Zhou, Ying; Zhang, Meijuan; Liu, Hui
2015-01-01
Objectives. To develop a new method for determining total antioxidants in serum and to evaluate the total antioxidant capacity of organisms. Design and Methods. Sodium hyposulfite (Na2S2O3) and serum were used to evaluate the linearity and precision of the potassium permanganate agar method. The area of serum diffusion in samples from 30 intensive care unit (ICU) patients compared with 44 healthy subjects was determined by the potassium permanganate agar method. Results. The linearity (R2 in the linear experiment of Na2S2O3 was 0.994; R2 in the linear experiment of serum was 0.987) and precision (coefficient of variation of area of high level serum diffusion within-run, between-run, and between-day and coefficient of variation of area of low serum diffusion within-run, between-run, and between-day were all less than 10%) were acceptable using the potassium permanganate agar method. Total antioxidants of serum between the ICU group and the healthy group were different (p = 0.002, two tailed). Conclusions. Total antioxidants in serum can be determined by the potassium permanganate agar method. The total antioxidant capacity of an organism can be evaluated by the amount of total antioxidants in serum. PMID:26347595
Comparison of the antibacterial activity of chelating agents using the agar diffusion method
Technology Transfer Automated Retrieval System (TEKTRAN)
The agar diffusion assay was used to examine antibacterial activity of 2 metal chelators. Concentrations of 0 to 40 mM of ethylenediaminetetraacetic acid (EDTA) and ethylenediamine-N,N’-disuccinic acid (EDDS) were prepared in 1.0 M potassium hydroxide (KOH). The pH of the solutions was adjusted to 1...
Skóra, Magdalena; Macura, Anna B
2011-01-01
The genus Scopulariopsis is a common soil saprotroph and has been isolated from air, organic waste and also from plant, animal and human tissues. Scopulariopsis has mainly been associated in humans with superficial mycoses, but it has also been described as the cause of subcutaneous and invasive infections. The most common aetiological agent of infections in humans is Scopulariopsis brevicaulis. This species has been reported to be resistant in vitro to broad-spectrum antifungal agents available today. The aim of the study was to establish in vitro antifungal susceptibility of 35 S. brevicaulis strains against amphotericin B (AMB), flucytosine (FC), caspofungin (CAS), terbinafine (TER), ciclopirox (CIC), voriconazole (VOR), clotrimazole (CTR), miconazole (MCZ), econazole (ECO), ketoconazole (KET), itraconazole (ITR), and fluconazole (FLU). Antifungal susceptibility tests were evaluated by an agar diffusion method (Neo-Sensitabs, Rosco, Denmark). AMB, FC, CAS, ITR and FLU showed no antifungal activity against S. brevicaulis. TER, CIC, CTR, KET, VOR, ECO, and MCZ revealed inhibitory activity for S. brevicaulis, but it varied for each of the drugs. The best antifungal effect was observed for TER and CIC. All isolates had large inhibition zones for TER and CIC. CTR was also inhibitory for all tested S. brevicaulis isolates, but the diameters of inhibition zones were smaller than for TER and CIC. Nearly 89% isolates showed inhibition zones for KET and the mean diameter of the inhibition zone was comparable to CTR. The least antifungal activity exhibited VQR, ECO and MCZ. Because of the multiresistance of S. brevicaulis, infections due to this species may not respond to particular antifungal treatment and other therapeutic approaches should be considered, e.g., combined therapy and/or surgery. PMID:21682097
Evaluation of agar diffusion bioassay for nisin quantification.
Pongtharangkul, T; Demirci, A
2004-08-01
The agar diffusion bioassay is the most widely used method for the quantification of nisin, due to its high sensitivity, simplicity, and cost-effectiveness. This method is based on the measurement of the inhibition zone produced in nisin-sensitive microorganisms. The size of the zone is affected by many factors, such as nisin-sensitive strain, amount of added agar and surfactant, and pre-diffusion step. This research aims to evaluate the effects of nisin-sensitive strains and pre-diffusion on the accuracy and precision of nisin quantification. Three strains of nisin-sensitive microorganisms (Micrococcus luteus, Lactobacillus sakei, Brochothrix thermosphacta) were tested along with three different incubation processes. The best combination was the method using L. sakei as an indicator strain with pre-diffusion at 4 degrees C for 24 h. Compared with M. luteus and B. thermosphacta, L. sakei gave more accurate and reproducible results. Moreover, the pre-diffusion step resulted in larger inhibition zones and more precise results. Finally, the best combination was validated and compared with the method that is usually used and the result showed that the method using L. sakei with pre-diffusion gave more accurate and precise results. PMID:14963617
Lo-Ten-Foe, Jerome R.; de Smet, Anne Marie G. A.; Diederen, Bram M. W.; Kluytmans, Jan A. J. W.; van Keulen, Peter H. J.
2007-01-01
Increasing antibiotic resistance in gram-negative bacteria has recently renewed interest in colistin as a therapeutic option. The increasing use of colistin necessitates the availability of rapid and reliable methods for colistin susceptibility testing. We compared seven methods of colistin susceptibility testing (disk diffusion, agar dilution on Mueller-Hinton [MH] and Isosensitest agar, Etest on MH and Isosensitest agar, broth microdilution, and VITEK 2) on 102 clinical isolates collected from patient materials during a selective digestive decontamination or selective oral decontamination trial in an intensive-care unit. Disk diffusion is an unreliable method to measure susceptibility to colistin. High error rates and low levels of reproducibility were observed in the disk diffusion test. The colistin Etest, agar dilution, and the VITEK 2 showed a high level of agreement with the broth microdilution reference method. Heteroresistance for colistin was observed in six Enterobacter cloacae isolates and in one Acinetobacter baumannii isolate. This is the first report of heteroresistance to colistin in E. cloacae isolates. Resistance to colistin in these isolates seemed to be induced upon exposure to colistin rather than being caused by stable mutations. Heteroresistant isolates could be detected in the broth microdilution, agar dilution, Etest, or disk diffusion test. The VITEK 2 displayed low sensitivity in the detection of heteroresistant subpopulations of E. cloacae. The VITEK 2 colistin susceptibility test can therefore be considered to be a reliable tool to determine susceptibility to colistin in isolates of genera that are known not to exhibit resistant subpopulations. In isolates of genera known to (occasionally) exhibit heteroresistance, an alternative susceptibility testing method capable of detecting heteroresistance should be used. PMID:17646414
Modeling development of inhibition zones in an agar diffusion bioassay
Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C
2015-01-01
A two-temperature agar diffusion bioassay is commonly used to quantify the concentration of nisin using Micrococcus luteus as the indicator microorganism. A finite element computational model based on Fick's second law of diffusion was used to predict the radius of the inhibition zone in this diffusion bioassay. The model developed was used to calculate nisin concentration profiles as a function of time and position within the agar. The minimum inhibitory concentration (MIC) of nisin against M. luteus was determined experimentally. The critical time (Tc) for growth of M. luteus within the agar diffusion bioassay was experimentally determined using incubation studies with nisin. The radius of the inhibition zone was predicted from the computational model as the location where the predicted nisin concentration at Tc was equal to MIC. The MIC was experimentally determined to be 0.156 ?g mL?1, and Tc was determined to be 7 h. Good agreement (R2 = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii. PMID:26405525
Arendrup, Maiken Cavling; Garcia-Effron, Guillermo; Lass-Flörl, Cornelia; Lopez, Alicia Gomez; Rodriguez-Tudela, Juan-Luis; Cuenca-Estrella, Manuel; Perlin, David S.
2010-01-01
This study compared nine susceptibility testing methods and 12 endpoints for anidulafungin, caspofungin, and micafungin with the same collection of blinded FKS hot spot mutant (n = 29) and wild-type isolates (n = 94). The susceptibility tests included EUCAST Edef 7.1, agar dilution, Etest, and disk diffusion with RPMI-1640 plus 2% glucose (2G) and IsoSensitest-2G media and CLSI M27A-3. Microdilution plates were read after 24 and 48 h. The following test parameters were evaluated: fks hot spot mutants overlapping the wild-type distribution, distance between the two populations, number of very major errors (VMEs; fks mutants misclassified as susceptible), and major errors (MEs; wild-type isolates classified as resistant) using a wild-type-upper-limit value (WT-UL) (two twofold-dilutions higher than the MIC50) as the susceptibility breakpoint. The methods with the lowest number of errors (given as VMEs/MEs) across the three echinocandins were CLSI (12%/1%), agar dilution with RPMI-2G medium (14%/0%), and Etest with RPMI-2G medium (8%/3%). The fewest errors overall were observed for anidulafungin (4%/1% for EUCAST, 4%/3% for CLSI, and 3%/9% for Etest with RPMI-2G). For micafungin, VME rates of 10 to 71% were observed. For caspofungin, agar dilution with either medium was superior (VMEs/MEs of 0%/1%), while CLSI, EUCAST with IsoSensitest-2G medium, and Etest were less optimal (VMEs of 7%, 10%, and 10%, respectively). Applying the CLSI breakpoint (S ? 2 ?g/ml) for CLSI results, 89.2% fks hot spot mutants were classified as anidulafungin susceptible, 60.7% as caspofungin susceptible, and 92.9% as micafungin susceptible. In conclusion, no test was perfect, but anidulafungin susceptibility testing using the WT-UL to define susceptibility reliably identified fks hot spot mutants. PMID:19884370
Bailey, Tom A.
1983-01-01
The reliability, reproducibility, and usefulness of three screening methods -- the cellophane transfer, the agar plug transfer, and the agar dilution -- to screen aquatic fungicides were evaluated. Achlya flagellata and Saprolegnia hypogyna were exposed to 1, 10, and 100 mg/L of malachite green to test each method. The cellophane transfer and agar plug transfer techniques had similar reliability and reproducibility in rating fungicidal activity, and were both superior to the agar dilution technique. The agar plug transfer and agar dilution techniques adequately projected in vivo activity of malachite green, but the cellophane transfer technique overestimated its activity. Overall, the agar plug transfer technique most accurately rated the activity of malachite green and was the easiest test to perform. It therefore appears to be the method of choice for testing aquatic fungicides.
Simplified 48-hour IMVic test: an agar plate method.
Powers, E M; Latt, T G
1977-09-01
An agar plate method was developed for the performance of the IMVic (indole, methyl red, Voges-Proskauer, and citrate) tests in lieu of the conventional tubed liquid media. By modifying the composition of the media and adding agar, a single "X"-compartmented petri dish was prepared containing all four IMVic test media. Ease of performance and simplification of the test were achieved by inoculating all four media simultaneously from a single colony (single inoculum) on eosin-methylene blue agar. Tests with 87 cultures, representing 7 genera in the family Enterobacteriaceae, were completed with typical (correct) IMVic patterns for all cultures within 48 h. Parallel tests with conventional media showed that the agar plate method was superior, more sensitive, faster, and simpler to perform, and less time was required to identify Escherichia coli by 72 h. PMID:334074
Methods for identifying lipoxygenase producing microorganisms on agar plates
2012-01-01
Plate assays for lipoxygenase producing microorganisms on agar plates have been developed. Both potassium iodide-starch and indamine dye formation methods were effective for detecting soybean lipoxygenase activity on agar plates. A positive result was also achieved using the ?-carotene bleaching method, but the sensitivity of this method was lower than the other two methods. The potassium iodide-starch and indamine dye formation methods were also applied for detecting lipoxygenase production by Trichoderma reesei and Pichia pastoris transformants expressing the lipoxygenase gene of the fungus Gaeumannomyces graminis. In both cases lipoxygenase production in the transformants could be identified. For detection of the G. graminis lipoxygenase produced by Aspergillus nidulans the potassium iodide-starch method was successful. When Escherichia coli was grown on agar and soybean lipoxygenase was applied on the culture lipoxygenase activity could clearly be detected by the indamine dye formation method. This suggests that the method has potential for screening of metagenomic libraries in E. coli for lipoxygenase activity. PMID:22449314
Methods for identifying lipoxygenase producing microorganisms on agar plates.
Nyyssölä, Antti; Heshof, Ruud; Haarmann, Thomas; Eidner, Jasmin; Westerholm-Parvinen, Ann; Langfelder, Kim; Kruus, Kristiina; de Graaff, Leo; Buchert, Johanna
2012-01-01
Plate assays for lipoxygenase producing microorganisms on agar plates have been developed. Both potassium iodide-starch and indamine dye formation methods were effective for detecting soybean lipoxygenase activity on agar plates. A positive result was also achieved using the ?-carotene bleaching method, but the sensitivity of this method was lower than the other two methods. The potassium iodide-starch and indamine dye formation methods were also applied for detecting lipoxygenase production by Trichoderma reesei and Pichia pastoris transformants expressing the lipoxygenase gene of the fungus Gaeumannomyces graminis. In both cases lipoxygenase production in the transformants could be identified. For detection of the G. graminis lipoxygenase produced by Aspergillus nidulans the potassium iodide-starch method was successful. When Escherichia coli was grown on agar and soybean lipoxygenase was applied on the culture lipoxygenase activity could clearly be detected by the indamine dye formation method. This suggests that the method has potential for screening of metagenomic libraries in E. coli for lipoxygenase activity. PMID:22449314
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
Traub, W H; Geipel, U; Leonhard, B
1998-01-01
Forty-two isolates of Enterococcus faecalis and 56 isolates of Enterococcus faecium, including 8 vancomycin-resistant strains, were examined for comparative susceptibility to 27 antimicrobial drugs with the agar dilution method, employing Mueller-Hinton (MHA), Iso-Sensitest (ISTA), and Wilkins-Chalgren (WCA) agar. The Bauer-Kirby agar disk diffusion method was used to comparatively test 24 of the agents in parallel. The enterococci yielded better growth on ISTA and WCA. However, WCA completely antagonized co-trimoxazole and, though less, fosfomycin. Importantly, WCA slightly reduced the activities of teicoplanin (minimal inhibitory concentrations, MICs, raised up to twofold) and vancomycin (MICs raised two- to fourfold) against enterococci and staphylococcal quality control strains. Therefore, WCA was judged unsuitable for susceptibility testing of enterococci. For E. faecalis no discrepancies between agar dilution MICs and inhibition zone diameters were encountered with augmentin, ampicillin, ampicillin-sulbactam, chloramphenicol, mupirocin, oxacillin, teicoplanin, and co-trimoxazole. Overall, MHA yielded fewer very major (category I) and major (category II) discrepancies than ISTA. However, numerous minor (category III), slight (category IV), minimal (category V), and/or negligible (category VI) discrepancies were encountered with ciprofloxacin, doxycycline, erythromycin, fosfomycin, fusidic acid, meropenem, ofloxacin and rifampin. With respect to E. faecium, only cefotaxime, mupirocin, oxacillin, and teicoplanin yielded nondiscrepant results. Several very major (I) and major (II) discrepancies were observed with augmentin, ampicillin, ampicillin-sulbactam, doxycycline, fusidic acid, imipenem, and penicillin G. Minor discrepancies (categories III-VI) were particularly numerous with augmentin, chloramphenicol, ciprofloxacin, doxycycline, and piperacillin. The largest numbers of negligible (VI) discrepancies were noted with fosfomycin, fusidic acid, and ofloxacin. It is recommended to test one cephalosporin (cefuroxime or the like) in parallel for educational purposes and to exclude fosfomycin, fusidic acid, and rifampin from test batteries because of the wide scatter of test results. The large number of minimal (V) discrepancies of ciprofloxacin against E. faecalis, the numerous minor (III) and slight (IV) discrepancies of chloramphenicol against E. faecium, and the not insignificant number of very major (I) and minor (III) discrepancies observed with meropenem against isolates of E. faecalis necessitated proposals for new disk intermediate susceptibility criteria. PMID:9681198
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
DeCross, A J; Marshall, B J; McCallum, R W; Hoffman, S R; Barrett, L J; Guerrant, R L
1993-01-01
Since the methods for metronidazole susceptibility testing of Helicobacter pylori have not been standardized or validated, we compared three methods that are used to test the metronidazole susceptibilities of 25 isolates of H. pylori. Specifically, we examined the methods of Steer's replicator agar dilution, tube broth microdilution, and modified Kirby-Bauer disk diffusion. The metronidazole disk zone sizes obtained by the disk diffusion method correlated well (r = 0.74) with the MICs obtained by the agar dilution method. Afterward, the disk diffusion method was used to characterize the metronidazole susceptibilities of 44 isolates of H. pylori. Dual therapy (bismuth and metronidazole) proved to be highly effective against metronidazole-susceptible strains (81.6% eradication rate) but fared poorly against resistant strains (16.7% eradication rate; P < 0.01). Using agar dilution testing, we validated the modified Kirby-Bauer disk diffusion method for metronidazole susceptibility testing of H. pylori and conclude that it is practical, accurate, and clinically applicable. PMID:8370723
Pasquetti, M; Chiavassa, E; Tizzani, P; Danesi, P; Peano, A
2015-10-01
Aim of this study was to verify whether Mueller-Hinton agar supplemented with 2 % glucose and methylene blue (MH-GM), which is used for disk diffusion susceptibility testing of Candida species by the Clinical and Laboratory Standards Institute, is suitable for testing Malassezia pachydermatis. A variant of the disk diffusion procedure utilizing a 9-mm tablet was used to test 31 isolates against clotrimazole and miconazole using MH-GM as test medium. The MH-GM agar optimally supported the growth of all M. pachydermatis isolates, provided that the yeast inoculum was prepared with a lipid source (Tween 40 and 80). Zone edges were frequently definite and clear, facilitating the measurement of zone size and minimizing subjectivity. The inhibition zones correlated with MIC values obtained in a broth dilution assay. The agar diffusion method with MH-GM as the test medium appears as a suitable procedure for testing the susceptibility of M. pachydermatis to CTZ and MCZ in clinical laboratories. This test format may allow processing a large number of isolates in epidemiological studies. This may in turn facilitate clarifying to what extent the problem "drug resistance" accounts for cases of treatment failure in dogs with Malassezia otitis and dermatitis. PMID:26138434
Burns, Jane L.; Saiman, Lisa; Whittier, Susan; Larone, Davise; Krzewinski, Jay; Liu, Zhenling; Marshall, Steven A.; Jones, Ronald N.
2000-01-01
Pseudomonas aeruginosa is the most common pathogen infecting the lungs of patients with cystic fibrosis (CF). Improved antimicrobial chemotherapy has significantly increased the life expectancy of these patients. However, accurate susceptibility testing of P. aeruginosa isolates from CF sputum may be difficult because the organisms are often mucoid and slow growing. This study of 597 CF isolates of P. aeruginosa examined the correlation of disk diffusion and Etest (AB BIODISK, Solna, Sweden) results with a reference broth microdilution method. The rates of interpretive errors for 12 commonly used antipseudomonal antimicrobials were determined. The disk diffusion method correlated well (zone diameter versus MIC) for all of the agents tested. However, for mucoid isolates, correlation coefficients (r values) for piperacillin, piperacillin-tazobactam, and meropenem were <0.80. The Etest correlation with reference broth microdilution results (MIC versus MIC) was acceptable for all of the agents tested, for both mucoid and nonmucoid isolates. Category interpretation errors were similar for the disk diffusion and Etest methods with 0.4 and 0.1%, respectively, very major errors (false susceptibility) and 1.1 and 2.2% major errors (false resistance). Overall, both agar diffusion methods appear to be broadly acceptable for routine clinical use in susceptibility testing of CF isolates of P. aeruginosa. PMID:10790106
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...
MODIFIED AGAR MEDIUM FOR DETECTING ENVIRONMENTAL SALMONELLAE BY THE MOST-PROBABLE-NUMBER METHOD
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...
Jones, R N; Gavan, T L; Thornsberry, C; Fuchs, P C; Gerlach, E H; Knapp, J S; Murray, P; Washington, J A
1989-01-01
A six-laboratory study developed a standardized method for determining the susceptibilities of Neisseria gonorrhoeae strains to penicillin, tetracycline, spectinomycin, and ceftriaxone. Three quality control organisms were also selected, and quality assurance guidelines were initially generated for the disk diffusion and agar dilution methods. The medium recommended for gonococcal susceptibility testing was GC agar with a defined "XV-like" supplement. The supplement should be free of cysteine, a component implicated in the inactivation of some newer beta-lactam compounds. Penicillin, tetracycline, spectinomycin, and ceftriaxone were stable in agar plates stored at 3 to 5 degrees C for at least 2 weeks. Numerous GC agar and drug disk lots were used during the trials without significant variation in test results. Several other gonococcal strains were recommended for additional medium quality assurance. The disk quality control zone limits were established for N. gonorrhoeae ATCC 49226 (formerly CDC F-18) and Staphylococcus aureus ATCC 25923. MIC quality control ranges were also developed for N. gonorrhoeae ATCC 49226 and S. aureus ATCC 29213. The interpretive criteria for penicillin were as follows: susceptibility, greater than or equal to 47 mm (diameter of inhibition zone) (less than or equal to 0.06 micrograms/ml [MIC]); resistance, less than or equal to 26 mm (greater than or equal to 2 micrograms/ml). For tetracycline they were as follows: susceptibility, greater than or equal to 38 mm (less than or equal to 0.25 microgram/ml); resistance, less than or equal to 30 mm (greater than or equal to 2 micrograms/ml). For spectinomycin they were as follows: susceptibility, >/= 18 mm (/= 128 micrograms/ml). For ceftriaxone susceptibility, the criterion was >/= 35 mm (
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...
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
Wu, Guoyan; Yang, Qianru; Long, Mei; Guo, Lijuan; Li, Bei; Meng, Yue; Zhang, Anyun; Wang, Hongning; Liu, Shuliang; Zou, Likou
2015-11-01
A variety of disinfectants have been widely used in veterinary hygiene, food industries and environments, which could induce the development of bacterial resistance to disinfectants. The methods used to investigate antimicrobial effects of disinfectant vary considerably among studies, making comparisons difficult. In this study, agar dilution and broth microdilution methods were used to compare the antimicrobial activities of four quaternary ammonium compounds (QACs) against foodborne and zoonotic pathogens. The potential relationship between the presence of QACs resistance genes and phenotypic resistance to QACs was also investigated. Our results indicated that the minimum inhibitory concentrations (MICs) determined by two methods might be different depended upon different QACs and bacteria applied. Regardless of the testing methods, Klebsiella pneumoniae was more tolerant among Gram-negative strains to four QACs, followed by Salmonella and Escherichia coli. The agreement between MICs obtained by the two methods was good, for benzalkonium chloride (78.15%), didecyldimethylammonium chloride (DDAC) (82.35%), cetylpyridinium chloride (CTPC) (97.48%) and cetyltrimethylammonium bromide (CTAB) (99.16%), respectively. Among all Gram-negative bacteria, 94.55% (n=52) of qacE?1-positive strains showed higher MICs (512?mg?l(-1)) to CTAB. The qacE?1 gene was highly associated (P<0.05) with the high MICs of QACs (?512?mg?l(-1)). In addition, DDAC remained as the most effective disinfectant against both Gram-positive and Gram-negative bacteria. This is the first study that compared the agar dilution and broth microdilution methods to assess the antimicrobial activity of QACs. The study demonstrated the need to standardize method that would be used in evaluating QACs antimicrobial properties in the future. PMID:25944532
Technology Transfer Automated Retrieval System (TEKTRAN)
The agar diffusion assay was used to examine antibacterial activity of alkaline salts of caproic, caprylic, capric, lauric, and myristic acids. A 0.5M concentration of each fatty acid was dissolved in 1.0 M potassium hydroxide (KOH), and pH of the mixtures was adjusted to 10.5 with citric acid. Solu...
Park, Chang-Su; Yang, Hee-Jong; Kim, Dong-Ho; Kang, Dae-Ook; Kim, Min-Soo; Choi, Nack-Shick
2012-06-01
A new screening method for ?-(1,3-1,6) glucan hydrolase was developed using a pure ?-glucan from Aureobaisidum pullulans by zymography and an LB-agar plate. Paenibacillus sp. was screened as a producer a ?-glucan hydrolase on the Trypan Blue-coupled ?-glucan LB-agar plate and the activity of the enzyme was analyzed by SDS-?-glucan zymography. The ?-glucan was not hydrolyzed by Bacillus spp. strains, which exhibit cellulolytic activity on CMC zymography. The gene, obtaining by shotgun cloning and encoding the ?-glucan hydrolase of Paenibacillus sp. was sequenced. PMID:22350291
A Method for Cell Culture and Maintenance of Ammonia-Oxidizing Archaea in Agar Stab.
Chu, Yeon-Jin; Lee, Jin-Young; Shin, So-Ra; Kim, Geun-Joong
2015-12-01
Ammonia oxidizing archaea (AOA) are predominantly found and closely linked with geochemical cycling of nitrogen in non-extreme habitats. However, these strains have mainly been investigated using liquid cultures of enriched cells. Here, we provide an agar stab as a simple and reliable means of cultivating and maintaining AOA. PMID:26543273
Perçin, Duygu; Colako?lu, Selcan; Durmaz, Süleyman; Ekincio?lu, P?nar
2012-10-01
Detection of rectal colonization with carbapenem-resistant Klebsiella pneumoniae (CRKP) is the most important step in the infection control protocols in order to prevent infections caused by CRKP which has an increasing incidence all over the world. In this study, it was aimed to compare the detection rate of 2 mg/L ertapenem EMB agar medium with the other methods recommended by various international guidelines. These methods include direct plate method using ertapenem disc, enrichment method in tryptic soy broth containing 2 mg/L ertapenem and the investigation of the predominant betalactamases in the colonized patients. The lowest inoculum detected by different methods was determined by using simulative challenge test prepared for this purpose. The ability to detect CRKP from rectal swabs was evaluated by using the clinical specimens of 801 patients. For all bacteria isolated, carbapenem susceptibility was evaluated by using E-test method, the presence of beta-lactamases was determined by using modified Hodge test (MHT), and the carbapenemase genes were investigated by using multiplex polymerase chain reaction (PCR). The lowest inoculum detected by ertapenem-EMB agar was 50 CFU/mL whereas the lowest inocula were 1 x 105 and 1 x 103, respectively by tryptic soy broth with ertapenem and direct plate method. No resistance gene were identified by PCR in 13 (39.4%) of 33 isolates, whereas blaOXA-48 was detected in 19 (95%) and blaIMP in 1 (5%) of 20 positive isolates. All of the positive strains were resistant to imipenem and ertapenem, while 2 (10%) strains were found to be susceptible to doripenem and meropenem. While MHT was negative in all strains which were negative for resistance genes, all resistance gene positive strains except one blaOXA-48 strain that was also sensitive to doripenem and meropenem, were found to be positive with MHT. According to the results of PCR, the sensitivities of the three methods were found to be 80%. The specificities, positive and negative predictive values were found to be 15.4%, 59% and 33.3% for ertapenem-EMB agar, 23%, 61.5% and 42.9% for broth with ertapenem and 61.5%, 76% and 66.6% for direct plate method, respectively. Average labor time of the methods (isolation + identification + sensitivity + MHT) was determined as 48 hours for ertapenem-EMB agar, whereas it was 96 hours for the other methods. In conclusion, since ertapenem- EMB agar method is a sensitive and rapid method, it can be used safely for the preliminary detection of CRKP without increasing the workload of the laboratory. PMID:23188568
Woo, Patrick C. Y.; Ngan, Antonio H. Y.; Chui, Hon-Kit; Lau, Susanna K. P.; Yuen, Kwok-Yung
2010-01-01
We describe a novel method of fungal slide preparation named “agar block smear preparation.” A total of 510 agar block smears of 25 fungal strains obtained from culture collections, 90 QC fungal strains, and 82 clinical fungal strains from our clinical microbiology laboratory, which included a total of 137 species of yeasts, molds, and thermal dimorphic fungi, were prepared and examined. In contrast to adhesive tape preparation, agar block smears preserved the native fungal structures, such as intact conidiophores of Aspergillus species and arrangements of conidia in Scopulariopsis brevicaulis. Furthermore, agar block smears allowed examination of fungal structures embedded in the agar, such as the ascomata with ascomal hairs in Chaetomium funicola; pycnidium of Phoma glomerata; the intercalary ovoidal chlamydospores arranged in chains of Fusarium dimerum; and the lateral, spherical chlamydospores arranged in pairs of Fusarium solani. After 1 year of storage, morphological integrity was found to have been maintained in 459 (90%) of the 510 agar block smears. After 3 years of storage, morphological integrity was found to have been maintained in 72 (71%) of the 102 smears prepared in 2006. Agar block smear preparation preserves the native fungal structures and allows long-term storage and examination of fungal structures embedded in the agar, hence overcoming the major drawbacks of adhesive tape preparation. The major roles of agar block smear should be diagnosis for difficult cases, accurate identification of fungal species for clinical management of patients and epidemiological studies, and long-term storage for transportation of slides and education purposes. PMID:20660221
Electro-osmosis in gels: Application to Agar-Agar
NASA Astrophysics Data System (ADS)
Cherblanc, Fabien; Boscus, Jérôme; Bénet, Jean-Claude
2008-10-01
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 soils, even if Agar-Agar gel does not share any micro-structural characteristics with soils. To cite this article: F. Cherblanc et al., C. R. Mecanique 336 (2008).
Saeed, I; Roepstorff, A; Rasmussen, T; Høg, M; Jungersen, G
2001-01-01
Experiments on use of an agar-gel method for recovery of migrating Ascaris suum larvae from the liver and lungs of pigs were conducted to obtain fast standardized methods. Subsamples of blended tissues of pig liver and lungs were mixed with agar to a final concentration of 1% agar and the larvae allowed to migrate out of the agar-gel into 0.9% NaCl at 38°C. The results showed that within 3 h more than 88% of the recoverable larvae migrated out of the liver agar-gel and more than 83% of the obtained larvae migrated out of the lung agar-gel. The larvae were subsequently available in a very clean suspension which reduced the sample counting time. Blending the liver for 60 sec in a commercial blender showed significantly higher larvae recovery than blending for 30 sec. Addition of gentamycin to reduce bacterial growth during incubation, glucose to increase larval motility during migration or ice to increase sedimentation of migrated larvae did not influence larvae recovery significantly. PMID:11503373
Lavieri, Nicolas A; Sebranek, Joseph G; Cordray, Joseph C; Dickson, James S; Jung, Stephanie; Manu, David K; Mendonça, Aubrey F; Brehm-Stecher, Byron F; Stock, Joseph; Stalder, Kenneth J
2014-05-01
A sublethally injured bacterial cell has been defined as a cell that survives a stress such as heating, freezing, acid treatment, or other antimicrobial intervention but can repair the cellular damage exerted by the stressor and later regain its original ability to grow. Consequently, sublethally injured cells are not likely to be included in conventional enumeration procedures, which could result in unrealistically low counts unless efforts are made to encourage recovery of the injured cells before enumeration. The objective of this study was to evaluate the use of the thin agar layer (TAL) method for the recovery of pressure-injured and heat-injured Listeria monocytogenes in a tryptic soy broth with 0.6% yeast extract system. Pressure injury consisted of treatment of a culture of mixed L. monocytogenes strains with high hydrostatic pressure at 400 or 600 MPa for 1 s, 2 min, 4 min, or 6 min at a process temperature of 12±2 °C. Heat injury consisted of treatment of a culture of mixed L. monocytogenes strains at 60±1 °C for 3, 6, or 9 min. Growth media were tryptic soy agar (TSA) with 0.6% yeast extract, modified Oxford medium (MOX), and TAL, which consisted of a 7-ml layer of TSA overlaid onto solidified MOX. Counts of viable L. monocytogenes on TAL were higher than those on MOX in the heat-injury experiment but not in the pressure-injury experiment. Therefore, the effectiveness of the TAL method may be specific to the type of injury applied to the microorganism and should be investigated in a variety of cellular injury scenarios. PMID:24780340
A simple method for classification of antibiotics using ion exchange resins added to agar plates.
Yoshida, K; Kondo, F
1994-01-01
Using two different ion-exchange resins (Dowex 50W-X4 as cation and Dowex 1-X4 as anion) added directly to assay plates seeded with Bacillus subtilis or Micrococcus luteus, the size of the inhibitory zone produced by 36 antimicrobial agents around a disc or cup was characterized into various types, such as acidic, basic or amphoteric. An increase of the inhibition zone following addition of 15% Dowex 50W-X4 was evident in penicillins except for ampicillin and penicillin-G, and polyethers. Aminoglycosides, macrolides and colistin, lincomycin, and sulphonamides on assay medium treated with Dowex 1-X4 showed a similar effect on the inhibition zone. Tetracyclines, virginiamycin, oxolinic acid and furazoridone revealed no effects on the inhibition zone with either of the resins. These antibiotics could be divided into various groups on the basis of their chemical structure. This simple and rapid method may be useful for routine laboratory testing of residual antibiotics in meat. PMID:8152391
Butler, N J; Langley, G R; Winwood, J
1993-02-01
Synopsis An established cytotoxicity test for plastic materials in medical devices has been adapted and used to assess the relative potential irritancy of cosmetic ingredients and formulations during product development. Serum-free medium containing a novel protein supplement supported growth in suspension of LS mouse fibroblast cells. Release of the vital dye Neutral Red from pre-loaded cells suspended in agar was the endpoint. Test substances and reference standards were applied to a central well cut into the agar, a sensitive method which allowed accurate dose application and yielded consistent results. Relative irritancy potential was measured quantitatively by comparing the diameters of the clear zones of damaged cells which surround the central well. The test has been used with raw materials such as surfactants, preservatives and herbal extracts, as well as finished products ranging from shampoos and conditioners to creams, lotions and coloured cosmetics. The method is practical, versatile, reproducible and economic to use. Résumé Un test de cytotoxicité utilisé pour la détection de toxines dans les plastiques des appareils médicaux a été adapté pour prévenir le potentiel d'irritation relative. Le point mesuré est la libération de la teinture vitale rouge neutre des cellules chargées au préalable, résultant de l'incubation avec des substances tests. La mesure des diamétres de la zone claire de dilutions sequentielles de substances tests permet de calculer l'irritation potentielle d'un produit testé par rapport à un standard. Parmi les modifications, on a pu constater à l'aide d'une ligne de cellules en suspension dérivées de fibroblastes de souris L-929, la pousse en milieu sans sérum pour éviter les produits d'abattoir. A la place du sérum de veau, on a ajouté au milieu une nouvelle protéine innovatrice supportant la pousse normale en suspension. Durant la procédure de test les cellules se trouvaient en suspension dans une solution agar et les substances tests ont été appliquées sur une cellule centrale bien délimitéc sur la gélose plutôt qu'à l'aide d'un disque de papier filtre. L'application par une cellule centrale était plus sensible qu'avec un disque, permettant l'application d'une dose précise et fournissant des résultats plus fiables. Le test modifié a été utilisé sur une période de 4 ans pour des matiéres premières telles que tensioactifs, conservateurs et extraits de plantes, ainsi que des formules de shampooings, savons, lotions hydratantes et cosmétiques colorés. Ces produits ont étéévalués sur des panels de volontaires, et les produits testés sont commercialisés depuis 2 ans au moins. Le test est un moyen pratique, versatile, reproductible et économique de calculer le potentiel d'irritation relative d'une gamme de produits et ingrédients cosmktiques. PMID:19272118
Modeling of the Bacillus subtilis Bacterial Biofilm Growing on an Agar Substrate
Wang, Xiaoling; Wang, Guoqing; Hao, Mudong
2015-01-01
Bacterial biofilms are organized communities composed of millions of microorganisms that accumulate on almost any kinds of surfaces. In this paper, a biofilm growth model on an agar substrate is developed based on mass conservation principles, Fick's first law, and Monod's kinetic reaction, by considering nutrient diffusion between biofilm and agar substrate. Our results show biofilm growth evolution characteristics such as biofilm thickness, active biomass, and nutrient concentration in the agar substrate. We quantitatively obtain biofilm growth dependence on different parameters. We provide an alternative mathematical method to describe other kinds of biofilm growth such as multiple bacterial species biofilm and also biofilm growth on various complex substrates. PMID:26355542
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.
ERIC Educational Resources Information Center
Foy, Barry G.
1977-01-01
Two demonstrations are described. Materials and instructions for demonstrating movement of molecules into cytoplasm using agar blocks, phenolphthalein, and sodium hydroxide are given. A simple method for demonstrating that the rate of diffusion of a gas is inversely proportional to its molecular weight is also presented. (AJ)
Preparation of an agar-silver nanoparticles (A-AgNp) film for increasing the shelf-life of fruits.
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
Ingham, Steven C; Becker, Katie L; Fanslau, Melody A
2003-11-01
The recently developed 3M Petrifilm Staph Express Count plate (PFSE) method was compared with the U.S. Food and Drug Administration Bacteriological Analytical Manual's Baird-Parker agar spread plate (B-P) method for enumeration of Staphylococcus aureus in naturally contaminated, mechanically separated poultry (MSP; n = 92) and raw milk (n = 12). In addition, mozzarella and Parmesan cheeses and hot-smoked rainbow trout and chub were surface inoculated with a three-strain mixture of S. aureus, stored at 5 degrees C, and periodically analyzed with both methods for numbers of S. aureus. For naturally contaminated raw milk and MSP samples, the PFSE method yielded counts that were not significantly different (P > 0.05) from counts obtained using the B-P method. From raw milk and MSP samples, 60% (21 of 35) and 55% (124 of 226), respectively, of confirmed (DNAse-positive) isolates from PFSE plates were identified by further testing as S. aureus. Corresponding S. aureus identification rates for isolates forming typical colonies on B-P plates were 53% (19 of 36) and 50% (125 of 248). For both methods, other staphylococci composed the vast majority of tested isolates that were not identified as S. aureus. For inoculated hot-smoked fish, S. aureus counts from the PFSE method were not significantly different from counts from the B-P method. Compared to the B-P method, significantly lower numbers of inoculated S. aureus were recovered using the PFSE method in analyses of mozzarella cheese stored 28 and 42 days at 4 degrees C. The PFSE and B-P methods were not significantly different for inoculated cheeses at all other sampling times. DNAse-positive isolates from PFSE analyses of inoculated cheeses and smoked fish were identified as S. aureus 98% (51 of 52) and 86% (36 of 42) of the time, respectively, as compared with 100% (58 of 58) and 95% (40 of 42) of the time for typical B-P isolates. Overall, the PFSE and B-P methods appeared to perform similarly in enumeration of S. aureus in animal-derived foods. PMID:14627298
Automatic agar tray inoculation device
NASA Technical Reports Server (NTRS)
Wilkins, J. R.; Mills, S. M.
1972-01-01
Automatic agar tray inoculation device is simple in design and foolproof in operation. It employs either conventional inoculating loop or cotton swab for uniform inoculation of agar media, and it allows technician to carry on with other activities while tray is being inoculated.
Smith, Amanda R; Ellison, Alysha L; Robinson, Amanda L; Drake, Maryanne; McDowell, Susan A; Mitchell, James K; Gerard, Patrick D; Heckler, Rachel A; McKillip, John L
2013-04-01
Quality control procedures during food processing may involve direct inoculation of food samples onto appropriate selective media for subsequent enumeration. However, sublethally injured bacteria often fail to grow, enabling them to evade detection and intervention measures and ultimately threaten the health of consumers. This study compares traditional selective and nonselective agar-based overlays versus two commercial systems (Petrifilm and Easygel) for recovery of injured E. coli B-41560 and O157:H7 strains. Bacteria were propagated in tryptic soy broth (TSB), ground beef slurry, and infant milk formula to a density of 10(6) to 10(8) CFU/ml and then were stressed for 6 min either in lactic acid (pH 4.5) or heat shocked for 3 min at 60°C. Samples were pour plated in basal layers of either tryptic soy agar (TSA), sorbitol MacConkey agar (SMAC), or violet red bile agar (VRB) and were resuscitated for 4 h prior to addition of agar overlays. Other stressed bacteria were plated directly onto Petrifilm and Easygel. Results indicate that selective and nonselective agar overlays recovered significantly higher numbers (greater than 1 log) of acid- and heat-injured E. coli O157:H7 from TSB, ground beef, and infant milk formula compared with direct plating onto selective media, Petrifilm, or Easygel, while no significant differences among these media combinations were observed for stressed E. coli B-41560. Nonstressed bacteria from TSB and ground beef were also recovered at densities significantly higher in nonselective TSA-TSA and in VRB-VRB and SMAC-SMAC compared with Petrifilm and Easygel. These data underscore the need to implement food safety measures that address sublethally injured pathogens such as E. coli O157:H7 in order to avoid underestimation of true densities for target pathogens. PMID:23575132
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...
NASA Astrophysics Data System (ADS)
Zhang, Qianqian; Chen, Ran; Li, Ling
2012-12-01
The paper aims to expand the application of natural marine algae. Marine diatoms, which have intricate frustule structures, can serve as bio-template for preparing three-dimensional materials. A simple and effective approach to synthesize the corrugated agaric-like biomorphic TiO2 templated with frustule of Coscinodiscus sp. is reported. In the sol-gel preparation process, the titania-coating on the frustule is prepared through the deposition and condensation with the aid of acetylacetone (acac) as a controlling agent to make the precursor Ti(BuO)4 hydrolyze slowly. The as-prepared titania-coated frustule and biomorphic TiO2 is characterized by scanning electron microscopy (SEM) attached with energy dispersive X-ray spectrometer (EMAX) and X-ray diffraction (XRD). The microstructure of the corresponding titania nanoparticles appears to be sphere with the diameters distributed around 10-20 nm. The templating process is repeated for three cycles. Subsequently, the three-dimensional freestanding corrugated agaric-like biomorphic TiO2 structure is obtained by a selective removal in the NaOH solution. As far as we known, the 3D freestanding corrugated agaric-like biomorphic TiO2 with greatly increased surface area is obtained for the first time.
Fabrication of PMMA microfluidic chips using disposable agar hydrogel templates.
Yao, Xiao; Chen, Zhi; Chen, Gang
2009-12-01
A novel method based on disposable agar hydrogel temples have been developed for the fabrication of PMMA microfluidic chips. Molten agar hydrogel was sandwiched between a glass plate and a PMMA template bearing negative relief of microstructure. After cooling, the negative PMMA template could be easily separated from the solidified agar hydrogel and a layer of agar hydrogel temple bearing high-fidelity positive relief of the microstructure was left on the glass plate. Prepolymerized methyl methacrylate molding solution containing ultraviolet-initiator was subsequently sandwiched between the agar hydrogel template and a PMMA plate and was allowed to polymerize under ultraviolet light to fabricate the PMMA channel plate at room temperature. Complete microchips could be obtained by bonding the channel plates with covers. The prepared microfluidic microchips have been successfully employed in the electrophoresis separation and detection of several ions in connection with contactless conductivity detection. PMID:20013907
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
Matuschek, E; Brown, D F J; Kahlmeter, G
2014-04-01
With the support of ESCMID and European countries, EUCAST has developed a disk diffusion test with zone diameter breakpoints correlated with the EUCAST clinical MIC breakpoints. The development of the EUCAST disk diffusion method and quality control criteria are described, together with guidance on quality control and implementation of the method in clinical microbiology laboratories. The method includes the use of Mueller-Hinton agar without supplements for non-fastidious organisms and with 5% mechanically defibrinated horse blood and 20 mg/L ?-NAD for fastidious organisms, a standardized inoculum resulting in confluent growth, an incubation time of 16-20 h, a reading guide on how to read zone diameters on individual species-agent combinations and zone diameter breakpoints calibrated to the EUCAST clinical MIC breakpoints. EUCAST recommendations are described in detail and updated regularly on the EUCAST website (http://www.eucast.org). PMID:24131428
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)
New method to measure liquid diffusivity by analyzing an instantaneous diffusion image.
Sun, Licun; Meng, Weidong; Pu, Xiaoyun
2015-09-01
A novel optical method was applied to measure the binary liquid diffusion coefficient (D) quickly. Equipped with an asymmetric liquid-core cylindrical lens (ALCL), the spatially resolving ability of the ALCL in measuring refractive index of liquid was utilized to obtain the gradient distribution of the liquid concentration along diffusive direction. Based on Fick's second law, the D value was then calculated by analyzing diffusion images. It was worth mentioning that only one instantaneous diffusive image was required to measure D value by the method, reducing the measurement time greatly from several hours in traditional methods to a few seconds. The diffusion coefficients of ethylene glycol diffusing in pure water, at temperatures from 288.15 to 308.15 K, were measured by analyzing instantaneous diffusion images, the results were consistent well with the values measured by using holographic interferometry and Taylor dispersion methods. The method is characterized by faster measurement, direct observation of diffusive process, and easy operation, which provides a new method in measuring diffusion coefficient of liquids rapidly. PMID:26368418
Detection of encapsulation in Staphylococcus aureus by use of antiserum agar.
West, T E; Apicella, M A
1984-01-01
We examined an antiserum agar method to study its reliability in screening Staphylococcus aureus strains for capsule production. The encapsulated S. aureus Smith diffuse strain was compared with its nonencapsulated variant, Smith compact, in CCY medium containing 0.5% NaCl and 5.0% Smith diffuse rabbit antiserum. A halo was visible surrounding colonies of the Smith diffuse strain but not the Smith compact strain. On this same medium, the protein A-producing Cowan I strain possessed a halo that was visible on photographs. Single high-salt medium is known to inhibit protein A production, halo formation by the strains was also compared in 7.5% NaCl medium. The halo surrounding the Cowan I strain was not present when the salt content of the medium was increased. In contrast, the halo surrounding the Smith diffuse strain persisted in the 7.5% NaCl medium. By use of this medium, the antiserum agar technique may be valuable for the identification of encapsulated staphylococci without appreciable interference from protein A. Images PMID:6490810
Eigenmode analysis of advective-diffusive transport in micromixers by the diffusive mapping method
NASA Astrophysics Data System (ADS)
Anderson, Patrick; Speetjens, Michel; Gorodetskyi, Oleksandr; Giona, Max; Mixing Collaboration
2013-11-01
Advective-diffusive transport in microflows is studied by means of the diffusive map- ping method, a recent extension of the mapping method by Gorodetskyi et al. (Phys. Fluids 24, 2012) that includes molecular diffusion. This greatly expands the application area of the mapping technique and makes the powerful concepts of eigenmode decompo- sition and spectral analysis of scalar transport accessible to an important class of flows: inline micromixers with diffusion. The staggered herringbone micro-mixer is adopted as a prototypical three-dimensional micro mixer. Simulations with the diffusive mapping method are in close agreement with experimental observations in literature and expose a strong impact of diffusion on the transport. Diffusion enables crossing of Lagrangian trans- port barriers and thus smoothens concentration gradients and accelerates homogenization. Spectral analysis of the mapping matrix reveals this already occurs on a modal level in that individual eigenmodes progressively smoothen and spread out across transport bar- riers with stronger diffusion. Concurrently, the corresponding eigenvalues diminish and thus fundamentally alter the mixing process by invariably causing homogenization, irre- spective of the Lagrangian flow structure. This happens faster and exhibits an earlier emergence of the dominant eigenmode the stronger the diffusion. Lagrangian structures may still affect the spectral properties in that flows comprising both islands and chaotic seas typically result in a richer set of eigenmodes compared to cases with global chaos.
Capturing correlations in chaotic diffusion by approximation methods.
Knight, Georgie; Klages, Rainer
2011-10-01
We investigate three different methods for systematically approximating the diffusion coefficient of a deterministic random walk on the line that contains dynamical correlations that change irregularly under parameter variation. Capturing these correlations by incorporating higher-order terms, all schemes converge to the analytically exact result. Two of these methods are based on expanding the Taylor-Green-Kubo formula for diffusion, while the third method approximates Markov partitions and transition matrices by using a slight variation of the escape rate theory of chaotic diffusion. We check the practicability of the different methods by working them out analytically and numerically for a simple one-dimensional map, study their convergence, and critically discuss their usefulness in identifying a possible fractal instability of parameter-dependent diffusion, in the case of dynamics where exact results for the diffusion coefficient are not available. PMID:22181115
Diffuse-Interface Methods in Fluid Mechanics
NASA Technical Reports Server (NTRS)
Anderson, D. M.; McFadden, G. B.; Wheeler, A. A.
1997-01-01
The authors review the development of diffuse-interface models of hydrodynamics and their application to a wide variety of interfacial phenomena. The authors discuss the issues involved in formulating diffuse-interface models for single-component and binary fluids. Recent applications and computations using these models are discussed in each case. Further, the authors address issues including sharp-interface analyses that relate these models to the classical free-boundary problem, related computational approaches to describe interfacial phenomena, and related approaches describing fully-miscible fluids.
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.
Effect of Gravity on the Colonial Morphology of Staphylococci in Soft Agar
Wilkins, Judd R.; Hatten, Mary B.; Salmirs, Seymour
1969-01-01
After horizontal rotation on a clinostat at 1 rev/min, subsurface colonies of staphylococci in soft agar were compact and spherical; nonrotated colonies were diffuse and elongated. Images PMID:5369302
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.
An adaptive SUPG method for evolutionary convection-diffusion equations
John, Volker
An adaptive SUPG method for evolutionary convection-diffusion equations Javier de Frutos a,1 with results obtained by utilizing the adaptive algorithm proposed in [5]. Key words: Evolutionary convection and studying an adaptive algorithm for the evolutionary convection-diffusion equation which uses the natural ex
Kofler, Markus; Lenninger, Margit; Mayer, Gert; Neuwirt, Hannes; Grimm, Michael; Bechtold, Thomas
2016-01-20
Renal replacement therapy options are limited to hemodialysis and peritoneal dialysis (70% of US patients) or renal transplantation. Diffusion processes are the main physico-chemical principle behind hemodialysis. An alternative way to achieve liquid flow through membranes bases on the electroosmotic flow which is observed as electrokinetic phenomenon in porous membranes which bear surface charges. Agar consists of the non-ionic agarose and the negatively charged agaropectine thus an electroosmotic flux is observed in analytical electrophoresis. In this study the potential electroosmosis on textile reinforced agar membranes as separation method was investigated. Using a five-chamber electrolysis cell and an agar membrane/cellulose fabric composite an intensive electroosmotic flow of 1-2mlcm(2)h(-1) at 100mA cell current could be observed. The movement of cations in the negatively charged agar structure led to an intensive electroosmotic flux, which also transported uncharged molecules such as urea, glucose through the membrane. Separation of uncharged low molecular weight molecules is determined by the membrane characteristic. The transport of ions (K(+), PO4(3-), creatinine) and uncharged molecules (urea, glucose) in electroosmotic separation experiments was monitored using a pH 5.5 phosphate electrolyte with the aim to assess the overall transport processes in the electrochemical cell. The results demonstrate the potential of the method for filtration of biological fluids in the absence of external pressure or high shear rates. PMID:26572331
Adaptive streamline diffusion methods for compressible flow using conservation variables
NASA Astrophysics Data System (ADS)
Hansbo, Peter; Johnson, Claes
1991-06-01
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.
Crystal formation in furunculosis agar
Bullock, G.L.; Ross, A.J.
1964-01-01
SINCE ITS INTRODUCTION SOME MONTHS AGO, FURUNCULOSIS AGAR has been employed in the diagnosis of suspect furunculosis and also as a general purpose medium. During our work with this medium we have noticed discrete "colonies," of crystalline material, which very closely resemble microbial colonies. These crystal colonies are compact and appear on both the surface and subsurface; they occur in inoculated slants and plates incubated for long periods (2 to 3 weeks), as well as in uninoculated stored medium. As the crystal colonies could be confusing to workers using this medium, we decided to attempt to identify them and also to determine whether storage conditions and different lots of medium affect crystal formation.
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.
Preparation of hydroxypropyl agars and their properties.
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
Computing the effective diffusivity using a spectral method
2001-05-03
equation using a Fourier–Chebyshev spectral method. ... [3]. In the finite difference or finite element methods, the local property of a material is assumed ... in a microstructure by solving the time-dependent diffu- ... therefore the fact that grain boundary diffusivity Dgb is .... (9·D(r)9) is spectrally equivalent to the Laplacian op-.
Diffusion method in random matrix theory
NASA Astrophysics Data System (ADS)
Grela, Jacek
2016-01-01
We introduce a calculational tool useful in computing ratios and products of characteristic polynomials averaged over Gaussian measures with an external source. The method is based on Dyson’s Brownian motion and Grassmann/complex integration formulas for determinants. The resulting formulas are exact for finite matrix size N and form integral representations convenient for large N asymptotics. Quantities obtained by the method are interpreted as averages over standard matrix models. We provide several explicit and novel calculations with special emphasis on the ? =2 Girko-Ginibre ensembles.
Residual Agar Determination in Bacterial Spores by Electrospray Ionization Mass Spectrometry
Wahl, Karen L.; Colburn, Heather A.; Wunschel, David S.; Petersen, Catherine E.; Jarman, Kristin H.; Valentine, Nancy B.
2010-02-15
Presented here is an analytical method to detect residual agar from a bacterial spore sample as an indication of culturing on an agar plate. This method is based on the resolubilization of agar polysaccharide from a bacterial spore sample, enzymatic digestion, followed by electrospray ionization tandem mass spectrometry (ESI-MSn) analysis for detection of a specific agar fragment ion. A range of Bacillus species and strains were selected to demonstrate the effectiveness of this approach. The characteristic agar fragment ion was detected in the spores grown on agar that were washed from 1 to 5 times, irradiated or non-irradiated and not in the spores grown in broth. A sample containing approximately 108 spores is currently needed for confident detection of residual agar from culture on agar plates in the presence of bacterial spores with a limit of detection of approximately 1 ppm agar spiked into a broth-grown spore sample. The results of a proficiency test with 42 blinded samples are presented demonstrating the utility of this method with no false positives and only 3 false negatives for samples that were below the detection level of the method as documented.
Diffusion accessibility as a method for visualizing macromolecular surface geometry.
Tsai, Yingssu; Holton, Thomas; Yeates, Todd O
2015-10-01
Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. PMID:26189444
A Diffusion Synthetic Acceleration Method for Block Adaptive Mesh Refinement.
Ward, R. C.; Baker, R. S.; Morel, J. 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.
A method for thermal diffusivity measurement in fluids
NASA Astrophysics Data System (ADS)
Marín, E.; Hernández-Rosales, E.; Mansanares, A. M.; Ivanov, R.; Rojas-Trigos, J. B.; Calderón, A.
2013-10-01
A technique is proposed for thermal diffusivity measurement in fluids. It is based on the Angstrom method, but with excitation of thermal waves by electromagnetic energy absorption and pyroelectric detection. The good agreement between measured thermal diffusivity of air and some test liquids with literature values shows the validity of the method. It is free of some limitations of conventional photopyroelectric technique with length scanning because it is free of moving parts inside the sample and because it avoids problems associated with the non-parallelism between thermal wave generator surface and sensor. It does not require any data normalization procedure or special sample preparation.
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)
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.
The whole-block method and water diffusion in olivine
NASA Astrophysics Data System (ADS)
Ferriss, E.; Plank, T. A.; Walker, D.
2013-12-01
Accurate knowledge of the diffusion rates and mechanisms of water (hydrogen) in geologic materials is critical for geologic applications such as understanding the deep earth water cycle and determining ascent rates of pre-eruptive magmas. However, diffusion rates and mechanisms are often poorly known. Obtaining robust diffusion profile data for water with transmission FTIR traditionally requires cutting the sample after an experiment to isolate the central slice. Here we develop a method for interpreting diffusion profile data in three dimensions without cutting the sample. This 'whole-block' method is nondestructive, which simplifies the analytical procedure and allows multiple experiments on the same sample (e.g., a time series or reversal). Whole-block data represent concentration values that are integrated through the entire sample in the direction parallel to the infrared beam ray path during the measurement, and they are determined by taking the average value of a non-path-integrated 3 dimensional model (e.g., based on error functions or infinite sums in a rectangular parallelepiped) down the ray path for a given position. The whole-block method was tested by comparing whole-block profiles with profiles cut from the center of an oriented diopside sample after a dehydration experiment [1]. Water profiles were measured in the cut slice by both SIMS and FTIR. The results of the two methods are in good agreement both with each other and with diffusion profiles calculated based on the results of the whole-block method. Interpreting whole block measurements without taking into account the integration effects through the crystal can lead to errors in calculated diffusivities and inferred mechanisms. We have used numerical simulations to demonstrate as much as a half an order of magnitude error (typically indicating diffusivities that are too fast) if whole-block data are interpreted using non-path integrated diffusion models. The largest errors are in short and/or fast directions, in which diffusion profiles are well developed. Whole block data also inevitably involve central values that are contaminated by edge concentrations integrated in the signal. This integration effect results in a plateau in the whole-block data that may complicate the interpretation of the whole-block data. For example, previous experimental work on water diffusion in olivine has identified a central plateau using whole block measurements, and this plateau is interpreted to result from a transitional state between two diffusion mechanisms [2]. However, a whole-block model also produces a reasonable fit to this data using the observed initial concentration of zero and a single-step diffusion mechanism. Thus, whole block effects need to be taken into account for the accurate determination of diffusivities and mechanisms. [1] Ferriss et al 2012 AGU; [2] Demouchy&Mackwell 2006 Phys Chem Mineral 33(5).
Growth kinetics of three species of Tetrahymena on solid agar
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.
Watson, E. Bruce
Oxygen self-diffusion ``fast-paths'' in titanite single crystals and a general method., and Watson E. B. (2006) Oxygen diffusion in titanite: lattice and fast-path diffusion in single crystals most other minerals, titanite rarely if ever forms perfect crystals. In addition to the point defects
Method of making gas diffusion layers for electrochemical cells
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.
Modeling the flow in diffuse interface methods of solidification
NASA Astrophysics Data System (ADS)
Subhedar, A.; Steinbach, I.; Varnik, F.
2015-08-01
Fluid dynamical equations in the presence of a diffuse solid-liquid interface are investigated via a volume averaging approach. The resulting equations exhibit the same structure as the standard Navier-Stokes equation for a Newtonian fluid with a constant viscosity, the effect of the solid phase fraction appearing in the drag force only. This considerably simplifies the use of the lattice Boltzmann method as a fluid dynamics solver in solidification simulations. Galilean invariance is also satisfied within this approach. Further, we investigate deviations between the diffuse and sharp interface flow profiles via both quasiexact numerical integration and lattice Boltzmann simulations. It emerges from these studies that the freedom in choosing the solid-liquid coupling parameter h provides a flexible way of optimizing the diffuse interface-flow simulations. Once h is adapted for a given spatial resolution, the simulated flow profiles reach an accuracy comparable to quasiexact numerical simulations.
Correia, Teresa; Aguirre, Juan; Sisniega, Alejandro; Chamorro-Servent, Judit; Abascal, Juan; Vaquero, Juan J.; Desco, Manuel; Kolehmainen, Ville; Arridge, Simon
2011-01-01
Fluorescence diffuse optical tomography (fDOT) is an imaging modality that provides images of the fluorochrome distribution within the object of study. The image reconstruction problem is ill-posed and highly underdetermined and, therefore, regularisation techniques need to be used. In this paper we use a nonlinear anisotropic diffusion regularisation term that incorporates anatomical prior information. We introduce a split operator method that reduces the nonlinear inverse problem to two simpler problems, allowing fast and efficient solution of the fDOT problem. We tested our method using simulated, phantom and ex-vivo mouse data, and found that it provides reconstructions with better spatial localisation and size of fluorochrome inclusions than using the standard Tikhonov penalty term. PMID:22091447
Lin, Guoxing
2015-10-01
Pulsed field gradient (PFG) diffusion measurement has a lot of applications in NMR and MRI. Its analysis relies on the ability to obtain the signal attenuation expressions, which can be obtained by averaging over the accumulating phase shift distribution (APSD). However, current theoretical models are not robust or require approximations to get the APSD. Here, a new formalism, an effective phase shift diffusion (EPSD) equation method is presented to calculate the APSD directly. This is based on the idea that the gradient pulse effect on the change of the APSD can be viewed as a diffusion process in the virtual phase space (VPS). The EPSD has a diffusion coefficient, K(?)(t)D rad(?)/s(?), where ? is time derivative order and ? is a space derivative order, respectively. The EPSD equations of VPS are built based on the diffusion equations of real space by replacing the diffusion coefficients and the coordinate system (from real space coordinate to virtual phase coordinate). Two different models, the fractal derivative model and the fractional derivative model from the literature were used to build the EPSD fractional diffusion equations. The APSD obtained from solving these EPSD equations were used to calculate the PFG signal attenuation. From the fractal derivative model the attenuation is exp(-?(?)g(?)?(?) [Formula: see text] t(?)), a stretched exponential function (SEF) attenuation, while from the fractional derivative model the attenuation is E?,1(-?(?)g(?)?(?) [Formula: see text] t(?)), a Mittag-Leffler function (MLF) attenuation. The MLF attenuation can be reduced to SEF attenuation when ?=1, and can be approximated as a SEF attenuation when the attenuation is small. Additionally, the effect of finite gradient pulse widths (FGPW) is calculated. From the fractal derivative model, the signal attenuation including FGPW effect is [Formula: see text] . The results obtained in this study are in good agreement with the results in literature. Several expressions that describe signal attenuation have not been reported and that can be of great importance for the PFG experiments. This EPSD equation method provides a new, simple path to calculate signal attenuation of PFG NMR experiments. PMID:26384777
NASA Astrophysics Data System (ADS)
Lin, Guoxing
2015-10-01
Pulsed field gradient (PFG) diffusion measurement has a lot of applications in NMR and MRI. Its analysis relies on the ability to obtain the signal attenuation expressions, which can be obtained by averaging over the accumulating phase shift distribution (APSD). However, current theoretical models are not robust or require approximations to get the APSD. Here, a new formalism, an effective phase shift diffusion (EPSD) equation method is presented to calculate the APSD directly. This is based on the idea that the gradient pulse effect on the change of the APSD can be viewed as a diffusion process in the virtual phase space (VPS). The EPSD has a diffusion coefficient, K?(t)D rad?/s?, where ? is time derivative order and ? is a space derivative order, respectively. The EPSD equations of VPS are built based on the diffusion equations of real space by replacing the diffusion coefficients and the coordinate system (from real space coordinate to virtual phase coordinate). Two different models, the fractal derivative model and the fractional derivative model from the literature were used to build the EPSD fractional diffusion equations. The APSD obtained from solving these EPSD equations were used to calculate the PFG signal attenuation. From the fractal derivative model the attenuation is exp(-??g???Df1 t?), a stretched exponential function (SEF) attenuation, while from the fractional derivative model the attenuation is E?,1(-??g???Df2 t?), a Mittag-Leffler function (MLF) attenuation. The MLF attenuation can be reduced to SEF attenuation when ? = 1, and can be approximated as a SEF attenuation when the attenuation is small. Additionally, the effect of finite gradient pulse widths (FGPW) is calculated. From the fractal derivative model, the signal attenuation including FGPW effect is exp[ -Df1 ?0? K? (t)dt? ] . The results obtained in this study are in good agreement with the results in literature. Several expressions that describe signal attenuation have not been reported and that can be of great importance for the PFG experiments. This EPSD equation method provides a new, simple path to calculate signal attenuation of PFG NMR experiments.
Some Experiments With Agar-Grown Seedlings
ERIC Educational Resources Information Center
Freeland, P. W.
1973-01-01
Two percent agar gel is reported as a better medium for germination and growth studies. Students can be encouraged to undertake many simple experiments and make precise observations by using this medium. (PS)
Support Operators Method for the Diffusion Equation in Multiple Materials
Winters, Andrew R.; Shashkov, Mikhail J.
2012-08-14
A second-order finite difference scheme for the solution of the diffusion equation on non-uniform meshes is implemented. The method allows the heat conductivity to be discontinuous. The algorithm is formulated on a one dimensional mesh and is derived using the support operators method. A key component of the derivation is that the discrete analog of the flux operator is constructed to be the negative adjoint of the discrete divergence, in an inner product that is a discrete analog of the continuum inner product. The resultant discrete operators in the fully discretized diffusion equation are symmetric and positive definite. The algorithm is generalized to operate on meshes with cells which have mixed material properties. A mechanism to recover intermediate temperature values in mixed cells using a limited linear reconstruction is introduced. The implementation of the algorithm is verified and the linear reconstruction mechanism is compared to previous results for obtaining new material temperatures.
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.
Minutes to Millennia: Diffusion Methods in Subduction-Related Volcanism
NASA Astrophysics Data System (ADS)
Morgan, D. J.; Allan, A.; Wilson, C. J. N.; Charlier, B. L.; Davidson, J.
2014-12-01
Diffusion methods have several advantages as relative geochronometers in volcano-related magmatic processes: diffusion stops on eruption, locking in short timescale information; methods are relatively easy to implement; and suitable material is generally abundant. Such methods also pose significant, accompanying challenges: the need for accurate melt palaeothermometry, uncertainties in diffusion parameters, and sometimes even a cryptic connection between mineral zonation and timescale. As all timescales are relative to an event, timing is not absolute, and care must be taken in interpretation. Yet for all the difficulties, diffusion tools are seeing more widespread usage. This has come about because of the potential of diffusion methods to interrogate certain pre-eruptive processes operating over timescales of relevance to human timescales and responses, having direct bearing on hazard mitigation procedures. In studying subduction zone systems we have a wide range of minerals to choose from but will, in subduction-related, andesitic-to-rhyolitic systems, usually be operating away from the relatively well-constrained system of olivine, and instead be dealing with mineral phases that offer different challenges, such as plagioclase, quartz, sanidine, amphibole, orthopyroxene, Fe-Ti oxides and mica. Timescales here span a wide range across different mineral-element combinations, from minutes for Li in plagioclase and quartz to days by Fe-Ti oxides, years by orthopyroxene Fe-Mg and decades to millennia with plagioclase, sanidine and quartz. This contribution will focus on the interpretation of diffusion signals in minerals found in subduction-related volcanic systems. To understand what any modelled timescale means, the process which formed the relevant zonation pattern is absolutely key, yet often elusive. Variations in P, T, X conditions really drive the crystallisation process yet certain zonation patterns are non-unique. This ambiguity necessitates painstaking petrological and geochemical detective work to understand where the zoning came from to begin with, and which parameter or parameters were truly driving the zonation. The rewards are insights into short-lived processes occurring in the build up to, or process of, eruption, which are not accessible via other mechanisms.
Data analysis methods for flash thermal diffusivity experiments
Sweet, J.N.
1989-02-01
New methods, based on nonlinear least squares techniques, are presented for reducing flash diffusivity data obtained on layered composite samples. Analytical solutions to the transient heat conduction equation are derived by the Laplace transform technique for the cases of two and three layer samples with interfacial thermal resistance between the layers and thermal losses at the external boundaries. The use of the analytical solutions in least squares fitting programs is then discussed, with emphasis on the two layer problem. A description of FORTRAN computer programs which implement the calculations is given, with emphasis on the non-linear least squares fitting routine LSTSQRSL3. This program can determine the external boundary thermal loss factor and either the thermal diffusivity of one of the layers or the interfacial resistance between the layers. Two examples of the use of this program are given. In the first, the thermal diffusivity of an alumina layer in a graphite-alumina sample is determined, and in the second, the diffusivity of an enamel paint on a stainless steel substrate is determined. 34 refs., 12 figs., 2 tabs.
Diffusion-based MR methods for bone structure and evolution.
Sigmund, E E; Cho, H; Chen, P; Byrnes, S; Song, Y-Q; Guo, X E; Brown, T R
2008-01-01
A new approach to MR trabecular bone characterization is presented. This method probes the diffusion of spins through internal magnetic field gradients due to the susceptibility contrast between the bone and water (or marrow) phases. The resulting spin magnetization decay encodes properties of the underlying structure. This method, termed decay due to diffusion in the internal field (DDIF), is well established as a probe of pore size and structure. In the present work its application is shown for in vitro experiments on excised bovine tibiae samples. A comparison with pulsed field gradient (PFG) measurement of restricted diffusion shows a strong correlation of DDIF with the surface-to-volume ratio (SVR) of bones. Calculation of the internal magnetic field within the bone structure also supports this interpretation. These NMR measurements compare well with the image analysis from microscopic computed tomography (muCT). The SVR is not accessible in the clinically standard densitometry measurements, and provides vital information on bone strength and therefore on its fracture risk. The DDIF and PFG methods derive this information from a straightforward pulse sequence that does not employ either high applied field gradients or microimaging, and thus may have clinical potential. PMID:18098292
Drop deformation and breakup with diffuse interface method
NASA Astrophysics Data System (ADS)
Chen, S. L.; Lin, C. Z.; Guo, L. J.; Wang, Y. S.
2010-03-01
Two-dimensional numerical simulation of the deformation and breakup of an isolated liquid drop suspended in immiscible viscous fluid under shear flow was performed with the diffuse interface method. The governing equations of the model were described by Navier—Stokes—Cahn—Hilliard equations. The surface tension was treated as a modified stress. In the paper, the critical Capillary number was plotted as a function of viscosity ratios with the method of approximation. Besides, From the numerical observations, the breakup of the droplets occurred by three mechanisms, namely, necking, end pinching, and capillary instability. Quantitative results for the deformation and breakup of drop are presented.
Effective Thermal Diffusivity Study of Powder Biocomposites via Photoacoustic Method
NASA Astrophysics Data System (ADS)
Mariucci, V. V. G.; da Cruz, J. A.; Bonadio, T. G. M.; Picolloto, A. M.; Weinand, W. R.; Lima, W. M.; Medina, A. N.; Bento, A. C.
2015-10-01
The effective thermal diffusivity for biocomposites of hydroxyapatite (HAp), and niobium pentoxide (Nb2O5) on powder form was studied via photoacoustic method adapted for porous materials. The concentration of each element was accompanied with the results of X-ray diffractometer (XRD) and scanning electron microscopy (SEM). A theoretical model for the thermal coupling of a three layered sample, designed to contain the powder material is proposed. The method for mixtures obeyed the formula [(1 - x) H A p + ( x) N b 2O5] for 0.0 ? x ? 1.0. Experimental results for effective thermal diffusivity ranged between (6.4 ± 0.3) × 10-6 m2 s-1 and (9.8 ± 0.4) × 10-6 m2 s-1 for x ? 0.7. Values of the effective thermal diffusivity have decreased sharply to (0.7 ± 0.03) ×10-6 m2 s-1 for x > 0.7. SEM micrographs showed a coating of HAp over the particles of Nb2O5 for some mixtures.
Wuthiekanun, Vanaporn; Amornchai, Premjit; Langla, Sayan; White, Nicholas J; Day, Nicholas P J; Limmathurotsakul, Direk; Peacock, Sharon J
2015-08-01
Leptospira Vanaporn Wuthiekanun (LVW) agar was used to develop a disk diffusion assay for Leptospira spp. Ten pathogenic Leptospira isolates were tested, all of which were susceptible to 17 antimicrobial agents (amoxicillin/clavulanic acid, amoxicillin, azithromycin, cefoxitin, ceftazidime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, doripenem, doxycycline, gentamicin, linezolid, nitrofurantoin, penicillin, piperacillin/tazobactam, and tetracycline). All 10 isolates had no zone of growth inhibition for four antimicrobials (fosfomycin, nalidixic acid, rifampicin, and trimethoprim/sulfamethoxazole). Of the ten Leptospira, seven had a growth inhibition zone of ? 21 mm for aztreonam, the zone diameter susceptibility break point for Enterobacteriaceae. This assay could find utility as a simple screening method during the epidemiological surveillance of antimicrobial resistance in Leptospira spp. PMID:26055750
Wuthiekanun, Vanaporn; Amornchai, Premjit; Langla, Sayan; White, Nicholas J.; Day, Nicholas P. J.; Limmathurotsakul, Direk; Peacock, Sharon J.
2015-01-01
Leptospira Vanaporn Wuthiekanun (LVW) agar was used to develop a disk diffusion assay for Leptospira spp. Ten pathogenic Leptospira isolates were tested, all of which were susceptible to 17 antimicrobial agents (amoxicillin/clavulanic acid, amoxicillin, azithromycin, cefoxitin, ceftazidime, ceftriaxone, chloramphenicol, ciprofloxacin, clindamycin, doripenem, doxycycline, gentamicin, linezolid, nitrofurantoin, penicillin, piperacillin/tazobactam, and tetracycline). All 10 isolates had no zone of growth inhibition for four antimicrobials (fosfomycin, nalidixic acid, rifampicin, and trimethoprim/sulfamethoxazole). Of the ten Leptospira, seven had a growth inhibition zone of ? 21 mm for aztreonam, the zone diameter susceptibility break point for Enterobacteriaceae. This assay could find utility as a simple screening method during the epidemiological surveillance of antimicrobial resistance in Leptospira spp. PMID:26055750
Newton-Krylov methods applied to nonequilibrium radiation diffusion
Knoll, D.A.; Rider, W.J.; Olsen, G.L.
1998-03-10
The authors present results of applying a matrix-free Newton-Krylov method to a nonequilibrium radiation diffusion problem. Here, there is no use of operator splitting, and Newton`s method is used to convert the nonlinearities within a time step. Since the nonlinear residual is formed, it is used to monitor convergence. It is demonstrated that a simple Picard-based linearization produces a sufficient preconditioning matrix for the Krylov method, thus elevating the need to form or store a Jacobian matrix for Newton`s method. They discuss the possibility that the Newton-Krylov approach may allow larger time steps, without loss of accuracy, as compared to an operator split approach where nonlinearities are not converged within a time step.
A diffusive information preservation method for small Knudsen number flows
Fei, Fei; Fan, Jing
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.
New method to diffusion bond superalloys A. A. Shirzadi and E. R. Wallach
Cambridge, University of
New method to diffusion bond superalloys A. A. Shirzadi and E. R. Wallach A new method for diffusion bonding nickel base and cobalt base superalloys has been developed, which is based on non-chemical oxide removal before the bonding process. Using this method, diffusion bonds were produced in nickel
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
The streamline diffusion finite element method for compressible and incompressible fluid flow
NASA Astrophysics Data System (ADS)
Johnson, C.
The streamline diffusion finite element method is applied as a general method for hyperbolic type problems including convection-dominated scalar convection-diffusion problems, the incompressible Euler and Navier-Stokes equations, and the incompressible Euler equations. Results on adaptive forms of the streamline diffusion, based on a priori estimates are included. A form of the streamline diffusion method for time-dependent problems, using space-time finite elements oriented along characteristics, is presented.
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.
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.
Migration of chemotactic bacteria in soft agar: role of gel concentration.
Croze, Ottavio A; Ferguson, Gail P; Cates, Michael E; Poon, Wilson C K
2011-08-01
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?0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria 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. PMID:21806920
Migration of Chemotactic Bacteria in Soft Agar: Role of Gel Concentration
Croze, Ottavio A.; Ferguson, Gail P.; Cates, Michael E.; Poon, Wilson C.K.
2011-01-01
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?0.35%, expanding bacterial colonies display characteristic chemotactic rings. At C = 0.35%, however, bacteria 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. PMID:21806920
Domain decomposition multigrid methods for nonlinear reaction-diffusion problems
NASA Astrophysics Data System (ADS)
Arrarás, A.; Gaspar, F. J.; Portero, L.; Rodrigo, C.
2015-03-01
In this work, we propose efficient discretizations for nonlinear evolutionary reaction-diffusion problems on general two-dimensional domains. The spatial domain is discretized through an unstructured coarse triangulation, which is subsequently refined via regular triangular grids. Following the method of lines approach, we first consider a finite element spatial discretization, and then use a linearly implicit splitting time integrator related to a suitable decomposition of the triangulation nodes. Such a procedure provides a linear system per internal stage. The equations corresponding to those nodes lying strictly inside the elements of the coarse triangulation can be decoupled and solved in parallel using geometric multigrid techniques. The method is unconditionally stable and computationally efficient, since it avoids the need for Schwarz-type iteration procedures. In addition, it is formulated for triangular elements, thus yielding much flexibility in the discretization of complex geometries. To illustrate its practical utility, the algorithm is shown to reproduce the pattern-forming dynamics of the Schnakenberg model.
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.
Modelling of transient heat conduction with diffuse interface methods
NASA Astrophysics Data System (ADS)
Ettrich, J.; Choudhury, A.; Tschukin, O.; Schoof, E.; August, A.; Nestler, B.
2014-12-01
We present a survey on different numerical interpolation schemes used for two-phase transient heat conduction problems in the context of interface capturing phase-field methods. Examples are general transport problems in the context of diffuse interface methods with a non-equal heat conductivity in normal and tangential directions to the interface. We extend the tonsorial approach recently published by Nicoli M et al (2011 Phys. Rev. E 84 1-6) to the general three-dimensional (3D) transient evolution equations. Validations for one-dimensional, two-dimensional and 3D transient test cases are provided, and the results are in good agreement with analytical and numerical reference solutions.
A Hidden Pitfall in the Preparation of Agar Media Undermines Microorganism Cultivability
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
A hidden pitfall in the preparation of agar media undermines microorganism cultivability.
Tanaka, Tomohiro; Kawasaki, Kosei; Daimon, Serina; Kitagawa, Wataru; Yamamoto, Kyosuke; Tamaki, Hideyuki; Tanaka, Michiko; Nakatsu, Cindy H; Kamagata, Yoichi
2014-12-01
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-27(T) 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
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
Colony morphology of Staphylococcus aureus in serum-soft agar following in vivo and in vitro growth.
Opdebeeck, J P; Watson, D L; Frost, A J
1988-01-01
Staphylococcus aureus isolated from cases of mastitis in ruminants were grown in vitro and in vivo and subsequently examined for expression of diffuse colony morphology in serum-soft agar. Growth in the bovine mammary gland, but not in the ovine mammary gland or ovine peritoneal cavity, resulted in subsequent expression of diffuse colony morphology. PMID:3354194
Low density, microcellular, dopable, agar/gelatin foams for pulsed power experiments
McNamara, W.F.; Aubert, J.H.
1997-04-01
Low-density, microcellular foams prepared from the natural polymers agar and gelatin have been developed for pulsed-power physics experiments. Numerous experiments were supported with foams having densities at or below 10 mg/cm{sup 3}. For some of the experiments, the agar/gelatin foam was uniformly doped with metallic elements using soluble salts. Depending on the method of preparation, cell sizes were typically below 10 microns and for one process were below 1.0 micron.
A Critical Study of Agglomerated Multigrid Methods for Diffusion
NASA Technical Reports Server (NTRS)
Nishikawa, Hiroaki; Diskin, Boris; Thomas, James L.
2011-01-01
Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Convergence rates of multigrid cycles are verified with quantitative analysis methods in which parts of the two-grid cycle are replaced by their idealized counterparts.
A Critical Study of Agglomerated Multigrid Methods for Diffusion
NASA Technical Reports Server (NTRS)
Thomas, James L.; Nishikawa, Hiroaki; Diskin, Boris
2009-01-01
Agglomerated multigrid techniques used in unstructured-grid methods are studied critically for a model problem representative of laminar diffusion in the incompressible limit. The studied target-grid discretizations and discretizations used on agglomerated grids are typical of current node-centered formulations. Agglomerated multigrid convergence rates are presented using a range of two- and three-dimensional randomly perturbed unstructured grids for simple geometries with isotropic and highly stretched grids. Two agglomeration techniques are used within an overall topology-preserving agglomeration framework. The results show that multigrid with an inconsistent coarse-grid scheme using only the edge terms (also referred to in the literature as a thin-layer formulation) provides considerable speedup over single-grid methods but its convergence deteriorates on finer grids. Multigrid with a Galerkin coarse-grid discretization using piecewise-constant prolongation and a heuristic correction factor is slower and also grid-dependent. In contrast, grid-independent convergence rates are demonstrated for multigrid with consistent coarse-grid discretizations. Actual cycle results are verified using quantitative analysis methods in which parts of the cycle are replaced by their idealized counterparts.
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.
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.
Hombach, Michael; Maurer, Florian P; Pfiffner, Tamara; Böttger, Erik C; Furrer, Reinhard
2015-12-01
Parameters like zone reading, inoculum density, and plate streaking influence the precision and accuracy of disk diffusion antibiotic susceptibility testing (AST). While improved reading precision has been demonstrated using automated imaging systems, standardization of the inoculum and of plate streaking have not been systematically investigated yet. This study analyzed whether photometrically controlled inoculum preparation and/or automated inoculation could further improve the standardization of disk diffusion. Suspensions of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213 of 0.5 McFarland standard were prepared by 10 operators using both visual comparison to turbidity standards and a Densichek photometer (bioMérieux), and the resulting CFU counts were determined. Furthermore, eight experienced operators each inoculated 10 Mueller-Hinton agar plates using a single 0.5 McFarland standard bacterial suspension of E. coli ATCC 25922 using regular cotton swabs, dry flocked swabs (Copan, Brescia, Italy), or an automated streaking device (BD-Kiestra, Drachten, Netherlands). The mean CFU counts obtained from 0.5 McFarland standard E. coli ATCC 25922 suspensions were significantly different for suspensions prepared by eye and by Densichek (P < 0.001). Preparation by eye resulted in counts that were closer to the CLSI/EUCAST target of 10(8) CFU/ml than those resulting from Densichek preparation. No significant differences in the standard deviations of the CFU counts were observed. The interoperator differences in standard deviations when dry flocked swabs were used decreased significantly compared to the differences when regular cotton swabs were used, whereas the mean of the standard deviations of all operators together was not significantly altered. In contrast, automated streaking significantly reduced both interoperator differences, i.e., the individual standard deviations, compared to the standard deviations for the manual method, and the mean of the standard deviations of all operators together, i.e., total methodological variation. PMID:26468500
CLOSED-LOOP CONTROL OF VORTEX SHEDDING IN A SEPARATED DIFFUSER USING AN INVERSE METHOD
Colonius, Tim
CLOSED-LOOP CONTROL OF VORTEX SHEDDING IN A SEPARATED DIFFUSER USING AN INVERSE METHOD Takao Suzuki for vortex shedding in a separated diffuser. We intro- duce pulses of zero-net-mass injection (consecutive shedding from a bluff body, a va- riety of closed-loop control methods has been stud- ied. The main
Biological treatment of textile dyes by agar-agar immobilized consortium in a packed bed reactor.
Patel, Yogesh; Gupte, Akshaya
2015-03-01
The decolorization of Acid Maroon V was investigated using bacterial consortium EDPA containing Enterobacter dissolvens AGYP1 and Pseudomonas aeruginosa AGYP2 immobilized in different entrapment matrices. The consortium displayed 96% removal of dye (100 mg/l) within 6 h when immobilized in agar-agar. Under optimum concentrations of agar-agar (3.0% w/v) and cell biomass (0.9 g% w/v), the consortium displayed decolorization for 18 successive batches of Acid Maroon V and also decolorized 14 other different textile dyes. A packed bed reactor under batch mode showed 89% decolorization of dye after 56 repetitive cycles. Under continuous flow mode, maximum color removal was achieved with bed length of 36 cm, hydraulic retention time of 2.66 h, and dye concentration of 100 mg/l. Additionally, the reactor decolorized relatively higher concentrations (100-2000 mg/l) of dye. The synthetic dye wastewater containing five textile dyes was decolorized 92% with 62% COD reduction using an immobilized consortium. PMID:25842535
Improving agar electrospinnability with choline-based deep eutectic solvents.
Sousa, Ana M M; Souza, Hiléia K S; Uknalis, Joseph; Liu, Shih-Chuan; Gonçalves, Maria P; Liu, LinShu
2015-09-01
Very recently our group has produced novel agar-based fibers by an electrospinning technique using water as solvent and polyvinyl alcohol (PVA) as co-blending polymer. Here, we tested the deep eutectic solvent (DES), (2-hydroxyethyl)trimethylammonium chloride/urea prepared at 1:2 molar ratio, as an alternative solvent medium for agar electrospinning. The electrospun materials were collected with an ethanol bath adapted to a previous electrospinning set-up. One weight percent agar-in-DES showed improved viscoelasticity and hence, spinnability, when compared to 1 wt% agar-in-water and pure agar nanofibers were successfully electrospun if working above the temperature of sol-gel transition (?80 °C). By changing the solvent medium we decreased the PVA concentration (5 wt% starting solution) and successfully produced composite fibers with high agar contents (50/50 agar/PVA). Best composite fibers were formed with the 50/50 and 30/70 agar/PVA solutions. These fibers were mechanically resistant, showed tailorable surface roughness and diverse size distributions, with most of the diameters falling in the sub-micron range. Both nano and micro forms of agar fibers (used separately or combined) may have potential for the design of new and highly functional agar-based materials. PMID:26116384
Uzun, Meltem; Bozdogan, Bulent
2013-01-01
The performance of sheep sera instead of sheep blood in agar-based media was investigated for susceptibility testing of Mycobacterium tuberculosis against primary drugs. The levels of agreement between agar-based medium supplemented with sheep sera and the proportion method on Middlebrook 7H11 agar as the reference method for determining susceptibility to isoniazid (INH), rifampin (RIF), ethambutol (EMB), and streptomycin (STR) were 98.4, 98.4, 95.3, and 100%, respectively. PMID:24131699
T. Koide; T. Kodama
2011-08-24
The stochastic variational method is applied to particle systems and continuum mediums. As the brief review of this method, we first discuss the application to particle Lagrangians and derive a diffusion-type equation and the Schr\\"{o}dinger equation with the minimum gauge coupling. We further extend the application of the stochastic variational method to Lagrangians of continuum mediums and show that the Navier-Stokes, Gross-Pitaevskii and generalized diffusion equations are derived. The correction term for the Navier-Stokes equation is also obtained in this method. We discuss the meaning of this correction by comparing with the diffusion equation.
Characterization of bionanocomposite films prepared with agar and paper-mulberry pulp nanocellulose.
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
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
Bale, M J; Yang, C; Pfaller, M A
1997-06-01
Candida albicans and Candida (Torulopsis) glabrata are the most common species of yeast encountered in the clinical laboratory. In this study, we sought to evaluate simple means of screening cultures for the presence or absence of C. glabrata. Twelve thousand five hundred (12,500) consecutive cultures were evaluated for sufficient yeast growth to warrant identification. When detected (369 isolates), the amount of growth on eosin methylene blue agar (EMB) versus sheep blood agar (BAP) (both incubated in 5% CO2), wet mount morphology, and germ tube production were evaluated. All germ tube-negative yeasts were definitively identified using the Vitek YBC card. Of the 369 yeast isolates included in this study, 225 were C. albicans, 102 C. glabrata, and 42 other Candida species. Growth on EMB was greater than BAP for 92 isolates; all identified as C. glabrata. When EMB growth was equal to or less than BAP, 10 isolates were C. glabrata and 267 were other Candida ssp. An accurate presumptive identification of C. glabrata may be made using the observation of greater growth on EMB versus BAP. When coupled with the germ tube test, the majority of yeast isolates could be identified by these simple methods in our laboratory. PMID:9239496
Preparation of oxidized agar and characterization of its properties.
Zhang, Xiaodong; Liu, Xin; Xia, Kai; Luan, Jimei
2014-11-01
A series of oxidized agars with different carboxyl content were prepared, and their properties were determined and analyzed. The results showed that the gelling temperature, the optical rotation and the apparent viscosity of the agar solution, and the melting temperature, the strength, the hardness, the fracturability, the springiness, the chewiness and the gumminess of agar gel all decreased except that the cohesiveness increased after oxidation. The gel skeleton structures of agar before and after oxidation were all of the porous network structures, but the pores of gel skeleton structure became smaller and denser after oxidation. PMID:25129785
A fully implicit method for 3D quasi-steady state magnetic advection-diffusion.
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.
A multigrid Newton-Krylov method for flux-limited radiation diffusion
Rider, W.J.; Knoll, D.A.; Olson, G.L.
1998-09-01
The authors focus on the integration of radiation diffusion including flux-limited diffusion coefficients. The nonlinear integration is accomplished with a Newton-Krylov method preconditioned with a multigrid Picard linearization of the governing equations. They investigate the efficiency of the linear and nonlinear iterative techniques.
Diffusion NMR methods applied to xenon gas for materials study
NASA Technical Reports Server (NTRS)
Mair, R. W.; Rosen, M. S.; Wang, R.; Cory, D. G.; Walsworth, R. L.
2002-01-01
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. c2002 John Wiley & Sons, Ltd.
Lou, Shishu; Zhu, Huishi; Hu, Shaoxu; Zhao, Chunhua; Han, Peide
2015-01-01
Characterization of the diffusion length of solar cells in space has been widely studied using various methods, but few studies have focused on a fast, simple way to obtain the quantified diffusion length distribution on a silicon wafer. In this work, we present two different facile methods of doing this by fitting photoluminescence images taken in two different wavelength ranges or from different sides. These methods, which are based on measuring the ratio of two photoluminescence images, yield absolute values of the diffusion length and are less sensitive to the inhomogeneity of the incident laser beam. A theoretical simulation and experimental demonstration of this method are presented. The diffusion length distributions on a polycrystalline silicon wafer obtained by the two methods show good agreement. PMID:26364565
Lou, Shishu; Zhu, Huishi; Hu, Shaoxu; Zhao, Chunhua; Han, Peide
2015-01-01
Characterization of the diffusion length of solar cells in space has been widely studied using various methods, but few studies have focused on a fast, simple way to obtain the quantified diffusion length distribution on a silicon wafer. In this work, we present two different facile methods of doing this by fitting photoluminescence images taken in two different wavelength ranges or from different sides. These methods, which are based on measuring the ratio of two photoluminescence images, yield absolute values of the diffusion length and are less sensitive to the inhomogeneity of the incident laser beam. A theoretical simulation and experimental demonstration of this method are presented. The diffusion length distributions on a polycrystalline silicon wafer obtained by the two methods show good agreement. PMID:26364565
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.
Sutra, L; Mendolia, C; Rainard, P; Poutrel, B
1990-01-01
A total of 193 Staphylococcus aureus isolates from bovine, caprine, and ovine mastitis producing type 5 or 8 capsular polysaccharides were investigated for colony morphology in serum-soft agar and agglutinability by an anti-teichoic acid serum, after cultivation in modified staphylococcus medium no. 110. Also, 40 of these strains were cultivated in brain heart infusion and submitted to clumping factor and protein A detection tests. Considering capsular serotyping as a reference method, diffuse growth in serum-soft agar and inagglutinability by anti-teichoic acid serum identified, respectively, 57.5 and 45% of encapsulated strains cultivated in brain heart infusion and 85.5 and 77.2% of those cultivated in modified staphylococcus medium 110. Consequently, these indirect techniques underestimated encapsulation and were greatly influenced by culture conditions. Whatever the medium used, diffuse colony morphology in serum-soft agar was generally characterized by a masking of teichoic acid and protein A. By contrast, these surface antigens were detected in association with compact morphology; the presence of a thin or discontinuous capsular material could explain this result. Moreover, the masking of teichoic acid and the removal of capsular polysaccharide by washing in saline suggest that type 8 capsular polysaccharide is more abundant and labile than type 5. PMID:2324272
Sutra, L; Mendolia, C; Rainard, P; Poutrel, B
1990-03-01
A total of 193 Staphylococcus aureus isolates from bovine, caprine, and ovine mastitis producing type 5 or 8 capsular polysaccharides were investigated for colony morphology in serum-soft agar and agglutinability by an anti-teichoic acid serum, after cultivation in modified staphylococcus medium no. 110. Also, 40 of these strains were cultivated in brain heart infusion and submitted to clumping factor and protein A detection tests. Considering capsular serotyping as a reference method, diffuse growth in serum-soft agar and inagglutinability by anti-teichoic acid serum identified, respectively, 57.5 and 45% of encapsulated strains cultivated in brain heart infusion and 85.5 and 77.2% of those cultivated in modified staphylococcus medium 110. Consequently, these indirect techniques underestimated encapsulation and were greatly influenced by culture conditions. Whatever the medium used, diffuse colony morphology in serum-soft agar was generally characterized by a masking of teichoic acid and protein A. By contrast, these surface antigens were detected in association with compact morphology; the presence of a thin or discontinuous capsular material could explain this result. Moreover, the masking of teichoic acid and the removal of capsular polysaccharide by washing in saline suggest that type 8 capsular polysaccharide is more abundant and labile than type 5. PMID:2324272
Continuous and Discontinuous Finite Element Methods for Convection-Diffusion Problems: A Comparison
Continuous and Discontinuous Finite Element Methods for Convection-Diffusion Problems: A Comparison the performance of a new continuous-discontinuous finite element method (CDFEM) for linear convection Petrov-Galerkin finite element method, the residual- free bubble method and the discontinuous Galerkin
NASA Astrophysics Data System (ADS)
Hoffmann, Thomas; Dorrestein, Pieter C.
2015-11-01
Matrix deposition on agar-based microbial colonies for MALDI imaging mass spectrometry is often complicated by the complex media on which microbes are grown. This Application Note demonstrates how consecutive short spray pulses of a matrix solution can form an evenly closed matrix layer on dried agar. Compared with sieving dry matrix onto wet agar, this method supports analyte cocrystallization, which results in significantly more signals, higher signal-to-noise ratios, and improved ionization efficiency. The even matrix layer improves spot-to-spot precision of measured m/z values when using TOF mass spectrometers. With this technique, we established reproducible imaging mass spectrometry of myxobacterial cultures on nutrient-rich cultivation media, which was not possible with the sieving technique.
A comparison of the point kinetics equations with the QUANDRY analytic nodal diffusion method
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...
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.
New selective agar medium for isolation of virulent Yersinia enterocolitica.
Fukushima, H
1987-06-01
A selective agar medium for isolation of virulent Yersinia enterocolitica (VYE agar) was developed for the rapid and accurate isolation of virulent Y. enterocolitica from environmental samples highly contaminated with environmental Yersinia organisms, as well as for isolation from clinical specimens. VYE agar provided a quantitative recovery of 51 different strains of virulent Y. enterocolitica at 32 degrees C after incubation for 24 h. The cefsulodin, irgasan, josamycin, and oleandomycin content of the medium resulted in a high selectivity, and the mannitol and esculin content provided some differentiation. The greatest advantage of VYE agar is that virulent Y. enterocolitica, which forms red colonies, is easily differentiated from most environmental Yersinia organisms and other gram-negative bacteria, which form dark colonies with a dark peripheral zone as a result of esculin hydrolysis. Use of VYE agar led to a high recovery of Y. enterocolitica biotype 3B serotype O:3 strains from experimentally inoculated meat samples, compared with use of CIN agar. Biotype 2 serotypes O:5,27 and O:9 and biotype 1 esculin-negative serotypes O:4,32, O:8, O:13a,13b, O:18, O:20, and O:21 (American types) were readily differentiated from other environmental organisms able to grow on VYE agar. Epidemiological studies on Y. enterocolitica should be greatly facilitated by the use of this selective agar medium. PMID:3597750
Development of a numerical method for the prediction of turbulent flows in dump diffusers
NASA Astrophysics Data System (ADS)
Ando, Yasunori; Kawai, Masafumi; Sato, Yukinori; Toh, Hidemi
1987-01-01
In order to obtain an effective tool to design dump diffusers for gas turbine combustors, a finite-volume numerical calculation method has been developed for the solution of two-dimensional/axisymmetric incompressible steady Navier-Stokes equation in general curvilinear coordinate system. This method was applied to the calculations of turbulent flows in a two-dimensional dump diffuser with uniform and distorted inlet velocity profiles as well as an annular dump diffuser with uniform inlet velocity profile, and the calculated results were compared with experimental data. The numerical results showed a good agreement with experimental data in case of both inlet velocity profiles; eventually, the numerical method was confirmed to be an effective tool for the development of dump diffusers which can predict the flow pattern, velocity distribution and the pressure loss.
Normal force controlled rheology applied to agar gelation
Bosi Mao; Thibaut Divoux; Patrick Snabre
2015-10-24
A wide range of thermoreversible gels are prepared by cooling down to ambient temperature hot aqueous solutions of polymers. During the sol-gel transition, such soft solids may experience a volume contraction which is traditionally overlooked as rheological measurements are usually performed in geometries of constant volume. In this article, we revisit the impact of thermal history on the formation of agar gels through a series of benchmark experiments conducted with a plate-plate geometry. We demonstrate that the sample contraction cannot be neglected, and that monitoring the gelation while imposing a constant gap width results in the strain hardening of the sample, as evidenced by the slow drift in time of the gel elastic modulus G'. Furthermore, we show that imposing a constant normal force equals to zero during the gelation, instead of a constant gap width, suppresses the hardening as the decrease of the gap width compensates for the sample contraction. The latter method provides a way to measure more reliably the gel linear properties and is remarkably proved efficient with either rough or smooth boundary conditions. Varying the thermal history, we show by using normal force controlled rheology that neither the value of the cooling rate, nor the addition of a constant temperature stage during the cooling process influence the gel elastic properties. Instead, G' is controlled by the terminal temperature at the end of the cooling ramp as confirmed by direct imaging of the gel microstructure by electron microscopy. The present work offers an extensive review of the artifacts associated with the rheology of agar gels and paves the way for a more systematic use of normal force controlled rheology to monitor non-isochoric processes.
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
Zhao, Su; Ovadia, Jeremy; Liu, Xinfeng; Zhang, Yong-Tao; Nie, Qing
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) 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
Development of advanced methods for analysis of experimental data in diffusion
NASA Astrophysics Data System (ADS)
Jaques, Alonso V.
There are numerous experimental configurations and data analysis techniques for the characterization of diffusion phenomena. However, the mathematical methods for estimating diffusivities traditionally do not take into account the effects of experimental errors in the data, and often require smooth, noiseless data sets to perform the necessary analysis steps. The current methods used for data smoothing require strong assumptions which can introduce numerical "artifacts" into the data, affecting confidence in the estimated parameters. The Boltzmann-Matano method is used extensively in the determination of concentration - dependent diffusivities, D(C), in alloys. In the course of analyzing experimental data, numerical integrations and differentiations of the concentration profile are performed. These methods require smoothing of the data prior to analysis. We present here an approach to the Boltzmann-Matano method that is based on a regularization method to estimate a differentiation operation on the data, i.e., estimate the concentration gradient term, which is important in the analysis process for determining the diffusivity. This approach, therefore, has the potential to be less subjective, and in numerical simulations shows an increased accuracy in the estimated diffusion coefficients. We present a regression approach to estimate linear multicomponent diffusion coefficients that eliminates the need pre-treat or pre-condition the concentration profile. This approach fits the data to a functional form of the mathematical expression for the concentration profile, and allows us to determine the diffusivity matrix directly from the fitted parameters. Reformulation of the equation for the analytical solution is done in order to reduce the size of the problem and accelerate the convergence. The objective function for the regression can incorporate point estimations for error in the concentration, improving the statistical confidence in the estimated diffusivity matrix. Case studies are presented to demonstrate the reliability and the stability of the method. To the best of our knowledge there is no published analysis of the effects of experimental errors on the reliability of the estimates for the diffusivities. For the case of linear multicomponent diffusion, we analyze the effects of the instrument analytical spot size, positioning uncertainty, and concentration uncertainty on the resulting values of the diffusivities. These effects are studied using Monte Carlo method on simulated experimental data. Several useful scaling relationships were identified which allow more rigorous and quantitative estimates of the errors in the measured data, and are valuable for experimental design. To further analyze anomalous diffusion processes, where traditional diffusional transport equations do not hold, we explore the use of fractional calculus in analytically representing these processes is proposed. We use the fractional calculus approach for anomalous diffusion processes occurring through a finite plane sheet with one face held at a fixed concentration, the other held at zero, and the initial concentration within the sheet equal to zero. This problem is related to cases in nature where diffusion is enhanced relative to the classical process, and the order of differentiation is not necessarily a second--order differential equation. That is, differentiation is of fractional order alpha, where 1 ? alpha < 2. For alpha = 2, the presented solutions reduce to the classical second-order diffusion solution for the conditions studied. The solution obtained allows the analysis of permeation experiments. Frequently, hydrogen diffusion is analyzed using electrochemical permeation methods using the traditional, Fickian-based theory. Experimental evidence shows the latter analytical approach is not always appropiate, because reported data shows qualitative (and quantitative) deviation from its theoretical scaling predictions. Preliminary analysis of data shows better agreement with fractional diffusion analysis when compared to tr
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.
Diffusion Rate Tomography for Time Domain Electromagnetic Induction Methods
NASA Astrophysics Data System (ADS)
Kazlauskas, E. M.; Weiss, C. J.
2010-12-01
Although it is now routine to invert near-surface electromagnetic induction data in terms of ground conductivity, geoelectromagnetic inversion remains an open research problem because of its intrinsic non-uniqueness and the need to balance computational efficiency with recovering models bearing some resemblance to real geologic structure. The most popular approach for fitting electromagnetic data is analogous to seismic full-waveform inversion. Whether the data are in the time- or frequency-domain, a model is sought which recovers either the amplitude and phase, or the transient response of some measured waveform. However, imperfect knowledge of the source waveform has the potential to erroneously introduce unwarranted geologic structure in the final recovered earth model. Hence, we explore here an alternative approach that mitigates these effects in highly attenuated electromagnetic data. Rather than inverting for the full waveform response, Diffusion Rate Tomography (DiRT) is based on inverting for the arrival time of some key, diagnostic feature in the measured data. This procedure eliminates any error introduced by incomplete knowledge of the source amplitude due to miscalibration, instrument drift, or battery drainage. Time-domain electromagnetic sounding experiments conducted with a horizontal loop transmitter and offset receiver coil provide a useful test of the concept. As induced eddy currents from the transmitter diffuse beneath the receiver, a polarity change occurs in the vertical component of the observed magnetic field. This polarity change (or zero crossing) is our invertible diagnostic, and given a range of offsets between the transmitter and receiver antennae, the zero-crossing moveout curve constitutes the data we invert. Examples of DiRT for a range of geologic settings will be presented and compared against results from smooth, full-waveform inversion. Interestingly, although DiRT works on fewer data than the full-waveform inversion, there is strong similarity in the recovered models, suggesting future work in examining redundancy in electromagnetic data or optimal regularization schemes.
A LEVEL SET METHOD FOR ANISOTROPIC GEOMETRIC DIFFUSION IN 3D IMAGE PROCESSING
Rumpf, Martin
. Introduction. Multiscale methods have proved to be successful tools in image de- noising, edge enhancementA 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 processing is presented which
Akter, Laila; Haque, Rezwana; Salam, Md. Abdus
2014-01-01
Objective: Urine is the most frequent specimen received for culture/sensitivity by clinical laboratories. The microbiological performance of HiCrome UTI agar medium was compared with Blood agar and MacConkey agar for isolation and presumptive identification of bacteria from urine culture. Methods: A total of 443 consecutively collected midstream and/or catheter-catch urine samples from patients attending the Islami Bank Medical College Hospital, Rajshahi, Bangladesh during January to December, 2012 were cultured. Urine samples showing pus cells ? 5/HPF were inoculated on to Blood agar (BA), MacConkey agar (MAC) and HiCrome UTI agar (CA) media simultaneously and incubated overnight aerobically at 370C. Rate of isolation and presumptive identification of bacterial species were compared for different media. Results: Culture yielded a total of 199 bacterial isolates from 189 (42.67%) positive plates including 179 (40.40%) unimicrobial and 10 (2.26%) polymicrobial (mixed growth of pair of bacteria) growths. Both HiCrome UTI agar and Blood agar media supported 100% growths while 151 (75.88%) growths were observed on MacConkey agar. The rate of presumptive identification was found significantly higher on HiCrome UTI agar (97.49%) than MAC agar (67.34%) (P<0.001) as primary urine culture medium. Of 199 isolates, E. coli was found to be the leading uropathogen isolated from 118 (59.30%) samples with its presumptive identification rate of 95.76%, 93.22% and 5.93% on CA, MAC and BA respectively. All 10 (100%) polymicrobial growths were demonstrated distinctly on CA against only 01(10%) on each BA and MAC. Conclusion: HiCrome UTI agar was found to be more useful as primary urine culture medium in both higher rate of isolation and presumptive identification of uropathogens in comparison to conventional media. Its inherent characteristics in demonstrating polymicrobial growth and ease of rapid identification by distinct colony colour are unique. PMID:25225521
Study of acid diffusion behaves form PAG by using top coat method
NASA Astrophysics Data System (ADS)
Sekiguchi, Atsushi; Matsumoto, Yoko
2014-03-01
Our past research on measurements of simulation parameters for ArF resists focused on establishing methods for measuring the following parameters:[1]-[4] • Development parameters[1] • PEB parameters[2] • Dill's ABC parameters[3] • Quencher parameter[4] We entered these parameters into a lithography simulator and performed ArF resist simulations.We then explored ways to optimize the ArF resist material and process. This paper reports on our study of methods for measuring the diffusion length of acid generated from PAG during exposures. In our experiment, we applied a PAG-containing top coat (TC) material (second layer) to a PAG-free ArF resist (first layer), then performed the exposure and PEB processes. The acid generated in the TC during the exposure diffused into the ArF resist in the lower layer (first layer) when PEB was performed. The process of developing this sample removed the TC in the second layer and the parts of the first layer into which the acid had diffused.We obtained the acid diffusion length based on the quantity of film removed by the development. We calculated the acid diffusion coefficient after varying the exposure value and repeating the measurement. For this report, we also performed measurements to determine how differences in PAG anion size, amount of quencher additive, and PEB temperature affected the acid diffusion coefficient.We entered the measurements obtained into the PROLITH simulator and explored the effects of acid diffusion on pattern profile.
Method of applying a cerium diffusion coating to a metallic alloy
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).
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.
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.
NASA Astrophysics Data System (ADS)
Saha Ray, Santanu
2009-04-01
Spatially fractional order diffusion equations are generalizations of classical diffusion equations which are increasingly used in modeling practical superdiffusive problems in fluid flow, finance and other areas of application. This paper presents the analytical solutions of the space fractional diffusion equations by two-step Adomian Decomposition Method (TSADM). By using initial conditions, the explicit solutions of the equations have been presented in the closed form and then their solutions have been represented graphically. Two examples, the first one is one-dimensional and the second one is two-dimensional fractional diffusion equation, are presented to show the application of the present technique. The solutions obtained by the standard decomposition method have been numerically evaluated and presented in the form of tables and then compared with those obtained by TSADM. The present TSADM performs extremely well in terms of efficiency and simplicity.
Antimicrobial potentials of Mentha longifolia by disc diffusion method.
Bakht, Jehan; Shaheen, Salma; Shafi, Mohammad
2014-07-01
This study was conducted for the assessment of the antimicrobial activities of different solvents extracted samples from the aerial parts of Mentha longifolia against ten microbial species through the disc diffusion assay using two different concentrations of 1 and 2 mg disc1. All extracts from Mentha longifolia showed different ranges of antimicrobial activities. Butanol and ethyl acetate fractions showed inhibitory activities against all microbial species. Methanol fraction showed inhibitory effects against all the tested microbial species except Salmonella typhi. Salmonella typhi was also not controlled by methanol, petroleum ether and dichloromethane extracted samples. The most susceptible gram positive bacteria was Bacillus atropheus and Bacillus subtilis and were inhibited by all extracts and Staphylococus aureus was least susceptible among gram positive bacteria. Klebsiella pneumoniae was the most susceptible gram negative bacterium and Salmonella typhi was highly resistant among the gram negative bacteria. Erwinia carotovora and Agrobacterium tumefaciene were susceptible to all fractions. All fractions showed antifungal activities against Candida albicans except water extracted samples. PMID:25015464
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.
Direct Protocol for Ambient Mass Spectrometry Imaging on Agar Culture.
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
Giri, Sidhartha; Kindo, Anupma Jyoti
2014-01-01
With the increase in invasive fungal infections due to Candida species and resistance to antifungal therapy, in vitro antifungal susceptibility testing is becoming an important part of clinical microbiology laboratories. Along with broth microdilution and disk diffusion method, various commercial methods are being increasingly used for antifungal susceptibility testing, especially in the developed world. In our study, we compared the antifungal susceptibility patterns of 39 isolates of Candida to three antifungal drugs (fluconazole, amphotericin B, ketoconazole) by Candifast and disk diffusion method. The following resistance pattern was found by Candifast: Fluconazole (30.8%), ketoconazole (12.8%), amphotericin B (0%). The results obtained by disk diffusion method were in complete agreement with Candifast results. PMID:25308014
Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.
Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael; 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.
Diffusion Systems for Evaluation of Biomineralization
Silverman, L.
2005-01-01
A variety of in vitro study methods have been used to elucidate the roles of matrix molecules in biomineralization processes. Among these, gel diffusion-precipitation studies have proved to be an effective tool. This methodology is uniquely capable of characterizing the effects of matrix molecules on mineralization while only using very small quantities of material. Furthermore, gel methods have been extended for use as a mineralization assay system to characterize modified matrix molecules and synthetic analogues. Here we discuss the advantages and limitations of gelatin, agar, agarose, and other systems for studying the mechanisms of biomineralization. PMID:15455184
A First-Passage Kinetic Monte Carlo method for reaction–drift–diffusion processes
Mauro, Ava J.; Sigurdsson, Jon Karl; Shrake, Justin; Atzberger, Paul J.; Isaacson, Samuel A.
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.
The Local Discontinuous Galerkin Method for Time-Dependent Convection-Diffusion Systems
NASA Technical Reports Server (NTRS)
Cockburn, Bernardo; Shu, Chi-Wang
1997-01-01
In this paper, we study the Local Discontinuous Galerkin methods for nonlinear, time-dependent convection-diffusion systems. These methods are an extension of the Runge-Kutta Discontinuous Galerkin methods for purely hyperbolic systems to convection-diffusion systems and share with those methods their high parallelizability, their high-order formal accuracy, and their easy handling of complicated geometries, for convection dominated problems. It is proven that for scalar equations, the Local Discontinuous Galerkin methods are L(sup 2)-stable in the nonlinear case. Moreover, in the linear case, it is shown that if polynomials of degree k are used, the methods are k-th order accurate for general triangulations; although this order of convergence is suboptimal, it is sharp for the LDG methods. Preliminary numerical examples displaying the performance of the method are shown.
The Galerkin/least-squares method for advective-diffusive equations
NASA Technical Reports Server (NTRS)
Hughes, T. J. R.; Franca, L. P.; Hulbert, G. M.; Johan, Z.; Shakib, F.
1988-01-01
Galerkin/least-squares finite-element methods are presented for advective-diffusive equations. Galerkin/least-squares represents a conceptual simplification of streamline-upwind Petrov-Galerkin methods, and is in fact applicable to a wide variety of other problem types. A convergence analysis and error estimates are presented. Some numerical results for compressible Navier-Stokes flows are presented.
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.
A Monte Carlo Synthetic Acceleration Method for the Non-Linear, Time-Dependent Diffusion Equation
Evans, Thomas M; Mosher, Scott W
2009-01-01
We present a synthetic-acceleration based Monte Carlo method for solving the 1T thermal radiation diffusion equations. We show that this method can be an effective solver for sparse matrix systems. We also discuss its general applicability to broader classes of problems.
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)...
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)...
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)...
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.
Chen, Li; Kang, Qinjun; Yao, Jun; Tao, Wenquan
2014-01-01
Porous structures of shales are reconstructed based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analyzes of the nanoscale reconstructed shales are performed, including porosity, pore size distribution, specific surface area and pore connectivity. The multiple-relaxation-time (MRT) lattice Boltzmann method (LBM) fluid flow model and single-relaxation-time (SRT) LBM diffusion model are adopted to simulate the fluid flow and Knudsen diffusion process within the reconstructed shales, respectively. Tortuosity, intrinsic permeability and effective Knudsen diffusivity are numerically predicted. The tortuosity is much higher than that commonly employed in Bruggeman equation. Correction of the intrinsic permeability by taking into consideration the contribution of Knudsen diffusion, which leads to the apparent permeability, is performed. The correction factor under different Knudsen number and pressure are estimated and compared with existing corrections re...
Negative Magnetic Eddy Diffusivities from the Test-field Method and Multiscale Stability Theory
NASA Astrophysics Data System (ADS)
Andrievsky, Alexander; Brandenburg, Axel; Noullez, Alain; Zheligovsky, Vladislav
2015-10-01
The generation of a large-scale magnetic field in the kinematic regime in the absence of an ?-effect is investigated by following two different approaches: the test-field method and the multiscale stability theory relying on the homogenization technique. Our computations of the magnetic eddy diffusivity tensor of the parity-invariant flow IV of G. O. Roberts and the modified Taylor-Green flow confirm the findings of previous studies and also explain some of their apparent contradictions. The two flows have large symmetry groups; this is used to considerably simplify the eddy diffusivity tensor. Finally, a new analytic result is presented: upon expressing the eddy diffusivity tensor in terms of solutions to auxiliary problems for the adjoint operator, we derive relations between the magnetic eddy diffusivity tensors that arise for mutually reverse small-scale flows {\\boldsymbol{v}}(x) and -{\\boldsymbol{v}}(x).
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.
Rapid diagnosis of acanthamoeba keratitis using non-nutrient agar with a lawn of E. coli
2013-01-01
Background A patient presented with a corneal foreign body in his only eye. He was treated with prophylactic antibiotics and sent home, but deteriorated. Findings He returned to the hospital 5 days later, and on slit-lamp examination, there was ciliary injection, corneal oedema and a 1 mm × 1 mm corneal abscess with mild anterior uveitis. Corneal scrapings were taken for culture on a non-nutrient agar with a lawn of Escherichia coli, on chocolate agar and on blood agar. He was treated with fortified gentamicin and cefazolin drops. He improved and was discharged 4 days after admission. On day 5, the culture results showed acanthamoeba. He was brought back to the hospital and treated with hourly chlorhexidine drops, ofloxacin six times daily and neomycin/dexamethasone drops once daily. On day 7, he was discharged to continue treatment at home, at which time his visual acuity in that eye was 6/9, and slit-lamp examination showed punctate keratitis and a stromal opacity with mild peripheral infiltration. Conclusions Culture on non-nutrient agar with a lawn of E. coli is a rapid, reliable and less invasive alternative to corneal biopsy for the diagnosis of acanthamoeba infection. We suggest using this method where acanthamoeba is suspected. Owing to the risk of corneal abscess, orthokeratology should be avoided in an amblyopic patient or an only eye. Acanthamoeba infection may be masked by other eye diseases. PMID:23514313
USE OF MUELLER-HINTON BROTH AND AGAR IN THE GERM TUBE TEST
Mattei, Antonella Souza; Alves, Sydney Hartz; Severo, Cecília Bittencourt; Guazzelli, Luciana da Silva; Oliveira, Flávio de Mattos; Severo, Luiz Carlos
2014-01-01
Candida albicans is often isolated from clinical samples, thus its presumptive differentiation from other species of the same genus can be based on its ability to form the germ tube in human serum. Nevertheless, there are two other species that share this characteristic: C. dubliniensis and C. africana. The aim of this study was to compare four different substrates to perform the germ tube (GT) test. The Candida spp. isolates were identified using a manual system (135 C. albicans, 24 C. tropicalis and one C. dubliniensis). The germ tube test was performed with fresh, previously frozen serum and Mueller-Hinton (MH) broth and agar. GT was observed in 96% (130/136) of the isolates through the fresh serum technique, 94% (128/136) through previously frozen serum, 92% (125/136) in MH agar, and 90% (122/136) in MH broth. The sensitivity of each test was higher than 90%, with 100% specificity. Both the MH agar and broth were able to identify the true positives, and false positives were not found. However, some C. albicans isolates were not identified. MH agar and broth may be used in laboratory for the rapid presumptive identification of C. albicans, as an alternative method for germ tube test. PMID:25351541
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.
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.
NUMERICAL METHODS FOR SOLVING THE MULTI-TERM TIME-FRACTIONAL WAVE-DIFFUSION EQUATION.
Liu, F; Meerschaert, M M; McGough, R J; Zhuang, P; Liu, Q
2013-03-01
In this paper, the multi-term time-fractional wave-diffusion equations are considered. The multi-term time fractional derivatives are defined in the Caputo sense, whose orders belong to the intervals [0,1], [1,2), [0,2), [0,3), [2,3) and [2,4), respectively. Some computationally effective numerical methods are proposed for simulating the multi-term time-fractional wave-diffusion equations. The numerical results demonstrate the effectiveness of theoretical analysis. These methods and techniques can also be extended to other kinds of the multi-term fractional time-space models with fractional Laplacian. PMID:23772179
MRI Phantoms – Are There Alternatives to Agar?
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
A gradient random walk method for two-dimensional reaction-diffusion equations
Sherman, A. ); Mascagni, M. Inst. for Defense Analyses, Bowie, MD . Supercomputing Research Center)
1994-11-01
An extension to two space dimensions of the gradient random walk algorithm for reaction-diffusion equations is presented. This family of algorithms is related closely to the random vortex method of computational fluid dynamics. Although the computational cost is high, the method has the desirable features of being grid free and of automatically adapting to the solution by concentrating elements where the gradient is large. In addition, the method can be extended easily to more than two space dimensions. A key feature of the method is discretization in terms of the dependent, rather than independent, variable, giving it features in common with Lagrangian particle methods. The method is derived here and its application to some simple reaction-diffusion wave propagation problems is illustrated.
NASA Astrophysics Data System (ADS)
Bodammer, N. C.; Kaufmann, J.; Kanowski, M.; Tempelmann, C.
2009-02-01
Diffusion tensor tractography (DTT) allows one to explore axonal connectivity patterns in neuronal tissue by linking local predominant diffusion directions determined by diffusion tensor imaging (DTI). The majority of existing tractography approaches use continuous coordinates for calculating single trajectories through the diffusion tensor field. The tractography algorithm we propose is characterized by (1) a trajectory propagation rule that uses voxel centres as vertices and (2) orientation probabilities for the calculated steps in a trajectory that are obtained from the diffusion tensors of either two or three voxels. These voxels include the last voxel of each previous step and one or two candidate successor voxels. The precision and the accuracy of the suggested method are explored with synthetic data. Results clearly favour probabilities based on two consecutive successor voxels. Evidence is also provided that in any voxel-centre-based tractography approach, there is a need for a probability correction that takes into account the geometry of the acquisition grid. Finally, we provide examples in which the proposed fibre-tracking method is applied to the human optical radiation, the cortico-spinal tracts and to connections between Broca's and Wernicke's area to demonstrate the performance of the proposed method on measured data.
Method of fabricating reflection-mode EUV diffusers
Anderson, Erik; Naulleau, Patrick P.
2005-03-01
Techniques for fabricating well-controlled, random relief, engineered surfaces that serve as substrates for EUV optical devices are accomplished with grayscale exposure. The method of fabricating a multilevel EUV optical element includes: (a) providing a substrate; (b) depositing a layer of curable material on a surface of the substrate; (c) creating a relief profile in a layer of cured material from the layer of curable material wherein the relief profile comprises multiple levels of cured material that has a defined contour; and (d) depositing a multilayer reflection film over the relief profile wherein the film has an outer contour that substantially matches that of the relief profile. The curable material can comprise photoresist or a low dielectric constant material.
Stability and error analysis of nodal expansion method for convection-diffusion equation
Deng, Z.; Rizwan-Uddin; Li, F.; Sun, Y.
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)
Peev, G; Nikolova, A; Beschkov, V; Christov, G
2001-07-01
A modified method for determination of diffusivities of low molecular substances in non-Newtonian liquids described by the power-law model has been proposed. It is based on the dissolution of Geiss body, with a parameter m=1/3 rotating in an infinite fluid. In this case, the solution of the differential equations of motion and mass transfer is available as an analytical formula for calculating the diffusivity coefficient.The method allows the extension of the variety of media and diffusing species. It has been illustrated with dissolving of gypsum in water and five non-Newtonian liquids. The results obtained have been interpreted taking into account the interaction between calcium ions and polymer molecules of the non-Newtonian system, as well as the heterogeneity of the system near to the dissolving surface. PMID:11356373
Numerical simulation of diffusion MRI signals using an adaptive time-stepping method.
Li, Jing-Rebecca; Calhoun, Donna; Poupon, Cyril; Le Bihan, Denis
2014-01-20
The effect on the MRI signal of water diffusion in biological tissues in the presence of applied magnetic field gradient pulses can be modelled by a multiple compartment Bloch-Torrey partial differential equation. We present a method for the numerical solution of this equation by coupling a standard Cartesian spatial discretization with an adaptive time discretization. The time discretization is done using the explicit Runge-Kutta-Chebyshev method, which is more efficient than the forward Euler time discretization for diffusive-type problems. We use this approach to simulate the diffusion MRI signal from the extra-cylindrical compartment in a tissue model of the brain gray matter consisting of cylindrical and spherical cells and illustrate the effect of cell membrane permeability. PMID:24351275
Susceptibility testing of Propionibacterium acnes comparing agar dilution with E test.
Smith, M A; Alperstein, P; France, K; Vellozzi, E M; Isenberg, H D
1996-04-01
Propionibacterium acnes has been identified as a significant agent of nosocomial infections, including endophthalmitis. Data concerning susceptibility of P. acnes to newer beta-lactam antibiotics and fluoroquinolones are limited. Recent reports suggest that quinolones have activity against these organisms sufficient to warrant further study. We undertook a study to select appropriate antimicrobial agents for use in a rabbit model of P. acnes endophthalmitis. We compared the antibiotic susceptibilities of P. acnes by using the National Committee for Clinical Laboratory Standards method of agar dilution with the E test. Thirteen clinical isolates obtained from eye specimens and three American Type Culture Collection control strains were tested against 14 antibiotics. All the clinical isolates were susceptible by both methods to piperacillin, piperacillin-tazobactam, ampicillin-sulbactam, ticarcillin-clavulanate, cefotaxime, cefotetan, ceftriaxone, cefoxitin, and imipenem in addition to clindamycin but were resistant to metronidazole. The clinical P. acnes isolates also displayed high-level susceptibility to ciprofloxacin, sparfloxacin, and ofloxacin. Almost all the P. acnes strains demonstrated E-test MICs within 2 dilutions of the MICs observed by the agar dilution method. Those few strains for which discrepancies were noted exhibited E-test susceptibilities three- to fivefold dilutions lower than the agar dilution method susceptibilities but only with ampicillin-sulbactam, ticarcillin-clavulanate, and/or clindamycin. On the basis of our study, all of clinical eye isolates were susceptible to these newer antimicrobial agents and the two methods demonstrated similar susceptibility patterns. PMID:8815076
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry
NASA Astrophysics Data System (ADS)
Pham Tu Quoc, S.; Cheymol, G.; Semerok, A.
2014-05-01
Modulated photothermal radiometry is a non-destructive and contactless technique for the characterization of materials. It has two major advantages: a good signal-to-noise ratio through a synchronous detection and a low dependence on the heating power and the optical properties of the sample surface. This paper presents a new method for characterizing the thermal diffusivity of a material when the phase shift between a modulated laser power signal and the thermal signal of a plate sample is known at different frequencies. The method is based on a three-dimensional analytical model which is used to determine the temperature amplitude and the phase in the laser heating of the plate. A new simple formula was developed through multi-parametric analysis to determine the thermal diffusivity of the plate with knowledge of the frequency at the minimum phase shift, the laser beam radius r0 and the sample thickness L. This method was developed to control the variation of the thermal diffusivity of nuclear components and it was first applied to determine the thermal diffusivity of different metals: 304 L stainless steel, nickel, titanium, tungsten, molybdenum, zinc, and iron. The experimental results were obtained with 5%-10% accuracy and corresponded well with the reference values. The present paper also demonstrates the limit of application of this method for plate with thickness r0/100 ? L ? r0/2. The technique is deemed interesting for the characterization of barely accessible components that require a contactless measurement.
Lattice simulation method to model diffusion and NMR spectra in porous materials
Merlet, Céline; Forse, Alexander C.; Griffin, John M.; Frenkel, Daan; Grey, Clare P.
2015-03-02
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...
Diffusion blotting: a rapid and simple method for production of multiple blots from a single gel.
Olsen, Ingrid; Wiker, Harald G
2015-01-01
A very simple and fast method for diffusion blotting of proteins from precast SDS-PAGE gels on a solid plastic support was developed. Diffusion blotting for 3 min gives a quantitative transfer of 10 % compared to 1-h electroblotting. For each subsequent blot from the same gel a doubling of transfer time is necessary to obtain the same amount of protein onto each blot. High- and low-molecular-weight components are transferred equally efficiently when compared to electroblotting. However, both methods do give a higher total transfer of the low-molecular-weight proteins compared to the large proteins. The greatest advantage of diffusion blotting is that several blots can be made from each lane, thus enabling testing of multiple antisera on virtually identical blots. The gel remains on the plastic support, which prevents it from stretching or shrinking. This ensures identical blots and facilitates more reliable molecular weight determination. Furthermore the proteins remaining in the gel can be stained with Coomassie Brilliant Blue or other methods for exact and easy comparison with the developed blots. These advantages make diffusion blotting the method of choice when quantitative protein transfer is not required. PMID:26043991
rKnowledge: The Spatial Diffusion of rDNA Methods Maryann P. Feldman
1 rKnowledge: The Spatial Diffusion of rDNA Methods Maryann P. Feldman Department of Public Policy for their development of rDNA technology played a critical role in the establishment of the modern biotechnology industry. From the birth of this general purpose technology in the San Francisco Bay area, rDNA
Hamilton, Richard P; Heal, Mathew R
2004-01-01
% (n = 112), respectively) consistent with augmentation of within-tube NO2 flux by chemical reaction between co-diffusing NO and O3. Overall, it is recommended that the pipetting method of PDT grid preparation is avoided, or at least investigated...
DEVELOPMENT OF LOW-DIFFUSION FLUX-SPLITTING METHODS FOR DENSE GAS-SOLID FLOWS
The development of a class of low-diffusion upwinding methods for computing dense gas-solid flows is presented in this work. An artificial compressibility/low-Mach preconditioning strategy is developed for a hyperbolic two-phase flow equation system consisting of separate solids ...
Kovalishin, A. A. Laletin, N. I.
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.
INVERSION: a robust method for co-registration of T1 and diffusion weighted MRI images
Leahy, Richard M.
INVERSION: a robust method for co-registration of T1 and diffusion weighted MRI images Chitresh · Multi-contrast images registration is useful to fuse information from different modalities. · Normalized in a T1w brain image is approximately the inverse of the contrast in a T2w image. · Intensity order
Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column
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.
Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column
Rutherford, W.M.
1985-12-04
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 obtained in the prior art.
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.
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.
COMPARISON OF THE COMPLETE FOURIER DIRECT MRI WITH EXISTING DIFFUSION WEIGHTED MRI METHODS
Özcan, Alpay
2011-01-01
The Complete Fourier Direct (CFD) MRI method introduced in earlier work for modeling the diffusion weighted MRI signal is compared with the existing methods. The preservation of Hermitian symmetry in the diffusion weighted MRI signal without affecting its energy is the key point that differentiates CFD–MRI from the existing methods. By keeping the correct Fourier relationship intact, the joint distribution function is represented ‘as it is’, without any constraints, e.g. being symmetric. The necessity to model or assume models for spin motion and try to fit the model to the samples of the Fourier transform as in case of model matching methods is not required because the Discrete Fourier Transform applied to correctly processed signal in CFD–MRI gives more accurate results. PMID:21918715
Numerical solution of a diffusion problem by exponentially fitted finite difference methods.
D'Ambrosio, Raffaele; Paternoster, Beatrice
2014-01-01
This paper is focused on the accurate and efficient solution of partial differential differential equations modelling a diffusion problem by means of exponentially fitted finite difference numerical methods. After constructing and analysing special purpose finite differences for the approximation of second order partial derivatives, we employed them in the numerical solution of a diffusion equation with mixed boundary conditions. Numerical experiments reveal that a special purpose integration, both in space and in time, is more accurate and efficient than that gained by employing a general purpose solver. PMID:26034665
Diffuse interface methods for inverse problems: case study for an elliptic Cauchy problem
NASA Astrophysics Data System (ADS)
Burger, Martin; Løseth Elvetun, Ole; Schlottbom, Matthias
2015-12-01
Many inverse problems have to deal with complex, evolving and often not exactly known geometries, e.g. as domains of forward problems modeled by partial differential equations. This makes it desirable to use methods which are robust with respect to perturbed or not well resolved domains, and which allow for efficient discretizations not resolving any fine detail of those geometries. For forward problems in partial differential equations methods based on diffuse interface representations have gained strong attention in the last years, but so far they have not been considered systematically for inverse problems. In this work we introduce a diffuse domain method as a tool for the solution of variational inverse problems. As a particular example we study ECG inversion in further detail. ECG inversion is a linear inverse source problem with boundary measurements governed by an anisotropic diffusion equation, which naturally cries for solutions under changing geometries, namely the beating heart. We formulate a regularization strategy using Tikhonov regularization and, using standard source conditions, we prove convergence rates. A special property of our approach is that not only operator perturbations are introduced by the diffuse domain method, but more important we have to deal with topologies which depend on a parameter \\varepsilon in the diffuse domain method, i.e. we have to deal with \\varepsilon -dependent forward operators and \\varepsilon -dependent norms. In particular the appropriate function spaces for the unknown and the data depend on \\varepsilon . This prevents the application of some standard convergence techniques for inverse problems, in particular interpreting the perturbations as data errors in the original problem does not yield suitable results. We consequently develop a novel approach based on saddle-point problems. The numerical solution of the problem is discussed as well and results for several computational experiments are reported. In particular investigations of convergence rates support our theoretical findings.
A semi-discrete finite element method for a class of time-fractional diffusion equations
HongGuang Sun; Wen Chen; K. Y. Sze
2013-04-10
As fractional diffusion equations can describe the early breakthrough and the heavy-tail decay features observed in anomalous transport of contaminants in groundwater and porous soil, they have been commonly employed in the related mathematical descriptions. These models usually involve long-time range computation, which is a critical obstacle for its application, improvement of the computational efficiency is of great significance. In this paper, a semi-analytical method is presented for solving a class of time-fractional diffusion equations which overcomes the critical long-time range computation problem of time fractional differential equations. In the procedure, the spatial domain is discretized by the finite element method which reduces the fractional diffusion equations into approximate fractional relaxation equations. As analytical solutions exist for the latter equations, the burden arising from long-time range computation can effectively be minimized. To illustrate its efficiency and simplicity, four examples are presented. In addition, the method is employed to solve the time-fractional advection-diffusion equation characterizing the bromide transport process in a fractured granite aquifer. The prediction closely agrees with the experimental data and the heavy-tail decay of anomalous transport process is well-represented.
Novel front-surface thermal-diffusivity measurement method based on phase analysis
NASA Astrophysics Data System (ADS)
Braggiotti, Alberto; Marinetti, Sergio
2000-05-01
The technique described in this paper is for one-side thermal diffusivity measurement. A single stripe-shaped pulse provided by a flash lamp is used to heat the front surface of a specimen slab. Classical methods for estimating a parameter out of a distribution involve fitting the temperature distribution with its theoretical model. With the technique described in this paper the evolution of the temperature distribution along a line perpendicular to the heated stripe is analyzed in the frequency domain. An estimate of the thermal diffusivity is then obtained from comparison of the phase component behavior with an abacus similarly built from the theoretical model. This technique is valid for any shape of flash lamp pulse (i.e. laser spot), and can be used also for estimating the thermal diffusivity of anisotropic materials. The choice of the stripe shape is due to the limitations of the simulation environment used.
Chau, Jessica Furrer; Or, Dani; Sukop, Michael C
2005-08-01
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. PMID:16173154
NASA Astrophysics Data System (ADS)
Toth, G.; Meng, X.; Gombosi, T. I.
2009-12-01
We are introducing a new scheme to model the global magnetosphere with less numerical diffusion. The new scheme combines the stability of an implicit solver with a limited diffusive numerical flux. The new scheme is an alternative to the standard "Boris correction" that solves the semi-relativistic MHD equations with an artificially reduced speed of light. While the Boris correction is an efficient and well established method, it changes the time dependent behavior of the equations, since it artificially reduces the propagation speeds. The new scheme on the other hand does not modify the physics, only the numerical algorithm. We are comparing the limited numerical diffusion scheme with the Boris correction for idealized problems as well as for magnetic storm simulations.
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.
[Disk diffusion method for fluconazole susceptibility testing of Candida spp. isolates].
Rodero, L; Córdoba, S; Vivot, W; Campo, M; Corfield, P; Olguín, C; Cuirolo, A; Soria, M; Guelfand, L; Canteros, C E; Davel, G
2006-01-01
In order to standardize and evaluate a disk diffusion method with visual reading to detect in vitro fluconazole susceptibility of yeast, 1193 clinical isolates were tested. These included 584 Candida albicans, 196 Candida parapsilosis, 200 Candida tropicalis, 113 Candida glabrata, 50 Candida krusei and 50 Candida spp. and other opportunistic yeasts. The disks were manufactured in the INEI-ANLIS "Dr. Carlos G. Malbrán. The disk diffusion method results were compared to MIC results obtained by the reference CLSI M27-A2 broth microdilution method modified by EUCAST. The interpretative breakpoints for in vitro susceptibility testing of fluconazole were established at: zone diameter > or =16 mm for MIC < or =8 microg/ml (susceptible isolates), between 9 and 15 mm for MIC = 16-32 microg/ml (susceptible dose-dependent isolates), and < or =8 mm for MIC > or =64 microg/ml (resistant isolates). Overall agreement between the two methods was 94.7%, with 0.2% very major errors, and 0.3% major errors. Inter - and intralaboratory agreement was good. The disk diffusion method for drug susceptibility testing of Candida spp. isolates is inexpensive, reliable and reproducible. However, when the inhibition zone diameter is < or =15 mm, it is advisable to test the isolate by the reference microdilution method. PMID:17152217
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
A quantitative radioluminographic imaging method for evaluating lateral diffusion rates in skin.
Rush, Allison K; Miller, Matthew A; Smith, Edward D; Kasting, Gerald B
2015-10-28
A method is presented for measuring the lateral diffusion coefficients of exogenously applied compounds on excised skin. The method involves sequential high resolution imaging of the spatial distribution of ?-radiation associated with [(14)C]-labeled compounds to monitor the development of the concentration profile on the skin surface. It is exemplified by measurements made on three radiolabeled test compounds--caffeine, testosterone, and zinc pyrithione (ZnPT)--administered as solutions. Lateral diffusivity is expected to be an important determinant of the topical bioavailability of ZnPT, which is characteristically administered as a fine suspension and must reach microorganisms in molecular form to exert biocidal activity. Application of the test compounds at levels below and above their estimated saturation doses in the upper stratum corneum allows one to distinguish between diffusion-limited and dissolution rate-limited kinetics. The effective lateral diffusivities of the two chemically stable reference compounds, caffeine and testosterone, were (1-4) × 10(-9) cm(2)/s and (3-9) × 10(-9) cm(2)/s, respectively. Lateral transport of [(14)C] associated with ZnPT was formulation-dependent, with effective diffusivities of (1-2) × 10(-9) cm(2)/s in water and (3-9) × 10(-9) cm(2)/s in a 1% body wash solution. These differences are thought to be related to molecular speciation and/or the presence of a residual surfactant phase on the skin surface. All values were greater than those estimated for the transverse diffusivities of these compounds in stratum corneum by factors ranging from 250 to over 2000. Facile lateral transport on skin, combined with a low transdermal permeation rate, may thus be seen to be a key factor in the safe and effective use of ZnPT as a topical antimicrobial agent. PMID:26241749
GPU-accelerated 3D neutron diffusion code based on finite difference method
Xu, Q.; Yu, G.; Wang, K.
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)
A Monte Carlo synthetic-acceleration method for solving the thermal radiation diffusion equation
Evans, Thomas M.; Mosher, Scott W.; Slattery, Stuart R.; Hamilton, Steven P.
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.
Gillin, F D; Diamond, L S
1978-01-01
A new technique for growing single Entamoeba trophozoites into colonies in agar has been developed. This method depended upon axenic cultivation and utilized Diamond's new TYI-S-33 medium. The present paper describes several different types of experiment which have utilized the agar technique. a) Cloning. The isolation of clones from agar way easy and successful. Clones of the HM-1 strain did not differ in virulence for newborn hamster liver or in colony morphology or colony forming efficiency. b) Viability measurements. Colony forming efficiency (CFE) was proportional to the number of viable cells in a culture. Pilot studies with the amebacides, metronidazole and emetine, showed that the agar method should be useful in drug testing. Colchicine at high concentration inhibited clonal growth in a non-specific manner. c) E. histolytica HM-1 and E. invadens cells were rapidly killed by exposure to 42 degree C but survived relatively well at 0 degree C. d) Hemolysis. In a preliminary experiment HM-1 colonies did not produce halo's of hemolysis when grown in agar containing sheep red blood cells. PMID:211957
Novikova, N; Rodrigues, A; Mårdh, P A
2002-01-01
OBJECTIVE: To investigate if introital and vaginal flushing samples inoculated on chromogenic agar could increase the recovery rate and rapid identification of Candida and non-albicans species, as compared to culture of posterior vaginal fornix samples on Sabouraud agar and speciation of isolates by biochemical tests. METHODS: Samples from the introitus and the posterior vaginal fornix and vaginal lavage samples were collected from 91 women with a history suggestive of recurrent vulvovaginal candidosis (RVVC), and with a suspected new attack of the condition. The specimens were cultured on Sabouraud and CHROMagar. Speciation of yeast isolates was made on the chromogenic agar by API 32C kits and by an atomized system (Vitek). RESULTS: Forty-six (51%) women were positive for Candida from one or more of the samples. The introital cultures were positive in 43 (47%) women, both on Sabouraud and chromogenic agar. From the posterior vaginal fomix, 42 (46%) women were positive on the Sabouraud and 43 (47%) on chromogenic agar cultures, while the vaginal lavage cultures yielded Candida on those two media in 40 (44%) and 41 (45%) cases, respectively. Candida albicans was the most frequent species recovered, from 40 (87%) cases, followed by C. krusei in 4 (9%), C. glabrata in 2 (4%), and C. parapsilosis in one case. There was only one woman who had a mixed yeast infection, by C. albicans and C. krusei. There was only one discrepancy in the speciation as demonstrated by mean of chromogenic agar and API 32C kit. CONCLUSIONS: Neither cultures of introital nor of vaginal lavage samples increases the detection rate of Candida in RVVC cases as compared to cultures of posterior vaginal fornix samples. Use of chromogenic agar is a convenient and reliable means to detect colonization by Candida and differentiate between C. albicans and non-albicans species. PMID:12530485
Evaluation of a new chromogenic agar medium for Alicyclobacillus acidoterrestris.
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
Phase-contrast diffuse optical tomography for in vivo breast imaging: a two-step method
Jiang Ruixin; Liang Xiaoping; Zhang Qizhi; Grobmyer, Stephen; Fajardo, Laurie L.; Jiang Huabei
2009-08-20
We present a two-step reconstruction method that can qualitatively and quantitatively improve the reconstruction of tissue refractive index (RI) distribution by phase-contrast diffuse optical tomography (PCDOT). In this two-step method, we first recover the distribution of tissue absorption and scattering coefficients by conventional diffuse optical tomography to obtain the geometrical information of lesions, allowing the incorporation of geometrical information as a priori in the PCDOT reconstruction using a locally refined mesh. The method is validated by a series of phantom experiments and evaluated using in vivo data from 42 human subjects. The results demonstrate clear contrast of RI between the lesion and the surroundings, making the image interpretation straightforward. The sensitivity and specificity from these 42 cases are both 81% when RI is used as an imaging parameter for distinguishing between malignant and benign lesions.
Tchitchekova, Deyana S.; Morthomas, Julien; Perez, Michel; Ribeiro, Fabienne; Ducher, Roland
2014-07-21
A novel method for accurate and efficient evaluation of the change in energy barriers for carbon diffusion in ferrite under heterogeneous stress is introduced. This method, called Linear Combination of Stress States, is based on the knowledge of the effects of simple stresses (uniaxial or shear) on these diffusion barriers. Then, it is assumed that the change in energy barriers under a complex stress can be expressed as a linear combination of these already known simple stress effects. The modifications of energy barriers by either uniaxial traction/compression and shear stress are determined by means of atomistic simulations with the Climbing Image-Nudge Elastic Band method and are stored as a set of functions. The results of this method are compared to the predictions of anisotropic elasticity theory. It is shown that, linear anisotropic elasticity fails to predict the correct energy barrier variation with stress (especially with shear stress) whereas the proposed method provides correct energy barrier variation for stresses up to ?3 GPa. This study provides a basis for the development of multiscale models of diffusion under non-uniform stress.
NASA Astrophysics Data System (ADS)
Nakatsuka, Yutaka; Nakajima, Takahito
2012-10-01
A diffusion Monte Carlo (DMC) method for the relativistic zeroth-order regular approximation (ZORA) is proposed. In this scheme, a novel approximate Green's function is derived for the spin-free ZORA Hamiltonian. Several numerical tests on atoms and small molecules showed that by combining with the relativistic cusp-correction scheme, the present approach can include both relativistic and electron-correlation effects simultaneously. The correlation energies recovered by the ZORA-DMC method are comparable with the nonrelativistic DMC results and superior to the coupled cluster singles and doubles with perturbative triples correction results when the correlation-consistent polarized valence triple-zeta Douglas-Kroll basis set is used. For the heavier CuH molecule, the ZORA-DMC estimation of its dissociation energy agrees with the experimental value within the error bar.
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.
A modified evaluation method to reduce finite pulse time effects in flash diffusivity measurement.
Tao, Ye; Yang, Liping; Zhong, Qiu; Xu, Zijun; Luo, Caiyun
2015-12-01
A modified evaluation method for laser flash is proposed. In this method, the moment of laser-heating cutoff time is considered as zero point. The penetration depth and formula equation of the sample temperature distribution are obtained with the approximate analytical solution before time zero (during laser heating) for the physical model of a continuously heated half-infinite, well-distributed sample. The weighted-average and approximate-equation methods are then used to quantitatively determine the laser effect depth, which leads to the formulation of a modified evaluation method in flash thermal diffusivity measurement. Results of the simulation calculations and experiments confirm the correctness of the modified method, which remarkably increases flash method applications. The modified method is applicable only to cases in which ?(x) does not exceed the sample thickness (12??0?L) during laser heating. PMID:26724057
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.
[Poisoning with deadly agaric (Amanita virosa). Symptoms, diagnosis and treatment].
Madsen, S; Jenssen, K M
1990-05-30
Amatoxin poisonings are uncommon in Norway. We describe a case where a young couple was poisoned after accidental ingestion of Amanita virosa (deadly agaric). After hospital treatment they recovered without serious damage to the liver. We briefly review the biological actions of amatoxins, discuss the symptoms and signs of amatoxin poisoning in detail, and outline current recommendations on therapy. PMID:2363148
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2012 CFR
2012-04-01
... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Ouchterlony agar plate. 866.4600 Section 866.4600 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents §...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2014 CFR
2014-04-01
... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Ouchterlony agar plate. 866.4600 Section 866.4600 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents §...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Ouchterlony agar plate. 866.4600 Section 866.4600 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents §...
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Ouchterlony agar plate. 866.4600 Section 866.4600 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents §...
Improving agar electrospinnability with choline-based deep eutectic solvents
Technology Transfer Automated Retrieval System (TEKTRAN)
One percent agar (% wt) was dissolved in the deep eutectic solvent (DES), (2-hydroxyethyl) trimethylammonium chloride/urea at a 1:2 molar ratio, and successfully electrospun into nanofibers. An existing electrospinning set-up, operated at 50 deg C, was adapted for use with an ethanol bath to collect...
Multistage Classification for Bacterial Colonies Recognition on Solid Agar Images
Signoroni, Alberto
. As an essential part of these systems, digital recording and processing of cultured bacteria images is expectedMultistage Classification for Bacterial Colonies Recognition on Solid Agar Images Alessandro to improve plate reading, with a key role of image analysis tools in guaranteeing cost
[Salmonella diagnosis and expanded bacteriologic differential diagnosis using Rambach agar].
Wermter, R; Müller, U
1995-05-01
The present study gives not only additional advises and ideas for the use of Rambach agar but also diagnostic support. Resulting from several years of diagnostic experience the medium can be recommended for enlarged routine differential-diagnosis of bacteria and also for improved Salmonella-diagnosis as an alternative medium (under section 35 LMBG; Untersuchung von Lebensmitteln; Nachweis von Salmonellen). PMID:7575387
21 CFR 866.4600 - Ouchterlony agar plate.
Code of Federal Regulations, 2010 CFR
2010-04-01
... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Ouchterlony agar plate. 866.4600 Section 866.4600 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunology Laboratory Equipment and Reagents §...
Internal structure and thermo-viscoelastic properties of agar ionogels.
Sharma, Anshu; Rawat, Kamla; Solanki, Pratima R; Aswal, V K; Kohlbrecher, J; Bohidar, H B
2015-12-10
Ionic liquids (IL) can alter the physical properties of agar hydrogels. Rheology studies show that gels with wide range of storage moduli (gel strength) G0 values ranging from 1 to 20 KPa could be made in imidazolium based IL solutions where the IL concentration may not exceed 5% (w/v). Gelation and gel melting temperatures (tgel and Tm) could be altered by as much as ? 10 °C. Small angle neutron scattering studies revealed the presence of fibre bundles of agar double helices having typical length of 120 nm that increased to ? 180 nm under favorable conditions. These structures gain flexibility from the cladding of the agar bundles by IL molecules which in turn caused partial charge neutralization of its surface. Raman spectroscopy revealed differential hydration of these bundles. It was found that IL molecules with longer alkyl chain (more hydrophobic) altered the gel homogeneity, and changed its thermal and mechanical properties significantly. Therefore, customization of agar hydrogels in green solvent medium (IL solutions) widens the scope of its application potential that may include sensing. PMID:26428165
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...
Non-invasive measurements of tissue hemodynamics with hybrid diffuse optical methods
NASA Astrophysics Data System (ADS)
Durduran, Turgut
Diffuse optical techniques were used to measure hemodynamics of tissues non-invasively. Spectroscopy and tomography of the brain, muscle and implanted tumors were carried out in animal models and humans. Two qualitatively different methods, diffuse optical tomography and diffuse correlation tomography, were hybridized permitting simultaneous measurement of total hemoglobin concentration, blood oxygen saturation and blood flow. This combination of information was processed further to derive estimates of oxygen metabolism (e.g. CMRO 2) in tissue. The diffuse correlation measurements of blood flow were demonstrated in human tissues, for the first time, demonstrating continous, non-invasive imaging of oxygen metabolism in large tissue volumes several centimeters below the tissue surface. The bulk of these investigations focussed on cerebral hemodynamics. Extensive validation of this methodology was carried out in in vivo rat brain models. Three dimensional images of deep tissue hemodynamics in middle cerebral artery occlusion and cortical spreading depression (CSD) were obtained. CSD hemodynamics were found to depend strongly on partial pressure of carbon dioxide. The technique was then adapted for measurement of human brain. All optical spectroscopic measurements of CMRO2 during functional activation were obtained through intact human skull non-invasively. Finally, a high spatio-temporal resolution measurement of cerebral blood flow due to somatosensory cortex activation following electrical forepaw stimulation in rats was carried out with laser speckle flowmetry. New analysis methods were introduced for laser speckle flowmetry. In other organs, deep tissue hemodynamics were measured on human calf muscle during exercise and cuff-ischemia and were shown to have some clinical utility for peripheral vascular disease. In mice tumor models, the measured hemodynamics were shown to be predictive of photodynamic therapy efficacy, again suggesting promise of clinical utility. In total, the research has pioneered the development of diffuse optical measurements of blood flow, oxygenation and oxygen metabolism in a large range of research and clinical applications.
NASA Astrophysics Data System (ADS)
Kang, Q.; Chen, L.
2014-12-01
Although short-term production of unconventional gas depends on the area of contact created by hydraulic fracturing and connections with pre-existing natural fracture networks, sustainable recovery is limited by transfer of gas from nanoporous matrix into the fractures, because the permeability of hydraulic fractures is orders of magnitude higher than that of the shale matrix. Therefore, a fundamental understanding of hydrocarbon mobility in shale matrix is urgently needed for improving recovery efficiencies. Shale transport properties (diffusivity, permeability, and electronic conductivity), which are critical for understanding the fundamental transport mechanisms, are still poorly understood. There have been some studies using experimental techniques such as scanning electron microscopy (SEM) to visualize the nanoscale structures of shale. Due to the ultra-low porosity and permeability, it is difficult to experimentally investigate the fundamental transport processes inside the shale or accurately measure the transport properties. Advanced pore-scale numerical methods, e.g., the lattice Boltzman method (LBM) may provide an alternative approach. In the present study, three-dimensional nanoscale porous structures of shale are reconstructed based on SEM images of shale samples. Characterization analysis of the nanoscale reconstructed shale is performed, including determination of porosity, pore size distribution, specific surface area, and pore connectivity. The LBM flow model and diffusion model are adopted to simulate fluid flow and Knudsen diffusion in the reconstructed shale, respectively. Tortuosity, intrinsic permeability, and effective Knudsen diffusivity are numerically predicted. The tortuosity is much higher than what is commonly employed in Bruggeman equation. Correction of the intrinsic permeability by taking into consideration the contribution of Knudsen diffusion, which leads to the apparent permeability, is performed. The correction factor under different Knudsen number and pressure conditions are estimated and compared with existing corrections reported in the literature.
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry
Pham Tu Quoc, S. Cheymol, G.; Semerok, A.
2014-05-15
Modulated photothermal radiometry is a non-destructive and contactless technique for the characterization of materials. It has two major advantages: a good signal-to-noise ratio through a synchronous detection and a low dependence on the heating power and the optical properties of the sample surface. This paper presents a new method for characterizing the thermal diffusivity of a material when the phase shift between a modulated laser power signal and the thermal signal of a plate sample is known at different frequencies. The method is based on a three-dimensional analytical model which is used to determine the temperature amplitude and the phase in the laser heating of the plate. A new simple formula was developed through multi-parametric analysis to determine the thermal diffusivity of the plate with knowledge of the frequency at the minimum phase shift, the laser beam radius r{sub 0} and the sample thickness L. This method was developed to control the variation of the thermal diffusivity of nuclear components and it was first applied to determine the thermal diffusivity of different metals: 304 L stainless steel, nickel, titanium, tungsten, molybdenum, zinc, and iron. The experimental results were obtained with 5%–10% accuracy and corresponded well with the reference values. The present paper also demonstrates the limit of application of this method for plate with thickness r{sub 0}/100 ? L ? r{sub 0}/2. The technique is deemed interesting for the characterization of barely accessible components that require a contactless measurement.
Thermal diffusivity of BaTiO{sub 3} ceramics analyzed by the photoacoustic method
Todorovic, D. M.; Vasiljevic-Radovic, D.; Stojanovic, B. D.; Ristic, M. M.; Bojicic, A. I.; Pavlovic, V. B.
1999-03-15
The thermophysical properties of BaTiO{sub 3}-based ferroelectric ceramics were investigated using the photoacoustic frequency transmission method. The photoacoustic amplitude signals as a function of modulating frequency, for various sample thicknesses, were measured and fitted with theoretically calculated spectra. Obtained data show the presence of thermal wave diffraction within the sample. The change of the thermal diffusivity vs the modulating frequency is also discussed.
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.
Studies on the accuracy of time-integration methods for the radiation-diffusion equations
NASA Astrophysics Data System (ADS)
Ober, Curtis C.; Shadid, John N.
2004-04-01
The governing equations for the radiation-diffusion approximation to radiative transport are a system of highly nonlinear, multiple time-scale, partial-differential equations. The numerical solution of these equations for very large-scale simulations is most often carried out using semi-implicit linearization or operator-splitting techniques. These techniques do not fully converge the nonlinearities of the system so as to reduce the cost and complexity of the transient solution at each time step. For a given time-step size, this process exchanges temporal accuracy for computational efficiency. This study considers the temporal-accuracy issue by presenting detailed numerical-convergence studies for problems related to radiation-diffusion simulations. In this context a particular spatial discretization based on a Galerkin finite-element technique is used. The time-integration methods that we consider include: fully implicit, semi-implicit, and operator-splitting techniques. Results are presented for the relative accuracy and the asymptotic order of accuracy of the various methods. The results demonstrate both first-order and second-order asymptotic order of accuracy for the fully implicit, semi-implicit, and the operator-splitting schemes. Additionally a second-order operator-splitting linearized-diffusion method is also presented.
Method and apparatus for determining minority carrier diffusion length in semiconductors
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.
Contribution to an effective design method for stationary reaction-diffusion patterns.
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. PMID:26117122
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.
The diffuse-scattering method for investigating locally ordered binary solid solutions
Epperson, J.E. ); Anderson, J.P. ); Chen, H. . Materials Science and Engineering Dept.)
1994-01-01
Diffuse-scattering investigations comprise a series of maturing methods for detailed characterization of the local-order structure and atomic displacements of binary alloy systems. The distribution of coherent diffuse scattering is determined by the local atomic ordering, and analytical techniques are available for extracting the relevant structural information. An extension of such structural investigations, for locally ordered alloys at equilibrium, allows one to obtain pairwise interaction energies. Having experimental pairwise interaction energies for the various coordination shells offers one the potential for more realistic kinetic Ising modeling of alloy systems as they relax toward equilibrium. Although the modeling of atomic displacements in conjunction with more conventional studies of chemical ordering is in its infancy, the method appears to offer considerable promise for revealing additional information about the strain fields in locally ordered and clustered alloys. The diffuse-scattering methods for structural characterization and for the recovery of interaction energies are reviewed, and some preliminary results are used to demonstrate the potential of the kinetic Ising modeling technique to follow the evolution of ordering or phase separation in an alloy system.
A deterministic particle method for one-dimensional reaction-diffusion equations
NASA Technical Reports Server (NTRS)
Mascagni, Michael
1995-01-01
We derive a deterministic particle method for the solution of nonlinear reaction-diffusion equations in one spatial dimension. This deterministic method is an analog of a Monte Carlo method for the solution of these problems that has been previously investigated by the author. The deterministic method leads to the consideration of a system of ordinary differential equations for the positions of suitably defined particles. We then consider the time explicit and implicit methods for this system of ordinary differential equations and we study a Picard and Newton iteration for the solution of the implicit system. Next we solve numerically this system and study the discretization error both analytically and numerically. Numerical computation shows that this deterministic method is automatically adaptive to large gradients in the solution.
Arabski, Micha?; Wasik, S?awomir; Piskulak, Patrycja; Gó?d?, Natalia; Slezak, Andrzej; Kaca, Wies?aw
2011-01-01
The aim of this study was to analysis of antibiotics (ampicilin, streptomycin, ciprofloxacin or colistin) release from agarose gel by spectrophotmetry and laser interferometry methods. The interferometric system consisted of a Mach-Zehnder interferometer with a He-Ne laser, TV-CCD camera, computerised data acquisition system and a gel system. The gel system under study consists of two cuvettes. We filled the lower cuvette with an aqueous 1% agarose solution with the antibiotics at initial concentration of antibiotics in the range of 0.12-2 mg/ml for spectrophotmetry analysis or 0.05-0.5 mg/ml for laser interferometry methods, while in the upper cuvette there was pure water. The diffusion was analysed from 120 to 2400 s with a time interval of deltat = 120 s by both methods. We observed that 0.25-1 mg/ml and 0,05 mg/ml are minimal initial concentrations detected by spectrophotometric and laser interferometry methods, respectively. Additionally, we observed differences in kinetic of antibiotic diffusion from gel measured by both methods. In conclusion, the laser interferometric method is a useful tool for studies of antibiotic release from agarose gel, especially for substances are not fully soluble in water, for example: colistin. PMID:22046824
Numerical methods of solving a system of multi-dimensional nonlinear equations of the diffusion type
NASA Technical Reports Server (NTRS)
Agapov, A. V.; Kolosov, B. I.
1979-01-01
The principles of conservation and stability of difference schemes achieved using the iteration control method were examined. For the schemes obtained of the predictor-corrector type, the conversion was proved for the control sequences of approximate solutions to the precise solutions in the Sobolev metrics. Algorithms were developed for reducing the differential problem to integral relationships, whose solution methods are known, were designed. The algorithms for the problem solution are classified depending on the non-linearity of the diffusion coefficients, and practical recommendations for their effective use are given.
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.
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S.; Yao, Jun; Tao, Wenquan
2015-01-01
Porous structures of shales are reconstructed using the markov chain monte carlo (MCMC) method based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analysis of the reconstructed shales is performed, including porosity, pore size distribution, specific surface area and pore connectivity. The lattice Boltzmann method (LBM) is adopted to simulate fluid flow and Knudsen diffusion within the reconstructed shales. Simulation results reveal that the tortuosity of the shales is much higher than that commonly employed in the Bruggeman equation, and such high tortuosity leads to extremely low intrinsic permeability. Correction of the intrinsic permeability is performed based on the dusty gas model (DGM) by considering the contribution of Knudsen diffusion to the total flow flux, resulting in apparent permeability. The correction factor over a range of Knudsen number and pressure is estimated and compared with empirical correlations in the literature. For the wide pressure range investigated, the correction factor is always greater than 1, indicating Knudsen diffusion always plays a role on shale gas transport mechanisms in the reconstructed shales. Specifically, we found that most of the values of correction factor fall in the slip and transition regime, with no Darcy flow regime observed. PMID:25627247
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S; Yao, Jun; Tao, Wenquan
2015-01-01
Porous structures of shales are reconstructed using the markov chain monte carlo (MCMC) method based on scanning electron microscopy (SEM) images of shale samples from Sichuan Basin, China. Characterization analysis of the reconstructed shales is performed, including porosity, pore size distribution, specific surface area and pore connectivity. The lattice Boltzmann method (LBM) is adopted to simulate fluid flow and Knudsen diffusion within the reconstructed shales. Simulation results reveal that the tortuosity of the shales is much higher than that commonly employed in the Bruggeman equation, and such high tortuosity leads to extremely low intrinsic permeability. Correction of the intrinsic permeability is performed based on the dusty gas model (DGM) by considering the contribution of Knudsen diffusion to the total flow flux, resulting in apparent permeability. The correction factor over a range of Knudsen number and pressure is estimated and compared with empirical correlations in the literature. For the wide pressure range investigated, the correction factor is always greater than 1, indicating Knudsen diffusion always plays a role on shale gas transport mechanisms in the reconstructed shales. Specifically, we found that most of the values of correction factor fall in the slip and transition regime, with no Darcy flow regime observed. PMID:25627247
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.
A balancing domain decomposition method by constraints for advection-diffusion problems
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.
Calculating diffusion and permeability coefficients with the oscillating forward-reverse method
NASA Astrophysics Data System (ADS)
Holland, Bryan W.; Gray, Chris G.; Tomberli, Bruno
2012-09-01
The forward-reverse or FR method is an efficient bidirectional work method for determining the potential of mean force w(z) and also supposedly gives in principle the position-dependent diffusion coefficient D(z). Results from a variation called the OFR (oscillating FR) method suggest inconsistencies in the D(z) values when calculated as prescribed by the FR method. A new steering protocol has thus been developed and applied to the OFR method for the accurate determination of D(z) and also provides greater convergence for w(z) in molecular dynamics simulations. The bulk diffusion coefficient for water was found to be (6.03±0.16)×10-5 cm2/s at 350 K with system size dependence within the statistical error bars. Using this steering protocol, D(z) and w(z) for water permeating a dipalmitoylphosphatidylcholine (DPPC) bilayer were determined. The potential of mean force is shown to have a barrier of peak height, wmax/(kBT)=8.4, with a width of about 10 Å on either side from the membrane center. The diffusion constant is shown to be highest in the core region of the membrane [peak value ˜(8.0±0.8)×10-5 cm2/s], lowest in the head-group region [minimum value ˜(2.0±0.3)×10-5 cm2/s], and to tend toward the bulk value as the water molecule leaves the membrane. The permeability coefficient P for H2O in DPPC was determined using the simulated D(z) and w(z) to give values of (0.129±0.075) cm/s at 323 K and (0.141±0.043) cm/s at 350 K. The results show more spatial detail than results presented in previous work while reducing the computational and user effort.
Improved method for quantification of the bacteriocin nisin.
Wolf, C E; Gibbons, W R
1996-04-01
Nisin, a bacteriocin produced by Lactococcus lactis subsp. lactis, is used in some types of food preservation due to its inhibitory action on Gram-positive bacteria and their spores. A commonly used agar diffusion bioassay technique for quantification of nisin in food samples was modified to increase its sensitivity, accuracy and precision. Several variables were evaluated. Results showed Micrococcus luteus as the most sensitive organism tested, a lower agar concentration (0 x 75% compared 1 x 5%) increased the sensitivity of the assay (21% improvement over standard method), and incorporation of 1% Na2HPO4 buffer into the bioassay agar made it possible to prevent false inhibitory zones from developing due to the low pH of the test solutions. This resulted in a 57% improvement in accuracy and a 12% improvement in precision compared to the standard method. PMID:8849648
NASA Astrophysics Data System (ADS)
Price, H. C.; Murray, B. J.; Mattsson, J.; O'Sullivan, D.; Wilson, T. W.; Baustian, K. J.; Benning, L. G.
2014-04-01
Recent research suggests that under certain temperature and relative humidity conditions atmospheric aerosol may be present in the form of a glassy solid. In order to understand the impacts that this may have on aerosol-cloud interactions and atmospheric chemistry, knowledge of water diffusion within such aerosol particles is required. Here, a method is described in which Raman spectroscopy is used to observe D2O diffusion in high-viscosity aqueous solutions, enabling a quantitative assessment of water diffusion coefficients, Dwater, as a function of relative humidity. Results for sucrose solutions compare well with literature data at 23.5 ± 0.3 °C, and demonstrate that water diffusion is slow (Dwater ~5 × 10-17 m2 s-1), but not arrested, just below the glass transition at a water activity of 0.2. Room temperature water diffusion coefficients are also presented for aqueous levoglucosan and an aqueous mixture of raffinose, dicarboxylic acids and ammonium sulphate: at low humidity, diffusion is retarded but still occurs on millisecond to second timescales in atmospherically relevant-sized particles. The effect of gel formation on diffusion in magnesium sulfate solutions is shown to be markedly different from the gradual decrease in diffusion coefficients of highly viscous liquids. We show that using the Stokes-Einstein equation to determine diffusion timescales from viscosity leads to values which are more than 5 orders of magnitude too big, which emphasises the need to make measurements of diffusion coefficients. In addition, comparison of bounce fraction data for levoglucosan with measured diffusion data reveals that even when particles bounce the diffusion timescales for water are a fraction of a second for a 100 nm particle. This suggests a high bounce fraction does not necessarily indicate retarded water diffusion.
Fast non-overlapping Schwarz domain decomposition methods for solving the neutron diffusion equation
Jamelot, Erell; Ciarlet, Patrick
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.
A diffuse-interface method for two-phase flows with soluble surfactants
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
Local DG method using WENO type limiters for convection-diffusion problems
NASA Astrophysics Data System (ADS)
Zhu, Jun; Qiu, Jianxian
2011-05-01
The local discontinuous Galerkin (LDG) method is a spatial discretization procedure for convection-diffusion equations, which employs useful features from high resolution finite volume schemes, such as the exact or approximate Riemann solvers serving as numerical fluxes and limiters, which is termed as Runge-Kutta LDG (RKLDG) when TVD Runge-Kutta method is applied for time discretization. It has the advantage of flexibility in handling complicated geometry, h- p adaptivity, and efficiency of parallel implementation and has been used successfully in many applications. However, the limiters used to control spurious oscillations in the presence of strong shocks are less robust than the strategies of essentially non-oscillatory (ENO) and weighted ENO (WENO) finite volume and finite difference methods. In this paper, we investigated RKLDG methods with WENO and Hermite WENO (HWENO) limiters for solving convection-diffusion equations on unstructured meshes, with the goal of obtaining a robust and high order limiting procedure to simultaneously obtain uniform high order accuracy and sharp, non-oscillatory shock transition. Numerical results are provided to illustrate the behavior of these procedures.
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
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
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
Vandenhove, H; Antunes, K; Wannijn, J; Duquène, L; Van Hees, M
2007-02-15
The measurement of diffusive gradients in thin films (DGT) has been proposed as a surrogate for metal uptake by plants. A small-scale experiment was performed to test the predictive capacity of the DGT method with respect to uranium availability and uptake by ryegrass. Correlation analyses were performed to compare the results obtained with the DGT device with more conventional bioavailability indices - concentration of uranium in pore water or in selective extracts. Six soils with different uranium contamination history and with distinct soil characteristics were used for the availability tests and the uptake experiment. The four uranium bioavailability indices screened were highly correlated, indicating that at least partially comparable uranium pools were assessed. The uranium concentration in the pore water was a better predictor for uranium uptake by ryegrass than amounts of uranium recovered following extraction with 0.11 M CH3COOH or 0.4 M MgCl2, the fractions considered exchangeable according to, respectively, the BCR or NIST standardized sequential extraction methods. The DGT measured concentration, C(DGT), was also highly correlated with plant uptake but the significance level was sensitive to the value of the diffusion coefficient (pH depend or not) used to calculate C(DGT). From the results obtained it could not be concluded that the DGT method would have an additional value in assessing uranium bioavailability. PMID:17241652
A method to analyze the diffuse gamma-ray emission with the Fermi Large Area Telescope
Ackermann, Markus; Johannesson, Gueolaugur; Digel, Seth; Moskalenko, Igor V.; Reimer, Olaf; Porter, Troy; Strong, Andrew
2008-12-24
The Fermi Gamma-Ray Space Telescope with its main instrument the LAT is the most sensitive {gamma}-ray telescope in the energy region between 30 MeV and 100 GeV. One of the prime scientific goals of this mission is the measurement and interpretation of the diffuse Galactic and extragalactic {gamma}-ray emission. While not limited by photon statistics, this analysis presents several challenges: Instrumental response functions, residual background from cosmic rays as well as resolved and unresolved foreground {gamma}-ray sources have to be taken carefully into account in the interpretation of the data. Detailed modeling of the diffuse {gamma}-ray emission is being performed and will form the basis of the investigations. We present the analysis approach to be applied to the Fermi LAT data, namely the modeling of the diffuse emission components and the background contributions, followed by an all-sky maximum-likelihood fitting procedure. We also report on the performance of this method evaluated in tests on simulated Fermi LAT and real EGRET data.
A new method for choosing the computational cell in stochastic reaction–diffusion systems
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
NASA Astrophysics Data System (ADS)
Price, H. C.; Murray, B. J.; Mattsson, J.; O'Sullivan, D.; Wilson, T. W.; Baustian, K. J.; Benning, L. G.
2013-11-01
Recent research suggests that under certain temperature and relative humidity conditions atmospheric aerosol may be present in the form of a glassy solid. In order to understand the impacts that this may have on aerosol-cloud interactions and atmospheric chemistry, knowledge of water diffusion within such aerosol particles is required. Here, a method is described in which Raman spectroscopy is used to observe D2O diffusion in high-viscosity aqueous solutions, enabling a quantitative assessment of water diffusion coefficients, Dwater, as a function of relative humidity. Results for sucrose solutions compare well with literature data at 23.5 ± 0.3 °C, and demonstrate that water diffusion is slow (Dwater~5 ×10-17m2s-1), but not arrested, just below the glass transition. Room temperature water diffusion coefficients are also presented for aqueous levoglucosan and an aqueous mixture of raffinose, dicarboxylic acids and ammonium sulphate: at low humidity, diffusion is retarded but still occurs on millisecond to second timescales in atmospherically relevant-sized particles. The effect of gel formation on diffusion in magnesium sulfate solutions is shown to be markedly different from the gradual decrease in diffusion coefficients of highly viscous liquids. We show that using the Stokes-Einstein equation to determine diffusion timescales from viscosity leads to values which are more than five orders of magnitude too big, which emphasises the need to make measurements of diffusion coefficients. In addition, comparison of bounce fraction data for levoglucosan with measured diffusion data reveals that even when particles bounce the equilibration timescales for water are a fraction of a second for a 100 nm particle. This suggests a high bounce fraction does not necessarily indicate retarded water diffusion.
cAMP diffusion in Dictyostelium discoideum: A Green's function method
NASA Astrophysics Data System (ADS)
Calovi, Daniel S.; Brunnet, Leonardo G.; de Almeida, Rita M. C.
2010-07-01
A Green’s function method is developed to approach the spatiotemporal equations describing the cAMP production in Dictyostelium discoideum, markedly reducing numerical calculations times: cAMP concentrations and gradients are calculated just at the amoeba locations. A single set of parameters is capable of reproducing the different observed behaviors, from cAMP synchronization, spiral waves and reaction-diffusion patterns to streaming and mound formation. After aggregation, the emergence of a circular motion of amoebas, breaking the radial cAMP field symmetry, is observed.
Sinc-Chebyshev Collocation Method for a Class of Fractional Diffusion-Wave Equations
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
Akhgari, Abbas; Sadeghi, Hasti; Dabbagh, Mohammad Ali
2014-01-01
Objective(s): The aim of this study was to improve flowability and compressibility characteristics of starch to use as a suitable excipient in direct compression tabletting. Quasi-emulsion solvent diffusion was used as a crystal modification method. Materials and Methods: Corn starch was dissolved in hydrochloric acid at 80°C and then ethanol as a non-solvent was added with lowering temperature until the formation of a precipitate of modified starch. Flow parameters, particle size and thermal behavior of the treated powders were compared with the native starch. Finally, the 1:1 mixture of naproxen and each excipient was tabletted, and hardness and friability of different tablets were evaluated. Results: Larger and well shaped agglomerates were formed which showed different thermal behavior. Treated starch exhibited suitable flow properties and tablets made by the treated powder had relatively high hardness. Conclusion: It was found that recrystallization of corn starch by quasi emulsion solvent diffusion method could improve its flowability and compressibility characteristics. PMID:25422746
Liu, Cong; Kolarik, Barbara; Gunnarsen, Lars; Zhang, Yinping
2015-10-20
Polychlorinated biphenyls (PCBs) have been found to be persistent in the environment and possibly harmful. Many buildings are characterized with high PCB concentrations. Knowledge about partitioning between primary sources and building materials is critical for exposure assessment and practical remediation of PCB contamination. This study develops a C-depth method to determine diffusion coefficient (D) and partition coefficient (K), two key parameters governing the partitioning process. For concrete, a primary material studied here, relative standard deviations of results among five data sets are 5%-22% for K and 42-66% for D. Compared with existing methods, C-depth method overcomes the inability to obtain unique estimation for nonlinear regression and does not require assumed correlations for D and K among congeners. Comparison with a more sophisticated two-term approach implies significant uncertainty for D, and smaller uncertainty for K. However, considering uncertainties associated with sampling and chemical analysis, and impact of environmental factors, the results are acceptable for engineering applications. This was supported by good agreement between model prediction and measurement. Sensitivity analysis indicated that effective diffusion distance, contacting time of materials with primary sources, and depth of measured concentrations are critical for determining D, and PCB concentration in primary sources is critical for K. PMID:26347992
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.
A comparison between the fission matrix method, the diffusion model and the transport model
Dehaye, B.; Hugot, F. X.; Diop, C. M.
2013-07-01
The fission matrix method may be used to solve the critical eigenvalue problem in a Monte Carlo simulation. This method gives us access to the different eigenvalues and eigenvectors of the transport or fission operator. We propose to compare the results obtained via the fission matrix method with those of the diffusion model, and an approximated transport model. To do so, we choose to analyse the mono-kinetic and continuous energy cases for a Godiva-inspired critical sphere. The first five eigenvalues are computed with TRIPOLI-4{sup R} and compared to the theoretical ones. An extension of the notion of the extrapolation distance is proposed for the modes other than the fundamental one. (authors)
A Sparse Representation Based Method to Classify Pulmonary Patterns of Diffuse Lung Diseases
Xu, Rui; Tachibana, Rie; Kido, Shoji
2015-01-01
We applied and optimized the sparse representation (SR) approaches in the computer-aided diagnosis (CAD) to classify normal tissues and five kinds of diffuse lung disease (DLD) patterns: consolidation, ground-glass opacity, honeycombing, emphysema, and nodule. By using the K-SVD which is based on the singular value decomposition (SVD) and orthogonal matching pursuit (OMP), it can achieve a satisfied recognition rate, but too much time was spent in the experiment. To reduce the runtime of the method, the K-Means algorithm was substituted for the K-SVD, and the OMP was simplified by searching the desired atoms at one time (OMP1). We proposed three SR based methods for evaluation: SR1 (K-SVD+OMP), SR2 (K-Means+OMP), and SR3 (K-Means+OMP1). 1161 volumes of interest (VOIs) were used to optimize the parameters and train each method, and 1049 VOIs were adopted to evaluate the performances of the methods. The SR based methods were powerful to recognize the DLD patterns (SR1: 96.1%, SR2: 95.6%, SR3: 96.4%) and significantly better than the baseline methods. Furthermore, when the K-Means and OMP1 were applied, the runtime of the SR based methods can be reduced by 98.2% and 55.2%, respectively. Therefore, we thought that the method using the K-Means and OMP1 (SR3) was efficient for the CAD of the DLDs. PMID:25821509
A sparse representation based method to classify pulmonary patterns of diffuse lung diseases.
Zhao, Wei; Xu, Rui; Hirano, Yasushi; Tachibana, Rie; Kido, Shoji
2015-01-01
We applied and optimized the sparse representation (SR) approaches in the computer-aided diagnosis (CAD) to classify normal tissues and five kinds of diffuse lung disease (DLD) patterns: consolidation, ground-glass opacity, honeycombing, emphysema, and nodule. By using the K-SVD which is based on the singular value decomposition (SVD) and orthogonal matching pursuit (OMP), it can achieve a satisfied recognition rate, but too much time was spent in the experiment. To reduce the runtime of the method, the K-Means algorithm was substituted for the K-SVD, and the OMP was simplified by searching the desired atoms at one time (OMP1). We proposed three SR based methods for evaluation: SR1 (K-SVD+OMP), SR2 (K-Means+OMP), and SR3 (K-Means+OMP1). 1161 volumes of interest (VOIs) were used to optimize the parameters and train each method, and 1049 VOIs were adopted to evaluate the performances of the methods. The SR based methods were powerful to recognize the DLD patterns (SR1: 96.1%, SR2: 95.6%, SR3: 96.4%) and significantly better than the baseline methods. Furthermore, when the K-Means and OMP1 were applied, the runtime of the SR based methods can be reduced by 98.2% and 55.2%, respectively. Therefore, we thought that the method using the K-Means and OMP1 (SR3) was efficient for the CAD of the DLDs. PMID:25821509
Gage, Daniel J.
6/15/10 4:46 PMMacConkey agar - Wikipedia, the free encyclopedia Page 1 of 3http://en.wikipedia.org/wikiConkey agar - Wikipedia, the free encyclopedia Page 2 of 3http://en.wikipedia.org/wiki-12-11. External links #12;6/15/10 4:46 PMMacConkey agar - Wikipedia, the free encyclopedia Page 3 of 3http://en.wikipedia.org/wiki
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...
Method and apparatus for determining minority carrier diffusion length in semiconductors
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.
Method and apparatus for determining minority carrier diffusion length in semiconductors
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.
A channel-dependent color error diffusion method based on distance constraint
NASA Astrophysics Data System (ADS)
Kang, Ki-Min; Lee, Eul-Hwan
2003-12-01
It is well known that the homogeneous dot distribution is one of the important features affecting the image quality for B/W error diffusion method. However, when B/W error diffusion method is independently applied to each color channel, homogeneity between channels would not appear in color binary image. Non-homogeneity in color binary image often generates the overlap of the dots between channels. Especially, the overlap of cyan dots and magenta dots is noticeable to human eyes in color highlights. In order to prevent the overlap of cyan dots and magenta dots, this paper modulates the threshold value that makes the distance between dots in cyan channel and magenta channel be equal to the principal distance. Therefore, cyan dots and magenta dots are homogeneously distributed and the overlap of cyan dots and magenta dots can be prevented. The threshold value is increasing or decreasing according to the difference between the principal distance and the minimum distance. In color highlights, the principal distance is adjusted for satisfying the homogeneity between channels and the homogeneity in the respective channel. For the calculation of the minimum distance, this paper describes the 2D-MPOA(two dimensional minor pixel offset array) that is able to calculate the minimum distance efficiently.
A Simple and Efficient Diffuse Interface Method for Compressible Two-Phase Flows
Ray A. Berry; Richard Saurel; Fabien Petitpas
2009-05-01
In nuclear reactor safety and optimization there are key issues that rely on in-depth understanding of basic two-phase flow phenomena with heat and mass transfer. For many reasons, to be discussed, there is growing interest in the application of two-phase flow models to provide diffuse, but nevertheless resolved, simulation of interfaces between two immiscible compressible fluids – diffuse interface method (DIM). Because of its ability to dynamically create interfaces and to solve interfaces separating pure media and mixtures for DNS-like (Direct Numerical Simulation) simulations of interfacial flows, we examine the construction of a simple, robust, fast, and accurate numerical formulation for the 5-equation Kapila et al. [1] reduced two-phase model. Though apparently simple, the Kapila et al. model contains a volume fraction differential transport equation containing a nonlinear, non-conservative term which poses serious computational challenges. To circumvent the difficulties encountered with the single velocity and single pressure Kapila et al. [1] multiphase flow model, a 6-equation relaxation hyperbolic model is built to solve interface problems with compressible fluids. In this approach, pressure non-equilibrium is first restored, followed by a relaxation to an asymptotic solution which is convergent to the solutions of the Kapila et al. reduced model. The apparent complexity introduced with this extended hyperbolic model actually leads to considerable simplifications regarding numerical resolution, and the various ingredients used by this method are general enough to consider future extensions to problems involving complex physics.
NASA Astrophysics Data System (ADS)
Täuber, Uwe C.; Howard, Martin; Vollmayr-Lee, Benjamin P.
2005-04-01
We review the application of field-theoretic renormalization group (RG) methods to the study of fluctuations in reaction-diffusion problems. We first investigate the physical origin of universality in these systems, before comparing RG methods to other available analytic techniques, including exact solutions and Smoluchowski-type approximations. Starting from the microscopic reaction-diffusion master equation, we then pedagogically detail the mapping to a field theory for the single-species reaction kA ? ellA(ell < k). We employ this particularly simple but non-trivial system to introduce the field-theoretic RG tools, including the diagrammatic perturbation expansion, renormalization and Callan-Symanzik RG flow equation. We demonstrate how these techniques permit the calculation of universal quantities such as density decay exponents and amplitudes via perturbative epsi = dc - d expansions with respect to the upper critical dimension dc. With these basics established, we then provide an overview of more sophisticated applications to multiple species reactions, disorder effects, Lévy flights, persistence problems and the influence of spatial boundaries. We also analyse field-theoretic approaches to non-equilibrium phase transitions separating active from absorbing states. We focus particularly on the generic directed percolation universality class, as well as on the most prominent exception to this class: even-offspring branching and annihilating random walks. Finally, we summarize the state of the field and present our perspective on outstanding problems for the future.
Numerical Modeling of Deep Mantle Convection: Advection and Diffusion Schemes for Marker Methods
NASA Astrophysics Data System (ADS)
Mulyukova, Elvira; Dabrowski, Marcin; Steinberger, Bernhard
2013-04-01
Thermal and chemical evolution of Earth's deep mantle can be studied by modeling vigorous convection in a chemically heterogeneous fluid. Numerical modeling of such a system poses several computational challenges. Dominance of heat advection over the diffusive heat transport, and a negligible amount of chemical diffusion results in sharp gradients of thermal and chemical fields. The exponential dependence of the viscosity of mantle materials on temperature also leads to high gradients of the velocity field. The accuracy of many numerical advection schemes degrades quickly with increasing gradient of the solution, while the computational effort, in terms of the scheme complexity and required resolution, grows. Additional numerical challenges arise due to a large range of length-scales characteristic of a thermochemical convection system with highly variable viscosity. To examplify, the thickness of the stem of a rising thermal plume may be a few percent of the mantle thickness. An even thinner filament of an anomalous material that is entrained by that plume may consitute less than a tenth of a percent of the mantle thickness. We have developed a two-dimensional FEM code to model thermochemical convection in a hollow cylinder domain, with a depth- and temperature-dependent viscosity representative of the mantle (Steinberger and Calderwood, 2006). We use marker-in-cell method for advection of chemical and thermal fields. The main advantage of perfoming advection using markers is absence of numerical diffusion during the advection step, as opposed to the more diffusive field-methods. However, in the common implementation of the marker-methods, the solution of the momentum and energy equations takes place on a computational grid, and nodes do not generally coincide with the positions of the markers. Transferring velocity-, temperature-, and chemistry- information between nodes and markers introduces errors inherent to inter- and extrapolation. In the numerical scheme that we use for this study, the velocity field is discretised using second order triangular elements, which gives second order accuracy of interpolation from grid-nodes to markers. A fourth order Runge-Kutta solver is used to compute marker-trajectories. We reevaluate the velocity field for each of the intermediate steps of the ODE-solver, rendering our advection scheme to be fourth-order accurate in time. We compare two different approaches for performing the thermal diffusion step. In the first, more conventional approach, the energy equation is solved on a static grid. For this grid, we use first-order triangular elements and a higher resolution than for the velocity-grid, to compensate for the lower order elements. The temperature field is transferred between grid-nodes and markers, and a subgrid diffusion correction step (Gerya and Yuen, 2003) is included to account for the different spatial resolutions of the markers and the grid. In the second approach, the energy equation is solved directly on markers. To do this, we compute a constrained Delaunay triangulation, with markers as nodes, at every time step. We wish to resolve the large range of spatial scales of the solution at lowest possible computational cost. In several existing codes this is achieved with dynamically adaptive meshes, which use high resolution in regions with high solution gradients, and vice versa. The numerical scheme used in this study can be extended to include a similar feature, by regenerating the thermal and mechanical grids in the course of computation, adapting them to the temperature and chemistry fields carried by the markers. We present the results of thermochemical convection simulations obtained using the schemes outlined above, as well as the results of the numerical benchmarks commonly used in the geodynamics community. The quality of the solutions, as well as the computational cost of our schemes, are discussed.
Yoshida, Kosaku; Ekstedt, Richard D.
1968-01-01
The growth characteristics of several strains of Staphylococcus aureus in Brain Heart Infusion and in a modified Staphylococcus Medium No. 110 were compared. In the latter medium all of the strains studied showed an increased mucoid character. Some of the strains studied showed a greater potential to synthesize excess slime layer material than others. The highly mucoid strains grew as diffuse-type colonies in modified Staphylococcus Medium No. 110 serum-soft agar and reacted as though they were negative in the test for clumping factor. These strains were also found to be more virulent when used to challenge normal mice intraperitoneally. Images PMID:5686016
Yoshida, K; Ekstedt, R D
1968-10-01
The growth characteristics of several strains of Staphylococcus aureus in Brain Heart Infusion and in a modified Staphylococcus Medium No. 110 were compared. In the latter medium all of the strains studied showed an increased mucoid character. Some of the strains studied showed a greater potential to synthesize excess slime layer material than others. The highly mucoid strains grew as diffuse-type colonies in modified Staphylococcus Medium No. 110 serum-soft agar and reacted as though they were negative in the test for clumping factor. These strains were also found to be more virulent when used to challenge normal mice intraperitoneally. PMID:5686016
Mansoor, Iman; Lai, Jacqueline; Ranamukhaarachchi, Sahan; Schmitt, Veronika; Lambert, Dana; Dutz, Jan; Häfeli, Urs O; Stoeber, Boris
2015-01-01
Hollow microneedles can overcome the stratum corneum (SC) barrier and deposit a compound directly into the viable epidermis or the dermis, unlike adhesive patches that rely on drug diffusion across the SC. The traditional one-dimensional methods used to study the diffusivity of drugs across the skin layers are not very accurate for hollow microneedles, since the ejection of compounds out of microneedle lumens resembles a point-source spreading in all directions and is highly dependent on injection depth. This paper presents a technique that is useful for studying drug injection using hollow microneedles at various depths below the SC. This technique uses confocal microscopy to image the distribution of a fluorescent compound in the skin after injection. The fluorescence distribution in the skin is observed over time and applied to a spherical Gaussian diffusion model for limited source diffusion to determine the diffusion coefficient of the compound in the skin. Applied to freshly excised pig skin, the diffusion coefficient for the anti-cancer drug doxorubicin was measured as 4.61?×?10(-9) cm(2)/s, while the diffusion coefficient in previously refrigerated or frozen pig skin was 1.31?×?10(-8) cm(2)/s and 4.21?×?10(-8) cm(2)/s, respectively. Our data suggests that skin storage conditions can substantially alter the diffusion of drugs. The use of refrigerated and, even more so, previously frozen skin should be avoided for quantitative transdermal drug delivery studies. PMID:26009275
Numerical Method Using Cubic B-Spline for a Strongly Coupled Reaction-Diffusion System
Abbas, Muhammad; Majid, Ahmad Abd.; Md. Ismail, Ahmad Izani; Rashid, Abdur
2014-01-01
In this paper, a numerical method for the solution of a strongly coupled reaction-diffusion system, with suitable initial and Neumann boundary conditions, by using cubic B-spline collocation scheme on a uniform grid is presented. The scheme is based on the usual finite difference scheme to discretize the time derivative while cubic B-spline is used as an interpolation function in the space dimension. The scheme is shown to be unconditionally stable using the von Neumann method. The accuracy of the proposed scheme is demonstrated by applying it on a test problem. The performance of this scheme is shown by computing and error norms for different time levels. The numerical results are found to be in good agreement with known exact solutions. PMID:24427270
Reprint of Domain decomposition multigrid methods for nonlinear reaction-diffusion problems
NASA Astrophysics Data System (ADS)
Arrarás, A.; Gaspar, F. J.; Portero, L.; Rodrigo, C.
2015-04-01
In this work, we propose efficient discretizations for nonlinear evolutionary reaction-diffusion problems on general two-dimensional domains. The spatial domain is discretized through an unstructured coarse triangulation, which is subsequently refined via regular triangular grids. Following the method of lines approach, we first consider a finite element spatial discretization, and then use a linearly implicit splitting time integrator related to a suitable decomposition of the triangulation nodes. Such a procedure provides a linear system per internal stage. The equations corresponding to those nodes lying strictly inside the elements of the coarse triangulation can be decoupled and solved in parallel using geometric multigrid techniques. The method is unconditionally stable and computationally efficient, since it avoids the need for Schwarz-type iteration procedures. In addition, it is formulated for triangular elements, thus yielding much flexibility in the discretization of complex geometries. To illustrate its practical utility, the algorithm is shown to reproduce the pattern-forming dynamics of the Schnakenberg model.
Numerical modeling of axisymmetric laminar diffusion flames by a parallel boundary value method
Smooke, M.D. ); Giovangigli, V. )
1991-01-01
This paper reports on the coupling of adaptive numerical methods with large-memory parallel/vector computers that has produced a powerful tool with which to probe flame structure. The authors have investigated numerically one such system - the axisymmetric laminar diffusion flame. The ability to predict the coupled effects of complex transport phenomena with detailed chemical kinetics in these flames is critical in modeling turbulent reacting flows, in improving engine efficiency, and in understanding the processes by which pollutants are formed. Computationally, the authors solve the governing conservation equations of mass, momentum, species balance, and energy with detailed transport and finite rate chemistry submodels. The authors utilize up to six processors of an IBM ES/3090 600J in parallel to obtain a discrete solution on a two- dimensional grid with Newton's method and adaptive mesh refinement.
Efficient method for near real-time diffuse optical tomography of the human brain
NASA Astrophysics Data System (ADS)
Wu, Xue; Eggebrecht, Adam T.; Ferradal, Silvina L.; Culver, Joseph P.; Dehghani, Hamid
2015-07-01
Previous studies have showed only regions with a sensitivity higher that 1% of the maximum value can affect the recovery result for diffuse optical tomography (DOT). Two methods of efficient sensitivity map generation based on Finite Element Models (FEM) are developed based on (1) reduced sensitivity matrix and (2) parallelisation process. Time and memory efficiency of these processes are evaluated and compared with conventional methods. It is shown that the computational time for a full head model containing 200k nodes is reduced from 3 hours to 48 minutes and the required memory is reduced from 5.5 GB to 0.5 GB. For a range of mesh densities up to 320k nodes, the required memory is improved by ~1000% and computational time by ~400% to allow near real-time image recovery.
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
Lattice Boltzmann methods for some 2-D nonlinear diffusion equations:Computational results
Elton, B.H.; Rodrigue, G.H. . Dept. of Applied Science Lawrence Livermore National Lab., CA ); Levermore, C.D. . Dept. of Mathematics)
1990-01-01
In this paper we examine two lattice Boltzmann methods (that are a derivative of lattice gas methods) for computing solutions to two two-dimensional nonlinear diffusion equations of the form {partial derivative}/{partial derivative}t u = v ({partial derivative}/{partial derivative}x D(u){partial derivative}/{partial derivative}x u + {partial derivative}/{partial derivative}y D(u){partial derivative}/{partial derivative}y u), where u = u({rvec x},t), {rvec x} {element of} R{sup 2}, v is a constant, and D(u) is a nonlinear term that arises from a Chapman-Enskog asymptotic expansion. In particular, we provide computational evidence supporting recent results showing that the methods are second order convergent (in the L{sub 1}-norm), conservative, conditionally monotone finite difference methods. Solutions computed via the lattice Boltzmann methods are compared with those computed by other explicit, second order, conservative, monotone finite difference methods. Results are reported for both the L{sub 1}- and L{sub {infinity}}-norms.
Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
Mark B Flegg; Stefan Hellander; Radek Erban
2013-04-27
In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is the ghost cell method (GCM). Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step $\\Delta t$ (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter $h$, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) \\Delta t approaches 0 and h is fixed; and (ii) \\Delta t approaches 0 and h approaches 0 such that \\Delta t/h^2 is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.
Testing the U-Th/4He dating method on carbonates I. Helium diffusion
NASA Astrophysics Data System (ADS)
Pinti, D. L.; Ghaleb, B. G.; Sano, Y.; Blanchette, S.; Mathouchanh, E.; Takahata, N.
2012-12-01
Corals and other carbonates, such as speleothems, are important climatic-change proxies which need to be precisely dated for paleoclimatic reconstructions. Yet, U-Th disequilibrium method is applicable up to ca. 500 ka old carbonates. Calcite is difficult to date precisely by U-Pb method because of the low U amounts often found and difficulties in correcting for the common lead. Radiogenic 4He produced by decay of 238U and 235U incorporated into carbonates is a potential chronometer of Quaternary, and possibly Tertiary, corals and speleothems. However, several limitations exist for this method, related to the few data on the He diffusion [1] and on the alpha recoil effect in carbonate minerals. We decided to measure 4He by step heating in carbonate samples dated previously by U-Th disequilibrium: a coral (Scleractinia) from Cape Verde dated at 125 ka; a stalagmite from Patagonia dated at 128 ka; and two hydrothermal travertines from the Ziz Valley in Morocco with ages ? 500 ka. A one cm3 of each sample was cut by saw, crushed, washed and sieved to 80-100?m and 100-125?m fractions. Crushed samples (0.5 to 1 gram) were loaded in a vacuum crucible and 4He extracted by step heating. Previous step heating experiments on a sub-Arctic flowstone suggested that 4He is mainly released between 400 and 600°C [2]. However, the first coral sample heated at 100°C steps, showed a release pattern profile with 4He mainly released between 200 and 400°C. Measured 4He amount of 2.05 x 10-8 (±0.03% 1?) ccSTP/g and U content of 2.7 ppm yield a U-4He age of 62.5 ka, lower than that obtained by U-Th disequilibrium. Data were not precise enough to calculate diffusion parameters using the Arrhenius diagram. The second step-heating pyrolysis of the coral using 50°C-steps indicated that all 4He is released between 250 and 350°C. The measured 4He amount was 2.27 x 10-8 (±0.04% 1?) ccSTP/g, yielding an age of 83 ka, again lower compared to that obtained by U-Th disequilibrium. The data were plotted on an Arrhenius diagram and the activation energy (E) and the ln(D0/a2) value were determined to be 26.2±3.7 kcal mol-1K-1 and 12.7±3.4 cm2 s-1. These values are in agreement with those of [1] for crinoids (E = 30.0±2.6; ln(D0/a2) = 11±2). Using our values, we estimated a diffusion coefficient for carbonate at ambient temperature (20°C) of 3.16 x 10-19 cm2 s-1. Assuming that all crushed material had an initial spherical shape and applying appropriate diffusion equations, the He fraction lost by the coral in the last 125 ka would be only 1 % of the total amount. Assuming a plane sheet (to better represent the septate structure of the coral) with a thickness ranging from 100 ?m to 1 mm, then the He fraction lost could reach 83% of the total, without taking into account the probable loss of He by ? recoil through the surface. These calculations suggests that more complex diffusion models need to be developed to test whether He is readily lost from the structure of corals in a short geological timescale. [1] Copeland, P. et al. (2007) Geochim. Cosmochim. Acta 71, 4488-4511. [2] Agosta, S. et al. (2011) GAC-MAC Annual Meeting, Ottawa (abstr.)
On the diffuse interface method using a dual-resolution Cartesian grid
NASA Astrophysics Data System (ADS)
Ding, Hang; Yuan, Cheng-jun
2014-09-01
We investigate the applicability and performance of diffuse interface methods on a dual-resolution grid in solving two-phase flows. In the diffuse interface methods, the interface thickness represents a cut-off length scale in resolving the interfacial dynamics, and it was found that an apparent loss of mass occurs when the interface thickness is comparable to the length scale of flows [24]. From the accuracy and mass conservation point of view, it is desirable to have a thin interface in simulations. We propose to use a dual-resolution Cartesian grid, on which a finer resolution is applied to the volume fraction C than that for the velocity and pressure fields. Because the computation of C field is rather inexpensive compared to that required by velocity and pressure fields, dual-resolution grids can significantly increase the resolution of the interface with only a slight increase of computational cost, as compared to the single-resolution grid. The solution couplings between the fine grid for C and the coarse grid (for velocity and pressure) are delicately designed, to make sure that the interpolated velocity is divergence-free at a discrete level and that the mass and surface tension force are conserved. A variety of numerical tests have been performed to validate the method and check its performance. The dual-resolution grid appears to save nearly 70% of the computational time in two-dimensional simulations and 80% in three-dimensional simulations, and produces nearly the same results as the single-resolution grid. Quantitative comparisons are made with previous studies, including Rayleigh Taylor instability, steadily rising bubble, and partial coalescence of a drop into a pool, and good agreement has been achieved. Finally, results are presented for the deformation and breakup of three-dimensional drops in simple shear flows.
Atomistic study of diffusion-mediated plasticity and creep using phase field crystal methods
NASA Astrophysics Data System (ADS)
Berry, Joel; Rottler, Jörg; Sinclair, Chad W.; Provatas, Nikolas
2015-10-01
The nonequilibrium dynamics of diffusion-mediated plasticity and creep in materials subjected to constant load at high homologous temperatures is studied atomistically using phase field crystal (PFC) methods. Creep stress and grain size exponents obtained for nanopolycrystalline systems, m ?1.02 and p ?1.98 , respectively, closely match those expected for idealized diffusional Nabarro-Herring creep. These exponents are observed in the presence of significant stress-assisted diffusive grain boundary migration, indicating that Nabarro-Herring creep and stress-assisted boundary migration contribute in the same manner to the macroscopic constitutive relation. When plastic response is dislocation-mediated, power-law stress exponents inferred from dislocation climb rates are found to increase monotonically from m ?3 , as expected for generic climb-mediated natural creep, to m ?5.8 as the dislocation density ?d is increased beyond typical experimental values. Stress exponents m ?3 directly measured from simulations that include dislocation nucleation, climb, glide, and annihilation are attributed primarily to these large ?d effects. Extrapolation to lower ?d suggests that m ?4 -4.5 should be obtained from our PFC description at typical experimental ?d values, which is consistent with expectations for power-law creep via mixed climb and glide. The anomalously large stress exponents observed in our atomistic simulations at large ?d may nonetheless be relevant to systems in which comparable densities are obtained locally within heterogeneous defect domains such as dislocation cell walls or tangles.
NASA Astrophysics Data System (ADS)
Nagasaka, Y.; Hatakeyama, T.; Okuda, M.; Nagashima, A.
1988-07-01
This article is devoted to the theory and experiment of the forced Rayleigh scattering method for measurement of thermal diffusivity of liquids which can be employed in the form of an instrument operated optically in a contact-free manner. The theoretical considerations included are: (1) effect of cell wall, (2) effect of dye, (3) effect of Gaussian beam intensity distribution, (4) effect of heating duration time, and (5) effect of coupled dye and wall for a heavily absorbing sample. The errors caused by inadequate setting of optical conditions are also analyzed: (1) effects of grating thickness and (2) effects of initial temperature amplitude. Experimental verifications of the theory have been carried out through the measurements on toluene and water as standard reference substances. As a result of these experiments and theory, the criteria for optimum measuring conditions became available. To demonstrate the applicability of the present theory and the apparatus, the thermal diffusivities of toluene and methanol have been measured near room temperature under atmospheric pressure. The accuracy of the present measurement is estimated to be ±3%.
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
Algebraic Methods for Direct and Feature Based Registration of Diffusion Tensor Images
Vidal, René
. We test our approach on synthetic, brain and heart diffusion tensor images. 1 Introduction Diffusion molecules in human and animal tissues. As the directional dependence of water diffusion rates is closely been extracted and segment these curves according to a certain cost function, or else segment
Janik, Paulina; Tylko, Grzegorz; Ostachowicz, Beata; Turnau, Katarzyna
2010-12-01
The elemental composition of spores, peridium walls, and lime nodes of Physarum compressum sporocarps, cultivated on rabbit dung as a natural growing environment for the slime mold and on artificial agar medium, was compared to evaluate differences that may be dependent on substrates. Whole fruiting bodies and samples of both experimental media were extracted with nitric acid or Parr digest bomb, respectively, and analyzed by means of total X-ray reflection fluorescence (TXRF). Electron probe microanalysis (EPMA) of spores, peridium walls, and lime nodes structure was carried out with the scanning electron microscope equipped with energy-dispersive spectrometer. Because of minute sizes and roughness of investigated structures, Monte Carlo simulations were utilized to establish analytical conditions of EPMA. Biological and geological standards were used in the quantification of element concentrations. According to TXRF, the fruiting bodies from agar medium revealed lower concentrations of K, Ca, Cr, Mn, and Fe in relation to fruiting bodies from the dung, reflecting elemental relationships in the experimental media. According to EPMA, the highest Ca concentration was found in the lime nodes followed by the peridium and the spores. Culturing of the slime molds on the rabbit dung indicated higher concentration of Ca in the lime nodes and peridium walls when compared with those obtained from the sporocarps grown on agar media. The opposite relation was found for the spores. The concentration of Na, Mg, P, S, and Cl was generally lower in all structures of the sporocarps harvested from the dung than from the agar medium. K was in higher concentration in analyzed structures from dung than from agar. Different element uptake (except for Ca and K) was revealed by the two methods: TXRF and EPMA. PMID:20981759
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.
Calvinho, L F; Dodd, K
1994-07-01
Six Staphylococcus aureus strains isolated from bovine mastitic milk representing the typical growth types in soft agar media were injected into mice via the intraperitoneal route. Strains showing diffuse colony morphology (DCM) in serum-soft agar (SSA) as a permanent characteristic which reacted against anti-capsular sera types A, B, and D were virulent for mice. A strain showing DCM in SSA that reacted only against anti-capsular serum D behaved as a compact-colony-morphology-type strain in the peritoneal cavity of the mouse. Diffuse-type colony morphology and presence of capsular antigens type A, B, and D correlated with increased virulence for mice, but a capsule could not be demonstrated. PMID:7839755
Boyanova, Lyudmila; Ilieva, Juliana; Gergova, Galina; Mitov, Ivan
2016-01-01
We compared levofloxacin (1?g/disk) disk diffusion method to E test against 212 Helicobacter pylori strains. Using diameter breakpoints for susceptibility (?15mm) and resistance (?9mm), very major error, major error rate, and categoric agreement were 0.0%, 0.6%, and 93.9%, respectively. The method may be useful in low-resource laboratories. PMID:26454324
A method for estimating the diffuse attenuation coefficient (KdPAR)from paired temperature sensors
Read, Jordan S.; Rose, Kevin C.; Winslow, Luke A.; Read, Emily Kara
2015-01-01
A new method for estimating the diffuse attenuation coefficient for photosynthetically active radiation (KdPAR) from paired temperature sensors was derived. We show that during cases where the attenuation of penetrating shortwave solar radiation is the dominant source of temperature changes, time series measurements of water temperatures at multiple depths (z1 and z2) are related to one another by a linear scaling factor (a). KdPAR can then be estimated by the simple equation KdPAR ln(a)/(z2/z1). A suggested workflow is presented that outlines procedures for calculating KdPAR according to this paired temperature sensor (PTS) method. This method is best suited for conditions when radiative temperature gains are large relative to physical noise. These conditions occur frequently on water bodies with low wind and/or high KdPARs but can be used for other types of lakes during time periods of low wind and/or where spatially redundant measurements of temperatures are available. The optimal vertical placement of temperature sensors according to a priori knowledge of KdPAR is also described. This information can be used to inform the design of future sensor deployments using the PTS method or for campaigns where characterizing sub-daily changes in temperatures is important. The PTS method provides a novel method to characterize light attenuation in aquatic ecosystems without expensive radiometric equipment or the user subjectivity inherent in Secchi depth measurements. This method also can enable the estimation of KdPAR at higher frequencies than many manual monitoring programs allow.
Thermal diffusivity of few-layers graphene measured by an all-optical method
NASA Astrophysics Data System (ADS)
Cabrera, H.; Mendoza, D.; Benítez, J. L.; Bautista Flores, C.; Alvarado, S.; Marín, E.
2015-11-01
We report on the measurement of the thermal diffusivity, D, of few-layers graphene obtained by chemical vapor deposition, using a noncontact optical microscopy method based on a mode mismatched thermal lens technique in a pump-probe two-laser beams configuration. It takes advantage of the coaxial counter propagating tightly focused excitation and collimated probe beams in an improved thermal lens microscopy setup. The obtained results: D??=??(6.5??±??0.09)??×??10-4 m2 s-1, D??=??(1.9??±??0.07)??×??10-4 m2 s-1 and D??=??(1.3??±??0.05)??×??10-4 m2 s-1 for four (on a glass slide), eight and sixteen graphene (freestanding) layers are reasonable values, as can be concluded from reported literature data.
InP synthesis by the synthesis, solute diffusion (SSD) method using glassy-carbon crucibles
Miskys, C.R.; Oliveira, C.E.M. de; Carvalho, M.M.G. de
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.
Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R; Berman, Marc; Greenbaum, Steve; Zawodzinski, Thomas; Sokolov, Alexei P
2013-01-01
Electrode polarization analysis is frequently used to determine free-ion diffusivity and number density in ionic conductors. In the present study, this approach is critically examined in a wide variety of electrolytes, including aqueous and nonaqueous solutions, polymer electrolytes, and ionic liquids. It is shown that the electrode polarization analysis based on theMacdonald-Trukhan model [J. Chem. Phys. 124, 144903 (2006); J. Non-Cryst. Solids 357, 3064 (2011)] progressively fails to give reasonable values of free-ion diffusivity and number density with increasing salt concentration. This should be expected because the original model of electrode polarization is designed for dilute electrolytes. An empirical correction method which yields ion diffusivities in reasonable agreement with pulsed-field gradient nuclear magnetic resonance measurements is proposed. However, the analysis of free-ion diffusivity and number density from electrode polarization should still be exercised with great caution because there is no solid theoretical justification for the proposed corrections.
Diffusion approximation-based simulation of stochastic ion channels: which method to use?
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
NASA Astrophysics Data System (ADS)
Girard, Timothy J.; Payton, Richard M.
1994-10-01
A method is presented that conservatively predicts long term outgassing for materials outgassing diffusely using short term test data. Accurate long term predictions require knowledge of the diffusion coefficient and initial concentrations of each species outgassed from a material which are obtainable only from often prohibitively long term testing. The method presented demonstrates how one can utilize standard 24 hour TML/CVCM data or short term outgassing rate testing data to conservatively predict long term outgassing. The method is based upon diffusion theory which predicts that the amount of material outgassing is proportional to the product of a constant, the square root of time, and a function that decays with time with maximum value of 1. The conservative approach taken is to assume that outgassing is proportional to a constant times the square root of time, replacing the decaying function with its maximum value of 1.
A reaction-diffusion model of the Darien Gap Sterile Insect Release Method
NASA Astrophysics Data System (ADS)
Alford, John G.
2015-05-01
The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.
An endoscopic diffuse optical tomographic method based on the effective detection range.
Qin, Zhuanping; Cui, Shanshan; Zhao, Huijuan; Zhou, Xiaoqing; Jia, Mengyu; Yang, Yanshuang; Fan, Ying; Gao, Feng
2013-01-01
Endoscopic diffuse optical tomography (DOT) is a new medical imaging modality with the potential applications in functional imaging of the internal organs. To cut down the measurement time and the computation burden of image reconstruction, in this paper, we developed the image reconstruction algorithm with the partial measurement in the effective detection range (EDR) of a tubular tissue and the corresponding endoscopic imaging system with a novel endoscopic probe for flexibly selecting the detection sites. For a typical inner size and optical properties of the cervix, it is found that EDR is less than half of the inner circumference. Comparing to the traditional method, the adoption of EDR results in a reduction of more than a factor of two in the time cost for a measurement cycle and for the total iteration reconstruction. Images reconstructed from the simulation data demonstrate that the proposed method achieves equivalent image quality to that obtained from the complete data set. The images reconstructed from the EDR measurements on cervix-like solid phantoms show that both the location and size of the targets are reconstructed correctly. The proposed method will be useful to the development of endoscopic DOT technologies for cancer detection in tubular organs including cervix. PMID:24191990
Visualization of Biosurfactant Film Flow in a Bacillus subtilis Swarm Colony on an Agar Plate
Kim, Kyunghoon; Kim, Jung Kyung
2015-01-01
Collective bacterial dynamics plays a crucial role in colony development. Although many research groups have studied the behavior of fluidic swarm colonies, the detailed mechanics of its motion remains elusive. Here, we developed a visualization method using submicron fluorescent beads for investigating the flow field in a thin layer of fluid that covers a Bacillus subtilis swarm colony growing on an agar plate. The beads were initially embedded in the agar plate and subsequently distributed spontaneously at the upper surface of the expanding colony. We conducted long-term live cell imaging of the B. subtilis colony using the fluorescent tracers, and obtained high-resolution velocity maps of microscale vortices in the swarm colony using particle image velocimetry. A distinct periodic fluctuation in the average speed and vorticity of flow in swarm colony was observed at the inner region of the colony, and correlated with the switch between bacterial swarming and growth phases. At the advancing edge of the colony, both the magnitudes of velocity and vorticity of flow in swarm colony were inversely correlated with the spreading speed of the swarm edge. The advanced imaging tool developed in this study would facilitate further understanding of the effect of micro vortices in swarm colony on the collective dynamics of bacteria. PMID:26343634
Visualization of Biosurfactant Film Flow in a Bacillus subtilis Swarm Colony on an Agar Plate.
Kim, Kyunghoon; Kim, Jung Kyung
2015-01-01
Collective bacterial dynamics plays a crucial role in colony development. Although many research groups have studied the behavior of fluidic swarm colonies, the detailed mechanics of its motion remains elusive. Here, we developed a visualization method using submicron fluorescent beads for investigating the flow field in a thin layer of fluid that covers a Bacillus subtilis swarm colony growing on an agar plate. The beads were initially embedded in the agar plate and subsequently distributed spontaneously at the upper surface of the expanding colony. We conducted long-term live cell imaging of the B. subtilis colony using the fluorescent tracers, and obtained high-resolution velocity maps of microscale vortices in the swarm colony using particle image velocimetry. A distinct periodic fluctuation in the average speed and vorticity of flow in swarm colony was observed at the inner region of the colony, and correlated with the switch between bacterial swarming and growth phases. At the advancing edge of the colony, both the magnitudes of velocity and vorticity of flow in swarm colony were inversely correlated with the spreading speed of the swarm edge. The advanced imaging tool developed in this study would facilitate further understanding of the effect of micro vortices in swarm colony on the collective dynamics of bacteria. PMID:26343634
Wetting dynamics of colloidal dispersions on agar gel surfaces.
Seino, Eri; Chida, Shigeki; Mayama, Hiroyuki; Hotta, Jun-ichi; Nonomura, Yoshimune
2014-10-01
The effects of silica particle addition on the wetting velocity on flat and fractal agar gel surfaces were analyzed along with the applicability of such particles for controlling the wetting dynamics of water. The contact angles (?D) of the colloidal dispersions obeyed the power law, i.e., ?D?t(-x), where t is time and x is a constant. Wetting was inhibited by the addition of a suitable amount of 20-nm-diameter silica particles. Specifically, the exponent x reached a minimum value for a silica composition of 0.1wt%. However, such inhibition effects were not observed upon the addition of silica particles with diameters of 100, 550, and, 1000nm. The mechanism of the inhibition of the liquid wetting on gel surfaces may be attributed to a slight increase in local viscosity around the contact line during wetting. PMID:25016539
Primer on Agar-Based Microbial Imaging Mass Spectrometry
Yang, Jane Y.; Phelan, Vanessa V.; Simkovsky, Ryan; Watrous, Jeramie D.; Trial, Rachelle M.; Fleming, Tinya C.; Wenter, Roland; Moore, Bradley S.; Golden, Susan S.; Pogliano, Kit
2012-01-01
Matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) imaging mass spectrometry (IMS) applied directly to microbes on agar-based medium captures global information about microbial molecules, allowing for direct correlation of chemotypes to phenotypes. This tool was developed to investigate metabolic exchange factors of intraspecies, interspecies, and polymicrobial interactions. Based on our experience of the thousands of images we have generated in the laboratory, we present five steps of microbial IMS: culturing, matrix application, dehydration of the sample, data acquisition, and data analysis/interpretation. We also address the common challenges encountered during sample preparation, matrix selection and application, and sample adherence to the MALDI target plate. With the practical guidelines described herein, microbial IMS use can be extended to bio-based agricultural, biofuel, diagnostic, and therapeutic discovery applications. PMID:22821974
Oxygen diffusion-concentration product in rhodopsin as observed by a pulse ESR spin labeling method.
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
NASA Astrophysics Data System (ADS)
Lin, Guoxing
2015-10-01
Inter-molecular multiple quantum coherence (iMQC) has important applications in NMR and MRI. However, the current theoretical methods still have some difficulties in analyzing the behavior of iMQC signal attenuation of pulsed field gradient diffusion experiments. In this paper, the iMQC diffusion experiments were analyzed by an effective phase shift diffusion equation (EPSDE) method, which is based on the idea that the accumulating phase shift (APS) can be viewed as the result of a diffusion process in virtual phase space (VPS) with effective diffusion coefficient K2(t) D (rad2/s) where K ( t ) = ?0 t ? g ( t ' ) d t ' is a wavenumber and D is the physical diffusion coefficient of the spin carrier in the real space. The term K(ttot) z1 needs to be added to the APS when K(ttot) is not zero. Most of the time, K(ttot) equals zero. However, in iMQC experiments, the condition K(ttot) equaling zero or being non-zero for each spin depends on the gradient pulse setting. The signal attenuations of these two types of iMQC, zero or non-zero K(ttot), were analyzed in detail for free and restricted diffusions, which shows that there are significant differences between these two types of iMQC. Particularly, if an apparent diffusion coefficient Dapp is used to analyze the signal attenuation, it equals nD for zero K(ttot) which agrees with current theoretical and experimental reports, while for non-zero K(ttot), it equals (2n - 1) D which agrees with experimental results from the literature; there are no similar theoretical results reported for comparison. The result that Dapp equals (2n - 1) D is important because the higher value of Dapp means that non-zero K(ttot) iMQC can potentially provide more contrast and measure slower diffusion rates than zero K(ttot) iMQC. The EPSDE method provides a new way to analyze iMQC diffusion experiments.
Pyrak-Nolte, Laura J.
rights reserved. Keywords: Mixing; Agar gels; Viscoelasticity; Ultrasound 1. Introduction Agar is a gelThe effect of mixing conditions on the material properties of an agar gel January 2005 Abstract The effect of mixing on the properties of agar gels was investigated
Convergence analysis of two-node CMFD method for two-group neutron diffusion eigenvalue problem
NASA Astrophysics Data System (ADS)
Jeong, Yongjin; Park, Jinsu; Lee, Hyun Chul; Lee, Deokjung
2015-12-01
In this paper, the nonlinear coarse-mesh finite difference method with two-node local problem (CMFD2N) is proven to be unconditionally stable for neutron diffusion eigenvalue problems. The explicit current correction factor (CCF) is derived based on the two-node analytic nodal method (ANM2N), and a Fourier stability analysis is applied to the linearized algorithm. It is shown that the analytic convergence rate obtained by the Fourier analysis compares very well with the numerically measured convergence rate. It is also shown that the theoretical convergence rate is only governed by the converged second harmonic buckling and the mesh size. It is also noted that the convergence rate of the CCF of the CMFD2N algorithm is dependent on the mesh size, but not on the total problem size. This is contrary to expectation for eigenvalue problem. The novel points of this paper are the analytical derivation of the convergence rate of the CMFD2N algorithm for eigenvalue problem, and the convergence analysis based on the analytic derivations.
Quantification of Al-goethite from diffuse reflectance spectroscopy and magnetic methods
NASA Astrophysics Data System (ADS)
Jiang, Zhaoxia; Liu, Qingsong; Colombo, Claudio; Barrón, Vidal; Torrent, José; Hu, Pengxiang
2014-01-01
As one of the most abundant iron oxides in soils, the presence and nature of goethite is controlled by the soil conditions and burial history. The visible diffuse reflectance spectroscopy (DRS) is a useful tool for quantifying goethite. However, aluminium (Al) substitution for goethite is very common in soils and the effects of Al content on the DRS properties of goethite have not been fully resolved. In this study, two series of Al substituted goethites (Al-goethite) and 20 Chinese loess/palaeosol samples were investigated using both DRS and magnetic methods to test the feasibility of quantifying Al-goethite with the DRS method. Results show that the peak positions and amplitudes of the goethite DRS band are significantly influenced by Al substitution. Specifically, the goethite concentration proxy, the amplitude of the DRS band, is relatively stable only when Al substitution ranged between about 4 and 16 mol per cent. Practically, in order to resolve the difficulty in measuring Al content in natural samples, the unblocking temperature (Tb) is proposed as the proxy for Al substitution of goethite. When Tb of Al-goethite was above 250 K, the amplitude of DRS can be used to reliably trace the goethite concentration variation in natural samples. For example, the DRS spectra for the Chinese loess-palaeosol samples support the idea that only haematite is enhanced via pedogenesis. In contrast, the origin of goethite seems to be mostly related to the aeolian inputs.
Bifurcation analysis of brown tide by reaction-diffusion equation using finite element method
Kawahara, Mutsuto; Ding, Yan
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.
AxCaliber: A Method for Measuring Axon Diameter Distribution from Diffusion MRI
Assaf, Yaniv; Blumenfeld-Katzir, Tamar; Yovel, Yossi; Basser, Peter J.
2015-01-01
The diameter of a myelinated nerve axon is directly proportional to its conduction velocity, so the axon diameter distribution helps determine the channel capacity of nervous transmission along fascicles in the central (CNS) and peripheral nervous systems (PNS). Previously, this histological information could only be obtained using invasive tissue biopsies. Here we propose a new NMR-based approach that employs a model of water diffusion within “restricted” cylindrical axons to estimate their diameter distribution within a nerve bundle. This approach can be combined with MRI to furnish an estimate of the axon diameter distribution within each voxel. This method is validated by comparing the diameter distributions measured using the NMR and histological techniques on sciatic and optic nerve tissue specimens. The axon diameter distribution measured in each voxel of porcine spinal cord using MRI and using histological methods were similar. Applications are expected in longitudinal studies designed to follow nerve growth in normal and abnormal development, as well as in diagnosing disorders and diseases affecting specific populations of axons in the CNS and PNS PMID:18506799
Jayawardena, Asitha; Boardman, Allison; Cook, Thomas; Oprescu, Florin; Morcuende, Jose A
2011-01-01
This ethnographic study evaluated the use of low-bandwidth web-conferencing to enhance diffusion of a specific best practice, the Ponseti method to treat clubfoot, in three economically diverse countries in Latin America. A “Ponseti Virtual Forum” (PVF) was organized in Guatemala, Peru and Chile to examine the influences of economic level and telecommunication infrastructure on the effectiveness of tins approach. Across the three countries, a total of 14 different sites participated in the PVFs. Thirty-three Ponseti-trained practitioners were interviewed before and after each PVF, which included interactions with a Spanish-speaking Ponseti method expert. Semi-structured interviews, observations, and IP address data were triangulated and analyzed. The results demonstrated that 100% of the practitioners rated the sessions as very useful and that they would use this approach again. The largest obstacles to using PVFs were financial (7 out of 9 practitioners) in Guatemala; a lack of equipment and network access (6 out of 11) in Peru; and the organization and implementation of the conferences themselves (7 out of 9) in Chile. This study illustrates the usefulness of Ponseti Virtual Forums in Latin America. Health officials in Peru are currently developing a large-scale information session for traumatologists about the Ponseti method, while practitioners in Guatemala and Chile are organizing monthly scholarly meetings for physicians in remote areas. This initial feedback suggests that low-bandwidth web-conferencing can be an important vehicle for the dissemination of best practices, such as the Ponseti method, in developing countries. PMID:22096417
Adaptive meshless local maximum-entropy finite element method for convection-diffusion problems
NASA Astrophysics Data System (ADS)
Wu, C. T.; Young, D. L.; Hong, H. K.
2014-01-01
In this paper, a meshless local maximum-entropy finite element method (LME-FEM) is proposed to solve 1D Poisson equation and steady state convection-diffusion problems at various Peclet numbers in both 1D and 2D. By using local maximum-entropy (LME) approximation scheme to construct the element shape functions in the formulation of finite element method (FEM), additional nodes can be introduced within element without any mesh refinement to increase the accuracy of numerical approximation of unknown function, which procedure is similar to conventional p-refinement but without increasing the element connectivity to avoid the high conditioning matrix. The resulted LME-FEM preserves several significant characteristics of conventional FEM such as Kronecker-delta property on element vertices, partition of unity of shape function and exact reproduction of constant and linear functions. Furthermore, according to the essential properties of LME approximation scheme, nodes can be introduced in an arbitrary way and the continuity of the shape function along element edge is kept at the same time. No transition element is needed to connect elements of different orders. The property of arbitrary local refinement makes LME-FEM be a numerical method that can adaptively solve the numerical solutions of various problems where troublesome local mesh refinement is in general necessary to obtain reasonable solutions. Several numerical examples with dramatically varying solutions are presented to test the capability of the current method. The numerical results show that LME-FEM can obtain much better and stable solutions than conventional FEM with linear element.
Basu, P.K.; Singh, S.N.; Arora, N.K.; Chakravarty, B.C. )
1994-03-01
A new method of determination of the minority carrier diffusion length (L) in the base region of an n[sup +]-p-p[sup +] silicon solar cell using the spectral response of the cell in a middle wavelength ([lambda]) range is presented. The minority carrier diffusion length (L) in the base region of an n[sup +]-p or n[sup +]-p-p[sup +] silicon solar cell has a profound effect on the solar cell performance. In this paper the authors report a new method of determination of diffusion length using the middle wavelength spectral response (MWSR) of the cell. It has been developed using a model of n[sup +]-p-p[sub +] silicon solar cells given by Singh and Jain and making some simplifying assumptions. It is equally applicable to cells with d/L > 2.5 and d/L < 2.5. In the following they give the theoretical basis of the method and present the result of the measurement of diffusion length of a few N[sup +]-p-p[sup +] silicon solar cells with d/L in the range 1.3--4.1 by using this method and the LWSR method.
Nguyen, Dang Van; Li, Jing-Rebecca; Grebenkov, Denis; Le Bihan, Denis
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.
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
Nusca, A; Orefice, L; Paradiso, R
2007-01-01
In the recent European Drinking Water Directive, Clostridium perfringens has assumed increasing importance so as to be considered a primary contamination indicator. Therefore it emerged the necessity to make culture methods, aimed at its recovery, more specific and sensitive. In this study we have verified the ability of Tryptose Sulphite Cycloserine Agar plates (TSC Agar), prepared and stored before the use at refrigeration temperature (+4 degrees) for different times, to show typical colonies, using both, the single layer and double layer techniques. Results show that storage of the prepared medium, even for a few days, decrease the recovery of typical colonies although such negative effect is minimized by using the double layer technique. PMID:17405507
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…
A Space-Time Spectral Method for the Time Fractional Diffusion Xianjuan Li
Xu, Chuanju
. Numerical tests are carried out to confirm the theoretical results. Thanks to the spectral accuracy in both of Education of China, and 973 High Performance Scientific Computation Research Program 2005CB321703. School the fractional diffusion equation to describe diffusion in media with fractal geometry. Mainardi [20] pointed out
ERIC Educational Resources Information Center
Artun, Huseyin; Costu, Bayram
2013-01-01
The aim of this study was to explore a group of prospective primary teachers' conceptual understanding of diffusion and osmosis as they implemented a 5E constructivist model and related materials in a science methods course. Fifty prospective primary teachers' ideas were elicited using a pre- and post-test and delayed post-test survey consisting…
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...
NASA Technical Reports Server (NTRS)
Stoker, Carol R.; Rages, Kathy
2002-01-01
We correct spectra of Yogi to remove diffuse illumination and show that the part of Yogi facing the wind is less red than other faces of the rock. Our method eliminates ambiguity in interpreting spectra obtained under Mars illumination conditions. Additional information is contained in the original extended abstract.
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, ...
Method of coating the interior surface of hollow objects with a diffusion coating
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.
Secure Multicast Tree Structure Generation Method for Directed Diffusion Using A* Algorithms
NASA Astrophysics Data System (ADS)
Kim, Jin Myoung; Lee, Hae Young; Cho, Tae Ho
The application of wireless sensor networks to areas such as combat field surveillance, terrorist tracking, and highway traffic monitoring requires secure communication among the sensor nodes within the networks. Logical key hierarchy (LKH) is a tree based key management model which provides secure group communication. When a sensor node is added or evicted from the communication group, LKH updates the group key in order to ensure the security of the communications. In order to efficiently update the group key in directed diffusion, we propose a method for secure multicast tree structure generation, an extension to LKH that reduces the number of re-keying messages by considering the addition and eviction ratios of the history data. For the generation of the proposed key tree structure the A* algorithm is applied, in which the branching factor at each level can take on different value. The experiment results demonstrate the efficiency of the proposed key tree structure against the existing key tree structures of fixed branching factors.
Comparison of dialysis membrane diffusion samplers and two purging methods in bedrock wells
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.
Erickson, Tim A.; Mazhar, Amaan; Cuccia, David; Durkin, Anthony J.; Tunnell, James W.
2010-01-01
Sinusoidally structured illumination is used in concert with a phantom-based lookup-table (LUT) to map wide-field optical properties in turbid media with reduced albedos as low as 0.44. A key advantage of the lookup-table approach is the ability to measure the absorption (?a) and reduced scattering coefficients (?s?) over a much broader range of values than permitted by current diffusion theory methods. Through calibration with a single reflectance standard, the LUT can extract ?s? from 0.8 to 2.4 mm?1 with an average root-mean-square (rms) error of 7% and extract ?a from 0 to 1.0 mm?1 with an average rms error of 6%. The LUT is based solely on measurements of two parameters, reflectance R and modulation M at an illumination period of 10 mm. A single set of three phase-shifted images is sufficient to measure both M and R, which are then used to generate maps of absorption and scattering by referencing the LUT. We establish empirically that each pair (M,R) maps uniquely to only one pair of (?s?,?a) and report that the phase function (i.e., size) of the scatterers can influence the accuracy of optical property extraction. PMID:20615015
Thickness Mapping of Eleven Retinal Layers Segmented Using the Diffusion Maps Method in Normal Eyes
Kafieh, Raheleh; Rabbani, Hossein; Abramoff, Michael D.; Sonka, Milan
2015-01-01
This study was conducted to determine the thickness map of eleven retinal layers in normal subjects by spectral domain optical coherence tomography (SD-OCT) and evaluate their association with sex and age. Mean regional retinal thickness of 11 retinal layers was obtained by automatic three-dimensional diffusion map based method in 112 normal eyes of 76 Iranian subjects. We applied our previously reported 3D intraretinal fast layer segmentation which does not require edge-based image information but rather relies on regional image texture. The thickness maps are compared among 9 macular sectors within 3 concentric circles as defined by ETDRS. The thickness map of central foveal area in layers 1, 3, and 4 displayed the minimum thickness. Maximum thickness was observed in nasal to the fovea of layer 1 and in a circular pattern in the parafoveal retinal area of layers 2, 3, and 4 and in central foveal area of layer 6. Temporal and inferior quadrants of the total retinal thickness and most of other quadrants of layer 1 were significantly greater in the men than in the women. Surrounding eight sectors of total retinal thickness and a limited number of sectors in layers 1 and 4 significantly correlated with age. PMID:25960888
Rule, Toby D.; Cai, Wei; Wang, Hsin
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.
Yeshurun, Lilach; Azhari, Haim
2016-01-01
Thermal diffusivity at the site ablated by high-intensity focused ultrasound (HIFU) plays an important role in the final therapeutic outcome, as it influences the temperature's spatial and temporal distribution. Moreover, as tissue thermal diffusivity is different in tumors as compared with normal tissue, it could also potentially be used as a new source of imaging contrast. The aim of this study was to examine the feasibility of combining through-transmission ultrasonic imaging and HIFU to estimate thermal diffusivity non-invasively. The concept was initially evaluated using a computer simulation. Then it was experimentally tested on phantoms made of agar and ex vivo porcine fat. A computerized imaging system combined with a HIFU system was used to heat the phantoms to temperatures below 42°C to avoid irreversible damage. Through-transmission scanning provided the time-of-flight values in a region of interest during its cooling process. The time-of-flight values were consequently converted into mean values of speed of sound. Using the speed-of-sound profiles along with the developed model, we estimated the changes in temperature profiles over time. These changes in temperature profiles were then used to calculate the corresponding thermal diffusivity of the studied specimen. Thermal diffusivity for porcine fat was found to be lower by one order of magnitude than that obtained for agar (0.313×10(-7)m(2)/s vs. 4.83×10(-7)m(2)/s, respectively, p < 0.041). The fact that there is a substantial difference between agar and fat implies that non-invasive all-ultrasound thermal diffusivity mapping is feasible. The suggested method may particularly be suitable for breast scanning. PMID:26489364
Bhattacharyya, Sayan; Gupta, Prashant; Banerjee, Gopa; Singh, Mastan
2015-01-01
Background Antifungal susceptibility testing remains an area of intense interest because of the increasing number of clinical isolates resistant to antifungal therapy. Clinical and Laboratory Standards Institute has proposed reference broth micro dilution (BMD) method for susceptibility testing. The reference method is time-consuming and poorly suited for the routine clinical laboratory setting. Agar-based susceptibility testing methods, disk diffusion (DD) method and the E-test method can be an easier, reliable and less time consuming alternative for the BMD method. Aim To compare the results of Amphotericin B, fluconazole, voriconazole, and Caspofungin susceptibility testing by DD, and the E-test method with the CLSI reference method for clinical Candida isolates. Materials and Methods Broth Microdilution (BMD), E-test and Disk diffusion testing of the various clinical Candida isolates was performed in accordance with CLSI documents. The results obtained were analysed and compared. Results The categorical agreement for Amphotericin B, fluconazole, voriconazole, and Caspofungin susceptibility results by E-test and DD method was 65.2%, 67.4%; 100%, 82.6%; 100%, 100%; 100%, 97.8% respectively. Conclusion The agar-based E-test and disk diffusion methods are reliable alternatives to the BMD method for Candida isolates when test susceptible to fluconazole, voriconazole, and Caspofungin, however the susceptibility testing results must be interpreted with caution in case of Amphotericin B. PMID:26675415
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.
Ganesh, P; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A; Kent, Paul R C
2014-12-01
Highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based on point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. The results demonstrate that the lithium-carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches. PMID:26583215
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.
DEVELOPMENT OF SPLIT-OPERATOR, PETROV-GALERKIN METHODS TO SIMULATE TRANSPORT AND DIFFUSION PROBLEMS
The rate at which contaminants in groundwater undergo sorption and desorption is routinely described using diffusion models. Such approaches, when incorporated into transport models, lead to large systems of coupled equations, often nonlinear. This has restricted applications of ...
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.
A method of determination of the thermal diffusivity of refractory powders in the 400-1200 K range
Litovskii, E.Ya.; Bondarenko, S.L.; Fedina, I.G.
1986-09-01
This paper describes a method of measurement of the thermal diffusivity of refractory powders at temperatures of 400-2100 K in different gaseous media in the p = 10/sup 2/-10/sup 5/ Pa pressure range. The method developed is based on the rules of steady heating of cylindrical specimens. The calculation equation has a form characteristic of regular conditions of the second order in an infinite cylinder with corrections for the deviation from quasisteadiness and for the nonuniformity of the temperature field in the specimen. Thermal diffusivities of magnesite powder and PIT-1 yttrium oxide powder are shown in different gaseous media. The method developed possesses satisfactory accuracy and makes it possible to obtain information on the thermal divusivity and conductivity of refractory powders in a broad temperature range and in the area of high temperature.
An improved design method and experimental performance of two dimensional curved wall diffusers
NASA Technical Reports Server (NTRS)
Yang, T.; Hudson, W. G.; El-Nashar, A. M.
1972-01-01
A computer design program was developed to incorporate the suction slots in solving the potential flow equations with prescribed boundary conditions. Using the contour generated from this program two Griffith diffusers were tested having area ratios AR = 3 and 4. The inlet Reynolds number ranged from 600,000 to 7 million. It was found that the slot suction required for metastable operation depends on the sidewall suction applied. Values of slot suction of 8% of the inlet flow rate was required for AR = 4 with metastable condition, provided that enough sidewall suction was applied. For AR = 3, the values of slot suction was about 25% lower than those required for AR = 4. For nearly all unseparated test runs, the effectiveness was 100% and the exit flow was uniform. In addition to the Griffith diffusers, dump and cusp diffusers of comparable area ratios were built and tested. The results obtained from these diffusers were compared with those of the Griffith diffusers. Flow separation occurred in all test runs with the dump and cusp diffusers.
NASA Astrophysics Data System (ADS)
Zhao, Peng; Zhang, Yan; Qian, Weiping
2015-10-01
Diffuse reflection laser ranging is one of the feasible ways to realize high precision measurement of the space debris. However, the weak echo of diffuse reflection results in a poor signal-to-noise ratio. Thus, it is difficult to realize the real-time signal extraction for diffuse reflection laser ranging when echo signal photons are blocked by a large amount of noise photons. The Genetic Algorithm, originally evolved from the idea of natural selection process, is a heuristic search algorithm which is famous for the adaptive optimization and the global search ability. To the best of our knowledge, this paper is the first one to propose a method of real-time signal extraction for diffuse reflection laser ranging based on Genetic Algorithm. The extraction results are regarded as individuals in the population. Besides, short-term linear fitting degree and data correlation level are used as selection criteria to search for an optimal solution. Fine search in the real-time data part gives the suitable new data quickly in real-time signal extraction. A coarse search in both historical data and real-time data after the fine search is designed. The co-evolution of both parts can increase the search accuracy of real-time data as well as the precision of the history data. Simulation experiments show that our method has good signal extraction capability in poor signal-to-noise ratio circumstance, especially for data with high correlation.
Kos, J.; Zwitter, T.; Grebel, E. K.; Bienayme, O.; Siebert, A.; Binney, J.; Bland-Hawthorn, J.; Freeman, K. C.; Gibson, B. K.; Gilmore, G.; Kordopatis, G.; Navarro, J. F.; Parker, Q.; Reid, W. A.; Seabroke, G.; Siviero, A.; Steinmetz, M.; Watson, F.; Wyse, R. F. G.
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.
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)…
Leonenko, Nikolai N.; Meerschaert, Mark M.
2013-01-01
Pearson diffusions are governed by diffusion equations with polynomial coefficients. Fractional Pearson diffusions are governed by the corresponding time-fractional diffusion equation. They are useful for modeling sub-diffusive phenomena, caused by particle sticking and trapping. This paper provides explicit strong solutions for fractional Pearson diffusions, using spectral methods. It also presents stochastic solutions, using a non-Markovian inverse stable time change. PMID:23626377
Manzini, Gianmarco; Cangiani, Andrea; Sutton, Oliver
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 H^{1}-norm. For the convection-dominated case, the streamline diffusion stabilization (aka SUPG) is also discussed.
Rovenská, Kate?ina; Jiránek, Martin
2012-04-01
This paper summarizes information about 16 measuring methods for determining the radon diffusion coefficient of waterproofing materials. We have found that the differences in results for identical membranes, which can be as high as two orders of magnitude, can mainly be attributed to insufficient duration of the tests, insufficient radon concentration to which the samples are exposed, and the use of steady state calculation procedures for data measured under non-steady state conditions. PMID:22285061
Factors Affecting Selectivity of Brilliant Green-Phenol Red Agar for Salmonellae
Moats, W. A.; Kinner, J. A.
1974-01-01
Commercial brilliant green (BG)-sulfa agar was found to be nonselective toward a test series of Enterobacteriaceae. Various formulations of BG were prepared by using Trypticase soy agar (BBL) as a base. Results were more reproducible when BG dye was added after sterilization than before. Sulfonamides improved selectivity as compared with brilliant green alone. Sulfanilamide (SN) was slightly more selective for salmonellae than other sulfonamides tested. Bile salts and sodium dodecyl sulfate markedly reduced the toxicity of BG to all the test bacteria. Enterobacter strains were most difficult to inhibit. A combination of 5 mg of BG and 1 g of SN/liter prevented growth of Proteus mirabilis and Escherichia coli and retarded growth of Enterobacter strains. The BG-SN agars were superior in selectivity to a series of commercial agars tested, and numbers of salmonellae recovered on BG-SN agar and Trypticase soy agar (BBL) were the same. Brilliant green agars with various degrees of selectivity are described. PMID:4589120
Technology Transfer Automated Retrieval System (TEKTRAN)
A four-year field study was conducted to test alternative control strategies for spotted knapweed and at Fort Carson, CO and diffuse knapweed at Yakima Training Center, WA. We evaluated the control of these alien invasive weeds with a combination of four manipulations to speed up restoration of des...
Propagation of Diffusing Pollutant by a Hybrid Eulerian-Lagrangian Method
Kurganov, Alexander
in shallow water. The flow is modeled by the Saint- Venant system of shallow water equations and the pollutant propagation is described by a convection-diffusion equation. In this paper, we extend the hybrid is to use different schemes for the flow and pollution compu- tations: the shallow water equations
ADAPTIVE FINITE VOLUME ELEMENT METHOD FOR CONVECTION-DIFFUSION-REACTION PROBLEMS IN 3-D
Lazarov, Raytcho
formulation. The mathematical model of steady state ground- water flows and transport in porous media yields. Computational re- sults of various model simulations of fluid flow and transport of passive chemicals in non mathematical models for both problems, flow and transport, are elliptic equations of second order (diffusion
Van Wyk, J A; Gerber, H M
1978-03-01
When gastro-intestinal ingesta and mucosa containing larvae or adult Haemonchus contortus, Ostertagia circumcincta. Trichostrongylus colubriformis, Strongyloides papillosus, Nematodirus spathiger, Gaigeria pachyscelis, Oesophagostomum columbianum or Chabertia ovina were suspended in 0,75--1,00% agar gel and incubated in physiological saline, a mean of 93,6% of the helminths migrated from the agar-ingesta or agar-mucosa into the physiological saline. The lowest suitable concentration of agar was 0,85--0,90% for one batch of agar and 0,65% for another. Although most of the worms had migrated from the agar gel after 3--4 h of incubation, migration usually continued for longer than 7 h. While low concentrations of formalin partially inhibited migration from the gel, slightly more worms were recovered from agar containing 1% bile than from agar alone. PMID:704042
EULERIAN-LAGRANGIAN LOCALIZED ADJOINT METHOD FOR THE ADVECTION-DIFFUSION EQUATION
Many numerical methods use characteristic analysis to accommodate the advective component of transport. uch characteristic methods include Eulerian-Lagrangian methods (ELM), modified method of characteristics (MMOC), and operator splitting methods. eneralization of characteristic...
AN EULERIAN-LAGRANGIAN LOCALIZED ADJOINT METHOD FOR THE ADVECTION-DIFFUSION EQUATION
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 characteri...
Scheau, C; Preda, EM; Popa, GA; Ghergus, AE; Capsa, RA; Lupescu, IG
2012-01-01
Magnetic Resonance Spectroscopy is a non-invasive method, which can be performed following a routine Magnetic Resonance investigation within the same examination, and can provide very useful molecular information related to the metabolism and function of the normal and pathological structures of the brain. Its role is increasing in the establishment of a clear diagnosis, in both focal and diffuse central nervous system diseases, and the tendency is to replace the histopathology test, in certain cases, with similar or sometimes better diagnostic accuracy. This paper summarizes the principle, method, and main clinical applications, standing as a guide to procedure performing and results interpretation. PMID:23346244
Diffusion Geometry Diffusion Geometry
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
Orlova, Darya Y.; Bártová, Eva; Maltsev, Valeri P.; Kozubek, Stanislav; Chernyshev, Andrei V.
2011-01-01
Determining averaged effective diffusion constants from experimental measurements of fluorescent proteins in an inhomogeneous medium in the presence of ligand-receptor interactions poses problems of analytical tractability. Here, we introduced a nonfitting method to evaluate the averaged effective diffusion coefficient of a region of interest (which may include a whole nucleus) by mathematical processing of the entire cellular two-dimensional spatial pattern of recovered fluorescence. Spatially and temporally resolved measurements of protein transport inside cells were obtained using the fluorescence recovery after photobleaching technique. Two-dimensional images of fluorescence patterns were collected by laser-scanning confocal microscopy. The method was demonstrated by applying it to an estimation of the mobility of green fluorescent protein-tagged heterochromatin protein 1 in the nuclei of living mouse embryonic fibroblasts. This approach does not require the mathematical solution of a corresponding system of diffusion-reaction equations that is typical of conventional fluorescence recovery after photobleaching data processing, and is most useful for investigating highly inhomogeneous areas, such as cell nuclei, which contain many protein foci and chromatin domains. PMID:21244847
Skelhon, Thomas S; Olsson, Patrik K A; Morgan, Adam R; Bon, Stefan A F
2013-09-01
Reducing the fat content of chocolate formulations is a major challenge for the confectionery industry. We report the suspension of aqueous microgel agar particles of up to 80% v/v within sunflower oil, cocoa butter, and ultimately chocolate. The optimised emulsification process involves a shear-cooling step. We demonstrate the versatility of our method when applied to white, milk, and dark chocolate formulations, whilst preserving the desired polymorph V of the cocoa butter matrix. In addition, we show that this technology can be used as a strategy to disperse alcoholic beverages into chocolate confectionery. PMID:23799607
Development of a rapid, reliable and quantitative method--"SPOTi" for testing antifungal efficacy.
Rizi, Khalida; Murdan, Sudaxshina; Danquah, Cynthia A; Faull, Jane; Bhakta, Sanjib
2015-10-01
A reference method for the antimicrobial susceptibility testing of common fungal pathogens such as dermatophytes, is currently lacking. In this study, we report the successful adaptation of solid agar-based spot culture growth inhibition assay (SPOTi) for dermatophytes, currently being used as a gold-standard in the anti-tubercular drug discovery field. The fungal-SPOTi assay correlated with the disc-diffusion method, and is validated using mycelial plugs. We propose the fungal-SPOTi as a high-throughput alternative to the disc-diffusion and broth micro-dilution anti-fungal assays to screen novel anti-fungals. PMID:26183763
Valdes, Claudia P; Varma, Hari M; Kristoffersen, Anna K; Dragojevic, Tanja; Culver, Joseph P; Durduran, Turgut
2014-08-01
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
Determination of the Solute Diffusion Coefficient by the Droplet Migration Method
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.
Intrauterine device for laser light diffusion and method of using the same
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.
Intrauterine device for laser light diffusion and method of using the same
Tadir, Y.; Berns, M.W.; Svaasand, L.O.; Tromberg, B.J.
1995-12-26
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. 5 figs.
Methods for measuring diffusion of a social media-based health intervention
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. PMID:26120501
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.
Primary isolation of Mycobacterium avium complex-serotype 6 on blood agar.
Thigpen, J E; Thierry, V L; Gupta, B N
1976-01-01
Mycobacterium avium complex-serotype 6 was isolated in pure culture on blood agar plates from inocula taken from the heart blood, lungs, liver, kidneys, and spleen of a naturally infected captive female opossum (Didelphis marsupialis virginiana). Repeat cultures from stored tissues and transfer of colonies from original blood agar plates revealed that the mycobacterium grew on tryptose, brilliant green, eosin-methylene blue. Sabouraud glucose, and mycobiotic agar plates and in Fletcher leptospira medium. The cultural, biochemical, and serological characteristics of the test isolate were compared with other mycobacteria. This is the first report to describe the primary isolation of a serotype from the M. avium complex from an animal species on blood agar or in Fletcher broth. In addition, this is the second documented report describing the isolation and identification of a mycobacterial species from the American opossum. PMID:972192
Hardboiled eggs petri dishes for growing tooth microbes (find proper agar)
Materials Hardboiled eggs cola OJ Water petri dishes for growing tooth microbes (find proper agar) activities: roleplay egg in acid grow microbes Intro so just a little about myself; name; Im a Chemist I go
Primary isolation of Mycobacterium avium complex-serotype 6 on blood agar.
Thigpen, J E; Thierry, V L; Gupta, B N
1976-09-01
Mycobacterium avium complex-serotype 6 was isolated in pure culture on blood agar plates from inocula taken from the heart blood, lungs, liver, kidneys, and spleen of a naturally infected captive female opossum (Didelphis marsupialis virginiana). Repeat cultures from stored tissues and transfer of colonies from original blood agar plates revealed that the mycobacterium grew on tryptose, brilliant green, eosin-methylene blue. Sabouraud glucose, and mycobiotic agar plates and in Fletcher leptospira medium. The cultural, biochemical, and serological characteristics of the test isolate were compared with other mycobacteria. This is the first report to describe the primary isolation of a serotype from the M. avium complex from an animal species on blood agar or in Fletcher broth. In addition, this is the second documented report describing the isolation and identification of a mycobacterial species from the American opossum. PMID:972192
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.
Salazar, A.; Sanchez-Lavega, A.
1998-03-01
The thermal diffusivity tensor of a polymer-carbon fiber composite with unidirectionally distributed fibers has been measured using a modulated photothermal mirage device. The thermal diffusivity along the fibers is k{sub {parallel}} = 6.0 {+-} 0.5 mm{sup 2}{center_dot}s{sup {minus}1}, that perpendicular to the fibers is k{sub {perpendicular}} = 0.35 {+-} 0.05 mm{sup 2}{center_dot}s{sup {minus}1}, and that perpendicular to the sample surface is k{sub z} = 0.40 {+-} 0.15 mm{sup 2}{center_dot}s{sup {minus}1}. These results have been confirmed by independent measurements on the sample by other laboratories using three other different photothermal techniques. A previous claim on anomalous results found on this sample (k{sub {parallel}} < k{sub {perpendicular}} and high thermal diffusivities) can be explained by the inappropriate use of the frequency range. The authors have also found that there is not perfect thermal contact between the fibers and the matrix, which can be characterized by the thermal contact resistance of R{sub th} = (9 {+-} 2) {times} 10{sup {minus}6} m{sup 2}{center_dot}K{center_dot}W{sup {minus}1}.
Xu, Chen; Kumavor, Patrick D.; Aguirre, Andres; Zhu, Quing
2012-01-01
Abstract. Photoacoustic tomography provides the distribution of absorbed optical energy density, which is the product of optical absorption coefficient and optical fluence distribution. We report the experimental investigation of a novel fitting procedure that quantitatively determines the optical absorption coefficient of chromophores. The experimental setup consisted of a hybrid system of a 64-channel photoacoustic imaging system with a frequency-domain diffused optical measurement system. The fitting procedure included a complete photoacoustic forward model and an analytical solution of a target chromophore using the diffusion approximation. The fitting procedure combines the information from the photoacoustic image and the background information from the diffuse optical measurements to minimize the photoacoustic measurements and forward model data and recover the target absorption coefficient quantitatively. 1-cm-cube phantom absorbers of high and low contrasts were imaged at depths of up to 3.0 cm. The fitted absorption coefficient results were at least 80% of their true values. The sensitivities of this fitting procedure to target location, target radius, and background optical properties were also investigated. We found that this fitting procedure was most sensitive to the accurate determination of the target radius and depth. Blood sample in a thin tube of radius 0.58 mm, simulating a blood vessel, was also studied. The photoacoustic images and fitted absorption coefficients are presented. These results demonstrate the clinical potential of this fitting procedure to quantitatively characterize small lesions in breast imaging. PMID:22734743
Lattice Boltzmann method for diffusion-limited partial dissolution of fluids
NASA Astrophysics Data System (ADS)
Aursjø, Olav; Pride, Steven R.
2015-07-01
A lattice Boltzmann model for two partially miscible fluids is developed. By partially miscible we mean that, although there is a definite interfacial region separating the two fluids with a surface tension force acting at all points of the transition region, each fluid can nonetheless accept molecules from the other fluid up to a set solubility limit. We allow each fluid to diffuse into the other with the solubility and diffusivity in each fluid being input parameters. The approach is to define two regions within the fluid: one interfacial region having finite width, across which most of the concentration change occurs, and in which a surface tension force and color separation step are allowed for and one miscible fluid region where the concentration of the binary fluids follows an advection-diffusion equation and the mixture as a whole obeys the Navier-Stokes incompressible flow equations. Numerical examples are presented in which the algorithm produces results that are quantitatively compared to exact analytical results as well as qualitatively examined for their reasonableness. The model has the ability to simulate how bubbles of one fluid flow through another while dissolving their contents as well as to simulate a range of practical invasion problems such as injecting supercritical CO2 into a porous material saturated with water for sequestration purposes.
Li, Liang; Du, Wenbin; Ismagilov, Rustem F.
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.
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.
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. PMID:26090423
van Wyk, J A; Gerber, H M; Groeneveld, H T
1980-09-01
A gelled-agar technique for worm recovery was adapted to facilitate the recovery of larval and adult nematodes from the total ingesta of large numbers of sheep. The technique was also used to recover nematodes from 4 calves. In one trial involving 120 sheep, 100% of 2013 4th stage larvae (L4) and 92,1% of 134,205 adult Haemonchus contortus migrated from the agar preparations. Highly significantly more male than female worms failed to migrate. Using 1 x 1/10 aliquot to estimate the numbers of worms that failed to migrate from the agar, the mean error in the total worm count (worms that migrated plus those that failed to migrate) per sheep was 2,2%; with an examination of 2 x 1/10 aliquot the error was 1,7%. We concluded from this that the gelled-agar method may be of value for quantitative worm recovery, for example, in anthelmintic tests. In a second trial, 98,5% of 17,056 L4 and adult nematodes of 5 genera migrated from the ingesta of 4 calves and 96,4% of 62,597 L4 and adult nematodes of 9 species from the ingesta of 15 sheep. In general, L4 migrated slightly more efficiently than adult worms. In sheep and, to a lesser extent, in calves, Haemonchus spp. did not migrate as efficiently as the other genera such as Ostertagia, Trichostrongylus, Nematodirus, Oesophagostomum, Marshallagia and Chabertia. PMID:7465167
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. PMID:26090423
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.
Wang, Zheng; Neves, Marcos A; Kobayashi, Isao; Uemura, Kunihiko; Nakajima, Mitsutoshi
2013-01-01
Soybean oil-in-water (O/W) emulsion-agar gel samples were prepared and their digestibility evaluated by using an in vitro gastrointestinal digestion model. Emulsion-agar sols were obtained by mixing the prepared O/W emulsions with a 1.5 wt % agar solution at 60 °C, and their subsequent cooling at 5 °C for 1 h formed emulsion-agar gels. Their gel strength values increased with increasing degree of polymerization of the emulsifiers, and the relative gel strength increased in the case of droplets with an average diameter smaller than 700 nm. Flocculation and coalescence of the released emulsion droplets depended strongly on the emulsifier type; however, the emulsifier type hardly affected the ?-potential of emulsion droplets released from the emulsion-agar gels during in vitro digestion. The total FFA content released from each emulsion towards the end of the digestion period was nearly twice that released from the emulsion-agar gel, indicating that gelation of the O/W emulsion may have delayed lipid hydrolysis. PMID:23470750
[GROWTH OF MICROMYCETES FROM DIFFERENT ECOLOGICAL NICHES ON AGAR NUTRIENT MEDIA].
Kurchenko, I M; Yurieva, E M; Voychuk, S I
2015-01-01
Radial growth rate of (K(r)) 153 strains 6 species of micromycetes from different ecological niches was studied on 7 agar media: three standard (malt extract agar, potato-dextrose agar, Czapek's agar), and on agar media with plant polymers (carboxymethylcellulose, xylan, soluble starch and apple pectin). Endophytic and plant pathogenic strains (biotrophs) of all studied species did not differ significantly in their ability to grow on nutrient media of different composition--average values of K(r) for these two groups were the same (0,200 and 0,199 mm/h, respectively). Soil micromycetes (saprophytes) characterized by the lowest average growth rate (0,169 mm/h) and significantly differed from the endophytic and plant pathogenic ones. Average of the radial growth rates of studied microscopic fungi were higher on standard nutrient media than with plant polymers ones. Growth parameters of endophytes and plant pathogens of all studied species on various agar media differed from the soil strains. High growth rate of endophytic and plant pathogenic strains of Fusarium poae, Alternaria alternata and Ceratocystis sp. provides them the rapid colonization of plants. Penicillium funiculosum strains equally can exist as saprophytes in soil and as endophytic plant symbionts. A wide range of K(r) variation of endophytic dark pigmented Mycelia sterilia indicates the presence in this group of different species of micromycetes, which have no sporulation. PMID:26638483
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.
Chai, Zhenhua; Zhao, T S
2014-07-01
In this paper, we propose a local nonequilibrium scheme for computing the flux of the convection-diffusion equation with a source term in the framework of the multiple-relaxation-time (MRT) lattice Boltzmann method (LBM). Both the Chapman-Enskog analysis and the numerical results show that, at the diffusive scaling, the present nonequilibrium scheme has a second-order convergence rate in space. A comparison between the nonequilibrium scheme and the conventional second-order central-difference scheme indicates that, although both schemes have a second-order convergence rate in space, the present nonequilibrium scheme is more accurate than the central-difference scheme. In addition, the flux computation rendered by the present scheme also preserves the parallel computation feature of the LBM, making the scheme more efficient than conventional finite-difference schemes in the study of large-scale problems. Finally, a comparison between the single-relaxation-time model and the MRT model is also conducted, and the results show that the MRT model is more accurate than the single-relaxation-time model, both in solving the convection-diffusion equation and in computing the flux. PMID:25122408
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.
NASA Astrophysics Data System (ADS)
Tønning, Erik; Polders, Daniel; Callaghan, Paul T.; Engelsen, Søren B.
2007-09-01
This paper demonstrates how the multi-linear PARAFAC model can with advantage be used to decompose 2D diffusion-relaxation correlation NMR spectra prior to 2D-Laplace inversion to the T2- D domain. The decomposition is advantageous for better interpretation of the complex correlation maps as well as for the quantification of extracted T2- D components. To demonstrate the new method seventeen mixtures of wheat flour, starch, gluten, oil and water were prepared and measured with a 300 MHz nuclear magnetic resonance (NMR) spectrometer using a pulsed gradient stimulated echo (PGSTE) pulse sequence followed by a Carr-Purcell-Meiboom-Gill (CPMG) pulse echo train. By varying the gradient strength, 2D diffusion-relaxation data were recorded for each sample. From these double exponentially decaying relaxation data the PARAFAC algorithm extracted two unique diffusion-relaxation components, explaining 99.8% of the variation in the data set. These two components were subsequently transformed to the T2- D domain using 2D-inverse Laplace transformation and quantitatively assigned to the oil and water components of the samples. The oil component was one distinct distribution with peak intensity at D = 3 × 10 -12 m 2 s -1 and T2 = 180 ms. The water component consisted of two broad populations of water molecules with diffusion coefficients and relaxation times centered around correlation pairs: D = 10 -9 m 2 s -1, T2 = 10 ms and D = 3 × 10 -13 m 2 s -1, T2 = 13 ms. Small spurious peaks observed in the inverse Laplace transformation of original complex data were effectively filtered by the PARAFAC decomposition and thus considered artefacts from the complex Laplace transformation. The oil-to-water ratio determined by PARAFAC followed by 2D-Laplace inversion was perfectly correlated with known oil-to-water ratio of the samples. The new method of using PARAFAC prior to the 2D-Laplace inversion proved to have superior potential in analysis of diffusion-relaxation spectra, as it improves not only the interpretation, but also the quantification.
Su, Jonathan T.; Duncan, P. Brent; Momaya, Amit; Jutila, Arimatti; Needham, David
2010-01-01
While the Stokes–Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5×10?5 cm2?s for water in n-pentane to 1.15×10?5 cm2?s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75×10?5 cm2?s in n-methanol to 0.364×10?5 cm2?s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid. PMID:20113048
Su, Jonathan T; Duncan, P Brent; Momaya, Amit; Jutila, Arimatti; Needham, David
2010-01-28
While the Stokes-Einstein (SE) equation predicts that the diffusion coefficient of a solute will be inversely proportional to the viscosity of the solvent, this relation is commonly known to fail for solutes, which are the same size or smaller than the solvent. Multiple researchers have reported that for small solutes, the diffusion coefficient is inversely proportional to the viscosity to a fractional power, and that solutes actually diffuse faster than SE predicts. For other solvent systems, attractive solute-solvent interactions, such as hydrogen bonding, are known to retard the diffusion of a solute. Some researchers have interpreted the slower diffusion due to hydrogen bonding as resulting from the effective diffusion of a larger complex of a solute and solvent molecules. We have developed and used a novel micropipette technique, which can form and hold a single microdroplet of water while it dissolves in a diffusion controlled environment into the solvent. This method has been used to examine the diffusion of water in both n-alkanes and n-alcohols. It was found that the polar solute water, diffusing in a solvent with which it cannot hydrogen bond, closely resembles small nonpolar solutes such as xenon and krypton diffusing in n-alkanes, with diffusion coefficients ranging from 12.5x10(-5) cm(2)/s for water in n-pentane to 1.15x10(-5) cm(2)/s for water in hexadecane. Diffusion coefficients were found to be inversely proportional to viscosity to a fractional power, and diffusion coefficients were faster than SE predicts. For water diffusing in a solvent (n-alcohols) with which it can hydrogen bond, diffusion coefficient values ranged from 1.75x10(-5) cm(2)/s in n-methanol to 0.364x10(-5) cm(2)/s in n-octanol, and diffusion was slower than an alkane of corresponding viscosity. We find no evidence for solute-solvent complex diffusion. Rather, it is possible that the small solute water may be retarded by relatively longer residence times (compared to non-H-bonding solvents) as it moves through the liquid. PMID:20113048
NASA Astrophysics Data System (ADS)
Rahman, Mohammad Shafiur; Al-Marhubi, Insaaf Mohd; Al-Mahrouqi, Abdullah
2007-06-01
Glass transition measured by DMTA from the change in slope in storage modulus was 55 °C, which was 10.5 °C lower than the value measured by tan ? peak. Initial glass transition measured by DSC, increased exponentially and reached a constant value of 55 °C at or higher heating rate of 30 °C/min. Transition temperature, measured by MDSC, remained constant up to heating rate 15 °C/min and then decreased. The glass transition values determined from reversible heat flow was 60 °C. The break in diffusivity and density (i.e. volume) was observed at 50 °C below the glass transition temperature measured by thermal and mechanical methods.
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.
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.
da Silva, Wilton Pereira; E Silva, Cleide M D P S
2014-09-01
Cooling of fruits and vegetables, immediately after the harvest, has been a widely used method for maximizing post-harvest life. In this paper, an optimization algorithm and a numerical solution are used to determine simultaneously the convective heat transfer coefficient, hH, and the thermal diffusivity, ?, for an individual solid with cylindrical shape, using experimental data obtained during its cooling. To this end, the one-dimensional diffusion equation in cylindrical coordinates is discretized and numerically solved through the finite volume method, with a fully implicit formulation. This solution is coupled to an optimizer based on the inverse method, in which the chi-square referring to the fit of the numerical simulation to the experimental data is used as objective function. The optimizer coupled to the numerical solution was applied to experimental data relative to the cooling of a cucumber. The obtained results for ? and hH were coherent with the values available in the literature. With the results obtained in the optimization process, the cooling kinetics of cucumbers was described in details. PMID:25190830
Lipp, V P; Garcia, M E; Ivanov, D S
2015-01-01
We present a finite-difference integration algorithm for solution of a system of differential equations containing a diffusion equation with nonlinear terms. The approach is based on Crank-Nicolson method with predictor-corrector algorithm and provides high stability and precision. Using a specific example of short-pulse laser interaction with semiconductors, we give a detailed description of the method and apply it for the solution of the corresponding system of differential equations, one of which is a nonlinear diffusion equation. The calculated dynamics of the energy density and the number density of photoexcited free carriers upon the absorption of laser energy are presented for the irradiated thin silicon film. The energy conservation within 0.2% has been achieved for the time step $10^4$ times larger than that in case of the explicit scheme, for the chosen numerical setup. We also present a few examples of successful application of the method demonstrating its benefits for the theoretical studies of la...
Mahalakshmi, M; Hariharan, G
2014-03-01
The mathematical model of Rahamathunissa and Rajendran (J Math Chem 44:849-861, 2008) in an amperometric biosensor response is discussed. In this paper, we have applied the shifted second kind Chebyshev wavelets (CW) to obtain the numerical solutions of reaction-diffusion equations containing a nonlinear term related to Michaelis-Menton kinetics of the enzymatic reaction. The application of the shifted second kind CW operational matrices for solving initial and boundary value problems is presented. The obtained numerical results demonstrate efficient and applicability of the proposed method. The power of the manageable method is confirmed. Moreover the use of shifted second kind CW method is found to be simple, efficient, accurate, small computation cost, and computationally attractive. PMID:24445748
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.
LaBombardi, Vincent J; Urban, Carl M; Kreiswirth, Barry N; Chen, Liang; Osorio, Giuliana; Kopacz, Joanna; Labaze, Georges; Segal-Maurer, Sorana
2015-09-01
We compared the Remel Spectra CRE agar plate to CDC standard methodology for the isolation of carbapenem-resistant Enterobacteriaceae (CRE) from 300 rectal swab specimens obtained from patients residing in a long-term-care facility (LTCF). Multiplex PCR experiments were performed on isolates to identify specific Klebsiella pneumoniae carbapenemases (KPC) and additional ?-lactamases. Of the 300 patients, 72 (24%) harbored CRE and were PCR positive for KPC enzymes. The Remel Spectra CRE plates detected KPC-type CRE in isolates from 70 of 72 patients (97.2%), while the CDC method detected CRE in 56 of 72 (77.8%). CRE identification results were available in 18 h compared to 36 h for the CDC method. Remel Spectra CRE agar plates can provide useful means for a fast and reliable method for detecting KPC-type CRE and for accelerated institution of appropriate infection control precautions. PMID:26085613
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.
Wind, Carolien M; de Vries, Henry J C; van Dam, Alje P
2015-03-01
In response to antimicrobial resistance of Neisseria gonorrhoeae to last-resort extended-spectrum cephalosporins, combination therapy of azithromycin+ceftriaxone is now recommended. Dual therapy can be effective to treat monoresistant strains as well as multidrug-resistant strains, preferably employing the effect of in vitro synergy. As reports on in vitro synergy of azithromycin+ceftriaxone in N. gonorrhoeae are conflicting, in this study an evaluation of this combination was performed using a cross-wise Etest method and agar dilution. Synergy was defined as a fractional inhibitory concentration index (FICI) of ?0.5. To identify other dual treatment options for gonorrhoea, in vitro synergy was evaluated for 65 dual antimicrobial combinations using Etest. Azithromycin, cefixime, ceftriaxone, colistin, ertapenem, fosfomycin, gentamicin, minocycline, moxifloxacin, rifampicin, spectinomycin and tigecycline were screened for synergy in all possible combinations. No synergy or antagonism was found for any of the 65 combinations. The geometric mean FICI ranged from 0.82 to 2.00. The mean FICI of azithromycin+ceftriaxone was 1.18 (Etest) and 0.55 (agar dilution). The difference between both methods did not result in a difference in interpretation of synergy. Ceftriaxone-resistant strain F89 was tested in all combinations and no synergy was found for any of them. Most importantly, the ceftriaxone minimum inhibitory concentration of F89 was not decreased below the breakpoint with any concentration of azithromycin. PMID:25532741
Ben Saïd, Noura Elmnasser; Federighi, Michel; Bakhrouf, Amina; Orange, Nicole
2010-11-01
In the present study, the efficiency of a broad-spectrum pulsed ultraviolet (UV)-light for the inactivation of Listeria monocytogenes Scott A, L. monocytogenes CNL 895807, and Pseudomonas fluorescens MF37 populations as agar seeded or suspended cells was investigated. The bacterial populations were treated by pulsed UV-light at different number of pulses (1 to 3), dose of energy (162, 243, or 324 J), and distance from the strobe (4, 9, or 12 cm). After pulsed UV-light treatment, the bacterial reduction was determined by standard plate count. The results showed that there was a significant reduction of population along with an increase of light energy and number of pulses. Decreasing the distance between the Petri dishes and the xenon lamp demonstrated an increase in bacterial reduction. Decontamination efficacy decreased significantly with the increase in level of contamination. This study demonstrates that pulsed UV-light can be used as an effective sterilizing method for the bacteria. PMID:20586608
Rivera-Posada, J A; Pratchett, M; Owens, L
2011-12-01
We assessed histological changes in the tissues of the crown-of-thorns starfish Acanthaster planci (COTS) after injection of thiosulfate-citrate-bile-sucrose agar (TCBS) which was used as a disease inducer (potential outbreak control method), by conventional and scanning electron microscopy. Digestive glands were processed and stained with hematoxylin and eosin to describe the histological architecture of the intestinal epithelium. Subsequently comparison of healthy versus infected tissues and Gram stains were carried out to confirm bacterial occurrence on infected tissues, characterize the structural changes induced by bacterial communities in COTS tissues, and to determine if the histopathological changes of intestinal tissues were consistent with vibrio infection. TCBS injections induced marked epithelial desquamation, hypertrophy and hypersecretion of glandular cells, epithelial cell destruction, pyknosis, reduction of thickness and disorganization of connective tissue and associated nerve plexus, presence of bacterial colonies, irregular eosinophilic foci in glandular cells, brush border disruption, atrophy and detachment of intestinal microvilli and cell debris in the lumen. All these changes were attributed to a fulminating systemic dysbiosis and were consistent with vibrio infections. PMID:22303626
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.
NASA Astrophysics Data System (ADS)
Hsu, Po Jen; Lai, S. K.; Rapallo, Arnaldo
2014-03-01
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.
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
Skov, Robert; Matuschek, Erika; Sjölund-Karlsson, Maria; Åhman, Jenny; Petersen, Andreas; Stegger, Marc; Torpdahl, Mia; Kahlmeter, Gunnar
2015-11-01
Fluoroquinolones (FQs) are among the drugs of choice for treatment of Salmonella infections. However, fluoroquinolone resistance is increasing in Salmonella due to chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of the topoisomerase genes gyrA, gyrB, parC, and parE and/or plasmid-mediated quinolone resistance (PMQR) mechanisms including qnr variants, aac(6')-Ib-cr, qepA, and oqxAB. Some of these mutations cause only subtle increases in the MIC, i.e., MICs ranging from 0.12 to 0.25 mg/liter for ciprofloxacin (just above the wild-type MIC of ?0.06 mg/liter). These isolates are difficult to detect with standard ciprofloxacin disk diffusion, and plasmid-mediated resistance, such as qnr, is often not detected by the nalidixic acid screen test. We evaluated 16 quinolone/fluoroquinolone disks for their ability to detect low-level-resistant Salmonella enterica isolates that are not serotype Typhi. A total of 153 Salmonella isolates characterized for the presence (n = 104) or absence (n = 49) of gyrA and/or parC topoisomerase mutations, qnrA, qnrB, qnrD, qnrS, aac(6')-Ib-cr, or qepA genes were investigated. All isolates were MIC tested by broth microdilution against ciprofloxacin, levofloxacin, and ofloxacin and by disk diffusion using EUCAST or CLSI methodology. MIC determination correctly categorized all isolates as either wild-type isolates (MIC of ?0.06 mg/liter and absence of resistance genes) or non-wild-type isolates (MIC of >0.06 mg/liter and presence of a resistance gene). Disk diffusion using these antibiotics and nalidixic acid failed to detect some low-level-resistant isolates, whereas the 5-?g pefloxacin disk correctly identified all resistant isolates. However, pefloxacin will not detect isolates having aac(6')-Ib-cr as the only resistance determinant. The pefloxacin disk assay was approved and implemented by EUCAST (in 2014) and CLSI (in 2015). PMID:26292292
Heinemann, Detlev
Motivation Methods Model configuration Results Forecasting Summary & Outlook 1/ 14 Retrieving. 17, 2015 #12;Motivation Methods Model configuration Results Forecasting Summary & Outlook 2/ 14 Motivation Sky Imager based shortest-term solar irradiance forecasts for local solar energy applications
A coarse-mesh nodal diffusion method based on response matrix considerations
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 ...
Diffusion-dispersion method of hardening the surface of austenitic steel
Belyakova, V.I.; Vereshchagina, A.A.; Banas, I.P.
1992-05-01
The basic procedure of enhancing wear resistance is so-called surface hardening - more accurately, the increase in surface hardness due to diffusion processes (carburizing, nitriding, etc.). Nitriding is used to harden austenitic corrosion-resistant (and, consequently, high-chromium) steels, although the latter submit to nitriding with difficulty. The thickness of the hardened layer does not exceed 0.1-0.2 mm. Instead of pure nitriding, which is universally adopted for these steels (at a temperature in the 500-700{degrees}C interval), we used carburizing and carbon nitriding at higher temperatures as compared with conventional nitriding (950-1050{degrees}C) in this study. High-strength layers were obtained with a thickness to 1 mm; subsequent heat treatment made it possible to elevate the hardness to 700 HV. The treatment regime that we propose for corrosion-resistant steels should be used to extend the longevity of components. 3 figs., 1 tab.
Nonlinear variants of the TR/BDF2 method for thermal radiative diffusion
Edwards, Jarrod D.; Morel, Jim E.; Knoll, Dana A.
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.
NASA Astrophysics Data System (ADS)
Tucker, Susan C.
1994-08-01
The Mori-Zwanzig memory function formalism is used to determine the behavior of the solute reactive flux in the energy diffusion regime. We show formally that in the case of slow vibrational energy relaxation the reactive flux can exhibit two plateaus corresponding to two phenomenological rate constants. The second of these plateaus corresponds to the overall solute reaction rate, while the first plateau is a ``false'' plateau. Such a scenario is equated with a Lindemann-type reaction phenomenology corresponding to two different energy relaxation mechanisms. Time scale arguments are used to show that such a scenario exists in an example of a cubic reaction coordinate coupled to a slow Gaussian friction bath. The geminate recombination of I2 in solution provides experimental confirmation that such behavior also occurs in real chemical systems.
Electron microscopy observations of MgB 2 wire prepared by an internal Mg diffusion method
NASA Astrophysics Data System (ADS)
Shimada, Y.; Kubota, Y.; Hata, S.; Ikeda, K.; Nakashima, H.; Matsumoto, A.; Togano, K.; Kumakura, H.
2011-11-01
Microstructure in a high-density MgB 2 wire fabricated by an internal Mg diffusion (IMD) process has been investigated by electron microscopy imaging and analysis at different scales. In the IMD process, a pure Mg rod was used as Mg source, and nanosized SiC powders were mixed with amorphous B powders. In the case of a heat treatment at 640 °C for 1 h carried out after rolling and drawing processes, the wire has two microstructural features that degrade critical current density: uncrystallized zones composed mainly of unreacted B and SiC powders, and cracks partly filled with course Mg 2Si crystals. Those cracks were formed in the uncrystallized zones as well as in crystallized MgB 2 zones. It indicate that the cracks formed by the mechanical milling and drawing remain after the heat treatment.
Davis, Julian L.; Dumont, Elizabeth R.; Strait, David S.; Grosse, Ian R.
2011-01-01
The ability to incorporate detailed geometry into finite element models has allowed researchers to investigate the influence of morphology on performance aspects of skeletal components. This advance has also allowed researchers to explore the effect of different material models, ranging from simple (e.g., isotropic) to complex (e.g., orthotropic), on the response of bone. However, bone's complicated geometry makes it difficult to incorporate complex material models into finite element models of bone. This difficulty is due to variation in the spatial orientation of material properties throughout bone. Our analysis addresses this problem by taking full advantage of a finite element program's ability to solve thermal-structural problems. Using a linear relationship between temperature and modulus, we seeded specific nodes of the finite element model with temperatures. We then used thermal diffusion to propagate the modulus throughout the finite element model. Finally, we solved for the mechanical response of the finite element model to the applied loads and constraints. We found that using the thermal diffusion analogy to control the modulus of bone throughout its structure provides a simple and effective method of spatially varying modulus. Results compare favorably against both experimental data and results from an FE model that incorporated a complex (orthotropic) material model. This method presented will allow researchers the ability to easily incorporate more material property data into their finite element models in an effort to improve the model's accuracy. PMID:21347288
Koumetz, Serge D. Martin, Patrick; Murray, Hugues
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.
Novel grafted agar disks for the covalent immobilization of ?-D-galactosidase.
Wahba, Marwa I; Hassan, Mohamed E
2015-12-01
Novel grafted agar disks were prepared for the covalent immobilization of ?-D-galactosidase (?-gal). The agar disks were activated through reacting with ethylenediamine or different molecular weights of Polyethyleneimine (PEI), followed by glutaraldehyde (GA). The modification of the agar gel and the binding of the enzyme were verified by Fourier Transform Infrared (FTIR) and elemental analysis. Moreover, the agar's activation process was optimized, and the amount of immobilized enzyme increased 3.44 folds, from 38.1 to 131.2 U/g gel, during the course of the optimization process. The immobilization of ?-gal onto the activated agar disks caused its optimum temperature to increase from 45°C to 45-55°C. The optimum pH of the enzyme was also shifted towards the acidic side (3.6-4.6) after its immobilization. Additionally, the Michaelis-Menten constant (Km ) increased for the immobilized ?-gal as compared to its free counterpart whereas the maximum reaction rate (Vmax ) decreased. The immobilized enzyme was also shown to retain 92.99% of its initial activity after being used for 15 consecutive times. PMID:26043937
Effects of shape and size of agar gels on heating uniformity during pulsed microwave treatment.
Soto-Reyes, Nohemí; Temis-Pérez, Ana L; López-Malo, Aurelio; Rojas-Laguna, Roberto; Sosa-Morales, María Elena
2015-05-01
Model gel systems with different shape (sphere, cylinder, and slab) and size (180 and 290 g) were prepared with agar (5%) and sucrose (5%). Dielectric constant (?'), loss factor (?"), thermophysical properties, and temperature distribution of the model system were measured. Each agar model system was immersed and suspended in water, and then, heated in a microwave oven with intermittent heating until the core temperature reached 50 °C. The ?' and ?" of agar gels decreased when frequency increased. The density and thermal conductivity values of the agar gels were 1033 kg/m(3) and 0.55 W/m °C, respectively. The temperature distribution of sphere, cylinder, and slab was different when similar power doses were applied. The slab reached 50 °C in less time (10 min) and showed a more uniform heating than spheres and cylinders in both sizes. Agar model systems of 180 g heated faster than those of 290 g. The coldest point was the center of the model systems in all studied cases. Shape and size are critical food factors that affect the heating uniformity during microwave heating processes. PMID:25827444
Sousa, Ana M M; Gonçalves, Maria P
2015-11-01
Agar films possess several properties adequate for food packaging applications. However, their high cost-production and quality variations caused by physiological and environmental factors affecting wild seaweeds make them less attractive for industries. In this work, native (NA) and alkali-modified (AA) agars obtained from sustainably grown seaweeds (integrated multi-trophic aquaculture) were mixed with locust bean gum (LBG) to make 'knife-coated' films with fixed final concentration (1 wt%) and variable agar/LBG ratios. Agar films were easier to process upon LBG addition (viscosity increase and gelling character decrease of the film-forming solutions observed by dynamic oscillatory and steady shear measurements). The mechanical properties and water resistance were optimal for films with 50 and/or 75% LBG contents and best in the case of NA (cheaper to extract). These findings can help reduce the cost-production of agar packaging films. Moreover, the controlled cultivation of seaweeds can provide continuous and reliable feedstock for transformation industries. PMID:26256341
NASA Astrophysics Data System (ADS)
Mukhurov, N.; Maschenko, A.; Khilo, N.; Ropot, P.
2011-05-01
A highly ordered structure and a relatively simple method of obtaining porous anodic alumina (PAA) have been attracting the attention of researchers to the potentialities of using such material in various fields of science and technology. The PAA- technology is oriented to mass production, does not require the use of expensive modern lithography and evaporation equipment. The technology makes it possible to produce PAA layers in a wide thickness range (0.1 - 800 ?m) and with a spatially ordered system of pores whose diameter and periodicity can be changed within the range from tens to hundreds of nanometers. By filling nanopores with conductive, semiconductive and dielectric materials or their combinations, possibilities arise of making micro-sensors based on various physical, chemical and biological effects. For numerous applications, there is a promising development direction associated with modification of PAA structures with nano-diamonds. To control the modification process and for subsequent use of films in energyabsorbing sensor systems, a real-time measurement is required of their thermal and physical parameters, and, in particular, the coefficient of thermal diffusion (CTD). In this report an optical method for determining CTD is developed which is based on an analysis of the spatialtemporal dynamics of the speckle field. The proposed method for measuring the coefficient of thermal diffusion is based on the measurement of an average speed of the speckle-field movement along the specimen surface. Due to statistical nature of speckles, their movement must be also described statistically. Our approach consists in the use of correlation functions describing the degree of change in a speckle-image of some element of the surface in the process of heating or cooling. The proposed method is fully optical, fast, non-invasive and can be customized for specific applications. Optical measurement of CTD has been carried out for PAA structures both modified and not modified with nano-diamonds. High resolution allows one to measure spatial inhomogeneities of thermophysical properties of PAA- films.
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
2015-06-15
Accurate knowledge of O{sup 6}-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. 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. 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). 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.
Rivadeneira, Josefina; Di Virgilio, Ana Laura; Audisio, M Carina; Boccaccini, Aldo R; Gorustovich, Alejandro A
2015-02-01
The aim of this work was to evaluate the perfomance of agar-gelatin (AG) composites and AG-containing 45S5 bioactive glass (BG) microparticles (AGBG) in relation to their water uptake capacity, sustained release of a drug over time, and antibacterial effects. The composites were fabricated by the gel-casting method. To impart the local drug release capacity, vancomycin hydrochloride (VC) was loaded in the composites in concentrations of 0.5 and 1?mg?ml(-1). VC release was assessed in distilled water at 37?°C up to 72?h and quantified spectrophotometrically. The antibacterial activity of composites was evaluated by the inhibition zone test and the plate count method. The experiments were performed in vitro up to 48?h on three staphylococcus strains: Staphylococcus aureus ATCC29213, S. aureus ATCC6538 and Staphylococcus epidermidis ATCC12228. The results showed that the addition of BG to AG composites did not affect the degree of water uptake. The release of VC was significantly affected by the presence of BG. VC release was higher from AGBGVC films than from AGVC ones over prolonged incubation times. Bacterial inhibition zones were found around the composites. The halos were larger when the cells were put in contact with AGVC composites than when they were put in contact with AGBGVC ones. Nevertheless, the viable count method demonstrated that the composites inhibited Staphylococcus cell growth with no statistical differences. In conclusion, the addition of BG did not reflect an improvement in the parameters studied. On the other hand, composites loaded with VC would have a role in prophylaxis against bacterial infection. PMID:25586240
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.
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.
A Monte Carlo Synthetic-Acceleration Method for Solving the Thermal Radiation Diffusion Equation
Evans, Thomas M; Mosher, Scott W; Slattery, Stuart
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.
NASA Astrophysics Data System (ADS)
Reaney, S. M.
2010-12-01
The processes related to diffuse pollution can be understood within a 'source -> mobilisation -> pathway -> impact' framework. Recently our ability to monitor the impact section of this framework has significantly increased. This has been achieved through the measurement of flow and water quality (e.g. Nitrogen and Phosphorus) on a continuous 10 minute basis. However, our ability to observe and understand the 'source', 'mobilisation' and 'pathway' sections has not progressed at the same rate. This lack of information of the source term is due to the larger spatial areas involved and the difficulty in performing repeat surveys. Within an agricultural catchment, there are two key, temporally dynamic factors that affect the diffuse pollution export [source-mobilisation-pathway]: 1. vegetation cover and 2. agricultural management. These factors influence the amount of bare soil, vulnerable to erosion (source) and the creation of flow pathways, for example, due to tractor wheelings (tram lines). Information on these factors could be acquired through the use of satellite remote sensing or light aircraft based aerial photography. However, to acquire images on a fine temporal scale (monthly) there are significant cost and practical barriers (e.g. cloud cover). A potential solution to the problem could be the use of small semi- autonomous helicopters (UAV) and is the approach that has been investigated in this research. The UAV helicopter that has been used in this research is a Microdrones MD4-200 and is capable of autonomously flying a pre-programmed route and acquiring images at set locations at heights of up to 120 metres. The use of the pre-programmed routes enables the acquisition of repeat images at the same locations. These images contain information on the vegetation cover that can be extracted with the use of standard image processing techniques. However, the images also contain a large amount of implicit information that may help to explain water quality trends. For example, information on changes in the direction of plough lines and the timing of canopy closure will give extra insight into the export of nutrients from the landscape. The extraction of the amount of vegetation cover from the images has been done through the use of a custom web based image processing service. Basing the analysis in a cloud computing framework enables greater collaboration within the project consortium and the effective dissemination of images and results to stakeholders. This presentation will discuss the results of the first four months of the UAV helicopter images and how the information has been extracted from the images. This work is part of the Defra Demonstration Test Catchments project and the NERC Pilot Virtual Observatory project.
NASA Astrophysics Data System (ADS)
Shishkin, G. I.; Shishkina, L. P.
2010-12-01
For the one-dimensional singularly perturbed parabolic reaction-diffusion equation with a perturbation parameter ?, where ? ? (0, 1], the grid approximation of the Dirichlet problem on a rectangular domain in the ( x, t)-plane is examined. For small ?, a parabolic boundary layer emerges in a neighborhood of the lateral part of the boundary of this domain. A new approach to the construction of ?-uniformly converging difference schemes of higher accuracy is developed for initial boundary value problems. The asymptotic construction technique is used to design the base decomposition scheme within which the regular and singular components of the grid solution are solutions to grid subproblems defined on uniform grids. The base scheme converges ?-uniformly in the maximum norm at the rate of O( N -2ln2 N + N {0/-1}), where N + 1 and N 0 + 1 are the numbers of nodes in the space and time meshes, respectively. An application of the Richardson extrapolation technique to the base scheme yields a higher order scheme called the Richardson decomposition scheme. This higher order scheme converges?-uniformly at the rate of O( N -4ln4 N + N {0/-2}). For fixed values of the parameter, the convergence rate is O( N -4 + N {0/-2}).
A new, coupled transport-diffusion method for radiative transfer calculations
Wollaber, A. B.; Warsa, J. S.
2013-07-01
We derive and present a new frequency- and angle-integrated low-order system of equations designed to enhance the accuracy of a coupled, high-order (transport) solution of the thermal radiative transfer equations. In particular, our new low-order system is designed to use intensity-weighted opacities and anisotropic diffusion coefficients generated by a solution of the Implicit Monte Carlo (IMC) equations in order to predict the spatial dependence of the material temperature and radiation energies in the ensuing time cycle. The predicted temperature solution can then be exploited to generate appropriately time-centered opacities, specific heats, and Planck emission spectra for the upcoming IMC solution. Additionally, the relatively inexpensive solution of the low-order system can be iteratively solved to recommend an adaptive time step size before the IMC solution is computed. A test implementation has been implemented using existing software available from the Jayenne and Capsaicin projects at Los Alamos National Laboratory. We present initial results from a new driver code that has integrated these stochastic and deterministic software packages. (authors)
Xiong, Jianyin; Huang, Shaodan; Zhang, Yinping
2012-01-01
The diffusion coefficient (Dm) and material/air partition coefficient (K) are two key parameters characterizing the formaldehyde and volatile organic compounds (VOC) sorption behavior in building materials. By virtue of the sorption process in airtight chamber, this paper proposes a novel method to measure the two key parameters, as well as the convective mass transfer coefficient (hm). Compared to traditional methods, it has the following merits: (1) the K, Dm and hm can be simultaneously obtained, thus is convenient to use; (2) it is time-saving, just one sorption process in airtight chamber is required; (3) the determination of hm is based on the formaldehyde and VOC concentration data in the test chamber rather than the generally used empirical correlations obtained from the heat and mass transfer analogy, thus is more accurate and can be regarded as a significant improvement. The present method is applied to measure the three parameters by treating the experimental data in the literature, and good results are obtained, which validates the effectiveness of the method. Our new method also provides a potential pathway for measuring hm of semi-volatile organic compounds (SVOC) by using that of VOC. PMID:23145156
NASA Astrophysics Data System (ADS)
Baum, K.; Hartmann, R.; Bischoff, T.; Himmelreich, F.; Heverhagen, J. T.
2011-07-01
In recent years optical methods became increasingly popular for pre-clinical research and small animal imaging. One main field in biomedical optics research is the diffuse optical tomography (DOT). Many new systems were invented for small animal imaging and breast cancer detection. In combination with the progress in the development of optical markers, optical detectors and near infrared light sources, these new systems have become a formidable source of information. Most of the systems detect the transmitted light which passes through an object and one observes the intensity variations on the detector side. The biggest challenge for all diffuse optical tomography systems is the enormous scattering of light in tissues and tissue-like phantoms resulting in loss of image information. Many systems work with contact gels and optical fibers that have direct contact with the object to neglect the light path between surface and detector. Highly developed mathematic models and reconstruction algorithms based on FEM and Monte Carlo simulations describe the light transport inside tissues and determine differences in absorption and scattering coefficients inside. The proposed method allows a more exact description of the orientation of surface elements from semi-transparent objects towards the detector. Using Polarization Difference Imaging (PDI) in combination with structured light 3D-scanning, it is possible to separate information from the surface from that of the subsurface. Thus, the actual surface shape can be determined. Furthermore, overlaying byproducts caused by inter-reflections and multiple scattering can be filtered from the basic image information with this method. To enhance the image quality, the intensity dispersion between surface and camera is calculated and the creation of 3D-FEM-meshes simplified.
NASA Astrophysics Data System (ADS)
Žalenkien?, S.; Krylova, V.; Baltrusaitis, J.
2015-01-01
Polyamide (PA) incorporated CdSe-CdS films were deposited using sorption-diffusion method. A single precursor - K2SeS2O6 was used as both sulfur and selenium source. In aqueous solution, SeS2O62- diffused into the polymer where it reacted with Cd2+ ions to form cadmium chalcogenide particles. Crystallinity of the composite material was analyzed via XRD and both CdSe and CdS were detected within the material at all deposition conditions of temperature and SeS2O62- - chalcogenization - exposure time. A complex surface speciation was obtained using XPS analysis. Formation of the protonated amide species was observed in combination with the adsorbed SO42- on the surface of the polymer confirming that SeS2O62- and its decomposition products hydrolyzed to form cadmium chalcogenides and H2SO4. A significant red shift in UV-vis spectrum was observed with the increasing chalcogenization time of PA, whereas Cd2+ solution temperature had very little effect on the apparent thickness and the optical properties of the composite materials. SEM surface analysis revealed sub-micron particles deposited on top of the PA-CdSe-CdS composite materials in continuous overlapping films, showing a possible dual crystal growth mechanism.
Gharooni, M.; Hosseini, M.; Mohajerzadeh, S. Taghinejad, M.; Taghinejad, H.; Abdi, Y.
2014-07-28
Morphologically controlled nanostructures have been increasingly important because of their strongly shape dependent physical and chemical properties. Formation of nanoscale silicon based structures that employ high levels of strain, intentional, and unintentional twins or grain boundaries can be dramatically different from the commonly conceived bulk processes. We report, realization of highly crystallographic 3D nanosheets with unique morphology and ultra-thin thickness by a stress-induced oriented-diffusion method, based on plasma processing of metal layer deposited on Si substrate and its post deep reactive ion etching. Annealing in plasma ambient creates rod-like metal alloy precursors which induce stress at its interface with Si substrate due to the mismatch of lattice constants. This stress opens facilitated gateways for orientated-diffusion of metal atoms in ?110? directions and leads to formation of NSs (nanosheets) with [111] crystalline essence. Nanosheets are mainly triangular, hexagonal, or pseudo hexagonal in shape and their thicknesses are well controlled from several to tens of nanometers. The structural and morphological evolution of features were investigated in detail using transmission electron microscope, atomic force microscope, scanning electron microscope and possible mechanism is proposed to explain the formation of the thermodynamically unfavorable morphology of nanosheets. Significant photoemission capability of NSs was also demonstrated by photoluminescence spectroscopy.
NASA Astrophysics Data System (ADS)
Liu, Xiaoyu; Guo, Zhishi; Roache, Nancy F.
2014-06-01
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 estimate parameters Dm and Kma. The SVOCs chosen for study were polychlorinated biphenyl (PCB) congeners, including PCB-52, PCB-66, PCB-101, PCB-110, and PCB-118. The test materials included polypropylene, high density polyethylene, low density polyethylene, polytetrafluoroethylene, polyether ether ketone, glass, stainless steel and concrete. Two 53-L environmental chambers were connected in series, with the relatively stable SVOCs source in the source chamber and the test materials, made as small “buttons”, in the test chamber. Prior to loading the test chamber with the test materials, the test chamber had been dosed with SVOCs for 12 days to “coat” the chamber walls. During the tests, the material buttons were removed from the test chamber at different exposure times to determine the amount of SVOC absorbed by the buttons. SVOC concentrations at the inlet and outlet of the test chamber were also monitored. The data were used to estimate the partition and diffusion coefficients by fitting a sink model to the experimental data. The parameters obtained were employed to predict the accumulation of SVOCs in the sink materials using an existing mass transfer model. The model prediction agreed reasonably well with the experimental data.
Clayden, Jonathan D
2008-01-01
Diffusion magnetic resonance imaging (dmri) is a technique that can be used to examine the diffusion characteristics of water in the living brain. A recently developed application of this technique is tractography, in ...
On the Accuracy of the Finite Volume Element Method for Diffusion ...
Dec 6, 2003 ... SIAM Journal on Numerical Analysis is currently published by Society ... control volume ?nite element method but tailored to composite grid applications. ..... Practical computation would normally use some numerical integra-.
Leung, Jacob C K; Taylor-Kamall, Rhodri W; Hilliker, Arthur J; Rezai, Pouya
2015-05-01
Drosophila melanogaster (fruit fly) is a model organism and its behaviours including oviposition (egg-laying) on agar substrates have been widely used for assessment of a variety of biological processes in flies. Physical and chemical properties of the substrate are the dominant factors affecting Drosophila's oviposition, but they have not been investigated precisely and parametrically with the existing manual approaches. As a result, many behavioral questions about Drosophila oviposition, such as the combined effects of the aforementioned substrate properties (e.g., exposure area, sugar content, and stiffness) on oviposition and viability, and their threshold values, are yet to be answered. In this paper, we have devised a simple, easily implementable, and novel methodology that allows for modification of physical and chemical composition of agar substrates in order to quantitatively study survival and oviposition of adult fruit flies in an accurate and repeatable manner. Agar substrates have been modified by surface patterning using single and hexagonally arrayed through-hole polydimethylsiloxane (PDMS) membranes with various diameters and interspacing, as well as by substrate stiffness and sugar content modification via alteration of chemical components. While pure PDMS substrates showed a significant lethal effect on flies, a 0.5?mm diameter through-hole access to agar was found to abruptly increase the survival of adult flies to more than 93%. Flies avoided ovipositing on pure PDMS and on top of substrates with 0.5?mm diameter agar exposure areas. At a hole diameter of 2?mm (i.e., 0.25% exposure area) or larger, eggs were observed to be laid predominately inside the through-holes and along the edges of the PDMS-agar interface, showing a trending increase in site selection with 4?mm (i.e., 1% exposure area threshold) demonstrating natural oviposition rates similar to pure agar. The surface-modified agar-PDMS hybrid devices and the threshold values reported for the substrate physical and chemical conditions affecting oviposition are novel; therefore, we advocate their use for future in-depth studies of oviposition behaviour in Drosophila melanogaster with accuracy and repeatability. The technique is also useful for development of novel assays for learning and decision-making studies as well as miniaturized devices for self-assembly of eggs and embryonic developmental investigations. PMID:26180569
Grilli, Anthony; Sutton, Scott
2015-01-01
This article provides the results of a study evaluating the sampling efficiency of a flat paddle sampling device against a round surface sampling device in controlled studies. Each device is supplied with identical microbial-growth media, and laboratory studies document equivalent performance of the media in the devices. Both devices perform sampling by the same process (agar transfer of microorganisms from the facility surface to the agar surface), and the performance of the two devices was shown to be equivalent in laboratory studies. Either the commonly used flat paddle sampler or the round contact plate is suitable for surface monitoring in the compounding pharmacy. PMID:25902625
NASA Technical Reports Server (NTRS)
Wang, Xiao-Yen; Chow, Chuen-Yen; Chang, Sin-Chung
1995-01-01
The existing 2-D alpha-mu scheme and alpha-epsilon scheme based on the method of space-time conservation element and solution element, which were constructed for solving the linear 2-D unsteady advection-diffusion equation and unsteady advection equation, respectively, are tested. Also, the alpha-epsilon scheme is modified to become the V-E scheme for solving the nonlinear 2-D inviscid Burgers equation. Numerical solutions of six test problems are presented in comparison with their exact solutions or numerical solutions obtained by traditional finite-difference or finite-element methods. It is demonstrated that the 2-D alpha-mu, alpha-epsilon, and nu-epsilon schemes can be used to obtain numerical results which are more accurate than those based on some of the traditional methods but without using any artificial tuning in the computation. Similar to the previous 1-D test problems, the high accuracy and simplicity features of the space-time conservation element and solution element method have been revealed again in the present 2-D test results.
Diffuse sources of human fecal pollution allow for the direct discharge of waste into receiving waters with minimal or no treatment. Traditional culture-based methods are commonly used to characterize fecal pollution in ambient waters, however these methods do not discern between...
NASA Astrophysics Data System (ADS)
Jeon, Dong Hyup; Kim, Hansang
2015-10-01
The effect of the compression ratio on the dynamic behavior of liquid water transport in a gas diffusion layer (GDL) is studied both experimentally and numerically. We experimentally study the emergence and growth of liquid droplets in a channel at various compression ratios by adopting a direct visualization device. The results of the experiment show that water breakthrough occurs at the channel for a low compression ratio, whereas it is observed at the channel/rib interface for a high compression ratio. To determine the mechanism of water transport in the GDL, a multiphase lattice Boltzmann method (LBM) is developed for a simplified porous structure of the GDL. The observation of lattice Boltzmann (LB) simulation shows that the compression ratio significantly affects the water transport in the GDL. The results indicate that the lower compression ratio reduces the water saturation in the GDL. The simulation and experimental result are similar.
Mason, Harris E.; Walsh, Stuart D. C.; DuFrane, Wyatt L.; Carroll, Susan A.
2014-06-17
The development of accurate, predictive models for use in determining wellbore integrity requires detailed information about the chemical and mechanical changes occurring in hardened Portland cements. X-ray computed tomography (XRCT) provides a method that can nondestructively probe these changes in three dimensions. Here, we describe a method for extracting subvoxel mineralogical and chemical information from synchrotron XRCT images by combining advanced image segmentation with geochemical models of cement alteration. The method relies on determining “effective linear activity coefficients” (ELAC) for the white light source to generate calibration curves that relate the image grayscales to material composition. The resulting data set supports the modeling of cement alteration by CO_{2}-rich brine with discrete increases in calcium concentration at reaction boundaries. The results of these XRCT analyses can be used to further improve coupled geochemical and mechanical models of cement alteration in the wellbore environment.
Frank, Damian; Eyres, Graham T; Piyasiri, Udayasika; Cochet-Broch, Maeva; Delahunty, Conor M; Lundin, Leif; Appelqvist, Ingrid M
2015-10-21
The density and composition of a food matrix affect the rates of oral breakdown and in-mouth flavor release as well as the overall sensory experience. Agar gels of increasing concentration (1.0, 1.7, 2.9, and 5% agarose) with and without added fat (0, 2, 5, and 10%) were spiked with seven aroma volatiles. Differences in oral processing and sensory perception were systematically measured by a trained panel using a discrete interval time intensity method. Volatile release was measured in vivo and in vitro by proton transfer reaction mass spectrometry. Greater oral processing was required as agar gel strength increased, and the intensity of flavor-related sensory attributes decreased. Volatile release was inversely related to gel strength, showing that physicochemical phenomena were the main mechanisms underlying the perceived sensory changes. Fat addition reduced the amount of oral processing and had differential effects on release, depending on the fat solubility or lipophilicity of the volatiles. PMID:26435196
Anandh, K R; Sujatha, C M; Ramakrishnan, S
2015-01-01
Alzheimer?s Disease (AD) is a common form of dementia that affects gray and white matter structures of brain. Manifestation of AD leads to cognitive deficits such as memory impairment problems, ability to think and difficulties in performing day to day activities. Although the etiology of this disease is unclear, imaging biomarkers are highly useful in the early diagnosis of AD. Magnetic resonance imaging is an indispensible non-invasive imaging modality that reflects both the geometry and pathology of the brain. Corpus Callosum (CC) is the largest white matter structure as well as the main inter-hemispheric fiber connection that undergoes regional alterations due to AD. Therefore, segmentation and feature extraction are predominantly essential to characterize the CC atrophy. In this work, an attempt has been made to segment CC using edge based level set method. Prior to segmentation, the images are pre-processed using Total Variation (TV) based diffusion filtering to enhance the edge information. Shape based geometric features are extracted from the segmented CC images to analyze the CC atrophy. Results show that the edge based level set method is able to segment CC in both the normal and AD images. TV based diffusion filtering has performed uniform region specific smoothing thereby preserving the texture and small scale details of the image. Consequently, the edge map of CC in both the normal and AD are apparently sharp and distinct with continuous boundaries. This facilitates the final contour to correctly segment CC from the nearby structures. The extracted geometric features such as area, perimeter and minor axis are found to have the percentage difference of 5.97%, 22.22% and 9.52% respectively in the demarcation of AD subjects. As callosal atrophy is significant in the diagnosis of AD, this study seems to be clinically useful. PMID:25996739
Shor, Leslie McCabe
were investigated to enhance understanding of plant growth conditions in microgravity. We used a single of the lattice Boltzmann method for rapid and cost-effective evaluation of alternative plant growth media designs gravity conditions play an important role in advanced life support systems for NASA's long-duration space
NASA Astrophysics Data System (ADS)
Bouklas, Nikolaos; Landis, Chad M.; Huang, Rui
2015-06-01
Hydrogels are capable of coupled mass transport and large deformation in response to external stimuli. In this paper, a nonlinear, transient finite element formulation is presented for initial boundary value problems associated with swelling and deformation of hydrogels, based on a nonlinear continuum theory that is consistent with classical theory of linear poroelasticity. A mixed finite element method is implemented with implicit time integration. The incompressible or nearly incompressible behavior at the initial stage imposes a constraint to the finite element discretization in order to satisfy the Ladyzhenskaya-Babuska-Brezzi (LBB) condition for stability of the mixed method, similar to linear poroelasticity as well as incompressible elasticity and Stokes flow; failure to choose an appropriate discretization would result in locking and numerical oscillations in transient analysis. To demonstrate the numerical method, two problems of practical interests are considered: constrained swelling and flat-punch indentation of hydrogel layers. Constrained swelling may lead to instantaneous surface instability for a soft hydrogel in a good solvent, which can be regulated by assuming a stiff surface layer. Indentation relaxation of hydrogels is simulated beyond the linear regime under plane strain conditions, in comparison with two elastic limits for the instantaneous and equilibrium states. The effects of Poisson's ratio and loading rate are discussed. It is concluded that the present finite element method is robust and can be extended to study other transient phenomena in hydrogels.
NASA Astrophysics Data System (ADS)
Efimov, S. V.; Khodov, I. A.; Ratkova, E. L.; Kiselev, M. G.; Berger, S.; Klochkov, V. V.
2016-01-01
An intriguing property of the multistep magnetization transfer, so-called spin diffusion, is that it can affect the results of NMR-based analysis of conformer distribution of small molecules in solution. Therefore, the contribution of spin diffusion should be subtracted in order to obtain accurate data on molecular conformations and their distributions. Several methods have been developed for this purpose, but many of them have a lack of versatility. These methods were critically analysed, and two approaches to eliminate spin diffusion were tested during the study of felodipine as the drug molecule of small size. QUIET-NOESY was found to be a powerful technique to solve this problem. The second method, combined analysis of two sets of spectra, NOESY and T-ROESY, was tested and proved to be the most correct way of obtaining exact internuclear distances in a flexible molecule in solution.
DIMENSION REDUCTION NUMERICAL CLOSURE METHOD FOR ADVECTION-DIFFUSION-REACTION SYSTEMS
Tartakovsky, Alexandre M.; Scheibe, Timothy D.
2011-11-30
Many natural physical processes exhibit a multiscale behavior, that is the same processes allow different mathematical description on different scales. The microscale description is usually based on fundamental conservation laws that form a closed system of ordinary differential equations (ODEs) or partial differential equations (PDEs) but the numerical discretization of these equations may produce a system of ODEs with an enormous number of unknowns. Furthermore, a time integration of the microscale equations usually requires time steps that are smaller than the observation time by many orders of magnitude. A direct solution of these ODEs can be extremely expensive. This necessitates development of advanced algorithms for model (or dimension) reduction. Often, we are only interested in the average behavior of the system rather than the exact solution of the ODEs. Here we developed a novel dimension reduction method that gives an approximate solution of the ODEs and gives an accurate prediction of the average behavior. The method relies on a computational closure of averaged evolution balance equations. The computational closure is achieved via short bursts of microscale simulation. The dimension reduction model was used to simulate flow and transport with mixing controlled reactions and mineral precipitation. A pore-scale model was used as a microscale model. A good agreement between microscale simulations and the accelerated microscale simulations confirms the accuracy and computational efficiency of the dimension reduction model. The method significant accelerates microscale simulations, while providing accurate approximation of the solution and accurate prediction of the average behavior of the system.
EFFECT OF IMPACT STRESS ON MICROBIAL RECOVERY ON AN AGAR SURFACE
Microbial stress due to the impaction of microorganisms onto an agar collection surface was studied experimentally. he relative recovery rates of aerosolized Pseudomonas fluorescens and Micrococcus luteus were determined as a function of the impaction velocity by using a moving a...
Sousa, Ana M M; Morais, Simone; Abreu, Maria H; Pereira, Rui; Sousa-Pinto, Isabel; Cabrita, Eurico J; Delerue-Matos, Cristina; Gonçalves, Maria Pilar
2012-05-16
Native agars from Gracilaria vermiculophylla produced in sustainable aquaculture systems (IMTA) were extracted under conventional (TWE) and microwave (MAE) heating. The optimal extracts from both processes were compared in terms of their properties. The agars' structure was further investigated through Fourier transform infrared and NMR spectroscopy. Both samples showed a regular structure with an identical backbone, ?-d-galactose (G) and 3,6-anhydro-?-l-galactose (LA) units; a considerable degree of methylation was found at C6 of the G units and, to a lesser extent, at C2 of the LA residues. The methylation degree in the G units was lower for MAE(opt) agar; the sulfate content was also reduced. MAE led to higher agar recoveries with drastic extraction time and solvent volume reductions. Two times lower values of [?] and M(v) obtained for the MAE(opt) sample indicate substantial depolymerization of the polysaccharide backbone; this was reflected in its gelling properties; yet it was clearly appropriate for commercial application in soft-texture food products. PMID:22540146
THE MICROGARDENING COOKBOOK, DIRECTIONS FOR PREPARING DISHES AND TUBES OF STERILE NUTRIENT AGAR.
ERIC Educational Resources Information Center
CHANDLER, MARION N.
THIS BOOKLET WAS PREPARED FOR TEACHER USE IN ASSOCIATION WITH THE ELEMENTARY SCIENCE STUDY UNIT "MICROGARDENING." IT CONTAINS DIRECTIONS FOR PREPARING CULTURE DISHES AND TUBES OF NUTRIENT STERILE AGAR FOR FUNGAL AND/OR BACTERIAL GROWTH. IT INCLUDES (1) LISTS OF NEEDED SUPPLIES AND EQUIPMENT, (2) DIRECTIONS FOR THE PREPARATION AND STERILIZATION OF…
Irvine, Cynthia E.
to the management of system performance [17]. A Quality of Protection parameter, which manages the levelIPsec Modulation for Quality of Security Service Evdoxia Spyropoulou Chris Agar Timothy Levin and how security can be treated as a dimension of Quality of Service in distributed systems is described
Alternative plasticizers for the production of thermo-compressed agar films
Technology Transfer Automated Retrieval System (TEKTRAN)
One percent agar (% wt) was dissolved in the deep eutectic solvent (DES), (2-hydroxyethyl) trimethylammonium chloride/urea at a 1:2 molar ratio, and successfully Electrospun into nanofibers. An existing electrospinning set-up, operated at 50 deg C, was adapted for use with an ethanol bath to collect...
ERIC Educational Resources Information Center
Norris, Lindy; Tsedendamba, Nara
2015-01-01
This paper reports part of a broader qualitative case study of Asian students "translation" (Agar, 2006) to study in an Australian university. The paper is concerned with the experiences of eight participants and their involvement in a training programme in the use of language learning strategies (LLS) to support their engagement with…
Hyperspectral image reconstruction using RGB color for foodborne pathogen detection on agar plates
Technology Transfer Automated Retrieval System (TEKTRAN)
This paper reports the latest development of a color vision technique for detecting colonies of foodborne pathogens grown on agar plates with a hyperspectral image classification model that was developed using full hyperspectral data. The hyperspectral classification model depended on reflectance sp...
A Simple Experiment for Visualizing Diffusion
ERIC Educational Resources Information Center
Helseth, L. E.
2011-01-01
We propose a simple and fascinating experiment for studying diffusion in gels using a pH-sensitive dye. By doping agar with methyl red, we obtain a gel which rapidly reacts to changes in pH by changing its absorption spectrum. The pH gradients can be followed using a digital camera, and we demonstrate here that the pH-sensitive colour changes can…
Farzad Rahnema
2003-09-30
Most modern nodal methods in use by the reactor vendors and utilities are based on the generalized equivalence theory (GET) that uses homogenized cross sections and flux discontinuity factors. These homogenized parameters, referred to as infinite medium parameters, are precomputed by performing single bundle fine-mesh calculations with zero current boundary conditions. It is known that for configurations in which the node-to-node leakage (e.g., surface current-to-flux ratio) is large the use of the infinite medium parameters could lead to large errors in the nodal solution. This would be the case for highly heterogeneous core configurations, typical of modern reactor core designs.
Gong, Chunye; Bao, Weimin; Tang, Guojian; Jiang, Yuewen; Liu, Jie
2014-01-01
It is very time consuming to solve fractional differential equations. The computational complexity of two-dimensional fractional differential equation (2D-TFDE) with iterative implicit finite difference method is O(M(x)M(y)N(2)). In this paper, we present a parallel algorithm for 2D-TFDE and give an in-depth discussion about this algorithm. A task distribution model and data layout with virtual boundary are designed for this parallel algorithm. The experimental results show that the parallel algorithm compares well with the exact solution. The parallel algorithm on single Intel Xeon X5540 CPU runs 3.16-4.17 times faster than the serial algorithm on single CPU core. The parallel efficiency of 81 processes is up to 88.24% compared with 9 processes on a distributed memory cluster system. We do think that the parallel computing technology will become a very basic method for the computational intensive fractional applications in the near future. PMID:24744680
Nazaruk, Ewa; Miszta, Przemys?aw; Filipek, S?awomir; Górecka, Ewa; Landau, Ehud M; Bilewicz, Renata
2015-11-24
Lyotropic liquid crystalline systems are excellent carriers for drugs due to their biocompatibility, stability in aqueous environment, and well-defined structure that allow them to host significantly larger amounts of drugs than carriers such as liposomes or gold nanoparticles. Incorporating the drug within the mesophase gel, or the cubosome/hexosome nanoparticles, decreased its toxic effects toward healthy cells, while appropriate mechanisms can stimulate the release of the drug from the carrier when it approaches the cancerous cell environment. Electrochemical methods-chronocoulometry and voltammetry at micro and normal size electrodes-are used for the first time to simultaneously determine the diffusion coefficients and effective concentrations of a toxic anticancer drug, doxorubicin, in the channels of three liquid-crystalline lipidic cubic phases. This approach was instrumental in demonstrating that the drug diffusion and kinetics of release from the mesophases depend on the aqueous channel size, which in turn is related to the identity and structure of the amphiphilic molecules used for the formation of the mesophase. Structural parameters of the cubic phases with the incorporated drug were characterized by small-angle X-ray scattering (SAXS), and molecular dynamics simulations were applied in order to describe the differences in the distribution of doxorubicin in the cubic phase matrix at acidic and neutral pH. The release of the drug from the phase was retarded at physiological pH, while at lower pH, corresponding to the cancer environment, it was accelerated, provided that suitable amphiphilic molecules were employed for the construction of the liquid crystal drug delivery system. PMID:26513537
Glinz, Dominik; Silué, Kigbafori D.; Knopp, Stefanie; Lohourignon, Laurent K.; Yao, Kouassi P.; Steinmann, Peter; Rinaldi, Laura; Cringoli, Giuseppe; N'Goran, Eliézer K.; Utzinger, Jürg
2010-01-01
Background Infections with schistosomes and soil-transmitted helminths exert a considerable yet underappreciated economic and public health burden on afflicted populations. Accurate diagnosis is crucial for patient management, drug efficacy evaluations, and monitoring of large-scale community-based control programs. Methods/Principal Findings The diagnostic accuracy of four copromicroscopic techniques (i.e., Kato-Katz, Koga agar plate, ether-concentration, and FLOTAC) for the detection of Schistosoma mansoni and soil-transmitted helminth eggs was compared using stool samples from 112 school children in Côte d'Ivoire. Combined results of all four methods served as a diagnostic ‘gold’ standard and revealed prevalences of S. mansoni, hookworm, Trichuris trichiura, Strongyloides stercoralis and Ascaris lumbricoides of 83.0%, 55.4%, 40.2%, 33.9% and 28.6%, respectively. A single FLOTAC from stool samples preserved in sodium acetate-acetic acid-formalin for 30 or 83 days showed a higher sensitivity for S. mansoni diagnosis (91.4%) than the ether-concentration method on stool samples preserved for 40 days (85.0%) or triplicate Kato-Katz using fresh stool samples (77.4%). Moreover, a single FLOTAC detected hookworm, A. lumbricoides and T. trichiura infections with a higher sensitivity than any of the other methods used, but resulted in lower egg counts. The Koga agar plate method was the most accurate diagnostic assay for S. stercoralis. Conclusion/Significance We have shown that the FLOTAC method holds promise for the diagnosis of S. mansoni. Moreover, our study confirms that FLOTAC is a sensitive technique for detection of common soil-transmitted helminths. For the diagnosis of S. stercoralis, the Koga agar plate method remains the method of choice. PMID:20651931
A two-grid method with Richardson extrapolation for a semilinear convection-diffusion problem
NASA Astrophysics Data System (ADS)
Tikhovskaya, S. V.; Zadorin, A. I.
2015-10-01
A boundary value problem for a second-order semilinear singularly perturbed ordinary differential equation is considered. We use Newton and Picard iterations for a linearization. To solve the problem at each iteration we apply the difference scheme with the property of uniform with respect to the singular perturbation parameter convergence. A modified Samarskii and central difference schemes on Shishkin mesh are considered. It is known that these schemes are almost second order accuracy uniformly with respect to the singular perturbation parameter. To decrease the required number of arithmetical operations for resolving the difference scheme, a two-grid method is proposed. To increase the accuracy of difference scheme, we investigate the possibility to apply Richardson extrapolation using known solutions of the difference scheme on both meshes. The comparison of modified Samarskii and central difference schemes is carried out. The results of some numerical experiments are discussed.
NASA Astrophysics Data System (ADS)
Pop, Mihaela; Ghugre, Nilesh R.; Ramanan, Venkat; Morikawa, Lily; Stanisz, Greg; Dick, Alexander J.; Wright, Graham A.
2013-08-01
Many have speculated that MRI signal characteristics can be used to identify regions of heterogeneous infarct associated with an arrhythmogenic substrate; however, direct evidence of this relationship is limited. The aim of this study was to demonstrate the remodelling characteristics of fibrosis by means of histology and high-resolution MR imaging. For this purpose, we performed whole-mount histology in heart samples (n = 9) collected from five swine at six weeks post-infarction and compared the extent of fibrosis in the infarcted areas delineated in these histological images with that obtained ex vivo by MRI using late gadolinium-enhancement (LGE) and diffusion-weighted imaging (DWI) methods. All MR images were obtained at a submillimetre resolution (i.e., voxel size of 0.6×0.6×1.2 mm3). Specifically, in the histology images, we differentiated moderate fibrosis (consisting of a mixture of viable and non-viable myocytes, known as border zone, BZ) from severe fibrosis (i.e., the dense scar). Correspondingly, tissue heterogeneities in the MR images were categorized by a Gaussian mixture model into healthy, BZ and scar. Our results showed that (a) both MRI methods were capable of qualitatively distinguishing sharp edges between dense scar and healthy tissue from regions of heterogeneous BZ; (b) the BZ and dense scar areas had intermediate-to-high increased values of signal intensity in the LGE images and of apparent diffusion coefficient in the DWI, respectively. In addition, as demonstrated by the Picrosirius Red and immunohistochemistry stains, the viable bundles in the BZ were clearly separated by thin collagen strands and had reduced expression of Cx43, whereas the core scar was composed of dense fibrosis. A quantitative analysis demonstrated that the comparison between BZ/scar extent in LGE and DWI to the corresponding areas identified in histology yielded very good correlations (i.e., for the scar identified by LGE, R2 was 0.96 compared to R2 = 0.93 for the scar identified in ADC maps, whereas the BZ had R2 = 0.95 for the correlation between LGE and histology compared to R2 = 0.91 obtained for ADC). This novel study represents an intermediate step in translating such research to the in vivo stages, as well as in establishing the best and most accurate MR method to help identify arrhythmia substrate in patients with structural heart disease.
Chauhan, Ashvini; Williams, Henry N
2008-05-01
Characterization of Bdellovibrio- and like organisms (BALOs) from environmental samples involves growing them in the presence of Gram-negative prey bacteria and isolation of BALO plaques. This labor-intensive enrichment and isolation procedure may impede the detection and phylogenetic characterization of uncultivable BALOs. In this article, we describe a simple slide biofilm assay to improve detection and characterization of BALO microbiota. Agar spiked with biostimulants such as yeast extract (YE), casamino acids (CA), or concentrated cells of Vibrio parahaemolyticus P5 (most widely used prey bacteria for isolation of halophilic BALOs) was plated onto buffed glass slides and exposed to water samples collected from Apalachicola Bay, Florida. After incubating for a week, diversity of the biofilm bacterial community was studied by culture-dependent and culture-independent molecular methods. The results revealed that most probable numbers (MPNs) of BALOs and total culturable bacteria recovered from YE agar slide were significantly higher than the numbers on CA- or P5-spiked agar slides. Polymerase chain reaction-restriction fragment length polymorphism followed by 16S rDNA sequencing of clones from different biostimulants resulted in identification of a plethora of Gram-negative bacteria predominantly from the alpha, gamma, delta-proteobacteria, and the Cytophaga-Flavobacterium-Bacteroides group. Corresponding to the higher biomass on the YE agar slide, the BALO clone library from YE was most diverse, consisting of Bacteriovorax spp. and a novel clade representing Peredibacter spp. Microbiota from all three biostimulated biofilms were exclusively Gram-negative, and each bacterial guild represented potential prey for BALOs. We propose the use of this simple yet novel slide biofilm assay to study oligotrophic aquatic bacterial diversity which could also potentially be utilized to isolate marine bacteria with novel traits. PMID:17968612
NASA Astrophysics Data System (ADS)
da Silva, Aline Santana; Fernandes, Flávio Cesar Bedatty; Tognolli, João Olímpio; Pezza, Leonardo; Pezza, Helena Redigolo
2011-09-01
This article describes a simple, inexpensive, and environmentally friendly method for the monitoring of glyphosate using diffuse reflectance spectroscopy. The proposed method is based on reflectance measurements of the colored compound produced from the spot test reaction between glyphosate and p-dimethylaminocinnamaldehyde ( p-DAC) in acid medium, using a filter paper as solid support. Experimental designs were used to optimize the analytical conditions. All reflectance measurements were carried out at 495 nm. Under optimal conditions, the glyphosate calibration graphs obtained by plotting the optical density of the reflectance signal (A R) against the concentration were linear in the range 50-500 ?g mL -1, with a correlation coefficient of 0.9987. The limit of detection (LOD) for glyphosate was 7.28 ?g mL -1. The technique was successfully applied to the direct determination of glyphosate in commercial formulations, as well as in water samples (river water, pure water and mineral drinking water) after a previous clean-up or pre-concentration step. Recoveries were in the ranges 93.2-102.6% and 91.3-102.9% for the commercial formulations and water samples, respectively.
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. Productivity Change in U.S. Catch Shares Fisheries. U.S. Dept. of Commer., NOAA Technical Memorandum NMFS
Daly, C C; Hoffman, I; Hobbs, M; Maida, M; Zimba, D; Davis, R; Mughogho, G; Cohen, M S
1997-01-01
Susceptibility of Neisseria gonorrhoeae to gentamicin, the primary treatment for gonorrhea in Malawi since 1993, was determined by using agar dilution MICs, E-test MICs, disc diffusion, and clinical cure rate. Agar dilution MICs were slightly higher in 1996 than in 1993 isolates, with a concomitant drop in the clinical cure rate. E-test MICs were substantially lower than agar dilution determinations, with only 77.4% within 1 log2 concentration. PMID:9350775
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 grids. Theses studies have...
Fritz, B G; Walker, D K; Goveia, D E; Parker, A E; Goeres, D M
2015-03-01
This paper compares Petrifilm™ aerobic count (AC) plates to drop plating on R2A agar plates as an alternative method for biofilm bacteria enumeration after application of a disinfectant. A Pseudomonas aeruginosa biofilm was grown in a Centers for Disease Control and Prevention biofilm reactor (ASTM E2562) and treated with 123 ppm sodium hypochlorite (as free chlorine) according to the Single Tube Method (ASTM E2871). Aliquots from the same dilution tubes were plated on Petrifilm™ AC plates and drop plated on R2A agar plates. The Petrifilm™ AC and R2A plates were incubated for 48 and 24 h, respectively, at 36 ± 1 °C. After nine experimental runs performed by two technicians, the mean difference in biofilm log densities [log biofilm density (LD) = log10(CFU/cm(2))] between the two methods for control coupons, treated coupons, and log reduction (LR) was 0.052 (p = 0.451), -0.102 (p = 0.303), and 0.152 (p = 0.313). Equivalence testing was used to assess equivalence of the two plating methods. The 90 % confidence intervals for the difference in control and treated mean LDs between methods were (-0.065, 0.170) and (-0.270, 0.064), both of which fall within a (-0.5, +0.5) equivalence criterion. The 90 % confidence interval for the mean LR difference (-0.113, 0.420) also falls within this equivalence criterion. Thus, Petrifilm™ AC plates were shown to be statistically equivalent to drop plating on R2A agar for the determination of control LDs, treated LDs, and LR values in an anti-biofilm efficacy test. These are the first published results that establish equivalency to a traditional plate counting technique for biofilms and for a disinfectant assay. PMID:25471267
NASA Astrophysics Data System (ADS)
Artun, Hüseyin; Co?tu, Bayram
2013-02-01
The aim of this study was to explore a group of prospective primary teachers' conceptual understanding of diffusion and osmosis as they implemented a 5E constructivist model and related materials in a science methods course. Fifty prospective primary teachers' ideas were elicited using a pre- and post-test and delayed post-test survey consisting of ten two-tier questions of which an explanatory part was integral. Individual interviews were conducted with six prospective teachers at the end of the implementation of the unit using four questions. Test scores were analyzed quantitatively and qualitatively. Post-instructional interviews were analyzed qualitatively. Statistical analysis using one-way ANOVA of student test scores pointed to statistically significant differences between pre- and post- and delayed post-test ( p < 0.05). A qualitative analysis of the prospective teachers' explanations in the two-tier questions revealed changes in their ideas overtime. Both quantitative and qualitative analyses suggest that the teaching activities promoted students' conceptual understanding. No statistically significant differences were found between post-test and delayed post-test scores, suggesting that the teaching activities based on 5E model enabled students to retain their new conceptual understanding.
Mallory, Joel D; Mandelshtam, Vladimir A
2015-01-01
The Diffusion Monte Carlo (DMC) method is applied to the water monomer, dimer, and hexamer, using q-TIP4P/F, one of the most simple, empirical water models with flexible monomers. The bias in the time step ($\\Delta\\tau$) and population size ($N_w$) is investigated. For the binding energies, the bias in $\\Delta\\tau$ cancels nearly completely, while a noticeable bias in $N_w$ still remains. However, for the isotope shift, (e.g, in the dimer binding energies between (H$_2$O)$_2$ and (D$_2$O)$_2$) the systematic errors in $N_w$ do cancel. Consequently, very accurate results for the latter (within $\\sim 0.01$ kcal/mol) are obtained with relatively moderate numerical effort ($N_w\\sim 10^3$). For the water hexamer and its (D$_2$O)$_6$ isotopomer the DMC results as a function of $N_w$ are examined for the cage and prism isomers. For a given isomer, the issue of the walker population leaking out of the corresponding basin of attraction is addressed by using appropriate geometric constraints. The population size bias f...
Lyon, B.F.
1996-02-01
During the summer of 1995, ultrasonic wall thickness data were collected for 100 steel cylinders containing depleted uranium (DU) hexafluoride located at Paducah Gaseous Diffusion Plant (PGDP) in Paducah, Kentucky. The cylinders were selected for measurement to assess the condition of the more vulnerable portion of the cylinder inventory at PGDP. The purpose of this report is to apply the method used in Lyon to estimate the effects of corrosion for larger unsampled populations as a function of time. The scope of this report is limited and is not intended to represent the final analyses of available data. Future efforts will include continuing analyses of available data to investigate defensible deviations from the conservative assumptions made to date. For each cylinder population considered, two basic types of analyses were conducted: (1) estimates were made of the number of cylinders as a function of time that will have a minimum wall thickness of either 0 mils (1 mil = 0.00 1 in.) or 250 mils and (2) the current minimum wall thickness distributions across cylinders were estimated for each cylinder population considered. Additional analyses were also performed investigating comparisons of the results for F and G yards with the results presented in Lyon (1995).
Ning, Lipeng; Laun, Frederik; Gur, Yaniv; DiBella, Edward V R; Deslauriers-Gauthier, Samuel; Megherbi, Thinhinane; Ghosh, Aurobrata; Zucchelli, Mauro; Menegaz, Gloria; Fick, Rutger; St-Jean, Samuel; Paquette, Michael; Aranda, Ramon; Descoteaux, Maxime; Deriche, Rachid; O'Donnell, Lauren; Rathi, Yogesh
2015-12-01
Diffusion magnetic resonance imaging (dMRI) is the modality of choice for investigating in-vivo white matter connectivity and neural tissue architecture of the brain. The diffusion-weighted signal in dMRI reflects the diffusivity of water molecules in brain tissue and can be utilized to produce image-based biomarkers for clinical research. Due to the constraints on scanning time, a limited number of measurements can be acquired within a clinically feasible scan time. In order to reconstruct the dMRI signal from a discrete set of measurements, a large number of algorithms have been proposed in recent years in conjunction with varying sampling schemes, i.e., with varying b-values and gradient directions. Thus, it is imperative to compare the performance of these reconstruction methods on a single data set to provide appropriate guidelines to neuroscientists on making an informed decision while designing their acquisition protocols. For this purpose, the SPArse Reconstruction Challenge (SPARC) was held along with the workshop on Computational Diffusion MRI (at MICCAI 2014) to validate the performance of multiple reconstruction methods using data acquired from a physical phantom. A total of 16 reconstruction algorithms (9 teams) participated in this community challenge. The goal was to reconstruct single b-value and/or multiple b-value data from a sparse set of measurements. In particular, the aim was to determine an appropriate acquisition protocol (in terms of the number of measurements, b-values) and the analysis method to use for a neuroimaging study. The challenge did not delve on the accuracy of these methods in estimating model specific measures such as fractional anisotropy (FA) or mean diffusivity, but on the accuracy of these methods to fit the data. This paper presents several quantitative results pertaining to each reconstruction algorithm. The conclusions in this paper provide a valuable guideline for choosing a suitable algorithm and the corresponding data-sampling scheme for clinical neuroscience applications. PMID:26606457
Zecchinel, E; Brito, L; Lárez, G
2000-12-01
The yield, gel strength, gelling and melting temperatures of Gracilariopsis tenuifrons agar from Guayacán, Araya Peninsula, Sucre State, Venezuela were determined. Yield values with and without alkali treatment ranged from 23.22 to 39.57% and from 16.29 to 22.42% respectively, while gel strength with alkali treatment fluctuated betwen 699.31 and 1231.69 g/cm2 and without treatment varied from 278.0 to 691.06 g/cm2. Gelling and melting temperatures were in the range reported for other agarophytes. Considering gel strength, the agar quality of G. tenuifrons was higher than in other species and its exploitation in economically feasible. PMID:15266808
Evaluation of Rambach agar for detection of Salmonella subspecies I to VI.
Kühn, H; Wonde, B; Rabsch, W; Reissbrodt, R
1994-01-01
Salmonella strains belonging to subspecies I to VI were investigated for colony color when grown on Rambach agar. Most strains of Salmonella subspecies I, II, IV, and VI behaved as described. All strains of Salmonella subspecies IIIa, IIIb, and V produced beta-D-galactosidase and blue-green colonies which could not be distinguished in color from Escherichia coli and other lactose-fermenting members of the family Enterobacteriaceae. PMID:8135525
Nilsson, Annica M.; Jonsson, Andreas; Jonsson, Jacob C.; Roos, Arne
2011-03-01
For most integrating sphere measurements, the difference in light distribution between a specular reference beam and a diffused sample beam can result in significant errors. The problem becomes especially pronounced in integrating spheres that include a port for reflectance or diffuse transmittance measurements. The port is included in many standard spectrophotometers to facilitate a multipurpose instrument, however, absorption around the port edge can result in a detected signal that is too low. The absorption effect is especially apparent for low-angle scattering samples, because a significant portion of the light is scattered directly onto that edge. In this paper, a method for more accurate transmittance measurements of low-angle light-scattering samples is presented. The method uses a standard integrating sphere spectrophotometer, and the problem with increased absorption around the port edge is addressed by introducing a diffuser between the sample and the integrating sphere during both reference and sample scan. This reduces the discrepancy between the two scans and spreads the scattered light over a greater portion of the sphere wall. The problem with multiple reflections between the sample and diffuser is successfully addressed using a correction factor. The method is tested for two patterned glass samples with low-angle scattering and in both cases the transmittance accuracy is significantly improved.
Ganesh, Panchapakesan; Kim, Jeongnim; Park, Changwon; Yoon, Mina; Reboredo, Fernando A; Kent, Paul R
2014-01-01
Highly accurate diffusion quantum Monte Carlo (QMC) studies of the adsorption and diffusion of atomic lithium in AA-stacked graphite are compared with van der Waals-including density functional theory (DFT) calculations. Predicted QMC lattice constants for pure AA graphite agree with experiment. Pure AA-stacked graphite is shown to challenge many van der Waals methods even when they are accurate for conventional AB graphite. Highest overall DFT accuracy, considering pure AA-stacked graphite as well as lithium binding and diffusion, is obtained by the self-consistent van der Waals functional vdW-DF2, although errors in binding energies remain. Empirical approaches based on point charges such as DFT-D are inaccurate unless the local charge transfer is assessed. The results demonstrate that the lithium carbon system requires a simultaneous highly accurate description of both charge transfer and van der Waals interactions, favoring self-consistent approaches.
Cavitation-enhanced delivery of insulin in agar and porcine models of human skin
NASA Astrophysics Data System (ADS)
Feiszthuber, Helga; Bhatnagar, Sunali; Gyöngy, Miklós; Coussios, Constantin-C.
2015-03-01
Ultrasound-assisted transdermal insulin delivery offers a less painful and less invasive alternative to subcutaneous insulin injections. However, ultrasound-based drug delivery, otherwise known as sonophoresis, is a highly variable phenomenon, in part dependent on cavitation. The aim of the current work is to investigate the role of cavitation in transdermal insulin delivery. Fluorescently stained, soluble Actrapid insulin was placed on the surface of human skin-mimicking materials subjected to 265?kHz, 10% duty cycle focused ultrasound. A confocally and coaxially aligned 5?MHz broadband ultrasound transducer was used to detect cavitation. Two different skin models were used. The first model, 3% agar hydrogel, was insonated with a range of pressures (0.25-1.40?MPa peak rarefactional focal pressure—PRFP), with and without cavitation nuclei embedded within the agar at a concentration of 0.05% w/v. The second, porcine skin was insonated at 1.00 and 1.40?MPa PRFP. In both models, fluorescence measurements were used to determine penetration depth and concentration of delivered insulin. Results show that in agar gel, both insulin penetration depth and concentration only increased significantly in the presence of inertial cavitation, with up to a 40% enhancement. In porcine skin the amount of fluorescent insulin was higher in the epidermis of those samples that were exposed to ultrasound compared to the control samples, but there was no significant increase in penetration distance. The results underline the importance of instigating and monitoring inertial cavitation during transdermal insulin delivery.
Wessig, Martin; Spitzbarth, Martin; Drescher, Malte; Winter, Rainer; Polarz, Sebastian
2015-06-28
Mass transport of molecular compounds through porous solids is a decisive step in numerous, important applications like chromatography or heterogeneous catalysis. It is a multi-scale, hierarchical phenomenon: macrodiffusion (>?m) is influenced, in addition to parameters like grain boundaries and particle packing, by meso-scale (>10 nm, diffusion and macro-scale diffusion are first and foremost determined directly by processes on the molecular scale (<10 nm), which depend on numerous factors like pore-size, interactions of the host with the solid surfaces and with the solvent. Due to the high complexity of the latter and the fact that current analytical techniques enable only limited insights into solvent-filled pores with sufficient spatial and temporal resolution, the knowledge about the molecular origins of diffusive processes in porous materials is still restricted. The main focus of the current paper is on the development of continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy into a tool shedding some new light on molecular diffusion inside mesoporous silica materials differing systematically in pore size and surface functionalities. The advantages of CW-EPR are that its spatial resolution fits ideally to the size of mesopores (2-10 nm), it is fast enough for spotting molecular processes, and any conventional solvent and the porous matrix are EPR silent. Diffusion coefficients have been calculated considering spin exchange occurring from the diffusive collision of radicals, and are compared to complementary analytical techniques like MAS PFG NMR (sensitive for meso-scale) and EPR-imaging (sensitive to macroscale diffusion). Our results show that the choice of surface bound functional groups influences diffusion much stronger than pore-size. There are indications that this is not only due to different guest-surface interactions but also due to an altered mobility within the solvent under confinement. PMID:26027653
Nagasaka, Y.; Nagashima, A.
1988-11-01
This paper describes measurement of the thermal diffusivity of molten KCl in the temperature range from 804 to 1,030/degree/C by the forced Rayleigh scattering method. In this contact-free optical measuring technique for the thermal diffusivity of liquids, a sample needs to be colored by the admixture of a dye for suitable absorption of a heating laser beam. The dye substances employed are CoCl/sub 2/ and NiCl/sub 2/, which were chosen through the experimental evaluation. The accuracy is estimated to be /plus minus/7% for molten KCl colored with NiCl/sub 2/. The results converted to thermal conductivity show one of the smallest values among other previous data; the difference is a factor of four. The present study demonstrates the promising applicability of the forced Rayleigh scattering method to the measurement of high-temperature molten salts, which has never been attained by other conventional methods.
Mason, Sean; Hamon, Rebecca; Zhang, Hao; Anderson, Jenny
2008-01-15
The effect of potential chemical constraints on the performance of two relatively new soil P testing methods, anion exchange membrane (AEM) and diffusive gradients in thin films (DGT), were evaluated. Exposures to ranges of anion (Cl(-), NO(3)(-), SO(4)(2-) and HCO(3)(-)) concentrations relevant to agricultural soils had minimal effect on P recoveries using DGT. It has also been shown previously that DGT P recoveries are unaffected by varying pH (3-9). In contrast, increasing NO(3)(-) and SO(4)(2-) concentrations in solution reduced the recovery of P using the resin method (anion exchange membrane, AEM) by 24% at 50mgL(-1) NO(3)(-) and by 47% at 12mgL(-1) SO(4)(2-) when the P concentration of the test solution was 2mgL(-1). Phosphorus sorption by the resin decreased with increasing Cl(-) concentrations until there was a 100% decrease at 300mgL(-1) Cl(-) when the P concentration of the test solution was 2mgL(-1) and a 92% reduction at 700mgL(-1) Cl(-) when the P concentration of the test solution was 0.2mgL(-1). There was also a small but significant effect of carbonate species on P sorption to the resin at carbonate concentrations that can occur in agricultural soils. Changing the pH of the solution had minimal effects on the resin P measurements in solutions above pH 4, but below pH 4, resin P measurements decreased dramatically. A poor coefficient of determination for the regression fit between DGT and resin measurements on eight agricultural soils suggested that these two methods are measuring different amounts of P for different soils. Resin P measurements increased significantly, but non-uniformly across soils, when the soil:water ratio was decreased but this did not result in an improved relationship with DGT P. There was a minimal effect on measured P using either Cl(-) or HCO(3)(-) as counter ions on the resin. PMID:18371709
NASA Astrophysics Data System (ADS)
Fouvry, J. B.; Pichon, C.; Magorrian, J.; Chavanis, P. H.
2015-12-01
The secular evolution of an infinitely thin tepid isolated galactic disc made of a finite number of particles is investigated using the inhomogeneous Balescu-Lenard equation expressed in terms of angle-action variables. The matrix method is implemented numerically in order to model the induced gravitational polarisation. Special care is taken to account for the amplification of potential fluctuations of mutually resonant orbits and the unwinding of the induced swing amplified transients. Quantitative comparisons with N-body simulations yield consistent scalings with the number of particles and with the self-gravity of the disc: the fewer the particles and the colder the disc, the faster the secular evolution. Secular evolution is driven by resonances, but does not depend on the initial phases of the disc. For a Mestel disc with Q ~ 1.5, the polarisation cloud around each star boosts its secular effect by a factor of a thousand or more, accordingly promoting the dynamical relevance of self-induced collisional secular evolution. The position and shape of the induced resonant ridge are found to be in very good agreement with the prediction of the Balescu-Lenard equation, which scales with the square of the susceptibility of the disc. In astrophysics, the inhomogeneous Balescu-Lenard equation may describe the secular diffusion of giant molecular clouds in galactic discs, the secular migration and segregation of planetesimals in proto-planetary discs, or even the long-term evolution of population of stars within the Galactic centre. It could be used as a valuable check of the accuracy of N-body integrators on secular timescales. Appendices are available in electronic form at http://www.aanda.orgA copy of the linear matrix response code is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/584/A129
ERIC Educational Resources Information Center
Mitchell, James K.; Carter, William E.
2000-01-01
Describes using a computer statistical software package called Minitab to model the sensitivity of several microbes to the disinfectant NaOCl (Clorox') using the Kirby-Bauer technique. Each group of students collects data from one microbe, conducts regression analyses, then chooses the best-fit model based on the highest r-values obtained.…
'Acinetobacter calcoaceticus', frequently found in drinking waters and implicated in nosocomial infections, was presumptively identified by its tiny, blue colonial appearance on Levine eosin methylene blue agar. All of the 33 isolates from drinking water showing this distinctive ...
Instrumentation in Diffuse Optical Imaging
Zhang, Xiaofeng
2014-01-01
Diffuse optical imaging is highly versatile and has a very broad range of applications in biology and medicine. It covers diffuse optical tomography, fluorescence diffuse optical tomography, bioluminescence, and a number of other new imaging methods. These methods of diffuse optical imaging have diversified instrument configurations but share the same core physical principle – light propagation in highly diffusive media, i.e., the biological tissue. In this review, the author summarizes the latest development in instrumentation and methodology available to diffuse optical imaging in terms of system architecture, light source, photo-detection, spectral separation, signal modulation, and lastly imaging contrast. PMID:24860804
Hara, Shintaro; Isoda, Reika; Tahvanainen, Teemu; Hashidoko, Yasuyuki
2012-01-01
Background Many investigators have recognised that a significant proportion of environmental bacteria exist in a viable but non-culturable state on agar plates, and some researchers have also noticed that some of such bacteria clearly recover their growth on matrices other than agar. However, the reason why agar is unsuitable for the growth of some bacteria has not been addressed. Methodology/Principal Findings According to the guide of a bioassay for swarming inhibition, we identified 5-hydroxymethylfuran-2-carboxylic acid (5-HMFA) and furan-2-carboxylic acid (FA) as factors that inhibit bacterial swarming and likely inhibit extracellular polysaccharide production on agar. The furan-2-carboxylic acids 5-HMFA and FA effectively inhibited the swarming and swimming of several environmental bacteria at concentrations of 1.8 and 2.3 µg L?1 (13 and 21 nmol L?1), respectively, which are equivalent to the concentrations of these compounds in 0.3% agar. On Luria-Bertani (LB) plates containing 1.0% agar that had been previously washed with MeOH, a mixture of 5-HMFA and FA in amounts equivalent to their original concentrations in the unwashed agar repressed the swarming of Escherichia coli K12 strain W3110, a representative swarming bacterium. Conclusions/Significance Agar that contains trace amounts of 5-HMFA and FA inhibits the proliferation of some slow-growing or difficult-to-culture bacteria on the plates, but it is useful for single colony isolation due to the ease of identification of swarmable bacteria as the non-swarmed colonies. PMID:22848437
Turbo fluid machinery and diffusers
NASA Technical Reports Server (NTRS)
Sakurai, T.
1984-01-01
The general theory behind turbo devices and diffusers is explained. Problems and the state of research on basic equations of flow and experimental and measuring methods are discussed. Conventional centrifugation-type compressor and fan diffusers are considered in detail.
Shankar, Shiv; Rhim, Jong-Whan
2015-10-01
Silver nanoparticles (AgNPs) were synthesized using amino acids (tyrosine and tryptophan) as reducing and capping agents, and they were incorporated into the agar to prepare antimicrobial composite films. The AgNPs solutions exhibited characteristic absorption peak at 420 nm that showed a red shift to ?434 nm after forming composite with agar. XRD data demonstrated the crystalline structure of AgNPs with dominant (111) facet. Apparent surface color and transmittance of agar films were greatly influenced by the AgNPs. The incorporation of AgNPs into agar did not exhibit any change in chemical structure, thermal stability, moisture content, and water vapor permeability. The water contact angle, tensile strength, and modulus decreased slightly, but elongation at break increased after AgNPs incorporation. The agar/AgNPs nanocomposite films possessed strong antibacterial activity against Listeria monocytogenes and Escherichia coli. The agar/AgNPs film could be applied to the active food packaging by controlling the food-borne pathogens. PMID:26076636
Clonal proliferation of PHA-stimulated human lymphocytes in soft agar culture.
Rozenszajn, L A; Shoham, D; Kalechman, I
1975-01-01
The purpose of this investigation was the induction of clonal proliferation of PHA-stimulated normal human lymphocytes using a two-layer soft agar technique. Essential conditions for colony formation include preceding sensitization of lymphocytes with PHA, and continuous presence of PHA in the soft agar culture. Two types of colonies developed: large colonies which appeared 3-4 days after seeding and comprised, after 5-6 days, 200-500 cells, and small colonies which were seen after 6-7 days of culture, resulting in production of 50-150 cells. Morphological study showed that all cells were blast-like and the mitotic index exceeded that in liquid medium by a factor of 50. Comparison between the number of colonies developing from cultured bone marrow and spleen cells with those from peripheral blood showed that, in proportion to the number of lymphocytes seeded, a larger number of colonies developed from bone marrow cells and a lower number of colonies developed from spleen cells. The time required for sensitization of lymphocytes in liquid medium with PHA was found to be no less than 12 hours. The greatest number of colonies appeared when the optimal concentration of PHA was placed in the lower agar layer. A linear relation between the number of cells seeded and the number of resulting colonies was found. One out of 2 X 10(3) or 3 X 10(3) lymphocytes in peripheral blood has the potential to develop as colony. The rosette-forming ability and morphological identification of the cells suggest that the colonies are composed of T lymphocytes. Images FIG. 1 FIG. 2 FIG. 3 FIG. 4 FIG. 5 PMID:1081491
Cavitation-enhanced delivery of insulin in agar and porcine models of human skin.
Feiszthuber, Helga; Bhatnagar, Sunali; Gyöngy, Miklós; Coussios, Constantin-C
2015-03-21
Ultrasound-assisted transdermal insulin delivery offers a less painful and less invasive alternative to subcutaneous insulin injections. However, ultrasound-based drug delivery, otherwise known as sonophoresis, is a highly variable phenomenon, in part dependent on cavitation. The aim of the current work is to investigate the role of cavitation in transdermal insulin delivery. Fluorescently stained, soluble Actrapid insulin was placed on the surface of human skin-mimicking materials subjected to 265?kHz, 10% duty cycle focused ultrasound. A confocally and coaxially aligned 5?MHz broadband ultrasound transducer was used to detect cavitation. Two different skin models were used. The first model, 3% agar hydrogel, was insonated with a range of pressures (0.25-1.40?MPa peak rarefactional focal pressure-PRFP), with and without cavitation nuclei embedded within the agar at a concentration of 0.05% w/v. The second, porcine skin was insonated at 1.00 and 1.40?MPa PRFP. In both models, fluorescence measurements were used to determine penetration depth and concentration of delivered insulin. Results show that in agar gel, both insulin penetration depth and concentration only increased significantly in the presence of inertial cavitation, with up to a 40% enhancement. In porcine skin the amount of fluorescent insulin was higher in the epidermis of those samples that were exposed to ultrasound compared to the control samples, but there was no significant increase in penetration distance. The results underline the importance of instigating and monitoring inertial cavitation during transdermal insulin delivery. PMID:25716689
NASA Technical Reports Server (NTRS)
Bever, R. S.
1977-01-01
Several dummy tubes imitating the IUE Camera System design were encapsulated with Solithane 2, Conathane EN-11, Green and Black Hysols and SMRD 432. Various flaws were purposefully placed in some of these. Partial discharge testing in vacuum under direct voltage conditions was carried once a week for 12 weeks, 15 kv dc being applied during normal working hours for 40 hours duration per week. None of the units showed much damage during this time judging by the P.D. energy histograms. A more complete mathematical presentation is given on diffusion and permeation than previously. Measurements of diffusion constants for various silicone rubbers are carried out by the Time-Lag method and compared to other determinations in the literature. Calculations of the time required for diffusion through a thick wall are demonstrated in the long time approximation and for dimensions pertaining to void and wall sizes of a delamination problem in the LANDSAT-C vidicon tubes. An actual delaminated LANDSAT-C tube and some facsimiles are immersed in vacuum for long periods and tested for catastrophic breakdown due to diffusion of gas, by application of high voltage.
Smith, Shaun; Meade, Joseph; McGill, Kevina; Gibbons, James; Bolton, Declan; Whyte, Paul
2015-10-01
Extended spectrum ?-lactamase (ESBL) producing Escherichia coli have emerged as a contaminant on modified charcoal cefoperazone deoxycholate agar (mCCDA) when attempting to selectively isolate Campylobacter spp. from poultry. E. coli are particularly problematic given their ability to grow under microaerophilic conditions and have been shown to outcompete Campylobacter species making Campylobacter detection or enumeration difficult. This paper recommends a novel method for restoring the selectivity of mCCDA using tazobactam, a ?-lactamase inhibitor. The method significantly inhibited ESBL E. coli growth in spiked or naturally contaminated broiler caecal samples (p?0.01) when compared to conventional mCCDA. This effect was seen at concentrations as low as 1mg/L tazobactam. TmCCDA(1) was found to inhibit up to 8 log10 CFU/mL of ESBL E. coli in mixed pure cultures and 7.5 log10 CFU/mL in caecal samples. Furthermore TmCCDA concentrations up to 10 mg/L had no statistically significant inhibitory effect (p?0.05) on the recovery of a panel of 27 Campylobacter jejuni and 5 Campylobacter coli isolates when compared to conventional mCCDA. From this study it is suggested that tazobactam, which is more chemically stable than clavulanic acid or sulbactam, is more suitable for restoring the selectivity of mCCDA for the detection or isolation of campylobacters. PMID:26119190
Chang, Wenjiao; Ding, Ding; Zhang, Shanshan; Dai, Yuanyuan; Pan, Qing; Lu, Huaiwei; Luo, Qingli; Shen, Jilong; Ma, Xiaoling
2015-12-01
Brain heart infusion agar containing 3 mg/liter vancomycin (BHI-V3) was used to screen for heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA). There was markedly greater biofilm formation by isolates that grew on BHI-V3 than by strains that did not grow on BHI-V3. Increased biofilm formation by hVISA may be mediated by FnbA- and polysaccharide intercellular adhesin-dependent pathways, and upregulation of atlA and sarA may also contribute to enhanced biofilm formation by hVISA upon prolonged exposure to vancomycin. PMID:26459889
Beltrami, Hugo
the rate at which diffusivity decreased with increasing soil moisture content were typically quite, soil respiration accounts for approximately half of total forest respiration and is regarded efforts have been aimed at determining the physical controls on total soil respiration [Risk et al., 2002a
Technology Transfer Automated Retrieval System (TEKTRAN)
Diffuse-Reflectance Fourier-Transform Mid-Infrared Spectroscopy (FTIR) can be used quickly and non destructively to identify and quantify the presence of important organic functional groups in environmental samples. However, soils contain myriad organic and inorganic components that absorb in the M...
Technology Transfer Automated Retrieval System (TEKTRAN)
Diffuse-Reflectance Fourier-Transform Mid-Infrared Spectroscopy (MidIR) can identify the presence of important organic functional groups in soil organic matter (SOM). Soils contain myriad organic and inorganic components that absorb in the MidIR so spectral interpretation needs to be validated in or...
The report gives results of Phase I of a laboratory assessment of the permeability and diffusion characteristics of Florida concretes. (NOTE: The ability of concrete to permit air flow under pressure (permeability) and the passage of radon gas without any pressure difference (dif...
The report gives results of Phase I of a laboratory assessment of the permeability and diffusion characteristics of Florida concretes. (NOTE: The ability of concrete to permit air flow under pressure (permeability) and the passage of radon gas without any pressure difference (dif...
NASA Astrophysics Data System (ADS)
Yamamoto, Utako; Kobayashi, Tetsuo; Kito, Shinsuke; Koga, Yoshihiko
We have analyzed cerebral white matter using magnetic resonance diffusion tensor imaging (MR-DTI) to measure the diffusion anisotropy of water molecules. The goal of this study is the quantitative evaluation of schizophrenia. Diffusion tensor images are acquired for patients with schizophrenia and healthy comparison subjects, group-matched for age, sex, and handedness. Fiber tracking is performed on the superior longitudinal fasciculus for the comparison between the patient and comparison groups. We have analysed and compared the cross-sectional area on the starting coronal plane and the mean and standard deviation of the fractional anisotropy and the apparent diffusion coefficient along fibers in the right and left hemispheres. In the right hemisphere, the cross-sectional areas in patient group are significantly smaller than those in the comparison group. Furthermore, in the comparison group, the cross-sectional areas in the right hemisphere are significantly larger than those in the left hemisphere, whereas there is no significant difference in the patient group. These results suggest that we may evaluate the disruption in white matter integrity in schizophrenic patients quantitatively by comparing the cross-sectional area of the superior longitudinal fasciculus in the right and left hemispheres.
Oun, Ahmed A; Rhim, Jong-Whan
2015-12-10
Cellulose nanocrystals (CNCs) were prepared by acid hydrolysis of cotton linter pulp fibers and three different purification methods, i.e., without post purification (CNC1), dialyzed against distilled water (CNC2), and neutralized with NaOH (CNC3), and their effect on film properties was evaluated by preparation of agar/CNCs composite films. All the CNCs were rod in shape with diameter of 15-50 nm and length of 210-480 nm. FTIR result indicated that there was no distinctive differences in the chemical structure between CNCs and cotton linter cellulose fiber. No significant relationship was observed between the sulfate content and crystallinity index of CNCs. The CNC3 showed higher thermal stability than the other type of CNCs due to the less adverse effect on the thermal stability of sulfate groups induced by the neutralization with NaOH. The tensile strength (TS) of agar film increased by 15% with incorporation of 5 wt% of CNC3, on the contrary, it decreased by 10% and 15% with incorporation of CNC1 and CNC2, respectively. Other performance properties of agar/CNCs composite films such as optical and water vapor barrier properties showed that the CNC3 was more effective filler than the other CNCs. In the range of concentration of CNC3 tested (1-10 wt%), inclusion of 5 wt% of CNC3 was the maximum concentration for improving or maintaining film properties of the composite films. The neutralization of acid hydrolyzed cellulose using NaOH was simple and convenient for the preparation of CNC and bionanocomposite films. PMID:26428095
Huff, Karleigh; Aroonnual, Amornrat; Littlejohn, Amy E Fleishman; Rajwa, Bartek; Bae, Euiwon; Banada, Padmapriya P; Patsekin, Valery; Hirleman, E Daniel; Robinson, J Paul; Richards, Gary P; Bhunia, Arun K
2012-09-01
The three most common pathogenic species of Vibrio, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus, are of major concerns due to increased incidence of water- and seafood-related outbreaks and illness worldwide. Current methods are lengthy and require biochemical and molecular confirmation. A novel label-free forward light-scattering sensor was developed to detect and identify colonies of these three pathogens in real time in the presence of other vibrios in food or water samples. Vibrio colonies grown on agar plates were illuminated by a 635?nm laser beam and scatter-image signatures were acquired using a CCD (charge-coupled device) camera in an automated BARDOT (BActerial Rapid Detection using Optical light-scattering Technology) system. Although a limited number of Vibrio species was tested, each produced a unique light-scattering signature that is consistent from colony to colony. Subsequently a pattern recognition system analysing the collected light-scatter information provided classification in 1-2?min with an accuracy of 99%. The light-scattering signatures were unaffected by subjecting the bacteria to physiological stressors: osmotic imbalance, acid, heat and recovery from a viable but non-culturable state. Furthermore, employing a standard sample enrichment in alkaline peptone water for 6?h followed by plating on selective thiosulphate citrate bile salts sucrose agar at 30°C for ??12?h, the light-scattering sensor successfully detected V.?cholerae, V.?parahaemolyticus and V.?vulnificus present in oyster or water samples in 18?h even in the presence of other vibrios or other bacteria, indicating the suitability of the sensor as a powerful screening tool for pathogens on agar plates. PMID:22613192
Huff, Karleigh; Aroonnual, Amornrat; Littlejohn, Amy E. Fleishman; Rajwa, Bartek; Bae, Euiwon; Banada, Padmapriya P.; Patsekin, Valery; Hirleman, E. Daniel; Robinson, J. Paul; Richards, Gary P.; Bhunia, Arun K.
2012-01-01
Summary The three most common pathogenic species of Vibrio, Vibrio cholerae, Vibrio parahaemolyticus and Vibrio vulnificus, are of major concerns due to increased incidence of water? and seafood?related outbreaks and illness worldwide. Current methods are lengthy and require biochemical and molecular confirmation. A novel label?free forward light?scattering sensor was developed to detect and identify colonies of these three pathogens in real time in the presence of other vibrios in food or water samples. Vibrio colonies grown on agar plates were illuminated by a 635?nm laser beam and scatter?image signatures were acquired using a CCD (charge?coupled device) camera in an automated BARDOT (BActerial Rapid Detection using Optical light?scattering Technology) system. Although a limited number of Vibrio species was tested, each produced a unique light?scattering signature that is consistent from colony to colony. Subsequently a pattern recognition system analysing the collected light?scatter information provided classification in 1?2?min with an accuracy of 99%. The light?scattering signatures were unaffected by subjecting the bacteria to physiological stressors: osmotic imbalance, acid, heat and recovery from a viable but non?culturable state. Furthermore, employing a standard sample enrichment in alkaline peptone water for 6?h followed by plating on selective thiosulphate citrate bile salts sucrose agar at 30°C for ??12?h, the light?scattering sensor successfully detected V.?cholerae, V.?parahaemolyticus and V.?vulnificus present in oyster or water samples in 18?h even in the presence of other vibrios or other bacteria, indicating the suitability of the sensor as a powerful screening tool for pathogens on agar plates. PMID:22613192
Starch-Ampicillin Agar for the Quantitative Detection of Aeromonas hydrophila.
Palumbo, S A; Maxino, F; Williams, A C; Buchanan, R L; Thayer, D W
1985-10-01
Interest in Aeromonas hydrophila as a food-borne and human pathogen is increasing. Isolation media from the clinical laboratory were evaluated for food use and either did not give quantitative recovery of A. hydrophila or did not permit ready differentiation of A. hydrophila from the background microflora. A new medium was developed which permitted quantitative recovery of A. hydrophila from foods. The medium consisted of phenol red agar base (Difco Laboratories), soluble starch (10 g/liter), and ampicillin (10 mg/liter). All foods surveyed contained A. hydrophila. Foods sampled included red meats, chicken, raw milk, and seafood (fish, shrimp, scallops, crab, and oysters). The count of A. hydrophila at the time of purchase ranged from 1 x 10/g (lower limit of detection) to 5 x 10/g. In most instances, the count of A. hydrophila increased during 1 week of storage at 5 degrees C. The starch-ampicillin agar developed permitted rapid quantitative recovery of A. hydrophila from foods in the presence of very large numbers of competing microflora. PMID:16346899
Evaluation of a Modified Cefsulodin-Irgasan-Novobiocin Agar for Isolation of Yersinia spp
Tan, Lai Kuan; Ooi, Peck Toung; Carniel, Elisabeth; Thong, Kwai Lin
2014-01-01
Y. enterocolitica and Y. pseudotuberculosis are important food borne pathogens. However, the presence of competitive microbiota makes the isolation of Y. enterocolitica and Y. pseudotuberculosis from naturally contaminated foods difficult. We attempted to evaluate the performance of a modified Cefsulodin-Irgasan-Novobiocin (CIN) agar in the differentiation of Y. enterocolitica from non-Yersinia species, particularly the natural intestinal microbiota. The modified CIN enabled the growth of Y. enterocolitica colonies with the same efficiency as CIN and Luria-Bertani agar. The detection limits of the modified CIN for Y. enterocolitica in culture medium (10 cfu/ml) and in artificially contaminated pork (104 cfu/ml) were also comparable to those of CIN. However, the modified CIN provided a better discrimination of Yersinia colonies from other bacteria exhibiting Yersinia-like colonies on CIN (H2S-producing Citrobacter freundii, C. braakii, Enterobacter cloacae, Aeromonas hydrophila, Providencia rettgeri, and Morganella morganii). The modified CIN exhibited a higher recovery rate of Y. enterocolitica from artificially prepared bacterial cultures and naturally contaminated samples compared with CIN. Our results thus demonstrated that the use of modified CIN may be a valuable means to increase the recovery rate of food borne Yersinia from natural samples, which are usually contaminated by multiple types of bacteria. PMID:25170941
Atef, Maryam; Rezaei, Masoud; Behrooz, Rabi
2014-09-01
Nanocrystalline cellulose (NCC) was prepared from microcrystalline cellulose (MCC) with particle size of 24.7 ?m using sulfuric acid hydrolysis technique. The obtained NCC revealed size of 0-100 nm, which the major part of them was about 30 nm. Then different contents (2.5, 5 and 10 wt%) of these NCC incorporated in agar film solution and the morphology, structure, and properties of the nanocomposite films were characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), Fourier transforms infrared (FTIR) spectroscopy, differential scanning calorimetry (DSC), mechanical, physical and optical testing. Results showed that the water vapor permeability (WVP) and water solubility (WS) of the agar-based nanocomposite films significantly (P<0.05) decreased about 13% and 21%, respectively, upon increasing the NCC content to 10%. Tensile strength (TS) and Young's modulus (YM) values of nanocomposite films significantly increased (P?0.05) with addition of NCC, whereas the elongation percent (E%) decreased not significantly (P>0.05). In addition, swelling percentage, transparency and light transmission of the films were decreased by incorporating NCC into polymer matrix. PMID:25036597
Pourreza, N; Ghanemi, K
2009-01-30
A novel solid phase extraction method for the determination of mercury has been developed. The Hg(II) ions were retained on a mini-column packed with agar powder modified with 2-mercaptobenzimidazole at a flow rate of 6 mL min(-1). The retained Hg(II) ions were eluted with 3 mol L(-1) solution of HCl and measured by cold vapor atomic absorption spectrometry (CV-AAS). The effect of different variables such as pH, sample flow rate, amounts of 2-mercaptobenzimidazole loaded on agar and SnCl(2) concentration was investigated and optimum conditions were established. The calibration curve was linear in the range of 0.040-2.40 ng mL(-1) with r=0.9994 (n=8). The limit of detection based on three times the standard deviation (3S(b)) (n=10) obtained under optimum conditions was 0.02 ng mL(-1). The relative standard deviation (R.S.D.) for the determination of 0.4 and 2.0 ng mL(-1) of Hg(II) was 2.6 and 1.9% (n=8), respectively. The method was successfully applied to determine Hg(II) in water, wastewater and fish samples. PMID:18513869
Yang, L.H.; Ding, Y.M.
2009-07-01
The aim of this article is to discuss the distribution law of the gasification agent concentration in a deep-going way during underground coal gasification and the new method of solving the problem for the convection diffusion of the gas. In this paper, the basic features of convection diffusion for the gas produced in underground coal gasification are studied. On the basis of the model experiment, through the analysis of the distribution and patterns of variation for the fluid concentration field in the process of the combustion and gasification of the coal seams within the gasifier, the 3-D non-linear unstable mathematical models on the convection diffusion for oxygen are established. In order to curb such pseudo-physical effects as numerical oscillation and surfeit which frequently occurred in the solution of the complex mathematical models, the novel finite unit algorithm, the upstream weighted multi-cell balance method is advanced in this article, and its main derivation process is introduced.
NASA Astrophysics Data System (ADS)
Tabaka, Marcin; Burdzy, Krzysztof; Ho?yst, Robert
2015-08-01
DNA-binding protein searches for its target, a specific site on DNA, by means of diffusion. The search process consists of many recurrent steps of one-dimensional diffusion (sliding) along the DNA chain and three-dimensional diffusion (hopping) after dissociation of a protein from the DNA chain. Here we propose a computational method that allows extracting the contribution of sliding and hopping to the search process in vivo from the measurements of the kinetics of the target search by the lac repressor in Escherichia coli [P. Hammar et al., Science 336, 1595 (2012), 10.1126/science.1221648]. The method combines lattice Monte Carlo simulations with the Brownian excursion theory and includes explicitly steric constraints for hopping due to the helical structure of DNA. The simulation results including all experimental data reveal that the in vivo target search is dominated by sliding. The short-range hopping to the same base pair interrupts one-dimensional sliding while long-range hopping does not contribute significantly to the kinetics of the search of the target in vivo.
Hirsch, Elizabeth B; Raux, Brian R; Zucchi, Paola C; Kim, Yisu; McCoy, Christopher; Kirby, James E; Wright, Sharon B; Eliopoulos, George M
2015-12-01
Fosfomycin is recommended as first-line treatment for acute uncomplicated cystitis in women. It has demonstrated in vitro activity against a variety of pathogens; however, a paucity of data are available from the USA. We determined the susceptibility of a collection of urine isolates to fosfomycin and compared multiple methods of susceptibility testing. Consecutive non-duplicate Enterobacteriaceae, enterococci and Pseudomonas aeruginosa isolates were collected from the clinical microbiology laboratory between August 2013 and January 2014. Isolates represented hospitalised or emergency department patients with monomicrobial bacteriuria. Fosfomycin MICs were determined in duplicate, on separate days, by Etest and disk diffusion and results were compared with agar dilution. Nitrofurantoin and ciprofloxacin were used as comparators. MIC results were categorised using Clinical and Laboratory Standards Institute interpretive criteria for Escherichia coli and Enterococcus faecalis. Correlation between the three testing methods was evaluated. Overall susceptibility to fosfomycin was 94.4%, 93.5% and 87.9% by agar dilution, disk diffusion and Etest, respectively. Five fosfomycin-resistant isolates were identified, including two Morganella morganii, one P. aeruginosa, one Proteus mirabilis and one Enterobacter aerogenes. Across all organisms, rates of essential agreement, categorical agreement, minor errors, major errors and very major errors for Etest/disk diffusion compared with agar dilution were 77.3%/NA, 89.5/93.8%, 7.1/5.0%, 3.6/1.3% and 0/0%, respectively. Fosfomycin displayed fairly consistent activity against a majority of isolates collected when using the susceptibility breakpoint of 64?g/mL. MICs for E. coli were particularly low (?2?g/mL). These data lend support to current guidelines that recommend fosfomycin as empirical first-line therapy for uncomplicated UTI. PMID:26498988
NASA Astrophysics Data System (ADS)
Lipnikov, Konstantin; Manzini, Gianmarco; Moulton, J. David; Shashkov, Mikhail
2016-01-01
Numerical schemes for nonlinear parabolic equations based on the harmonic averaging of cell-centered diffusion coefficients break down when some of these coefficients go to zero or their ratio grows. To tackle this problem, we propose new mimetic finite difference schemes that use a staggered discretization of the diffusion coefficient. The primary mimetic operator approximates div (k ?); the derived (dual) mimetic operator approximates - ? (?). The new mimetic schemes preserve symmetry and positive-definiteness of the continuum problem which allows us to use algebraic solvers with optimal complexity. We perform detailed numerical analysis of the new schemes for linear elliptic problems and a specially designed linear parabolic problem that has solution dynamics typical for nonlinear problems. We show that the new schemes are competitive with the state-of-the-art schemes for steady-state problems but provide much more accurate solution dynamics for the transient problem.
Zhang, Yulin; Mason, Sean; McNeill, Ann; McLaughlin, Michael J
2013-09-15
Potassium (K) and phosphorus (P) are two important macronutrients for crops, and are usually applied to soils as granular fertilizer before seeding. Therefore, accurate soil tests prior to planting to predict crop response to fertilizers are important in optimizing crop yields. Traditional methods used for testing both available K and P in soils, which are based on chemical extraction procedures, are to be soil-type dependent, and the predictive relationships across a broad range of soils are generally poor. The diffusive gradients in thin films (DGT) technique, based on diffusion theory, is extensively used to measure the diffusive supply of trace elements, metals and some nutrients in soils and water. When DGT is used to assess plant-available P in soils, a good relationship is found between crop response to P fertilizer and concentrations of P in soil measured by DGT, and therefore the DGT method provides a more precise recommendation of P fertilizer requirements. Adaptation of the DGT method to measure plant-available K in soils has already been attempted [1], but limitations were reported due to the non-uniform size of the resin gel, decreased K binding rate of the gel at long deployment times and a limited ability to measure a wide range of K concentrations. To eliminate these problems, a new resin gel has been developed by combining Amberlite and ferrihydrite. This mixed Amberlite and ferrihydrite (MAF) gel has improved properties in terms of handling and even distribution of Amberlite in the gel. The elution efficiencies of the MAF gel for K and P were 90% and 96%, respectively. The diffusion coefficient of K through the diffusive gel was 1.30 × 10(-5)cm(2)s(-1) at 22 ± 1°C and was stable through time. Since ferrihydrite is already used in DGT P testing, the ability of the MAF gel to assess available P simultaneously was also assessed. The MAF gel performed the same as the traditional ferrihydrite gel for available P assessment in a wide variety of agricultural soils. This means that the newly developed gel has the potential to measure K and plant-available P in soils simultaneously. PMID:23708633
NASA Astrophysics Data System (ADS)
Liu, Hao-Ran; Ding, Hang
2015-08-01
We propose an approach to simulate flows with moving contact lines (MCLs) on curved substrates on a Cartesian mesh. The approach combines an immersed boundary method with a three-component diffuse-interface model and a characteristic MCL model. The immersed boundary method is able to accurately enforce the no-slip boundary condition at the solid surface, thereby circumventing the penetration of the gas and the liquid into the solid by convection. On the other hand, using the three-component diffuse-interface model can prevent the gas and liquid from infiltrating into the solid substrate through the diffusive fluxes during the interface evolution. A combination of these two methods appears to effectively conserve the mass of the phases in the computation. The characteristic MCL model not only allows the contact lines to move on the curved boundaries, but makes the gas-liquid interface to intersect the solid object at an angle in consistence with the prescribed contact angle, even with the variation of surface tangent at the solid substrate. We examine the performance of the approach through a variety of numerical experiments. The mass conservation and interface shapes at equilibrium were tested through the simulation of drop spreading on a circular cylinder. The dynamic behaviors of moving contact lines were validated by simulating the droplet spreading on a flat substrate, and we compared the numerical results against theoretical predictions and previous experimental observations. The method was also applied to the simulations of flows with curved boundaries and moving contact lines, such as drop impact on a sphere and water entry of a sphere. Finally, we studied the penetration process of a two-dimensional drop into a porous substrate that consists of a cluster of circular cylinders.
Sousa, A M M; Alves, V D; Morais, S; Delerue-Matos, C; Gonçalves, M P
2010-05-01
Microwave-assisted extraction (MAE) of agar from Gracilaria vermiculophylla, produced in an integrated multitrophic aquaculture (IMTA) system, from Ria de Aveiro (northwestern Portugal), was tested and optimized using response surface methodology. The influence of the MAE operational parameters (extraction time, temperature, solvent volume and stirring speed) on the physical and chemical properties of agar (yield, gel strength, gelling and melting temperatures, as well as, sulphate and 3,6-anhydro-L-galactose contents) was evaluated in a 2(4) orthogonal composite design. The quality of the extracted agar compared favorably with the attained using traditional extraction (2 h at 85 degrees Celsius) while reducing drastically extraction time, solvent consumption and waste disposal requirements. Agar MAE optimum results were: an yield of 14.4 + or - 0.4%, a gel strength of 1331 + or - 51 g/cm(2), 40.7 + or - 0.2 degrees Celsius gelling temperature, 93.1 + or - 0.5 degrees Celsius melting temperature, 1.73 + or - 0.13% sulfate content and 39.4 + or - 0.3% 3,6-anhydro-L-galactose content. Furthermore, this study suggests the feasibility of the exploitation of G. vermiculophylla grew in IMTA systems for agar production. PMID:20056408
Roumen Tsekov
2011-04-20
Quantum diffusion is studied via dissipative Madelung hydrodynamics. Initially the wave packet spreads ballistically, than passes for an instant through normal diffusion and later tends asymptotically to a sub-diffusive law. It is shown that the apparent quantum diffusion coefficient is not a universal physical parameter since it depends on the initial wave packet preparation. The overdamped quantum diffusion of an electron in the field of a periodic potential is also investigated; in this case the wave packet spreads logarithmically in time. Thermo-quantum diffusion of heavier particles as hydrogen, deuterium and tritium atoms in periodic potentials is studied and a simple estimate of the tunneling effect is obtained in the frames of a quasi-equilibrium semiclassical approach. The effective thermo-quantum temperature is also discussed in relation to the known temperature dependence of muon diffusivity in solids.
2014-01-01
Background Magnetite used in an 8-MHz radiofrequency (RF) capacitive heating device can increase the temperature of a specific site up to 45°C. When treating a metastatic lesion around large abdominal vessels via hyperthermia with magnetite, heating-induced adverse effects on these vessels need to be considered. Therefore, this study examined hyperthermia-induced damage to blood vessel walls in vitro. Methods A large agar phantom with a circulatory system consisting of a swine artery and vein connected to a peristaltic pump was prepared. The blood vessels were placed on the magnetite-containing agar piece. Heating was continued for 30 min at 45°C. After heating, a histological study for injury to the blood vessels was performed. Results The inner membrane temperature did not reach 45°C due to the cooling effect of the blood flow. In the heated vessels, vascular wall collagen degenerated and smooth muscle cells were narrowed; however, no serious changes were noted in the vascular endothelial cells or vascular wall elastic fibers. The heated vessel wall was not severely damaged; this was attributed to cooling by the blood flow. Conclusions Our findings indicate that RF capacitive heating therapy with magnetite may be used for metastatic lesions without injuring the surrounding large abdominal vessels. PMID:25114787
Agar hydrogel with silver nanoparticles to prolong the shelf life of Fior di Latte cheese.
Incoronato, A L; Conte, A; Buonocore, G G; Del Nobile, M A
2011-04-01
The objective of this work was to evaluate the effectiveness of an antimicrobial packaging system containing active nanoparticles on the quality deterioration of Fior di Latte cheese. To this aim, 3 concentrations of silver montmorillonite embedded in agar were used. The cell loads of spoilage and useful microorganisms were monitored during a refrigerated storage period. Moreover, cheese sensory quality (i.e., odor, color, consistency, and overall quality) was evaluated by means of a panel test. Results showed that the active packaging system markedly increased the shelf life of Fior di Latte cheese, due to the ability of silver cations to control microbial proliferation, without affecting the functional dairy microbiota and the sensory characteristics of the product. The active packaging system developed in this work could be used to prolong the shelf life of Fior di Latte and boost its distribution beyond local market borders. PMID:21426957