-free. The symmetric part that describes the diapycnal and isopycnal diffusions requires a special treatment. A stable and physically sound isopycnal tracer diffusion scheme is needed. Here, an interior penalty method is chosen that enables to build stable diffusion terms. However, due to the strong anisotropy of the diffusion, the common-usual penalty factor by Ern et al. (2008) is not sufficient. A novel method for computing the penalty term of Ern is then proposed for diffusion equations when both the diffusivity and the mesh are strongly anisotropic. Two test cases are resorted to validate the methodology and two more realistic applications illustrate the diapycnal and isopycnal diffusions, as well as the Gent-McWilliams velocity.

  17. Some new discretization and adaptation and multigrid methods for 2-D 3-T diffusion equations

    SciTech Connect

    Jiang, Jun [Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan City, YangGuTang, Xiangtan, Hunan 411105 (China); Huang, Yunqing [Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan City, YangGuTang, Xiangtan, Hunan 411105 (China)]. E-mail: huangyq@xtu.edu.cn; Shu, Shi [Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Xiangtan City, YangGuTang, Xiangtan, Hunan 411105 (China); Zeng, Shi [Department of Engineering Physics, Tsinghua University, Beijing 100084 (China)

    2007-05-20

    In the simulation of laser-driven implosion of a fuel capsule in inertial confinement fusion experiments, a system of two-dimensional diffusion equations coupled with electron, iron and photon temperature are widely used to approximately describe the process of energy across multiple materials and the exchange of energy among electrons, irons and photons. The numerical solution of such equations is always challenging because of its strong nonlinear phenomena and strong discontinuous interfaces. In this article, we design a symmetric finite volume method, develop the corresponding preconditioning technique, and propose a mesh adaptation algorithm based on Hessian matrix and a two-grid method. Using these new methods, we demonstrate that the energy conservation error and computation efficiency of the integrated algorithm are much better than classical method.

  18. Fast non-overlapping Schwarz domain decomposition methods for solving the neutron diffusion equation

    SciTech Connect

    Jamelot, Erell [Commissariat à l’Énergie Atomique et aux Énergie Alternatives, CEA Saclay, 91191 Gif-sur-Yvette Cedex (France)] [Commissariat à l’Énergie Atomique et aux Énergie Alternatives, CEA Saclay, 91191 Gif-sur-Yvette Cedex (France); Ciarlet, Patrick, E-mail: patrick.ciarlet@ensta.fr [POEMS Laboratory, CNRS-INRIA-ENSTA UMR 7231, ENSTA ParisTech 32, Boulevard Victor, 75739 Paris Cedex 15 (France)] [POEMS Laboratory, CNRS-INRIA-ENSTA UMR 7231, ENSTA ParisTech 32, Boulevard Victor, 75739 Paris Cedex 15 (France)

    2013-05-15

    Studying numerically the steady state of a nuclear core reactor is expensive, in terms of memory storage and computational time. In order to address both requirements, one can use a domain decomposition method, implemented on a parallel computer. We present here such a method for the mixed neutron diffusion equations, discretized with Raviart–Thomas–Nédélec finite elements. This method is based on the Schwarz iterative algorithm with Robin interface conditions to handle communications. We analyse this method from the continuous point of view to the discrete point of view, and we give some numerical results in a realistic highly heterogeneous 3D configuration. Computations are carried out with the MINOS solver of the APOLLO3® neutronics code.

  19. A diffuse-interface method for two-phase flows with soluble surfactants

    PubMed Central

    Teigen, Knut Erik; Song, Peng; Lowengrub, John; Voigt, Axel

    2010-01-01

    A method is presented to solve two-phase problems involving soluble surfactants. The incompressible Navier–Stokes equations are solved along with equations for the bulk and interfacial surfactant concentrations. A non-linear equation of state is used to relate the surface tension to the interfacial surfactant concentration. The method is based on the use of a diffuse interface, which allows a simple implementation using standard finite difference or finite element techniques. Here, finite difference methods on a block-structured adaptive grid are used, and the resulting equations are solved using a non-linear multigrid method. Results are presented for a drop in shear flow in both 2D and 3D, and the effect of solubility is discussed. PMID:21218125

  20. A Numerical Method for Pricing Electricity Derivatives for Jump-Diffusion Processes Based on Continuous Time Lattices

    E-print Network

    Albanese, Claudio

    A Numerical Method for Pricing Electricity Derivatives for Jump-Diffusion Processes Based.tompaidis@mccombs.utexas.edu Corresponding author. Tel. 512-4715252, Fax 512-4710587. #12;A Numerical Method for Pricing Electricity method for pricing derivatives on electricity prices. The method is based on approximating the generator

  1. Nuclemeter: A Reaction-Diffusion Based Method for Quantifying Nucleic Acids Undergoing Enzymatic Amplification

    PubMed Central

    Liu, Changchun; Sadik, Mohamed M.; Mauk, Michael G.; Edelstein, Paul H.; Bushman, Frederic D.; Gross, Robert; Bau, Haim H.

    2014-01-01

    Real-time amplification and quantification of specific nucleic acid sequences plays a major role in medical and biotechnological applications. In the case of infectious diseases, such as HIV, quantification of the pathogen-load in patient specimens is critical to assess disease progression and effectiveness of drug therapy. Typically, nucleic acid quantification requires expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low-resource settings. This paper describes a simple, low-cost, reaction-diffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. The method was tested for HIV viral load monitoring and performed on par with conventional benchtop methods. The proposed method is suitable for nucleic acid quantification at point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. PMID:25477046

  2. In vitro antibacterial activity of minocycline and effect of agar medium utilized in its susceptibility testing.

    PubMed

    Washington, J A; Yu, P K; Martin, W J

    1970-02-01

    The in vitro activity of minocycline against 1,028 bacterial strains was determined in parallel in Mueller Hinton Agar and Trypticase Soy Agar. The broad antibacterial effect of minocycline against gram-positive cocci and gram-negative bacilli is confirmed. Minimal inhibitory concentrations for gram-positive bacteria in Mueller Hinton Agar were at least twofold less than in Trypticase Soy Agar. Minimal inhibitory concentrations for gram-negative bacilli in Mueller Hinton Agar were usually fourfold less than in Trypticase Soy Agar. PMID:4392357

  3. Lattice simulation method to model diffusion and NMR spectra in porous materials.

    PubMed

    Merlet, Céline; Forse, Alexander C; Griffin, John M; Frenkel, Daan; Grey, Clare P

    2015-03-01

    A coarse-grained simulation method to predict nuclear magnetic resonance (NMR) spectra of ions diffusing in porous carbons is proposed. The coarse-grained model uses input from molecular dynamics simulations such as the free-energy profile for ionic adsorption, and density-functional theory calculations are used to predict the NMR chemical shift of the diffusing ions. The approach is used to compute NMR spectra of ions in slit pores with pore widths ranging from 2 to 10 nm. As diffusion inside pores is fast, the NMR spectrum of an ion trapped in a single mesopore will be a sharp peak with a pore size dependent chemical shift. To account for the experimentally observed NMR line shapes, our simulations must model the relatively slow exchange between different pores. We show that the computed NMR line shapes depend on both the pore size distribution and the spatial arrangement of the pores. The technique presented in this work provides a tool to extract information about the spatial distribution of pore sizes from NMR spectra. Such information is difficult to obtain from other characterisation techniques. PMID:25747093

  4. Supersaturation patterns in counter-diffusion crystallisation methods followed by Mach Zehnder interferometry

    NASA Astrophysics Data System (ADS)

    García-Ruiz, J. M.; Novella, M. L.; Otálora, F.

    1999-01-01

    We present experimental observation of the spatio-temporal pattern of supersaturation in counter-diffusion methods. These complex patterns were recorded by dynamical interferometric analysis using a Mach-Zehnder configuration. Tetragonal hen egg white lysozyme crystals were grown inside APCF (advanced protein crystallisation facility) reactors. Salt and protein diffusion profiles were obtained independently by performing duplicated experiments with and without protein in the protein chamber; salt gradients were observed directly while protein concentration profiles are computed from the differences in refractive index between the two experiments. As expected from computer simulations, the time evolution of supersaturation shows a maximum about 45 h after activation (although this value can change as a function of the starting conditions and the geometry of the reactor). Nucleation takes place before this maximum supersaturation is reached. This explains the trend of the growth rate versus time curves for experiments performed within APCF reactors (both on ground and in space) and in capillaries by the gel acupuncture technique. By using very low concentration agarose gel in the protein chamber, sedimentation and buoyancy effects are eliminated so that the effects of gravity on fluid dynamics and hence on the spatio-temporal evolution of supersaturation can be assessed. These results confirm experimentally the predicted behaviour of counter-diffusion systems and support their use in growing large high-quality protein single crystals.

  5. Impaction onto a Glass Slide or Agar versus Impingement into a Liquid for the Collection and Recovery of Airborne Microorganisms

    PubMed Central

    Juozaitis, Arvydas; Willeke, Klaus; Grinshpun, Sergey A.; Donnelly, Jean

    1994-01-01

    To study impaction versus impingement for the collection and recovery of viable airborne microorganisms, three new bioaerosol samplers have been designed and built. They differ from each other by the medium onto which the bioaerosol particles are collected (glass, agar, and liquid) but have the same inlet and collection geometries and the same sampling flow rate. The bioaerosol concentrations recorded by three different collection techniques have been compared with each other: impaction onto a glass slide, impaction onto an agar medium, and impingement into a liquid. It was found that the particle collection efficiency of agar slide impaction depends on the concentration of agar in the collection medium and on the sampling time, when samples are collected on a nonmoving agar slide. Impingement into a liquid showed anomalous behavior with respect to the sampling flow rate. Optimal sampling conditions in which all three new samplers exhibit the same overall sampling efficiency for nonbiological particles have been established. Inlet and collection efficiencies of about 100% have been achieved for all three devices at a sampling flow rate of 10 liters/min. The new agar slide impactor and the new impinger were then used to study the biological factors affecting the overall sampling efficiency. Laboratory experiments on the total recovery of a typical environmental microorganism, Pseudomonas fluorescens ATCC 13525, showed that both sampling methods, impaction and impingement, provided essentially the same total recovery when relatively nonstressed microorganisms were sampled under optimal sampling conditions. Comparison tests of the newly developed bioaerosol samplers with those commercially available showed that the incorporation of our research findings into the design of the new samplers yields better performance data than data from currently available samplers. PMID:16349217

  6. A new method for choosing the computational cell in stochastic reaction–diffusion systems

    PubMed Central

    Kang, Hye-Won; Zheng, Likun; Othmer, Hans G.

    2013-01-01

    How to choose the computational compartment or cell size for the stochastic simulation of a reaction–diffusion system is still an open problem, and a number of criteria have been suggested. A generalized measure of the noise for finite-dimensional systems based on the largest eigenvalue of the covariance matrix of the number of molecules of all species has been suggested as a measure of the overall fluctuations in a multivariate system, and we apply it here to a discretized reaction–diffusion system. We show that for a broad class of first-order reaction networks this measure converges to the square root of the reciprocal of the smallest mean species number in a compartment at the steady state. We show that a suitably re-normalized measure stabilizes as the volume of a cell approaches zero, which leads to a criterion for the maximum volume of the compartments in a computational grid. We then derive a new criterion based on the sensitivity of the entire network, not just of the fastest step, that predicts a grid size that assures that the concentrations of all species converge to a spatially-uniform solution. This criterion applies for all orders of reactions and for reaction rate functions derived from singular perturbation or other reduction methods, and encompasses both diffusing and non-diffusing species. We show that this predicts the maximal allowable volume found in a linear problem, and we illustrate our results with an example motivated by anterior-posterior pattern formation in Drosophila, and with several other examples. PMID:22071651

  7. Pore size distribution of bioresorbable films using a 3-D diffusion NMR method.

    PubMed

    Benjamini, Dan; Elsner, Jonathan J; Zilberman, Meital; Nevo, Uri

    2014-06-01

    Pore size distribution (PSD) within porous biomaterials is an important microstructural feature for assessing their biocompatibility, longevity and drug release kinetics. Scanning electron microscopy (SEM) is the most common method used to obtain the PSD of soft biomaterials. The method is highly invasive and user dependent, since it requires fracturing of the sample and then considers only the small portion that the user had acquired in the image. In the current study we present a novel nuclear magnetic resonance (NMR) method as an alternative method for estimation of PSD in soft porous materials. This noninvasive 3-D diffusion NMR method considers the entire volume of the specimen and eliminates the user's need to choose a specific field of view. Moreover, NMR does not involve exposure to ionizing radiation and can potentially have preclinical and clinical uses. The method was applied on four porous 50/50 poly(dl-lactic-co-glycolic acid) bioresorbable films with different porosities, which were created using the freeze-drying of inverted emulsions technique. We show that the proposed NMR method is able to address the main limitations associated with SEM-based PSD estimations by being non-destructive, depicting the full volume of the specimens and not being dependent on the magnification factor. Upon comparison, both methods yielded a similar PSD in the smaller pore size range (1-25?m), while the NMR-based method provided additional information on the larger pores (25-50?m). PMID:24534719

  8. Operator splitting methods for degenerate convection–diffusion equations II: numerical examples with emphasis on reservoir simulation and sedimentation

    Microsoft Academic Search

    Helge Holden; Kenneth Hvistendahl Karlsen; Knut-Andreas Lie

    2000-01-01

    We present an accurate numerical method for a large class of scalar, strongly degenerate convection–diffusion equations. Important subclasses are hyperbolic conservation laws, porous medium type equations, two-phase reservoir flow equations, and strongly degenerate equations coming from the recent theory of sedimentation–consolidation processes. The method is based on splitting the convective and the diffusive terms. The nonlinear, convective part is solved

  9. Axial Expansion Methods for Solution of the Multi - Neutron Diffusion Equation.

    NASA Astrophysics Data System (ADS)

    Beaklini Filho, Jose Felippe

    The feasibility and practical implementation of axial expansion methods for the solution of the multi-dimensional multigroup neutron diffusion (MGD) equations is investigated. The theoretical examination which is applicable to the general MGD equations in arbitrary geometry includes the derivation of a new weak (reduced) form of the MGD equations by expanding the axial component of the neutron flux in a series of known trial functions and utilizing the Galerkin weighting. A general two-group albedo boundary condition is included in the weak form as a natural boundary condition. The application of different types of trial functions is presented. The practical implementation of the axial expansion method has involved two major tasks: (1) the development of a computer code for solving the MGD equations in two dimensions and (2) the unique implementation of two versions of the three-dimensional (3-D) method within a production level two-dimensional (2-D) MGD code 2DB-UM. Both the 2-D and 3-D computer codes solve the reduced weak form of the diffusion equation with conventional finite difference methods. The 3-D code is intended as a practical engineering tool which can be used for realistic reactor analysis. Both the Fourier sine series and the Legendre polynomial expansion were used as expansion functions for the 3-D application. Numerical results using the 2-D version of the code have indicated the advantage of the Fourier expansion method versus a conventional finite difference method due to an improved convergence rate, which was observed to be quadratic with the number of trial functions. The 3-D implementation has been constrained by the existing iteration methodology contained in the 2DB -UM code and optimum convergence rates similar to the 2 -D method have not been obtained. Recommendations for further improvements of the iteration scheme and the use of alternative axial trial functions are made.

  10. Calculation methods for ventricular diffusion-weighted imaging thermometry: phantom and volunteer studies.

    PubMed

    Sakai, Koji; Yamada, Kei; Sugimoto, Naozo

    2012-02-01

    A method for the measurement of temperature in the lateral ventricle using diffusion-weighted imaging (DWI) has been proposed recently. This method uses predetermined arbitrary thresholds, but a more objective method of calculation would be useful. We therefore compared four different calculation methods, two of which were newly created and did not require predetermined thresholds. A rectangular polyethylene terephthalate bottle (8?×?10?×?28?cm(3)) was filled with heated water (35.0-38.8?°C) and used as a water phantom. The DWI data of 23 healthy subjects (aged 26-75?years; mean?±?standard deviation, 50.13?±?19.1?years) were used for this study. The temperature was calculated using the following equation: T(°C)?=?2256.74/ln(4.39221/D)?-?273.15, where D is the diffusion coefficient. The mean ventricular temperature was calculated by four methods: two thresholding methods and two histogram curve-fitting methods. As a reference, we used the temperature measured at the tympanic membrane, which is known to be approximately 1?°C lower than the brain temperature. The averaged differences in temperature between mercury thermometry and classical predetermined thresholding methods for the water phantom were 0.10?±?0.42 and 0.05?±?0.41?°C, respectively. The histogram curve-fitting methods, however, yielded temperatures a little lower (averaged differences of -0.24?±?0.32 and -0.14?±?0.31?°C, respectively) than mercury thermometry. There was very little difference in temperature between tympanic thermometry and classical predetermined thresholding methods (+0.01 and -0.07?°C, respectively). In humans, however, the histogram curve-fitting methods yielded temperatures approximately 1?°C higher (+1.04?°C and +1.36?°C, respectively), suggesting that temperatures measured in this way more closely approximate the true brain temperature. The histogram curve-fitting methods were more objective and better matched the estimated brain temperature than did classical predetermined thresholding methods, although the standard deviation was wider in the former methods. PMID:21805517

  11. CCMR: Method Development of Dynamic Mass Diffusion Monte Carlo using Lennard-Jones Clusters

    NSDL National Science Digital Library

    Craig, Helen A.

    2007-08-29

    The Lennard-Jones clusters, clusters of inert particles have a long history of being studied. Many algorithms have been proposed and used with a varying level of success from "basin hopping" [1] to “greedy search” [2]. Despite these achievements, the Lennard-Jones potential continues to be a widely studied model. Not only is it a good test case for new particle structure algorithms, but it is still an interesting model that we can yet learn from. In this project we proposed to study these cluster using a method never before attempted: dynamic mass diffusion Monte Carlo.

  12. Sinc-Chebyshev Collocation Method for a Class of Fractional Diffusion-Wave Equations

    PubMed Central

    Mao, Zhi; Xiao, Aiguo; Yu, Zuguo; Shi, Long

    2014-01-01

    This paper is devoted to investigating the numerical solution for a class of fractional diffusion-wave equations with a variable coefficient where the fractional derivatives are described in the Caputo sense. The approach is based on the collocation technique where the shifted Chebyshev polynomials in time and the sinc functions in space are utilized, respectively. The problem is reduced to the solution of a system of linear algebraic equations. Through the numerical example, the procedure is tested and the efficiency of the proposed method is confirmed. PMID:24977177

  13. 3D modeling for solving forward model of no-contact fluorescence diffuse optical tomography method

    NASA Astrophysics Data System (ADS)

    Nouizi, F.; Chabrier, R.; Torregrossa, M.; Poulet, P.

    2009-07-01

    This paper presents detailed computational aspects of a new 3D modeling for solving the direct problem in a no-contact time-resolved Fluorescent Diffuse Optical Tomography (FDOT) method that rely on near-infrared scattered and fluorescent photons to image the optical properties and distribution of fluorescent probes in small laboratory animals. An optical scanner allowing performing in-vivo measurements in no-contact scheme was built in our laboratory and is presented. We use the three-dimensional Finite Element Method (FEM) to solve the coupled diffusion equations of excitation and fluorescence photons in highly scattering objects. The computed results allowed yielding photon density maps and the temporal profiles of photons on the surface of the small animal. Our 3D modeling of propagation of photons in the void space between the surface of the object and the detectors allows calculating the quantity of photons reaching the optodes. Simulations were carried-out on two test objects: a resin cylinder and a mouse phantom. The results demonstrate the potential applications of the method to pre-clinical imaging.

  14. An Ion Diffusion Method for Visualising a Solid-like Water Nanofilm

    PubMed Central

    Wang, Ya; Duan, Zhiguang; Fan, Daidi

    2013-01-01

    A nano-thick solid-like water film on solid surfaces plays an important role in various fields, including biology, materials science, atmospheric chemistry, catalysis and astrophysics. Visualising the water nanofilm has been a challenge due to its dynamic nature and nanoscale thickness. Here we report an ion diffusion method to address this problem using a membrane formed with a BSA-Na2CO3 (BSA, bovine serum albumin) mixture. After a solid-like water nanofilm deposits onto the membrane, Na+ and CO32? ions diffuse into the film to form a solid Na2CO3 phase in its place. Consequently, the morphology of the nanofilm can be visualised by the space filled by the Na2CO3. Using this method, we successfully observed polygon-like, ribbon-like and spot-like nanofilms at 193?K, 253?K and room temperature, respectively. Our method may provide a tool for characterising confined water films ranging from a few nanometres to hundreds of nanometres in thickness. PMID:24336341

  15. An ADI extrapolated Crank-Nicolson orthogonal spline collocation method for nonlinear reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Fernandes, Ryan I.; Fairweather, Graeme

    2012-08-01

    An alternating direction implicit (ADI) orthogonal spline collocation (OSC) method is described for the approximate solution of a class of nonlinear reaction-diffusion systems. Its efficacy is demonstrated on the solution of well-known examples of such systems, specifically the Brusselator, Gray-Scott, Gierer-Meinhardt and Schnakenberg models, and comparisons are made with other numerical techniques considered in the literature. The new ADI method is based on an extrapolated Crank-Nicolson OSC method and is algebraically linear. It is efficient, requiring at each time level only O(N) operations where N is the number of unknowns. Moreover, it is shown to produce approximations which are of optimal global accuracy in various norms, and to possess superconvergence properties.

  16. Modeling of extinction in turbulent diffusion flames by the velocity-dissipation-composition PDF method

    SciTech Connect

    Norris, A.T. (NASA Lewis Research Center, Brookpark, OH (United States). Inst. for Computational Mechanics in Propulsion); Pope, S.B. (Cornell Univ., Ithaca, NY (United States). Sibley School of Mechanical and Aerospace Engineering)

    1995-01-01

    The velocity-dissipation-composition probability density function (pdf) method is used to model a turbulent CO/H[sub 2]/N[sub 2]-air-piloted jet diffusion flame in the regime of extinction. The thermochemistry is modeled by a three-scalar simplified formulation obtained by the intrinsic low-dimensional manifold (ILDM) method. Calculations are performed for five different jet velocities, and the scalar pdfs are compared with experimental data. Overall good agreement is obtained between the calculations and the experimental results, with the only significant difference being the high level of scatter in the experimental data compared with the pdf results: reasons for this difference are discussed. The pdf method is found to predict flame extinction at approximately the same jet velocity as that of the experiment. A small amount of local extinction is observed in the pdf results for the high-jet-velocity cases.

  17. Combination of Boundary Element Method and Finite Element Method in Diffuse Optical Tomography

    Microsoft Academic Search

    Josias Pierrick Elisee; Adam Gibson; Simon Arridge

    2010-01-01

    This paper presents a new numerical method for optical tomography: the combined boundary element\\/finite element method (BEM-FEM), designed to tackle reconstructions in layered turbid media. The BEM-FEM focuses on the region of interest by creating a volume mesh and reconstructing in this region only. All other regions are treated as piecewise constant in a surface-integral approach. We validate the model

  18. Electrochemical methods for the determination of the diffusion coefficient of ionophores and ionophore-ion complexes in plasticized PVC membranes.

    PubMed

    Bodor, Sándor; Zook, Justin M; Lindner, Erno; Tóth, Klára; Gyurcsányi, Róbert E

    2008-05-01

    The diffusion coefficients of active components in ion-selective membranes have a decisive influence on the life-time and detection limit of the respective ion-selective electrodes, as well as influencing the rate of polarization and relaxation processes of electrically perturbed ion sensors. Therefore, the rational design of mass transport controlled ion-selective electrodes with sub-nanomolar detection limits requires reliable data on the diffusion coefficients. We have implemented electrochemical methods for the quantitative assessment of both the diffusion coefficients of free ionophores and ion-ionophore complexes. The diffusion coefficients of the pH-sensitive chromoionophore ETH 5294 and the calcium-selective ionophore ETH 5234 were determined in plasticized PVC membranes with different PVC to plasticizer ratios. The diffusion coefficient of the free chromoionophore determined by a chronoamperometric method was validated with optical methods for a variety of membrane compositions. The calcium-selective ionophore ETH 5234 was used as a model compound to assess the diffusion coefficient of the ion-ionophore complex calculated from the time required for the complexes to cross a freshly prepared membrane during potentiometric ion-breakthrough experiments. The difference between the diffusion coefficients of the free ionophore ETH 5234 and the ion-ionophore complex was found to be significant and correlated well with the geometry of the respective species. PMID:18427685

  19. Characterization of biogenic iron oxides collected by the newly designed liquid culture method using diffusion chambers.

    PubMed

    Kikuchi, S; Makita, H; Takai, K; Yamaguchi, N; Takahashi, Y

    2014-03-01

    We designed a new culture method for neutrophilic iron-oxidizing bacteria using liquid medium (i) to study the formation and mineralogical characteristics of biogenic iron oxides (BIOS) and (ii) to apply BIOS to various scientific and engineering applications. An iron-oxidizing bacterium, Mariprofundus ferrooxydans PV-1(T) (ATCC, BAA-1020), was cultured using a set of diffusion chambers to prepare a broad anoxic-oxic interface, upon which BIOS formation is typically observed in natural environments. Iron oxide precipitates were generated in parallel with bacterial growth. A scanning electron microscopy analysis indicated that the morphological features of the iron oxide precipitates in the medium (in vitro BIOS) were similar to those of BIOS collected from natural deep-sea hydrothermal environments in the Northwest Eifuku Seamount field in the northern Mariana Arc (in situ BIOS). Further chemical speciation of both the in vitro and in situ BIOS was examined with X-ray absorption fine structure (XAFS). A bulk XAFS analysis showed that the minerals in both BIOS were mainly ferrihydrite and oligomeric stages of amorphous iron oxyhydroxides with edge-sharing octahedral linkages. The amount of in vitro BIOS produced with the diffusion-chamber method was greater than those produced previously with other culture methods, such as gel-stabilized gradient and batch liquid culture methods. The larger yields of BIOS produced with the new culture method will allow us to clarify in the future the mineralization mechanisms during bacterial growth and to examine the physicochemical properties of BIOS, such as their adsorption to and coprecipitation with various elements and substances. PMID:24382149

  20. Method and apparatus for determining minority carrier diffusion length in semiconductors

    DOEpatents

    Moore, Arnold R. (Princeton, NJ)

    1984-02-21

    Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon, which has a significantly small minority carrier diffusion length using the constant magnitude surface-photovoltage (SPV) method. Steady or modulated illumination at several wavelengths provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV for each wavelength. A probe electrode immersed in an electrolyte solution containing redox couples (preferably quinhydrone) having an oxidation-reduction potential (E) in the order of +0.6 to -1.65 volts couples the SPV to a measurement system. The redox couple solution functions to create a liquid Schottky barrier at the surface of the material. The Schottky barrier is contacted by merely placing the probe in the solution. The redox solution is placed over and in contact with the material to be tested and light is passed through the solution to generate the SPV. To compensate for colored redox solutions a portion of the redox solution not over the material is also illuminated for determining the color compensated light intensity. Steady red light is also used as an optical bias to reduce deleterious space-charge effects that occur in amorphous silicon.

  1. Method and apparatus for determining minority carrier diffusion length in semiconductors

    DOEpatents

    Moore, Arnold R. (Princeton, NJ)

    1984-01-01

    Method and apparatus are provided for determining the diffusion length of minority carriers in semiconductor material, particularly amorphous silicon which has a significantly small minority carrier diffusion length using the constant magnitude surface-photovoltage (SPV) method. Steady or modulated illumination at several wavelengths provides the light excitation on the surface of the material to generate the SPV. A manually controlled or automatic servo system maintains a constant predetermined value of the SPV for each wavelength. A drop of a transparent electrolyte solution containing redox couples (preferably quinhydrone) having an oxidation-reduction potential (E) in the order of +0.6 to -1.65 volts couples the SPV to a measurement system. The drop of redox couple solution functions to create a liquid Schottky barrier at the surface of the material. Illumination light is passed through a transparent rod supported over the surface and through the drop of transparent electrolyte. The drop is held in the gap between the rod and the surface. Steady red light is also used as an optical bias to reduce deleterious space-charge effects that occur in amorphous silicon.

  2. An artificial nonlinear diffusivity method for supersonic reacting flows with shocks

    NASA Astrophysics Data System (ADS)

    Fiorina, B.; Lele, S. K.

    2007-03-01

    A computational approach for modeling interactions between shocks waves, contact discontinuities and reactions zones with a high-order compact scheme is investigated. To prevent the formation of spurious oscillations around shocks, artificial nonlinear viscosity [A.W. Cook, W.H. Cabot, A high-wavenumber viscosity for high resolution numerical method, J. Comput. Phys. 195 (2004) 594-601] based on high-order derivative of the strain rate tensor is used. To capture temperature and species discontinuities a nonlinear diffusivity based on the entropy gradient is added. It is shown that the damping of 'wiggles' is controlled by the model constants and is largely independent of the mesh size and the shock strength. The same holds for the numerical shock thickness and allows a determination of the L2 error. In the shock tube problem, with fluids of different initial entropy separated by the diaphragm, an artificial diffusivity is required to accurately capture the contact surface. Finally, the method is applied to a shock wave propagating into a medium with non-uniform density/entropy and to a CJ detonation wave. Multi-dimensional formulation of the model is presented and is illustrated by a 2D oblique wave reflection from an inviscid wall, by a 2D supersonic blunt body flow and by a Mach reflection problem.

  3. A new selective blood agar medium for Streptococcus pyogenes and other haemolytic streptococci

    Microsoft Academic Search

    E. J. L. Lowbury; A. Kidson; H. A. Lilly

    1964-01-01

    Horse blood agar containing polymyxin B sulphate, neomycin sulphate, and fusidic acid inhibited the growth of Staph. aureus, Ps. pyocyanea, Proteus mirabilis, E. coli, and Klebsiella pneumoniae but allowed good growth of, and haemolysis by, Str. pyogenes.In a comparison with blood agar, blood 4% agar, and gentian violet blood agar, the selective medium (P.N.F.) yielded a significantly higher proportion of

  4. Application of a Particle Method to the Advection-Diffusion-Reaction Equation

    NASA Astrophysics Data System (ADS)

    Paster, A.; Bolster, D.; Benson, D. A.

    2012-12-01

    A reaction between two chemical species can only happen if molecules collide and react. Thus, the mixing of a system can become a limiting factor in the onset of reaction. Solving for reaction rate in a well-mixed system is typically a straightforward task. However, when incomplete mixing kicks in, obtaining a solution becomes more challenging. Since reaction can only happen in regions where both reactants co-exist, the incomplete mixing may slow down the reaction rate, when compared to a well-mixed system. The effect of incomplete mixing upon reaction is a highly important aspect of various processes in natural and engineered systems, ranging from mineral precipitation in geological formations to groundwater remediation in aquifers. We study a relatively simple system with a bi-molecular irreversible kinetic reaction A+B ? Ø where the underlying transport of reactants is governed by an advection-diffusion equation, and the initial concentrations are given in terms of an average and a perturbation. Such a system does not have an analytical solution to date, even for the zero advection case. We model the system by a Monte Carlo particle tracking method, where particles represent some reactant mass. In this method, diffusion is modeled by a random walk of the particles, and reaction is modeled by annihilation of particles. The probability of the annihilation is proportional to the reaction rate constant and the probability density associated with particle co-location. We study the numerical method in depth, characterizing typical numerical errors and time step restrictions. In particular, we show that the numerical method converges to the advection-diffusion-reaction equation at the limit ?t ?0. We also rigorously derive the relationship between the initial number of particles in the system and the initial concentrations perturbations represented by that number. We then use the particle simulations of zero-advection system to demonstrate the well-known phenomena of incomplete mixing (Ovchinnikov-Zeldovich segregation). The numerical results of the particle-tracking simulations are compared to an approximate analytical solution and the late time discrepancy is explained. We also study, for a two dimensional system, how shear flow effects the reaction rate. We do so since shear flow is the simplest form of a spatially variable advection. For the shear flow system, we find that shear flow leads to better mixing of the system on one hand, and a surprising one dimensional segregation at late times, on the other hand. This is in contrast with zero-advection two-dimensional system, where the late time behavior is characterized by the formation of two-dimensional islands. References (Manuscripts in submission): Paster A., D. Bolster and D.A. Benson. Connecting the dots: application of a particle method to the diffusion-reaction equation. Submitted to Advances in Water Resources. Paster A., D. Bolster and D.A. Benson. Particle Tracking and the Diffusion-Reaction Equation. Submitted to Water Resources Research.

  5. Electrospinning of agar/PVA aqueous solutions and its relation with rheological properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this work, we report the successful fabrication of agar-based nanofibers by an electrospinning technique using water as the solvent media. A tubeless spinneret was attached inside the electrospinning chamber, operated at 50 deg C, to avoid agar gelation. Pure agar solution 1% (w/w) showed inadequ...

  6. Biology and agar composition of Gelidium sesquipedale harvested along the Atlantic coast of Morocco

    Microsoft Academic Search

    Aziza Mouradi-Givernaud; Lalla Amina Hassani; Thierry Givernaud; Yves Lemoine; Oumaima Benharbet

    1999-01-01

    Gelidium sesquipedale (Clem.) Bornet et Thuret is the main raw material used for agar production in Morocco. The biology and biochemistry of this slow growing alga collected monthly over one year has been studied. The agar content varied around 40% of algal dry weight and reached a maximum of 44.5% in November. Agar gel strength was maximum in May and

  7. Mechanical response of agar gel irradiated with Nd:YAG nanosecond laser pulses.

    E-print Network

    Aguilar, Guillermo

    Mechanical response of agar gel irradiated with Nd:YAG nanosecond laser pulses. Francisco G. Pérez transients originated when 6 ns laser pulses are incident on agar gels with varying linear absorption to mechanical effects in agar gel. Real time pressure transients are recorded with PVDF piezoelectric sensors

  8. Classification methods for the differentiation of atypical meningiomas using diffusion and perfusion techniques at 3-T MRI.

    PubMed

    Svolos, Patricia; Tsolaki, Evangelia; Theodorou, Kyriaki; Fountas, Konstantinos; Kapsalaki, Eftychia; Fezoulidis, Ioannis; Tsougos, Ioannis

    2013-01-01

    The purpose was to investigate the contribution of machine learning algorithms using diffusion and perfusion techniques in the differentiation of atypical meningiomas from glioblastomas and metastases. Apparent diffusion coefficient, fractional anisotropy, and relative cerebral blood volume were measured in different tumor regions. Naive Bayes, k-Nearest Neighbor, and Support Vector Machine classifiers were used in the classification procedure. The application of classification methods adds incremental differential diagnostic value. Differentiation is mainly achieved using diffusion metrics, while perfusion measurements may provide significant information for the peritumoral regions. PMID:23849831

  9. Diffusion approximations and domain decomposition method of linear transport equations: Asymptotics and numerics

    NASA Astrophysics Data System (ADS)

    Li, Qin; Lu, Jianfeng; Sun, Weiran

    2015-07-01

    In this paper we construct numerical schemes to approximate linear transport equations with slab geometry by diffusion equations. We treat both the case of pure diffusive scaling and the case where kinetic and diffusive scalings coexist. The diffusion equations and their data are derived from asymptotic and layer analysis which allows general scattering kernels and general data. We apply the half-space solver in [20] to resolve the boundary layer equation and obtain the boundary data for the diffusion equation. The algorithms are validated by numerical experiments and also by error analysis for the pure diffusive scaling case.

  10. CCMR: Sisal Fiber Reinforced Green Composite Using Soy Flour Resin Modified With Sorbitol, Agar and NB416 Microfibers

    NSDL National Science Digital Library

    Khalsa, Amrit

    2009-08-15

    Fully biodegradable green composites were prepared using natural sisal fiber and soy flour (SF) resin modified with sorbitol, agar, and NB416 microfiber. The SF resin modified with agar and NB416 microfibers had a higher Tensile Stress and Young’s Modulus, 8.73 + 0.60 MPa, 232.61 + 25.44 MPa, and 12.15 + 1.53 MPa, 327.87 + 27.62 respectively, compared to the Tensile Stress and Young’s Modulus of the sorbitol modified SF resin. The composites fabricated with sorbitol modified SF resin showed the highest Tensile Stress of 141.45 + 16.72 MPa which was significantly greater than the Tensile Stress of the pure SF resin. Problems arose in preparing the composites with the resins modified with agar and NB416. The method for coating the fibers with the more viscous resin solutions was not an adequate way to prepare the composite. The mechanical properties of the SF resins modified with agar and NB416 microfibers suggests that if the resin was equally dispersed in the composites then the composite properties would be very high. These composites are very useful in replacing some of the petroleum based composites in use today and reducing the amount of plastics in the landfills.

  11. How do microorganisms influence trace element uptake by plants? Screening in an agar model rhizosphere.

    NASA Astrophysics Data System (ADS)

    Marchetti, M.; Robinson, B. H.; Evangelou, M. W. H.; Vachey, A.; Schwitzguebel, J. P.; Bernier-Latmani, R.; Schulin, R.

    2009-04-01

    Trace elements (TE) are essential for humans and plants, but they may be toxic if their concentration is too high. For this reason, the management of TE in soils is very important. In some cases it may be necessary to increase the uptake of nutrients or TE by plants, for example in a biofortification perspective. Conversely, in some other cases TE uptake by plants should be decreased, for instance to avoid heavy metals entering the food chain via edible crops. Microorganisms living in the rhizosphere affect trace element (TE) uptake by plants. However, due to the complexity of this space and the variety of microorganisms that occur there, it is difficult to isolate the effect of any particular strain. To overcome this hurdle, we developed a system in which we grew plants under sterile conditions in agar and inoculated their rhizosphere with a single, well-defined microbial strain. For many years, agar has been used as a growth substrate for microorganisms and plant tissues. It is cheap, easy to use, and can be autoclaved to ensure its sterility. Because of its widespread use, an experiment conducted using this substrate can be reproduced under the same conditions in any laboratory. In contrast to soil, there is little interaction between the trace elements and the agar matrix. There are many studies investigating the influence of microorganisms on TE uptake by plants. However, so far only a small variety of microorganisms has been tested on few plant species. Therefore, the first objective of our research was to develop a method to rapidly screen a large variety of microorganisms on various plant species. Once this goal was achieved, we sought to study the effect of single, well-defined microbial strains on TE uptake by sunflower and wheat. The substrate for plants growth was a 10% agar solution prepared with modified Hoagland's solution and a TE solution containing 1 mg/kg Pb and molar equivalents of Cu, Ni and Zn. The agar solution was autoclaved and poured into sterile, transparent plastic boxes, whose lid was equipped with a filter allowing gas exchanges without contamination by external microorganisms. The seed surface was sterilised and the plants grew one week in agar before their rhizosphere was inoculated with LB broth containing a pure bacterial strain or agar plugs colonized by fungal hyphae. We tested 14 strains, with 5 replicates per treatment and a control where the system was inoculated with sterile LB broth. The plants grew for 2 weeks in a climate chamber and their shoots were analysed for their TEs by ICP-OES. Samples of agar and roots were collected to confirm microbial colonization of the rhizosphere, respectively sterile conditions in the control treatments. Concerning the method development, the plants grew without visible toxicity in all the boxes, and the analysis of root and agar samples indicated that the controls were sterile and the strains inoculated were growing along the roots. More than 90% of the TE and nutrients added to the system were in the liquid fraction of the agar medium, thus available for root uptake. The screening showed that the microorganisms in general decreased TE uptake by wheat and sunflower, although some of them had an opposite effect on the plants. However, with the same plant species, the microorganisms had a consistent effect on all TE tested, i.e. a given single strain caused the same effect (increase or decrease of TE uptake) on all TE tested. In sunflower, 3 microorganisms (Paenibacillus polymyxa, Pythium ultimum and Rhizoctonia solani) decreased Cu and Zn uptake by 50% compared to the control treatment. These three species are common soil microorganisms. All three are known to exude auxin, a phytohormone. This hormone can modify root morphology and physiology and thus may affect TE uptake by plants. R. solani and P. ultimum are root pathogens. Their effect was opposite to what we expected. If roots are damaged, TE should have flooded into the plant and accumulate in the tissues, but this was not the case. One explanation could be the biosorption of TE by these mi

  12. Suggestions regarding thermal diffusivity measurements on pyrolytic graphite and pyrolytic boron nitride by the laser pulse method/sup 1/

    SciTech Connect

    He, G.H.; Di, Z.Q.; Dong, S.Q.; Wei, Z.; Zhang, X.Z.; Hanley, H.J.M.; Cezairliyan, A.

    1986-07-01

    The laser pulse method can be successfully applied to the measurement of thermal diffusivity of isotropic materials subject to some assumptions. For anisotropic materials, this method is applicable to the measurement of principal thermal diffusivity only on the condition that there is no difference in direction between the principal axis and that of the temperature gradient. After analyzing the heat conduction process in an anisotropic solid, it has been shown that large errors in the measurement of thermal diffusivity would exist if the direction of the principal axis deviates inconspicously from that of the temperature gradient. The experimental results of thermal diffusivity of highly oriented pyrolytic graphite (HOPG) samples with various deviation angles have been compared with the analytical results. The laser pulse method is not applicable to measurements on semitransparent pyrolytic boron nitride (PBN). We adopted a two-layer composite sample to measure the thermal diffusivity of PBN in the c direction and a particular graphite-PBN composite sample has been prepared which has a very low thermal resistance at the interface. The thermal diffusivity and thermal conductivity of PG (below 2300/sup 0/C) and PBN (below 1000/sup 0/C) are given.

  13. Basic principles for the development of a common standardised method for determining the radon diffusion coefficient in waterproofing materials.

    PubMed

    Jiránek, Martin; Rovenská, Kate?ina

    2012-04-01

    Paper presents the principles for unified test methods for determining the radon diffusion coefficient in waterproof materials in order to increase the accuracy, repeatability and reproducibility of the results. We consider this very important, because an assessment of the radon diffusion coefficient is required by several national technical standards when waterproofing acts as a radon-proof membrane. The requirements for key parameters for one test method performed under non-stationary conditions and for two methods performed under stationary conditions are described in this paper. PMID:22245288

  14. High temperature diffusion chromizing as a successful method for CVD-diamond coating of steel

    Microsoft Academic Search

    S. Schwarz; Y. Musayev; S. M. Rosiwal; C. Schaufler; R. F. Singer; H. Meerkamm

    2002-01-01

    Using chromium carbide intermediate layers, generated by a novel diffusion process, well adherent CVD-diamond coatings were deposited onto large surfaces of 41Cr4 steel substrates. The chromium carbide intermediate layers feature excellent barrier properties against the diffusion of iron from the substrate and against the diffusion of carbon from the gas phase during the diamond deposition. The diamond coatings show also

  15. A modified method for diffusive monitoring of 3-ethenylpyridine as a specific marker of environmental tobacco smoke

    NASA Astrophysics Data System (ADS)

    Kuusimäki, Leea; Peltonen, Kimmo; Vainiotalo, Sinikka

    A previously introduced method for monitoring environmental tobacco smoke (ETS) was further validated. The method is based on diffusive sampling of a vapour-phase marker, 3-ethenylpyridine (3-EP), with 3 M passive monitors (type 3500). Experiments were done in a dynamic chamber to assess diffusive sampling in comparison with active sampling in charcoal tubes or XAD-4 tubes. The sampling rate for 3-EP collected on the diffusive sampler was 23.1±0.6 mL min -1. The relative standard deviation for parallel samples ( n=6) ranged from 4% to 14% among experiments ( n=9). No marked reverse diffusion of 3-EP was detected nor any significant effect of relative humidity at 20%, 50% or 80%. The diffusive sampling of 3-EP was validated in field measurements in 15 restaurants in comparison with 3-EP and nicotine measurements using active sampling. The 3-EP concentration in restaurants ranged from 0.01 to 9.8 ?g m -3, and the uptake rate for 3-EP based on 92 parallel samples was 24.0±0.4 mL min -1. A linear correlation ( r=0.98) was observed between 3-EP and nicotine concentrations, the average ratio of 3-EP to nicotine being 1:8. Active sampling of 3-EP and nicotine in charcoal tubes provided more reliable results than sampling in XAD-4 tubes. All samples were analysed using gas chromatography-mass spectrometry after elution with a 15% solution of pyridine in toluene. For nicotine, the limit of quantification of the charcoal tube method was 4 ng per sample, corresponding to 0.04 ?g m -3 for an air sample of 96 L. For 3-EP, the limit of quantification of the diffusive method was 0.5-1.0 ng per sample, corresponding to 0.04-0.09 ?g m -3 for 8 h sampling. The diffusive method proved suitable for ETS monitoring, even at low levels of ETS.

  16. Simulation of a diffusion flame in turbulent mixing layer by the flame hole dynamics model with level-set method

    Microsoft Academic Search

    J. Kim; S. H. Chung; K. Y. Ahn; J. S. Kim

    2006-01-01

    The partial quenching structure of diffusion flames, arising from the phenomenon of turbulent flame lift off, is investigated in a turbulent mixing layer by the method of flame hole dynamics. Modification of the flame hole dynamics by including the level-set method is specifically aimed to properly take into account the effect of slow flame-edge response near the crossover scalar dissipation

  17. Folding a 20 amino acid ?? peptide with the diffusion process-controlled Monte Carlo method

    NASA Astrophysics Data System (ADS)

    Derreumaux, Philippe

    1997-08-01

    In this study we report on the application of the diffusion process-controlled Monte Carlo method to a 20 amino acid ?? peptide (Ac-E-T-Q-A-A-L-L-A-A-Q-K-A-Y-H-P-M-T-M-T-G-Am). The polypeptide chain is represented by a set of 126 particles, the side chains are modeled by spheres, and the backbone dihedral angles ? and ? of each of the amino acid residue are essentially restricted to a set of ten high probability regions, although the whole ?-? space may be visited in the course of the simulation. The method differs from other off-lattice Monte Carlo methods, in that the escape time from one accepted conformation to the next is estimated and limited at each iteration. The conformations are evaluated on the basis of pairwise nonbonded side chain energies derived from statistical distributions of contacts in real proteins and a simple main chain hydrogen bonding potential. As a result of four simulations starting from random extended conformations and one starting from a structure consistent with NMR data, the lowest-energy conformation (i.e., the ?? fold) is detected in ˜103 Monte Carlo steps, although the estimated probability of getting the ?? motif is ˜10-12. The predicted conformations deviate by 3.0 Å rms from a model structure compatible with the experimental results. In this work further evidence is provided that this method is useful in determining the lowest-energy region of medium-size polypeptide chains.

  18. InP synthesis by the synthesis, solute diffusion (SSD) method using glassy-carbon crucibles

    SciTech Connect

    Miskys, C.R.; Oliveira, C.E.M. de; Carvalho, M.M.G. de [UNICAMP-IFGW-DFA-LPD, Campinas, Sao Paulo (Brazil)

    1996-12-31

    An Indium Phosphide (InP) Synthesis system by the Synthesis, Solute Diffusion (SSD) method has been built. It provides high purity InP charges with low carrier densities (3 {times} 10{sup 14} to 2 {times} 10{sup 15} cm{sup {minus}3}) to be used as starting material for InP single-crystal Liquid Encapsulated Czochralski (LEC) growth. Glassy-carbon is a refractory material with low vapor pressure that can be moulded in various forms and sizes. Indeed the glassy-carbon crucible is reusable after the synthesis because InP does not stick to its walls. Preliminary electrical characteristics measurements showed residual carrier concentration below 3 {times} 10{sup 15} cm{sup {minus}3}. These results are comparable with those achieved utilizing quartz crucibles. The features denoted makes glassy-carbon an interesting alternative in comparison with quartz and PBN crucibles.

  19. A systematic investigation of reflectance diffuse optical tomography using nonlinear reconstruction methods and continuous wave measurements

    PubMed Central

    Yuan, Zhen; Zhang, Jiang; Wang, Xiaodong; Li, Changqing

    2014-01-01

    We conducted a systematic investigation of the reflectance diffuse optical tomography using continuous wave (CW) measurements and nonlinear reconstruction algorithms. We illustrated and suggested how to fine-tune the nonlinear reconstruction methods in order to optimize target localization with depth-adaptive regularizations, reduce boundary noises in the reconstructed images using a logarithm based objective function, improve reconstruction quantification using transport models, and resolve crosstalk problems between absorption and scattering contrasts with the CW reflectance measurements. The upgraded nonlinear reconstruction algorithms were evaluated with a series of numerical and experimental tests, which show the potentials of the proposed approaches for imaging both absorption and scattering contrasts in the deep targets with enhanced image quality. PMID:25401014

  20. A high throughput and efficient visualization method for diffusion tensor imaging of human brain white matter employing diffusion-map space.

    PubMed

    Aarabi, Mohammad Hadi; Kazerooni, Anahita Fathi; Salehi, Narges; Rad, Hamidreza Saligheh

    2014-01-01

    Diffusion tensor imaging (DTI) possesses high dimension and complex structure, so that detecting available pattern information and its analysis based on conventional linear statistics and classification methods become inefficient. In order to facilitate classification, segmentation, compression or visualization of the data, dimension reduction is far-reaching. There have been many approaches proposed for this purpose, which mostly rely on complex low dimensional manifold embedding of the high-dimensional space. Dimension reduction is commonly applicable through linear algorithms, such as principal component analysis and multi-dimensional scaling; however, they are not able to deal with complex and high dimensional data. In this light, nonlinear algorithms with the capability to preserve the distance of high dimensional data have been developed. The purpose of this paper is to propose a new method for meaningful visualization of brain white matter using diffusion tensor data to map the 6-dimensional tensor to a three dimensional space employing Markov random walk and diffusion distance algorithms, leading to a new distance-preserving map for the DTI data with lower dimension and higher throughput information. PMID:25570465

  1. Sediment transport via needle ice: a new method for diffusive transport on laboratory-scale hillslopes

    NASA Astrophysics Data System (ADS)

    Sweeney, K. E.; Roering, J. J.; Rempel, A. W.

    2012-12-01

    Convex hilltops formed by diffusive sediment transport are a fundamental feature of soil-mantled landscapes worldwide. Additionally, the competition and interaction between hillslopes and valleys control basic topographic metrics, such as relief, drainage density, and breaks in slope-area scaling. Despite recent progress in erosive landscape experiments, no published work has explored the competition of hillslope diffusion and channel advection experimentally. Here, we present preliminary findings on the plausibility of needle ice driven frost creep as a mechanism for laboratory hillslope transport of wet sediment. In nature, needle ice is a diurnal form of ice segregation, whereby liquid water held in sediment pore space is driven upward toward a near-surface freezing front by a temperature-controlled liquid pressure gradient. As needles grow perpendicular to the surface, sediment is incorporated in the growing needle ice by temperature perturbations and associated downward shifts in the freezing front. Sediment then moves downslope due to melting or sublimation of the ice needles. We constructed a slope of saturated sediment in a freezer to constrain the temperature, grain size, and soil moisture limits on laboratory needle ice growth and sediment transport. Surficial sediment transport is measured during experimentation by tracking the movement of colored grains. Additionally, at the end of each run we measure depth-dependent sediment transport by taking slices of the experimental slope and observing the displacement of buried columns of colored grains. In agreement with past work, we find that with temperatures just below freezing, soil moisture above 35%, and silt-sized sediment, the moisture migration induced by freezing releases enough latent heat to maintain the location of the freezing front and encourage needle ice growth. Our experiments demonstrate that the amount of sediment incorporated during needle growth, i.e., the transport efficiency, can be controlled by systematically varying the frequency and/or duration of temperature perturbations. The rate of sediment transport on soil mantled hillslopes depends on topographic slope and transport occurs in an "active layer", i.e., the soil mantle. We show that needle ice transports sediment diffusively and has great potential as a method for laboratory simulation of a soil-mantled hillslope since transport is confined to a layer only a few millimeters from the surface. Furthermore, while past experiments are limited to modeling landscape response to precipitation or uplift, our method to systematically control the vigor of hillslope processes will enable us to model potential climate-driven changes in hillslope transport efficiency.

  2. Growth characteristics of Bacillus anthracis compared to other Bacillus spp. on the selective nutrient media Anthrax Blood Agar ® and Cereus Ident Agar ®

    Microsoft Academic Search

    Herbert Tomaso; Carsten Bartling; Sascha Al Dahouk; Ralf M. Hagen; Holger C. Scholz; Wolfgang Beyer; Heinrich Neubauer

    2006-01-01

    Anthrax Blood Agar® (ABA) and Cereus Ident Agar® (CEI) were evaluated as selective growth media for the isolation of Bacillus anthracis using 92 B. anthracis and 132 other Bacillus strains from 30 species. The positive predictive values for the identification of B. anthracis on ABA, CEI, and the combination of both were 72%, 71%, and 90%, respectively. Thus, less than

  3. Comparison of Oxford Agar, PALCAM and Listeria monocytogenes Blood Agar for the recovery of L. monocytogenes from foods and environmental samples

    Microsoft Academic Search

    Marlene Pinto; Solange Burri; Cristina Mena; Gonçalo Almeida; Lu??sa Carneiro; Paula Teixeira; Paul A Gibbs

    2001-01-01

    This work had as the main objective a comparison between Listeria monocytogenes Blood Agar (LMBA) and the conventional selective agar media, Oxford and PALCAM, relative to its efficacy in the detection of L. monocytogenes in naturally contaminated food and environmental samples. 173 environmental samples and 272 samples of foods were analysed. A higher sensitivity for detection of L. monocytogenes was

  4. Embryo Staining Protocol. 1. Keep the flies for egg laying on agar sucrose plates (1.5% agar, 1.5% sucrose)

    E-print Network

    Embryo Staining Protocol. 1. Keep the flies for egg laying on agar sucrose plates (1.5% agar, 1. With a brush and distilled water transfer the embryos into an egg basket. (egg baskets can be made by cutting the embryos in distilled water. 5. Soak in 50% bleach for 2 minutes. This removes the chorion. Look under

  5. Diffusion approximation-based simulation of stochastic ion channels: which method to use?

    PubMed Central

    Pezo, Danilo; Soudry, Daniel; Orio, Patricio

    2014-01-01

    To study the effects of stochastic ion channel fluctuations on neural dynamics, several numerical implementation methods have been proposed. Gillespie's method for Markov Chains (MC) simulation is highly accurate, yet it becomes computationally intensive in the regime of a high number of channels. Many recent works aim to speed simulation time using the Langevin-based Diffusion Approximation (DA). Under this common theoretical approach, each implementation differs in how it handles various numerical difficulties—such as bounding of state variables to [0,1]. Here we review and test a set of the most recently published DA implementations (Goldwyn et al., 2011; Linaro et al., 2011; Dangerfield et al., 2012; Orio and Soudry, 2012; Schmandt and Galán, 2012; Güler, 2013; Huang et al., 2013a), comparing all of them in a set of numerical simulations that assess numerical accuracy and computational efficiency on three different models: (1) the original Hodgkin and Huxley model, (2) a model with faster sodium channels, and (3) a multi-compartmental model inspired in granular cells. We conclude that for a low number of channels (usually below 1000 per simulated compartment) one should use MC—which is the fastest and most accurate method. For a high number of channels, we recommend using the method by Orio and Soudry (2012), possibly combined with the method by Schmandt and Galán (2012) for increased speed and slightly reduced accuracy. Consequently, MC modeling may be the best method for detailed multicompartment neuron models—in which a model neuron with many thousands of channels is segmented into many compartments with a few hundred channels. PMID:25404914

  6. An implicit high-order hybridizable discontinuous Galerkin method for nonlinear convection-diffusion equations

    NASA Astrophysics Data System (ADS)

    Nguyen, N. C.; Peraire, J.; Cockburn, B.

    2009-12-01

    In this paper, we present hybridizable discontinuous Galerkin methods for the numerical solution of steady and time-dependent nonlinear convection-diffusion equations. The methods are devised by expressing the approximate scalar variable and corresponding flux in terms of an approximate trace of the scalar variable and then explicitly enforcing the jump condition of the numerical fluxes across the element boundary. Applying the Newton-Raphson procedure and the hybridization technique, we obtain a global equation system solely in terms of the approximate trace of the scalar variable at every Newton iteration. The high number of globally coupled degrees of freedom in the discontinuous Galerkin approximation is therefore significantly reduced. We then extend the method to time-dependent problems by approximating the time derivative by means of backward difference formulae. When the time-marching method is (p+1)th order accurate and when polynomials of degree p?0 are used to represent the scalar variable, each component of the flux and the approximate trace, we observe that the approximations for the scalar variable and the flux converge with the optimal order of p+1 in the L2-norm. Finally, we apply element-by-element postprocessing schemes to obtain new approximations of the flux and the scalar variable. The new approximate flux, which has a continuous interelement normal component, is shown to converge with order p+1 in the L2-norm. The new approximate scalar variable is shown to converge with order p+2 in the L2-norm. The postprocessing is performed at the element level and is thus much less expensive than the solution procedure. For the time-dependent case, the postprocessing does not need to be applied at each time step but only at the times for which an enhanced solution is required. Extensive numerical results are provided to demonstrate the performance of the present method.

  7. Oxygen diffusion-concentration product in rhodopsin as observed by a pulse ESR spin labeling method.

    PubMed Central

    Subczynski, W K; Renk, G E; Crouch, R K; Hyde, J S; Kusumi, A

    1992-01-01

    Permeation of molecular oxygen in rhodopsin, an integral membrane protein, has been investigated by monitoring the bimolecular collision rate between molecular oxygen and the nitroxide spin label using a pulse electron spin resonance (ESR) T1 method. Rhodopsin was labeled by regeneration with the spin-labeled 9-cis retinal analogue in which the beta-ionone ring of retinal is replaced by the nitroxide tetramethyl-oxypyrrolidine ring. The bimolecular collision rate was evaluated in terms of an experimental parameter W(x), defined as T1(-1)(air,x)--T1(-1)(N2,x) where T1's are the spin-lattice relaxation times of the nitroxide in samples equilibrated with atmospheric air and nitrogen respectively, which is proportional to the product of local oxygen concentration and local diffusion coefficient (transport). W-values at the beta-ionone binding site in spin-labeled rhodopsin are in the range of 0.02-0.13 microseconds-1, which are 10-60 times smaller than W's in water and 1.1-20 times smaller than in model membranes in the gel phase, indicating that membrane proteins create significant permeation resistance to transport of molecular oxygen inside and across the membrane. W(thereby the oxygen diffusion-concentration product) is larger in the meta II-enriched sample than in rhodopsin, indicating light-induced conformational changes of opsin around the beta-ionone binding site. W decreases with increase of temperature for both rhodopsin and meta II-enriched samples, suggesting that temperature-induced conformational changes take place in both samples. These changes were not observable using conventional ESR spectroscopy. It is concluded that W is a sensitive monitor of conformational changes of proteins. PMID:1330032

  8. Use of the Chrome Azurol S Agar Plate Technique To Differentiate Strains and Field Isolates of Rhizobium leguminosarum biovar trifolii

    PubMed Central

    Ames-Gottfred, N. P.; Christie, B. R.; Jordan, D. C.

    1989-01-01

    Identification of Rhizobium and Bradyrhizobium strains and especially of indigenous isolates continues to be one of the major difficulties associated with competition studies. Because there is no universally accepted method, the method of choice depends on preference, experience, and equipment. Here, an agar plate technique was used to distinguish strains and field isolates of Rhizobium leguminosarum biovar trifolii to provide a basis for identifying nodule occupants in further competition studies. A rapid plate technique, based on differential growth characteristics, complements other techniques such as serological reactions, particularly when antisera cross-react with nonhomologous strains. The technique involves culturing strains and isolates on chrome azurol S agar. Although similar responses were observed among some strains, the response was highly reproducible and was considered an ideal complementary technique used in conjunction with serological procedures. Strains with similar responses could often be differentiated by varying media components, such as the source of carbon. Images PMID:16347877

  9. A finite elements method to solve the Bloch–Torrey equation applied to diffusion magnetic resonance imaging

    SciTech Connect

    Nguyen, Dang Van [INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau Cedex (France); NeuroSpin, Bat145, Point Courrier 156, CEA Saclay Center, 91191 Gif-sur-Yvette Cedex (France); Li, Jing-Rebecca, E-mail: jingrebecca.li@inria.fr [INRIA Saclay, Equipe DEFI, CMAP, Ecole Polytechnique, Route de Saclay, 91128 Palaiseau Cedex (France); NeuroSpin, Bat145, Point Courrier 156, CEA Saclay Center, 91191 Gif-sur-Yvette Cedex (France); Grebenkov, Denis [Laboratoire de Physique de la Matiere Condensee, CNRS, Ecole Polytechnique, 91128 Palaiseau Cedex (France); Le Bihan, Denis [NeuroSpin, Bat145, Point Courrier 156, CEA Saclay Center, 91191 Gif-sur-Yvette Cedex (France)

    2014-04-15

    The complex transverse water proton magnetization subject to diffusion-encoding magnetic field gradient pulses in a heterogeneous medium can be modeled by the multiple compartment Bloch–Torrey partial differential equation (PDE). In addition, steady-state Laplace PDEs can be formulated to produce the homogenized diffusion tensor that describes the diffusion characteristics of the medium in the long time limit. In spatial domains that model biological tissues at the cellular level, these two types of PDEs have to be completed with permeability conditions on the cellular interfaces. To solve these PDEs, we implemented a finite elements method that allows jumps in the solution at the cell interfaces by using double nodes. Using a transformation of the Bloch–Torrey PDE we reduced oscillations in the searched-for solution and simplified the implementation of the boundary conditions. The spatial discretization was then coupled to the adaptive explicit Runge–Kutta–Chebyshev time-stepping method. Our proposed method is second order accurate in space and second order accurate in time. We implemented this method on the FEniCS C++ platform and show time and spatial convergence results. Finally, this method is applied to study some relevant questions in diffusion MRI.

  10. FAST MONTE CARLO SIMULATION METHODS FOR BIOLOGICAL REACTION-DIFFUSION SYSTEMS IN SOLUTION AND ON SURFACES

    PubMed Central

    KERR, REX A.; BARTOL, THOMAS M.; KAMINSKY, BORIS; DITTRICH, MARKUS; CHANG, JEN-CHIEN JACK; BADEN, SCOTT B.; SEJNOWSKI, TERRENCE J.; STILES, JOEL R.

    2010-01-01

    Many important physiological processes operate at time and space scales far beyond those accessible to atom-realistic simulations, and yet discrete stochastic rather than continuum methods may best represent finite numbers of molecules interacting in complex cellular spaces. We describe and validate new tools and algorithms developed for a new version of the MCell simulation program (MCell3), which supports generalized Monte Carlo modeling of diffusion and chemical reaction in solution, on surfaces representing membranes, and combinations thereof. A new syntax for describing the spatial directionality of surface reactions is introduced, along with optimizations and algorithms that can substantially reduce computational costs (e.g., event scheduling, variable time and space steps). Examples for simple reactions in simple spaces are validated by comparison to analytic solutions. Thus we show how spatially realistic Monte Carlo simulations of biological systems can be far more cost-effective than often is assumed, and provide a level of accuracy and insight beyond that of continuum methods. PMID:20151023

  11. [Two cases of Paragonimiasis westermani in a Chinese family diagnosed with the Ouchterlony double diffusion method].

    PubMed

    Hoshina, Tokio; Tamura, Kumi; Kawano, Shinji; Kato, Tetsurou; Sato, Fumiya; Horino, Tetsuya; Nakazawa, Yasushi; Yosikawa, Kouji; Yoshida, Masaki; Kumagai, Masahiro; Hori, Seiji

    2014-11-01

    We report two cases of Paragonimus westermani infection in a Chinese family in Japan. A 41-year-old husband and his 40-year-old wife were infected with P. westermani after consuming a homemade Chinese traditional "Drunken Crab." They were a family with two children who had lived in Japan for 19 years. The crabs were Eriocheir japonica sent from the Kyusyu area that they had pickled at home with soy sauce and Chinese liquor for 5 days. Their children did not eat any of the crabs. One month after consuming the crabs, the husband came to our outpatient clinic with fever and chest pain and his wife also presented with a persistent cough. Both patients had a high peripheral blood eosinophil count (husband:18,900/?L, wife:10,600/?L) with pulmonary effusion, nodular shadow, and pneumothorax in chest X-ray findings. Paragonimiasis was suspected from the episode of consuming the crabs. No parasite eggs were seen in their sputum and stool samples. A multiple-dot ELISA was performed with the sera to screen for parasitic infections, but the result was only weakly positive for P. westermani antigen in the husband and a slightly positive reaction in the wife. The diagnosis of P. westermani was achieved with the double diffusion Ouchterlony method using P. westermani antigen and P. miyazakii antigen. Praziquantel administration for three days improved the symptoms in both patients. The Ouchterlony method proved useful in diagnosing paragonimiasis in these cases. PMID:25764810

  12. Towards Correlated Sampling for the Fixed-Node Diffusion Quantum Monte Carlo Method

    NASA Astrophysics Data System (ADS)

    Berner, Raphael; Petz, René; Lüchow, Arne

    2014-07-01

    Most methods of quantum chemistry calculate total energies rather than directly the energy differences that are of interest to chemists. In the case of statistical methods like quantum Monte Carlo the statistical errors in the absolute values need to be considerably smaller than their difference. The calculation of small energy differences is therefore particularly time consuming. Correlated sampling techniques provide the possibility to compute directly energy differences by simulating the underlying systems with the same stochastic process. The smaller the energy difference the smaller its statistical error. Correlated sampling is well established in variational quantum Monte Carlo, but it is much more difficult to implement in diffusion quantum Monte Carlo because of the fixed node approximation. A correlated sampling formalism and a corresponding algorithm based on a transformed Schrödinger equation having the form of a Kolmogorov's backward equation is derived. The numerical verification of the presented algorithm is given for the harmonic oscillator. The extension of the algorithm to electron structure calculations is discussed.

  13. Bifurcation analysis of brown tide by reaction-diffusion equation using finite element method

    SciTech Connect

    Kawahara, Mutsuto; Ding, Yan [Chuo Univ., Tokyo (Japan)] [Chuo Univ., Tokyo (Japan)

    1997-03-01

    In this paper, we analyze the bifurcation of a biodynamics system in a two-dimensional domain by virtue of reaction-diffusion equations. The discretization method in space is the finite element method. The computational algorithm for an eigenspectrum is described in detail. On the basis of an analysis of eigenspectra according to Helmholtz`s equation, the discrete spectra in regards to the physical variables are numerically obtained in two-dimensional space. In order to investigate this mathematical model in regards to its practical use, we analyzed the stability of two cases, i.e., hydranth regeneration in the marine hydroid Tubularia and a brown tide in a harbor in Japan. By evaluating the stability according to the linearized stability definition, the critical parameters for outbreaks of brown tide can be theoretically determined. In addition, results for the linear combination of eigenspectrum coincide with the distribution of the observed brown tide. Its periodic characteristic was also verified. 10 refs., 8 figs., 5 tabs.

  14. Mean Apparent Propagator (MAP) MRI: a novel diffusion imaging method for mapping tissue microstructure

    PubMed Central

    Özarslan, Evren; Koay, Cheng Guan; Shepherd, Timothy M.; Komlosh, Michal E.; ?rfano?lu, M. Okan; Pierpaoli, Carlo; Basser, Peter J.

    2014-01-01

    Diffusion-weighted magnetic resonance (MR) signals reflect information about underlying tissue microstructure and cytoarchitecture. We propose a quantitative, efficient, and robust mathematical and physical framework for representing diffusion-weighted MR imaging (MRI) data obtained in “q-space,” and the corresponding “mean apparent propagator (MAP)” describing molecular displacements in “r-space.” We also define and map novel quantitative descriptors of diffusion that can be computed robustly using this MAP-MRI framework. We describe efficient analytical representation of the three-dimensional q-space MR signal in a series expansion of basis functions that accurately describes diffusion in many complex geometries. The lowest order term in this expansion contains a diffusion tensor that characterizes the Gaussian displacement distribution, equivalent to diffusion tensor MRI (DTI). Inclusion of higher order terms enables the reconstruction of the true average propagator whose projection onto the unit “displacement” sphere provides an orientational distribution function (ODF) that contains only the orientational dependence of the diffusion process. The representation characterizes novel features of diffusion anisotropy and the non-Gaussian character of the three-dimensional diffusion process. Other important measures this representation provides include the return-to-the-origin probability (RTOP), and its variants for diffusion in one- and two-dimensions—the return-to-the-plane probability (RTPP), and the return-to-the-axis probability (RTAP), respectively. These zero net displacement probabilities measure the mean compartment (pore) volume and cross-sectional area in distributions of isolated pores irrespective of the pore shape. MAP-MRI represents a new comprehensive framework to model the three-dimensional q-space signal and transform it into diffusion propagators. Experiments on an excised marmoset brain specimen demonstrate that MAP-MRI provides several novel, quantifiable parameters that capture previously obscured intrinsic features of nervous tissue microstructure. This should prove helpful for investigating the functional organization of normal and pathologic nervous tissue. PMID:23587694

  15. Comparison of microbial adherence to antiseptic and antibiotic central venous catheters using a novel agar subcutaneous infection model

    Microsoft Academic Search

    Trupti A. Gaonkar; Shanta M. Modak

    An agar subcutaneous infection model (agar model), which simulates the rat subcutaneous infection model (rat model), was developed to assess the ability of antimicrobial catheters to resist microbial colonization. The catheters were implanted in the agar and rat models and the insertion sites were infected immediately or on day 7, 14 or 21 post-implantation. The catheters implanted in the agar

  16. A finite analytic method for solving the 2-D time-dependent advection diffusion equation with time-invariant coefficients

    NASA Astrophysics Data System (ADS)

    Lowry, Thomas; Li, Shu-Guang

    2005-02-01

    Difficulty in solving the transient advection-diffusion equation (ADE) stems from the relationship between the advection derivatives and the time derivative. For a solution method to be viable, it must account for this relationship by being accurate in both space and time. This research presents a unique method for solving the time-dependent ADE that does not discretize the derivative terms but rather solves the equation analytically in the space-time domain. The method is computationally efficient and numerically accurate and addresses the common limitations of numerical dispersion and spurious oscillations that can be prevalent in other solution methods. The method is based on the improved finite analytic (IFA) solution method [Lowry TS, Li S-G. A characteristic based finite analytic method for solving the two-dimensional steady-state advection-diffusion equation. Water Resour Res 38 (7), 10.1029/2001WR000518] in space coupled with a Laplace transformation in time. In this way, the method has no Courant condition and maintains accuracy in space and time, performing well even at high Peclet numbers. The method is compared to a hybrid method of characteristics, a random walk particle tracking method, and an Eulerian-Lagrangian Localized Adjoint Method using various degrees of flow-field heterogeneity across multiple Peclet numbers. Results show the IFALT method to be computationally more efficient while producing similar or better accuracy than the other methods.

  17. Simultaneous Determination of Thermal Conductivity and Thermal Diffusivity of Food and Agricultural Materials Using a Transient Plane-Source Method

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thermal conductivity and thermal diffusivity are two important physical properties essential for designing any food engineering processes. Recently a new transient plane-source method was developed to measure a variety of materials, but its application in foods has not been documented. Therefore, ...

  18. Experimental Method Development for Estimating Solid-phase Diffusion Coefficients and Material/Air Partition Coefficients of SVOCs

    EPA Science Inventory

    The solid-phase diffusion coefficient (Dm) and material-air partition coefficient (Kma) are key parameters for characterizing the sources and transport of semivolatile organic compounds (SVOCs) in the indoor environment. In this work, a new experimental method was developed to es...

  19. An asymptotically fitted finite element method for convection dominated convection-diffusion-reaction problems

    NASA Astrophysics Data System (ADS)

    Lube, G.

    The convergence of an asymptotically fitted variant (SDFEM-A) of the streamline-diffusion type FEMs (SDFEM) for singularly perturbed elliptical boundary value modeling of convection-dominated convection-diffusion problems is presented. It is concluded that the SDFEM-A approximates boundary layers better than SDFEM. Global error and local estimates for the variant are given, and numerical examples are presented.

  20. Diffusion chromizing using a method of applying a plasma coating to a steel surface

    Microsoft Academic Search

    I. Ya. Ryazantsev; I. A. Goncharenko; N. G. Filatov; V. V. Kazanskii; V. T. Seroshtan

    1986-01-01

    1.Application to a steel billet surface of a plasma coating as an initial chromizing stage makes it possible to carry out diffusion annealing in normal flame furnaces without using special protective atmospheres.2.A diffusion layer forms at the steel billet surface in accordance with rules for equilibrium phase transformation at the annealing temperature, and it has increased corrosion resistance even on

  1. A Simple Educational Method for the Measurement of Liquid Binary Diffusivities

    ERIC Educational Resources Information Center

    Rice, Nicholas P.; de Beer, Martin P.; Williamson, Mark E.

    2014-01-01

    A simple low-cost experiment has been developed for the measurement of the binary diffusion coefficients of liquid substances. The experiment is suitable for demonstrating molecular diffusion to small or large undergraduate classes in chemistry or chemical engineering. Students use a cell phone camera in conjunction with open-source image…

  2. Laboratory evaluation of different agar media for isolation of carbapenem-resistant Acinetobacter spp.

    PubMed

    Moran-Gilad, J; Adler, A; Schwartz, D; Navon-Venezia, S; Carmeli, Y

    2014-11-01

    The optimal method for surveillance of carbapenem-resistant Acinetobacter spp. (CRAB) is unknown. A collection of CRAB strains (n?=?42), carbapenem-susceptible strains (CSAB), and non-Acinetobacter strains (n?=?18) was used to evaluate six laboratory surveillance methods: MacConkey (MAC), MAC?+?1 ?g/ml imipenem (MAC-IPM), minimal salts agar?+?1 % acetate (MSA), MSA with IPM disk (MSA-IPM), CHROMagarKPC, and CHROMagar Acinetobacter with CR102 (CHROMAcineto). CHROMAcineto was 100 % sensitive and specific. CHROMagarKPC and MAC-IPM were highly sensitive (>95 %), but their specificity was substantially hampered by the breakthrough growth of CSAB. MSA was unsuitable for CRAB detection. CHROMAcineto is a promising medium for CRAB detection and warrants further clinical evaluation. PMID:24865248

  3. Towards automated high-throughput screening of C. elegans on agar

    E-print Network

    Kabra, Mayank; O'Rourke, Eyleen J; Xie, Xin; Ljosa, Vebjorn; Jones, Thouis R; Ausubel, Frederick M; Ruvkun, Gary; Carpenter, Anne E; Freund, Yoav

    2010-01-01

    High-throughput screening (HTS) using model organisms is a promising method to identify a small number of genes or drugs potentially relevant to human biology or disease. In HTS experiments, robots and computers do a significant portion of the experimental work. However, one remaining major bottleneck is the manual analysis of experimental results, which is commonly in the form of microscopy images. This manual inspection is labor intensive, slow and subjective. Here we report our progress towards applying computer vision and machine learning methods to analyze HTS experiments that use Caenorhabditis elegans (C. elegans) worms grown on agar. Our main contribution is a robust segmentation algorithm for separating the worms from the background using brightfield images. We also show that by combining the output of this segmentation algorithm with an algorithm to detect the fluorescent dye, Nile Red, we can reliably distinguish different fluorescence-based phenotypes even though the visual differences are subtle....

  4. Optochin Revisited: Defining the Optimal Type of Blood Agar for Presumptive Identification of Streptococcus pneumoniae

    Microsoft Academic Search

    M. A. GARDAM; M. A. MILLER; B. Davis-Jewish

    1998-01-01

    To determine the optimal media for optochin susceptibility testing of Streptococcus pneumoniae, we measured inhibition zones for 72 S. pneumoniae and 22 Streptococcus viridans isolates on three blood-containing media. Because 15.3, 0, and 22.2% of S. pneumoniae organisms were misidentified on Columbia agar, Trypticase soy agar (TSA), and Mueller-Hinton agar, respectively, each containing sheep blood, we recommend that TSA- sheep

  5. Measuring thermal diffusivity of mechanical and optical grades of polycrystalline diamond using an AC laser calorimetry method

    SciTech Connect

    Rule, Toby D. [II-VI Incorporated; Cai, Wei [ORNL; Wang, Hsin [ORNL

    2013-01-01

    Because of its extremely high thermal conductivity, measuring the thermal conductivity or diffusivity of optical-grade diamond can be challenging. Various methods have been used to measure the thermal conductivity of thick diamond films. For the purposes of commercial quality control, the AC laser calorimetry method is appealing because it enables fairly rapid and convenient sample preparation and measurement. In this paper, the method is used to measure the thermal diffusivity of optical diamond. It is found that sample dimensions and measurement parameters are critical, and data analysis must be performed with great care. The results suggest that the method as it is applied to optical-grade diamond could be enhanced by a more powerful laser, higher frequency beam modulation, and post-processing based on 2D thermal simulation.

  6. Efficient gradient-free simplex method for estimation of optical properties in image-guided diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Jagannath, Ravi Prasad K.; Yalavarthy, Phaneendra K.

    2013-03-01

    Typical image-guided diffuse optical tomographic image reconstruction procedures involve reduction of the number of optical parameters to be reconstructed equal to the number of distinct regions identified in the structural information provided by the traditional imaging modality. This makes the image reconstruction problem less ill-posed compared to traditional underdetermined cases. Still, the methods that are deployed in this case are same as those used for traditional diffuse optical image reconstruction, which involves a regularization term as well as computation of the Jacobian. A gradient-free Nelder-Mead simplex method is proposed here to perform the image reconstruction procedure and is shown to provide solutions that closely match ones obtained using established methods, even in highly noisy data. The proposed method also has the distinct advantage of being more efficient owing to being regularization free, involving only repeated forward calculations.

  7. Efficient gradient-free simplex method for estimation of optical properties in image-guided diffuse optical tomography.

    PubMed

    Jagannath, Ravi Prasad K; Yalavarthy, Phaneendra K

    2013-03-01

    Typical image-guided diffuse optical tomographic image reconstruction procedures involve reduction of the number of optical parameters to be reconstructed equal to the number of distinct regions identified in the structural information provided by the traditional imaging modality. This makes the image reconstruction problem less ill-posed compared to traditional underdetermined cases. Still, the methods that are deployed in this case are same as those used for traditional diffuse optical image reconstruction, which involves a regularization term as well as computation of the Jacobian. A gradient-free Nelder-Mead simplex method is proposed here to perform the image reconstruction procedure and is shown to provide solutions that closely match ones obtained using established methods, even in highly noisy data. The proposed method also has the distinct advantage of being more efficient owing to being regularization free, involving only repeated forward calculations. PMID:23515862

  8. Continuous measurement of nitrous acid (HONO) in indoor environment using a diffusion scrubber and chemiluminescence method

    NASA Astrophysics Data System (ADS)

    Park, S.; Hong, J.; Lee, J.; Cho, S.

    2006-12-01

    Recent study has demonstrated that the use of combustion appliances in indoor environments, e.g., gas stoves and heaters, results in significant concentrations of NO2 and nitrous acid (HONO). Indoor HONO is formed by both direct emissions from combustion processes and the heterogeneous reaction of NO2 with water vapor on surfaces present indoors. In this study in-situ instrument was constructed for measuring HONO concentration in both indoor and outdoor environments, utilizing diffusion scrubber and peroxynitrite-induced luminol chemiluminescent methods. We measured the HONO concentration under the conditions existing in living room of an apartment, along with NO, NO2, temperature, and relative humidity, to investigate the sources, chemical transformation, and lifetimes of nitrogen oxides and HONO. Some experiments investigated the emissions and transformations of nitrogen species from operation of unvented or vented gas appliance. Measurement data of NO, NO2, and HONO will be reported, and formation pathway of the HONO under the experimental conditions will also be discussed. In addition to measurement of indoor HONO, comparison of HONO measurements by luminol chemiluminescence and annular denuder integrated samples was made in outdoor environment. HONO in ambient air was sampled with annular denuders (Teflon-coated PM2.5 cyclone inlet followed by two Na2CO3-coated denuders coupled in series) operated at 16.7 L/min. Acknowledgement This study was supported by grant No. (# R01-2005-000-10775-0) from the Basic Research Program of the Korea Science and Engineering Foundation (KOSEF).

  9. Comparison of dialysis membrane diffusion samplers and two purging methods in bedrock wells

    USGS Publications Warehouse

    Imbrigiotta, T.E.; Ehlke, T.A.; Lacombe, P.J.; Dale, J.M.

    2002-01-01

    Collection of ground-water samples from bedrock wells using low-flow purging techniques is problematic because of the random spacing, variable hydraulic conductivity, and variable contamination of contributing fractures in each well's open interval. To test alternatives to this purging method, a field comparison of three ground-water-sampling techniques was conducted on wells in fractured bedrock at a site contaminated primarily with volatile organic compounds. Constituent concentrations in samples collected with a diffusion sampler constructed from dialysis membrane material were compared to those in samples collected from the same wells with a standard low-flow purging technique and a hybrid (high-flow/low-flow) purging technique. Concentrations of trichloroethene, cis-1,2-dichloroethene, vinyl chloride, calcium, chloride, and alkalinity agreed well among samples collected with all three techniques in 9 of the 10 wells tested. Iron concentrations varied more than those of the other parameters, but their pattern of variation was not consistent. Overall, the results of nonparametric analysis of variance testing on the nine wells sampled twice showed no statistically significant difference at the 95-percent confidence level among the concentrations of volatile organic compounds or inorganic constituents recovered by use of any of the three sampling techniques.

  10. Method of coating the interior surface of hollow objects with a diffusion coating

    DOEpatents

    Knowles, Shawn D.; Senor, David J.; Forbes, Steven V.; Johnson, Roger N.; Hollenberg, Glenn W.

    2005-03-15

    A method for forming a diffusion coating on the interior of surface of a hollow object wherein a filament, extending through a hollow object and adjacent to the interior surface of the object, is provided, with a coating material, in a vacuum. An electrical current is then applied to the filament to resistively heat the filament to a temperature sufficient to transfer the coating material from the filament to the interior surface of the object. The filament is electrically isolated from the object while the filament is being resistively heated. Preferably, the filament is provided as a tungsten filament or molybdenum filament. Preferably, the coating materials are selected from the group consisting of Ag, Al, As, Au, Ba, Be, Bi, Ca, Cd, Co, Cr, Cu, Dy, Er, Eu, Fe, Ga, Ge, Hg, In, K, Li, Mg, Mn, Na, Ni P, Pb, Pd, Pr, S, Sb, Sc, Se, Si, Sn, Sr, Te, Tl, Y, Yb, Zn, and combinations thereof. The invention additionally allows for the formation of nitrides, hydrides, or carbides of all the possible coating materials, where such compounds exist, by providing a partial pressure of nitrogen, hydrogen, hydrocarbons, or combination thereof, within the vacuum.

  11. Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation

    PubMed Central

    Roberts, Elijah; Stone, John E.; Luthey-Schulten, Zaida

    2013-01-01

    Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing, the method is poised to allow integration of data from structural, single-molecule, and biochemical studies into coherent computational models of cells. Here we introduce the Lattice Microbes software package for simulating such cell models on high-performance computing systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA GPUs and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of ?0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm. PMID:23007888

  12. Optimal Analysis Method for Dynamic Contrast-Enhanced Diffuse Optical Tomography

    PubMed Central

    Ghijsen, Michael; Lin, Yuting; Hsing, Mitchell; Nalcioglu, Orhan; Gulsen, Gultekin

    2011-01-01

    Diffuse Optical Tomography (DOT) is an optical imaging modality that has various clinical applications. However, the spatial resolution and quantitative accuracy of DOT is poor due to strong photon scatting in biological tissue. Structural a priori information from another high spatial resolution imaging modality such as Magnetic Resonance Imaging (MRI) has been demonstrated to significantly improve DOT accuracy. In addition, a contrast agent can be used to obtain differential absorption images of the lesion by using dynamic contrast enhanced DOT (DCE-DOT). This produces a relative absorption map that consists of subtracting a reconstructed baseline image from reconstructed images in which optical contrast is included. In this study, we investigated and compared different reconstruction methods and analysis approaches for regular endogenous DOT and DCE-DOT with and without MR anatomical a priori information for arbitrarily-shaped objects. Our phantom and animal studies have shown that superior image quality and higher accuracy can be achieved using DCE-DOT together with MR structural a priori information. Hence, implementation of a combined MRI-DOT system to image ICG enhancement can potentially be a promising tool for breast cancer imaging. PMID:21811492

  13. Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.

    PubMed

    Roberts, Elijah; Stone, John E; Luthey-Schulten, Zaida

    2013-01-30

    Spatial stochastic simulation is a valuable technique for studying reactions in biological systems. With the availability of high-performance computing (HPC), the method is poised to allow integration of data from structural, single-molecule and biochemical studies into coherent computational models of cells. Here, we introduce the Lattice Microbes software package for simulating such cell models on HPC systems. The software performs either well-stirred or spatially resolved stochastic simulations with approximated cytoplasmic crowding in a fast and efficient manner. Our new algorithm efficiently samples the reaction-diffusion master equation using NVIDIA graphics processing units and is shown to be two orders of magnitude faster than exact sampling for large systems while maintaining an accuracy of !0.1%. Display of cell models and animation of reaction trajectories involving millions of molecules is facilitated using a plug-in to the popular VMD visualization platform. The Lattice Microbes software is open source and available for download at http://www.scs.illinois.edu/schulten/lm PMID:23007888

  14. Comparison of diffusion- and pumped-sampling methods to monitor volatile organic compounds in ground water, Massachusetts Military Reservation, Cape Cod, Massachusetts, July 1999-December 2002

    USGS Publications Warehouse

    Archfield, Stacey A.; LeBlanc, Denis R.

    2005-01-01

    To evaluate diffusion sampling as an alternative method to monitor volatile organic compound (VOC) concentrations in ground water, concentrations in samples collected by traditional pumped-sampling methods were compared to concentrations in samples collected by diffusion-sampling methods for 89 monitoring wells at or near the Massachusetts Military Reservation, Cape Cod. Samples were analyzed for 36 VOCs. There was no substantial difference between the utility of diffusion and pumped samples to detect the presence or absence of a VOC. In wells where VOCs were detected, diffusion-sample concentrations of tetrachloroethene (PCE) and trichloroethene (TCE) were significantly lower than pumped-sample concentrations. Because PCE and TCE concentrations detected in the wells dominated the calculation of many of the total VOC concentrations, when VOC concentrations were summed and compared by sampling method, visual inspection also showed a downward concentration bias in the diffusion-sample concentration. The degree to which pumped- and diffusion-sample concentrations agreed was not a result of variability inherent within the sampling methods or the diffusion process itself. A comparison of the degree of agreement in the results from the two methods to 13 quantifiable characteristics external to the sampling methods offered only well-screen length as being related to the degree of agreement between the methods; however, there is also evidence to indicate that the flushing rate of water through the well screen affected the agreement between the sampling methods. Despite poor agreement between the concentrations obtained by the two methods at some wells, the degree to which the concentrations agree at a given well is repeatable. A one-time, well-bywell comparison between diffusion- and pumped-sampling methods could determine which wells are good candidates for the use of diffusion samplers. For wells with good method agreement, the diffusion-sampling method is a time-saving and cost-effective alternative to pumped-sampling methods in a long-term monitoring program, such as at the Massachusetts Military Reservation.

  15. Thermal diffusivity measurement of LiNbO 3 melts doped with MgO by the laser flash method

    NASA Astrophysics Data System (ADS)

    Ogawa, Hiroshi; Ohta, Hiromichi; Waseda, Yoshio

    1993-10-01

    Thermal diffusivities of LiNbO 3 melts doped with 0, 2 and 5 mol% MgO at 1523-1604 K have been determined by the laser flash method. The experimental values are in the range of (2.7×3.2) x10 -7m2? s with weak positive temperature dependence for each composition. The variation of thermal diffusivity by adding MgO up to 5 mol% is negligibly small, in contrast to the results of density, surface tension and shear viscosity. No anomalous behavior of thermal diffusivity was also observed at temperature near the melting point where a certain change in melt structure has been suggested by the measurements of shear viscosity and small angle X-ray scattering.

  16. Engineering Instruction In Nondestructive Testing Of Materials (NDT) Using The Capillary Diffusion Method

    NSDL National Science Digital Library

    Berezkina, Nadezda

    In a great majority of educational cases, testing of materials in the laboratory implies destructive techniques consisting of using universal testing machines (UTMs), where materials are brought to a failure condition under tension, compression, shear, bending or torsion. Common objectives associated with these types of tests are: the evaluation of materials moduli of elasticity and rigidity, yield strength, strain, ultimate strength, etc. In engineering practice, however, in-situ nondestructive testing (NDT) of materials are highly preferable, in order to evaluate rapidly the condition, failure potential, usefulness and serviceability of engineering materials. Thus, nondestructive testing of materials ought to be an essential ingredient of engineering education and training, since it plays a significant role in design, manufacturing and evaluation of engineering equipment. This paper presents an inexpensive, simple and effective method to convey to engineering students the underlying principles of NDT, based on an innovative technique referred to as Capillary Diffusion Method (CDM), which is classified within the category of non-destructive Penetrant Testing (PT). CDM is relatively unknown in the United States, but, it has been used for several years in the former Soviet Union, and more recently, in the Russian Federation. CDM proves to be quite versatile and considerably faster than conventional PT techniques used in the U.S. In this paper, the underlying science behind the CDM technique is discussed in detail, as well as, the academic benefits and educational potential derived from the inclusion of CDM in engineering academic curriculum. Mathematical, graphical and numerical documentation are presented in order to substantiate the suitability of CDM as an educational tool to teach Nondestructive Testing in engineering programs such as: Mechanical engineering, Chemical engineering, Civil engineering, Aeronautical, Aerospace engineering, Power Plant Engineering, and Nuclear engineering.

  17. A comparison of methods for the measurement of bacteriocin activity

    Microsoft Academic Search

    Eugenio Parente; Carla Brienza; Marcella Moles; Annamaria Ricciardi

    1995-01-01

    Agar diffusion (spot and well) and photometric (tube or microtiter) assays, both in the form of critical dilution and quantitative assays, were compared for 4 bacteriocins (enterocin 1146, lactococcin 140, leucocin F10 and nisin) against 2 indicator strains each. In the agar well diffusion assay (AWDA) a linear relationship existed between response (diameter or area of the zone of inhibition)

  18. An implicit high-order hybridizable discontinuous Galerkin method for linear convection-diffusion equations

    NASA Astrophysics Data System (ADS)

    Nguyen, N. C.; Peraire, J.; Cockburn, B.

    2009-05-01

    We present a hybridizable discontinuous Galerkin method for the numerical solution of steady and time-dependent linear convection-diffusion equations. We devise the method as follows. First, we express the approximate scalar variable and corresponding flux within each element in terms of an approximate trace of the scalar variable along the element boundary. We then define a unique value for the approximate trace by enforcing the continuity of the normal component of the flux across the element boundary; a global equation system solely in terms of the approximate trace is thus obtained. The high number of globally coupled degrees of freedom in the discontinuous Galerkin approximation is therefore significantly reduced. If the problem is time-dependent, we discretize the time derivative by means of backward difference formulae. This results in efficient schemes capable of producing high-order accurate solutions in space and time. Indeed, when the time-marching method is (p+1)th order accurate and when polynomials of degree p?0 are used to represent the scalar variable, the flux and the approximate trace, we observe that the approximations for the scalar variable, the flux and the trace of the scalar variable converge with the optimal order of p+1 in the L2-norm. Finally, we introduce a simple element-by-element postprocessing scheme to obtain new approximations of the flux and the scalar variable. The new approximate flux, which has a continuous inter-element normal component, is shown to converge with order p+1 in the L2-norm. The new approximate scalar variable is shown to converge with order p+2 in the L2-norm. For the time-dependent case, the postprocessing does not need to be applied at each time-step but only at the times for which an enhanced solution is required. Moreover, the postprocessing procedure is less expensive than the solution procedure, since it is performed at the element level. Extensive numerical results are presented to demonstrate the convergence properties of the method.

  19. An artificial nonlinear diffusivity method for supersonic reacting flows with shocks

    E-print Network

    Paris-Sud XI, Université de

    of different initial entropy separated by the diaphragm, an artificial diffusivity is required to accurately is presented and is il- lustrated by a 2D oblique wave reflection from an inviscid wall, by a 2D supersonic

  20. Investigation to develop a method to apply diffusion barrier to high strength fibers

    NASA Technical Reports Server (NTRS)

    Veltri, R. D.; Paradis, R. D.; Douglas, F. C.

    1975-01-01

    A radio frequency powered ion plating process was used to apply the diffusion barriers of aluminum oxide, yttrium oxide, hafnium oxide and titanium carbide to a substrate tungsten fiber. Each of the coatings was examined as to its effect on both room temperature strength and tensile strength of the base tungsten fiber. The coated fibers were then overcoated with a nickel alloy to become single cell diffusion couples. These diffusion couples were exposed to 1093 C for 24 hours, cycled between room temperature and 1093 C, and given a thermal anneal for 100 hours at 1200 C. Tensile testing and metallographic examinations determined that the hafnium oxide coating produced the best high temperature diffusion barrier for tungsten of the four coatings.

  1. A STABILIZED FINITE ELEMENT METHOD FOR ADVECTION-DIFFUSION EQUATIONS ON SURFACES

    E-print Network

    Olshanskii, Maxim A.

    is sufficiently fine. The paper introduces a stabilized finite element formulation based on the SUPG technique, advection-diffusion equation, SUPG stabilization AMS subject classifications. 58J32, 65N12, 65N30, 76D45, 76

  2. Antibacterial properties of Au doped polycarbonate synthesized by gamma radiation assisted diffusion method

    NASA Astrophysics Data System (ADS)

    Hareesh, K.; Deore, Avinash V.; Dahiwale, S. S.; Sanjeev, Ganesh; Kanjilal, D.; Ojha, Sunil; Dhole, N. A.; Kodam, K. M.; Bhoraskar, V. N.; Dhole, S. D.

    2015-07-01

    Gold (Au)-Polycarbonate (PC) matrix was prepared by gamma radiation assisted diffusion of Au nanoparticles in PC matrix. UV-Visible spectroscopy showed the surface plasmon resonance around 550 nm which corresponds to Au and this peak shift towards lower wavelength i.e. blue shift indicating the decrease in particle size of Au. Rutherford Backscattering (RBS) experiment confirmed the diffusion of Au in PC and depth of diffusion is found to be around 0.85 ?m. X-ray Diffractogram (XRD) results also revealed the diffusion of Au in PC where the peak observed at 2??38.29° which correspond to the FCC structure. Scanning Electron Microscope (SEM) images showed the hexagonal shaped Au nanoparticles and average particle size is found to be around 110 nm. These samples also showed anti-bacterial properties with both gram positive and gram negative bacteria's and revealed the inhibition of the overall growth of the bacteria with gamma dose.

  3. The 4D Hyperspherical Diffusion Wavelet: A New Method for the Detection of Localized Anatomical Variation

    PubMed Central

    Hosseinbor, A. Pasha; Kim, Won Hwa; Adluru, Nagesh; Acharya, Amit; Vorperian, Houri K.; Chung, Moo K.

    2014-01-01

    Recently, the HyperSPHARM algorithm was proposed to parameterize multiple disjoint objects in a holistic manner using the 4D hyperspherical harmonics. The HyperSPHARM coefficients are global; they cannot be used to directly infer localized variations in signal. In this paper, we present a unified wavelet framework that links HyperSPHARM to the diffusion wavelet transform. Specifically, we will show that the HyperSPHARM basis forms a subset of a wavelet-based multiscale representation of surface-based signals. This wavelet, termed the hyperspherical diffusion wavelet, is a consequence of the equivalence of isotropic heat diffusion smoothing and the diffusion wavelet transform on the hypersphere. Our framework allows for the statistical inference of highly localized anatomical changes, which we demonstrate in the firstever developmental study on the hyoid bone investigating gender and age effects. We also show that the hyperspherical wavelet successfully picks up group-wise differences that are barely detectable using SPHARM. PMID:25320783

  4. DEVELOPMENT OF SPLIT-OPERATOR, PETROV-GALERKIN METHODS TO STIMULATE TRANSPORT AND DIFFUSION PROBLEMS

    EPA Science Inventory

    The rate at which contaminants in groundwater undergo sorption and desorption is routinely described using diffusion models. uch approaches, when incorporated into transport models, lead to large systems of coupled equations, often nonlinear. his has restricted applications of co...

  5. A diffuse-interface method for simulating two-phase flows of complex fluids

    Microsoft Academic Search

    P ENGTAO Y UE; J AMES J. F ENG

    2004-01-01

    Two-phase systems of microstructured complex fluids are an important class of engineering materials. Their flow behaviour is interesting because of the coupling among three disparate length scales: molecular or supra-molecular conformation inside each component, mesoscopic interfacial morphology and macroscopic hydrodynamics. In this paper, we propose a diffuse-interface approach to simulating the flow of such materials. The diffuse-interface model circumvents certain

  6. ADAPTIVE FINITE VOLUME ELEMENT METHOD FOR CONVECTION-DIFFUSION-REACTION PROBLEMS IN 3-D

    Microsoft Academic Search

    R. D. LAZAROV; S. Z. TOMOV

    We present an adaptive numerical technique for solving steady-state diffusion and convection-diffusion-reaction equations in 3-D using finite volume approximations. Computational re- sults of various model simulations of fluid flow and transport of passive chemicals in non-homogeneous aquifers are presented and discussed. 1. Introduction. We aim to develop, implement, and test a computational tech- nique for simulation of fluid flow and

  7. Detection of oxacillin-resistance in Staphylococcus aureus by MicroScan MIC panels in comparison to four other methods

    Microsoft Academic Search

    S. C. Dillard; K. B. Waites; E. S. Brookings; S. A. Moser

    1996-01-01

    Two hundred fifty-two isolates of Staphylococcus aureus were tested for oxacillin susceptibility by MicroScan Gram positive overnight and rapid MIC panels. Results were compared with nonautomated methods including disk diffusion, MRSA Crystal ID, and Etests using MRSA Screen Agar as reference. One hundred sixty-nine isolates (67.1%) were oxacillin-susceptible and 83 (32.9%) were resistant. All methods agreed for 234 (92.9%) isolates.

  8. Evaluation of ceramic and membrane diffusers under operating conditions with the dynamic offgas method.

    PubMed

    Libra, J A; Sahlmann, C; Schuchardt, A; Handschag, J; Wiesmann, U; Gnirss, R

    2005-01-01

    The aeration systems of two full-scale, activated-sludge basins were compared during a period of three years, under the same operating conditions, using dynamic offgas testing. Only the material of the diffuser was different (membrane versus ceramic-tube diffusers). The investigation has shown that, although the membrane diffusers have higher initial standard-oxygen-transfer efficiency (alphaSOTE) and standard-aeration efficiency (alphaSAE), these decreased over time, while the alphaSAE of the ceramic diffusers started lower, but increased slightly over the whole period. A cost comparison makes clear how important it is to evaluate the aeration system under process conditions. The operating costs were the dominant factor (approximately 10x higher than capital costs), and operating costs were approximately 20% higher for membrane versus ceramic diffusers. The poor performance of the membrane-tube diffusers under process conditions could be explained on the basis of the actual alphaAE values in the basin, not the standardized values. PMID:16274078

  9. Stimulating growth and xylindein production of Chlorociboria aeruginascens in agar-based systems.

    PubMed

    Robinson, Sara C; Tudor, Daniela; Snider, Hilary; Cooper, Paul A

    2012-01-01

    Four isolates of Chlorociboria aeruginascens were tested for possible stimulatory effects when grown on malt agar media containing wood additives. The addition of any of the four types of test wood (Acer saccharum, Populus tremuloides, spalted P. tremuloides, and Ailanthus altissima), stimulated colony growth and xylindein production in C. aeruginascens. Addition of any amount of wood produced more growth than no wood additions, while ground wood produced more growth than chopped wood. Of the wood types tested, A. saccharum wood stimulated all four isolates, while spalted Populus tremuloides stimulated three of the four isolates. High glucose and sucrose amounts may be partially responsible for the greater stimulatory affect of some woods over others. The development of this simple and reliable method for growth and pigment stimulation of C. aeruginascens in laboratory conditions will allow for further development of this fungus for decorative and commercial use. PMID:22409931

  10. Sheep poxvirus identification from clinical specimens by PCR, cell culture, immunofluorescence and agar gel immunoprecipitation assay.

    PubMed

    Mangana-Vougiouka, O; Markoulatos, P; Koptopoulos, G; Nomikou, K; Bakandritsos, N; Papadopoulos, P

    2000-10-01

    Some 40 clinical specimens of skin lesions from sheep pox suspected cases were investigated by four different diagnostic assays: PCR, virus isolation in lamb testis cell cultures, direct immunofluorescent assay (DIFA) and antigen detecting agar gel immune precipitation test (AGIPT). All the specimens were positive by PCR and virus isolation, 29 were positive by DIFA and 16 by AGIPT. Using virus isolation on cell cultures as the gold standard, the PCR sensitivity was 100%, while that of DIFA and AGIPT was 73% and 40%, respectively. Skin samples with orf lesions or normal skin biopsies were PCR-negative. Cross-reactions with orf virus were observed in three samples only in the AGIPT assay. The PCR described combines high specificity and sensitivity with speed. PCR was therefore shown to be the method of choice for sheep poxvirus diagnosis directly from clinical specimens. PMID:11040094

  11. Exact correlations in the one-dimensional coagulation-diffusion process by the empty-interval method

    E-print Network

    Xavier Durang; Jean-Yves Fortin; Diego Del Biondo; Malte Henkel; Jean Richert

    2010-04-09

    The long-time dynamics of reaction-diffusion processes in low dimensions is dominated by fluctuation effects. The one-dimensional coagulation-diffusion process describes the kinetics of particles which freely hop between the sites of a chain and where upon encounter of two particles, one of them disappears with probability one. The empty-interval method has, since a long time, been a convenient tool for the exact calculation of time-dependent particle densities in this model. We generalise the empty-interval method by considering the probability distributions of two simultaneous empty intervals at a given distance. While the equations of motion of these probabilities reduce for the coagulation-diffusion process to a simple diffusion equation in the continuum limit, consistency with the single-interval distribution introduces several non-trivial boundary conditions which are solved for the first time for arbitrary initial configurations. In this way, exact space-time-dependent correlation functions can be directly obtained and their dynamic scaling behaviour is analysed for large classes of initial conditions.

  12. Diffuse interstellar band at 8620 Å in rave: A new method for detecting the diffuse interstellar band in spectra of cool stars

    SciTech Connect

    Kos, J.; Zwitter, T. [Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana (Slovenia); Grebel, E. K. [Astronomisches Rechen-Institut, Zentrum für Astronomie der Universität Heidelberg, Mönchhofstraße 12-14, D-69120 Heidelberg (Germany); Bienayme, O.; Siebert, A. [Observatorie astronomique de Strasbourg, Université de Strasbourg, 11 rue de l'Université, F-67000 Strasbourg (France); Binney, J. [Rudolf Peierls Centre for Theoretical Physics, Keble Road, Oxford OX1 3NP (United Kingdom); Bland-Hawthorn, J. [Sydney Institute for Astronomy, School of Physics A28, University of Sydney, NSW 2008 (Australia); Freeman, K. C. [Research School of Astronomy and Astrophysics, Australian National University, Canberra (Australia); Gibson, B. K. [Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE (United Kingdom); Gilmore, G.; Kordopatis, G. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Navarro, J. F. [University of Victoria, Victoria, BC V8P 5C2 (Canada); Parker, Q.; Reid, W. A. [Department of Physics and Astronomy, Macquarie University, Sydney, NSW 2109 (Australia); Seabroke, G. [Mullard Space Science Laboratory, University College London, Holmbury St Mary, Dorking RH5 6NT (United Kingdom); Siviero, A.; Steinmetz, M. [Leibniz-Institut für Astrophysik Potsdam (AIP), An der Sternwarte 16, D-14482 Potsdam (Germany); Watson, F. [Australian Astronomical Observatory, P.O. Box 915, North Ryde, NSW 1670 (Australia); Wyse, R. F. G., E-mail: janez.kos@fmf.uni-lj.si [Johns Hopkins University, Homewood Campus, 3400 North Charles Street, Baltimore, MD 21218 (United States)

    2013-12-01

    Diffuse interstellar bands (DIBs) are usually observed in spectra of hot stars, where interstellar lines are rarely blended with stellar ones. The need for hot stars is a strong limitation in the number of sightlines we can observe and their distribution in the Galaxy, as hot stars are rare and concentrated in the Galactic plane. We are introducing a new method, where interstellar lines can be observed in spectra of cool stars in large spectroscopic surveys. The method is completely automated and does not require prior knowledge of the stellar parameters. The main step is a construction of the stellar spectrum, which is done by finding other observed spectra that lack interstellar features and are otherwise very similar to the spectrum in question. Such spectra are then combined into a single stellar spectrum template, matching the stellar component of the observed spectrum. We demonstrate the performance of this new method on a sample of 482,430 Radial Velocity Experiment survey spectra. However, many spectra have to be combined (48 on average) in order to achieve a signal-to-noise ratio high enough to measure the profile of the DIB at 8620 Å, hence limiting the spatial information about the interstellar medium. We compare its equivalent width with extinction maps and with Bayesian reddening, calculated for individual stars, and provide a linear relation between the equivalent width and reddening. Separately from the introduced method, we calculate equivalent widths of the DIB in spectra of hot stars with known extinction and compare all three linear relations.

  13. Rotational self-diffusion in suspensions of charged particles: simulations and revised Beenakker-Mazur and pairwise additivity methods.

    PubMed

    Makuch, Karol; Heinen, Marco; Abade, Gustavo Coelho; Nägele, Gerhard

    2015-07-14

    We present a comprehensive joint theory-simulation study of rotational self-diffusion in suspensions of charged particles whose interactions are modeled by the generic hard-sphere plus repulsive Yukawa (HSY) pair potential. Elaborate, high-precision simulation results for the short-time rotational self-diffusion coefficient, D(r), are discussed covering a broad range of fluid-phase state points in the HSY model phase diagram. The salient trends in the behavior of D(r) as a function of reduced potential strength and range, and particle concentration, are systematically explored and physically explained. The simulation results are further used to assess the performance of two semi-analytic theoretical methods for calculating D(r). The first theoretical method is a revised version of the classical Beenakker-Mazur method (BM) adapted to rotational diffusion which includes a highly improved treatment of the salient many-particle hydrodynamic interactions. The second method is an easy-to-implement pairwise additivity (PA) method in which the hydrodynamic interactions are treated on a full two-body level with lubrication corrections included. The static pair correlation functions required as the only input to both theoretical methods are calculated using the accurate Rogers-Young integral equation scheme. While the revised BM method reproduces the general trends of the simulation results, it significantly underestimates D(r). In contrast, the PA method agrees well with the simulation results for D(r) even for intermediately concentrated systems. A simple improvement of the PA method is presented which is applicable for large concentrations. PMID:26054032

  14. Strain Storage Typically, mycobacteria can be stored as lyophilized stocks, agar slants, or frozen stocks.

    E-print Network

    Strain Storage Typically, mycobacteria can be stored as lyophilized stocks, agar slants, or frozen stocks. Since lyophilization is not a cost-effective product storage alternative for virulent M. tuberculosis and agar slants can take up considerable BSL3 storage space, the best alternative for strain

  15. Ceftibuten-containing agar plate for detecting group B streptococci with reduced penicillin susceptibility (PRGBS).

    PubMed

    Kamiya, Chitose; Kimura, Kouji; Doyama, Yo; Miyazaki, Akira; Morimoto, Makiko; Banno, Hirotsugu; Nagano, Noriyuki; Jin, Wanchun; Wachino, Jun-Ichi; Yamada, Keiko; Arakawa, Yoshichika

    2015-08-01

    Penicillins remain first-line agents for treatment of group B Streptococcus (Streptococcus agalactiae; GBS) infections; however, several reports have confirmed the existence of GBS with reduced penicillin susceptibility (PRGBS). Because no selective agar plates for detection of PRGBS are available to date, in this investigation, we developed the selective agar plate for detection of PRGBS. We used 19 genetically well-confirmed PRGBS isolates and 38 penicillin-susceptible GBS isolates identified in Japan. For preparation of trial PRGBS-selective agar plates, we added 1 of antimicrobial agents (among oxacillin, ceftizoxime, and ceftibuten) to a well-established GBS-selective agar plate. Among 12 trial PRGBS-selective agar plates, Muller-Hinton agar containing 128?g/mL ceftibuten with 5% sheep blood, 8?g/mL gentamicin, and 12?g/mL nalidixic acid was the most appropriate selective agar for PRGBS, showing 100% sensitivity and 81.6% specificity. In cases of potential nosocomial spread of PRGBS, the selective agar plate could be useful and reliable. PMID:25959629

  16. Susceptibilities of Mycobacterium tuberculosis to Isoniazid and Rifampin on Blood Agar

    Microsoft Academic Search

    Ahmet Yilmaz Coban; Kemal Bilgin; Meltem Uzun; Nuriye Tasdelen Fisgin; Alper Akgunes; Cigdem Cekic Cihan; Asuman Birinci; Belma Durupinar

    2005-01-01

    In this study, blood agar was used instead of 7H10 agar for the susceptibility testing of 34 clinical isolates of Mycobacterium tuberculosis to isoniazid (INH) and rifampin (RIF) in accordance with the NCCLS. The BACTEC 460 TB system (Becton Dickinson, Sparks, Md.) was used as a \\

  17. Effect of Activated Charcoal in Agar on the Culture of Lower Plants

    Microsoft Academic Search

    Berthold Klein; Martin Bopp

    1971-01-01

    Proskauer and Berman1 have described a technique for culturing green organisms such as filamentous algae and moss protonema on an agar substrate containing activated charcoal which may simulate conditions found in nature. They ascribed the resulting morphological changes primarily to a decrease in the amount of light transmitted by the blackened agar, and considered their technique a simulation of natural

  18. Development of novel agar media for isolating guaiacol producing Alicyclobacillus spp.

    PubMed

    Chang, S S; Park, S H; Kang, D H

    2013-06-01

    The purpose of this study is to develop a selective and differential medium (SK2 agar) for isolating guaiacol producing Alicyclobacillus. Forty-one selected dyes and vanillic acid were incorporated in SK agar for screening selective and differential agents. Two guaiacol producing (1016, 1101) and two non-guaiacol producing (19220, C-GD 1-1) Alicyclobacillus isolates were streaked onto media and color differentiation of the isolates was assessed. Among 41 tested dyes, Chrome Azurol S (CAS) allowed color differentiation of the two types of Alicyclobacillus. Colonies of guaiacol producing Alicyclobacillus isolates appeared as dark purple to royal blue color with yellow background, whereas non-guaiacol producing Alicyclobacillus isolates produced cream colored colonies with yellow background. Vanillic acid not only served as a precursor for guaiacol formation but also inhibited non-guaiacol producing Alicyclobacillus. Non-guaiacol producing isolates did not grow on SK agar containing more than 70 ppm vanillic acid, whereas the recovery of guaiacol producing isolates was unaffected. When compared with other Alicyclobacillus isolation media, not only was SK2 agar capable of selectively recovering guaiacol-producing Alicyclobacillus, the degree of growth was also approximately equal if not better than orange serum agar, potato dextrose agar, and K agar. The development of SK2 agar provides the fruit juice industry with an inexpensive, simple to use alternative for the detection of guaiacol producing Alicyclobacillus. PMID:23587706

  19. Caprylate-thallous agar medium for selectively isolating Serratia and its utility in the clinical laboratory.

    PubMed Central

    Starr, M P; Grimont, P A; Grimont, F; Starr, P B

    1976-01-01

    A defined agar medium (hereinafter designated caprylate-thallous [CT5 agar) containing 0.01% yeast extract, 0.1% caprylic (n-octanoic) acid, and 0.025% thallous sulfate is highly selective for all Serratia species and effectively discriminates against most non-Serratia strains likely to be in the same habitats. The selectivity of CT agar is demonstrated by the very high efficiency of colony formation (mean, 80.7% of that on a nonselective complex medium) on CT agar by known Serratia strains and the very low efficiency of colony formation (close to zero) on CT agar by bacterial strains known not to be Serratia. The utility of this medium in actual clinical laboratory practice is demonstrated by the more rapid and higher recovery of Serratia on this selective medium as compared to conventional procedures of in-tandem runs of 513 consecutive urine, feces, and sputum specimens. Pigmented and nonpigmented Serratia strains deliberately added to fecal specimens can be selectively and quantitatively recovered on CT agar. CT agar compares favorably with, or in some cases is an improvement over, other selective media which have been recommended for isolating Serratia. This selective CT agar medium could be quite useful in ecological surveys, especially those related to hospital-acquired infections. PMID:972193

  20. Improved agar bottle plate for isolation of methanogens or other anaerobes in a defined gas atmosphere

    SciTech Connect

    Hermann, M.; Noll, K.M.; Wolfe, R.S.

    1986-05-01

    A bottle plate for the cultivation of methanogens or other organisms in a defined pressurized-gas atmosphere was developed. The bottle provides the convenience of an agar streak plate, solves the problem of the water exudate from agar medium, and provides a convenient way of adding or sampling a defined gas atmosphere.

  1. How selective are agar cultures for malignant transformation?

    PubMed

    Klein, J C

    1981-01-01

    In vitro assays that permit cloning of tumour cells in soft agar have been improved during the last 5 years. Two of them (2, 10) are claimed to be useful as test systems for the screening of new anticancer drugs and even for drug sensitivity testing of individual human tumours in the devicing of individualized cancer chemotherapy regimens. Three assays were investigated for this report: those of Toshio Kuroki (TK) (11) and Hamburger and Salmon (HS) (5, 10) and that in use for bone marrow cell cultures (BM) (3). Cells of various origins were tested for their growth capacity and colony formation in these three assays. Included were cells of 10 established lines classified as malignant or nonmalignant according to the in vivo malignancy test (6). Cells freshly derived from two tumours ans those from five tumours after 2-10 passages in monolayer culture were also used as test cells. The BM assay gave the best results. Up to now, a 100 per cent correlation has been found between the in vivo and in vitro test. Investigations are under way to determine whether this assay can also be used as a transformation assay using cells with a low transformation rate. PMID:7259442

  2. Pulsed photothermal temperature profiling of agar tissue phantoms.

    PubMed

    Milanic, Matija; Majaron, Boris; Nelson, J Stuart

    2007-11-01

    We determine experimentally the accuracy of pulsed photothermal radiometric (PPTR) temperature depth profiling in water-based samples. We use custom tissue phantoms composed of agar gel layers separated by very thin absorbing layers. Two configurations of the acquisition system are compared, one using the customary spectral band of the InSb radiation detector (3.0-5.5 microm) and the other with a spectrally narrowed acquisition band (4.5-5.5 microm). The laser-induced temperature depth profiles are reconstructed from measured radiometric signals using a custom minimization algorithm. The results correlate very well with phantom geometry as determined by optical coherence tomography (OCT) and histology in all evaluated samples. Determination of the absorbing layer depth shows good repeatability with spatial resolution decreasing with depth. Spectral filtering improves the accuracy and resolution, especially for shallow absorption layers (~120 microm) and more complex structures (e.g., with two absorbing layers). The average full width at half maximum (FWHM) of the temperature peaks equals 23% of the layer depth. PMID:17522951

  3. Rotational self-diffusion in suspensions of charged particles: Revised Beenakker-Mazur and Pairwise Additivity methods versus numerical simulations

    E-print Network

    Karol Makuch; Marco Heinen; Gustavo C. Abade; Gerhard Nägele

    2015-01-07

    To the present day, the Beenakker-Mazur (BM) method is the most comprehensive statistical physics approach to the calculation of short-time transport properties of colloidal suspensions. A revised version of the BM method with an improved treatment of hydrodynamic interactions is presented and evaluated regarding the rotational short-time self-diffusion coefficient, $D^r$ , of suspensions of charged particles interacting by a hard-sphere plus screened Coulomb (Yukawa) pair potential. To assess the accuracy of the method, elaborate simulations of $D^r$ have been performed, covering a broad range of interaction parameters and particle concentrations. The revised BM method is compared in addition with results by a simplifying pairwise additivity (PA) method in which the hydrodynamic interactions are treated on a two-body level. The static pair correlation functions re- quired as input to both theoretical methods are calculated using the Rogers-Young integral equation scheme. While the revised BM method reproduces the general trends of the simulation results, it systematically and significantly underestimates the rotational diffusion coefficient. The PA method agrees well with the simulation data at lower volume fractions, but at higher concentrations $D^r$ is likewise underestimated. For a fixed value of the pair potential at mean particle distance comparable to the thermal energy, $D^r$ increases strongly with increasing Yukawa potential screening parameter.

  4. Screening of tannin acyl hydrolase (E.C.3.1.1.20) producing tannery effluent fungal isolates using simple agar plate and SmF process.

    PubMed

    Murugan, K; Saravanababu, S; Arunachalam, M

    2007-03-01

    Industrially important tannase producing fungi were isolated from tannery effluent using simple agar plate method. The isolates were screened by submerged fermentation using auto-controlled bioreactor. The colony diameter on the solid surface media shows high correlation with quantitative production of tannase. The isolate Aspergillus niger shows maximum production of both extracellular and intracellular enzyme. PMID:16839759

  5. Oral Actinomyces Isolates Forming Red Colonies on Brain Heart Blood Agar Can Be Unambiguously Classified as A. odontolyticus by Macroscopic Examination

    Microsoft Academic Search

    Annette Kaetzke; Henrike Korner; Susanne Kneist; Klaus Eschrich

    2003-01-01

    The accurate classification of oral Actinomyces isolates as one species is difficult. Out of 18 Actinomyces isolates forming red colonies on brain heart blood agar, 12 could be straightforwardly assigned as Actinomyces odontolyticus by biochemical, morphological, and chemotaxonomic characteristics. For the remaining six isolates, the results of the different identification methods were inconsistent. By sequencing a 16S ribosomal DNA fragment

  6. Determining Enzyme Activity by Radial Diffusion

    ERIC Educational Resources Information Center

    Davis, Bill D.

    1977-01-01

    Discusses advantages of radial diffusion assay in determining presence of enzyme and/or rough approximation of amount of enzyme activities. Procedures are included for the preparation of starch-agar plates, and the application and determination of enzyme. Techniques using plant materials (homogenates, tissues, ungerminated embryos, and seedlings)…

  7. Rheological and structural characterization of agar/whey proteins insoluble complexes.

    PubMed

    Rocha, Cristina M R; Souza, Hiléia K S; Magalhães, Natália F; Andrade, Cristina T; Gonçalves, Maria Pilar

    2014-09-22

    Complex coacervation between whey proteins and carboxylated or highly sulphated polysaccharides has been widely studied. The aim of this work was to characterise a slightly sulphated polysaccharide (agar) and whey protein insoluble complexes in terms of yield, composition and physicochemical properties as well as to study their rheological behaviour for better understanding their structure. Unlike other sulphated polysaccharides, complexation of agar and whey protein at pH 3 in the absence of a buffering agent resulted in a coacervate that was a gel at 20°C with rheological properties and structure similar to those of simple agar gels, reinforced by proteins electrostatically aggregated to the agar network. The behaviour towards heat treatment was similar to that of agar alone, with a high thermal hysteresis and almost full reversibility. In the presence of citrate buffer, the result was a "flocculated solid", with low water content (75-81%), whose properties were governed by protein behaviour. PMID:24906765

  8. Migration of chemotactic bacteria in soft agar: role of gel concentration

    E-print Network

    Croze, O A; Cates, M E; Poon, W C K

    2011-01-01

    We study the migration of chemotactic wild type Escherichia coli populations in semi-solid (`soft') agar in the concentration range C = 0.15-0.5% (w/v). For C agar and have not been previously reported experimentally. For C=0.4-0.5% expanding colonies do not span the depth of the agar and develop pronounced front instabilities. The rate of increase of the colony radius (front speed) v_F, is weakly dependent of agar concentration below C = 0.25%, but decreases sharply above this value. We discuss these observations in terms of an extended Keller-Segel model for which we derived novel expressions for transport parameters accounting for perturbations of the chemotactic response by collisions with the agar. The observed front speed decay could be well fitted with the model i...

  9. The Conforming Virtual Element Method for the convection-diffusion-reaction equation with variable coeffcients.

    SciTech Connect

    Manzini, Gianmarco [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cangiani, Andrea [University of Leicester, Leicester (United Kingdom); Sutton, Oliver [University of Leicester, Leicester (United Kingdom)

    2014-10-02

    This document describes the conforming formulations for virtual element approximation of the convection-reaction-diffusion equation with variable coefficients. Emphasis is given to construction of the projection operators onto polynomial spaces of appropriate order. These projections make it possible the virtual formulation to achieve any order of accuracy. We present the construction of the internal and the external formulation. The difference between the two is in the way the projection operators act on the derivatives (laplacian, gradient) of the partial differential equation. For the diffusive regime we prove the well-posedness of the external formulation and we derive an estimate of the approximation error in the H1-norm. For the convection-dominated case, the streamline diffusion stabilization (aka SUPG) is also discussed.

  10. A new measurement method for nitrogen oxides in the air using an annular diffusion scrubber coated with titanium dioxide

    Microsoft Academic Search

    Yuichi Komazaki; Hiroki Shimizu; Shigeru Tanaka

    1999-01-01

    A new convenient measurement method of nitrogen oxides (NOx) in the ambient air was developed. The collection of NOx is performed by an annular diffusion scrubber coated with a mixture of titanium dioxide (TiO2) and hydroxyapatite (Ca10(PO4)6(OH)2) and the analysis is carried out by ion chromatography with conductivity detection. Under ultraviolet light (UV) illumination, TiO2 produces reactive oxygen species such

  11. Binary diffusion coefficients and retention factors for polar compounds in supercritical carbon dioxide by chromatographic impulse response method

    Microsoft Academic Search

    Chang Yi Kong; Toshitaka Funazukuri; Seiichiro Kagei

    2006-01-01

    The chromatographic impulse response (CIR) method with curve fitting was employed for measuring binary diffusion coefficients D12 at infinite dilution for polar compounds such as benzoic acid and C1 to C3 mono-alcohols in supercritical (SC) carbon dioxide at 313.2K and pressures higher than 9.5MPa. The measured D12 values for the polar compounds were expressed with two correlations which well represent

  12. Autonomous basin climbing method with sampling of multiple transition pathways: application to anisotropic diffusion of point defects in hcp Zr

    NASA Astrophysics Data System (ADS)

    Fan, Yue; Yip, Sidney; Yildiz, Bilge

    2014-09-01

    This paper presents an extension of the autonomous basin climbing (ABC) method, an atomistic activation-relaxation technique for sampling transition-state pathways. The extended algorithm (ABC-E) allows the sampling of multiple transition pathways from a given minimum, with the additional feature of identifying the pathways in the order of increasing activation barriers, thereby prioritizing them according to their importance in the kinetics. Combined with on-the-fly kinetic Monte Carlo calculations, the method is applied to simulate the anisotropic diffusion of point defects in hcp Zr. Multiple migration mechanisms are identified for both the interstitials and vacancies, and benchmarked against results from other methods in the literature. The self-interstitial atom (SIA) diffusion kinetics shows a maximum anisotropy at intermediate temperatures (400~700?K), a non-monotonic behavior that we explain to originate from the stabilities and migration mechanisms associated with different SIA sites. The accuracy of the ABC-E calculations is validated, in part, by the existing results in the literature for point defect diffusion in hcp Zr, and by benchmarking against analytical results on a hypothetical rough-energy landscape. Lastly, sampling prioritization and computational efficiency are demonstrated through a direct comparison between the ABC-E and the activation relaxation technique.

  13. A one-level FETI method for the drift-diffusion-Poisson system with discontinuities at an interface

    NASA Astrophysics Data System (ADS)

    Baumgartner, Stefan; Heitzinger, Clemens

    2013-06-01

    A 3d FETI method for the drift-diffusion-Poisson system including discontinuities at a 2d interface is developed. The motivation for this work is to provide a parallel numerical algorithm for a system of PDEs that are the basic model equations for the simulation of semiconductor devices such as transistors and sensors. Moreover, discontinuities or jumps in the potential and its normal derivative at a 2d surface are included for the simulation of nanowire sensors based on a homogenized model. Using the FETI method, these jump conditions can be included with the usual numerical properties and the original Farhat-Roux FETI method is extended to the drift-diffusion-Poisson equations including discontinuities. We show two numerical examples. The first example verifies the correct implementation including the discontinuities on a 2d grid divided into eight subdomains. The second example is 3d and shows the application of the algorithm to the simulation of nanowire sensors with high aspect ratios. The Poisson-Boltzmann equation and the drift-diffusion-Poisson system with jump conditions are solved on a 3d grid with real-world boundary conditions.

  14. Simulation of gaseous diffusion in partially saturated porous media under variable gravity with lattice Boltzmann methods

    E-print Network

    Shor, Leslie McCabe

    Simulation of gaseous diffusion in partially saturated porous media under variable gravity under variable gravity. Citation: Chau, J. F., D. Or, and M. C. Sukop (2005), Simulation of gaseous-component, multiphase lattice Boltzmann code to simulate liquid configurations in two-dimensional porous media

  15. Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods

    E-print Network

    of the space. It can be thought of as global Fourier analysis. The multiscale analysis proposed hereGeometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale, CT 06510; and Department of Computer Science, Yale University, 51 Prospect Street, New Haven, CT

  16. A posteriori error estimations of a SUPG method for anisotropic diffusion–convection–reaction problems

    Microsoft Academic Search

    Thomas Apel; Serge Nicaise

    2007-01-01

    This Note presents an a posteriori residual error estimator for diffusion–convection–reaction problems approximated by a SUPG scheme on isotropic or anisotropic meshes in Rd, d=2 or 3. This estimator is based on the jump of the flux and the interior residual of the approximated solution. It is constructed to work on anisotropic meshes which account for the eventual anisotropic behavior

  17. A periodic surface heating method for determining thin film thermal diffusivity: Effects of interfacial resistance

    SciTech Connect

    Peterson, R.B.; Sauvage, E.C.

    1997-07-01

    An analytical model is developed for the periodic surface heating of thin samples attached to thermally thick substrates. The model gives the temperature response of the material at the interface between the sample and substrate in terms of the thermal properties of each material and an interfacial thermal resistance. For determining thermal diffusivity from experimental data, a simplified model valid for the high frequency limit is derived from the full analytical solution. This simplified model, in addition to the frequency restrictions, neglects interfacial resistance. As a consequence, significant error could result if interfacial effects exceed certain limiting values. This paper explores the influence thermal resistance has on experimentally determined thermal diffusivity and sets limits on its magnitude. For a specific case relevant to ongoing work, the thermal properties of thin film polymeric materials are used in the analysis. The specific material chosen is the polydimide family of materials characterized by the brand name Kapton. This material was chosen for its availability and close thickness tolerances in the 25 {micro}m size range. Results from this study show that as the true sample diffusivity decreases, the effect of interfacial resistance also decreases. Furthermore, under the conditions studied, an interfacial resistance of less than 1 x 10{sup {minus}5} m{sup 2}-KW should result in an apparent diffusivity reduction of no greater than approximately 10%.

  18. E. coli swimming over agar in a thin aqueous film

    NASA Astrophysics Data System (ADS)

    Berg, Howard

    2010-11-01

    When cells of Escherichia coli are grown in a rich medium over somewhat soft agar (0.45%) they elongate, produce more flagella, and swarm (or flock). Their behavior is dominated by collisions: an individual cell's velocity is randomized in about 0.2 s [1]. However, cells do not swim in spirals, as they do when in a thick layer of fluid near a solid boundary [2]. This suggests that the surface of the swarm is stationary, i.e., that the cells swim in a thin film of fluid between two fixed surfaces. We showed that this is the case by following the motion of MgO smoke particles deposited at the fluid-air interface [3]. By visualizing flagella of cells in swarms, we found that cells can escape from a confined environment by swimming back through the flagellar bundle, without changing the orientation of the cell body. This maneuver involves normal-to-curly and curly-to-normal polymorphic transformations [4]. These phenomena will be illustrated.[4pt] [1] Darnton NC, Turner L, Rojevsky S, & Berg HC (2010) Dynamics of bacterial swarming. Biophys. J. 98:2082-2090.[0pt] [2] Lauga E, DiLuzio WR, Whitesides GM, & Stone HA (2006) Swimming in circles: motion of bacteria near solid boundaries. Biophys. J. 90:400-412.[0pt] [3] Zhang R, Turner L, & Berg HC (2010) The upper surface of an Escherichia coli swarm is stationary. Proc. Natl. Acad. Sci. USA 107:288-290.[0pt] [4] Turner L, Zhang R, Darnton NC, & Berg HC (2010) Visualization of flagella during bacterial swarming. J. Bacteriol. 192:3259-3267.

  19. Multigrid method based on the transformation-free HOC scheme on nonuniform grids for 2D convection diffusion problems

    NASA Astrophysics Data System (ADS)

    Ge, Yongbin; Cao, Fujun

    2011-05-01

    In this paper, a multigrid method based on the high order compact (HOC) difference scheme on nonuniform grids, which has been proposed by Kalita et al. [J.C. Kalita, A.K. Dass, D.C. Dalal, A transformation-free HOC scheme for steady convection-diffusion on non-uniform grids, Int. J. Numer. Methods Fluids 44 (2004) 33-53], is proposed to solve the two-dimensional (2D) convection diffusion equation. The HOC scheme is not involved in any grid transformation to map the nonuniform grids to uniform grids, consequently, the multigrid method is brand-new for solving the discrete system arising from the difference equation on nonuniform grids. The corresponding multigrid projection and interpolation operators are constructed by the area ratio. Some boundary layer and local singularity problems are used to demonstrate the superiority of the present method. Numerical results show that the multigrid method with the HOC scheme on nonuniform grids almost gets as equally efficient convergence rate as on uniform grids and the computed solution on nonuniform grids retains fourth order accuracy while on uniform grids just gets very poor solution for very steep boundary layer or high local singularity problems. The present method is also applied to solve the 2D incompressible Navier-Stokes equations using the stream function-vorticity formulation and the numerical solutions of the lid-driven cavity flow problem are obtained and compared with solutions available in the literature.

  20. A method of determining the dissolved oxygen in the moisture of a porous medium and some oxygen diffusion studies 

    E-print Network

    Runkles, Jack Ralph

    1952-01-01

    tsoasure of the dissolved oxygen in the ~isture while it is in the porous wadi~' A method of measuring the dissolved oxygen in the 'moisture in oon$une tion with the method for measuring gaseous oxygen would help in determin1ng the rate of equilibrius... betseen gaseous and dissolved oxygen and open the ?ay for detailed study of root, funotion1ng snd of the diffusion prooessea by shish oxygen novas into the soil It was the purpose of this 1nvestigation to deviae a nethod of measuring the dissolved...

  1. Agar-screew specimen carrier for bulk processing of biopsy material for electron microscopy.

    PubMed

    Tio, F O; Cowley, L H; Garber, M C

    1975-03-01

    A specimen carrier for processing large numbers of biopsy materials for epoxy embedding and electron microscopy is described. Commercially available 18-mesh stainless steel or 16-mesh aluminum wire screening is used. The screening is cut into 1 x 3-inch strips. One corner is snipped off for orientation purposes. Four drops of warm 4% agar is placed on a prewarmed standard microscopic glass slide. A thin agar support film is formed on the bottom side of the horizontally held wire screen by lightly running it against the agar. Tissue blocks trimmed to 1 mm-3 are blotted on filter paper and placed in a prearranged order on the top surface of the support film. A thin top coating of agar is applied on the specimen by touching it with the tip of a pasteur pipette containing warm 4% agar. The agar-screen unit with the mounted specimens is stabilized in 4% buffered formalin and rinsed with Sorenson's phosphate buffer, pH 7.4, with 6.8% sucrose. It is then processed as a unit through routine osmium tetroxide postfixation, alcohol dehydration, and Epon 812 filtration. The tissue blocks are plucked off the agar support film with fine-tipped tweezers and embedded in individual capsules. No difficulty in thin sectioning was encountered and examination of the sections under the electron microscope showed good infiltration by the epoxy resin. PMID:1096371

  2. An Eulerian-Lagrangian localized adjoint method for the advection-diffusion equation

    Microsoft Academic Search

    Michael A. Celia; Thomas F. Russell

    1990-01-01

    Many numerical methods use characteristic analysis to accommodate the advective component of transport. Such characteristic methods include Eulerian-Lagrangian methods (ELM), modified method of characteristics (MMOC), and operator splitting methods. A generalization of characteristic methods can be developed using an approach that we refer to as an Eulerian- Lagrangian localized adjoint method (ELLAM). This approach is a space-time extension of the

  3. Speckle contrast optical spectroscopy, a non-invasive, diffuse optical method for measuring microvascular blood flow in tissue

    PubMed Central

    Valdes, Claudia P.; Varma, Hari M.; Kristoffersen, Anna K.; Dragojevic, Tanja; Culver, Joseph P.; Durduran, Turgut

    2014-01-01

    We introduce a new, non-invasive, diffuse optical technique, speckle contrast optical spectroscopy (SCOS), for probing deep tissue blood flow using the statistical properties of laser speckle contrast and the photon diffusion model for a point source. The feasibility of the method is tested using liquid phantoms which demonstrate that SCOS is capable of measuring the dynamic properties of turbid media non-invasively. We further present an in vivo measurement in a human forearm muscle using SCOS in two modalities: one with the dependence of the speckle contrast on the source-detector separation and another on the exposure time. In doing so, we also introduce crucial corrections to the speckle contrast that account for the variance of the shot and sensor dark noises. PMID:25136500

  4. A new method of boundary parameter estimation for a two-dimensional diffusion system under noisy observations

    NASA Technical Reports Server (NTRS)

    Sunahara, Y.; Kojima, F.

    1987-01-01

    The purpose of this paper is to establish a method for identifying unknown parameters involved in the boundary state of a class of diffusion systems under noisy observations. A mathematical model of the system dynamics is given by a two-dimensional diffusion equation. Noisy observations are made by sensors allocated on the system boundary. Starting with the mathematical model mentioned above, an online parameter estimation algorithm is proposed within the framework of the maximum likelihood estimation. Existence of the optimal solution and related necessary conditions are discussed. By solving a local variation of the cost functional with respect to the perturbation of parameters, the estimation mechanism is proposed in a form of recursive computations. Finally, the feasibility of the estimator proposed here is demonstrated through results of digital simulation experiments.

  5. A finite difference method on layer-adapted meshes for an elliptic reaction-diffusion system in two dimensions

    NASA Astrophysics Data System (ADS)

    Kellogg, R. Bruce; Linss, Torsten; Stynes, Martin

    2008-12-01

    An elliptic system of M (ge 2) singularly perturbed linear reaction-diffusion equations, coupled through their zero-order terms, is considered on the unit square. This system does not in general satisfy a maximum principle. It is solved numerically using a standard difference scheme on tensor-product Bakhvalov and Shishkin meshes. An error analysis for these numerical methods shows that one obtains nodal O(N^{-2}) convergence on the Bakhvalov mesh and O(N^{-2}ln^2 N) convergence on the Shishkin mesh, where N mesh intervals are used in each coordinate direction and the convergence is uniform in the singular perturbation parameter. The analysis is much simpler than previous analyses of similar problems, even in the case of a single reaction-diffusion equation, as it does not require the construction of an elaborate decomposition of the solution. Numerical results are presented to confirm our theoretical error estimates.

  6. Diffusion Geometry Diffusion Geometry

    E-print Network

    Hirn, Matthew

    Diffusion Geometry Diffusion Geometry for High Dimensional Data Matthew J. Hirn July 3, 2013 #12;Diffusion Geometry Introduction Embedding of closed curve Figure: Left: A closed, non-self-intersecting curve in 3 dimensions. Right: Its embedding as a circle. #12;Diffusion Geometry Introduction Cartoon

  7. Intrauterine device for laser light diffusion and method of using the same

    DOEpatents

    Tadir, Yona (Irvine, CA); Berns, Michael W. (Trabuco Canyon, CA); Svaasand, Lars O. (Trondheim, NO); Tromberg, Bruce J. (Irvine, CA)

    1995-01-01

    An improved device for delivery of photoenergy from a light source, such as a laser, into a uterine cavity for photodynamic therapy is comprised of a plurality of optic fibers, which are bundled together and inserted into the uterine cavity by means of a uterine cannula. The cannula is positioned within the uterine cavity at a preferred location and then withdrawn thereby allowing the plurality of optic fibers to splay or diverge one from the other within the cavity. Different portions of the distal tip of the optic fiber is provided with a light diffusing tip, the remainder being provided with a nondiffusing tip portion. The fiber optic shape, as well as the segment which is permitted to actively diffuse light through the tip, is selected in order to provide a more uniform exposure intensity of the photo energy or at least sufficient radiation directed to each segment of the uterine walls.

  8. Determination of the Solute Diffusion Coefficient by the Droplet Migration Method

    SciTech Connect

    Shan Liu; Jing Teng; Jeongyun Choi

    2007-07-01

    Further analysis of droplet migration in a temperature gradient field indicates that different terms can be used to evaluate the solute diffusion coefficient in liquid (D{sub L}) and that there exists a characteristic curve that can describe the motion of all the droplets for a given composition and temperature gradient. Critical experiments are subsequently conducted in succinonitrile (SCN)-salol and SCN-camphor transparent alloys in order to observe dynamic migration processes of a number of droplets. The derived diffusion coefficients from different terms are the same within experimental error. For SCN-salol alloys, D{sub L} = (0.69 {+-} 0.05) x 10{sup -3} mm{sup 2}/s, and for SCN-camphor alloys, D{sub L} = (0.24 {+-} 0.02) x 10{sup -3} mm{sup 2}/s.

  9. Methods for measuring diffusion of a social media-based health intervention

    PubMed Central

    Young, Sean D.; Belin, Thomas R.; Klausner, Jeffrey D.; Valente, Thomas W.

    2015-01-01

    This study evaluated the feasibility of measuring diffusion from a social networking community-level intervention. One year after completion of a randomized controlled HIV prevention trial on Facebook, 112 minority men who have sex with men (MSM) were asked to refer African-American and/or Latino sex partners to complete a survey. Results suggest that, compared to non-referrers, referrers spent more time online, controlling for age, race, education, and condition. Over 60% of referrals reported hearing about the intervention, and over half reported that the referrer talked to them about changing health behaviors. Results provide support and initial feasibility of using social networking for diffusing community-based HIV interventions.

  10. Application of inverse methods to contaminant source identification from aquitard diffusion profiles at Dover AFB, Delaware

    Microsoft Academic Search

    Chongxuan Liu; William P. Ball

    1999-01-01

    This paper presents a refinement and expansion of our previously described efforts to estimate contaminant plume history from observed contaminant concentrations within a low-permeability aquitard at the site of a field-scale groundwater remediation experiment at Dover Air Force Base. At this site, a two-layer aquitard has been contaminated with tetrachloroethene and trichloroethene through diffusive mass transfer from an overlying contaminated

  11. A cooled quartz crystal microbalance method for measuring diffusion pump backstreaming

    Microsoft Academic Search

    M A Baker

    1968-01-01

    A cooled quartz crystal microbalance has been used to study the backstreaming characteristics of an oil diffusion pump. The change of backstreaming rate of two pumps (diameters 7·6 cm and 12·7 cm) has been measured during warming and cooling. The variation in backsteaming rate across the pump mouth of the 12·7 cm diameter pump is shown. Backstreaming rates as high

  12. The boundedness-by-entropy method for cross-diffusion systems

    NASA Astrophysics Data System (ADS)

    Jüngel, Ansgar

    2015-06-01

    The global-in-time existence of bounded weak solutions to a large class of physically relevant, strongly coupled parabolic systems exhibiting a formal gradient-flow structure is proved. The main feature of these systems is that the diffusion matrix may be generally neither symmetric nor positive semi-definite. The key idea is to employ a transformation of variables, determined by the entropy density, which is defined by the gradient-flow formulation. The transformation yields at the same time a positive semi-definite diffusion matrix, suitable gradient estimates as well as lower and/or upper bounds of the solutions. These bounds are a consequence of the transformation of variables and are obtained without the use of a maximum principle. Several classes of cross-diffusion systems are identified which can be solved by this technique. The systems are formally derived from continuous-time random walks on a lattice modeling, for instance, the motion of ions, cells, or fluid particles. The key conditions for this approach are identified and previous results in the literature are unified and generalized. New existence results are obtained for the population model with or without volume filling.

  13. Methods for in vitro percutaneous absorption studies IV: The flow-through diffusion cell.

    PubMed

    Bronaugh, R L; Stewart, R F

    1985-01-01

    A flow-through diffusion cell system for percutaneous absorption studies has been developed. The results of initial studies with a limited number of compounds are reported. The cells were constructed from Teflon and contained a glass window in the bottom for viewing the receptor contents. A flow rate of at least 5 mL/h is required through the receptor (volume, 0.4 mL) for accurate results. The skin permeation of water, cortisone, and benzoic acid was determined in the flow-through cell and a standard static-diffusion cell. The absorption profiles and quantitative values obtained were similar for the two types of cells. The permeation of cortisone and benzoic acid applied in a petrolatum vehicle was determined in vivo in rats and with rat skin in the flow-through and static-diffusion cells. Good agreement was obtained between the results of the in vivo and in vitro procedures. The percutaneous absorption of a hydrophobic compound [3-phenyl-2-propenyl 2-aminobenzoate (cinnamyl anthranilate)] was enhanced with normal saline receptor solution in the flow-through cell when compared with results in the static cell. Maximum in vitro absorption was obtained with either cell using a 6% solution in water of the nonionic surfactant polyethylene glycol 20 oleyl ether (PEG-20 oleyl ether). PMID:3981421

  14. Multiparameter Screening on SlipChip Used for Nanoliter Protein Crystallization Combining Free Interface Diffusion and Microbatch Methods

    SciTech Connect

    Li, Liang; Du, Wenbin; Ismagilov, Rustem F. (UC)

    2010-08-04

    This paper describes two SlipChip-based approaches to protein crystallization: a SlipChip-based free interface diffusion (FID) method and a SlipChip-based composite method that simultaneously performs microbatch and FID crystallization methods in a single device. The FID SlipChip was designed to screen multiple reagents, each at multiple diffusion equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis, against 48 different reagents at five different equilibration times each, consuming 12 {micro}L of each protein for a total of 480 experiments using three SlipChips. The composite SlipChip was designed to screen multiple reagents, each at multiple mixing ratios and multiple equilibration times, and was validated by screening conditions for crystallization of two proteins, enoyl-CoA hydratase from Mycobacterium tuberculosis and dihydrofolate reductase/thymidylate synthase from Babesia bovis. To prevent cross-contamination while keeping the solution in the neck channels for FID stable, the plates of the SlipChip were etched with a pattern of nanowells. This nanopattern was used to increase the contact angle of aqueous solutions on the surface of the silanized glass. The composite SlipChip increased the number of successful crystallization conditions and identified more conditions for crystallization than separate FID and microbatch screenings. Crystallization experiments were scaled up in well plates using conditions identified during the SlipChip screenings, and X-ray diffraction data were obtained to yield the protein structure of dihydrofolate reductase/thymidylate synthase at 1.95 {angstrom} resolution. This free-interface diffusion approach provides a convenient and high-throughput method of setting up gradients in microfluidic devices and may find additional applications in cell-based assays.

  15. Method for producing components with internal architectures, such as micro-channel reactors, via diffusion bonding sheets

    DOEpatents

    Alman, David E. (Corvallis, OR); Wilson, Rick D. (Corvallis, OR); Davis, Daniel L. (Albany, OR)

    2011-03-08

    This invention relates to a method for producing components with internal architectures, and more particularly, this invention relates to a method for producing structures with microchannels via the use of diffusion bonding of stacked laminates. Specifically, the method involves weakly bonding a stack of laminates forming internal voids and channels with a first generally low uniaxial pressure and first temperature such that bonding at least between the asperites of opposing laminates occurs and pores are isolated in interfacial contact areas, followed by a second generally higher isostatic pressure and second temperature for final bonding. The method thereby allows fabrication of micro-channel devices such as heat exchangers, recuperators, heat-pumps, chemical separators, chemical reactors, fuel processing units, and combustors without limitation on the fin aspect ratio.

  16. Productivity Change in U.S. Catch Share Fisheries John Walden, Juan Agar, Ron Felthoven, Abigail Harley, Stephen Kasperski,

    E-print Network

    Productivity Change in U.S. Catch Share Fisheries John Walden, Juan Agar, Ron Felthoven, Abigail.S. Catch Share Fisheries John Walden, Juan Agar, Ron Felthoven, Abigail Harley, Stephen Kasperski, Jean Lee, Assistant Administrator for Fisheries #12;ii Recommended citation: Walden, J., J. Agar, R. Felthoven, A

  17. Webb & Agar (1991). The Application of Machine Learning to the Diagnosis of Glomerular Disease. Page 1 of 7

    E-print Network

    Webb, Geoff

    1991-01-01

    Webb & Agar (1991). The Application of Machine Learning to the Diagnosis of Glomerular Disease and John W. M. Agar Deakin University and Geelong Hospital, Geelong, Victoria, Australia. Abstract A pilot undergone diagnostic renal biopsy (Agar & Webb, in preparation). The results of this study lead us

  18. The effect of absorbent grid preparation method on precision and accuracy of ambient nitrogen dioxide measurements using Palmes passive diffusion tubes 

    E-print Network

    Heal, Mathew R

    2008-01-01

    A few studies have suggested that the precision and accuracy of measurement of NO2 by Palmes-type passive diffusion tube (PDT) are affected by the method of preparation of the triethanolamine (TEA) absorbent coating on the ...

  19. Thermal-Diffusivity and Heat-Capacity Measurements of Sandstone at High Temperatures Using Laser Flash and DSC Methods

    NASA Astrophysics Data System (ADS)

    Abdulagatov, I. M.; Abdulagatova, Z. Z.; Kallaev, S. N.; Bakmaev, A. G.; Ranjith, P. G.

    2015-04-01

    The well-known contact-free, laser-flash method was used for measurement of the thermal diffusivity of natural sandstone samples. The experimental procedure was conducted using the microflash apparatus (LFA 457). The measurements have been made over the temperature range from (302.9 to 774.3) K. The isobaric heat capacities of the same sample were measured over the temperature range from (308 to 763) K using DSC 204 F1. Uncertainties are 3 % and 1 % for and , respectively. Measured values of and together with density data were used to calculate the thermal conductivity of sandstone. Theoretically based correlations for the thermal diffusivity (damped harmonic oscillator, DHO) and heat capacity (Debye and Einstein theories) were adopted to accurately represent the measured data. Correlation equations for the thermal diffusivity and heat capacity have been developed using the well-known theoretical asymptotic behavior of and for various temperature ranges (low- and high-temperature limits). The microscopic nature of the effect of temperature on and behavior of sandstone is discussed. Detailed interpretation and testing of the measured property data for sandstone using various existing theoretical and empirical models, in order to check their accuracy, predictive capability, and applicability, are provided.

  20. A Posteriori Error Estimates and Mesh Adaptation Strategy for Discontinuous Galerkin Methods Applied to Diffusion Problems

    Microsoft Academic Search

    Béatrice Rivière; Mary F. Wheeler

    . A posteriori error estimates for locally mass conservative methods forsubsurface ow are presented. These methods are based on discontinuous approximationspaces and referred as Discontinuous Galerkin methods. In the case wherepenalty terms are added to the bilinear form, one obtain the Non-symmetric InteriorPenalty Galerkin methods. In a previous work, we proved a priori exponentialrates of convergence of the methods applied

  1. Optimization of modified Middlebrook 7H11 agar for isolation of Mycobacterium bovis from raw milk cheese.

    PubMed

    Forgrave, R; Donaghy, J A; Fisher, A; Rowe, M T

    2014-10-01

    Reports have highlighted the absence of contemporary peer reviewed publications pertaining to Mycobacterium bovis culture from raw milk and cheese. By replicating traditional methods, cheese-making methodology and equipment were devised to produce Cheddar (n = 6) and Caerphilly (n = 3) artificially contaminated with M. bovis (three genotypes) under stringent laboratory-containment guidelines for handling hazardous microbiological material. Middlebrook 7H11, modified for M. bovis isolation, was assessed for capacity to enumerate M. bovis despite changing cheese microflora and prolonged M. bovis exposure to the cheese matrix using maturing cheese test portions (n = 63; up to 16 weeks). Malachite green (MG) containing media isolated M. bovis at significantly (P < 0·05) lower levels than unmodified Middlebrook 7H11 agar despite MG being a common adjunct of Middlebrook 7H11 agar modified for M. bovis growth. Subsequently, a selective MG-free Middlebrook 7H11 agar modified using haemolysed red cells and calf serum was demonstrated as the best performing (P < 0·05) medium for recovery of M. bovis from typical UK cheese types, Cheddar and Caerphilly. Significance and impact of the study: Following increased M. bovis infection of UK cattle, the risk posed to consumers from consumption of unpasteurized milk and dairy products has changed. Furthermore, published methods for the culture and molecular detection of M. bovis in raw milk products are limited. Cheese-making protocols and M. bovis culture media reported here provide tools for further investigation of M. bovis survival during all stages of cheese manufacture and could inform future assessment of the risk to consumers from M. bovis contamination of unpasteurized dairy products. PMID:24888395

  2. A fresh liver agar substrate for rearing small numbers of forensically important blow flies (Diptera: Calliphoridae)

    USGS Publications Warehouse

    Gruner, Susan V.; Slone, Daniel H.

    2014-01-01

    Forensically important calliphorids can be reared on a mixture of beef liver and agar. Small pieces of meat, especially fresh or frozen beef liver, will desiccate in 2–6 h, but this simple-to-make feeding substrate remains moist for at least 12 h at 25 and 30°C without desiccation, even in small (5 g) amounts. We determined the survivorship of small numbers of Chrysomya megacephala (F.) (first-instar larvae to adult eclosion) raised on 5 g of liver agar and fresh beef liver. We found that all larvae raised on 5 g of liver died due to desiccation, but survivorship on 5 g of liver agar was equivalent to that on larger (50 g) pieces of either liver agar or beef liver.

  3. Proton beam writing of microstructures in Agar gel for patterned cell growth

    NASA Astrophysics Data System (ADS)

    Larisch, Wolfgang; Koal, Torsten; Werner, Ronald; Hohlweg, Marcus; Reinert, Tilo; Butz, Tilman

    2011-10-01

    A rather useful prerequisite for many biological and biophysical studies, e.g., for cell-cell communication or neuronal networks, is confined cell growth on micro-structured surfaces. Solidified Agar layers have smooth surfaces which are electrically neutral and thus inhibit receptor binding and cell adhesion. For the first time, Agar microstructures have been manufactured using proton beam writing (PBW). In the irradiated Agar material the polysaccharides are split into oligosaccharides which can easily be washed off leaving Agar-free areas for cell adhesion. The beam diameter of 1 ?m allows the fabrication of compartments accommodating single cells which are connected by micrometer-sized channels. Using the external beam the production process is very fast. Up to 50 Petri dishes can be produced per day which makes this technique very suitable for biological investigations which require large throughputs.

  4. Preparation, Optimization, and Screening of the Effect of Processing Variables on Agar Nanospheres Loaded with Bupropion HCl by a D-Optimal Design

    PubMed Central

    Varshosaz, Jaleh; Zaki, Mohammad Reza; Minaiyan, Mohsen; Banoozadeh, Jaafar

    2015-01-01

    Bupropion is an atypical antidepressant drug. Fluctuating in its serum levels following oral administration of immediate release dosage forms leads to occasional seizure. The aim of the present work was designing of sustained release bupropion HCl nanospheres suited for pulmonary delivery. Agar nanospheres were prepared by transferring the w/o emulsion to solid in oil (s/o) suspension. Calcium chloride was used as cross-linking agent and hydroxypropyl ?-cyclodextrin (HP?CD) was used as permeability enhancer. A response surface D-optimal design was used for optimization of nanospheres. Independent factors included in the design were calcium chloride percent, speed of homogenization, agar percent, and HP?CD percent. Optimum condition was predicted to be achieved when the calcium chloride was set at 7.19%, homogenization speed at 8500?rpm, agar content at 2%, and HP?CD at 0.12%. The optimized nanoparticles showed particle size of 587?nm, zeta potential of ?30.9?mV, drug loading efficiency of 38.6%, and release efficiency of 51% until 5?h. The nanospheres showed high degree of bioadhesiveness. D-optimal response surface method is a satisfactory design to optimize the fabrication of bupropion HCl loaded agar nanospheres and these nanospheres can be successively exploited to deliver bupropion in a controlled manner for a sufficiently extended period.

  5. A posteriori optimization of parameters in stabilized methods for convection-diffusion

    E-print Network

    John, Volker

    . Exemplarily, this framework is applied to the SUPG finite element method and the minimization of a residual: Stabilized finite element methods, parameter optimization by minimizing a target functional, SUPG method 1

  6. Iterative Local Solvers for Distributed KrylovSchwarz Method Applied to ConvectionDiffusion Problems

    E-print Network

    Coutinho, Alvaro L. G. A.

    , as first proposed with the SUPG Method (Stream­ line Upwind Petrov Galerkin Method) [1] to the scalar, the SUPG method is used to solve convection dominated problems to verify the behavior of the proposed

  7. A new measurement method for nitrogen oxides in the air using an annular diffusion scrubber coated with titanium dioxide

    NASA Astrophysics Data System (ADS)

    Komazaki, Yuichi; Shimizu, Hiroki; Tanaka, Shigeru

    A new convenient measurement method of nitrogen oxides (NO x) in the ambient air was developed. The collection of NO x is performed by an annular diffusion scrubber coated with a mixture of titanium dioxide (TiO 2) and hydroxyapatite (Ca 10(PO 4) 6(OH) 2) and the analysis is carried out by ion chromatography with conductivity detection. Under ultraviolet light (UV) illumination, TiO 2 produces reactive oxygen species such as super oxide (O 2-), hydroxyl radical (OH·) and peroxyhydroxyl radical (HO 2·), by which nitric oxide (NO) is oxidized to nitrogen dioxide (NO 2), and is further oxidized to nitric acid (HNO 3). The yielded HNO 3 and NO 2 are effectively adsorbed on the surface of TiO 2 and hydroxyapatite. The collection efficiencies of NO and NO 2 by the annular diffusion scrubber coated with the catalysts under UV illumination are higher than 98%, respectively, at the air flow rate of 0.2-1.0 l min -1. After the collection of NO x, by feeding deionized water into the annular diffusion scrubber, HNO 3 and NO 2 which adsorbed on the catalysts are extracted as forms of nitrite ion (NO 2-) and nitrate ion (NO 3-). The extraction efficiencies of NO and NO 2 are almost 100%. The activity of the washed catalysts can be completely recovered by drying with the purified air. Further, a simultaneous separated measurement of NO and NO 2 can be performed by utilizing the UV illumination dependence. This method was applied to the measurement of NO x in the ambient air. The NO x concentration measured by this method was in good agreement with that obtained using the chemiluminescence NO x analyzer.

  8. Plasma processing of the silicon surface: A novel method to reduce transient enhanced diffusion of boron

    NASA Astrophysics Data System (ADS)

    Mannino, Giovanni; Priolo, Francesco; Privitera, Vittorio; Raineri, Vito; Spinella, Corrado; Napolitani, Enrico; Carnera, Alberto; Arena, Giuseppe; Messina, Alberto; Rapisarda, Cirino

    1998-12-01

    We investigate in detail the effect of plasma processing on the transient enhanced diffusion of implanted boron in silicon. Thermally oxidized silicon wafers were first processed with CHF3/CF4 plasma and subsequently implanted with boron, with energies ranging from 3 to 20 keV and a dose of 1×1013/cm2. Chemical profiles were measured by secondary ion mass spectrometry while lattice extended defects induced in silicon by plasma processing were characterized by transmission electron microscopy. Secondary ion mass spectrometry measurements reveal that the transient enhanced diffusion of boron after rapid thermal annealing is strongly reduced in plasma processed samples with respect to unprocessed samples. Defects induced by plasma processing are responsible for the reduction by acting as very efficient traps for the interstitial atoms generated during the implant. We note that the trapping efficiency is critically dependent on the projected range of the boron implant, being extremely evident at low energies and less marked as the energy is increased (i.e., when the interstitials generated by the B implant are far away from the trapping sites). By varying the plasma conditions (an argon plasma is used instead of a CHF3/CF4 plasma), we are able to establish a general correlation between trapping defect centers and transient enhanced diffusion reduction. Finally, spreading resistance measurements reveal that the amount of electrically active boron in plasma processed pure epitaxial Si is almost equal to that obtained in samples not exposed to plasma bombardment, thus demonstrating that the plasma processing has no detrimental effect on the boron electrical activation.

  9. Gas diffusion liquid storage bag and method of use for storing blood

    NASA Technical Reports Server (NTRS)

    Bank, H.; Cleland, E. L. (inventors)

    1979-01-01

    The shelf life of stored whole blood may be doubled by adding a buffer which maintains a desired pH level. However, this buffer causes the generation of CO2 which, if not removed at a controlled rate, causes the pH value of the blood to decrease, which shortens the useful life of the blood. A blood storage bag is described which permits the CO2 to be diffused out at a controlled rate into the atmosphere, thereby maintaining the desired pH value and providing a bag strong enough to permit handling.

  10. A remark on least-squares mixed element methods for reaction-diffusion problems

    NASA Astrophysics Data System (ADS)

    Rui, Hongxing; Kim, Seokchan; Kim, Sang Dong

    2007-05-01

    In this paper, we propose a least-squares mixed element procedure for a reaction-diffusion problem based on the first-order system. By selecting the least-squares functional properly, the resulting procedure can be split into two independent symmetric positive definite schemes, one of which is for the unknown variable and the other of which is for the unknown flux variable, which lead to the optimal order H1([Omega]) and L2([Omega]) norm error estimates for the primal unknown and optimal H(div;[Omega]) norm error estimate for the unknown flux. Finally, we give some numerical examples.

  11. Influence of agar gel properties on the in vitro micropropagation of different clones of Thuja plicata.

    PubMed

    Pochet, B; Scoman, V; Mestdagh, M M; Moreau, B; Andre, P

    1991-10-01

    The influence of four agar-type polysaccharides, used as solidifying agents for culture media and differing in their sulfate content (0.14 to 10.95 % w/w), was tested on the budding and the elongation of five clones of Thuja plicata. Budding is reduced on the most sulfated polysaccharide and the differences observed between clones in elongation are as important as those observed between agar types. PMID:24221734

  12. Application of the Space-Time Conservation Element and Solution Element Method to One-Dimensional Advection-Diffusion Problems

    NASA Technical Reports Server (NTRS)

    Wang, Xiao-Yen; Chow, Chuen-Yen; Chang, Sin-Chung

    1999-01-01

    Test problems are used to examine the performance of several one-dimensional numerical schemes based on the space-time conservation and solution element (CE/SE) method. Investigated in this paper are the CE/SE schemes constructed previously for solving the linear unsteady advection-diffusion equation and the schemes derived here for solving the nonlinear viscous and inviscid Burgers equations. In comparison with the numerical solutions obtained using several traditional finite-difference schemes with similar accuracy, the CE/SE solutions display much lower numerical dissipation and dispersion errors.

  13. The combination methodic of diffusion and implantation technologies for creating optic wave-guided layers in lithium niobate

    NASA Astrophysics Data System (ADS)

    Orlikov, L. N.; Orlikov, N. L.; Arestov, S. I.; Mambetova, K. M.; Shandarov, S. M.

    2015-04-01

    The implantation of copper into Lithium Niobate in the prohibited crystal zone forms a definite energetic level for optic transits. This paper examines conditions of optic wave-guided layers formation on Niobate Lithium due to the method of implantation copper ions with the next diffusion. Reflect Spectrum in consequences implantation is extended. The transfer of the optical power from the primary beam into the another beam was discovered and in reverse. Photo galvanic characteristics of implantation specimen identity of crystal by traditional technology and doping CuO manufacture.

  14. Evaluation of a central-difference-like method for the solution of the convection-diffusion equation

    SciTech Connect

    Tzanos, C.P.

    1990-01-01

    For the numerical solution of the transport equation that describes the convection and diffusion of various physical quantities (e.g., momentum, heat, and material concentrations) first-order upwind schemes are widely used. For example, first order upwind differencing is used in codes like COMMIX and PHOENICS. These schemes are simple and always give oscillation-free and physically plausible solutions. However, due to false diffusion, at high Peclet numbers their accuracy on practical meshes is poor. In previous work, a central-difference-like method was presented that even with a coarse mesh produces oscillation-free solutions and of superior accuracy than the upwind scheme. For the evaluation of this method, previous work used the test problem of Smith and Hutton for Peclet numbers ranging from 10 to {infinity}. To further evaluate this method, in this work results are presented from its application to another benchmark problem of computational fluid dynamics. This problem is laminar isothermal flow in a square cavity driven by a sliding lid. 7 refs., 1 fig.

  15. Reaction-diffusion textures

    Microsoft Academic Search

    Andrew P. Witkin; Michael Kass

    1991-01-01

    We present a method for texture synthesis based on the simulation of a process of local nonlinear interaction, called reaction-diffusion, which has been proposed as a model of biological pattern formation. We extend traditional reaction-diffusion systems by allowing anisotropic and spatially non-uniform diffusion, as well as multiple competing directions of diffusion. We adapt reaction-diffusion system to the needs of computer

  16. Cultivation characteristics and gene expression profiles of Aspergillus oryzae by membrane-surface liquid culture, shaking-flask culture, and agar-plate culture

    Microsoft Academic Search

    Hiroyuki Imanaka; Soukichi Tanaka; Bin Feng; Koreyoshi Imamura; Kazuhiro Nakanishi

    2010-01-01

    We cultivated a filamentous fungus, Aspergillus oryzae IAM 2706 by three different cultivation methods, i.e., shaking-flask culture (SFC), agar-plate culture (APC), and membrane-surface liquid culture (MSLC), to elucidate the differences of its behaviors by different cultivation methods under the same media, by measuring the growth, secretion of proteases and ?-amylase, secreted protein level, and gene transcriptional profile by the DNA

  17. Complex impedance and conductivity of agar-based ion-conducting polymer electrolytes

    NASA Astrophysics Data System (ADS)

    Nwanya, A. C.; Amaechi, C. I.; Udounwa, A. E.; Osuji, R. U.; Maaza, M.; Ezema, F. I.

    2015-04-01

    Agar-based electrolyte standing films with different salts and weak acids as ion and proton conductors were prepared and characterized by X-ray diffraction, UV-visible spectrophotometry, photoluminescence emission spectroscopy and electrochemical impedance spectroscopy. The salts used are lithium perchlorate (LiClO4) and potassium perchlorate (KClO4), while the weak acids used are acetic acid (CH3COOH) and lactic acid (C3H6O3). The values of the ion conductivity obtained for the agar-based polymer films are 6.54 × 10-8, 9.12 × 10-8, 3.53 × 10-8, 2.24 × 10-8 S/cm for the agar/acetic acid, agar/lactic acid, agar/LiClO4 and agar/KClO4 polymer films, respectively. As a function of temperature, the ion conductivity exhibits an Arrhenius behavior and the estimated activation energy is ?0.1 eV for all the samples. The samples depicted high values of dielectric permittivity toward low frequencies which is due mostly to electrode polarization effect. The samples showed very high transparency (85-98 %) in the visible region, and this high transparency is one of the major requirements for application in electrochromic devices (ECD). The values of conductivity and activation energy obtained indicate that the electrolytes are good materials for application in ECD.

  18. [Methicillin resistance detection in Staphylococcus aureus: comparison between conventional methods and MRSA-Screen latex agglutination technique].

    PubMed

    Soloaga, R; Corso, A; Gagetti, P; Faccone, D; Galas, M

    2004-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a significant pathogen that has emerged over the last four decades, causing both nosocomial and community-acquired infections. Rapid and accurate detection of methicillin resistance in S. aureus is important for the use of appropriate antimicrobial therapy and for the control of nosocomial spread of MRSA strains. We evaluated the efficiency of conventional methods for detection of methicillin resistance such as the disk diffusion, agar dilution, oxacillin agar screen test, and the latex agglutination test MRSA-Screen latex, in 100 isolates of S. aureus, 79 mecA positive and 21 mecA negative. The MRSA-Screen latex (Denka Seiken, Niigata, Japón), is a latex agglutination method that detects the presence of PLP-2a, product of mecA gene in S. aureus. The PCR of the mecA gene was used as the "gold standard" for the evaluation of the different methods tested. The percentages of sensitivity and specificity were as follows: disk difusión 97 and 100%, agar dilution 97 and 95%, oxacillin agar screen test 100 and 100%, and MRSA-Screen latex, 100 and 100 %. All methods presented high sensitivity and specificity, but MRSA-Screen latex had the advantage of giving a reliable result, equivalent to PCR, in only 15 minutes. PMID:15174748

  19. A comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries

    NASA Astrophysics Data System (ADS)

    Tauriello, Gerardo; Koumoutsakos, Petros

    2015-02-01

    We present a comparative study of penalization and phase field methods for the solution of the diffusion equation in complex geometries embedded using simple Cartesian meshes. The two methods have been widely employed to solve partial differential equations in complex and moving geometries for applications ranging from solid and fluid mechanics to biology and geophysics. Their popularity is largely due to their discretization on Cartesian meshes thus avoiding the need to create body-fitted grids. At the same time, there are questions regarding their accuracy and it appears that the use of each one is confined by disciplinary boundaries. Here, we compare penalization and phase field methods to handle problems with Neumann and Robin boundary conditions. We discuss extensions for Dirichlet boundary conditions and in turn compare with methods that have been explicitly designed to handle Dirichlet boundary conditions. The accuracy of all methods is analyzed using one and two dimensional benchmark problems such as the flow induced by an oscillating wall and by a cylinder performing rotary oscillations. This comparative study provides information to decide which methods to consider for a given application and their incorporation in broader computational frameworks. We demonstrate that phase field methods are more accurate than penalization methods on problems with Neumann boundary conditions and we present an error analysis explaining this result.

  20. Diffuse Optical Tomography for Brain Imaging: Continuous Wave Instrumentation and Linear Analysis Methods

    NASA Astrophysics Data System (ADS)

    Giacometti, Paolo; Diamond, Solomon G.

    Diffuse optical tomography (DOT) is a functional brain imaging technique that measures cerebral blood oxygenation and blood volume changes. This technique is particularly useful in human neuroimaging measurements because of the coupling between neural and hemodynamic activity in the brain. DOT is a multichannel imaging extension of near-infrared spectroscopy (NIRS). NIRS uses laser sources and light detectors on the scalp to obtain noninvasive hemodynamic measurements from spectroscopic analysis of the remitted light. This review explains how NIRS data analysis is performed using a combination of the modified Beer-Lambert law (MBLL) and the diffusion approximation to the radiative transport equation (RTE). Laser diodes, photodiode detectors, and optical terminals that contact the scalp are the main components in most NIRS systems. Placing multiple sources and detectors over the surface of the scalp allows for tomographic reconstructions that extend the individual measurements of NIRS into DOT. Mathematically arranging the DOT measurements into a linear system of equations that can be inverted provides a way to obtain tomographic reconstructions of hemodynamics in the brain.

  1. A mass-conserved diffuse interface method and its application for incompressible multiphase flows with large density ratio

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Shu, C.; Shao, J. Y.; Wu, J.; Niu, X. D.

    2015-06-01

    In this work a mass-conserved diffuse interface method is proposed for simulating incompressible flows of binary fluids with large density ratio. In the method, a mass correction term is introduced into the Cahn-Hilliard equation to compensate the mass losses or offset the mass increases caused by the numerical and modeling diffusion. Since the mass losses or increases are through the phase interfaces and at each time step, their values are very small, to keep mass conservation, mass sources or sinks are introduced and uniformly distributed in the volume of diffuse layer. With the uniform distribution, the mass correction term representing mass sources or sinks is derived analytically by applying mass conservation principle. By including the mass correction, the modified Cahn-Hilliard equation is solved by the fifth-order upwind scheme to capture the phase field of the bindery fluids. The flow field is simulated by the newly-developed multiphase lattice Boltzmann flux solver [20]. The proposed approach is validated by simulating the Laplace law, the merging of two bubbles, Rayleigh-Taylor instability and bubble rising under gravity with density ratio of 1000 and viscosity ratio of 100. Numerical results of interface shapes and flow properties agree well with both analytical solutions and benchmark data in the literature. Numerical results also show that the mass is well-conserved in all cases considered. In addition, it is demonstrated that the mass correction term at each time step is in the order of 10-4 ?10-5, which is a small number compared with the magnitude of order parameter.

  2. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets

    SciTech Connect

    Hsu, Po Jen; Lai, S. K., E-mail: sklai@coll.phy.ncu.edu.tw [Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320, Taiwan and Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan (China); Rapallo, Arnaldo [Istituto per lo Studio delle Macromolecole (ISMAC) Consiglio Nazionale delle Ricerche (CNR), via E. Bassini 15, C.A.P 20133 Milano (Italy)] [Istituto per lo Studio delle Macromolecole (ISMAC) Consiglio Nazionale delle Ricerche (CNR), via E. Bassini 15, C.A.P 20133 Milano (Italy)

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in ?-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended ?-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form ? turns or ? helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations.

  3. Peptide dynamics by molecular dynamics simulation and diffusion theory method with improved basis sets.

    PubMed

    Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo

    2014-03-14

    Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in ?-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended ?-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form ? turns or ? helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit solvent, we performed in this work the classical molecular dynamics simulation on a realistic model solution with the peptide embedded in an explicit water environment, and calculated its dynamic properties both as an outcome of the simulations, and by the diffusion theory in reduced statistical-mechanical approach within HBA on the premise that the mode-coupling approach to the diffusion theory can give both the long-range and local dynamics starting from equilibrium averages which were obtained from detailed atomistic simulations. PMID:24628208

  4. Using the apparent diffusion coefficient to identifying MGMT promoter methylation status early in glioblastoma: importance of analytical method

    PubMed Central

    Rundle-Thiele, Dayle; Day, Bryan; Stringer, Brett; Fay, Michael; Martin, Jennifer; Jeffree, Rosalind L; Thomas, Paul; Bell, Christopher; Salvado, Olivier; Gal, Yaniv; Coulthard, Alan; Crozier, Stuart; Rose, Stephen

    2015-01-01

    Introduction Accurate knowledge of O6-methylguanine methyltransferase (MGMT) gene promoter subtype in patients with glioblastoma (GBM) is important for treatment. However, this test is not always available. Pre-operative diffusion MRI (dMRI) can be used to probe tumour biology using the apparent diffusion coefficient (ADC); however, its ability to act as a surrogate to predict MGMT status has shown mixed results. We investigated whether this was due to variations in the method used to analyse ADC. Methods We undertook a retrospective study of 32 patients with GBM who had MGMT status measured. Matching pre-operative MRI data were used to calculate the ADC within contrast enhancing regions of tumour. The relationship between ADC and MGMT was examined using two published ADC methods. Results A strong trend between a measure of ‘minimum ADC’ and methylation status was seen. An elevated minimum ADC was more likely in the methylated compared to the unmethylated MGMT group (U = 56, P = 0.0561). In contrast, utilising a two-mixture model histogram approach, a significant reduction in mean measure of the ‘low ADC’ component within the histogram was associated with an MGMT promoter methylation subtype (P < 0.0246). Conclusion This study shows that within the same patient cohort, the method selected to analyse ADC measures has a significant bearing on the use of that metric as a surrogate marker of MGMT status. Thus for dMRI data to be clinically useful, consistent methods of data analysis need to be established prior to establishing any relationship with genetic or epigenetic profiling.

  5. Synthesis and characterization of high-surface-area millimeter-sized silica beads with hierarchical multi-modal pore structure by the addition of agar

    SciTech Connect

    Han, Yosep; Choi, Junhyun [Department of Mineral Resources and Energy Engineering, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do 561–756 (Korea, Republic of); Tong, Meiping, E-mail: tongmeiping@iee.pku.edu.cn [The Key Laboratory of Water and Sediment Sciences, Ministry of Education, College of Environmental Sciences and Engineering, Peking University, Beijing 100871 (China); Kim, Hyunjung, E-mail: kshjkim@jbnu.ac.kr [Department of Mineral Resources and Energy Engineering, Chonbuk National University, 567 Baekje-daero, Deokjin-gu, Jeonju-si, Jeollabuk-do 561–756 (Korea, Republic of)

    2014-04-01

    Millimeter-sized spherical silica foams (SSFs) with hierarchical multi-modal pore structure featuring high specific surface area and ordered mesoporous frameworks were successfully prepared using aqueous agar addition, foaming and drop-in-oil processes. The pore-related properties of the prepared spherical silica (SSs) and SSFs were systematically characterized by field emission-scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), small-angle X-ray diffraction (SAXRD), Hg intrusion porosimetry, and N{sub 2} adsorption–desorption isotherm measurements. Improvements in the BET surface area and total pore volume were observed at 504 m{sup 2} g{sup ?1} and 5.45 cm{sup 3} g{sup ?1}, respectively, after an agar addition and foaming process. Despite the increase in the BET surface area, the mesopore wall thickness and the pore size of the mesopores generated from the block copolymer with agar addition were unchanged based on the SAXRD, TEM, and BJH methods. The SSFs prepared in the present study were confirmed to have improved BET surface area and micropore volume through the agar loading, and to exhibit interconnected 3-dimensional network macropore structure leading to the enhancement of total porosity and BET surface area via the foaming process. - Highlights: • Millimeter-sized spherical silica foams (SSFs) are successfully prepared. • SSFs exhibit high BET surface area and ordered hierarchical pore structure. • Agar addition improves BET surface area and micropore volume of SSFs. • Foaming process generates interconnected 3-D network macropore structure of SSFs.

  6. Nonlinear variants of the TR/BDF2 method for thermal radiative diffusion

    SciTech Connect

    Edwards, Jarrod D. [Department of Nuclear Engineering, 129 Zachry Engineering Center, TAMU 3133, Texas A and M University, College Station, Texas 77843 (United States); Morel, Jim E., E-mail: morel@tamu.ed [Department of Nuclear Engineering, 129 Zachry Engineering Center, TAMU 3133, Texas A and M University, College Station, Texas 77843 (United States); Knoll, Dana A. [Fluid Dynamics and Solid Mechanics Group T-3, Los Alamos National Laboratory, P.O. Box 1663, MS B216, Los Alamos, NM 87545 (United States)

    2011-02-20

    We apply the Trapezoidal/BDF2 (TR/BDF2) temporal discretization scheme to nonlinear grey radiative diffusion. This is a scheme that is not well-known within the radiation transport community, but we show that it offers many desirable characteristics relative to other second-order schemes. Several nonlinear variants of the TR/BDF2 scheme are defined and computationally compared with the Crank-Nicholson scheme. It is found for our test problems that the most accurate TR/BDF2 schemes are those that are fully iterated to nonlinear convergence, but the most efficient TR/BDF2 scheme is one based upon a single Newton iteration. It is also shown that neglecting the contributions to the Jacobian matrix from the cross-sections, which is often done due to a lack of smooth interpolations for tabular cross-section data, has a significant impact upon efficiency.

  7. A coarse-mesh nodal diffusion method based on response matrix considerations

    E-print Network

    Henry, Allan F.

    1977-01-01

    The overall objective of this thesis is to develop an economical computational method for multidimensional transient analysis of nuclear power reactors. Specifically, the application of nodal methods based on the multigroup ...

  8. Finite element methods for time-dependent convectiondiffusionreaction equations with small diffusion

    E-print Network

    John, Volker

    include the streamline-upwind Petrov­Galerkin (SUPG) method with different parameters, various spurious-upwind Petrov­Galerkin (SUPG) method [30,7] with the parameter from [49] was used. This approach led to computed

  9. Iterative Domain Decomposition Methods for Singularly Perturbed Nonlinear Convection-Diffusion Equations

    E-print Network

    Farrell, Paul A.

    Iterative Domain Decomposition Methods for Singularly Perturbed Nonlinear Convection method for a boundary value problem in the case of singularly perturbed nonlinear convection and parallel iterative schemes, for a singularly perturbed nonlinear boundary value problem consisting

  10. A combined kick-out and dissociative diffusion mechanism of grown-in Be in InGaAs and InGaAsP. A new finite difference-Bairstow method for solution of the diffusion equations

    SciTech Connect

    Koumetz, Serge D., E-mail: Serge.Koumetz@univ-rouen.fr; Martin, Patrick; Murray, Hugues [Normandie Université-Université de Rouen-ENSICAEN-UMR 6508 LaMIPS, Laboratoire commun CNRS-NXP-PRESTO-ENSICAEN-UCBN 2, rue de la Girafe BP 5120, F-14079 Caen (France)

    2014-09-14

    Experimental results on the diffusion of grown-in beryllium (Be) in indium gallium arsenide (In{sub 0.53}Ga{sub 0.47}As) and indium gallium arsenide phosphide (In{sub 0.73}Ga{sub 0.27}As{sub 0.58}P{sub 0.42}) gas source molecular beam epitaxy alloys lattice-matched to indium phosphide (InP) can be successfully explained in terms of a combined kick-out and dissociative diffusion mechanism, involving neutral Be interstitials (Be{sub i}{sup 0}), singly positively charged gallium (Ga), indium (In) self-interstitials (I{sub III}{sup +}) and singly positively charged Ga, In vacancies (V{sub III}{sup +}). A new numerical method of solution to the system of diffusion equations, based on the finite difference approximations and Bairstow's method, is proposed.

  11. A combined kick-out and dissociative diffusion mechanism of grown-in Be in InGaAs and InGaAsP. A new finite difference-Bairstow method for solution of the diffusion equations

    NASA Astrophysics Data System (ADS)

    Koumetz, Serge D.; Martin, Patrick; Murray, Hugues

    2014-09-01

    Experimental results on the diffusion of grown-in beryllium (Be) in indium gallium arsenide (In0.53Ga0.47As) and indium gallium arsenide phosphide (In0.73Ga0.27As0.58P0.42) gas source molecular beam epitaxy alloys lattice-matched to indium phosphide (InP) can be successfully explained in terms of a combined kick-out and dissociative diffusion mechanism, involving neutral Be interstitials (Bei0), singly positively charged gallium (Ga), indium (In) self-interstitials (IIII+) and singly positively charged Ga, In vacancies (VIII+). A new numerical method of solution to the system of diffusion equations, based on the finite difference approximations and Bairstow's method, is proposed.

  12. Equilibrium and kinetic modelling of Cd(II) biosorption by algae Gelidium and agar extraction algal waste.

    PubMed

    Vilar, Vítor J P; Botelho, Cidália M S; Boaventura, Rui A R

    2006-01-01

    In this study an industrial algal waste from agar extraction has been used as an inexpensive and effective biosorbent for cadmium (II) removal from aqueous solutions. This biosorbent was compared with the algae Gelidium itself, which is the raw material for agar extraction. Equilibrium data follow both Langmuir and Redlich-Peterson models. The parameters of Langmuir equilibrium model are q(max)=18.0 mgg(-1), b=0.19 mgl(-1) and q(max)=9.7 mgg(-1), b=0.16 mgl(-1), respectively for Gelidium and the algal waste. Kinetic experiments were conducted at initial Cd(II) concentrations in the range 6-91 mgl(-1). Data were fitted to pseudo-first- and second-order Lagergren models. For an initial Cd(II) concentration of 91 mgl(-1) the parameters of the pseudo-first-order Lagergren model are k(1,ads)=0.17 and 0.87 min(-1); q(eq)=16.3 and 8.7 mgg(-1), respectively, for Gelidium and algal waste. Kinetic constants vary with the initial metal concentration. The adsorptive behaviour of biosorbent particles was modelled using a batch reactor mass transfer kinetic model. The model successfully predicts Cd(II) concentration profiles and provides significant insights on the biosorbents performance. The homogeneous diffusivity, D(h), is in the range 0.5-2.2 x10(-8) and 2.1-10.4 x10(-8)cm(2)s(-1), respectively, for Gelidium and algal waste. PMID:16380148

  13. Differentiation between Primary Cerebral Lymphoma and Glioblastoma Using the Apparent Diffusion Coefficient: Comparison of Three Different ROI Methods

    PubMed Central

    Ahn, Sung Jun; Shin, Hyun Joo; Chang, Jong-Hee; Lee, Seung-Koo

    2014-01-01

    Objective Apparent diffusion coefficients (ADC) can help differentiate between central nervous system (CNS) lymphoma and Glioblastoma (GBM). However, overlap between ADCs for GBM and lymphoma have been reported because of various region of interest (ROI) methods. Our aim is to explore ROI method to provide the most reproducible results for differentiation. Materials and Methods We studied 25 CNS lymphomas and 62 GBMs with three ROI methods: (1) ROI1, whole tumor volume; (2) ROI2, multiple ROIs; and (3) ROI3, a single ROI. Interobserver variability of two readers for each method was analyzed by intraclass correlation(ICC). ADCs were compared between GBM and lymphoma, using two-sample t-test. The discriminative ability was determined by ROC analysis. Results ADCs from ROI1 showed most reproducible results (ICC >0.9). For ROI1, ADCmean for lymphoma showed significantly lower values than GBM (p?=?0.03). The optimal cut-off value was 0.98×10?3 mm2/s with 85% sensitivity and 90% specificity. For ROI2, ADCmin for lymphoma was significantly lower than GBM (p?=?0.02). The cut-off value was 0.69×10?3 mm2/s with 87% sensitivity and 88% specificity. Conclusion ADC values were significantly dependent on ROI method. ADCs from the whole tumor volume had the most reproducible results. ADCmean from the whole tumor volume may aid in differentiating between lymphoma and GBM. However, multi-modal imaging approaches are recommended than ADC alone for differentiation. PMID:25393543

  14. Chromium and zinc uptake by algae Gelidium and agar extraction algal waste: kinetics and equilibrium.

    PubMed

    Vilar, Vítor J P; Botelho, Cidália M S; Boaventura, Rui A R

    2007-11-19

    Biosorption of chromium and zinc ions by an industrial algal waste, from agar extraction industry has been studied in a batch system. This biosorbent was compared with the algae Gelidium itself, which is the raw material for agar extraction, and the industrial waste immobilized with polyacrylonitrile (composite material). Langmuir and Langmuir-Freundlich equilibrium models describe well the equilibrium data. The parameters of Langmuir equilibrium model at pH 5.3 and 20 degrees C were for the algae, q(L)=18 mg Cr(III)g(-1) and 13 mgZn(II)g(-1), K(L) = 0.021l mg(-1)Cr(III) and 0.026l mg(-1) Zn(II); for the algal waste, q(L)=12 mgCr(III)g(-1) and 7mgZn(II)g(-1), K(L)=0.033lmg(-1) Cr(III) and 0.042l mg(-1) Zn(II); for the composite material, q(L) = 9 mgCr(III)g(-1) and 6 mgZn(II)g(-1), K(L)=0.032l mg(-1)Cr(III) and 0.034l mg(-1)Zn(II). The biosorbents exhibited a higher preference for Cr(III) ions and algae Gelidium is the best one. The pseudo-first-order Lagergren and pseudo-second-order models fitted well the kinetic data for the two metal ions. Kinetic constants and equilibrium uptake concentrations given by the pseudo-second-order model for an initial Cr(III) and Zn(II) concentration of approximately 100 mgl(-1), at pH 5.3 and 20 degrees C were k(2,ads)=0.04 g mg(-1)Cr(III)min(-1) and 0.07 g mg(-1)Zn(II)min(-1), q(eq)=11.9 mgCr(III)g(-1) and 9.5 mgZn(II)g(-1) for algae; k(2,ads)=0.17 g mg(-1)Cr(III)min(-1) and 0.19 g mg(-1)Zn(II)min(-1), q(eq)=8.3 mgCr(III)g(-1) and 5.6 mgZn(II)g(-1) for algal waste; k(2,ads)=0.01 g mg(-1)Cr(III)min(-1) and 0.18 g mg(-1)Zn(II)min(-1), q(eq)=8.0 mgCr(III)g(-1) and 4.4 mgZn(II)g(-1) for composite material. Biosorption was modelled using a batch adsorber mass transfer kinetic model, which successfully predicts Cr(III) and Zn(II) concentration profiles. The calculated average homogeneous diffusivities, D(h), were 4.2 x 10(-8), 8.3 x 10(-8) and 1.4 x 10(-8)cm(2)s(-1) for Cr(III) and 4.8 x 10(-8), 9.7 x 10(-8) and 6.2 x 10(-8)cm(2)s(-1) for Zn(II), respectively, for Gelidium, algal waste and composite material. The algal waste has the lower intraparticle resistance. PMID:17507158

  15. Effect of Crystal Defects on Minority Carrier Diffusion Length in 6H SiC Measured Using the Electron Beam Induced Current Method

    NASA Technical Reports Server (NTRS)

    Tabib-Azar, Massood

    1997-01-01

    We report values of minority carrier diffusion length in n-type 6H SiC measured using a planar Electron Beam Induced Current (EBIC) method. Values of hole diffusion length in defect free regions of n-type 6H SiC, with a doping concentration of 1.7El7 1/cu cm, ranged from 1.46 microns to 0.68 microns. We next introduce a novel variation of the planar method used above. This 'planar mapping' technique measured diffusion length along a linescan creating a map of diffusion length versus position. This map is then overlaid onto the EBIC image of the corresponding linescan, allowing direct visualization of the effect of defects on minority carrier diffusion length. Measurements of the above n-type 6H SiC resulted in values of hole diffusion length ranging from 1.2 micron in defect free regions to below 0.1 gm at the center of large defects. In addition, measurements on p-type 6H SiC resulted in electron diffusion lengths ranging from 1.42 micron to 0.8 micron.

  16. Comparison of passive diffusion bag samplers and submersible pump sampling methods for monitoring volatile organic compounds in ground water at Area 6, Naval Air Station, Whidbey Island, Washington

    USGS Publications Warehouse

    Huffman, Raegan L.

    2002-01-01

    Ground-water samples were collected in April 1999 at Naval Air Station Whidbey Island, Washington, with passive diffusion samplers and a submersible pump to compare concentrations of volatile organic compounds (VOCs) in water samples collected using the two sampling methods. Single diffusion samplers were installed in wells with 10-foot screened intervals, and multiple diffusion samplers were installed in wells with 20- to 40-foot screened intervals. The diffusion samplers were recovered after 20 days and the wells were then sampled using a submersible pump. VOC concentrations in the 10-foot screened wells in water samples collected with diffusion samplers closely matched concentrations in samples collected with the submersible pump. Analysis of VOC concentrations in samples collected from the 20- to 40-foot screened wells with multiple diffusion samplers indicated vertical concentration variation within the screened interval, whereas the analysis of VOC concentrations in samples collected with the submersible pump indicated mixing during pumping. The results obtained using the two sampling methods indicate that the samples collected with the diffusion samplers were comparable with and can be considerably less expensive than samples collected using a submersible pump.

  17. A reduced-space basis function neural network method for diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Kim, Hyun Keol; Gunther, Jacqueline; Hoi, Jennifer; Hielscher, Andreas H.

    2015-03-01

    We propose here a reduced space image reconstruction method that makes use of basis function neural network (BFNN) within a framework of PDE-constrained algorithm. This method reduces the solution space using the basis function approach, and finds the optimal solution through the learning process of neural network. The basis function approach improves the ill-posed nature of an original inverse problem, reducing the number of unknowns as well as regularizing the solution automatically. The proposed method was applied to breast cancer imaging, and the reconstruction performance was evaluated on how well the method can identify the tumor location in breast tissue. The results show that the BFNN method gives better results in the identification of tumor location than the traditional element-based reconstruction method.

  18. A Monte Carlo Synthetic-Acceleration Method for Solving the Thermal Radiation Diffusion Equation

    SciTech Connect

    Evans, Thomas M [ORNL] [ORNL; Mosher, Scott W [ORNL] [ORNL; Slattery, Stuart [University of Wisconsin, Madison] [University of Wisconsin, Madison

    2014-01-01

    We present a novel synthetic-acceleration based Monte Carlo method for solving the equilibrium thermal radiation diusion equation in three dimensions. The algorithm performance is compared against traditional solution techniques using a Marshak benchmark problem and a more complex multiple material problem. Our results show that not only can our Monte Carlo method be an eective solver for sparse matrix systems, but also that it performs competitively with deterministic methods including preconditioned Conjugate Gradient while producing numerically identical results. We also discuss various aspects of preconditioning the method and its general applicability to broader classes of problems.

  19. An optical method for the analysis of the exitance diffused by light-transmitting fiber post

    NASA Astrophysics Data System (ADS)

    Cattini, Stefano; Rovati, Luigi

    2011-03-01

    The paper is focused on the description of a measurement procedure and image analysis technique able to easily estimate the exitance diffused by light-transmitting posts. The exitance has been measured by making use of a digital colour camera (DP20, Olympus) coupled to the optics of a microscope (SZX12, Olympus). Posts have been illuminated by using: a blue LED source (LS-450 Blue LED, Ocean Optics) with emission peak close to camphorquinone activator peak, an optical fibre and an ad-hoc realized post holder. The obtained results demonstrate that different translucent posts give rise to different exitance profiles, thus allowing to reach different polymerization depths along the post, providing different polymerization performances and, requiring different source powers and exposure times. Even though, other factors such us mechanical performances, biocompatibility and aesthetics have to be consider once choosing the more suitable post, the reported measurement procedure and data may help both in choosing the proper post and defining the optimum light-source power and exposure time.

  20. Two-step reconstruction method using global optimization and conjugate gradient for ultrasound-guided diffuse optical tomography

    NASA Astrophysics Data System (ADS)

    Tavakoli, Behnoosh; Zhu, Quing

    2013-01-01

    Ultrasound-guided diffuse optical tomography (DOT) is a promising method for characterizing malignant and benign lesions in the female breast. We introduce a new two-step algorithm for DOT inversion in which the optical parameters are estimated with the global optimization method, genetic algorithm. The estimation result is applied as an initial guess to the conjugate gradient (CG) optimization method to obtain the absorption and scattering distributions simultaneously. Simulations and phantom experiments have shown that the maximum absorption and reduced scattering coefficients are reconstructed with less than 10% and 25% errors, respectively. This is in contrast with the CG method alone, which generates about 20% error for the absorption coefficient and does not accurately recover the scattering distribution. A new measure of scattering contrast has been introduced to characterize benign and malignant breast lesions. The results of 16 clinical cases reconstructed with the two-step method demonstrates that, on average, the absorption coefficient and scattering contrast of malignant lesions are about 1.8 and 3.32 times higher than the benign cases, respectively.