Improved agar diffusion method for detecting residual antimicrobial agents.
Tsai, C E; Kondo, F
2001-03-01
The improved agar diffusion method for determination of residual antimicrobial agents was investigated, and the sensitivities of various combinations of test organisms and assay media were determined using 7 organisms, 5 media, and 31 antimicrobial agents. Bacillus stearothermophilus and synthetic assay medium (SAM) showed the greatest sensitivity for screening penicillins (penicillin G and ampicillin). The combination of Bacillus subtilis and minimum medium (MM) was the most sensitive for tetracyclines (oxytetracycline and chlortetracycline), B. stearothermophilus and SAM or Micrococcus luteus and Mueller-Hinton agar (MHA) for detecting tylosin and erythromycin, B. subtilis and MHA for aminoglycosides (streptomycin, kanamycin, gentamicin, and dihydrostreptomycin), B. stearothermophilus and SAM for polyethers (salinomycin and lasalocid), and B. subtilis and MM or Clostridium perfringens and GAM for polypeptides (thiopeptin, enramycin, virginiamycin, and bacitracin). However, gram-negative bacterium Escherichia coli ATCC 27166 and MM were better for screening for colistin and polymixin-B. For detecting the synthetic drugs tested, the best combination was B. subtilis and MM for sulfonamides, E. coli 27166 and MM for quinolones (oxolinic acid and nalidixic acid), B. subtilis and MM for furans (furazolidone), and the bioluminescent bacterium Photobacterium phosphoreum and luminescence assay medium for chloramphenicol and oxolinic acid. The results showed that the use of four assay plates, B. stearothermophilus and SAM, B. subtilis and MM, M. luteus and MHA, and E. coli 27166 and MM, was superior to the currently available techniques for screening for residual antimicrobial agents in edible animal tissues. PMID:11252480
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 (R (2) in the linear experiment of Na2S2O3 was 0.994; R (2) 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
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
Cytotoxicity of ferrite particles by MTT and agar diffusion methods for hyperthermic application
NASA Astrophysics Data System (ADS)
Kim, Dong-Hyun; Lee, Se-Ho; Kim, Kyoung-Nam; Kim, Kwang-Mahn; Shim, In-Bo; Lee, Yong-Keun
2005-05-01
We investigated the cytotoxicity of the prepared various ferrites (Fe-, Li-, Ni/Zn/Cu-, Ba-, Sr-, Co-, Co/Ni-ferrites) using MTT assay as well as agar diffusion method. Their cytotoxicity was compared with that of alginate-encapsulated ferrites. In the MTT assay, Fe 3O 4 and SrFe 12O 19 ferrite showed the highest cell viability of 90%. Alginate-encapsulated Ba-ferrite was ranked mildly cytotoxic, whereas their ferrite particles were ranked cytotoxic.
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...
Kotilainen, Pirkko; Puukka, Pauli; Nakari, Ulla-Maija; Siitonen, Anja; Eerola, Erkki; Huovinen, Pentti; Hakanen, Antti J.
2012-01-01
The agar dilution method has been standardized by the CLSI for the susceptibility testing of Campylobacter species, and according to these standards, the disk diffusion method should be used only in screening for macrolide and ciprofloxacin resistance. Nevertheless, the disk diffusion test is currently widely used, since it is easy to perform in clinical microbiology laboratories. In this study, the disk diffusion method was compared to the agar dilution method by analyzing the in vitro activities of seven antimicrobial agents against 174 Campylobacter strains collected in Finland between 2003 and 2008. Recommendations of the CLSI were followed using Mueller-Hinton agar plates with 5% of sheep blood. For each strain, the disk diffusion tests were performed two to four times. Of the 33 erythromycin-resistant strains (MIC, ≥16 μg/ml), 24 (73%) constantly showed a 6-mm erythromycin inhibition zone (i.e., no inhibition), while for seven strains the inhibition zone varied from 6 to 44 mm in repeated measurements. Among the 141 erythromycin-susceptible strains (MIC, <16 μg/ml), erythromycin inhibition zones varied between 6 and 61 mm. Of the 87 ciprofloxacin-resistant strains, 47 (54%) showed 6-mm inhibition zones, while 40 strains showed inhibition zones between 6 and 60 mm. Significant differences between the repetitions were observed in the disk diffusion for all antimicrobial agents and all strains except for the macrolide-resistant strains regarding the macrolides. For 17 (10%) strains, the variation in repeated measurements was substantial. These results show that the disk diffusion method may not be a reliable tool for the susceptibility testing of Campylobacter spp. Further studies are needed to assess whether the disk diffusion test could be improved or whether all susceptibilities of campylobacters should be tested using an MIC-based method. PMID:22075583
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
Disk Agar Diffusion Susceptibility Testing of Yeasts
Saubolle, Michael A.; Hoeprich, Paul D.
1978-01-01
A disk agar diffusion method was developed for testing the susceptibility of rapidly growing yeasts in vitro. A totally defined, completely synthetic agar culture medium (synthetic amino acid medium, fungal) and clinical isolates of Candida spp. and Torulopsis glabrata were used. Turbidimetric adjustment of cell suspensions resulted in standard, reproducible inocula, which gave sharp, clear zones of inhibition when applied by an agar overlay method. Optimal disk loads were determined for amphotericin B, amphotericin B methyl ester, 5-fluorocytosine, clotrimazole, and miconazole. Disk potencies were stable over a 2-month period when stored in a vacuum desiccator at −30°C. Using an error ratebounded classification, the zones of inhibition were correlated with both broth dilution and agar dilution minimum inhibitory concentrations (MICs). With amphotericin B and amphotericin B methyl ester, all isolates were susceptible, yielding zone diameters which clustered within 5 mm. Overall correlations between zone diameters and broth dilution MICs with 5-fluorocytosine, miconazole, and clotrimazole were 97, 96, and 82% (excluding T. glabrata), respectively; correlations of zone diameters with agar dilution MICs were 96, 92, and 88%, respectively. Disk diffusion susceptibility testing of yeasts appears to be generally applicable. However, when results are equivocal, quantitative test methods should be used. PMID:568910
Pusnik, Mascha; Imeri, Minire; Deppierraz, Grégoire; Bruinink, Arie; Zinn, Manfred
2016-01-01
A profound in vitro evaluation not only of the cytotoxic but also of bioactive potential of a given compound or material is crucial for predicting potential effects in the in vivo situation. However, most of the current methods have weaknesses in either the quantitative or qualitative assessment of cytotoxicity and/or bioactivity of the test compound. Here we describe a novel assay combining the ISO 10993-5 agar diffusion test and the scratch also termed wound healing assay. In contrast to these original tests this assay is able to detect and distinguish between cytotoxic, cell migration modifying and cytotoxic plus cell migration modifying compounds, and this at higher sensitivity and in a quantitative way. PMID:26861591
Korkeala, H; Sorvettula, O; Mäki-Petäys, O; Hirn, J
1983-01-01
Residue analyses of the kidneys of twenty-six pigs treated with various antimicrobial drugs 20 h before slaughter and of eleven untreated pigs were performed. The effects of storage temperature of the kidneys, and of sampling location, on the residue analysis were also studied. No method alone was sufficient for the detection of residues. Oxytetracycline residues could be detected at pH 6, dihydrostreptomycin residues at pH 8, and sulphonamide residues if trimethoprim was present in the medium. Chloramphenicol, penicillin G procaine, tylosin and lincomycin residues were not detectable with the methods used. The concentration of ampicillin decreased during the storage of samples at +4°C. Most methods also yielded zones of inhibition for the frozen kidneys from untreated pigs. It seems necessary to use agar media of two different pH values: the addition of trimethoprim to the medium is also needed. The use of fresh pig kidneys, and samples containing both kidney medulla and kidney cortex, is recommended in residue analysis. PMID:22055926
Modeling development of inhibition zones in an agar diffusion bioassay.
Chandrasekar, Vaishnavi; Knabel, Stephen J; Anantheswaran, Ramaswamy C
2015-09-01
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 (T c) 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 T c was equal to MIC. The MIC was experimentally determined to be 0.156 μg mL(-1), and T c was determined to be 7 h. Good agreement (R (2) = 0.984) was obtained between model-predicted and experimentally determined inhibition zone radii. PMID:26405525
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 μg 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
Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping
2016-01-01
Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm's shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here. PMID:27434099
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
Coughlan, A; Breed, S M; Ashraf, C; Cardinale, J A; Hall, M M; Towler, M R
2013-03-01
The authors have previously shown that it is possible to incorporate silver into a soda-zinc-silicate glass and subsequently form a glass polyalkenoate cement from it. The objective of the research described herein is to determine if incremental increases in the silver content of these glass polyalkenoate cements will increase their antibacterial efficacy against gram-positive and gram-negative bacteria using the accepted spread plate method. Four glass polyalkenoate cements were formulated; three contained increasing amounts of silver incorporated into them (cements A, B, and C, containing 0.33 mol%, 0.66 mol%, and 0.99 mol% silver, respectively) and a fourth contained no silver, which acted as a control (control cement). The handling properties of the glass polyalkenoate cements were evaluated, where working times were around 2 min and setting times ranged from 1 h 17 min to 2 h 41 min. Inductively coupled plasma atomic emission spectroscopy was employed to determine silver ion release with cement maturation for up to 14 days. The majority of silver ions were released within the first 24 h, with up to 2 mg/L cumulative ion release recorded up to 14 days. The antibacterial properties of the coatings were evaluated against Staphylococcus aureus and Pseudomonas aeruginosa bacteria. The silver-glass polyalkenoate cements exhibited antibacterial effect against both bacterial strains. The maximum inhibition zones recorded against S. aureus was 14.8 mm (SD ± 1.11) and against P. aeruginosa was 20.6 mm (SD ± 0.81). Cement B had a greater antibacterial effect compared to cement A, however, cements B and C had comparable antibacterial effects after 14 days even though cement C contained 0.33 mol% more silver than B. This indicates that by increasing the silver content in these cements, the antibacterial efficacy increases to a point, but there is a threshold where further silver ion release does not increase the antibacterial effect
NASA Astrophysics Data System (ADS)
Bante-Guerra, Jose; Macías, J. D.; Caballero-Aguilar, L.; Vales-Pinzón, C.; Alvarado-Gil, J. J.
2013-02-01
Recently, several treatments for fighting malignant tumors have been designed. However these procedures have well known inconveniences, depending on their applicability, tumor size and side effects, among others. Magnetic hyperthermia is a safe, non-invasive method for cancer therapy. This treatment is applied via elevation of target tissue temperature by dissipation of heat from Magnetic Nanoparticles (MNPs), previously located within the tumor. The induction of heat causes cell death and therefore the removal of the tumor. In this work the thermal diffusion in phantoms of agar loaded with magnetic nanoparticles (MNPs) is studied using the infrared thermography technique, which is widely used in biology/medicine (e.g. skin temperature mapping). Agar is one of the materials used to simulate different types of body tissues, these samples are known as "phantoms". Agar is of natural origin, low cost and high degree of biocompatibility. In this work the agar gel was embedded with MNPs by coprecipitation and placed in an alternating magnetic field radiation. As a consequence, the energy from the radiation source is dissipated as heat and then transferred from the MNP to the gel, increasing its temperature. For the temperature analysis, the samples of agar gel were stimulated by RF magnetic field generated by coils. Heating was measured with infrared thermography using a Thermovision A20M infrared camera. Thermographic images allowed obtaining the dependence of thermal diffusion in the phantom as a function of the magnitude of the applied RF magnetic field and the load of magnetic particles.
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
A modified agar plate method for detection of Strongyloides stercoralis.
Koga, K; Kasuya, S; Khamboonruang, C; Sukhavat, K; Ieda, M; Takatsuka, N; Kita, K; Ohtomo, H
1991-10-01
The agar plate method is a new technique with high detection rates for coprological diagnosis of human strongyloidiasis. This report details modifications of the technique and establishes a standardized procedure. We recommend that all plates should be carefully observed using a microscope because macroscopic observation can lead to false negative results. It is also advisable to pour formalin solution directly into microscopically positive dishes to collect worms by sedimentation. This procedure enables one to observe worms otherwise hidden. Sealing dishes with adhesive tape prevents larvae from crawling out of the dishes, eliminating any possibility in the reduction of detection rates, and greatly improves the safety conditions for the technician performing the procedure. We consider the agar plate method to be superior to the filter paper method in detecting Strongyloides, and we believe that it will eventually become the technique of choice. PMID:1951861
Diffusion of Methylene Blue in Phantoms of Agar Using a Photoacoustic Technique
NASA Astrophysics Data System (ADS)
Vilca-Quispe, L.; Alvarado-Gil, J. J.; Quintana, P.; Ordonez-Miranda, J.
2010-05-01
In this work, the kinetics of diffusion of methylene blue in agar aqueous solution is studied using a photoacoustic technique. Two agar phantoms solutions in water with a relation of mass/volume of 0.01% and 0.05% were analyzed. The study was performed using a modified Rosencwaig photoacoustic cell that is enclosed by transparent windows, on both sides. The sample is deposited directly on top of the upper window. A red light beam, at a fixed modulation frequency, is sent through the lower window illuminating the sample and inducing the photoacoustic effect inside the closed chamber of the cell. At the beginning of the experiment, a droplet of 100μL of agar solution is deposited; afterwards, the signal stabilizes, and 10μL of methylene blue aqueous solution (0.0125 g · mL-1) is added to the surface of the agar. During the first seconds of the experiment, the photoacoustic signal amplitude increases followed by a gradual and long decay. Results for modulation frequencies in the range from 10Hz to 80Hz for both agar concentrations are presented. A simple theoretical approach is presented to analyze the experimental data. It is demonstrated that the kinetics of the process can be parameterized as a function of the changes of an effective optical absorption coefficient. From these results, the characteristic time, in which the dye diffusion process stabilizes, is obtained. It is found that this time is larger for samples with a higher agar concentration. These differences provide important results for biomedical sciences in which agar gels are used as phantoms resembling some of the properties of living organs and tissues.
Aal-Saraj, Ali Burak; Ariffin, Zaihan; Masudi, Sam'an Malik
2012-08-01
The aim of this study was to evaluate the antimicrobial activity of a new experimental nano-hydroxyapatite epoxy resin-based sealer (Nanoseal) with several other commercially available sealers; AH26, Tubliseal, Sealapex and Roekoseal against Enterococcus faecalis, Pseudomonas aeruginosa, Streptococcus mutans, Streptococcus sobrinus and Escherichia coli for up to 7 days. Agar diffusion was used in this study. Fifty Muller-Hinton agar plates were prepared and divided into five experimental groups (n = 10), for each micro-organism. Another 10 agar plates were used as positive and negative controls. Endodontic sealers were tested against each micro-organism. Inhibition zones produced were recorded. The results of this study showed that all test materials exhibited inhibition zones towards the tested micro-organisms for 7 days except for Roekoseal, which showed no inhibition zones. Nanoseal and AH26 exhibited similar zones of inhibition. Significant difference was found between Nanoseal and the other tested sealers (P < 0.001). PMID:22827817
Ogata, Silvio Kazuo; Gales, Ana Cristina; Kawakami, Elisabete
2014-01-01
Antimicrobial susceptibility testing for Helicobacter pylori is increasingly important due to resistance to the most used antimicrobials agents. Only agar dilution method is approved by CLSI, but it is difficult to perform routinely. We evaluated the reliability of E-test and disk diffusion comparing to agar dilution method on Helicobacter pylori antimicrobial susceptibility testing. Susceptibility testing was performed for amoxicillin, clarithromycin, furazolidone, metronidazole and tetracycline using E-test, disk-diffusion and agar dilution method in 77 consecutive Helicobacter pylori strains from dyspeptic children and adolescents. Resistance rates were: amoxicillin - 10.4%, 9% and 68.8%; clarithromycin - 19.5%, 20.8%, 36.3%; metronidazole - 40.2%33.7%, 38.9%, respectively by agar dilution, E-test and disk diffusion method. Furazolidone and tetracycline showed no resistance rates. Metronidazole presented strong correlation to E-test (r = 0.7992, p < 0.0001) and disk diffusion method (r=-0.6962, p < 0.0001). Clarithromycin presented moderate correlation to E-test (r = 0.6369, p < 0.0001) and disk diffusion method (r=−0.5656, p < 0.0001). Amoxicillin presented weak correlation to E-test (r = 0.3565, p = 0.0015) and disk diffusion (r=−0.3565, p = 0.0015). Tetracycline presented weak correlation with E-test (r = 0.2346, p = 0.04) and furazolidone to disk diffusion (r=−0.0288, p = 0.8038). E-test presented better agreement with gold standard. It is an easy and reliable method for Helicobacter pylori susceptibility testing. Disk diffusion method presented high disagreement and high rates of major errors. PMID:25763052
Morioka, Ayako; Shimazaki, Yoko; Uchiyama, Mariko; Suzuki, Shoko
2016-05-01
We observed increasing unserotypable (UT) Actinobacillus pleuropneumoniae isolates using agar gel diffusion (AGD) test. To reanalyze their serovar, we performed rapid slide agglutination (RSA) test and multiplex PCR for 47 UT isolates. Of these, 25 were serovar 1 (UT-serovar 1), 20 were serovar 2 (UT-serovar 2) and 2 were serovar 15 (UT-serovar 15). We examined serotyping antigen extraction temperature to determine heat influence. UT-serovar 1 and 15 were influenced by heat, because their precipitation lines were observed in the case of low antigen extraction temperature. To investigate the relationship between antigenicity and genotype, we performed pulsed-field gel electrophoresis (PFGE) analysis using UT-serovar 2 and 15. The predominant PFGE pattern of UT-serovar 2 was identical to that of serovar 2. PMID:26726101
MORIOKA, Ayako; SHIMAZAKI, Yoko; UCHIYAMA, Mariko; SUZUKI, Shoko
2016-01-01
We observed increasing unserotypable (UT) Actinobacillus pleuropneumoniae isolates using agar gel diffusion (AGD) test. To reanalyze their serovar, we performed rapid slide agglutination (RSA) test and multiplex PCR for 47 UT isolates. Of these, 25 were serovar 1 (UT-serovar 1), 20 were serovar 2 (UT-serovar 2) and 2 were serovar 15 (UT-serovar 15). We examined serotyping antigen extraction temperature to determine heat influence. UT-serovar 1 and 15 were influenced by heat, because their precipitation lines were observed in the case of low antigen extraction temperature. To investigate the relationship between antigenicity and genotype, we performed pulsed-field gel electrophoresis (PFGE) analysis using UT-serovar 2 and 15. The predominant PFGE pattern of UT-serovar 2 was identical to that of serovar 2. PMID:26726101
Craven, D E; Frasch, C E; Robbins, J B; Feldman, H A
1978-01-01
A serum agar method for serogrouping Neisseria meningitidis is described and compared with conventional bacterial slide agglutination. There was 93% agreement for 300 strains examined individually by each method. Among strains from serogroups A, B, C, Y, and W135, there was 100% correlation, whereas strains from serogroup 29E (Z') had only 67% correlation. The serum agar method was rapid, as well as easy to perform and interpret. The potential benefits of this method for epidemiological studies and reference laboratories processing large numbers of meningococcal isolates are emphasized. Images PMID:96123
Lambert, Frank W.; Brown, June M.; Georg, Lucille K.
1967-01-01
This study was an attempt to develop a fluorescent-antibody (FA) test to differentiate Actinomyces israelii and A. naeslundii as an aid in their laboratory identification. Two strains of A. israelii (X522 and A601) and two strains of A. naeslundii (X454 and X600), which had received intensive study by several investigators, were used for the immunization of rabbits. Working titers, based on tests with antigens prepared from the homologous strains and from well-established heterologous strains, were determined for each labeled antibody preparation. These conjugates and their normal serum control conjugates were used separately to stain 85 cultures of Actinomyes species and 23 strains of other species that might be confused with them. Acetone-precipitated soluble antigens from these same strains were tested with different antisera in the agar-gel diffusion test. Results showed that A. israelii (X522 and A601) and A. naeslundii (X454 and X600) labeled antiglobulins, when used at their working titers, stained most strains of their homologous species. Agar-gel diffusion results showed general agreement with those of the FA tests. The two tests appear to be equal in sensitivity, but the FA test is more specific, since several cross-reactions were noted with the agar-gel diffusion test whereas no cross-reactions were obtained with the FA reagents. Agar-gel and FA studies suggest that at least two serotypes of A. israelii may be associated with human disease. Although the majority of strains tested in this study appear to belong to a common serotype, “serotype 1,” two strains of an apparent second serotype, “serotype 2,” were encountered. FA staining of tissue impression smears from experimentally infected mice was successful when a counterstain, Evans Blue dye, was used. PMID:4964473
Rhim, Jong-Whan; Wang, Long-Feng; Lee, Yonghoon; Hong, Seok-In
2014-03-15
Silver nanoparticles (AgNPs) were prepared by a laser ablation method and composite films with the AgNPs and agar were prepared by solvent casting method. UV-vis absorbance test and transmission electron microscopy (TEM) analysis results revealed that non-agglomerated spherical AgNPs were formed by the laser ablation method. The surface color of the resulting agar/AgNPs films exhibited the characteristic plasmonic effect of the AgNPs with the maximum absorption peaks of 400-407 nm. X-ray diffraction (XRD) test results also exhibited characteristic AgNPs crystals with diffraction peaks observed at 2θ values of 38.39°, 44.49°, and 64.45°, which were corresponding to (111), (200), and (220) crystallographic planes of face-centered cubic (fcc) silver crystals, respectively. Thermogravimetric analysis (TGA) results showed that thermal stability of the agar/AgNPs composite films was increased by the inclusion of metallic silver. Water vapor barrier properties and surface hydrophobicity of the agar/AgNPs films increased slightly with the increase in AgNPs content but they were not statistically significant (p>0.05), while mechanical strength and stiffness of the composite films decreased slightly (p<0.05). The agar/AgNPs films exhibited distinctive antimicrobial activity against both Gram-positive (Listeria monocytogenes) and Gram-negative (Escherichia coli O157:H7) bacterial pathogens. PMID:24528754
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...
The Resazurin-Agar Method - a Quick Test to Determine Water Quality
NASA Astrophysics Data System (ADS)
Huckfeldt, J.; Westphal, B.; Claußen, L.
2015-12-01
Rezasurin has been used as a smart tracer in stream ecosystems to indicate metabolic activity, specifically aerobic respiration by heterotrophic bacteria. Resazurin is a blue compound which is irreversibly reduced to the pink resorufin in the presence of aerobic bacteria. The degree and speed of colour change from blue to pink is a measure of the degree of oxygen consumption and thus an indirect indication of the concentration of aerobic bacteria in a given medium. A high concentration of bacteria in water indicates a bad water quality. In our work a method was developed using resazurin agar plates to find a quick and easy way for testing water quality and comparing concentrations of bacteria in freshwater and seawater samples. The theory was to concentrate bacteria from a defined volume of water sample onto polycarbonate filters (0.2 μm), which are then placed onto the resazurin agar plate. The presence of aerobic bacteria on the filter will reduce the resazurin in the agar and the compound changes its colour. First tests conducted with different dilutions of a pure culture of yoghurt bacteria showed promising results and confirmed the feasibility of the method. In a further assay, we used water samples from different water layers and different temperatures and were also able to observe differences in the concentration of bacteria, depending on these different environmental conditions.The assay was also successfully used with seawater samples, collected from 2 different stations at 3 different depths in the Baltic Sea (salinity=15). The discolouration of the plates showed good correlation with the oxygen concentrations in the water. The resazurin-agar plate method is economical and fast. Several samples could be investigated at the same time without sacrificing the reliability of the results. Thus it is a good pre-screening test for a quantitative evaluation of bacteria in a water sample.
An Agar-Based Method for Plating Marine Protozoan Parasites of the Genus Perkinsus
Cold, Emma R.; Freyria, Nastasia J.; Martínez Martínez, Joaquín; Fernández Robledo, José A.
2016-01-01
The genus Perkinsus includes protozoan parasites of mollusks responsible for losses in the aquaculture industry and hampering the recovery of natural shellfish beds worldwide, and they are a key taxon for understanding intracellular parasitism adaptations. The ability to propagate the parasite in liquid media, in the absence of the host, has been crucial for improving understanding of its biology; however, alternative techniques to grow the parasite are needed to explore other basic aspects of the Perkinsus spp. biology. We optimized a DME: Ham’s F12–5% FBS- containing solid agar medium for plating Perkinsus marinus. This solid medium supported trophozoite propagation both by binary fission and schizogony. Colonies were visible to the naked eye 17 days after plating. We tested the suitability of this method for several applications, including the following: 1) Subcloning P. marinus isolates: single discrete P. marinus colonies were obtained from DME: Ham’s F12–5% FBS– 0.75% agar plates, which could be further propagated in liquid medium; 2) Subcloning engineered Perkinsus mediterraneus MOE[MOE]: GFP by streaking cultures on plates; 3) Chemical susceptibility: Infusing the DME: Ham’s F12–5% FBS– 0.75% agar plates with triclosan resulted in inhibition of the parasite propagation in a dose-dependent manner. Altogether, our plating method has the potential for becoming a key tool for investigating diverse aspects of Perkinsus spp. biology, developing new molecular tools, and for biotechnological applications. PMID:27149378
Agar Plate Method for Detection and Enumeration of Alkylbenzenesulfonate-Degrading Microorganisms
Ohwada, Kouichi
1975-01-01
A simple method for detection and enumeration of alkylbenzenesulfonate (ABS)-degrading microorganisms by using agar plates was developed and used in microbiological studies of coastal marine and polluted river waters. The method depends upon the color responses of neutral red in alkaline medium. Neutral red changes from pink, when it enters into ABS micelles, to yellow, when the ABS is degraded, and does not form micelles. When neutral red-tris(hydroxymethyl)-aminomethane buffer solution and then cationic surfactant solution were sprayed onto the agar surface of ABS-nutrient agar cultures, transparent haloes appeared around the colonies of ABS-degrading microorganisms against a pink background. Viable counts of ABS-degrading bacteria isolated from both seawater and freshwater environments were considerably higher in polluted waters than in less polluted areas. Viable counts of ABS-degrading bacteria averaged 1.5 × 105/ml in samples from the surface water of polluted Tokyo Bay and 3.0 × 104/ml in samples from the surface water of polluted Tamagawa River but were fewer in number in samples from less polluted waters. Images PMID:234155
An Agar-Based Method for Plating Marine Protozoan Parasites of the Genus Perkinsus.
Cold, Emma R; Freyria, Nastasia J; Martínez Martínez, Joaquín; Fernández Robledo, José A
2016-01-01
The genus Perkinsus includes protozoan parasites of mollusks responsible for losses in the aquaculture industry and hampering the recovery of natural shellfish beds worldwide, and they are a key taxon for understanding intracellular parasitism adaptations. The ability to propagate the parasite in liquid media, in the absence of the host, has been crucial for improving understanding of its biology; however, alternative techniques to grow the parasite are needed to explore other basic aspects of the Perkinsus spp. biology. We optimized a DME: Ham's F12-5% FBS- containing solid agar medium for plating Perkinsus marinus. This solid medium supported trophozoite propagation both by binary fission and schizogony. Colonies were visible to the naked eye 17 days after plating. We tested the suitability of this method for several applications, including the following: 1) Subcloning P. marinus isolates: single discrete P. marinus colonies were obtained from DME: Ham's F12-5% FBS- 0.75% agar plates, which could be further propagated in liquid medium; 2) Subcloning engineered Perkinsus mediterraneus MOE[MOE]: GFP by streaking cultures on plates; 3) Chemical susceptibility: Infusing the DME: Ham's F12-5% FBS- 0.75% agar plates with triclosan resulted in inhibition of the parasite propagation in a dose-dependent manner. Altogether, our plating method has the potential for becoming a key tool for investigating diverse aspects of Perkinsus spp. biology, developing new molecular tools, and for biotechnological applications. PMID:27149378
Stone, M S; Wallace, R J; Swenson, J M; Thornsberry, C; Christensen, L A
1983-01-01
An agar disk elution method using round well plates, supplemented Mueller-Hinton agar, and commercial drug disks is described for susceptibility testing of Mycobacterium marinum and the rapidly growing mycobacteria to antibiotics and sulfonamides. By this method, 14 of 14 strains of M. marinum were susceptible to rifampin, doxycycline, minocycline, and trimethoprim-sulfamethoxazole. Identical results were obtained with Middlebrook 7H10 agar and drugs prepared from standard powders. With 58 isolates of Mycobacterium fortuitum and Mycobacterium chelonei, this method had a 92% correlation with broth minimal inhibitory concentration determinations for cefoxitin and greater than 98% for doxycycline, kanamycin, amikacin, and the sulfonamides. Sixty-nine percent of isolates of M. chelonei susceptible to amikacin on supplemented Mueller-Hinton agar were resistant on 7H10 agar, and 15 of 16 M. chelonei isolates susceptible to erythromycin in broth were resistant by disk elution when an endpoint of no growth was used with either agar. The agar disk elution method offers a practical method for testing of most antibacterial agents against these mycobacterial species. Images PMID:6651277
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...
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 qacEΔ1-positive strains showed higher MICs (512 mg l(-1)) to CTAB. The qacEΔ1 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
Yoshida, T; Jono, K; Okonogi, K
1997-01-01
In vitro activities of antifungal agents, including azole compounds, against yeasts were easily determined by using RPMI-1640 agar medium and by incubating the plates in the presence of 20% CO2. The end point of inhibition was clear by this method, even in the case of azole compounds, because of the almost complete inhibition of yeast growth at high concentrations which permitted weak growth of some Candida strains by traditional methods. MICs obtained by the agar dilution method were similar to those obtained by the broth dilution method proposed by the National Committee for Clinical Laboratory Standards. PMID:9174197
Kenny, G E; Hooton, T M; Roberts, M C; Cartwright, F D; Hoyt, J
1989-01-01
The increasing resistance of genital mycoplasmas to tetracycline poses a problem because tetracycline is one of the few antimicrobial agents active against Mycoplasma hominis, Ureaplasma urealyticum, chlamydiae, gonococci, and other agents of genitourinary-tract disease. Since the quinolones are a promising group of antimicrobial agents, the susceptibilities of M. hominis and U. urealyticum to the newer 6-fluoroquinolones were determined by the agar dilution method. Ciprofloxacin, difloxacin, and ofloxacin had good activity against M. hominis, with the MIC for 50% of isolates tested (MIC50) being 1 microgram/ml. Fleroxacin, lomefloxacin, pefloxacin, and rosoxacin had MIC50s of 2 micrograms/ml. Enoxacin, norfloxacin, and amifloxacin had MIC50s of 8 to 16 micrograms/ml, and cinoxacin and nalidixic acid were inactive (MIC50, greater than or equal to 256 micrograms/ml). Overall, the activities of 6-fluoroquinolones for ureaplasmas were similar to those for M. hominis, with MICs being the same or twofold greater. The most active 6-fluoroquinolones against ureaplasmas were difloxacin, ofloxacin, and pefloxacin, with MIC50s of 1 to 2 micrograms/ml. Ciprofloxacin was unusual in that the MIC50 for M. hominis was 1 microgram/ml, whereas the MIC50 for ureaplasmas was 8 micrograms/ml. Since the MIC50s for the most active quinolones approximate achievable concentrations in blood and urine, quinolones have promise in treating mycoplasmal infections. PMID:2712541
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; Colakoğlu, Selcan; Durmaz, Süleyman; Ekincioğlu, Pınar
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
Yasin, R M; Suan, K A; Meng, C Y
1997-05-01
A single dose of a new antibiotic, azithromycin, has been shown to be effective in the treatment of uncomplicated Neisseria gonorrhoeae. A clinical study was conducted to assess the in vitro susceptibility of N gonorrhoeae to azithromycin and compare the reliability of results obtained using the new E-test methodology for determination of the minimum inhibitory concentration (MIC) of antibiotic with those obtained through the standard agar dilution method. 135 clinical isolates of N gonorrhoeae were obtained from patients attending hospital-based sexually transmitted disease clinics in five geographic locations in Malaysia. 76 of the isolates were penicillinase-producing N gonorrhoeae and 69 were high-level tetracycline-resistant N gonorrhoeae. All isolates were susceptible to azithromycin based on the susceptible MIC breakpoint of 2.0 mcg/ml. The MICs ranged from 0.0078-0.25 mcg/ml by agar dilution method and from 0.016-0.50 mcg/ml by E-test. Agreement between these two methods was 97.8%. The single-dose regime and good antigonococcal and antichlamydial activity of azithromycin make this antibiotic a suitable treatment choice. Moreover, the findings of this study suggest that the simpler, faster E-test is as reliable as the agar dilution method. Given the tendency of the antimicrobial susceptibility pattern of N gonorrhoeae to change rapidly, it is important to monitor MICs to detect the emergence of resistance. PMID:9153733
Nagayama, Ariaki; Yamaguchi, Keizo; Watanabe, Kunitomo; Tanaka, Masatoshi; Kobayashi, Intetsu; Nagasawa, Zenzo
2008-10-01
In 1968, the agar dilution method was developed as an independent Japanese method for measuring the minimal inhibitory concentration (MIC) of antimicrobial agents. As this method differed in a few respects from the MIC measurement methods used in other countries, it was revised in 1981, by a committee headed by Susumu Mitsuhashi, and the revised method (Chemotherapy 29:76-79, 1981) has been used since then. In 1979, an agar dilution method for measuring the MIC of anaerobes was developed by a committee chaired by Nozomu Kosakai (Chemotherapy 27:559-561, 1979). In 1990, a committee headed by Sachiko Goto approved a broth microdilution method for nonfastidious bacteria (Chemotherapy 38:102-105, 1990). Later, a committee headed by Atsushi Saito examined media that would be suitable for nonfastidious bacteria and fastidious bacteria, and they endeavored to prepare a broth microdilution method for anaerobic bacteria. In this context, a new broth microdilution method was proposed at the 40th Annual Meeting of the Japanese Society of Chemotherapy (JSC) in Nagoya in 1992, and the proposal was adopted as the standard JSC method after some modification (Chemotherapy 41: 183-189, 1993). The agar dilution method has remained unrevised for approximately 20 years. A proposal to review this method was recently made, and the 2007 Committee on Antimicrobial Susceptibility Testing was formed, comprising the JSC members listed below. Under the auspices of this committee, the method revised in 1981 was reviewed in comparison to the international standard method (Clinical and Laboratory Standards Institute [CLSI] method). PMID:18936894
Use of urease-bromothymol blue-agar method for large-scale testing of urine on grain and seeds.
Valdes, P A; Ziobro, G C; Ferrera, R S
1996-01-01
The current AOAC method (963.28) for large-scale (50 g) testing of urine on grain is based on the reaction of sodium in urine with magnesium uranyl acetate. Detection of sodium suggests that urine is present and that a test for urea is appropriate. Urea is detected with urease-bromothymol blue-paper and is confirmed through its reaction with xanthydrol to form dixanthylurea crystals, which are detected microscopically. The initial nonspecific test for sodium can be influenced by the presence of salt or other sodium compounds. Furthermore, the magnesium uranyl acetate spray used in Method 963.28 potentially exposes the analyst to the aerosol of a volatile, toxic uranium compound. Excess reagents and analyzed test portions must be disposed of as radioactive waste. In addition, Method 963.28 requires several steps to determine the presence of urea. The alternative AOAC method (972.41) tests for the presence of urea from urine on individual seeds. Urea is enzymatically decomposed to ammonia and carbon dioxide by urease. Liberated ammonia shifts the pH, changing the color of the indicator in the agar from yellow to blue. This study adapts Method 972.41 to larger test samples. Up to 25 g grains and seeds are sprayed with urease test agar instead of being individually immersed in the urease test agar. The modified method was used to analyze urea on seeds and grains of 24 plants from 4 families. The method has a limit of detection of one seed contaminated with 1 microgram urea. PMID:8757445
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).
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
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
Gil-Romero, Yolanda; Regodón-Domínguez, Marta; Wilhelmi de Cal, Isabel; López-Fabal, Fátima; Gómez-Garcés, José Luis
2016-01-01
Carbapenems-resistance in Pseudomonas aeruginosa isolates has been widely reported. Fosfomycin has been shown to act synergistically with other antimicrobials. The agar dilution method was approved for susceptibility testing for fosfomycin and Pseudomonas aeruginosa. However, broth microdilution methods are the basis of systems currently used in clinical microbiology laboratories. The results of this study indicate that these methods are acceptable as susceptibility testing methods for fosfomycin against these organisms. PMID:26620604
Code of Federal Regulations, 2011 CFR
2011-04-01
... 21 Food and Drugs 6 2011-04-01 2011-04-01 false Agar-agar. 582.7115 Section 582.7115 Food and..., FEEDS, AND RELATED PRODUCTS SUBSTANCES GENERALLY RECOGNIZED AS SAFE Stabilizers § 582.7115 Agar-agar. (a) Product. Agar-agar. (b) Conditions of use. This substance is generally recognized as safe when used...
Code of Federal Regulations, 2010 CFR
2010-04-01
... 21 Food and Drugs 6 2010-04-01 2010-04-01 false Agar-agar. 582.7115 Section 582.7115 Food and..., FEEDS, AND RELATED PRODUCTS SUBSTANCES GENERALLY RECOGNIZED AS SAFE Stabilizers § 582.7115 Agar-agar. (a) Product. Agar-agar. (b) Conditions of use. This substance is generally recognized as safe when used...
Mathematical Methods for Diffusion MRI Processing
Lenglet, C.; Campbell, J.S.W.; Descoteaux, M.; Haro, G.; Savadjiev, P.; Wassermann, D.; Anwander, A.; Deriche, R.; Pike, G.B.; Sapiro, G.; Siddiqi, K.; Thompson, P.
2009-01-01
In this article, we review recent mathematical models and computational methods for the processing of diffusion Magnetic Resonance Images, including state-of-the-art reconstruction of diffusion models, cerebral white matter connectivity analysis, and segmentation techniques. We focus on Diffusion Tensor Images (DTI) and Q-Ball Images (QBI). PMID:19063977
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
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
Novicki, Thomas J.; Daly, Judy A.; Mottice, Susan L.; Carroll, Karen C.
2000-01-01
Enterohemorrhagic Escherichia coli (EHEC) and specifically serotype O157:H7 are a significant cause of hemorrhagic gastrointestinal disease and the hemolytic uremic syndrome. Methods currently used in clinical microbiology labs, such as sorbitol-MacConkey (SMAC) agar, reliably detect only O157:H7. We have evaluated a two-step method that has the potential to identify and isolate all EHEC serotypes, including serotype O157:H7. This method utilizes a chromogenic selective-differential medium for the isolation of E. coli together with an enzyme-linked immunosorbent assay (ELISA) that detects the Shiga-like toxins Stx1 and Stx2. Both are commercially available and usable in a wide range of clinical microbiology laboratories. Compared to a Vero cell cytotoxic assay, SMAC had sensitivities of 23.5% for the identification of all EHEC serotypes and of 50.0% for the identification of O157:H7 alone. The two-step method had sensitivities of 76.5 and 100%, respectively. The ELISA alone had a sensitivity of 82.4% in the detection of Stx1 and Stx2. The specificity was 100% in all cases. Overall, 14 EHEC isolates were obtained: 8 (58%) O157:H7, 2 (14%) O26, 2 (14%) O111:NM, 1 (7%) O103:H2, and 1 (7%) O121:H19. All but one were isolated during the months of May to September. The two-step method was found to be considerably more expensive than SMAC for both positive and negative samples. PMID:10655343
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.
Entis, P
1996-01-01
Twenty laboratories participated in a collaborative study to validate a 2-day hydrophobic grid membrane filter method using YM-11 agar for enumeration of yeast and mold in foods. Six naturally contaminated food products were included in the study: garlic powder, raw ground beef, walnuts, flour/meal, orange juice, and yogurt. The test method produced significantly higher results than the 5-day pour plate reference method for orange juice and significantly lower, though numerically similar, results for walnuts and yogurt. Differences between the test and reference methods were not significant for garlic powder, raw ground beef, or flour/meal. Repeatability and reproducibility were similar for both the test and reference methods in all cases. The hydrophobic grid membrane filter method for enumeration of yeast and mold in foods has been adopted by AOAC INTERNATIONAL. PMID:8823916
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)
Entis, P; Lerner, I
2000-03-01
A new culture medium, LM-137 agar, was developed for use with the ISO-GRID hydrophobic grid membrane filter system for direct presumptive enumeration of Listeria monocytogenes in 24 h. The method was validated against three-replicate, three-dilution most probable number procedures based on enrichment methods specified by the U.S. Department of Agriculture, the Association of Official Analytical Chemists International and the U.S. Food and Drug Administration. The study encompassed meats, dairy products, egg, produce, seafood, and environmental samples. The ISO-GRID filter method produced significantly higher recovery of L. monocytogenes from fermented sausage, hot dogs, pasteurized and raw milk, raw shrimp, and environmental swab samples (P < 0.05). The reference methods yielded significantly higher counts from frozen raw pork and cole slaw (P < 0.05). Confirmation rates of presumptive positive isolates from the filter method ranged from a low of 92% (frozen raw pork) to 100% (most other products). Neither the recovery efficiency nor the confirmation rate were affected by the presence of competing aerobic flora. PMID:10716565
Diffusion method of seperating gaseous mixtures
Pontius, Rex B.
1976-01-01
A method of effecting a relatively large change in the relative concentrations of the components of a gaseous mixture by diffusion which comprises separating the mixture into heavier and lighter portions according to major fraction mass recycle procedure, further separating the heavier portions into still heavier subportions according to a major fraction mass recycle procedure, and further separating the lighter portions into still lighter subportions according to a major fraction equilibrium recycle procedure.
Klancnik, Anja; Piskernik, Sasa; Jersek, Barbara; Mozina, Sonja Smole
2010-05-01
The aim of this study was to evaluate diffusion and dilution methods for determining the antibacterial activity of plant extracts and their mixtures. Several methods for measurement of the minimal inhibitory concentration (MIC) of a plant extract are available, but there is no standard procedure as there is for antibiotics. We tested different plant extracts, their mixtures and phenolic acids on selected gram-positive (Staphylococcus aureus, Bacillus cereus, and Listeria monocytogenes) and gram-negative bacteria (Escherichia coli O157:H7, Salmonella Infantis, Campylobacter jejuni, Campylobacter coli) with the disk diffusion, agar dilution, broth microdilution and macrodilution methods. The disk diffusion method was appropriate only as a preliminary screening test prior to quantitative MIC determination with dilution methods. A comparison of the results for MIC obtained by agar dilution and broth microdilution was possible only for gram-positive bacteria, and indicated the latter as the most accurate way of assessing the antimicrobial effect. The microdilution method with TTC (2,3,5-triphenyl tetrazolium chloride) or INT (2-p-iodophenyl-3-p-nitrophenyl-5-phenyl tetrazolium chloride) to indicate the viability of aerobic bacteria was found to be the best alternative approach, while only ATP determination was appropriate for microaerophilic Campylobacter spp. Using survival curves the kinetics of bacterial inactivation on plant extract exposure was followed for 24h and in this way the MIC values determined by the microdilution method were confirmed as the concentrations of extracts that inhibited bacterial growth. We suggest evaluation of the antibacterial activity of plant extracts using the broth microdilution method as a fast screening method for MIC determination and the macrodilution method at selected MIC values to confirm bacterial inactivation. Campylobacter spp. showed a similar sensitivity to plant extracts as the tested gram-positive bacteria, but S
Swenson, J M; Spargo, J; Tenover, F C; Ferraro, M J
2001-10-01
To define more precisely the inoculation methods to be used in the oxacillin screen test for Staphylococcus aureus, we tested agar screen plates prepared in house with 6 microg of oxacillin/ml and 4% NaCl using the four different inoculation methods that would most likely be used by clinical laboratories. The organisms selected for testing were 19 heteroresistant mecA-producing strains and 41 non-mecA-producing strains for which oxacillin MICs were near the susceptible breakpoint. The inoculation method that was preferred by all four readers and that resulted in the best combination of sensitivity and specificity was a 1-microl loopful of a 0.5 McFarland suspension. A second objective of the study was to then use this method to inoculate plates from five different manufacturers of commercially prepared media. Although all commercial media performed with acceptable sensitivity compared to the reference lot, one of the commercial lots demonstrated a lack of specificity. Those lots of oxacillin screen medium that fail to grow heteroresistant strains can be detected by using S. aureus ATCC 43300 as a positive control in the test and by using transmitted light to carefully examine the plates for any growth. However, lack of specificity with commercial lots may be difficult to detect using any of the current quality control organisms. PMID:11574618
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
Code of Federal Regulations, 2012 CFR
2012-04-01
... 21 Food and Drugs 3 2012-04-01 2012-04-01 false Agar-agar. 184.1115 Section 184.1115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) DIRECT FOOD SUBSTANCES AFFIRMED AS GENERALLY RECOGNIZED AS SAFE Listing of...
Code of Federal Regulations, 2010 CFR
2010-04-01
... 21 Food and Drugs 3 2010-04-01 2009-04-01 true Agar-agar. 184.1115 Section 184.1115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) DIRECT FOOD SUBSTANCES AFFIRMED AS GENERALLY RECOGNIZED AS SAFE Listing of Specific Substances Affirmed as GRAS §...
Code of Federal Regulations, 2011 CFR
2011-04-01
... 21 Food and Drugs 3 2011-04-01 2011-04-01 false Agar-agar. 184.1115 Section 184.1115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) DIRECT FOOD SUBSTANCES AFFIRMED AS GENERALLY RECOGNIZED AS SAFE Listing of Specific Substances Affirmed as GRAS § 184.1115...
Code of Federal Regulations, 2013 CFR
2013-04-01
... 21 Food and Drugs 3 2013-04-01 2013-04-01 false Agar-agar. 184.1115 Section 184.1115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) FOOD FOR HUMAN CONSUMPTION (CONTINUED) DIRECT FOOD SUBSTANCES AFFIRMED AS GENERALLY RECOGNIZED AS SAFE Listing of...
Code of Federal Regulations, 2014 CFR
2014-04-01
... 21 Food and Drugs 3 2014-04-01 2014-04-01 false Agar-agar. 184.1115 Section 184.1115 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DIRECT FOOD... ingredient meets the specifications of the “Food Chemicals Codex,” 3d Ed. (1981), p. 11, which...
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
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.
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...
Díez-Aguilar, María; Martínez-García, Laura; Morosini, María Isabel
2015-01-01
We analyzed fosfomycin susceptibility results in Pseudomonas aeruginosa clinical isolates obtained by MIC gradient strips and disk diffusion methods using two different inocula, 108 and 106 CFU/ml, and compared them to the agar dilution reference method. Essential and categorical agreements were 93.6% and 95%, respectively, for the 106 CFU/ml alternative inoculum, and they were 67.6% and 78.2%, respectively, for the standard inoculum (108 CFU/ml). The use of the 106 CFU/ml inoculum improves the agreement values and inhibition zone readings. PMID:26643341
Brazier, J S; Goldstein, E J; Citron, D M; Ostovari, M I
1990-11-01
Fastidious anaerobe agar supported the growth of 82 strains of fusobacteria better than brain heart infusion agar, brucella agar, and Wilkins-Chalgren agar. Fastidious anaerobe agar showed less hazing and fewer tailing endpoints with beta-lactam antibiotics. Whole-blood supplementation improved the performance of all media. Wilkins-Chalgren agar without blood failed to support the growth of 17% of the strains. All Fusobacterium ulcerans strains were resistant to clindamycin. PMID:2073122
Diffusion in Condensed Matter: Methods, Materials, Models
NASA Astrophysics Data System (ADS)
Heitjans, Paul; Kärger, Jög
This comprehensive, handbook-style survey of diffusion in condensed matter gives detailed insight into diffusion as the process of particle transport due to stochastic movement. It is understood and presented as a phenomenon of crucial relevance for a large variety of processes and materials. In this book, all aspects of the theoretical fundamentals, experimental techniques, highlights of current developments and results for solids, liquids and interfaces are presented.
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
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.
Development of a selective agar plate for the detection of Campylobacter spp. in fresh produce.
Yoo, Jin-Hee; Choi, Na-Young; Bae, Young-Min; Lee, Jung-Su; Lee, Sun-Young
2014-10-17
This study was conducted to develop a selective medium for the detection of Campylobacter spp. in fresh produce. Campylobacter spp. (n=4), non-Campylobacter (showing positive results on Campylobacter selective agar) strains (n=49) isolated from fresh produce, indicator bacteria (n=13), and spoilage bacteria isolated from fresh produce (n=15) were plated on four Campylobacter selective media. Bolton agar and modified charcoal cefoperazone deoxycholate agar (mCCDA) exhibited higher sensitivity for Campylobacter spp. than did Preston agar and Hunt agar, although certain non-Campylobacter strains isolated from fresh produce by using a selective agar isolation method, were still able to grow on Bolton agar and mCCDA. To inhibit the growth of non-Campylobacter strains, Bolton agar and mCCDA were supplemented with 5 antibiotics (rifampicin, polymyxin B, sodium metabisulfite, sodium pyruvate, ferrous sulfate) and the growth of Campylobacter spp. (n=7) and non-Campylobacter strains (n=44) was evaluated. Although Bolton agar supplemented with rifampicin (BR agar) exhibited a higher selectivity for Campylobacter spp. than did mCCDA supplemented with antibiotics, certain non-Campylobacter strains were still able to grow on BR agar (18.8%). When BR agar with various concentrations of sulfamethoxazole-trimethoprim were tested with Campylobacter spp. (n=8) and non-Campylobacter (n=7), sulfamethoxazole-trimethoprim was inhibitory against 3 of 7 non-Campylobacter strains. Finally, we validated the use of BR agar containing 50mg/L sulfamethoxazole (BRS agar) or 0.5mg/L ciprofloxacin (BRCS agar) and other selective agars for the detection of Campylobacter spp. in chicken and fresh produce. All chicken samples were positive for Campylobacter spp. when tested on mCCDA, BR agar, and BRS agar. In fresh produce samples, BRS agar exhibited the highest selectivity for Campylobacter spp., demonstrating its suitability for the detection of Campylobacter spp. in fresh produce. PMID:25126968
48 CFR 401.371 - AGAR Advisories.
Code of Federal Regulations, 2011 CFR
2011-10-01
... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false AGAR Advisories. 401.371... ACQUISITION REGULATION SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of the FAR and the AGAR, for the following purposes: (a)...
48 CFR 401.371 - AGAR Advisories.
Code of Federal Regulations, 2010 CFR
2010-10-01
... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false AGAR Advisories. 401.371... ACQUISITION REGULATION SYSTEM Agency Acquisition Regulations 401.371 AGAR Advisories. The SPE may issue AGAR Advisories, consistent with the policies of the FAR and the AGAR, for the following purposes: (a)...
A vertical diffusion method for the microbiological assay of isoniazid
Lloyd, Janet; Mitchison, D. A.
1964-01-01
A method is described for the assay of isoniazid in serum and other fluids by diffusion along slopes of Löwenstein-Jensen medium inoculated with tubercle bacilli. The method is convenient, rapid and robust, but is less accurate than diffusion systems for the assay of some other substances. PMID:14227431
Fokas method for a multi-domain linear reaction-diffusion equation with discontinuous diffusivity
NASA Astrophysics Data System (ADS)
Asvestas, M.; Sifalakis, A. G.; Papadopoulou, E. P.; Saridakis, Y. G.
2014-03-01
Motivated by proliferation-diffusion mathematical models for studying highly diffusive brain tumors, that also take into account the heterogeneity of the brain tissue, in the present work we consider a multi-domain linear reaction-diffusion equation with a discontinuous diffusion coefficient. For the solution of the problem at hand we implement Fokas transform method by directly following, and extending in this way, our recent work for a white-gray-white matter brain model pertaining to high grade gliomas. Fokas's novel approach for the solution of linear PDE problems, yields novel integral representations of the solution in the complex plane that, for appropriately chosen integration contours, decay exponentially fast and converge uniformly at the boundaries. Combining these method-inherent advantages with simple numerical quadrature rules, we produce an efficient method, with fast decaying error properties, for the solution of the discontinuous reaction-diffusion problem.
Kalwarf, D.R.; Nielson, K.K.; Rich, D.C.; Rogers, V.C.
1982-11-01
A method was developed and used to determine radon diffusion coefficients in compacted soils by transient-diffusion measurements. A relative standard deviation of 12% was observed in repeated measurements with a dry soil by the transient-diffusion method, and a 40% uncertainty was determined for moistures exceeding 50% of saturation. Excellent agreement was also obtained between values of the diffusion coefficient for radon in air, as measured by the transient-diffusion method, and those in the published literature. Good agreement was also obtained with diffusion coefficients measured by a steady-state method on the same soils. The agreement was best at low moistures, averaging less than ten percent difference, but differences of up to a factor of two were observed at high moistures. The comparison of the transient-diffusion and steady-state methods at low moistures provides an excellent verification of the theoretical validity and technical accuracy of these approaches, which are based on completely independent experimental conditions, measurement methods and mathematical interpretations.
Thermal characterization of magnetically aligned carbonyl iron/agar composites.
Diaz-Bleis, D; Vales-Pinzón, C; Freile-Pelegrín, Y; Alvarado-Gil, J J
2014-01-01
Composites of magnetic particles into polymeric matrices have received increasing research interest due to their capacity to respond to external magnetic or electromagnetic fields. In this study, agar from Gelidium robustum has been chosen as natural biocompatible polymer to build the matrix of the magnetic carbonyl iron particles (CIP) for their uses in biomedical fields. Heat transfer behavior of the CIP-agar composites containing different concentrations (5, 10, 15, 20, 25 and 30% w/w) of magnetically aligned and non-aligned CIP in the agar matrix was studied using photothermal radiometry (PTR) in the back-propagation emission configuration. The morphology of the CIP-agar composites with aligned and non-aligned CIP under magnetic field was also evaluated by scanning electron microscopy (SEM). The results revealed a dominant effect of CIP concentration over the alignment patterns induced by the magnetic field, which agrees with the behavior of the thermal diffusivity and thermal conductivity. Agar served as a perfect matrix to be used with CIP, and CIP-agar composites magnetically aligned at 20% CIP concentration can be considered as promising 'smart' material for hyperthermia treatments in the biomedical field. PMID:24274482
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
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)
NASA Astrophysics Data System (ADS)
Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping
2016-08-01
Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion–reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.
Syneresis and delayed detachment in agar plates.
Divoux, Thibaut; Mao, Bosi; Snabre, Patrick
2015-05-14
Biogels made of crosslinked polymers such as proteins or polysaccharides behave as porous soft solids and store large amounts of solvent. These gels undergo spontaneous aging, called syneresis, which consists of the shrinkage of the gel matrix and the progressive expulsion of solvent. As a result, a biogel originally casted in a container often loses contact with the container sidewalls, and the detachment time is difficult to anticipate a priori, since it may occur over variable time spans (from hours to days). Here we report on syneresis phenomena in agar plates, which consist of Petri dishes filled with a gel mainly composed of agar. Direct observations and speckle pattern correlation analysis allow us to rationalize the delayed detachment of the gel from the sidewall of the Petri dish. The detachment time t* is surprisingly not controlled by the mass loss as one would intuitively expect. Instead, t* is strongly correlated to the gel minimum thickness emin measured along the sidewall of the plate, and increases as a robust function of emin, independently of the prior mass-loss history. Time-resolved correlation spectroscopy atypically applied to such weakly diffusive media gives access to the local thinning rate of the gel. This technique also allows us to detect the gel micro-displacements that are triggered by water evaporation prior to the detachment, and even to anticipate the latter from a few hours. Our work provides observables to predict the detachment time of agar gels in dishes, and highlights the relevance of speckle pattern correlation analysis for the quantitative investigation of the syneresis dynamics in biopolymer gels. PMID:25812667
Lattice Boltzmann method for the fractional advection-diffusion equation
NASA Astrophysics Data System (ADS)
Zhou, J. G.; Haygarth, P. M.; Withers, P. J. A.; Macleod, C. J. A.; Falloon, P. D.; Beven, K. J.; Ockenden, M. C.; Forber, K. J.; Hollaway, M. J.; Evans, R.; Collins, A. L.; Hiscock, K. M.; Wearing, C.; Kahana, R.; Villamizar Velez, M. L.
2016-04-01
Mass transport, such as movement of phosphorus in soils and solutes in rivers, is a natural phenomenon and its study plays an important role in science and engineering. It is found that there are numerous practical diffusion phenomena that do not obey the classical advection-diffusion equation (ADE). Such diffusion is called abnormal or superdiffusion, and it is well described using a fractional advection-diffusion equation (FADE). The FADE finds a wide range of applications in various areas with great potential for studying complex mass transport in real hydrological systems. However, solution to the FADE is difficult, and the existing numerical methods are complicated and inefficient. In this study, a fresh lattice Boltzmann method is developed for solving the fractional advection-diffusion equation (LabFADE). The FADE is transformed into an equation similar to an advection-diffusion equation and solved using the lattice Boltzmann method. The LabFADE has all the advantages of the conventional lattice Boltzmann method and avoids a complex solution procedure, unlike other existing numerical methods. The method has been validated through simulations of several benchmark tests: a point-source diffusion, a boundary-value problem of steady diffusion, and an initial-boundary-value problem of unsteady diffusion with the coexistence of source and sink terms. In addition, by including the effects of the skewness β , the fractional order α , and the single relaxation time τ , the accuracy and convergence of the method have been assessed. The numerical predictions are compared with the analytical solutions, and they indicate that the method is second-order accurate. The method presented will allow the FADE to be more widely applied to complex mass transport problems in science and engineering.
Lattice Boltzmann method for the fractional advection-diffusion equation.
Zhou, J G; Haygarth, P M; Withers, P J A; Macleod, C J A; Falloon, P D; Beven, K J; Ockenden, M C; Forber, K J; Hollaway, M J; Evans, R; Collins, A L; Hiscock, K M; Wearing, C; Kahana, R; Villamizar Velez, M L
2016-04-01
Mass transport, such as movement of phosphorus in soils and solutes in rivers, is a natural phenomenon and its study plays an important role in science and engineering. It is found that there are numerous practical diffusion phenomena that do not obey the classical advection-diffusion equation (ADE). Such diffusion is called abnormal or superdiffusion, and it is well described using a fractional advection-diffusion equation (FADE). The FADE finds a wide range of applications in various areas with great potential for studying complex mass transport in real hydrological systems. However, solution to the FADE is difficult, and the existing numerical methods are complicated and inefficient. In this study, a fresh lattice Boltzmann method is developed for solving the fractional advection-diffusion equation (LabFADE). The FADE is transformed into an equation similar to an advection-diffusion equation and solved using the lattice Boltzmann method. The LabFADE has all the advantages of the conventional lattice Boltzmann method and avoids a complex solution procedure, unlike other existing numerical methods. The method has been validated through simulations of several benchmark tests: a point-source diffusion, a boundary-value problem of steady diffusion, and an initial-boundary-value problem of unsteady diffusion with the coexistence of source and sink terms. In addition, by including the effects of the skewness β, the fractional order α, and the single relaxation time τ, the accuracy and convergence of the method have been assessed. The numerical predictions are compared with the analytical solutions, and they indicate that the method is second-order accurate. The method presented will allow the FADE to be more widely applied to complex mass transport problems in science and engineering. PMID:27176431
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.
A novel method to evaluate spin diffusion length of Pt
NASA Astrophysics Data System (ADS)
Zhang, Yan-qing; Sun, Niu-yi; Che, Wen-ru; Shan, Rong; Zhu, Zhen-gang
2016-05-01
Spin diffusion length of Pt is evaluated via proximity effect of spin orbit coupling (SOC) and anomalous Hall effect (AHE) in Pt/Co2FeAl bilayers. By varying the thicknesses of Pt and Co2FeAl layer, the thickness dependences of AHE parameters can be obtained, which are theoretically predicted to be proportional to the square of the SOC strength. According to the physical image of the SOC proximity effect, the spin diffusion length of Pt can easily be identified from these thickness dependences. This work provides a novel method to evaluate spin diffusion length in a material with a small value.
Adaptive domain decomposition methods for advection-diffusion problems
Carlenzoli, C.; Quarteroni, A.
1995-12-31
Domain decomposition methods can perform poorly on advection-diffusion equations if diffusion is dominated by advection. Indeed, the hyperpolic part of the equations could affect the behavior of iterative schemes among subdomains slowing down dramatically their rate of convergence. Taking into account the direction of the characteristic lines we introduce suitable adaptive algorithms which are stable with respect to the magnitude of the convective field in the equations and very effective on bear boundary value problems.
Practical method for diffusion welding of steel plate in air.
NASA Technical Reports Server (NTRS)
Moore, T. J.; Holko, K. H.
1972-01-01
Description of a simple and easily applied method of diffusion welding steel plate in air which does not require a vacuum furnace or hot press. The novel feature of the proposed welding method is that diffusion welds are made in air with deadweight loading. In addition, the use of an autogenous (self-generated) surface-cleaning principle (termed 'auto-vac cleaning') to reduce the effects of surface oxides that normally hinder diffusion welding is examined. A series of nine butt joints were diffusion welded in thick sections of AISI 1020 steel plate. Diffusion welds were attempted at three welding temperatures (1200, 1090, and 980 C) using a deadweight pressure of 34,500 N/sq m (5 psi) and a two-hour hold time at temperature. Auto-vac cleaning operations prior to welding were also studied for the same three temperatures. Results indicate that sound welds were produced at the two higher temperatures when the joints were previously fusion seal welded completely around the periphery. Also, auto-vac cleaning at 1200 C for 2-1/2 hours prior to diffusion welding was highly beneficial, particularly when subsequent welding was accomplished at 1090 C.
Efficient stochastic Galerkin methods for random diffusion equations
Xiu Dongbin Shen Jie
2009-02-01
We discuss in this paper efficient solvers for stochastic diffusion equations in random media. We employ generalized polynomial chaos (gPC) expansion to express the solution in a convergent series and obtain a set of deterministic equations for the expansion coefficients by Galerkin projection. Although the resulting system of diffusion equations are coupled, we show that one can construct fast numerical methods to solve them in a decoupled fashion. The methods are based on separation of the diagonal terms and off-diagonal terms in the matrix of the Galerkin system. We examine properties of this matrix and show that the proposed method is unconditionally stable for unsteady problems and convergent for steady problems with a convergent rate independent of discretization parameters. Numerical examples are provided, for both steady and unsteady random diffusions, to support the analysis.
A method for thermal diffusivity measurement in fluids.
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. PMID:24182147
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.
Özcan, Alpay; Quirk, James D.; Wang, Yong; Wang, Qing; Sun, Peng; Spees, William M.; Song, Sheng–Kwei
2012-01-01
The equations of the Complete Fourier Direct (CFD) MR model are explicitly derived for diffusion weighted NMR experiments. The CFD–MR theory is validated by comparing a biological phantom constructed from nerve bundles and agar gel with its numerical implementation. The displacement integral distribution function estimated from the experimental data is in high agreement with the numerical phantom. CFD–MR’s ability to estimate accurately and fully spin diffusion properties demonstrated here, provides the experimental validation of the theoretical CFD–MR model. PMID:22255156
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 1-2 ml cm(2) h(-1) at 100 mA 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
Sun, Han; Liu, Zhengzhi; Hu, Chong; Ren, Kangning
2016-08-01
Antimicrobial resistance (AMR) is a rapidly increasing threat to the effective treatment of infectious diseases worldwide. The two major remedies include: (1) using narrow-spectrum antibiotics based on rapid diagnosis; and (2) developing new antibiotics. A key part of both remedies is the antimicrobial susceptibility test (AST). However, the current standard ASTs that monitor colony formation are costly and time-consuming and the new strategies proposed are not yet practical to be implemented. Herein, we report a strategy to fabricate whole-hydrogel microfluidic chips using alginate-doped agar. This agar-based microfabrication makes it possible to prepare inexpensive hydrogel devices, and allows a seamless link between microfluidics and conventional agar-based cell culture. Different from common microfluidic systems, in our system the cells are cultured on top of the device, similar to normal agar plate culture; on the other hand, the microfluidic channels inside the hydrogel allow precise generation of linear gradient of drugs, thus giving a better performance than the conventional disk diffusion method. Cells in this system are not exposed to any shear flow, which allows the reliable tracking of individual cells and AST results to be obtained within 2-3 hours. Furthermore, our system could test the synergistic effect of drugs through two-dimensional gradient generation. Finally, the platform could be directly implemented to new drug discovery and other applications wherein a fast, cost-efficient method for studying the response of microorganisms upon drug administration is desirable. PMID:27452345
Comparison of thermal diffusivity and thermal conductivity methods
Sheffield, G.S.; Schorr, J.R. )
1991-01-01
This paper reports on applications involving ceramics which require that this diverse group of materials act as either thermal insulators or thermal conductors. Values of thermal conductivity can range over more than 4 orders of magnitude from 0.1 W/(m {center dot} K) (0.7 BTU {center dot} in./(h {center dot} ft{sup 2} {center dot} {degrees}F)) for fiberboard insulation to 1300 W/(M {center dot} K) (9013 BTU {center dot} in./(h {center dot} {degrees}F)) for boron nitride. The magnitude of temperature gradients in materials is governed by thermal diffusivity and thermal conductivity. In ceramic materials, gradients can create significant thermal stresses, cause heat flow (causing furnaces to heat but also causing usually undesirable heat losses) and be a controlling factor in reaction rates. In general, no single method is dominant because of the wide range of temperatures involved, the large variations in diffusivity and conductivity encountered, the differences in sampling requirements (homogeneity), and the duration of measurement time. Five thermal diffusivity and conductivity methods, all of which have been successfully applied to ceramic materials are reviewed. The methods covered are dynamic radial heat flow, laser flash, hot wire, calorimeter, and guarded hot plate. The dynamic radial heat flow and laser flash methods are diffusivity methods, whereas the remaining three are representative of conductivity methods.
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.
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 Flux-integral Method for Multidimensional Convection and Diffusion
NASA Technical Reports Server (NTRS)
Leonard, B. P.; Macvean, M. K.; Lock, A. P.
1994-01-01
The flux-integral method is a procedure for constructing an explicit, single-step, forward-in-time, conservative, control volume update of the unsteady, multidimensional convection-diffusion equation. The convective plus diffusive flux at each face of a control-volume cell is estimated by integrating the transported variable and its face-normal derivative over the volume swept out by the convecting velocity field. This yields a unique description of the fluxes, whereas other conservative methods rely on nonunique, arbitrary pseudoflux-difference splitting procedures. The accuracy of the resulting scheme depends on the form of the subcell interpolation assumed, given cell-average data. Cellwise constant behavior results in a (very artificially diffusive) first-order convection scheme. Second-order convection-diffusion schemes correspond to cellwise linear (or bilinear) subcell interpolation. Cellwise quadratic subcell interpolants generate a highly accurate convection-diffusion scheme with excellent phase accuracy. Under constant-coefficient conditions, this is a uniformly third-order polynomial interpolation algorithm (UTOPIA).
Methods for diffusive relaxation in the Pn equation
Hauck, Cory D; Mcclarren, Ryan G; Lowrie, Robert B
2008-01-01
We present recent progress in the development of two substantially different approaches for simulating the so-called of P{sub N} equations. These are linear hyperbolic systems of PDEs that are used to model particle transport in a material medium, that in highly collisional regimes, are accurately approximated by a simple diffusion equation. This limit is based on a balance between function values and gradients of certain variables in the P{sub N} system. Conventional reconstruction methods based on upwinding approximate such gradients with an error that is dependent on the size of the computational mesh. Thus in order to capture the diffusion limit, a given mesh must resolve the dynamics of the continuum equation at the level of the mean-free-path, which tends to zero in the diffusion limit. The two methods analyzed here produce accurate solutions in both collisional and non-collisional regimes; in particular, they do not require resolution of the mean-free-path in order to properly capture the diffusion limit. The first method is a straight-forward application of the discrete Galerkin (DG) methodology, which uses additional variables in each computational cell to capture the balance between function values and gradients, which are computed locally. The second method uses a temporal splitting of the fast and slow dynamics in the P{sub N} system to derive so-called regularized equations for which the diffusion limit is built-in. We focus specifically on the P{sub N} equations for one-dimensional, slab geometries. Preliminary results for several benchmark problems are presented which highlight the advantages and disadvantages of each method. Further improvements and extensions are also discussed.
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.
Modeling the flow in diffuse interface methods of solidification.
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. PMID:26382542
Analytical method to estimate resin cement diffusion into dentin
NASA Astrophysics Data System (ADS)
de Oliveira Ferraz, Larissa Cristina; Ubaldini, Adriana Lemos Mori; de Oliveira, Bruna Medeiros Bertol; Neto, Antonio Medina; Sato, Fracielle; Baesso, Mauro Luciano; Pascotto, Renata Corrêa
2016-05-01
This study analyzed the diffusion of two resin luting agents (resin cements) into dentin, with the aim of presenting an analytical method for estimating the thickness of the diffusion zone. Class V cavities were prepared in the buccal and lingual surfaces of molars (n=9). Indirect composite inlays were luted into the cavities with either a self-adhesive or a self-etch resin cement. The teeth were sectioned bucco-lingually and the cement-dentin interface was analyzed by using micro-Raman spectroscopy (MRS) and scanning electron microscopy. Evolution of peak intensities of the Raman bands, collected from the functional groups corresponding to the resin monomer (C–O–C, 1113 cm-1) present in the cements, and the mineral content (P–O, 961 cm-1) in dentin were sigmoid shaped functions. A Boltzmann function (BF) was then fitted to the peaks encountered at 1113 cm-1 to estimate the resin cement diffusion into dentin. The BF identified a resin cement-dentin diffusion zone of 1.8±0.4 μm for the self-adhesive cement and 2.5±0.3 μm for the self-etch cement. This analysis allowed the authors to estimate the diffusion of the resin cements into the dentin. Fitting the MRS data to the BF contributed to and is relevant for future studies of the adhesive interface.
Thermal diffusivity of nonflat plates using the flash method
Salazar, Agustin; Fuente, Raquel; Apinaniz, Estibaliz; Mendioroz, Arantza
2011-01-15
The flash method is the standard technique to measure the thermal diffusivity of solid samples. It consists of heating the front surface of an opaque sample by a brief light pulse and detecting the temperature evolution at its rear surface. The thermal diffusivity is obtained by measuring the time corresponding to the half maximum of the temperature rise, which only depends on the sample thickness and thermal diffusivity through a simple formula. Up to now, the flash method has been restricted to flat samples. In this work, we extend the flash method to measure the thermal diffusivity of nonflat samples. In particular, we focus on plates with cylindrical and spherical shapes. The theoretical model indicates that the same expression for flat samples can also be applied to cylindrical and spherical plates, except for extremely curved samples. Accordingly, a curvature limit for the application of the expression for flat samples is established. Flash measurements on lead foils of cylindrical shape confirm the validity of the model.
Method of making gas diffusion layers for electrochemical cells
Frisk, Joseph William; Boand, Wayne Meredith; Larson, James Michael
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.
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, Kβ(t)D radβ/sα, where α is time derivative order and β 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(-γβgβδβDf1 tα), a stretched exponential function (SEF) attenuation, while from the fractional derivative model the attenuation is Eα,1(-γβgβδβDf2 tα), a Mittag-Leffler function (MLF) attenuation. The MLF attenuation can be reduced to SEF attenuation when α = 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 ∫0τ Kβ (t)dtα ] . The results obtained in this study are in good agreement with the results in literature. Several expressions that describe signal
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(β)(t)D rad(β)/s(α), where α is time derivative order and β 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(-γ(β)g(β)δ(β)Df1t(α)), a stretched exponential function (SEF) attenuation, while from the fractional derivative model the attenuation is Eα,1(-γ(β)g(β)δ(β)Df2t(α)), a Mittag-Leffler function (MLF) attenuation. The MLF attenuation can be reduced to SEF attenuation when α=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(τ) K(β)(t)dt(α)]. The results obtained in this study are in good agreement with the results in literature. Several expressions that
Instantaneous signal attenuation method for analysis of PFG fractional diffusions.
Lin, Guoxing
2016-08-01
An instantaneous signal attenuation (ISA) method for analyzing pulsed field gradient (PFG) fractional diffusion (FD) has been developed, which is modified from the propagator approach developed in 2001 by Lin et al. for analyzing PFG normal diffusion. Both, the current ISA method and the propagator method have the same fundamental basis that the total signal attenuation (SA) is the accumulation of all the ISA, and the ISA is the average SA of the whole diffusion system at each moment. However, the manner of calculating ISA is different. Unlike the use of the instantaneous propagator in the propagator method, the current method directly calculates ISA as A(K(t'),t'+dt')/A(K(t'),t'), where A(K(t'),t'+dt') and A(K(t'),t') are the SA. This modification makes the current method applicable to PFG FD as the instantaneous propagator may not be obtainable in FD. The ISA method was applied to study PFG SA including the effect of finite gradient pulse widths (FGPW) for free FD, restricted FD and the FD affected by a non-homogeneous gradient field. The SA expressions were successfully obtained for all three types of free FDs while other current methods still have difficulty in obtaining all of them. The results from this method agree with reported results such as that obtained by the effective phase shift diffusion equation (EPSDE) method. The M-Wright phase distribution approximation was also used to derive an SA expression for time FD as a comparison, which agrees with ISA method. Additionally, the continuous-time random walk (CTRW) simulation was performed to simulate the SA of PFG FD, and the simulation results agree with the analytical results. Particularly, the CTRW simulation results give good support to the analytical results including FGPW effect for free FD and restricted time FD based on a fractional derivative model where there have been no corresponding theoretical reports to date. The theoretical SA expressions including FGPW obtained here such as [Formula: see
Instantaneous signal attenuation method for analysis of PFG fractional diffusions
NASA Astrophysics Data System (ADS)
Lin, Guoxing
2016-08-01
An instantaneous signal attenuation (ISA) method for analyzing pulsed field gradient (PFG) fractional diffusion (FD) has been developed, which is modified from the propagator approach developed in 2001 by Lin et al. for analyzing PFG normal diffusion. Both, the current ISA method and the propagator method have the same fundamental basis that the total signal attenuation (SA) is the accumulation of all the ISA, and the ISA is the average SA of the whole diffusion system at each moment. However, the manner of calculating ISA is different. Unlike the use of the instantaneous propagator in the propagator method, the current method directly calculates ISA as A(K(t‧), t‧ + dt‧)/A(K(t‧), t‧), where A(K(t‧), t‧ + dt‧) and A(K(t‧), t‧) are the SA. This modification makes the current method applicable to PFG FD as the instantaneous propagator may not be obtainable in FD. The ISA method was applied to study PFG SA including the effect of finite gradient pulse widths (FGPW) for free FD, restricted FD and the FD affected by a non-homogeneous gradient field. The SA expressions were successfully obtained for all three types of free FDs while other current methods still have difficulty in obtaining all of them. The results from this method agree with reported results such as that obtained by the effective phase shift diffusion equation (EPSDE) method. The M-Wright phase distribution approximation was also used to derive an SA expression for time FD as a comparison, which agrees with ISA method. Additionally, the continuous-time random walk (CTRW) simulation was performed to simulate the SA of PFG FD, and the simulation results agree with the analytical results. Particularly, the CTRW simulation results give good support to the analytical results including FGPW effect for free FD and restricted time FD based on a fractional derivative model where there have been no corresponding theoretical reports to date. The theoretical SA expressions including FGPW obtained
Adsorptive removal of methylene blue by agar: effects of NaCl and ethanol
2012-01-01
Adsorption of methylene blue (MB) on agar was investigated as a function of temperature (308-328 K), different concentrations of NaCl and HCl and various weight percentages of binary mixtures of ethanol with water. It was observed that the maximum experimental adsorption capacity, qm, exp, in water is up to 50 mg g-1 and decreases with increase in weight percentage of ethanol and NaCl and HCl concentration compared to that of water. Analysis of data using ARIAN model showed that MB adsorbs as monomer and dimer on the surface of agar. Binding constants of MB to agar were calculated using the Temkin isotherm. The process is exothermic in water and other solutions. The mean adsorption energy (E) value indicated binding of MB to agar is chemical adsorption. Kinetics of this interaction obeys from the pseudo-second-order model and diffusion of the MB molecules into the agar is the main rate-controlling step. PMID:22339759
Individual based simulations of bacterial growth on agar plates
NASA Astrophysics Data System (ADS)
Ginovart, M.; López, D.; Valls, J.; Silbert, M.
2002-03-01
The individual based simulator, INDividual DIScrete SIMulations (INDISIM) has been used to study the behaviour of the growth of bacterial colonies on a finite dish. The simulations reproduce the qualitative trends of pattern formation that appear during the growth of Bacillus subtilis on an agar plate under different initial conditions of nutrient peptone concentration, the amount of agar on the plate, and the temperature. The simulations are carried out by imposing closed boundary conditions on a square lattice divided into square spatial cells. The simulator studies the temporal evolution of the bacterial population possible by setting rules of behaviour for each bacterium, such as its uptake, metabolism and reproduction, as well as rules for the medium in which the bacterial cells grow, such as concentration of nutrient particles and their diffusion. The determining factors that characterize the structure of the bacterial colony patterns in the presents simulations, are the initial concentrations of nutrient particles, that mimic the amount of peptone in the experiments, and the set of values for the microscopic diffusion parameter related, in the experiments, to the amount of the agar medium.
Measurement of gas diffusion through soils: comparison of laboratory methods.
Allaire, Suzanne E; Lafond, Jonathan A; Cabral, Alexandre R; Lange, Sébastien F
2008-11-01
Gas movement through soils is important for ecosystems and engineering in many ways such as for microbial and plant respiration, passive methane oxidation in landfill covers and oxidation of mine residues. Diffusion is one of the most important gas movement processes and the determination of the diffusion coefficient is a crucial step in any study. Five laboratory methods used for measuring the relative gas diffusion coefficient (D(s)/D(o)) were compared using a loamy sand, a porous media commonly found in agricultural fields and in several engineered structures, such as in landfill final covers. In the absence of macropores, all methods gave rather similar values of D(s)/D(o). Methods allowing the study of microscale variability indicated that the presence of macropores highly influenced gas movement, thus the value of D(s)/D(o), which, near a macropore may be one order of magnitude higher than in regions without macropores. Repacked columns do not allow the study of heterogeneity in D(s)/D(o). Natural spatial variability in D(s)/D(o) due to water distribution and preferential pathways can only be studied in large systems, but these systems are difficult to handle. Advantages and disadvantages of each method are discussed. PMID:18974902
Agar polysaccharides from Gracilaria species (Rhodophyta, Gracilariaceae).
Marinho-Soriano, E
2001-07-26
Yield, physical and chemical properties of agar from three agarophytes species (Gracilaria gracilis, G. dura and G. bursa-pastoris) were determined. The agar yield from the three species varied significantly (P<0.01). The highest yields of agar (34.8%) and the lowest (30%) were obtained from G. bursa-pastoris and G. gracilis, respectively. Highest gel strength (630+/-15 g cm(-2)) was obtained from agar extracted from G. gracilis and lowest from G. bursa-pastoris (26+/-3.6 g cm(-2)). The values of 3,6-anhydrogalactose were similar for G. gracilis and G. dura and there were no significant differences among the species. The sulfate contents varied significantly (P<0.01) and the higher value was obtained from G. bursa-pastoris. Among the three species, G. gracilis showed superior agar quality than the other two species, hence it can be considered a good potential source for industrial use. PMID:11472802
Some basic mathematical methods of diffusion theory. [emphasis on atmospheric applications
NASA Technical Reports Server (NTRS)
Giere, A. C.
1977-01-01
An introductory treatment of the fundamentals of diffusion theory is presented, starting with molecular diffusion and leading up to the statistical methods of turbulent diffusion. A multilayer diffusion model, designed to permit concentration and dosage calculations downwind of toxic clouds from rocket vehicles, is described. The concepts and equations of diffusion are developed on an elementary level, with emphasis on atmospheric applications.
A Numerical Method for Determining Diffusivity from Annealing Experiments
NASA Astrophysics Data System (ADS)
Harris-Kuhlman, K. R.; Kulcinski, G. L.
1998-12-01
Terrestrial analogs of lunar ilmenite (FeTiO3) have been implanted with solar-wind energy 4He at 4 keV and 3He at 3 keV using Plasma Source Ion Implantation (PSII). Isochronal annealing of the samples revealed thermally induced 4He evolution similar to the helium release of the Apollo 11 regoliths reported by Pepin, et. al., [1970]. These annealing experiments are analyzed with a three dimensional numerical method based on Fick's law for diffusion. An iterative method is used to calculate the diffusivity. The code uses an assumed diffusivity to calculate the amount of gas released during a temperature step. The initial depth profile of the implanted species is generated using the TRIM electronic stopping code [Ziegler, 1996]. The calculated value is compared to the measured value and a linear regression is used to calculate a new diffusivity until there is convergence within a specified tolerance level. The diffusivity as a function of temperature is then fitted to an Arrhenius equation. Analysis of results for 4 keV 4He on ilmenite shows two distinct regions of Arrehnius behavior with activation energies of 0.5 +/- 0.1 eV at emperatures below 800 deg C and 1.5 +/- 0.2 eV at temperatures from 800 deg C to 1100 deg C. Pepin, R. O., L. E. Nyquist, D. Phinney, and D. C. Black (1970) "Rare Gases in Apollo 11 Lunar Material," Proceedings of the Apollo 11 Lunar Science Conference, 2, pp. 1435-1454. Ziegler, J. P. (1996) SRIM Instruction Manual: The Stopping and Range of Ions in Matter, (Yorktown, New York: IBM - Research); based on Ziegler, J. P., J. P. Biersack and U. Littmark, The Stopping and Range of Ions in Solids, (New York: Pergamon Press, 1985).
Linear method of fluorescent source reconstruction in a diffusion medium.
Janunts, Edgar; Pöschinger, Thomas; Brünner, Holger; Langenbucher, Achim
2008-01-01
A new method is described for obtaining a 2D reconstruction of a fluorescent source distribution inside a diffusion medium from planar measurements of the emission light at the surface after excitation by a plane wave. Point sources are implanted at known locations of a rectangular phantom. The forward model of the photon transport is based on the diffusion approximation of the radiative transport equation (RTE) for homogeneous media. This can be described by a hierarchical system of two time-independent RTE's, one for the excitation plane wave originating from the external light source to the medium and another one for the fluorescence emission originating from the fluorophore marker to the detector. A linear inverse source problem was solved for image reconstruction. The applicability of the theoretical method is demonstrated in some representative working examples. For an optimization of the problem we used least squares minimization technique. PMID:18826162
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.
A localized meshless method for diffusion on folded surfaces
NASA Astrophysics Data System (ADS)
Cheung, Ka Chun; Ling, Leevan; Ruuth, Steven J.
2015-09-01
Partial differential equations (PDEs) on surfaces arise in a variety of application areas including biological systems, medical imaging, fluid dynamics, mathematical physics, image processing and computer graphics. In this paper, we propose a radial basis function (RBF) discretization of the closest point method. The corresponding localized meshless method may be used to approximate diffusion on smooth or folded surfaces. Our method has the benefit of having an a priori error bound in terms of percentage of the norm of the solution. A stable solver is used to avoid the ill-conditioning that arises when the radial basis functions (RBFs) become flat.
A radial basis function Galerkin method for inhomogeneous nonlocal diffusion
Lehoucq, Richard B.; Rowe, Stephen T.
2016-02-01
We introduce a discretization for a nonlocal diffusion problem using a localized basis of radial basis functions. The stiffness matrix entries are assembled by a special quadrature routine unique to the localized basis. Combining the quadrature method with the localized basis produces a well-conditioned, sparse, symmetric positive definite stiffness matrix. We demonstrate that both the continuum and discrete problems are well-posed and present numerical results for the convergence behavior of the radial basis function method. As a result, we explore approximating the solution to anisotropic differential equations by solving anisotropic nonlocal integral equations using the radial basis function method.
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.
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
Diffusely reflecting paints including polytetrafluoroethylene and method of manufacture
NASA Technical Reports Server (NTRS)
Schutt, J. B.; Shai, M. C. (Inventor)
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.
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)
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.
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.
A diffusive information preservation method for small Knudsen number flows
NASA Astrophysics Data System (ADS)
Fei, Fei; Fan, Jing
2013-06-01
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 ˜ 10-3-10-4 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.
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.
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.
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)
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 φm2RmDm / Lm2, whereas late-time behavior (long tracer tests) depends only on φmRm, 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 φm2RmDm / Lm2, alors que le comportement à long terme
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 φm2RmDm / Lm2, whereas late-time behavior (long tracer tests) depends only on φmRm, 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 φm2RmDm / Lm2, alors que le comportement à long terme
Diffuse optical methods for assessing breast cancer chemotherapy
NASA Astrophysics Data System (ADS)
Tromberg, Bruce J.
2014-03-01
In his talk, "Diffuse Optical Methods for Assessing Breast Cancer Chemotherapy," SPIE Fellow Bruce Tromberg (Beckman Laser Institute and Medical Clinic) describes a method combining frequency domain photon migration, essentially a method of tracking photon motion in tissue, with a NIR spectroscopy technique using 850nm LEDs. The result is a scatter corrected absorption spectra. The technique takes advantage of elevated blood and water levels and decreased lipid levels in the presence of tumors to provide a more accurate mapping of the breast, allowing more effective treatment. Tromberg's team recently completed their first full mapping of the breast and have taken the instrument from a standalone unit to a portable one suitable for travel. In addition to providing feedback to enhance breast cancer treatment, Tromberg expects that this technique will be applicable in treating other forms of cancer as well.
Agar composition affects in vitro screening of biocontrol activity of antagonistic microorganisms.
Bosmans, L; De Bruijn, I; De Mot, R; Rediers, H; Lievens, B
2016-08-01
Agar-based screening assays are the method of choice when evaluating antagonistic potential of bacterial biocontrol-candidates against pathogens. We showed that when using the same medium, but different agar compositions, the activity of a bacterial antagonist against Agrobacterium was strongly affected. Consequently, results from in vitro screenings should be interpreted cautiously. PMID:27166668
van Hal, S. J.; Stark, D.; Lockwood, B.; Marriott, D.; Harkness, J.
2007-01-01
Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing problem. Rapid detection of MRSA-colonized patients has the potential to limit spread of the organism. We evaluated the sensitivities and specificities of MRSA detection by two molecular methods (IDI-MRSA PCR assay and GenoType MRSA Direct PCR assay) and three selective MRSA agars (MRSA ID, MRSASelect, and CHROMagar MRSA), using 205 (101 nasal, 52 groin, and 52 axillary samples) samples from consecutive known MRSA-infected and/or -colonized patients. All detection methods had higher MRSA detection rates for nasal swabs than for axillary and groin swabs. Detection of MRSA by IDI-MRSA was the most sensitive method, independent of the site (94% for nasal samples, 80% for nonnasal samples, and 90% overall). The sensitivities of the GenoType MRSA Direct assay and the MRSA ID, MRSASelect, and CHROMagar MRSA agars with nasal swabs were 70%, 72%, 68%, and 75%, respectively. All detection methods had high specificities (95 to 99%), independent of the swab site. Extended incubation for a further 24 h with selective MRSA agars increased the detection of MRSA, with a corresponding decline in specificity secondary to a significant increase in false-positive results. There was a noticeable difference in test performance of the GenoType MRSA Direct assay in detection of MRSA (28/38 samples [74%]) compared with detection of nonmultiresistant MRSA (17/31 samples [55%]) (susceptible to two or more non-β-lactam antibiotics). This was not observed with selective MRSA agar plates or IDI-MRSA. Although it is more expensive, in addition to rapid turnaround times of 2 to 4 h, IDI-MRSA offers greater detection of MRSA colonization, independent of the swab site, than do conventional selective agars and GenoType MRSA Direct. PMID:17537949
Compact finite volume methods for the diffusion equation
NASA Technical Reports Server (NTRS)
Rose, Milton E.
1989-01-01
The paper describes an approach to treating initial-boundary-value problems by finite volume methods 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 ADI methods.
Extrapolation techniques applied to matrix methods in neutron diffusion problems
NASA Technical Reports Server (NTRS)
Mccready, Robert R
1956-01-01
A general matrix method is developed for the solution of characteristic-value problems of the type arising in many physical applications. The scheme employed is essentially that of Gauss and Seidel with appropriate modifications needed to make it applicable to characteristic-value problems. An iterative procedure produces a sequence of estimates to the answer; and extrapolation techniques, based upon previous behavior of iterants, are utilized in speeding convergence. Theoretically sound limits are placed on the magnitude of the extrapolation that may be tolerated. This matrix method is applied to the problem of finding criticality and neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron fluxes in a nuclear reactor with control rods. The two-dimensional finite-difference approximation to the two-group neutron-diffusion equations is treated. Results for this example are indicated.
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.
Berghaus, Londa J; Giguère, Steeve; Guldbech, Kristen; Warner, Eleanor; Ugorji, Ukachi; Berghaus, Roy D
2015-01-01
MICs of erythromycin, clarithromycin, azithromycin, rifampin, gentamicin, and doxycycline against 101 isolates of Rhodococcus equi were determined by broth macrodilution, disk diffusion, and Etest. Categorical agreement ranged between 85.1 and 100%. Overall, the agreement between Etest and disk diffusion was better than the agreement between broth macrodilution and the agar-based methods. PMID:25378571
Berghaus, Londa J.; Guldbech, Kristen; Warner, Eleanor; Ugorji, Ukachi; Berghaus, Roy D.
2014-01-01
MICs of erythromycin, clarithromycin, azithromycin, rifampin, gentamicin, and doxycycline against 101 isolates of Rhodococcus equi were determined by broth macrodilution, disk diffusion, and Etest. Categorical agreement ranged between 85.1 and 100%. Overall, the agreement between Etest and disk diffusion was better than the agreement between broth macrodilution and the agar-based methods. PMID:25378571
A method for quantitatively estimating diffuse and discrete hydrothermal discharge
NASA Astrophysics Data System (ADS)
Baker, Edward T.; Massoth, Gary J.; Walker, Sharon L.; Embley, Robert W.
1993-07-01
Submarine hydrothermal fluids discharge as undiluted, high-temperature jets and as diffuse, highly diluted, low-temperature percolation. Estimates of the relative contribution of each discharge type, which are important for the accurate determination of local and global hydrothermal budgets, are difficult to obtain directly. In this paper we describe a new method of using measurements of hydrothermal tracers such as Fe/Mn, Fe/heat, and Mn/heat in high-temperature fluids, low-temperature fluids, and the neutrally buoyant plume to deduce the relative contribution of each discharge type. We sampled vent fluids from the north Cleft vent field on the Juan de Fuca Ridge in 1988, 1989 and 1991, and plume samples every year from 1986 to 1991. The tracers were, on average, 3 to 90 times greater in high-temperature than in low-temperature fluids, with plume values intermediate. A mixing model calculates that high-temperature fluids contribute only ˜ 3% of the fluid mass flux but > 90% of the hydrothermal Fe and > 60% of the hydrothermal Mn to the overlying plume. Three years of extensive camera-CTD sled tows through the vent field show that diffuse venting is restricted to a narrow fissure zone extending for 18 km along the axial strike. Linear plume theory applied to the temperature plumes detected when the sled crossed this zone yields a maximum likelihood estimate for the diffuse heat flux of8.9 × 10 4 W/m, for a total flux of 534 MW, considering that diffuse venting is active along only one-third of the fissure system. For mean low- and high-temperature discharge of 25°C and 319°C, respectively, the discrete heat flux must be 266 MW to satisfy the mass flux partitioning. If the north Cleft vent field is globally representative, the assumption that high-temperature discharge dominates the mass flux in axial vent fields leads to an overestimation of the flux of many non-conservative hydrothermal species by about an order of magnitude.
An efficient method for model refinement in diffuse optical tomography
NASA Astrophysics Data System (ADS)
Zirak, A. R.; Khademi, M.
2007-11-01
Diffuse optical tomography (DOT) is a non-linear, ill-posed, boundary value and optimization problem which necessitates regularization. Also, Bayesian methods are suitable owing to measurements data are sparse and correlated. In such problems which are solved with iterative methods, for stabilization and better convergence, the solution space must be small. These constraints subject to extensive and overdetermined system of equations which model retrieving criteria specially total least squares (TLS) must to refine model error. Using TLS is limited to linear systems which is not achievable when applying traditional Bayesian methods. This paper presents an efficient method for model refinement using regularized total least squares (RTLS) for treating on linearized DOT problem, having maximum a posteriori (MAP) estimator and Tikhonov regulator. This is done with combination Bayesian and regularization tools as preconditioner matrices, applying them to equations and then using RTLS to the resulting linear equations. The preconditioning matrixes are guided by patient specific information as well as a priori knowledge gained from the training set. Simulation results illustrate that proposed method improves the image reconstruction performance and localize the abnormally well.
Agar agar-stabilized milled zerovalent iron particles for in situ groundwater remediation.
Velimirovic, Milica; Schmid, Doris; Wagner, Stephan; Micić, Vesna; von der Kammer, Frank; Hofmann, Thilo
2016-09-01
Submicron-scale milled zerovalent iron (milled ZVI) particles produced by grinding macroscopic raw materials could provide a cost-effective alternative to nanoscale zerovalent iron (nZVI) particles for in situ degradation of chlorinated aliphatic hydrocarbons in groundwater. However, the aggregation and settling of bare milled ZVI particles from suspension presents a significant obstacle to their in situ application for groundwater remediation. In our investigations we reduced the rapid aggregation and settling rate of bare milled ZVI particles from suspension by stabilization with a "green" agar agar polymer. The transport potential of stabilized milled ZVI particle suspensions in a diverse array of natural heterogeneous porous media was evaluated in a series of well-controlled laboratory column experiments. The impact of agar agar on trichloroethene (TCE) removal by milled ZVI particles was assessed in laboratory-scale batch reactors. The use of agar agar significantly enhanced the transport of milled ZVI particles in all of the investigated porous media. Reactivity tests showed that the agar agar-stabilized milled ZVI particles were reactive towards TCE, but that their reactivity was an order of magnitude less than that of bare, non-stabilized milled ZVI particles. Our results suggest that milled ZVI particles could be used as an alternative to nZVI particles as their potential for emplacement into contaminated zone, their reactivity, and expected longevity are beneficial for in situ groundwater remediation. PMID:26596889
Pigments of fly agaric (Amanita muscaria).
Stintzing, Florian; Schliemann, Willibald
2007-01-01
The complex pigment pattern of fly agaric (Amanita muscaria) cap skins has been studied by LC-DAD and mass spectrometry. Among the betaxanthins the corresponding derivatives of serine, threonine, ethanolamine, alanine, Dopa, phenylalanine and tryptophan are reported for the first time to contribute to the pigment pattern of fly agarics. Betalamic acid, the chromophoric precursor of betaxanthins and betacyanins, muscaflavin and seco-dopas were also detected. Furthermore, the red-purple muscapurpurin and the red muscarubrin were tentatively assigned while further six betacyanin-like components could not be structurally allocated. Stability studies indicated a high susceptibility of pigment extracts to degradation which led to rapid colour loss thus rendering a complete characterization of betacyanin-like compounds impossible at present. Taking into account these difficulties the presented results may be a starting point for a comprehensive characterization of the pigment composition of fly agarics. PMID:18274277
Le Page, S; van Belkum, A; Fulchiron, C; Huguet, R; Raoult, D; Rolain, J-M
2015-09-01
The disk diffusion (DD) method remains the most popular manual technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories. This is because of its simplicity, reproducibility, and limited cost compared to (automated) microdilution systems, which are usually less sensitive at detecting certain important mechanisms of resistance. Here, we evaluate the PREVI® Isola automated seeder system using a new protocol for spreading bacterial suspensions (eight deposits of calibrated inocula of bacteria, followed by two rounds of rotation) in comparison with manual DD reference testing on a large series of clinical and reference strains. The average time required for seeding one agar plate for DD with this new protocol was 51 s per plate, i.e., 70 agar plates/h. Reproducibility and repeatability was assessed on three reference and three randomly chosen clinical strains, as usually requested by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and was excellent compared to the manual method. The standard deviations of zones of growth inhibition showed no statistical discrimination. The correlation between the two methods, assessed using 294 clinical isolates and a panel of six antibiotics (n = 3,528 zones of growth inhibition measured), was excellent, with a correlation coefficient of 0.977. The new PREVI® Isola protocol adapted for DD had a sensitivity of 99 % and a specificity of 100 % compared to the manual technique for interpreting DD as recommended by the EUCAST. PMID:26092031
Madera-Santana, T J; Freile-Pelegrín, Y; Azamar-Barrios, J A
2014-08-01
The effects of the addition of glycerol (GLY) on the physicochemical and morphological properties of poly(vinyl alcohol) (PVA)-agar films were reported. PVA-agar films were prepared by solution cast method, and the addition of GLY in PVA-agar films altered the optical properties, resulting in a decrease in opacity values and in the color difference (ΔE) of the films. Structural characterization using Fourier transformation infrared (FTIR) spectroscopy and X-ray diffraction (XRD) indicated that the presence of GLY altered the intensity of the bands (from 1200 to 800cm(-1)) and crystallinity. The characterization of the thermal properties indicated that an increase in the agar content produces a decrease in the melting temperature and augments the heat of fusion. Similar tendencies were observed in plasticized films, but at different magnification. The formulation that demonstrated the lowest mechanical properties contained 25wt.% agar, whereas the formulation that contained 75wt.% agar demonstrated a significant improvement. The water vapor transmission rate (WVTR) and surface morphology analysis demonstrated that the structure of PVA-agar films is reorganized upon GLY addition. The physicochemical properties of PVA-agar films using GLY as a plasticizer provide information for the application of this formulation as packaging material for specific food applications. PMID:24875313
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
Standard operating procedure to prepare agar phantoms
NASA Astrophysics Data System (ADS)
Souza, R. M.; Santos, T. Q.; Oliveira, D. P.; Souza, R. M.; Alvarenga, A. V.; Costa-Felix, R. P. B.
2016-07-01
Agar phantoms are widely used as soft tissue mimics and some preparation techniques are described in the literature. There are also standards that describe the recipe of a soft tissue mimicking material (TMM). However some details of manufacture process are not clearly defined. The standardization of the phantom's preparation can produce a metrological impact on the results of the acoustic properties measured. In this direction, this paper presents a standard operating procedure (SOP) to prepare the agar TMM described on the IEC 60601-237.
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.
NASA Astrophysics Data System (ADS)
Yolcu, Cem; Memiç, Muhammet; Şimşek, Kadir; Westin, Carl-Fredrik; Özarslan, Evren
2016-05-01
We study the influence of diffusion on NMR experiments when the molecules undergo random motion under the influence of a force field and place special emphasis on parabolic (Hookean) potentials. To this end, the problem is studied using path integral methods. Explicit relationships are derived for commonly employed gradient waveforms involving pulsed and oscillating gradients. The Bloch-Torrey equation, describing the temporal evolution of magnetization, is modified by incorporating potentials. A general solution to this equation is obtained for the case of parabolic potential by adopting the multiple correlation function (MCF) formalism, which has been used in the past to quantify the effects of restricted diffusion. Both analytical and MCF results were found to be in agreement with random walk simulations. A multidimensional formulation of the problem is introduced that leads to a new characterization of diffusion anisotropy. Unlike the case of traditional methods that employ a diffusion tensor, anisotropy originates from the tensorial force constant, and bulk diffusivity is retained in the formulation. Our findings suggest that some features of the NMR signal that have traditionally been attributed to restricted diffusion are accommodated by the Hookean model. Under certain conditions, the formalism can be envisioned to provide a viable approximation to the mathematically more challenging restricted diffusion problems.
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
Stokkou, Sofia; Geginat, Gernot; Schlüter, Dirk; Tammer, Ina
2015-03-01
Sepsis represents a life-threatening infection requiring the immediate start of antibacterial treatment to reduce morbidity. Thus, laboratories use direct antimicrobial susceptibility testing (AST) to rapidly generate preliminary results from positive blood cultures. As the direct AST has not yet been published to be evaluated with EUCAST breakpoints, the purpose of the study was to investigate the reliability of the direct agar diffusion test to correctly produce AST results from positive monobacterial blood cultures compared with the VITEK2-based definitive AST, when current EUCAST breakpoints were used. A total of 428 isolates from unselected monobacterial routine blood cultures and 110 challenge strains were included. Direct agar diffusion-based and standard VITEK2-based AST of 2803 bacterium-drug combinations yielded a total clinical category agreement of 95.47% with 1.28% very major errors and 3.42% combined major and minor errors. On the species level, very major errors were observed in the species-drug combinations Enterococcus spp.-high-level gentamicin (10.87%) and Staphylococcus spp.-rifampicin (5%), only. No very major errors occurred with Enterobacteriaceae and Pseudomonas aeruginosa. In most species-drug combinations, the direct agar diffusion test using EUCAST breakpoints precisely predicted the result of the definitive antibiotic susceptibility test and, thus, it can be used to optimize empiric antibiotic therapy until definitive results are available. PMID:25883798
NASA Astrophysics Data System (ADS)
Almeida de Matos, Ricardo; da Silva Cordeiro, Thiago; Elgul Samad, Ricardo; Dias Vieira, Nilson; Coronato Courrol, Lilia
2012-11-01
We report a method to create gold nanoparticles of different sizes and shapes using agar-agar water solution and irradiation with light from a xenon lamp, followed by ultrashort laser pulses. No additives, such as solvents, surfactants or reducing agents, were used in the procedure. Laser irradiation (laser ablation) was important to the reduction of the nanoparticles diameter and formation of another shapes. Distilled water was used as solvent and agar-agar (hydrophilic colloid extracted from certain seaweeds) was important for the stabilization of gold nanoparticles, avoiding their agglomeration. The formation of gold nanoparticles was confirmed with ultraviolet-visible absorption and TEM microscopy. The gold nanoparticles acquired spherical, prism, and rod shapes depending on the laser parameters. Variation of laser irradiation parameters as pulse energy, irradiation time and repetition rate was assessed. The relevant mechanisms contributing for the gold nanoparticles production are discussed.
Three-dimensional characterization of bacterial microcolonies on solid agar-based culture media.
Drazek, Laurent; Tournoud, Maud; Derepas, Frédéric; Guicherd, Maryse; Mahé, Pierre; Pinston, Frédéric; Veyrieras, Jean-Baptiste; Chatellier, Sonia
2015-02-01
For the last century, in vitro diagnostic process in microbiology has mainly relied on the growth of bacteria on the surface of a solid agar medium. Nevertheless, few studies focused in the past on the dynamics of microcolonies growth on agar surface before 8 to 10h of incubation. In this article, chromatic confocal microscopy has been applied to characterize the early development of a bacterial colony. This technology relies on a differential focusing depth of the white light. It allows one to fully measure the tridimensional shape of microcolonies more quickly than classical confocal microscopy but with the same spatial resolution. Placing the device in an incubator, the method was able to individually track colonies growing on an agar plate, and to follow the evolution of their surface or volume. Using an appropriate statistical modeling framework, for a given microorganism, the doubling time has been estimated for each individual colony, as well as its variability between colonies, both within and between agar plates. A proof of concept led on four bacterial strains of four distinct species demonstrated the feasibility and the interest of the approach. It showed in particular that doubling times derived from early tri-dimensional measurements on microcolonies differed from classical measurements in micro-dilutions based on optical diffusion. Such a precise characterization of the tri-dimensional shape of microcolonies in their late-lag to early-exponential phase could be beneficial in terms of in vitro diagnostics. Indeed, real-time monitoring of the biomass available in a colony could allow to run well established microbial identification workflows like, for instance, MALDI-TOF mass-spectrometry, as soon as a sufficient quantity of material is available, thereby reducing the time needed to provide a diagnostic. Moreover, as done for pre-identification of macro-colonies, morphological indicators such as three-dimensional growth profiles derived from
Use of agar agar stabilized milled zero-valent iron particles for in situ groundwater remediation
NASA Astrophysics Data System (ADS)
Schmid, Doris; Velimirović, Milica; Wagner, Stephan; Micić 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
Evaluation of Hamaker coefficients using Diffusion Monte Carlo method
NASA Astrophysics Data System (ADS)
Maezono, Ryo; Hongo, Kenta
We evaluated the Hamaker's constant for Cyclohexasilane to investigate its wettability, which is used as an ink of 'liquid silicon' in 'printed electronics'. Taking three representative geometries of the dimer coalescence (parallel, lined, and T-shaped), we evaluated these binding curves using diffusion Monte Carlo method. The parallel geometry gave the most long-ranged exponent, ~ 1 /r6 , in its asymptotic behavior. Evaluated binding lengths are fairly consistent with the experimental density of the molecule. The fitting of the asymptotic curve gave an estimation of Hamaker's constant being around 100 [zJ]. We also performed a CCSD(T) evaluation and got almost similar result. To check its justification, we applied the same scheme to Benzene and compared the estimation with those by other established methods, Lifshitz theory and SAPT (Symmetry-adopted perturbation theory). The result by the fitting scheme turned to be twice larger than those by Lifshitz and SAPT, both of which coincide with each other. It is hence implied that the present evaluation for Cyclohexasilane would be overestimated.
Comparison of dosimetry gels prepared by agar and bovine gelatine
NASA Astrophysics Data System (ADS)
Sağsöz, M. E.; Korkut, Ö.; Alemdar, N.; Aktaş, S.; Çalı, E. B.; Kantarcı, M.
2016-04-01
Gel dosimeters are unique materials capable of showing three dimensional (3D) dose distributions of therapeutic or diagnostic exposures. Fricke gel dosimeters can be considered as chemical dosimeters that rely on a radiation-induced chemical reaction. Dose distribution of Fricke solutions containing Fe+2 ions determines the transformation of acidic, oxygen saturated Fe+2 ions to Fe+3 ions by the ionizing radiation in aqueous solutions. In this study we produced two different types of gel dosimeters using agar and bovine gelatin with similar fabrication methods. We compared the magnetic resonance (MR) T1 imaging responses of these two gel dosimeters to acquire a dose dependency of MR intensities. In conclusion agar gel dosimeters found to be produced easily and more consistent.
NASA Astrophysics Data System (ADS)
Wang, Fei; Kobayashi, Yasukazu; Muhammad, Usman; Wang, Dezheng; Wang, Yao
2016-03-01
The use of numerical analysis to solve the diffusion equation in the uptake method allowed the measurement of molecular diffusivity in a zeolite with a variable pressure around it. The diffusivity was obtained from the data in the measurement of the adsorption isotherm, which means that the diffusivity measurement now needs neither a special instrument nor procedure. The diffusivities of all the gases are readily available from the measurement of their adsorption isotherms and these data include how the diffusivity changes versus adsorbed concentration. The modeling introduced can also be used for a zeolite with a surface barrier.
Method for applying a diffusion barrier interlayer for high temperature components
Wei, Ronghua; Cheruvu, Narayana S.
2016-03-08
A coated substrate and a method of forming a diffusion barrier coating system between a substrate and a MCrAl coating, including a diffusion barrier coating deposited onto at least a portion of a substrate surface, wherein the diffusion barrier coating comprises a nitride, oxide or carbide of one or more transition metals and/or metalloids and a MCrAl coating, wherein M includes a transition metal or a metalloid, deposited on at least a portion of the diffusion barrier coating, wherein the diffusion barrier coating restricts the inward diffusion of aluminum of the MCrAl coating into the substrate.
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.
NASA Astrophysics Data System (ADS)
Ringermacher, Harry I.
2013-04-01
We describe an analysis of a flash thermographic method to measure thermal diffusivity that is particularly insensitive to heat loss mechanisms near thermal boundaries. This approach is an alternative to the "Parker method" which requires that a plate-like region subject to a uniform energy flux must reach a maximum constant temperature in order to obtain an accurate measurement of thermal diffusivity at the half-temperature point in time. The present approach relies on evaluating another unique point, the inflection point, of the same back-side thermal response curve as Parker's or, from the front side, using a contrast versus time curve in the sample region of interest. This inflection point occurs so early in the response history that little heat loss, for example, near heat-sink boundaries or surface convection, is expressed. Since the method is insensitive to the achieved temperature, it is also insensitive to surface emissivity variations.
Lessing, Paul A.
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.
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.
Sy, Cheng Len; Huang, Tsi-Shu; Chen, Chii Shiang; Chen, Yao-Shen; Tsai, Hung-Chin; Wann, Shue-Renn; Wu, Kuan-Sheng; Chen, Jui-Kuang; Lee, Susan Shin-Jung; Liu, Yung-Ching
2016-03-01
Modified disk diffusion (MDD) and checkerboard tests were employed to assess the synergy of combinations of vancomycin and β-lactam antibiotics for 59 clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Mu50 (ATCC 700699). Bacterial inocula equivalent to 0.5 and 2.0 McFarland standard were inoculated on agar plates containing 0, 0.5, 1, and 2 μg/ml of vancomycin. Oxacillin-, cefazolin-, and cefoxitin-impregnated disks were applied to the surface, and the zones of inhibition were measured at 24 h. The CLSI-recommended checkerboard method was used as a reference to detect synergy. The MICs for vancomycin were determined using the Etest method, broth microdilution, and the Vitek 2 automated system. Synergy was observed with the checkerboard method in 51% to 60% of the isolates when vancomycin was combined with any β-lactam. The fractional inhibitory concentration indices were significantly lower in MRSA isolates with higher vancomycin MIC combinations (P < 0.05). The overall agreement between the MDD and checkerboard methods to detect synergy in MRSA isolates with bacterial inocula equivalent to McFarland standard 0.5 were 33.0% and 62.5% for oxacillin, 45.1% and 52.4% for cefazolin, and 43.1% and 52.4% for cefoxitin when combined with 0.5 and 2 μg/ml of vancomycin, respectively. Based on our study, the simple MDD method is not recommended as a replacement for the checkerboard method to detect synergy. However, it may serve as an initial screening method for the detection of potential synergy when it is not feasible to perform other labor-intensive synergy tests. PMID:26677253
An integration factor method for stochastic and stiff reaction-diffusion systems
NASA Astrophysics Data System (ADS)
Ta, Catherine; Wang, Dongyong; Nie, Qing
2015-08-01
Stochastic effects are often present in the biochemical systems involving reactions and diffusions. When the reactions are stiff, existing numerical methods for stochastic reaction diffusion equations require either very small time steps for any explicit schemes or solving large nonlinear systems at each time step for the implicit schemes. Here we present a class of semi-implicit integration factor methods that treat the diffusion term exactly and reaction implicitly for a system of stochastic reaction-diffusion equations. Our linear stability analysis shows the advantage of such methods for both small and large amplitudes of noise. Direct use of the method to solving several linear and nonlinear stochastic reaction-diffusion equations demonstrates good accuracy, efficiency, and stability properties. This new class of methods, which are easy to implement, will have broader applications in solving stochastic reaction-diffusion equations arising from models in biology and physical sciences.
An integration factor method for stochastic and stiff reaction–diffusion systems
Ta, Catherine; Wang, Dongyong; Nie, Qing
2015-08-15
Stochastic effects are often present in the biochemical systems involving reactions and diffusions. When the reactions are stiff, existing numerical methods for stochastic reaction diffusion equations require either very small time steps for any explicit schemes or solving large nonlinear systems at each time step for the implicit schemes. Here we present a class of semi-implicit integration factor methods that treat the diffusion term exactly and reaction implicitly for a system of stochastic reaction–diffusion equations. Our linear stability analysis shows the advantage of such methods for both small and large amplitudes of noise. Direct use of the method to solving several linear and nonlinear stochastic reaction–diffusion equations demonstrates good accuracy, efficiency, and stability properties. This new class of methods, which are easy to implement, will have broader applications in solving stochastic reaction–diffusion equations arising from models in biology and physical sciences.
Luminescent DNA- and agar-based membranes.
Leones, R; Fernandes, M; Ferreira, R A S; Cesarino, I; Lima, J F; Carlos, L D; Bermudez, V de Zea; Magon, C J; Donoso, J P; Silva, M M; Pawlicka, A
2014-09-01
Luminescent materials containing europium ions are investigated for different optical applications. They can be obtained using bio-macromolecules, which are promising alternatives to synthetic polymers based on the decreasing oil resources. This paper describes studies of the DNA- and Agar-europium triflate luminescent membranes and its potential technological applications are expanded to electroluminescent devices. Polarized optical microscopy demonstrated that the samples are birefringent with submicrometer anisotropy. The X-ray diffraction analysis revealed predominantly amorphous nature of the samples and the atomic force microscopy images showed a roughness of the membranes of 409.0 and 136.1 nm for the samples of DNA10Eu and Agar1.11Eu, respectively. The electron paramagnetic resonance spectra of the DNA(n)Eu membranes with the principal lines at g ≈ 2.0 and g ≈ 4.8 confirmed uniform distribution of rare earth ions in a disordered matrix. Moreover, these strong and narrow resonance lines for the samples of DNA(n)Eu when compared to the Agar(n)Eu suggested a presence of paramagnetic radicals arising from the DNA matrix. The emission spectra suggested that the Eu3+ ions occupy a single local environment in both matrices and the excitation spectra monitored around the Eu emission lines pointed out that the Eu3+ ions in the Agar host were mainly excited via the broad band component rather than by direct intra-4f(6) excitation, whereas the opposite case occurred for the DNA-based sample. PMID:25924317
AEROSOL SIZE MEASUREMENT BY ELECTRICAL MOBILITY AND DIFFUSION ANALYSIS - A COMPARISON OF METHODS
The principle of the electrical aerosol analyzer method is reviewed and the diffusion battery method is described in detail. An appendix explains the basis of the calculations used. The diffusion battery method is complicated by counting losses of very small particles, inherent t...
A method for distinguishing between propagons, diffusions, and locons
NASA Astrophysics Data System (ADS)
Seyf, Hamid Reza; Henry, Asegun
2016-07-01
The majority of intuition on phonon transport has been derived from studies of homogenous crystalline solids, where the atomic composition and structure are periodic. For this specific class of materials, the solutions to the equations of motions for the atoms (in the harmonic limit) result in plane wave modulated velocity fields for the normal modes of vibration. However, it has been known for several decades that whenever a system lacks periodicity, either compositional or structural, the normal modes of vibration can still be determined (in the harmonic limit), but the solutions take on different characteristics and many modes may not be plane wave modulated. Previous work has classified the types of vibrations into three primary categories, namely, propagons, diffusions, and locons. One can use the participation ratio to distinguish locons, from propagons and diffusons, which measures the extent to which a mode is localized. However, distinguishing between propagons and diffusons has remained a challenge, since both are spatially delocalized. Here, we present a new method that quantifies the extent to which a mode's character corresponds to a propagating mode, e.g., exhibits plane wave modulation. This then allows for clear and quantitative distinctions between propagons and diffusons. By resolving this issue quantitatively, one can now automate the classification of modes for any arbitrary material or structure, subject to a single constraint that the atoms must vibrate stably around their respective equilibrium sites. Several example test cases are studied including crystalline silicon and germanium, crystalline silicon with different defect concentrations, as well as amorphous silicon, germanium, and silica.
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
Lecithin-agar assay for lecithinase antibodies in serum.
Sibinovic, K H; Brown, F A; Pettigrew, K D; Vought, R L
1971-01-01
A technique for assay of lecithinase antibodies in serum was developed in this laboratory by using a lecithin-agar plate diffusion procedure based on a combination of described plate assays. Egg yolk lipoprotein composed primarily of lecithin was used as a substrate for reaction with free or non-neutralized lecithinase C after incubation of known amounts of lecithinase C with various dilutions of control and test sera. It was found that the size of the reaction zone was a function of enzyme concentration and inversely proportional to the antibody concentration. Accuracy and precision of the assay were determined. In addition, lecithinase antibody levels in sera from experimentally inoculated rats and rabbits and sera from randomly selected human patients were studied. PMID:4322282
Lecithin-Agar Assay for Lecithinase Antibodies in Serum
Sibinovic, Kyle H.; Brown, Freddie A.; Pettigrew, Karen D.; Vought, Robert L.
1971-01-01
A technique for assay of lecithinase antibodies in serum was developed in this laboratory by using a lecithin-agar plate diffusion procedure based on a combination of described plate assays. Egg yolk lipoprotein composed primarily of lecithin was used as a substrate for reaction with free or non-neutralized lecithinase C after incubation of known amounts of lecithinase C with various dilutions of control and test sera. It was found that the size of the reaction zone was a function of enzyme concentration and inversely proportional to the antibody concentration. Accuracy and precision of the assay were determined. In addition, lecithinase antibody levels in sera from experimentally inoculated rats and rabbits and sera from randomly selected human patients were studied. Images PMID:4322282
A Multiresolution Method for Parameter Estimation of Diffusion Processes
Kou, S. C.; Olding, Benjamin P.; Lysy, Martin; Liu, Jun S.
2014-01-01
Diffusion process models are widely used in science, engineering and finance. Most diffusion processes are described by stochastic differential equations in continuous time. In practice, however, data is typically only observed at discrete time points. Except for a few very special cases, no analytic form exists for the likelihood of such discretely observed data. For this reason, parametric inference is often achieved by using discrete-time approximations, with accuracy controlled through the introduction of missing data. We present a new multiresolution Bayesian framework to address the inference difficulty. The methodology relies on the use of multiple approximations and extrapolation, and is significantly faster and more accurate than known strategies based on Gibbs sampling. We apply the multiresolution approach to three data-driven inference problems – one in biophysics and two in finance – one of which features a multivariate diffusion model with an entirely unobserved component. PMID:25328259
NASA Astrophysics Data System (ADS)
Bultinck, E.; Mahieu, S.; Depla, D.; Bogaerts, A.
2010-07-01
'Bohm diffusion' causes the electrons to diffuse perpendicularly to the magnetic field lines. However, its origin is not yet completely understood: low and high frequency electric field fluctuations are both named to cause Bohm diffusion. The importance of including this process in a Monte Carlo (MC) model is demonstrated by comparing calculated ionization rates with particle-in-cell/Monte Carlo collisions (PIC/MCC) simulations. A good agreement is found with a Bohm diffusion parameter of 0.05, which corresponds well to experiments. Since the PIC/MCC method accounts for fast electric field fluctuations, we conclude that Bohm diffusion is caused by fast electric field phenomena.
A new gauge-invariant method for diagnosing eddy diffusivities
NASA Astrophysics Data System (ADS)
Mak, J.; Maddison, J. R.; Marshall, D. P.
2016-08-01
Coarse resolution numerical ocean models must typically include a parameterisation for mesoscale turbulence. A common recipe for such parameterisations is to invoke mixing of some tracer quantity, such as potential vorticity or buoyancy. However, it is well known that eddy fluxes include large rotational components which necessarily do not lead to any mixing; eddy diffusivities diagnosed from unfiltered fluxes are thus contaminated by the presence of these rotational components. Here a new methodology is applied whereby eddy diffusivities are diagnosed directly from the eddy force function. The eddy force function depends only upon flux divergences, is independent of any rotational flux components, and is inherently non-local and smooth. A one-shot inversion procedure is applied, minimising the mis-match between parameterised force functions and force functions derived from eddy resolving calculations. This enables diffusivities associated with the eddy potential vorticity and Gent-McWilliams coefficients associated with eddy buoyancy fluxes to be diagnosed. This methodology is applied to multi-layer quasi-geostrophic ocean gyre simulations. It is found that: (i) a strictly down-gradient scheme for mixing potential vorticity and quasi-geostrophic buoyancy has limited success in reducing the mis-match compared to one with no sign constraint on the eddy diffusivity or Gent--McWilliams coefficient, with prevalent negative signals around the time-mean jet; (ii) the diagnostic is successful away from the jet region and wind-forced top layer; (iii) the locations of closed mean stream lines correlate with signals of positive eddy potential vorticity diffusivity; (iv) there is indication that the magnitude of the eddy potential vorticity diffusivity correlates well with the eddy energy. Implications for parameterisation are discussed in light of these diagnostic results.
Multilevel methods for transport equations in diffusive regimes
NASA Technical Reports Server (NTRS)
Manteuffel, Thomas A.; Ressel, Klaus
1993-01-01
We consider the numerical solution of the single-group, steady state, isotropic transport equation. An analysis by means of the moment equations shows that a discrete ordinate S(sub N) discretization in direction (angle) with a least squares finite element discretization in space does not behave properly in the diffusion limit. A scaling of the S(sub N) equations is introduced so that the least squares discretization has the correct diffusion limit. For the resulting discrete system a full multigrid algorithm was developed.
Thermal diffusivity measurement by lock-in photothermal shadowgraph method
NASA Astrophysics Data System (ADS)
Cifuentes, A.; Alvarado, S.; Cabrera, H.; Calderón, A.; Marín, E.
2016-04-01
Here, we present a novel application of the shadowgraph technique for obtaining the thermal diffusivity of an opaque solid sample, inspired by the orthogonal skimming photothermal beam deflection technique. This new variant utilizes the shadow projected by the sample when put against a collimated light source. The sample is then heated periodically by another light beam, giving rise to thermal waves, which propagate across it and through its surroundings. Changes in the refractive index of the surrounding media due to the heating distort the shadow. This phenomenon is recorded and lock-in amplified in order to determine the sample's thermal diffusivity.
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.
Diffusion NMR methods applied to xenon gas for materials study.
Mair, R W; Rosen, M S; Wang, R; Cory, D G; Walsworth, R L
2002-12-01
We report initial NMR studies of (i) xenon gas diffusion in model heterogeneous porous media and (ii) continuous flow laser-polarized xenon gas. Both areas utilize the pulsed gradient spin-echo (PGSE) techniques in the gas phase, with the aim of obtaining more sophisticated information than just translational self-diffusion coefficients--a brief overview of this area is provided in the Introduction. The heterogeneous or multiple-length scale model porous media consisted of random packs of mixed glass beads of two different sizes. We focus on observing the approach of the time-dependent gas diffusion coefficient, D(t) (an indicator of mean squared displacement), to the long-time asymptote, with the aim of understanding the long-length scale structural information that may be derived from a heterogeneous porous system. We find that D(t) of imbibed xenon gas at short diffusion times is similar for the mixed bead pack and a pack of the smaller sized beads alone, hence reflecting the pore surface area to volume ratio of the smaller bead sample. The approach of D(t) to the long-time limit follows that of a pack of the larger sized beads alone, although the limiting D(t) for the mixed bead pack is lower, reflecting the lower porosity of the sample compared to that of a pack of mono-sized glass beads. The Pade approximation is used to interpolate D(t) data between the short- and long-time limits. Initial studies of continuous flow laser-polarized xenon gas demonstrate velocity-sensitive imaging of much higher flows than can generally be obtained with liquids (20-200 mm s-1). Gas velocity imaging is, however, found to be limited to a resolution of about 1 mm s-1 owing to the high diffusivity of gases compared with liquids. We also present the first gas-phase NMR scattering, or diffusive-diffraction, data, namely flow-enhanced structural features in the echo attenuation data from laser-polarized xenon flowing through a 2 mm glass bead pack. PMID:12807139
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.
Hill, D R
1996-09-01
This project was undertaken to find ways to enhance fungus colony maturation, to make viewing of fungal cultures easier, and to reduce disruption of the fungal structures to be observed for identification. Accordingly, a technique using a thin (0.2-mm) agar film that avoids problems inherent in traditional methods of fungal culture and identification was developed. In addition, to accommodate the 0.2-mm layer of agar film and a contiguous thicker 4-mm section of agar, a sealable fungal culture case that fits within microscope stage calipers and under the objective lenses was invented. The growth and identification of 28 organisms were evaluated in the sealable fungal culture cases and on double-pour agar plates by using potato dextrose agar in both. Compared with results obtained with the double-pour agar plates (rated as "good"), fungal growth and identification with the sealable fungal culture case were superior (rated as "excellent") (P < 0.05, chi-square test). The thin agar film limits excessive mycelial growth, while it often promotes complete sporulation or other forms of maturation of the fungal colony. More importantly, the thin agar film allows direct microscopic viewing of the developing fungal colonies. The portion of the sealable fungal culture case with the 4-mm layer of agar can be used for evaluation of colony pigment and texture. In conclusion, this new sealable fungal culture case allows direct viewing and earlier fungal species identification with greater intrinsic safety. PMID:8862573
Agar-Gel Precipitin Technique in Anthrax Antibody Determinations1
Ray, John G.; Kadull, Paul J.
1964-01-01
A modification of the agar-gel precipitation inhibition technique of Thorne and Belton for detecting anthrax antibodies reduces inconsistency of visually determined end points on the same sera observed by different technicians. Determination of the minimal reacting concentrations of the anthrax antigen and antibody reagents, modifications of the visualization apparatus, methods for combining reagents, and length of incubation periods contribute to the ease of the end-point determinations and the uniformity of results. When compared with the previous technique, the modified procedure is less time-consuming while retaining satisfactory reproducibility, simplicity, specificity, and sensitivity. Images FIG. 1 FIG. 2 PMID:14201088
Bilal, Muhammad; Asgher, Muhammad; Shahid, Muhammad; Bhatti, Haq Nawaz
2016-05-01
Immobilization of enzymes has been regarded as an efficient approach to develop biocatalyst with improved activity and stability characteristics under reaction conditions. In the present study, purified manganese peroxidase (MnP) from Ganoderma lucidum IBL-05 was immobilized in agar-agar support using entrapment technique. Maximum immobilization yield was accomplished at 4.0% agar-agar gel. The immobilized MnP exhibited better resistance to changes in pH and temperature than the free enzyme, with optimal conditions being pH 6.0 and 50 °C. The kinetic parameters Km and Kcat/Km for free and entrapped MnP were calculated to be 65.6 mM and 6.99 M(-1) s(-1), and 82 mM and 8.15 M(-1) s(-1), respectively. Thermo-stability was significantly improved after immobilization. After 120 h, the insolubilized MnP retained its activity up to 71.9% and 60.3% at 30 °C and 40 °C, respectively. It showed activity until 10th cycle and retained 74.3% residual activity after 3th cycle. The effects of H2O2, ionic strength and potential inhibitors on activity of free and immobilized enzyme were investigated. Moreover, the decolorization of three structurally different dyes was monitored in order to assess the degrading capability of the entrapped MnP. The decolorization efficiencies for all the tested dyes were 78.6-84.7% after 12h. The studies concluded that the toxicity of dyes aqueous solutions was significantly reduced after treatment. The remarkable catalytic, thermo-stability and re-cycling features of the agar-agar immobilized MnP display a high potential for biotechnological applications. PMID:26854887
Neut, C; Pathak, J; Romond, C; Beerens, H
1985-01-01
The lactose sulfite (LS) medium recommended for the detection and identification of Clostridium perfringens in foods was compared with a reference method using tryptose-sulfite-cycloserine (TSC) agar for the enumeration of this organism in a variety of foods and food ingredients. C. perfringens was detected and enumerated in 17 of the 54 samples examined with LS broth, but its presence could be confirmed in only 9 of the samples with TSC agar. In only 2 instances, C. perfringens was detected on TSC agar but not in LS broth. A positive response (FeS + and gas +) in LS broth incubated at 46 degrees C always corresponded to the presence of C. perfringens; whereas the black colonies formed on TSC agar incubated at 37 degrees C were frequently found to be Clostridium species other than C. perfringens. Thus, because of its highly selective nature, LS broth was superior to TSC agar for enumerating and confirming the small numbers of C. perfringens that were present in a majority of the samples. This was especially true when other clostridia were also present. Besides its greater selectivity and sensitivity, LS broth had the additional advantages of requiring less work and giving confirmed results within 24-48 h compared with 3 days for the TSC agar method. PMID:2865247
Method of independently operating a group of stages within a diffusion cascade
Benedict, Manson; Fruit, Allen J.; Levey, Horace B.
1976-06-08
1. A method of operating a group of the diffusion stages of a productive diffusion cascade with countercurrent flow, said group comprising a top and a bottom stage, which comprises isolating said group from said cascade, circulating the diffused gas produced in said top stage to the feed of said bottom stage while at the same time circulating the undiffused gas from said bottom stage to the feed of said top stage whereby major changes in
Evaluation of use of a new chromogenic agar in detection of urinary tract pathogens.
Samra, Z; Heifetz, M; Talmor, J; Bain, E; Bahar, J
1998-04-01
CHROMagar Orientation, a new chromogenic medium, was evaluated for the detection and differentiation of gram-positive and gram-negative pathogenic microorganisms in 900 urine samples from hospitalized patients. Performance characteristics of the medium were evaluated in comparison to those of 5% sheep blood and MacConkey agars by direct inoculation of the urine samples on the three media. Four gram-negative and two gram-positive strains as well as one yeast control strain from the American Type Culture Collection were used to ensure quality control. CHROMagar Orientation succeeded in detecting all the urine pathogens that were detected by the reference media, including gram-negative bacilli, staphylococci, streptococci, and yeasts. Colony color and morphology on CHROMagar Orientation accurately differentiated Escherichia coli, Proteus mirabilis, Proteus vulgaris, Pseudomonas aeruginosa, and Acinetobacter spp. Owing to the similarity in the pigmentation produced by Klebsiella, Enterobacter, and Citrobacter isolates, the medium failed to distinguish among them; however, these isolates were easily recognized as coliforms because of their metallic blue coloration. Staphylococci were clearly perceptible: S. aureus and S. epidermidis grow in regular-size colonies that range from opaque white to yellowish, and S. saprophyticus produces opaque pink colonies. All streptococcus strains, including those from groups B and C, were detected. They grow as undifferentiated flat dry diffused colonies, and additional tests were required for identification. Enterococci were easily discriminated by their strong turquoise pigmentation and their typical growth on the agar's surface. Yeast grow in typical creamy wet convex colonies. The accuracy of antibiotic susceptibility determinations according to standard methods was also tested by picking isolates directly from CHROMagar Orientation. The results showed excellent correlation with those obtained with microorganisms picked from
Drinking water regulations under the Final Coliform Rule require that total coliform-positive drinking water samples be examined for the presence of Escherichia coli or fecal coliforms. The current U.S. Environmental Protection Agency-approved membrane filter (MF) method for E. c...
Kernel weights optimization for error diffusion halftoning method
NASA Astrophysics Data System (ADS)
Fedoseev, Victor
2015-02-01
This paper describes a study to find the best error diffusion kernel for digital halftoning under various restrictions on the number of non-zero kernel coefficients and their set of values. As an objective measure of quality, WSNR was used. The problem of multidimensional optimization was solved numerically using several well-known algorithms: Nelder- Mead, BFGS, and others. The study found a kernel function that provides a quality gain of about 5% in comparison with the best of the commonly used kernel introduced by Floyd and Steinberg. Other kernels obtained allow to significantly reduce the computational complexity of the halftoning process without reducing its quality.
Volume imaging with diffuse light: method, device, and clinical application
NASA Astrophysics Data System (ADS)
Hampel, Uwe; Schleicher, Eckhard; Freyer, Richard
2000-11-01
Diffuse optical imaging and tomography is of some interest in the diagnosis of testicular pathologies. For a clinical evaluation of 3D optical tomography a special laser scanning device as well as dedicated tomography algorithms have been developed. With the device we are able to obtain continuous- wave tomographic scans from an object under investigation using different laser wavelengths. Tomographic image reconstruction is based on the solution of the linearized inverse problem of optical absorption imaging for a three- dimensional volume. Priority is given to a spatial resolution adapted volume discretization and an efficient matrix solution algorithm based on singular value decomposition.
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.
A Review of Diffusion Tensor Magnetic Resonance Imaging Computational Methods and Software Tools
Hasan, Khader M.; Walimuni, Indika S.; Abid, Humaira; Hahn, Klaus R.
2010-01-01
In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766
A review of diffusion tensor magnetic resonance imaging computational methods and software tools.
Hasan, Khader M; Walimuni, Indika S; Abid, Humaira; Hahn, Klaus R
2011-12-01
In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766
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
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.
Validation of the diffusion-barrier charcoal canister method
Martz, D.E.; George, J.L.; Mamich, S.T.; Langner, G.H. Jr.
1989-05-01
A six-month study was conducted by the Technical Measurements Center, US Department of Energy Grand Junction Projects Office, to evaluate the accuracy and reliability of indoor radon measurements using an intermittent diffusion-barrier charcoal canister sampling protocol. Diffusion-barrier charcoal canisters (DBCC) were exposed for seven days in sixteen occupied residences each week during the 26-week study. The radon concentrations measured by the DBCCs were compared to radon concentrations measured by triplicate sets of four different types of alpha-track monitors and integrated hourly radon concentrations measured by a Pylon Model AB-5 continuous radon monitor. The results were also compared with radon-daughter concentrations measured in these same residences by an Eberline WLM-1 working level monitor. Excellent agreement was observed between the integrated mean radon concentrations measured by the DBCCs compared with the six-month alpha-track results, and between the weekly DBCC readings and average weekly radon concentrations measured by the Pylon radon monitors. An intermittent sampling protocol employing six weekly DBCC measurements spaced approximately every two months throughout the year should provide estimates of the average annual indoor radon concentrations that meet the criteria established for the Grand Junction Remedial Action Program. 9 refs., 17 figs., 9 tabs.
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.
Odlaug, T E; Pflug, I J
1977-10-01
Yeast extract agar, pork infusion agar, and modifications of these media were used to recover heated Clostridium botulinum spores. The D- and z-values were determined. Two type A strains and one type B strain of C. botulinum were studied. In all cases the D-values were largest when the spores were recovered in yeast extract agar, compared to the D-values for spores recovered in pork infusion agar. The z-values for strains 62A and A16037 were largest when the spores were recovered in pork infusion agar. The addition of sodium bicarbonate and sodium thioglycolate to pork infusion agar resulted in D-values for C. botulinum 62A spores similar to those for the same spores recovered in yeast extract agar. The results suggest that sodium bicarbonate and sodium thioglycolate should be added to recovery media for heated C. botulinum spores to obtain maximum plate counts. PMID:335970
Experimental Verification to Obtain Intrinsic Thermal Diffusivity by Laser-Flash Method
NASA Astrophysics Data System (ADS)
Akoshima, M.; Hay, B.; Neda, M.; Grelard, M.
2013-05-01
There is a need to obtain highly reliable values of thermophysical properties. The thermal conductivity of solids is often calculated from the thermal diffusivity, specific heat, and density, respectively, measured by the laser-flash method, differential scanning calorimetry, and Archimedes' method. The laser-flash method is one of the most well-known methods for measuring the thermal diffusivity of solids above room temperature. This method is very convenient to measure the thermal diffusivity without contact in a short time. On the other hand, it is considered as an absolute reference measurement method, in particular, because only measurements of basic quantities such as time, temperature, length, and electrical quantities are required, and because the uncertainty of measurement can be analytically evaluated. However, it could be difficult in some cases to obtain reliable thermal-diffusivity values. The measurement results can indeed depend on experimental conditions; in particular, the pulse heating energy. A procedure to obtain the intrinsic thermal-diffusivity value was proposed by National Metrology Institute of Japan (NMIJ). Here, "intrinsic" means unique for the material, independent of measurement conditions. In this method, apparent thermal-diffusivity values are first measured by changing the pulse heating energy at the same test temperature. Then, the intrinsic thermal diffusivity is determined by extrapolating these apparent thermal diffusivities to a zero energy pulse. In order to verify and examine the applicability of the procedure for intrinsic thermal-diffusivity measurements, we have measured the thermal diffusivity of some materials (metals, ceramics) using the laser-flash method with this extrapolation procedure. NMIJ and Laboratoire National de Metrologie et d'essais (LNE) have laser-flash thermal-diffusivity measurement systems that are traceable to SI units. The thermal diffusivity measured by NMIJ and LNE on four materials shows good
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
Maki, Yasuyuki; Furusawa, Kazuya; Yasuraoka, Sho; Okamura, Hideki; Hosoya, Natsuki; Sunaga, Mari; Dobashi, Toshiaki; Sugimoto, Yasunobu; Wakabayashi, Katsuzo
2014-08-01
Molecular orientation in anisotropic gels of chitosan, Curdlan and DNA obtained by dialysis of those aqueous solutions in gelation-inducing solutions was investigated. In this diffusion method (or dialysis method), the gel formation was induced by letting small molecules diffuse in or out of the polymer solutions through the surface. For the gels of DNA and chitosan, the polymer chains aligned perpendicular to the diffusion direction. The same direction of molecular orientation was observed for the Curdlan gel prepared in the dialysis cell. On the other hand, a peculiar nature was observed for the Curdlan gel prepared in the dialysis tube: the molecular orientation was perpendicular to the diffusion direction in the outermost layer of the gel, while the orientation was parallel to the diffusion direction in the inner translucent layer. The orientation parallel to the diffusion direction is attributed to a small deformation of the inner translucent layer caused by a slight shrinkage of the central region after the gel formation. At least near the surface of the gel, the molecular orientation perpendicular to the diffusion direction is a universal characteristic for the gels prepared by the diffusion method. PMID:24751255
NASA Technical Reports Server (NTRS)
Miller, Teresa Y.; He, Xiao-Min; Carter, Daniel C.
1992-01-01
Crystals of human serum albumin have been successfully grown in a variety of gels using crystallization conditions otherwise equivalent to those utilized in the popular hanging-drop vapor-equilibrium method. Preliminary comparisons of gel grown crystals with crystals grown by the vapor diffusion method via both ground-based and microgravity methods indicate that crystals superior in size and quality may be grown by limiting solutal convection. Preliminary X-ray diffraction statistics are presented.
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
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
Diffusion limitations of the lung - comparison of different measurement methods.
Preisser, A M; Seeber, M; Harth, V
2015-01-01
Pulmonary fibrosis leads to a decrease of oxygen diffusion, in particular during exercise. Bronchial obstruction also could decrease the partial pressure of oxygen (P(a)O(2)). In this study we investigated the validity of blood gas content, especially P(a)O(2) and P(a)O(2) affected by hyperventilation (P(a)O(2corr)) and alveolo-arterial oxygen gradient (P(A-a)O(2)) in comparison with the CO diffusion capacity (DLCO) in different lung diseases. A total of 250 subjects were studied (52.3 ± 12.5 year; F/M 40/210), among which there were 162 subjects with different lung disorders and 88 healthy controls. Pearson's correlation coefficients (r) of DLCO with P(a)O(2), P(a)O(2corr), and PA-aO(2) were analyzed in each group. The results show that the diagnostic power of P(A-a)O(2) against P(a)O(2corr) was equivalent, especially during exercise (r = -0.89 and -0.92, respectively). DLCO showed only weak correlations with P(a)O(2corr) and P(A-a)O(2) (r = 0.17 and -0.19, respectively). In conclusion, DLCO shows a better match with blood gas content during exercise than at rest during which it is routinely tested. Thus, the exercise test is advisable. The P(A-a)O(2) takes into account the level of ventilation, which makes it correlate better with DLCO rather than with blood gas content. The most significant problems in clinical evaluation of blood gas parameters during exercise are the insufficiently defined limits of normal-to-pathological range. PMID:25381558
Automatic Surface Inoculation of Agar Trays1
Wilkins, Judd R.; Mills, Stacey M.; Boykin, Elizabeth H.
1972-01-01
A machine is described which automatically inoculates a plastic tray containing agar media with a culture by use of either a conventional inoculating loop or a cotton swab. Isolated colonies were obtained with an inoculating loop when a heavy inoculum (109 cells/ml) was used or with a cotton swab when a light inoculum (ca. 104 cells/ml) was used. Trays containing combinations of differential or selective media were used to (i) separate mixtures of gram-positive and gram-negative bacteria, (ii) facilitate isolation of organisms from clinical specimens, and (iii) compare colony growth characteristics of pure cultures. The design of the machine is simple, it is easy to use, and it relieves the operator from the manual task of streaking cultures. Images PMID:16349943
Poisoning with brown fly agaric, Amanita regalis.
Elonen, E; Tarssanen, L; Härkönen, M
1979-01-01
Three patients ate different amounts of a common northern mushroom, brown fly agaric, Amanita regalis. All of them believed they had eaten delicious parasol mushrooms, Macrolepiota procera. The symptoms of poisoning began 1--2 hours after ingestion of the mushrooms. All the patients had marked gastrointestinal symptoms: nausea and heavy vomiting. Two had central nervous system manifestations and cholinergic symptoms: hallucinations, confusion, or loss of consciousness as well as copious salivation, or sweating. All patients recovered within 4--24 hours without any damage to liver, kidneys or central nervous system. It seems that cooking the mushrooms does not completely neutralize the toxic agents of Amanita regalis. The analysis of fried mushrooms shows that it may be possible to identify mushrooms reliably from the remains of a meal. PMID:760400
Comparative study of methods used to estimate ionic diffusion coefficients using migration tests
Narsilio, G.A. Li, R. Pivonka, P. Smith, D.W.
2007-08-15
Ionic diffusion coefficients are estimated rapidly using electromigration tests. In this paper, electromigration tests are accurately simulated by numerically solving the Nernst-Planck (NP) equation (coupled with the electroneutrality condition (EN)) using the finite element method. Numerical simulations are validated against experimental data obtained elsewhere [E. Samson, J. Marchand, K.A. Snyder, Calculation of ionic diffusion coefficients on the basis of migration test results, Materials and Structures/Materiaux et Constructions 36 (257) (2003) 156-165., H. Friedmann, O. Amiri, A. Ait-Mokhtar, A direct method for determining chloride diffusion coefficient by using migration test, Cement and Concrete Research 34 (11) (2004) 1967-1973.]. It is shown that migration due to the non-linear electric potential completely overwhelms diffusion due to concentration gradients. The effects of different applied voltage differences and chloride source concentrations on estimations of chloride diffusion coefficients are explored. We show that the pore fluid within concrete and mortar specimens generally differs from the curing solution, lowering the apparent diffusion coefficient, primarily due to interactions of chloride ions with other ions in the pore fluid. We show that the variation of source chloride concentration strongly affects the estimation of diffusion coefficients in non-steady-state tests; however this effect vanishes under steady-state conditions. Most importantly, a comparison of diffusion coefficients obtained from sophisticated analyses (i.e., NP-EN) and a variety of commonly used simplifying methods to estimate chloride diffusion coefficients allows us to identify those methods and experimental conditions where both approaches deliver good estimates for chloride diffusion coefficients. Finally, we demonstrate why simultaneous use and monitoring of current density and fluxes are recommended for both the non-steady and steady-state migration tests.
A method for optimizing the cosine response of solar UV diffusers
NASA Astrophysics Data System (ADS)
Pulli, Tomi; Kärhä, Petri; Ikonen, Erkki
2013-07-01
Instruments measuring global solar ultraviolet (UV) irradiance at the surface of the Earth need to collect radiation from the entire hemisphere. Entrance optics with angular response as close as possible to the ideal cosine response are necessary to perform these measurements accurately. Typically, the cosine response is obtained using a transmitting diffuser. We have developed an efficient method based on a Monte Carlo algorithm to simulate radiation transport in the solar UV diffuser assembly. The algorithm takes into account propagation, absorption, and scattering of the radiation inside the diffuser material. The effects of the inner sidewalls of the diffuser housing, the shadow ring, and the protective weather dome are also accounted for. The software implementation of the algorithm is highly optimized: a simulation of 109 photons takes approximately 10 to 15 min to complete on a typical high-end PC. The results of the simulations agree well with the measured angular responses, indicating that the algorithm can be used to guide the diffuser design process. Cost savings can be obtained when simulations are carried out before diffuser fabrication as compared to a purely trial-and-error-based diffuser optimization. The algorithm was used to optimize two types of detectors, one with a planar diffuser and the other with a spherically shaped diffuser. The integrated cosine errors—which indicate the relative measurement error caused by the nonideal angular response under isotropic sky radiance—of these two detectors were calculated to be f2=1.4% and 0.66%, respectively.
Efficacy of capsicum oleoresin nanocapsules formulation by the modified emulsion-diffusion method.
Surassmo, Suvimol; Min, Sang-Gi; Bejrapha, Piyawan; Choi, Mi-Jung
2011-01-01
In this study, we investigated the effect of high pressure homogenizer on the physico-chemical properties of capsicum oleoresin loaded nanoemulsion (NE) or nanocapsules (NCs) based on the emulsion-diffusion method. According to the application stage of high pressure process at principle emulsion-diffusion method, NCs was prepared by conventional-emulsion-diffusion method (CED), modified-emulsion-microfluidization-diffusion method (MEMD) and modified-emulsion-diffusion-microfluidization method (MEDM). The nanocapsules of MEMD showed homogeneous and the smallest particle size as compared with CED. In addition, MEMD presented the surface tension at the value 36.5 mN/m. The encapsulated capsicum oleoresin was generated the bright color and suppressed the dark red color. Furthermore, MEMD gave the high encapsulation efficiency of capsicum oleoresin around 95% and showed the slow release rate. On the other hand, MEDM presented the non-homogeneous and agglomerate of the particle, low percentage of encapsulation efficiency and the high initial release rate when compared with CED and MEMD methods. According these results, it was supposed that the microfluidization was interesting technique to ameliorate the physical properties and efficiency of NCs. However, it was depending on the appropriate combination of microfluidization based on the emulsion-diffusion method. PMID:21446515
A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems
Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing
2012-01-01
An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849
Laarhoven, Bob; Elissen, H J H; Temmink, H; Buisman, C J N
2016-01-01
An agar sediment test was developed to evaluate the suitability of organic waste streams from the food industry for recovering nutrients by the aquatic worm Lumbriculus variegatus (Lv). The effects of agar gel, sand, and food quantities in the sediment test on worm growth, reproduction, and water quality were studied. Agar gel addition ameliorated growth conditions by reducing food hydrolysis and altering sediment structure. Best results for combined reproduction and growth were obtained with 0.6% agar-gel (20 ml), 10 g. fine sand, 40 g. coarse sand, and 105 mg fish food (Tetramin). With agar gel, ingestion and growth is more the result of addition of food in its original quality. Final tests with secondary potato starch sludge and wheat bran demonstrated that this test is appropriate for the comparison of solid feedstuffs and suspended organic waste streams. This test method is expected to be suitable for organic waste studies using other sediment dwelling invertebrates. PMID:26937632
Laarhoven, Bob; Elissen, H. J. H.; Temmink, H.; Buisman, C. J. N.
2016-01-01
An agar sediment test was developed to evaluate the suitability of organic waste streams from the food industry for recovering nutrients by the aquatic worm Lumbriculus variegatus (Lv). The effects of agar gel, sand, and food quantities in the sediment test on worm growth, reproduction, and water quality were studied. Agar gel addition ameliorated growth conditions by reducing food hydrolysis and altering sediment structure. Best results for combined reproduction and growth were obtained with 0.6% agar-gel (20 ml), 10 g. fine sand, 40 g. coarse sand, and 105 mg fish food (Tetramin). With agar gel, ingestion and growth is more the result of addition of food in its original quality. Final tests with secondary potato starch sludge and wheat bran demonstrated that this test is appropriate for the comparison of solid feedstuffs and suspended organic waste streams. This test method is expected to be suitable for organic waste studies using other sediment dwelling invertebrates. PMID:26937632
Parameters estimation using the first passage times method in a jump-diffusion model
NASA Astrophysics Data System (ADS)
Khaldi, K.; Meddahi, S.
2016-06-01
The main purposes of this paper are two contributions: (1) it presents a new method, which is the first passage time (FPT method) generalized for all passage times (GPT method), in order to estimate the parameters of stochastic Jump-Diffusion process. (2) it compares in a time series model, share price of gold, the empirical results of the estimation and forecasts obtained with the GPT method and those obtained by the moments method and the FPT method applied to the Merton Jump-Diffusion (MJD) model.
An efficient wavelet analysis method to film-pore diffusion model arising in mathematical chemistry.
Hariharan, G
2014-04-01
In this paper, we have established an efficient Legendre wavelet based approximation method to solve film-pore diffusion model arising in engineering. Film-pore diffusion model is widely used to determine study the kinetics of adsorption systems. The use of Legendre wavelet based approximation method is found to be accurate, simple, fast, flexible, convenient, and computationally attractive. It is shown that film-pore diffusion model satisfactorily describe kinetics of methylene blue adsorption onto the three low-cost adsorbents, Guava, teak and gulmohar plant leaf powders, used in this study. PMID:24562792
Evaluation of CP Chromo Select Agar for the enumeration of Clostridium perfringens from water.
Manafi, Mammad; Waldherr, Kerstin; Kundi, Michael
2013-10-01
The European Directive on drinking water quality has included mCP agar as the reference method for recovering Clostridium perfringens from drinking waters. In the present study, three media (mCP, TSCF and CP Chromo Select Agar) were evaluated for recovery of C. perfringens in different surface water samples. Out of 139 water samples, using a membrane filtration technique, 131 samples (94.2%) were found to be presumptively positive for C. perfringens in at least one of the culture media. Green colored colonies on CP Chromo Select Agar (CCP agar) were counted as presumptive C. perfringens isolates. Out of 483 green colonies on CCP agar, 96.3% (465 strains, indole negative) were identified as C. perfringens, and 15 strains (3.1%) were indole positive and were identified as Clostridium sordellii, Clostridium bifermentans or Clostridium tetani. Only 3 strains (0.6%) gave false positive results and were identified as Clostridium fallax, Clostridium botulinum, and Clostridium tertium. Variance analysis of the data obtained shows statistically no significant differences in the counts obtained between media employed in this work. The mCP method is very onerous for routine screening and bacterial colonies could not be used for further biochemical testing. The colonies on CCP and TSCF were easy to count and subculture for confirmation tests. TSCF detects sulfite-reducing clostridia, including species other than C. perfringens, and in some cases excessive blackening of the agar frustrated counting of the colonies. If the contamination was too high, TSCF did not consistently produce black colonies and as a consequence, the colonies were white and gave false negative results. On the other hand, the identification of typical and atypical colonies isolated from all media demonstrated that CCP agar was the most useful medium for C. perfringens recovery in water samples. PMID:23816139
Performance of CHROMAGAR candida and BIGGY agar for identification of yeast species
Yücesoy, Mine; Marol, Serhat
2003-01-01
Background The importance of identifying the pathogenic fungi rapidly has encouraged the development of differential media for the presumptive identification of yeasts. In this study two differential media, CHROMagar Candida and bismuth sulphite glucose glycine yeast agar, were evaluated for the presumptive identification of yeast species. Methods A total number of 270 yeast strains including 169 Candida albicans, 33 C. tropicalis, 24 C. glabrata, 18 C. parapsilosis, 12 C. krusei, 5 Trichosporon spp., 4 C. kefyr, 2 C. lusitaniae, 1 Saccharomyces cerevisiae and 1 Geotrichum candidum were included. The strains were first identified by germ tube test, morphological characteristics on cornmeal tween 80 agar and Vitek 32 and API 20 C AUX systems. In parallel, they were also streaked onto CHROMagar Candida and bismuth sulphite glucose glycine yeast agar plates. The results were read according to the color, morphology of the colonies and the existance of halo around them after 48 hours of incubation at 37°C. Results The sensitivity and specificity values for C. albicans strains were found to be 99.4, 100% for CHROMagar Candida and 87.0, 75.2% for BiGGY agar, respectively. The sensitivity of CHROMagar Candida to identify C. tropicalis, C. glabrata and C. krusei ranged between 90.9 and 100% while the specificity was 100%. The sensitivity rates for BiGGY agar were 66.6 and 100% while the specificity values were found to be 95.4 and 100% for C. tropicalis and C. krusei, respectively. Conclusions It can be concluded that the use of CHROMagar Candida is an easy and reliable method for the presumptive identification of most commonly isolated Candida species especially C. albicans, C. tropicalis and C. krusei. The lower sensitivity and specificity of BiGGY agar to identify commonly isolated Candida species potentially limits the clinical usefulness of this agar. PMID:14613587
A fast finite volume method for conservative space-fractional diffusion equations in convex domains
NASA Astrophysics Data System (ADS)
Jia, Jinhong; Wang, Hong
2016-04-01
We develop a fast finite volume method for variable-coefficient, conservative space-fractional diffusion equations in convex domains via a volume-penalization approach. The method has an optimal storage and an almost linear computational complexity. The method retains second-order accuracy without requiring a Richardson extrapolation. Numerical results are presented to show the utility of the method.
Accurate determination of specific heat at high temperatures using the flash diffusivity method
NASA Technical Reports Server (NTRS)
Vandersande, J. W.; Zoltan, A.; Wood, C.
1989-01-01
The flash diffusivity method of Parker et al. (1961) was used to measure accurately the specific heat of test samples simultaneously with thermal diffusivity, thus obtaining the thermal conductivity of these materials directly. The accuracy of data obtained on two types of materials (n-type silicon-germanium alloys and niobium), was + or - 3 percent. It is shown that the method is applicable up to at least 1300 K.
Note on coefficient matrices from stochastic Galerkin methods for random diffusion equations
Zhou Tao; Tang Tao
2010-11-01
In a recent work by Xiu and Shen [D. Xiu, J. Shen, Efficient stochastic Galerkin methods for random diffusion equations, J. Comput. Phys. 228 (2009) 266-281], the Galerkin methods are used to solve stochastic diffusion equations in random media, where some properties for the coefficient matrix of the resulting system are provided. They also posed an open question on the properties of the coefficient matrix. In this work, we will provide some results related to the open question.
Diffuse interface method for a compressible binary fluid.
Liu, Jiewei; Amberg, Gustav; Do-Quang, Minh
2016-01-01
Multicomponent, multiphase, compressible flows are very important in real life, as well as in scientific research, while their modeling is in an early stage. In this paper, we propose a diffuse interface model for compressible binary mixtures, based on the balance of mass, momentum, energy, and the second law of thermodynamics. We show both analytically and numerically that this model is able to describe the phase equilibrium for a real binary mixture (CO_{2} + ethanol is considered in this paper) very well by adjusting the parameter which measures the attraction force between molecules of the two components in the model. We also show that the calculated surface tension of the CO_{2} + ethanol mixture at different concentrations match measurements in the literature when the mixing capillary coefficient is taken to be the geometric mean of the capillary coefficient of each component. Three different cases of two droplets in a shear flow, with the same or different concentration, are simulated, showing that the higher concentration of CO_{2} the smaller the surface tension and the easier the drop deforms. PMID:26871168
Diffuse interface method for a compressible binary fluid
NASA Astrophysics Data System (ADS)
Liu, Jiewei; Amberg, Gustav; Do-Quang, Minh
2016-01-01
Multicomponent, multiphase, compressible flows are very important in real life, as well as in scientific research, while their modeling is in an early stage. In this paper, we propose a diffuse interface model for compressible binary mixtures, based on the balance of mass, momentum, energy, and the second law of thermodynamics. We show both analytically and numerically that this model is able to describe the phase equilibrium for a real binary mixture (CO2 + ethanol is considered in this paper) very well by adjusting the parameter which measures the attraction force between molecules of the two components in the model. We also show that the calculated surface tension of the CO2 + ethanol mixture at different concentrations match measurements in the literature when the mixing capillary coefficient is taken to be the geometric mean of the capillary coefficient of each component. Three different cases of two droplets in a shear flow, with the same or different concentration, are simulated, showing that the higher concentration of CO2 the smaller the surface tension and the easier the drop deforms.
A combined reconstruction-classification method for diffuse optical tomography.
Hiltunen, P; Prince, S J D; Arridge, S
2009-11-01
We present a combined classification and reconstruction algorithm for diffuse optical tomography (DOT). DOT is a nonlinear ill-posed inverse problem. Therefore, some regularization is needed. We present a mixture of Gaussians prior, which regularizes the DOT reconstruction step. During each iteration, the parameters of a mixture model are estimated. These associate each reconstructed pixel with one of several classes based on the current estimate of the optical parameters. This classification is exploited to form a new prior distribution to regularize the reconstruction step and update the optical parameters. The algorithm can be described as an iteration between an optimization scheme with zeroth-order variable mean and variance Tikhonov regularization and an expectation-maximization scheme for estimation of the model parameters. We describe the algorithm in a general Bayesian framework. Results from simulated test cases and phantom measurements show that the algorithm enhances the contrast of the reconstructed images with good spatial accuracy. The probabilistic classifications of each image contain only a few misclassified pixels. PMID:19820265
NASA Astrophysics Data System (ADS)
Kang, Hyesung; Jones, T. W.
1995-07-01
Direct comparisons of diffusive particle acceleration numerical simulations have been made against Monte Carlo and hybrid plasma simulations by Ellison et al. (1993) and against observations at the Earth's bow shock presented by Ellison et al. (1990). Toward this end we have introduced a new numerical scheme for injection of cosmic-ray particles out of the thermal plasma, modeled by way of the diffusive scattering process itself; that is, the diffusion and acceleration across the shock front of particles out of the suprathermal tail of the Maxwellian distribution. Our simulations take two forms. First, we have solved numerically the timedependent diffusion-advection equation for the high-energy (cosmic-ray) protons in one-dimensional quasiparallel shocks. Dynamical feedback between the particles and thermal plasma is included. The proton fluxes on both sides of the shock derived from our method are consistent with those calculated by Ellison et al. (1993). A similar test has compared our methods to published measurements at the Earth's bow shock when the interplanetary magnetic field was almost parallel to the solar wind velocity (Ellison et al. 1990). Again our results are in good agreement. Second, the same shock conditions have been simulated with the two-fluid version of diffusive shock acceleration theory by adopting injection rates and the closure parameters inferred from the diffusion-advection equation calculations. The acceleration efficiency and the shock structure calculated with the two-fluid method are in good agreement with those computed with the diffusion-advection method. Thus, we find that all of these computational methods (diffusion-advection, two-fluid, Monte Carlo, and hybrid) are in substantial agreement on the issues they can simultaneously address, so that the essential physics of diffusive particle acceleration is adequately contained within each. This is despite the fact that each makes what appear to be very different assumptions or
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.
NASA Astrophysics Data System (ADS)
Sweilam, N. H.; Abou Hasan, M. M.
2016-08-01
This paper reports a new spectral algorithm for obtaining an approximate solution for the Lévy-Feller diffusion equation depending on Legendre polynomials and Chebyshev collocation points. The Lévy-Feller diffusion equation is obtained from the standard diffusion equation by replacing the second-order space derivative with a Riesz-Feller derivative. A new formula expressing explicitly any fractional-order derivatives, in the sense of Riesz-Feller operator, of Legendre polynomials of any degree in terms of Jacobi polynomials is proved. Moreover, the Chebyshev-Legendre collocation method together with the implicit Euler method are used to reduce these types of differential equations to a system of algebraic equations which can be solved numerically. Numerical results with comparisons are given to confirm the reliability of the proposed method for the Lévy-Feller diffusion equation.
Convergence of the binomial tree method for Asian options in jump-diffusion models
NASA Astrophysics Data System (ADS)
Kim, Kwang Ik; Qian, Xiao-Song
2007-06-01
The binomial tree methods (BTM), first proposed by Cox, Ross and Rubinstein [J. Cox, S. Ross, M. Rubinstein, Option pricing: A simplified approach, J. Finan. Econ. 7 (1979) 229-264] in diffusion models and extended by Amin [K.I. Amin, Jump diffusion option valuation in discrete time, J. Finance 48 (1993) 1833-1863] to jump-diffusion models, is one of the most popular approaches to pricing options. In this paper, we present a binomial tree method for Asian options in jump-diffusion models and show its equivalence to certain explicit difference scheme. Employing numerical analysis and the notion of viscosity solution, we prove the uniform convergence of the binomial tree method for European-style and American-style Asian options.
Data on the verification and validation of segmentation and registration methods for diffusion MRI.
Esteban, Oscar; Zosso, Dominique; Daducci, Alessandro; Bach-Cuadra, Meritxell; Ledesma-Carbayo, María J; Thiran, Jean-Philippe; Santos, Andres
2016-09-01
The verification and validation of segmentation and registration methods is a necessary assessment in the development of new processing methods. However, verification and validation of diffusion MRI (dMRI) processing methods is challenging for the lack of gold-standard data. The data described here are related to the research article entitled "Surface-driven registration method for the structure-informed segmentation of diffusion MR images" [1], in which publicly available data are used to derive golden-standard reference-data to validate and evaluate segmentation and registration methods in dMRI. PMID:27508235
A comparison of the Monte Carlo and the flux gradient method for atmospheric diffusion
Lange, R.
1990-05-01
In order to model the dispersal of atmospheric pollutants in the planetary boundary layer, various methods of parameterizing turbulent diffusion have been employed. The purpose of this paper is to use a three-dimensional particle-in-cell transport and diffusion model to compare the Markov chain (Monte Carlo) method of statistical particle diffusion with the deterministic flux gradient (K-theory) method. The two methods are heavily used in the study of atmospheric diffusion under complex conditions, with the Monte Carlo method gaining in popularity partly because of its more direct application of turbulence parameters. The basis of comparison is a data set from night-time drainage flow tracer experiments performed by the US Department of Energy Atmospheric Studies in Complex Terrain (ASCOT) program at the Geysers geothermal region in northern California. The Atmospheric Diffusion Particle-In-Cell (ADPIC) model used is the main model in the Lawrence Livermore National Laboratory emergency response program: Atmospheric Release Advisory Capability (ARAC). As a particle model, it can simulate diffusion in both the flux gradient and Monte Carlo modes. 9 refs., 6 figs.
Mass production of spores of lactic acid-producing Rhizopus oryzae NBRC 5384 on agar plate.
Yamane, Tsuneo; Tanaka, Ryosuke
2013-01-01
Mass production of sporangiospores (spores) of Rhizopus oryzae NBRC 5384 (identical to NRRL 395 and ATCC 9363) on potato-dextrose-agar medium was studied aiming at starting its L(+)-lactic acid fermentation directly from spore inoculation. Various parameters including harvest time, sowed spore density, size of agar plate, height of air space, and incubation mode of plate (agar-on-bottom or agar-on-top) were studied. Ordinarily used shallow Petri dishes were found out to be unsuitable for the full growth of R. oryzae sporangiophores. In a very wide range of the sowed spore density, the smaller it was, the greater the number of the harvested spores was. It was also interesting to find out that R. oryzae grown downward vertically with a deep air space in an agar-on-top mode gave larger amount of spores than in an agar-on-bottom mode at 30°C for 7-day cultivation. Scale-up of the agar plate culture from 26.4 to 292 cm(2) was studied, resulting in the proportional relationship between the number of the harvested spores/plate and the plate area in the deep Petri dishes. The number of plates of 50 cm in diameter needed for 100 m(3) industrial submerged fermentation started directly from 2 × 10(5) spores/mL inoculum size was estimated as about 6, from which it was inferred that such a fermentation would be feasible. Designing a 50 cm plate and a method of spreading and collecting the spores were suggested. Bioprocess technological significance of the "full-scale industrial submerged fermentation started directly from spore inoculation omitting pre-culture" has been discussed. PMID:23658025
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
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.; Alman, David E.
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 for the Calculation of Diffusion Coefficients with Monte Carlo
NASA Astrophysics Data System (ADS)
Dorval, Eric
2014-06-01
This paper presents a new Monte Carlo-based method for the calculation of diffusion coefficients. One distinctive feature of this method is that it does not resort to the computation of transport cross sections directly, although their functional form is retained. Instead, a special type of tally derived from a deterministic estimate of Fick's Law is used for tallying the total cross section, which is then combined with a set of other standard Monte Carlo tallies. Some properties of this method are presented by means of numerical examples for a multi-group 1-D implementation. Calculated diffusion coefficients are in general good agreement with values obtained by other methods.
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.
A coarse-mesh nodal method-diffusive-mesh finite difference method
Joo, H.; Nichols, W.R.
1994-05-01
Modern nodal methods have been successfully used for conventional light water reactor core analyses where the homogenized, node average cross sections (XSs) and the flux discontinuity factors (DFs) based on equivalence theory can reliably predict core behavior. For other types of cores and other geometries characterized by tightly-coupled, heterogeneous core configurations, the intranodal flux shapes obtained from a homogenized nodal problem may not accurately portray steep flux gradients near fuel assembly interfaces or various reactivity control elements. This may require extreme values of DFs (either very large, very small, or even negative) to achieve a desired solution accuracy. Extreme values of DFs, however, can disrupt the convergence of the iterative methods used to solve for the node average fluxes, and can lead to a difficulty in interpolating adjacent DF values. Several attempts to remedy the problem have been made, but nothing has been satisfactory. A new coarse-mesh nodal scheme called the Diffusive-Mesh Finite Difference (DMFD) technique, as contrasted with the coarse-mesh finite difference (CMFD) technique, has been developed to resolve this problem. This new technique and the development of a few-group, multidimensional kinetics computer program are described in this paper.
NASA Astrophysics Data System (ADS)
Bouffard, M.; Labrosse, M.; Choblet, M.; Fournier, M.; Aubert, M.; Tackley, M.
2015-10-01
Convection in the liquid layers of planetary interiors is usually driven by a combination of thermal and compositional sources of buoyancy. The low molecular diffusivity of composition causes troubles in the description of this field on the Eulerian grids typically employed in current codes of geodynamo because numerical diffusion on these grids is potentially larger than the real diffusivity. We developed a Lagrangian description of composition based on a method of tracers. The absence of numerical diffusion inherent to this method allows modeling of thermo-chemical convection with infinite Lewis number. The validation of this new tool on benchmark cases will be presented at EPSC as well as its first applications to the ocean of Ganymede with consistently coupled boundary condi- tions for temperature and composition.
NASA Astrophysics Data System (ADS)
Ziemys, A.; Kojic, M.; Milosevic, M.; Kojic, N.; Hussain, F.; Ferrari, M.; Grattoni, A.
2011-06-01
We present a successful hierarchical modeling approach which accounts for interface effects on diffusivity, ignored in classical continuum theories. A molecular dynamics derived diffusivity scaling scheme is incorporated into a finite element method to model transport through a nanochannel. In a 5 nm nanochannel, the approach predicts 2.2 times slower mass release than predicted by Fick's law by comparing time spent to release 90% of mass. The scheme was validated by predicting experimental glucose diffusion through a nanofluidic membrane with a correlation coefficient of 0.999. Comparison with experiments through a nanofluidic membrane showed interface effects to be crucial. We show robustness of our discrete continuum model in addressing complex diffusion phenomena in biomedical and engineering applications by providing flexible hierarchical coupling of molecular scale effects and preserving computational finite element method speed.
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.
Densmore, Jeffery D.; Thompson, Kelly G.; Urbatsch, Todd J.
2012-08-15
Discrete Diffusion Monte Carlo (DDMC) is a technique for increasing the efficiency of Implicit Monte Carlo radiative-transfer simulations in optically thick media. In DDMC, particles take discrete steps between spatial cells according to a discretized diffusion equation. Each discrete step replaces many smaller Monte Carlo steps, thus improving the efficiency of the simulation. In this paper, we present an extension of DDMC for frequency-dependent radiative transfer. We base our new DDMC method on a frequency-integrated diffusion equation for frequencies below a specified threshold, as optical thickness is typically a decreasing function of frequency. Above this threshold we employ standard Monte Carlo, which results in a hybrid transport-diffusion scheme. With a set of frequency-dependent test problems, we confirm the accuracy and increased efficiency of our new DDMC method.
The arbitrary order mixed mimetic finite difference method for the diffusion equation
Gyrya, Vitaliy; Lipnikov, Konstantin; Manzini, Gianmarco
2016-05-01
Here, we propose an arbitrary-order accurate mimetic finite difference (MFD) method for the approximation of diffusion problems in mixed form on unstructured polygonal and polyhedral meshes. As usual in the mimetic numerical technology, the method satisfies local consistency and stability conditions, which determines the accuracy and the well-posedness of the resulting approximation. The method also requires the definition of a high-order discrete divergence operator that is the discrete analog of the divergence operator and is acting on the degrees of freedom. The new family of mimetic methods is proved theoretically to be convergent and optimal error estimates for flux andmore » scalar variable are derived from the convergence analysis. A numerical experiment confirms the high-order accuracy of the method in solving diffusion problems with variable diffusion tensor. It is worth mentioning that the approximation of the scalar variable presents a superconvergence effect.« less
NASA Astrophysics Data System (ADS)
Sarwar, S.; Rashidi, M. M.
2016-07-01
This paper deals with the investigation of the analytical approximate solutions for two-term fractional-order diffusion, wave-diffusion, and telegraph equations. The fractional derivatives are defined in the Caputo sense, whose orders belong to the intervals [0,1], (1,2), and [1,2], respectively. In this paper, we extended optimal homotopy asymptotic method (OHAM) for two-term fractional-order wave-diffusion equations. Highly approximate solution is obtained in series form using this extended method. Approximate solution obtained by OHAM is compared with the exact solution. It is observed that OHAM is a prevailing and convergent method for the solutions of nonlinear-fractional-order time-dependent partial differential problems. The numerical results rendering that the applied method is explicit, effective, and easy to use, for handling more general fractional-order wave diffusion, diffusion, and telegraph problems.
Method of fluxless brazing and diffusion bonding of aluminum containing components
NASA Technical Reports Server (NTRS)
Featherston, A. B.; Okelly, K. P. (Inventor)
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.
Kanmani, Paulraj; Rhim, Jong-Whan
2014-02-15
The use of synthetic petroleum based packaging films caused serious environmental problems due to their difficulty in recycling and poor biodegradability. Therefore, present study was aimed to develop natural biopolymer-based antimicrobial packaging films as an alternative for the synthetic packaging films. As a natural antimicrobial agent, grapefruit seed extract (GSE) has been incorporated into agar to prepare antimicrobial packaging film. The films with different concentrations of GSE were prepared by a solvent casting method and the resulting composite films were examined physically and mechanically. In addition, the films were characterized by FE-SEM, XRD, FT-IR and TGA. The incorporation of GSE caused increase in color, UV barrier, moisture content, water solubility and water vapor permeability, while decrease in surface hydrophobicity, tensile strength and elastic modulus of the films. As the concentration of GSE increased from 0.6 to 13.3 μg/mL, the physical and mechanical properties of the films were affected significantly. The addition of GSE changed film microstructure of the film, but did not influence the crystallinity of agar and thermal stability of the agar-based films. The agar/GSE films exhibited distinctive antimicrobial activity against three test food pathogens, such as Listeria monocytogenes, Bacillus cereus and Escherichia coli. These results suggest that agar/GSE films have potential to be used in an active food packaging systems for maintaining food safety and extending the shelf-life of the packaged food. PMID:24507339
Martelli, Fabrizio; Zaccanti, Giovanni
2007-01-22
In spite of many progresses achieved both with theories and with experiments in studying light propagation through diffusive media, a reliable method for accurate measurements of the optical properties of diffusive media at NIR wavelengths is, in our opinion, still missing. It is therefore difficult to create a diffusive medium with well known optical properties to be used as a reference. In this paper we describe a method to calibrate the reduced scattering coefficient, mu'(s) , of a liquid diffusive medium and the absorption coefficient, mu(a), of an absorbing medium with a standard error smaller than 2% both on mu'(s) and on mu(a). The method is based on multidistance measurements of fluence into an infinite medium illuminated by a CW source. The optical properties are retrieved with simple inversion procedures (linear fits) exploiting the knowledge of the absorption coefficient of the liquid into which the diffuser and the absorber are dispersed. In this study Intralipid diluted in water has been used as diffusive medium and Indian ink as absorber. For a full characterization of these media measurements of collimated transmittance have also been carried out, from which the asymmetry factor of the scattering function of Intralipid and the single scattering albedo of Indian ink have been determined. PMID:19532267
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.
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.
Advanced computational methods for nodal diffusion, Monte Carlo, and S[sub N] problems
Martin, W.R.
1993-01-01
This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. A alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.
Advanced computational methods for nodal diffusion, Monte Carlo, and S(sub N) problems
NASA Astrophysics Data System (ADS)
Martin, W. R.
1993-01-01
This document describes progress on five efforts for improving effectiveness of computational methods for particle diffusion and transport problems in nuclear engineering: (1) Multigrid methods for obtaining rapidly converging solutions of nodal diffusion problems. An alternative line relaxation scheme is being implemented into a nodal diffusion code. Simplified P2 has been implemented into this code. (2) Local Exponential Transform method for variance reduction in Monte Carlo neutron transport calculations. This work yielded predictions for both 1-D and 2-D x-y geometry better than conventional Monte Carlo with splitting and Russian Roulette. (3) Asymptotic Diffusion Synthetic Acceleration methods for obtaining accurate, rapidly converging solutions of multidimensional SN problems. New transport differencing schemes have been obtained that allow solution by the conjugate gradient method, and the convergence of this approach is rapid. (4) Quasidiffusion (QD) methods for obtaining accurate, rapidly converging solutions of multidimensional SN Problems on irregular spatial grids. A symmetrized QD method has been developed in a form that results in a system of two self-adjoint equations that are readily discretized and efficiently solved. (5) Response history method for speeding up the Monte Carlo calculation of electron transport problems. This method was implemented into the MCNP Monte Carlo code. In addition, we have developed and implemented a parallel time-dependent Monte Carlo code on two massively parallel processors.
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.
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.
NASA Astrophysics Data System (ADS)
Punegov, V. I.; Sivkov, D. V.
2015-03-01
Two independent approaches to calculate the angular distribution of X-ray diffusion scattering from a crystalline medium with spheroidal quantum dots (QDs) have been proposed. The first method is based on the analytical solution involving the multipole expansion of elastic strain fields beyond QDs. The second approach is based on calculations of atomic displacements near QDs by the Green's function method. An analysis of the diffuse scattering intensity distribution in the reciprocal space within these two approaches shows that both methods yield similar results for the chosen models of QD spatial distribution.
Gentile, N A
2000-10-01
We present a method for accelerating time dependent Monte Carlo radiative transfer calculations by using a discretization of the diffusion equation to calculate probabilities that are used to advance particles in regions with small mean free path. The method is demonstrated on problems with on 1 and 2 dimensional orthogonal grids. It results in decreases in run time of more than an order of magnitude on these problems, while producing answers with accuracy comparable to pure IMC simulations. We call the method Implicit Monte Carlo Diffusion, which we abbreviate IMD.
Punegov, V. I. Sivkov, D. V.
2015-03-15
Two independent approaches to calculate the angular distribution of X-ray diffusion scattering from a crystalline medium with spheroidal quantum dots (QDs) have been proposed. The first method is based on the analytical solution involving the multipole expansion of elastic strain fields beyond QDs. The second approach is based on calculations of atomic displacements near QDs by the Green’s function method. An analysis of the diffuse scattering intensity distribution in the reciprocal space within these two approaches shows that both methods yield similar results for the chosen models of QD spatial distribution.
Selected elements in fly agaric Amanita muscaria.
Falandysz, J; Kunito, T; Kubota, R; Lipka, K; Mazur, A; Falandysz, Justyna J; Tanabe, S
2007-09-01
Concentrations of Ag, Al, Ba, Ca, Cd, Co, Cu, Cr, Cs, Fe, Ga, Hg, K, Mg, Mn, Mo, Na, Pb, Rb, Se, Sb, Sr, V, Tl and Zn have been determined in the whole fruiting bodies, as well as separately in caps and stalks, of fly agaric collected from three geographically distant sites in northern part of Poland. The elements were determined using ICP-MS, ICP-OES, HG-AAS and CV-AAS, respectively. For elements such as Al, Ba, Cr, Fe, Ga, Mo, Mn, Pb, Sb, Sr, Tl, and V concentrations were similar in the caps and stalks, respectively, and for K, Zn, Ag, Ca, Cd, Cu, Hg, Mg, Rb and Se were greater in the caps, while for Co, Cs and Na in the stalks. For Ag, Al, Ba, Ca, Cd, Co, Cr, Cs, Fe, Ga, Hg, Mn, Mo, Pb, Rb, Sb, Sr, Tl and V concentration in the caps showed spatial variations (P<0.05), while for Cu, K, Mg, Na, Se and Zn was independent of the site. The elements such as K with median or mean in the caps between 37,000 and 43,000 microg/g.dm and Mg with 920 and 1,100 microg/g dm were most abundant. Next, within median values range from approximately 100 to 500 microg/g dm were such as Ca, Fe and Al, and in descending order they followed by Rb (100-400 microg/g dm); V, Na, Zn (50-200 microg/g dm); Cu, Mn (10-50 microg/g dm); Cd (10-20 microg/g dm); Se (5 microg/g dm); Ba (<1-3); Cr, Ag, Pb, Sr (<1-2 microg/g dm); Cs, Co, Hg (<1-1 microg/g dm); Ga (<0.5), Sb, Mo and Tl (<0.1 microg/g dm). PMID:17849303
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.
FUJIHARA, Masatoshi; TABUCHI, Hiroyuki; UEGAKI, Kaho
2015-01-01
To determine the appropriate method for isolating Salmonella enterica, we compared the growth of S. enterica serovars using three selective enrichment media. S. enterica was more successfully isolated from artificially contaminated fecal samples after enrichment in Hajna tetrathionate broth or modified semisolid Rappaport agar than in Rappaport broth. Since most bacteria (other than motile S. enterica) do not migrate on modified semisolid Rappaport agar, the growth characteristics of S. enterica can be interpreted easily and quickly. Two S. enterica isolates did not migrate on modified semisolid Rappaport agar, but did grow in Hajna tetrathionate broth, which suggests that the combined use of these selective enrichment media is appropriate for isolating S. enterica. PMID:26498402
Yang, J; Köhler, K; Davis, D M; Burroughs, N J
2010-06-01
Fluorescence recovery after photobleaching is a widely established method for the estimation of diffusion coefficients, strip bleaching with an associated recovery curve analysis being one of the simplest techniques. However, its implementation requires near 100% bleaching in the region of interest with negligible fluorescence loss outside, both constraints being hard to achieve concomitantly for fast diffusing molecules. We demonstrate that when these requirements are not met there is an error in the estimation of the diffusion coefficient D, either an under- or overestimation depending on which assumption is violated the most. We propose a simple modification to the recovery curve analysis incorporating the concept of the relative bleached mass m giving a revised recovery time parametrization tau=m(2)w(2)/4piD for a strip of width w. This modified model removes the requirement of 100% bleaching in the region of interest and allows for limited diffusion of the fluorophore during bleaching. We validate our method by estimating the (volume) diffusion coefficient of FITC-labelled IgG in 60% glycerol solution, D= 4.09 +/- 0.21 microm(2) s(-1), and the (surface) diffusion coefficient of a green-fluorescent protein-tagged class I MHC protein expressed at the surface of a human B cell line, D= 0.32 +/- 0.03 microm(2) s(-1) for a population of cells. PMID:20579262
A new Sumudu transform iterative method for time-fractional Cauchy reaction-diffusion equation.
Wang, Kangle; Liu, Sanyang
2016-01-01
In this paper, a new Sumudu transform iterative method is established and successfully applied to find the approximate analytical solutions for time-fractional Cauchy reaction-diffusion equations. The approach is easy to implement and understand. The numerical results show that the proposed method is very simple and efficient. PMID:27386314
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.
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.
Liu, Hsi; Taylor, Thomas H; Pettus, Kevin; Trees, David
2014-05-01
We studied whether the Etest can be used as an alternative to agar dilution to determine antimicrobial susceptibilities of ceftriaxone, cefixime, and cefpodoxime in Neisseria gonorrhoeae surveillance. One hundred fifteen clinical and laboratory isolates of N. gonorrhoeae were tested following the Clinical Laboratory Improvement Amendments (CLIA)-approved CLSI standard agar dilution method and, separately, by the Etest according to the manufacturer's recommendations. The MICs were determined and compared. Ten laboratory-generated mutants were used to simulate substantially nonsusceptible specimens. The Etest and agar dilution methods were well correlated. Statistical tests produced regression R2 values of 88%, 82%, and 85% and Pearson correlation coefficients of 92%, 91%, and 92% for ceftriaxone, cefixime, and cefpodoxime, respectively. When paired comparisons were made, the two tests were 88.7%, 80%, and 87% within 1 log2 dilution from each other for ceftriaxone, cefixime, and cefpodoxime, respectively. The within-2-log2 agreements were 99.1%, 98.3%, and 94.8% for ceftriaxone, cefixime, and cefpodoxime, respectively. Notwithstanding the good correlations and the within-2-log2 general agreement, the Etest results produced slightly lower MICs than the agar dilution results. In conclusion, we found that the Etest can be effectively used as an alternative to agar dilution testing to determine the susceptibility of N. gonorrhoeae to ceftriaxone, cefixime, and cefpodoxime, although we recommend further research into extremely resistant isolates. For isolates within the typical range of clinical MICs, reexamination of the Etest interpretation of susceptible and nonsusceptible categories would likely allow for successful transition from agar dilution to the Etest. PMID:24554750
Taylor, Thomas H.; Pettus, Kevin; Trees, David
2014-01-01
We studied whether the Etest can be used as an alternative to agar dilution to determine antimicrobial susceptibilities of ceftriaxone, cefixime, and cefpodoxime in Neisseria gonorrhoeae surveillance. One hundred fifteen clinical and laboratory isolates of N. gonorrhoeae were tested following the Clinical Laboratory Improvement Amendments (CLIA)-approved CLSI standard agar dilution method and, separately, by the Etest according to the manufacturer's recommendations. The MICs were determined and compared. Ten laboratory-generated mutants were used to simulate substantially nonsusceptible specimens. The Etest and agar dilution methods were well correlated. Statistical tests produced regression R2 values of 88%, 82%, and 85% and Pearson correlation coefficients of 92%, 91%, and 92% for ceftriaxone, cefixime, and cefpodoxime, respectively. When paired comparisons were made, the two tests were 88.7%, 80%, and 87% within 1 log2 dilution from each other for ceftriaxone, cefixime, and cefpodoxime, respectively. The within-2-log2 agreements were 99.1%, 98.3%, and 94.8% for ceftriaxone, cefixime, and cefpodoxime, respectively. Notwithstanding the good correlations and the within-2-log2 general agreement, the Etest results produced slightly lower MICs than the agar dilution results. In conclusion, we found that the Etest can be effectively used as an alternative to agar dilution testing to determine the susceptibility of N. gonorrhoeae to ceftriaxone, cefixime, and cefpodoxime, although we recommend further research into extremely resistant isolates. For isolates within the typical range of clinical MICs, reexamination of the Etest interpretation of susceptible and nonsusceptible categories would likely allow for successful transition from agar dilution to the Etest. PMID:24554750
Diffusion constant of K+ inside Gramicidin A: A comparative study of four computational methods
Mamonov, Artem B.; Kurnikova, Maria G.; Coalson, Rob D.
2007-01-01
The local diffusion constant of K+ inside the Gramicidin A (GA) channel has been calculated using four computational methods based on molecular dynamics (MD) simulations, specifically: Mean Square Displacement (MSD), Velocity Autocorrelation Function (VACF), Second Fluctuation Dissipation Theorem (SFDT) and analysis of the Generalized Langevin Equation for a Harmonic Oscillator (GLE-HO). All methods were first tested and compared for K+ in bulk water—all predicted the correct diffusion constant. Inside GA, MSD and VACF methods were found to be unreliable because they are biased by the systematic force exerted by the membrane-channel system on the ion. SFDT and GLE-HO techniques properly unbias the influence of the systematic force on the diffusion properties and predicted a similar diffusion constant of K+ inside GA, namely, ca. 10 times smaller than in the bulk. It was found that both SFDT and GLE-HO methods require extensive MD sampling on the order of tens of nanoseconds to predict a reliable diffusion constant of K+ inside GA. PMID:16797116
Diffused interface ghost fluid method for incompressible multiphase, phase change simulations
NASA Astrophysics Data System (ADS)
Lee, Moon Soo; Riaz, Amir
2013-11-01
Sharp interface methods for simulating multiphase flow often suffer from unstable pressure and velocity fluctuations for problems involving mass transfer. An improved sharp interface method is developed for multiphase flow with phase change using both sharp and diffused interfacial properties. The approach is based on defining continuous, phase averaged velocity and density fields within a diffused interfacial region while using the sharp treatment for the implementation of the jumps in the pressure and the temperature gradient. The method implements interface advection with diffused and stable velocity field but can represent accurate movement of the sharp interface. Two-dimensional film boiling problems are solved on a horizontal surface to demonstrate the performance of the new approach.
Laser interferometric method for determining the carrier diffusion length in semiconductors
Manukhov, V. V.; Fedortsov, A. B.; Ivanov, A. S.
2015-09-15
A new laser interferometric method for measuring the carrier diffusion length in semiconductors is proposed. The method is based on the interference–absorption interaction of two laser radiations in a semiconductor. Injected radiation generates additional carriers in a semiconductor, which causes a change in the material’s optical constants and modulation of the probing radiation passed through the sample. When changing the distance between carrier generation and probing points, a decrease in the carrier concentration, which depends on the diffusion length, is recorded. The diffusion length is determined by comparing the experimental and theoretical dependences of the probe signal on the divergence of the injector and probe beams. The method is successfully tested on semiconductor samples with different thicknesses and surface states and can be used in scientific research and the electronics industry.
Individual Differences and Fitting Methods for the Two-Choice Diffusion Model of Decision Making
Ratcliff, Roger; Childers, Russ
2015-01-01
Methods of fitting the diffusion model were examined with a focus on what the model can tell us about individual differences. Diffusion model parameters were obtained from the fits to data from two experiments and consistency of parameter values, individual differences, and practice effects were examined using different numbers of observations from each subject. Two issues were examined, first, what sizes of differences between groups can be obtained to distinguish between groups and second, what sizes of differences would be needed to find individual subjects that had a deficit relative to a control group. The parameter values from the experiments provided ranges that were used in a simulation study to examine recovery of individual differences. This study used several diffusion model fitting programs, fitting methods, and published packages. In a second simulation study, 64 sets of simulated data from each of 48 sets of parameter values (spanning the range of typical values obtained from fits to data) were fit with the different methods and biases and standard deviations in recovered model parameters were compared across methods. Finally, in a third simulation study, a comparison between a standard chi-square method and a hierarchical Bayesian method was performed. The results from these studies can be used as a starting point for selecting fitting methods and as a basis for understanding the strengths and weaknesses of using diffusion model analyses to examine individual differences in clinical, neuropsychological, and educational testing. PMID:26236754
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.
Albertson, B J; Blue, T E; Niemkiewicz, J
2001-09-01
This paper outlines a method for determining proper removal-diffusion parameters to be used in removal-diffusion theory calculations for the purpose of BNCT treatment planning. Additionally, this paper demonstrates that, given the proper choice of removal-diffusion parameters, removal-diffusion theory may provide an accurate calculation technique for determining absorbed dose distributions for the purpose of BNCT treatment planning. For a four-group, one-dimensional calculation in water, this method was used to determine values for the neutron scattering cross sections, neutron removal cross sections, neutron diffusion coefficients, and extrapolation distances. These values were then used in a one-dimensional DIF3D calculation. The results of the DIF3D calculation showed a maximum deviation of 2.5% from a MCNP calculation performed for the same geometry. PMID:11585220
Technology Transfer Automated Retrieval System (TEKTRAN)
Salmonella is a common cause of foodborne disease resulting from the consumption of contaminated food products. Although a direct plating method is widely used for presumptive positive screening of pathogenic Salmonella colonies on agar plates, it is labor-intensive, time-consuming and also prone to...
NASA Technical Reports Server (NTRS)
Penner, Reginald M.; Vandyke, Leon S.; Martin, Charles R.
1987-01-01
The current pulse E sub oc relaxation method and its application to the determination of diffusion coefficients in electrochemically synthesized polypyrrole thin films is described. Diffusion coefficients for such films in Et4NBF4 and MeCN are determined for a series of submicron film thicknesses. Measurement of the double-layer capacitance, C sub dl, and the resistance, R sub u, of polypyrrole thin films as a function of potential obtained with the galvanostatic pulse method is reported. Measurements of the electrolyte concentration in reduced polypyrrole films are also presented to aid in the interpretation of the data.
Calculation of the neutron diffusion equation by using Homotopy Perturbation Method
NASA Astrophysics Data System (ADS)
Koklu, H.; Ersoy, A.; Gulecyuz, M. C.; Ozer, O.
2016-03-01
The distribution of the neutrons in a nuclear fuel element in the nuclear reactor core can be calculated by the neutron diffusion theory. It is the basic and the simplest approximation for the neutron flux function in the reactor core. In this study, the neutron flux function is obtained by the Homotopy Perturbation Method (HPM) that is a new and convenient method in recent years. One-group time-independent neutron diffusion equation is examined for the most solved geometrical reactor core of spherical, cubic and cylindrical shapes, in the frame of the HPM. It is observed that the HPM produces excellent results consistent with the existing literature.
An asymptotic induced numerical method for the convection-diffusion-reaction equation
NASA Technical Reports Server (NTRS)
Scroggs, Jeffrey S.; Sorensen, Danny C.
1988-01-01
A parallel algorithm for the efficient solution of a time dependent reaction convection diffusion equation with small parameter on the diffusion term is presented. The method is based on a domain decomposition that is dictated by singular perturbation analysis. The analysis is used to determine regions where certain reduced equations may be solved in place of the full equation. Parallelism is evident at two levels. Domain decomposition provides parallelism at the highest level, and within each domain there is ample opportunity to exploit parallelism. Run time results demonstrate the viability of the method.
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.
Development of Reference Materials for Thermal-Diffusivity Measurements by the Flash Method
NASA Astrophysics Data System (ADS)
Akoshima, M.; Abe, H.; Baba, T.
2015-12-01
The thermal conductivity of solid materials used for thermal simulations and thermal designs can be obtained as the product of thermal diffusivity, specific heat capacity, and bulk density in many cases. The thermal diffusivity is usually measured by the flash method, and the specific heat capacity is usually measured by differential scanning calorimetry. In order to obtain reliable thermal conductivities for strict thermal design, it is necessary to measure the thermal diffusivity using the flash method, a well-validated apparatus. Reference materials are an effective means for validation of most practical measurement apparatus. For the flash method, isotropic graphite was selected as a candidate reference material. A batch of isotropic graphite samples was prepared and characterized in detail in order to be a certified reference material for thermal-diffusivity measurement. The detailed characterization ensures the traceability of the measurement results to the international system of units (SI). A convenient reference material for thermal conductivity was also obtained by using the known thermal-diffusivity measurements, specific heat capacity, and density of the material.
A hybrid transport-diffusion method for Monte Carlo radiative-transfer simulations
Densmore, Jeffery D. . E-mail: jdd@lanl.gov; Urbatsch, Todd J. . E-mail: tmonster@lanl.gov; Evans, Thomas M. . E-mail: tme@lanl.gov; Buksas, Michael W. . E-mail: mwbuksas@lanl.gov
2007-03-20
Discrete Diffusion Monte Carlo (DDMC) is a technique for increasing the efficiency of Monte Carlo particle-transport simulations in diffusive media. If standard Monte Carlo is used in such media, particle histories will consist of many small steps, resulting in a computationally expensive calculation. In DDMC, particles take discrete steps between spatial cells according to a discretized diffusion equation. Each discrete step replaces many small Monte Carlo steps, thus increasing the efficiency of the simulation. In addition, given that DDMC is based on a diffusion equation, it should produce accurate solutions if used judiciously. In practice, DDMC is combined with standard Monte Carlo to form a hybrid transport-diffusion method that can accurately simulate problems with both diffusive and non-diffusive regions. In this paper, we extend previously developed DDMC techniques in several ways that improve the accuracy and utility of DDMC for nonlinear, time-dependent, radiative-transfer calculations. The use of DDMC in these types of problems is advantageous since, due to the underlying linearizations, optically thick regions appear to be diffusive. First, we employ a diffusion equation that is discretized in space but is continuous in time. Not only is this methodology theoretically more accurate than temporally discretized DDMC techniques, but it also has the benefit that a particle's time is always known. Thus, there is no ambiguity regarding what time to assign a particle that leaves an optically thick region (where DDMC is used) and begins transporting by standard Monte Carlo in an optically thin region. Also, we treat the interface between optically thick and optically thin regions with an improved method, based on the asymptotic diffusion-limit boundary condition, that can produce accurate results regardless of the angular distribution of the incident Monte Carlo particles. Finally, we develop a technique for estimating radiation momentum deposition during the
Ryabov, Yaroslav E; Geraghty, Charles; Varshney, Amitabh; Fushman, David
2006-12-01
We propose a new computational method for predicting rotational diffusion properties of proteins in solution. The method is based on the idea of representing protein surface as an ellipsoid shell. In contrast to other existing approaches this method uses principal component analysis of protein surface coordinates, which results in a substantial increase in the computational efficiency of the method. Direct comparison with the experimental data as well as with the recent computational approach (Garcia de la Torre; et al. J. Magn. Reson. 2000, B147, 138-146), based on representation of protein surface as a set of small spherical friction elements, shows that the method proposed here reproduces experimental data with at least the same level of accuracy and precision as the other approach, while being approximately 500 times faster. Using the new method we investigated the effect of hydration layer and protein surface topography on the rotational diffusion properties of a protein. We found that a hydration layer constructed of approximately one monolayer of water molecules smoothens the protein surface and effectively doubles the overall tumbling time. We also calculated the rotational diffusion tensors for a set of 841 protein structures representing the known protein folds. Our analysis suggests that an anisotropic rotational diffusion model is generally required for NMR relaxation data analysis in single-domain proteins, and that the axially symmetric model could be sufficient for these purposes in approximately half of the proteins. PMID:17132010
Lee, Eun Joo
2014-01-01
Background ChromID Clostridium difficile agar (IDCd; bioMérieux SA, France) is a recently developed chromogenic medium for rapid and specific isolation of C. difficile. We compared the performance of IDCd with that of Clostridium difficile Selective Agar (CDSA). Methods A total of 530 fresh stool specimens were collected from patients with clinical signs compatible with C. difficile infection, and cultures for C. difficile were performed on IDCd and CDSA. C. difficile colonies were identified by spore staining, odor, use of an ANI identification test kit (bioMérieux SA), and multiplex PCR for tcdA, tcdB, and tpi. Results The concordance rate between IDCd and CDSA was 90.6% (480/530). The positivity rates on IDCd on days 1 and 2 (55.6% and 85.0%, respectively) were significantly higher than those on CDSA (19.4% and 75.6%, respectively) (P<0.001 for day 1 and P=0.02 for day 2), but the detection rates on IDCd and CDSA on day 3 were not different (89.4% vs. 82.8%, P=0.0914). On day 3, the recovery rates for non-C. difficile isolates on IDCd and CDSA were 30.2% (160/530) and 22.1% (117/530), respectively (P=0.0075). Clostridium spp. other than C. difficile were the most prevalent non-C. difficile isolates on both media. Conclusions The culture positivity rates on IDCd and CDSA were not different on day 3 but IDCd may allow for rapid and sensitive detection of C. difficile within 2 days of cultivation. PMID:24422190
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
Numerical simulation of diffusion MRI signals using an adaptive time-stepping method
NASA Astrophysics Data System (ADS)
Li, Jing-Rebecca; Calhoun, Donna; Poupon, Cyril; Le Bihan, Denis
2014-01-01
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.
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
Spectral approximation to advection-diffusion problems by the fictitious interface method
NASA Astrophysics Data System (ADS)
Frati, A.; Pasquarelli, F.; Quarteroni, A.
1993-08-01
The algorithmic aspects of the 'fictitious interface' method used in numerical approximations of convection-dominated flows are discussed. The solution algorithm presented alternates the advection-equation solution with that of the advection-diffusion equation within complementary subdomains. For the problems presently considered, spatial discretization is obtained by the spectral collocation method via Legendre-Gaussian modes. Attention is given to the the fictitious interface method's application to the Burgers equation.
Group iterative methods for the solution of two-dimensional time-fractional diffusion equation
NASA Astrophysics Data System (ADS)
Balasim, Alla Tareq; Ali, Norhashidah Hj. Mohd.
2016-06-01
Variety of problems in science and engineering may be described by fractional partial differential equations (FPDE) in relation to space and/or time fractional derivatives. The difference between time fractional diffusion equations and standard diffusion equations lies primarily in the time derivative. Over the last few years, iterative schemes derived from the rotated finite difference approximation have been proven to work well in solving standard diffusion equations. However, its application on time fractional diffusion counterpart is still yet to be investigated. In this paper, we will present a preliminary study on the formulation and analysis of new explicit group iterative methods in solving a two-dimensional time fractional diffusion equation. These methods were derived from the standard and rotated Crank-Nicolson difference approximation formula. Several numerical experiments were conducted to show the efficiency of the developed schemes in terms of CPU time and iteration number. At the request of all authors of the paper an updated version of this article was published on 7 July 2016. The original version supplied to AIP Publishing contained an error in Table 1 and References 15 and 16 were incomplete. These errors have been corrected in the updated and republished article.
A deterministic Lagrangian particle separation-based method for advective-diffusion problems
NASA Astrophysics Data System (ADS)
Wong, Ken T. M.; Lee, Joseph H. W.; Choi, K. W.
2008-12-01
A simple and robust Lagrangian particle scheme is proposed to solve the advective-diffusion transport problem. The scheme is based on relative diffusion concepts and simulates diffusion by regulating particle separation. This new approach generates a deterministic result and requires far less number of particles than the random walk method. For the advection process, particles are simply moved according to their velocity. The general scheme is mass conservative and is free from numerical diffusion. It can be applied to a wide variety of advective-diffusion problems, but is particularly suited for ecological and water quality modelling when definition of particle attributes (e.g., cell status for modelling algal blooms or red tides) is a necessity. The basic derivation, numerical stability and practical implementation of the NEighborhood Separation Technique (NEST) are presented. The accuracy of the method is demonstrated through a series of test cases which embrace realistic features of coastal environmental transport problems. Two field application examples on the tidal flushing of a fish farm and the dynamics of vertically migrating marine algae are also presented.
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
Multiscale numerical methods for passive advection-diffusion in incompressible turbulent flow fields
NASA Astrophysics Data System (ADS)
Lee, Yoonsang; Engquist, Bjorn
2016-07-01
We propose a seamless multiscale method which approximates the macroscopic behavior of the passive advection-diffusion equations with steady incompressible velocity fields with multi-spatial scales. The method uses decompositions of the velocity fields in the Fourier space, which are similar to the decomposition in large eddy simulations. It also uses a hierarchy of local domains with different resolutions as in multigrid methods. The effective diffusivity from finer scale is used for the next coarser level computation and this process is repeated up to the coarsest scale of interest. The grids are only in local domains whose sizes decrease depending on the resolution level so that the overall computational complexity increases linearly as the number of different resolution grids increases. The method captures interactions between finer and coarser scales but has to sacrifice some of interactions between different scales. The proposed method is numerically tested with 2D examples including a successful approximation to a continuous spectrum flow.
New contactless method for thermal diffusivity measurements using modulated photothermal radiometry.
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. PMID:24880399
A moving mesh finite difference method for equilibrium radiation diffusion equations
Yang, Xiaobo; Huang, Weizhang; Qiu, Jianxian
2015-10-01
An efficient moving mesh finite difference method is developed for the numerical solution of equilibrium radiation diffusion equations in two dimensions. The method is based on the moving mesh partial differential equation approach and moves the mesh continuously in time using a system of meshing partial differential equations. The mesh adaptation is controlled through a Hessian-based monitor function and the so-called equidistribution and alignment principles. Several challenging issues in the numerical solution are addressed. Particularly, the radiation diffusion coefficient depends on the energy density highly nonlinearly. This nonlinearity is treated using a predictor–corrector and lagged diffusion strategy. Moreover, the nonnegativity of the energy density is maintained using a cutoff method which has been known in literature to retain the accuracy and convergence order of finite difference approximation for parabolic equations. Numerical examples with multi-material, multiple spot concentration situations are presented. Numerical results show that the method works well for radiation diffusion equations and can produce numerical solutions of good accuracy. It is also shown that a two-level mesh movement strategy can significantly improve the efficiency of the computation.
A moving mesh finite difference method for equilibrium radiation diffusion equations
NASA Astrophysics Data System (ADS)
Yang, Xiaobo; Huang, Weizhang; Qiu, Jianxian
2015-10-01
An efficient moving mesh finite difference method is developed for the numerical solution of equilibrium radiation diffusion equations in two dimensions. The method is based on the moving mesh partial differential equation approach and moves the mesh continuously in time using a system of meshing partial differential equations. The mesh adaptation is controlled through a Hessian-based monitor function and the so-called equidistribution and alignment principles. Several challenging issues in the numerical solution are addressed. Particularly, the radiation diffusion coefficient depends on the energy density highly nonlinearly. This nonlinearity is treated using a predictor-corrector and lagged diffusion strategy. Moreover, the nonnegativity of the energy density is maintained using a cutoff method which has been known in literature to retain the accuracy and convergence order of finite difference approximation for parabolic equations. Numerical examples with multi-material, multiple spot concentration situations are presented. Numerical results show that the method works well for radiation diffusion equations and can produce numerical solutions of good accuracy. It is also shown that a two-level mesh movement strategy can significantly improve the efficiency of the computation.
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.
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 ...
Liquid-phase thermal diffusion isotope separation apparatus and method having tapered column
Rutherford, William M.
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.
Anti-diffusion method for interface steepening in two-phase incompressible flow
NASA Astrophysics Data System (ADS)
So, K. K.; Hu, X. Y.; Adams, N. A.
2011-06-01
In this paper, we present a method for obtaining sharp interfaces in two-phase incompressible flows by an anti-diffusion correction, that is applicable in a straight-forward fashion for the improvement of two-phase flow solution schemes typically employed in practical applications. The underlying discretization is based on the volume-of-fluid (VOF) interface-capturing method on unstructured meshes. The key idea is to steepen the interface, independently of the underlying volume-fraction transport equation, by solving a diffusion equation with reverse time, i.e. an anti-diffusion equation, after each advection time step of the volume fraction. As the solution of the anti-diffusion equation requires regularization, a limiter based on the directional derivative is developed for calculating the gradient of the volume fraction. This limiter ensures the boundedness of the volume fraction. In order to control the amount of anti-diffusion introduced by the correction algorithm we propose a suitable stopping criterion for interface steepening. The formulation of the limiter and the algorithm for solving the anti-diffusion equation are applicable to 3-dimensional unstructured meshes. Validation computations are performed for passive advection of an interface, for 2-dimensional and 3-dimensional rising-bubbles, and for a rising drop in a periodically constricted channel. The results demonstrate that sharp interfaces can be recovered reliably. They show that the accuracy is similar to or even better than that of level-set methods using comparable discretizations for the flow and the level-set evolution. Also, we observe a good agreement with experimental results for the rising drop where proper interface evolution requires accurate mass conservation.
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.
Klevay, Michael; Ebinger, Alex; Diekema, Daniel; Messer, Shawn; Hollis, Richard; Pfaller, Michael
2005-01-01
We compared results of disk diffusion antifungal susceptibility testing from Candida sp. strains passaged on CHROMagar and on potato dextrose agar. The overall categorical agreements for fluconazole and voriconazole disk testing were 95% and 98% with 0% and 0.5% very major errors, respectively. Disk diffusion testing by the CLSI (formerly NCCLS) M44-A method can be performed accurately by taking inocula directly from CHROMagar. PMID:16000489
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
Zemlianitskaia, E P; Kurbanova, I Z; Sergeeva, T I
1979-02-01
An express method for determination of antibiotic sensitivity in the strains of Cl. perfringens of type A using Soviet dry nutrient media and antibiotics is proposed. The criteria for estimation of the level of the antibiotic sensitivity of the causative agent of gas gangrene in short periods on the basis of comparison of the data of the antibiotic agar diffusion procedure and the antibiotic MIC were worked out. Twelve antibiotics and 45 collection strains of Cl. perfringens of type A were used in the experiment. The antibiotic agar diffusion method with the use of the nutrient media, microbial load and cultivation conditions developed by the authors is recommended for tentative determination of the antibiotic sensitivity in Cl. perfringens of type A for 4 hours. The use of the agar diffusion method and determination of the antibiotic MIC provided complete estimation of tha antibiotic sensitivity of Cl. perfringens of type A within not more than 24 hours. PMID:219770
Kempka, S.N.; Strickland, J.H.
1993-08-01
A numerical method to simulate viscous diffusion of vorticity using vortex blobs (i.e., without a grid) is presented. The method consists of casting the effects of viscous diffusion into an effective ``diffusion velocity`` at which vortex blobs convect. The diffusion velocity was proposed previously by Ogami and Akamatsu, but they did not consider the effects of the divergence of the diffusion velocity. In fact, the diffusion velocity is highly non-solenoidal, which significantly affects the area over which a vortex blob diffuses. A formulation is presented that relates the area expansion to the diffusion velocity divergence. By taking into account the area expansion, more accurate simulations of diffusion are obtained, as demonstrated by a comparison of numerical and analytical diffusion solutions. Results from simulations show that vortex areas expand significantly in regions of large vorticity gradients. As a result of the area expansion, adjacent vortices remain overlapped, thereby maintaining smooth solution fields. The non-solenoidal diffusion velocity method is easily implemented in vortex blob algorithms, thus facilitating the development of vortex methods to simulate flows with finite Reynolds numbers.
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
An efficient and positivity-preserving layer method for modeling radiation belt diffusion processes
NASA Astrophysics Data System (ADS)
Tao, X.; Zhang, L.; Wang, C.; Li, X.; Albert, J. M.; Chan, A. A.
2016-01-01
An efficient and positivity-preserving layer method is introduced to solve the radiation belt diffusion equation and is applied to study the bounce resonance interaction between relativistic electrons and magnetosonic waves. The layer method with linear interpolation, denoted by LM-L (layer method-linear), requires the use of a large number of grid points to ensure accurate solutions. We introduce a monotonicity- and positivity-preserving cubic interpolation method to be used with the Milstein-Tretyakov layer method. The resulting method, called LM-MC (layer method-monotone cubic), can be used to solve the radiation belt diffusion equation with a much smaller number of grid points than LM-L while still being able to preserve the positivity of the solution. We suggest that LM-MC can be used to study long-term dynamics of radiation belts. We then develop a 2-D LM-MC code and use it to investigate the bounce resonance diffusion of radiation belt electrons by magnetosonic waves. Using a previously published magnetosonic wave model, we demonstrate that bounce resonance with magnetosonic waves is as important as gyroresonance; both can cause several orders of magnitude increase of MeV electron fluxes within 1 day. We conclude that bounce resonance with magnetosonic waves should be taken into consideration together with gyroresonance.
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.
Zheng, Y.P.; Zhang, T.Y.
1998-12-31
In order to verify the results predicted by the model in Part 1 of this work, permeation experiments were conducted at room and high temperatures on fully-annealed-commercially-pure iron with two kinds of surface treatment, one group with plasma cleaning and presputtering and the other without it. The experimental results show that the diffusivity evaluated by the new model is independent of sample thickness and surface treatment, while the diffusivity evaluated by the time-lag model varies two orders of magnitude. The experimental results confirm that a fine surface treatment yields a low energy barrier for desorption. The energy barrier for either group is higher than the activation energy of diffusion. Consequently, the ratio of drift velocity through surface to that in bulk increases with increasing temperature and makes the time-lag method appropriate at elevated temperatures.
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.
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.
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
Preconditioned time-difference methods for advection-diffusion-reaction equations
Aro, C.; Rodrigue, G.; Wolitzer, D.
1994-12-31
Explicit time differencing methods for solving differential equations are advantageous in that they are easy to implement on a computer and are intrinsically very parallel. The disadvantage of explicit methods is the severe restrictions placed on stepsize due to stability. Stability bounds for explicit time differencing methods on advection-diffusion-reaction problems are generally quite severe and implicit methods are used instead. The linear systems arising from these implicit methods are large and sparse so that iterative methods must be used to solve them. In this paper the authors develop a methodology for increasing the stability bounds of standard explicit finite differencing methods by combining explicit methods, implicit methods, and iterative methods in a novel way to generate new time-difference schemes, called preconditioned time-difference methods.
METHOD FOR REMOVAL OF LIGHT ISOTOPE PRODUCT FROM LIQUID THERMAL DIFFUSION UNITS
Hoffman, J.D.; Ballou, J.K.
1957-11-19
A method and apparatus are described for removing the lighter isotope of a gaseous-liquid product from a number of diffusion columns of a liquid thermal diffusion system in two stages by the use of freeze valves. The subject liquid flows from the diffusion columns into a heated sloping capsule where the liquid is vaporized by the action of steam in a heated jacket surrounding the capsule. When the capsule is filled the gas flows into a collector. Flow between the various stages is controlled by freeze valves which are opened and closed by the passage of gas and cool water respectively through coils surrounding portions of the pipes through which the process liquid is passed. The use of the dual stage remover-collector and the freeze valves is an improvement on the thermal diffusion separation process whereby the fraction containing the lighter isotope many be removed from the tops of the diffusion columns without intercolumn flow, or prior stage flow while the contents of the capsule is removed to the final receiver.
Britos, Leticia; Goyenola, Guillermo; Oroño, Silvia Umpiérrez
2004-09-01
An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical parameters of the electrophoretic system. Furthermore, the laboratory is framed in a more comprehensive pedagogical setting, which addresses the methodological aspects of a pivotal scientific enterprise such as the Human Genome Project. In this setting, the hands-on activity is complemented with animations, paper models, and discussions. Additionally, our results indicate that the use of borate buffer and agar-agar gels suits many of the experiments included in college-level laboratory activities, which currently make use of more expensive agarose gels and TBE or TAE buffers. PMID:21706751
Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.
Daducci, Alessandro; Canales-Rodríguez, Erick Jorge; Descoteaux, Maxime; Garyfallidis, Eleftherios; Gur, Yaniv; Lin, Ying-Chia; Mani, Merry; Merlet, Sylvain; Paquette, Michael; Ramirez-Manzanares, Alonso; Reisert, Marco; Reis Rodrigues, Paulo; Sepehrband, Farshid; Caruyer, Emmanuel; Choupan, Jeiran; Deriche, Rachid; Jacob, Mathews; Menegaz, Gloria; Prčkovska, Vesna; Rivera, Mariano; Wiaux, Yves; Thiran, Jean-Philippe
2014-02-01
Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies. PMID:24132007
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 β-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
Data Assimilation Using a Variational Method for a 1D Radiation Belt Diffusion Model
NASA Astrophysics Data System (ADS)
Marchand, R.; Degeling, A. W.; O'Donnell, S.; Rankin, R.; Kabin, K.
2009-12-01
A variational data assimilation algorithm has been developed to incorporate electron flux time-series data from satellites into a simple one dimensional diffusion model for the radial transport of radiation belt electrons. The model developed assumes a power law scaling for the radial diffusion coefficient with L shell. The effectiveness of this method is investigated by means of a series of identical twin numerical experiments. This involves using the diffusion model to produce synthetic observations along various satellite trajectories. These observations are in turn used to estimate time-dependent parameters input to the diffusion model, which are compared against the values initially used. The data assimilation algorithm considers the time dependent source located at the outer boundary as a function to be determined. Using synthetic satellite electron flux observations, the algorithm computes a source function that, when used as an input to the diffusion model, most closely reproduces the synthetic observations in a least-squares sense. Observational errors are taken into account, and an estimate of the uncertainty in the output source function is also produced. This uncertainty is found to consistently reflect the quality of the source function estimation during identical twin numerical experiments. Initial tests indicate that the quality of the outer boundary source estimation is strongly dependent on the satellite location, indicating that the outer boundary source estimation becomes poor as information relating to the outer boundary contained in the observations is reduced. The potential of using this data assimilation method to estimate one or more parameters that determine the radial diffusion coefficient, and the possibility of determining whether physical processes affecting the observations are missing in the dynamical model will be discussed.
An in situ method for real-time monitoring of soil gas diffusivity
NASA Astrophysics Data System (ADS)
Laemmel, Thomas; Maier, Martin; Schack-Kirchner, Helmer; Lang, Friederike
2016-04-01
Soil aeration is an important factor for the biogeochemistry of soils. Generally, gas exchange between soil and atmosphere is assumed to be governed by molecular diffusion and by this way fluxes can be calculated using by Fick's Law. The soil gas diffusion coefficient DS represents the proportional factor between the gas flux and the gas concentration gradient in the soil and reflects the ability of the soil to "transport passively" gas through the soil. One common way to determine DS is taking core samples in the field and measuring DS in the lab. Unfortunately this method is destructive and laborious and it can only reflect a small fraction of the whole soil. As a consequence, uncertainty about the resulting effective diffusivity on the profile scale, i.e. the real aeration status remains. We developed a method to measure and monitor DS in situ. The set-up consists of a custom made gas sampling device, the continuous injection of an inert tracer gas and inverse gas transport modelling in the soil. The gas sampling device has seven sampling depths (from 0 to -43 cm of depth) and can be easily installed into vertical holes drilled by an auger, which allows for fast installation of the system. Helium (He) as inert tracer gas was injected continuously at the lower end of the device. The resulting steady state distribution of He was used to deduce the DS depth distribution of the soil. For Finite Element Modeling of the gas-sampling-device/soil system the program COMSOL was used. We tested our new method both in the lab and in a field study and compared the results with a reference lab method using soil cores. DS profiles obtained by our in-situ method were consistent with DS profiles determined based on soil core analyses. Soil gas profiles could be measured with a temporal resolution of 30 minutes. During the field study, there was an important rain event and we could monitor the decrease in soil gas diffusivity in the top soil due to water infiltration. The effect
Garrido, T; Etxabide, A; Guerrero, P; de la Caba, K
2016-10-20
Agar/soy protein biocomposite films were successfully processed by extrusion and compression moulding, obtaining transparent and homogeneous films. The conformational changes occurred during the extrusion process and the effect of agar on the final properties were analyzed. As shown by differential scanning calorimetry (DSC) and specific mechanical energy (SME) values, during the extrusion process protein denatured and unfolded protein chains could interact with agar. These interactions were analyzed by Fourier transform infrared spectroscopy (FTIR) and the secondary structure was determined from the amide I band. Those interactions were supported by the decrease of film solubility. Furthermore, the good compatibility between agar and soy protein was confirmed by the images from scanning electron microscopy (SEM). PMID:27474583
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)
NASA Astrophysics Data System (ADS)
Lu, Yao; Chan, Heang-Ping; Wei, Jun; Hadjiiski, Lubomir M.
2013-02-01
Digital breast tomosynthesis (DBT) has strong promise to improve sensitivity for detecting breast cancer. DBT reconstruction estimates the breast tissue attenuation using projection views (PVs) acquired in a limited angular range. Because of the limited field of view (FOV) of the detector, the PVs may not completely cover the breast in the x-ray source motion direction at large projection angles. The voxels in the imaged volume cannot be updated when they are outside the FOV, thus causing a discontinuity in intensity across the FOV boundaries in the reconstructed slices, which we refer to as the truncated projection artifact (TPA). Most existing TPA reduction methods were developed for the filtered backprojection method in the context of computed tomography. In this study, we developed a new diffusion-based method to reduce TPAs during DBT reconstruction using the simultaneous algebraic reconstruction technique (SART). Our TPA reduction method compensates for the discontinuity in background intensity outside the FOV of the current PV after each PV updating in SART. The difference in voxel values across the FOV boundary is smoothly diffused to the region beyond the FOV of the current PV. Diffusion-based background intensity estimation is performed iteratively to avoid structured artifacts. The method is applicable to TPA in both the forward and backward directions of the PVs and for any number of iterations during reconstruction. The effectiveness of the new method was evaluated by comparing the visual quality of the reconstructed slices and the measured discontinuities across the TPA with and without artifact correction at various iterations. The results demonstrated that the diffusion-based intensity compensation method reduced the TPA while preserving the detailed tissue structures. The visibility of breast lesions obscured by the TPA was improved after artifact reduction.
Lu, Yao; Chan, Heang-Ping; Wei, Jun; Hadjiiski, Lubomir M
2013-02-01
Digital breast tomosynthesis (DBT) has strong promise to improve sensitivity for detecting breast cancer. DBT reconstruction estimates the breast tissue attenuation using projection views (PVs) acquired in a limited angular range. Because of the limited field of view (FOV) of the detector, the PVs may not completely cover the breast in the x-ray source motion direction at large projection angles. The voxels in the imaged volume cannot be updated when they are outside the FOV, thus causing a discontinuity in intensity across the FOV boundaries in the reconstructed slices, which we refer to as the truncated projection artifact (TPA). Most existing TPA reduction methods were developed for the filtered backprojection method in the context of computed tomography. In this study, we developed a new diffusion-based method to reduce TPAs during DBT reconstruction using the simultaneous algebraic reconstruction technique (SART). Our TPA reduction method compensates for the discontinuity in background intensity outside the FOV of the current PV after each PV updating in SART. The difference in voxel values across the FOV boundary is smoothly diffused to the region beyond the FOV of the current PV. Diffusion-based background intensity estimation is performed iteratively to avoid structured artifacts. The method is applicable to TPA in both the forward and backward directions of the PVs and for any number of iterations during reconstruction. The effectiveness of the new method was evaluated by comparing the visual quality of the reconstructed slices and the measured discontinuities across the TPA with and without artifact correction at various iterations. The results demonstrated that the diffusion-based intensity compensation method reduced the TPA while preserving the detailed tissue structures. The visibility of breast lesions obscured by the TPA was improved after artifact reduction. PMID:23318346
Yohem, K. H.; Slymen, D. J.; Bregman, M. D.; Meyskens, F. L.
1988-01-01
The radiation response of murine and human melanoma cells assayed in bilayer soft agar and monolayer was examined. Cells from the murine melanoma Cloudman S91 CCL 53.1 cell line and three human melanoma cell strains (C8146C, C8161, and R83-4) developed in our laboratory were irradiated by single dose X-rays and plated either in agar or on plastic. D0 values were the same within 95% confidence intervals for cells from the human melanoma cell strains C8146C, C8161, and R83-4 but were dissimilar for the murine cell line CCL 53.1 Dq values were different for all cells studied. The shape of the survival curve for all four melanomas was not identical for cells assayed in soft agar versus cells grown on plastic. This would indicate that apparent radiosensitivity was influenced by the method of assay although there were no apparent consistent differences between the curves generated by monolayer or bilayer soft agar assays. PMID:3348949
Hyperspectral image reconstruction using RGB color for foodborne pathogen detection on agar plates
NASA Astrophysics Data System (ADS)
Yoon, Seung-Chul; Shin, Tae-Sung; Park, Bosoon; Lawrence, Kurt C.; Heitschmidt, Gerald W.
2014-03-01
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 spectra measured in the visible and near-infrared spectral range from 400 and 1,000 nm (473 narrow spectral bands). Multivariate regression methods were used to estimate and predict hyperspectral data from RGB color values. The six representative non-O157 Shiga-toxin producing Eschetichia coli (STEC) serogroups (O26, O45, O103, O111, O121, and O145) were grown on Rainbow agar plates. A line-scan pushbroom hyperspectral image sensor was used to scan 36 agar plates grown with pure STEC colonies at each plate. The 36 hyperspectral images of the agar plates were divided in half to create training and test sets. The mean Rsquared value for hyperspectral image estimation was about 0.98 in the spectral range between 400 and 700 nm for linear, quadratic and cubic polynomial regression models and the detection accuracy of the hyperspectral image classification model with the principal component analysis and k-nearest neighbors for the test set was up to 92% (99% with the original hyperspectral images). Thus, the results of the study suggested that color-based detection may be viable as a multispectral imaging solution without much loss of prediction accuracy compared to hyperspectral imaging.
Use of Dehydrated Agar to Estimate Microbial Water Quality for Horticulture Irrigation.
Meador, Dustin P; Fisher, Paul R; Guy, Charles L; Harmon, Philip F; Peres, Natalia A; Teplitski, Max
2016-07-01
Petrifilms are dehydrated agar culture plates that have been used to quantify colony forming units (CFU) mL of either aerobic bacteria (Petrifilm-AC) or fungus (Petrifilm-YM), depending on substrate composition. Microbes in irrigation systems can indicate biofilm risk and potential clogging of irrigation emitters. The research objective was to compare counts on Petrifilms versus traditional, hydrated-agar plates using samples collected from recirculated irrigation waters and cultures of isolated known species. The estimated count (in CFU mL) from a recirculated irrigation sample after 7 d of incubation on Petrifilm-YM was only 5.5% of the count quantified using sabouraud dextrose agar (SDA) with chloramphenicol after 14 d. In a separate experiment with a known species, Petrifilm-YM did not successfully culture zoospores of . Isolates of viable zoospores were cultured successfully on potato-dextrose agar (PDA), with comparable counts with a vegetable juice medium supplemented with the antibiotics pimaricin, ampicillin, rifamycin, pentochloronitrobenzene and hymexazol (PARP-H). The quantification of pv. Begoniaceae on Petrifilm-AC was not significantly different ( < 0.05) than on PDA, but was lower than on Reasoner and Goldrich agar (R2A) or with a hemocytometer. The current formulation of Petrifilm-YM is unlikely to be a useful monitoring method for plant pathogens in irrigation water because of the inability to successfully culture oomycetes. However, Petrifilm-AC was an effective method to quantify bacteria and can provide an easy-to-use on-farm tool to monitor biofilm risk and microbial density. PMID:27380096
Application of Electrode Methods in Studies of Nitric Oxide Metabolism and Diffusion Kinetics
Liu, Xiaoping; Zweier, Jay L.
2012-01-01
Nitric oxide (NO) has many important physiological roles in the body. Since NO electrodes can directly measure NO concentration in the nM range and in real time, NO electrode methods have been generally used in laboratories for measuring NO concentration in vivo and in vitro. This review focuses on the application of electrode methods in studies of NO diffusion and metabolic kinetics. We have described the physical and chemical properties that need to be considered in the preparation of NO stock solution, discussed the effect of several interfering factors on the measured curves of NO concentration that need to be eliminated in the experimental setup for NO measurements, and provided an overview of the application of NO electrode methods in measuring NO diffusion and metabolic kinetics in solution and in biological systems. This overview covers NO metabolism by oxygen (O2), superoxide, heme proteins, cells and tissues. Important conclusions and physiological implication of these studies are discussed. PMID:23730264
Application of numerical methods for diffusion-based modeling of skin permeation.
Frasch, H Frederick; Barbero, Ana M
2013-02-01
The application of numerical methods for mechanistic, diffusion-based modeling of skin permeation is reviewed. Methods considered here are finite difference, method of lines, finite element, finite volume, random walk, cellular automata, and smoothed particle hydrodynamics. First the methods are briefly explained with rudimentary mathematical underpinnings. Current state of the art numerical models are described, and then a chronological overview of published models is provided. Key findings and insights of reviewed models are highlighted. Model results support a primarily transcellular pathway with anisotropic lipid transport. Future endeavors would benefit from a fundamental analysis of drug/vehicle/skin interactions. PMID:22261307
Preconditioned iterative methods for space-time fractional advection-diffusion equations
NASA Astrophysics Data System (ADS)
Zhao, Zhi; Jin, Xiao-Qing; Lin, Matthew M.
2016-08-01
In this paper, we propose practical numerical methods for solving a class of initial-boundary value problems of space-time fractional advection-diffusion equations. First, we propose an implicit method based on two-sided Grünwald formulae and discuss its stability and consistency. Then, we develop the preconditioned generalized minimal residual (preconditioned GMRES) method and preconditioned conjugate gradient normal residual (preconditioned CGNR) method with easily constructed preconditioners. Importantly, because resulting systems are Toeplitz-like, fast Fourier transform can be applied to significantly reduce the computational cost. We perform numerical experiments to demonstrate the efficiency of our preconditioners, even in cases with variable coefficients.
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.
Asgari, Setareh; Jahanshahi, Mohsen; Rahimpour, Ahmad
2014-09-26
In the present work a novel kind of dense nanoporous composite matrix for expanded bed application has been successfully first prepared with Nickel powder as a densifier and was covered with Agar-Agar layer as a skeleton, through the method of water-in-oil emulsification. Agar-Agar is a porous and inexpensive polymer. In order to fabricate cost-effective adsorbent with favorable qualities Agar-Agar polymer was used. Thereafter, the customized composite particle was modified by pseudo-affinity dye-ligand, Reactive Blue 4 (RB4), aimed at preparing a pseudo-affinity adsorbent (RB4-Agar-Ni) for bioprodut adsorption from aqueous solution. Bovine Serum Albumin (BSA) was selected as a model protein to investigate the adsorption behavior in batchwise and expanded bed chromatography, and the obtained results were evaluated with that of Streamline™ (Amersham-Pharmacia Biotech, Sweden). Spherical appearance and porous structure of composite particles were observed by the optical microscope (OM) and scanning electronic microscope (SEM). The results suggested that the matrices followed the logarithmic normal size distribution with the range of 65-300 μm and average diameter of 126.81-151.47 μm, proper wet density of 1.64-2.78 g/ml, water content of 62.74-34%, porosity of 98-90% and pore size of about 38-130 nm. For better comprehension of the impact of solid phase properties on the performance of the expanded bed, the expansion and hydrodynamic properties of a composite matrix with a series of densities was evaluated and estimated by the retention time distribution method (RTD) in an expanded bed and was compared with that of other matrices. According to obtained results the expansion factors under the same fluid velocity decreased by increasing the matrix density. Moreover, the axial dispersion coefficient (Dax) is the most appropriate parameter for evaluating the stability of expanded bed, on various operating conditions, such as different flow velocity, bed expansion
Ku, Bon Ki; Kulkarni, Pramod
2015-01-01
We compare different approaches to measure surface area of aerosol agglomerates. The objective was to compare field methods, such as mobility and diffusion charging based approaches, with laboratory approach, such as Brunauer, Emmett, Teller (BET) method used for bulk powder samples. To allow intercomparison of various surface area measurements, we defined ‘geometric surface area’ of agglomerates (assuming agglomerates are made up of ideal spheres), and compared various surface area measurements to the geometric surface area. Four different approaches for measuring surface area of agglomerate particles in the size range of 60–350 nm were compared using (i) diffusion charging-based sensors from three different manufacturers, (ii) mobility diameter of an agglomerate, (iii) mobility diameter of an agglomerate assuming a linear chain morphology with uniform primary particle size, and (iv) surface area estimation based on tandem mobility–mass measurement and microscopy. Our results indicate that the tandem mobility–mass measurement, which can be applied directly to airborne particles unlike the BET method, agrees well with the BET method. It was also shown that the three diffusion charging-based surface area measurements of silver agglomerates were similar within a factor of 2 and were lower than those obtained from the tandem mobility–mass and microscopy method by a factor of 3–10 in the size range studied. Surface area estimated using the mobility diameter depended on the structure or morphology of the agglomerate with significant underestimation at high fractal dimensions approaching 3. PMID:26692585
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.
Tchitchekova, Deyana S; Morthomas, Julien; Ribeiro, Fabienne; Ducher, Roland; Perez, Michel
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. PMID:25053312
NASA Astrophysics Data System (ADS)
Tchitchekova, Deyana S.; Morthomas, Julien; Ribeiro, Fabienne; Ducher, Roland; Perez, Michel
2014-07-01
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.
Theoretical principles of experimental methods for determining the thermal diffusivity of soils
NASA Astrophysics Data System (ADS)
Mikayilov, F. D.; Shein, E. V.
2010-05-01
Mathematical models for predicting the heat transfer in soils are used for the management of the soil thermal conditions; the development of different soil constructions; the analysis of the thermal effects related to the loosening or compaction of the surface soil layers, the sanding of peat, and the application of friable mulching materials; and the description of many other phenomena and processes. The experimental support of the development and functioning of these models is provided by the function of thermal diffusivity, which describes the thermal diffusivity as a function of the water content and can be derived using the methods based on the solution of direct and inverse problems of heat transfer. On the basis of the different boundary conditions and sine-shaped daily and annual temperature cycles, a number of equations were proposed for calculating the thermal diffusivity that contained logarithms, arctangents of amplitudes, and the phase shift between the daily temperatures at two depths. A mean-integral solution was obtained for the estimation of the average temperature in a specific soil layer. A number of methods were developed starting from the analysis of the temperature dynamics on the basis of four daily observations at the same depth with 6-hour intervals, and nomograms were given for the rapid and simple calculation of the soil thermal diffusivity at a specific depth. The developed methods can be used for assessing the soil thermal diffusivity under natural conditions, which should improve the reliability, accuracy, and adequacy and expand the application range of predictive mathematical models for the thermal regime of soils.
NASA Astrophysics Data System (ADS)
Jiang, Tian; Zhang, Yong-Tao
2016-04-01
Implicit integration factor (IIF) methods were developed in the literature for solving time-dependent stiff partial differential equations (PDEs). Recently, IIF methods were combined with weighted essentially non-oscillatory (WENO) schemes in Jiang and Zhang (2013) [19] to efficiently solve stiff 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 non-stiff hyperbolic part of the system. To efficiently calculate large matrix exponentials, Krylov subspace approximation is directly applied to the implicit integration factor (IIF) methods. So far, the IIF methods developed in the literature are multistep methods. In this paper, we develop Krylov single-step IIF-WENO methods for solving stiff advection-diffusion-reaction equations. The methods are designed carefully to avoid generating positive exponentials in the matrix exponentials, which is necessary for the stability of the schemes. We analyze the stability and truncation errors of the single-step IIF schemes. Numerical examples of both scalar equations and systems are shown to demonstrate the accuracy, efficiency and robustness of the new methods.
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
Andualem, Berhanu; Gessesse, Amare
2013-01-01
Objective To investigate and optimize microbial media that substitute peptone agar using brebra seed defatted flour. Methods 'Defatted process, inoculums preparation, evaluation of bacterial growth, preparation of cooked and hydrolyzed media and growth turbidity of tested bacteria were determined. Results Two percent defatted flour was found to be suitable concentration for the growth of pathogenic bacteria: Escherichia coli (ATCC 25922) (E. coli), Pseudomonas aeruginosa (ATCC 27853), Salmonella (NCTC 8385) and Shigella flexneri (ATCC 12022) (S. flexneri), while 3% defatted flour was suitable for Staphylococcus aureus (ATCC 25923) (S. aureus). E. coli (93±1) and S. flexneri (524±1) colony count were significantly (P≤0.05) greater in defatted flour without supplement than in supplemented medium. E. coli [(3.72×109±2) CFU/mL], S. aureus [(7.4×109±2) CFU/mL], S. flexneri [(4.03×109±2) CFU/mL] and Salmonella [(2.37×109±1) CFU/mL] in non-hydrolyzed sample were statistically (P≤0.05) greater than hydrolyzed one and commercial peptone agar. Colony count of Salmonella [(4.55×109±3) CFU/mL], S. flexneri [(5.40×109±3) CFU/mL] and Lyesria moncytogenes (ATCC 19116) [(5.4×109±3) CFU/mL] on raw defatted flour agar was significantly (P≤0.05) greater than cooked defatted flour and commercial peptone agar. Biomass of E. coli, S. aureus, Salmonella and Enterococcus faecalis in non-hydrolyzed defatted flour is highly increased over hydrolyzed defatted flour and commercial peptone broth. Conclusions The defatted flour agar was found to be better microbial media or comparable with peptone agar. The substances in it can serve as sources of carbon, nitrogen, vitamins and minerals that are essential to support the growth of microorganisms without any supplements. Currently, all supplements of peptone agar are very expensive in the market. PMID:24075344
A simple method for the determination of resistance to gas diffusion in plant organs.
Cameron, A C; Yang, S F
1982-07-01
A simple method was developed for the determination of resistance coefficients for ethylene diffusion in plant tissues based on the kinetic analysis of the efflux of preloaded ethane gas. Efflux curves were analyzed to obtain first-order rate constants and resistance coefficients. Resistance coefficients determined by the ethane efflux and steady-state methods were found to agree well. Employing the ethane efflux method, it was shown that over 97% of gas exchange of tomato (Lycopersicum esculentum Mill., cv. ;Ace') fruits occurs through the stem scar. The resistances to diffusion of tomato skin and stem scar were found to be 280,000 and 300 seconds per centimeter, respectively; the combined resistance of intact tomato fruits was approximately 7,800 seconds per centimeter. The ethane efflux method was employed to show that plastic shrink-wrapping of English cucumbers (Cucumis sativus L. var anglicus Bailey) increased the resistance to ethane diffusion from 1.1 x 10(3) to 23 x 10(3) seconds per centimeter. PMID:16662447
A novel model for diffusion based release kinetics using an inverse numerical method.
Mohammadi, Hadi; Herzog, Walter
2011-10-01
We developed and analyzed an inverse numerical model based on Fick's second law on the dynamics of drug release. In contrast to previous models which required two state descriptions of diffusion for long- and short-term release processes, our model is valid for the entire release process. The proposed model may be used for identifying and reducing experimental errors associated with measurements of diffusion based release kinetics. Knowing the initial and boundary conditions, and assuming Fick's second law to be appropriate, we use the methods of Lagrange multiplier along with least-square algorithms to define a cost function which is discretized using finite difference methods and is optimized so as to minimize errors. Our model can describe diffusion based release kinetics for static and dynamic conditions as accurately as finite element methods, but results are obtained in a fraction of CPU time. Our method can be widely used for drug release procedures and for tissue engineering/repair applications where oxygenation of cells residing within a matrix is important. PMID:21382735
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
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
Cu diffusion as an alternative method for nanopatterned CuTCNQ film growth
NASA Astrophysics Data System (ADS)
Capitán, M. J.; Álvarez, J.; Navío, C.; Miranda, R.
2016-05-01
In this paper we show by means of ‘in situ’ x-ray diffraction studies that CuTCNQ formation from Cu(solid)–TCNQ(solid tetracyanoquinodimethane) goes through Cu diffusion at room temperature. The film quality depends on the TCNQ evaporation rate. At low evaporation rate we get a single phase-I CuTCNQ film very well crystallized and well oriented. The film has a CuTCNQ(0 2 0) orientation. The film is formed by CuTCNQ nanorods of a very homogeneous size. The film homogeneity has also been seen by atomic force microscopy (AFM). The electronic properties of the film have been measured by x-ray photoelectron spectroscopy (XPS) and ultra-violet photoelectron spectroscopy (UPS). Thus, the Cu-diffusion method has arisen as a very simple, clean and efficient method to grow localized CuTCNQ nanorods on Cu, opening up new insights for technological applications.
Does diffusion MRI tell us anything about the white matter? An overview of methods and pitfalls
O’Donnell, Lauren J.; Pasternak, Ofer
2014-01-01
One key pitfall in diffusion magnetic resonance imaging (dMRI) clinical neuroimaging research is the challenge of understanding and interpreting the results of a complex analysis pipeline. The sophisticated algorithms employed by the analysis software, combined with the relatively non-specific nature of many diffusion measurements, lead to challenges in interpretation of the results. This paper is aimed at an intended audience of clinical researchers who are learning about dMRI or trying to interpret dMRI results, and who may be wondering “Does dMRI tell us anything about the white matter?” We present a critical review of dMRI methods and measures used in clinical neuroimaging research, focusing on the most commonly used analysis methods and the most commonly reported measures. We describe important pitfalls in every section, and provide extensive references for the reader interested in more detail. PMID:25278106
Errors associated with standard nodal diffusion methods as applied to mixed oxide fuel problems
Brantley, P. S., LLNL
1998-07-24
The evaluation of the disposition of plutonium using light water reactors is receiving increased attention. However, mixed-oxide (MOX) fuel assemblies possess much higher absorption and fission cross- sections when compared to standard UO2 assemblies. Those properties yield very high thermal flux gradients at the interfaces between MOX and UO2 assemblies. It has already been reported that standard flux reconstruction methods (that recover the homogeneous intranodal flux shape using the converged nodal solution) yield large errors in the presence of MOX assemblies. In an accompanying paper, we compare diffusion and simplified PN calculations of a mixed-oxide benchmark problem to a reference transport calculation. In this paper, we examine the errors associated with standard nodal diffusion methods when applied to the same benchmark problem. Our results show that a large portion of the error is associated with the quadratic leakage approximation (QLA) that is commonly used in the standard nodal codes.
An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems
NASA Astrophysics Data System (ADS)
Padgett, Jill M. A.; Ilie, Silvana
2016-03-01
Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating the solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.
Hyperspectral imaging for detecting pathogens grown on agar plates
NASA Astrophysics Data System (ADS)
Yoon, Seung Chul; Lawrence, Kurt C.; Siragusa, Gregory R.; Line, John E.; Park, Bosoon; Windham, William R.
2007-09-01
This paper is concerned with the development of a hyperspectral imaging technique for detecting and identifying one of the most common foodborne pathogens, Campylobacter. Direct plating using agars is an effective tool for laboratory tests and analyses of microorganisms. The morphology (size, growth pattern, color, etc.) of colonies grown on agar plates has been widely used to tentatively differentiate organisms. However, it is sometimes difficult to differentiate target organisms like Campylobacters from other contaminants grown together on the same agar plates. A hyperspectral imaging system operating at the visible and near infrared (VNIR) spectral region from 400 nm to 900 nm was set up to measure spectral signatures of 17 different Campylobacter and non-Campylobacter subspecies. Protocols for culturing, imaging samples and for calibrating measured data were developed. The VNIR spectral library of all 17 organisms commonly encountered in poultry was established from calibrated hyperspectral images. A classification algorithm was developed to locate and identify Campylobacters, non-Campylobacter contaminants, and background agars with 99.29% accuracy. This research has a potential to be expanded to detect other pathogens grown on agar media.
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.
Method for the measurement of the diffusion coefficient of benzalkonium chloride.
Smith, M J; Flowers, T H; Cowling, M J; Duncan, H J
2002-03-01
Biofilm formation on the optical ports of cameras and underwater sensors is the primary cause of their reduced useful deployment time. The use of a transparent hydrogel coating containing the cationic surfactant benzalkonium chloride has been shown to extend the deployment times for up to 12 weeks for these instruments. In order to predict the effective lifetime of these coatings it was necessary to obtain the diffusion coefficient of the benzalkonium chloride used in the coatings. Benzalkonium chloride can have different alkyl chain lengths ranging from C8H17 to C18H37 with chain length greatly affecting its chemical properties. The benzalkonium chloride materials investigated here were mixtures of C12H25 and C14H29 as well as C14H29 on its own. These materials were selected for their proven biofilm resistant qualities. The diaphragm diffusion cell technique was investigated for its applicability to the measurement of diffusion coefficients of molecules with surfactant properties and the ability to form micelles. The method was found to be satisfactory for the cationic surfactant benzalkonium chloride. The average value of the membrane cell integral diffusion coefficient D was 7.78 x 10(-6) cm2 s(-1) at 25 degrees C and there was no significant effect of alkyl chain length on the measured value of D. PMID:11996332
A Proposal for a Novel Method to Measure the Diffusivity of Species in Slag
NASA Astrophysics Data System (ADS)
Muhmood, Luckman; Viswanathan, Nurni Neelakantan; Seetharaman, Seshadri
2011-04-01
The rate of reactions involved in steel-refining operations largely depend on the transport of species through the slag or metal phase at steel refining temperatures; the intrinsic reaction rates are expected to be high. Therefore, the study of diffusivity of species in slag is of great importance. The present work proposes a new methodology, in which experiments can be designed to determine the diffusivity of species in liquid slag. In this article, a mathematical description for the methodology is formulated and subsequently solved using numerical methods. This exercise will help in identifying appropriate bounds for experimental parameters for a desired accuracy. The proposed methodology is generic for any species in the liquid slag phase. However, diffusion of sulfur through slag has been illustrated as a case study. The order of magnitude for the diffusion coefficient for sulfur was taken from the classic works of Saito and Kawai, the sulfide capacity and sulfur partition ratio were retrieved from the works of Taniguchi et al., and the slag density was retrieved from earlier experimental results of the present authors. The slag density was obtained from earlier experimental results from the present group. The Henrian activity coefficients were retrieved from literature. Subsequent to the present work, the design of experiments and measurements carried out using the proposed methodology and the results obtained are presented as the second article on this subject.
A hybrid method for efficient and accurate simulations of diffusion compartment imaging signals
NASA Astrophysics Data System (ADS)
Rensonnet, Gaëtan; Jacobs, Damien; Macq, Benoît; Taquet, Maxime
2015-12-01
Diffusion-weighted imaging is sensitive to the movement of water molecules through the tissue microstructure and can therefore be used to gain insight into the tissue cellular architecture. While the diffusion signal arising from simple geometrical microstructure is known analytically, it remains unclear what diffusion signal arises from complex microstructural configurations. Such knowledge is important to design optimal acquisition sequences, to understand the limitations of diffusion-weighted imaging and to validate novel models of the brain microstructure. We present a novel framework for the efficient simulation of high-quality DW-MRI signals based on the hybrid combination of exact analytic expressions in simple geometric compartments such as cylinders and spheres and Monte Carlo simulations in more complex geometries. We validate our approach on synthetic arrangements of parallel cylinders representing the geometry of white matter fascicles, by comparing it to complete, all-out Monte Carlo simulations commonly used in the literature. For typical configurations, equal levels of accuracy are obtained with our hybrid method in less than one fifth of the computational time required for Monte Carlo simulations.
A novel grating-imaging method to measure carrier diffusion coefficient in graphene
NASA Astrophysics Data System (ADS)
Chen, Ke; Wang, Yaguo; Akinwande, Deji; Bank, Seth; Lin, Jung-Fu
Similar to carrier mobility, carrier diffusion coefficient in graphene determines the response rate of future graphene-based electronics. Here we present a simple, sensitive and non-destructive technique integrated with ultrafast pump-probe spectroscopy to measure carrier diffusion in CVD-grown graphene. In the method, the pump and the probe beams pass through the same area of a photomask with metal strips i.e. a transmission amplitude grating, and get diffracted. The diffracted light is collected by an objective lens and focused onto the sample to generate carrier density grating. Relaxation of this carrier density grating is governed by both carrier recombination and carrier diffusion in the sample. Transient transmission change of the probe beams, which reflects this relaxation process, is recorded. The measured diffusion coefficients of multilayer and monolayer CVD-grown graphene are 2000cm2/s and 10000cm2/s, respectively, comparable with the reported values of epitaxial graphene and reduced graphene. This transmission grating technique can be used to measure carrier dynamics in versatile 2D materials.
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.
Bowen, Constance Mary; Stanton, Marietta; Manno, Martin
2012-01-01
Routine screening of mechanically ventilated patients for delirium is essential for prompt recognition and management; however, this represents a change in practice. Rogers' Diffusion of Innovations Theory can be useful as a strategy to facilitate adoption of a practice change. This case study describes the effectiveness of identifying barriers to a change in practice and developing strategies, specific to Rogers' innovation decision process, for implementing the Confusion Assessment Method for the intensive care unit. PMID:22367153
NASA Astrophysics Data System (ADS)
Lai, Yongzeng; Zeng, Yan; Xi, Xiaojing
2011-11-01
In this paper, we discuss control variate methods for Asian option pricing under exponential jump diffusion model for the underlying asset prices. Numerical results show that the new control variate XNCV is much more efficient than the classical control variate XCCV when used in pricing Asian options. For example, the variance reduction ratios by XCCV are no more than 120 whereas those by XNCV vary from 15797 to 49171 on average over sample sizes 1024, 2048, 4096, 8192, 16384 and 32768.
NASA Astrophysics Data System (ADS)
Liu, Quan; Ramanujam, Nirmala
2007-04-01
A scaling Monte Carlo method has been developed to calculate diffuse reflectance from multilayered media with a wide range of optical properties in the ultraviolet-visible wavelength range. This multilayered scaling method employs the photon trajectory information generated from a single baseline Monte Carlo simulation of a homogeneous medium to scale the exit distance and exit weight of photons for a new set of optical properties in the multilayered medium. The scaling method is particularly suited to simulating diffuse reflectance spectra or creating a Monte Carlo database to extract optical properties of layered media, both of which are demonstrated in this paper. Particularly, it was found that the root-mean-square error (RMSE) between scaled diffuse reflectance, for which the anisotropy factor and refractive index in the baseline simulation were, respectively, 0.9 and 1.338, and independently simulated diffuse reflectance was less than or equal to 5% for source-detector separations from 200 to 1500 μm when the anisotropy factor of the top layer in a two-layered epithelial tissue model was varied from 0.8 to 0.99; in contrast, the RMSE was always less than 5% for all separations (from 0 to 1500 μm) when the anisotropy factor of the bottom layer was varied from 0.7 to 0.99. When the refractive index of either layer in the two-layered tissue model was varied from 1.3 to 1.4, the RMSE was less than 10%. The scaling method can reduce computation time by more than 2 orders of magnitude compared with independent Monte Carlo simulations.
Impact of the emulsification-diffusion method on the development of pharmaceutical nanoparticles.
Quintanar-Guerrero, David; Zambrano-Zaragoza, María de la Luz; Gutierrez-Cortez, Elsa; Mendoza-Munoz, Nestor
2012-12-01
Nanotechnology is having a profound impact in many scientific fields and it has become one of the most important and exciting discipline. Like all technological advances, nanotechnology has its own scientific basis with a broad interdisciplinary effect. Perhaps, we are witnessing an exponential growth of nanotechnology, reflection of this is the important increase in the number of patents, scientific papers and specialized "nano" meetings and journals. The impact in the pharmaceutical area is related to the use of colloidal drug delivery systems as carriers for bioactive agents, in particular, the nanoparticle technology. The term nanoparticles designates solid submicronic particles formed of acceptable materials (e.g. polymers, lipids, etc.) containing an active substance. It includes both nanospheres (matricial systems) and nanocapsules (membrane systems). The knowledge of the nanoparticle preparation methods is a key issue for the formulator involved with drug-delivery research and development. In general, the methods based on preformed polymers, in particular biodegradable polymers, are preferred due to their easy implementation and lower potential toxicity. One of the most widely used methods to prepare polymeric nanoparticles is emulsification-diffusion. This method has been discussed in some reviews that compile research works but has a small number of patents. In this review, the emulsification-diffusion method is discussed from a technological point of view in order to show the operating conditions and formulation variables from data extracted of recent patents and experimental works. The main idea is to provide the reader with a general guide for formulators to make decisions about the usefulness of this method to develop specific nanoparticulate systems. The first part of this review provides an overview of the emulsification-diffusion method to prepare polymeric nanoparticles, while the second part evaluates the influence of preparative variables on the
A modified evaluation method to reduce finite pulse time effects in flash diffusivity measurement
NASA Astrophysics Data System (ADS)
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 δ(x) does not exceed the sample thickness ( √{ 12 α τ 0 } ≤ L ) during laser heating.
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 δ(x) does not exceed the sample thickness (√(12ατ0)≤L) during laser heating. PMID:26724057
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.
Method for Calculating the Optical Diffuse Reflection Coefficient for the Ocular Fundus
NASA Astrophysics Data System (ADS)
Lisenko, S. A.; Kugeiko, M. M.
2016-07-01
We have developed a method for calculating the optical diffuse reflection coefficient for the ocular fundus, taking into account multiple scattering of light in its layers (retina, epithelium, choroid) and multiple refl ection of light between layers. The method is based on the formulas for optical "combination" of the layers of the medium, in which the optical parameters of the layers (absorption and scattering coefficients) are replaced by some effective values, different for cases of directional and diffuse illumination of the layer. Coefficients relating the effective optical parameters of the layers and the actual values were established based on the results of a Monte Carlo numerical simulation of radiation transport in the medium. We estimate the uncertainties in retrieval of the structural and morphological parameters for the fundus from its diffuse reflectance spectrum using our method. We show that the simulated spectra correspond to the experimental data and that the estimates of the fundus parameters obtained as a result of solving the inverse problem are reasonable.
Song, Yun S.; Steinrücken, Matthias
2012-01-01
The transition density function of the Wright–Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright–Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation–selection balance. PMID:22209899
Computing quasi-linear diffusion coefficients using the delta-f particle-in-cell method
Austin, T. M.; Smithe, D. N.; Ranjbar, V.
2009-11-26
Linear wave codes AORSA and TORIC couple to the bounce-averaged nonlinear Fokker-Planck code CQL3D through quasi-linear diffusion coefficients. Both linear wave codes rely on the quasi-local approximation that includes only first-order parallel and perpendicular gradient variations of cyclotron frequency and ignores field line curvature along with temperature and density gradient effects. The delta-f particle-in-cell (DFPIC) method has been successfully used for simulating ion-cyclotron fast wave behavior. This method also permits particle behavior such as multiple pass resonance, banana orbits, and superadiabaticity. We present new work on generating quasi-linear diffusion coefficients using the DFPIC method that will permit the electromagnetic particle-in-cell (EMPIC) code, VORPAL, to couple to CQL3D and to compare to AORSA and TORIC. A new multiple weight delta-f approach will be presented that converts velocity derivatives to action derivatives and yields a full tensor quasi-linear diffusion coefficient.
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.
Contribution to an effective design method for stationary reaction-diffusion patterns
Szalai, István; Horváth, Judit; De Kepper, Patrick
2015-06-15
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.
Method and apparatus for determining minority carrier diffusion length in semiconductors
Goldstein, Bernard; Dresner, Joseph; Szostak, Daniel J.
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.
Susceptibility testing of Propionibacterium acnes comparing agar dilution with E test.
Smith, M A; Alperstein, P; France, K; Vellozzi, E M; Isenberg, H D
1996-01-01
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
Fabrication of graded-index plastic optical fiber by the diffusion-assisted coextrusion method
NASA Astrophysics Data System (ADS)
Sohn, In-Sung
Recently, plastic optical fibers (POFs) have drawn significant attention as high-speed transmission media due to their advantages over conventional glass optical fibers such as flexibility and durability. In addition, Grade-Index (GRIN) POFs with smoothly varying refractive indices provide increased data transmission speeds suitable for the short-distance communications such as local area networking or home networking. In this research, the diffusion-assisted coextrusion process is introduced as a method to fabricate GRIN POFs. In this process, two or more polymeric materials containing additives for refractive index modification are fed separately into a coextrusion die where a concentric multi-layer structure is formed. Subsequently, the diffusion of additives take places in a diffusion zone creating a non-equilibrium concentration profile, hence the refractive index profile. A theoretical analysis for the prediction of the refractive index profile obtainable by this process indicates that it is difficult to obtain a near-parabolic refractive index profile with the tubular flow design unless a very large residence time in the diffusion zone is provided. However, significant changes in the refractive index profile can be induced by adopting a multi-layer approach and an annulus flow design. Furthermore, the bandwidth estimated by the ray analysis indicates that even a small variation of the refractive index profile created by the additive diffusion can result in a significant increase in the bandwidth. To verify the findings from theoretical analysis, poly(methyl methacrylate)-base GRIN POFs with diphenyl sulfide and diphenyl sulfoxide as refractive index-modifying dopants were prepared and the effects of various operating conditions such as melt temperatures, flow rates and core-cladding interface positions were investigated. The dopant concentration profile, thus the refractive index profile, characterized by FT-IR spectroscopy, has been shown to be controllable
Fly agaric (Amanita muscaria) poisoning, case report and review.
Satora, Leszek; Pach, Dorota; Butryn, Beata; Hydzik, Piotr; Balicka-Slusarczyk, Barbara
2005-06-01
Gathering and eating mushrooms and other plants containing psychoactive substances has become increasingly popular among young people experimenting with drugs. Dried fly agaric Amanita muscaria fruiting bodies were eaten by five young persons (18-21 years of age) at a party in order to evoke hallucinations. Visual and auditory hallucinations occurred in four of them, whereas a 18-year-old girl lost consciousness. The following morning, she went to the Clinic of Toxicology. Due to the fact that not all the active substances present in the fly agaric have been identified, and some of them have an effect after a period of latency, the patient was admitted for several days of observation during which check-up examinations were performed. After four days without any problems, she was discharged. The poisoning regressed with no organ complications. The remaining persons who had eaten the fly agaric were free from any complaints. PMID:15904689
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.
Li, Xiaofan; Nie, Qing
2015-01-01
Many applications in materials involve surface diffusion of elastically stressed solids. Study of singularity formation and long-time behavior of such solid surfaces requires accurate simulations in both space and time. Here we present a high-order boundary integral method for an elastically stressed solid with axi-symmetry due to surface diffusions. In this method, the boundary integrals for isotropic elasticity in axi-symmetric geometry are approximated through modified alternating quadratures along with an extrapolation technique, leading to an arbitrarily high-order quadrature; in addition, a high-order (temporal) integration factor method, based on explicit representation of the mean curvature, is used to reduce the stability constraint on time-step. To apply this method to a periodic (in axial direction) and axi-symmetric elastically stressed cylinder, we also present a fast and accurate summation method for the periodic Green’s functions of isotropic elasticity. Using the high-order boundary integral method, we demonstrate that in absence of elasticity the cylinder surface pinches in finite time at the axis of the symmetry and the universal cone angle of the pinching is found to be consistent with the previous studies based on a self-similar assumption. In the presence of elastic stress, we show that a finite time, geometrical singularity occurs well before the cylindrical solid collapses onto the axis of symmetry, and the angle of the corner singularity on the cylinder surface is also estimated. PMID:26487788
NASA Astrophysics Data System (ADS)
Zhang, Xiaofeng
2012-03-01
Image formation in fluorescence diffuse optical tomography is critically dependent on construction of the Jacobian matrix. For clinical and preclinical applications, because of the highly heterogeneous characteristics of the medium, Monte Carlo methods are frequently adopted to construct the Jacobian. Conventional adjoint Monte Carlo method typically compute the Jacobian by multiplying the photon density fields radiated from the source at the excitation wavelength and from the detector at the emission wavelength. Nonetheless, this approach assumes that the source and the detector in Green's function are reciprocal, which is invalid in general. This assumption is particularly questionable in small animal imaging, where the mean free path length of photons is typically only one order of magnitude smaller than the representative dimension of the medium. We propose a new method that does not rely on the reciprocity of the source and the detector by tracing photon propagation entirely from the source to the detector. This method relies on the perturbation Monte Carlo theory to account for the differences in optical properties of the medium at the excitation and the emission wavelengths. Compared to the adjoint methods, the proposed method is more valid in reflecting the physical process of photon transport in diffusive media and is more efficient in constructing the Jacobian matrix for densely sampled configurations.
NASA Astrophysics Data System (ADS)
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.
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S.; Yao, Jun; Tao, Wenquan
2015-01-28
Here, 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 intrinsicmore » 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. We find that 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.« less
Fixed and pulsed gradient diffusion methods in low-field core analysis.
Leu, Gabriela; Fordham, Edmund J; Hürlimann, Martin D; Frulla, Phil
2005-02-01
We review diffusion-weighted relaxation protocols for two-dimensional diffusion/relaxation time (D, T(2)) distributions and their application to fluid-saturated sedimentary rocks at low fields typical of oil-well logging tools (< or = 2 MHz for 1H). Fixed field gradient (FFG) protocols may be implemented in logging tools and in the laboratory; there, pulsed field gradient (PFG) protocols are also available. In either category, direct or stimulated echoes may be used for the diffusion evolution periods. We compare the results of several variant FFG and PFG protocols obtained on liquids and two contrasting sedimentary rocks. For liquids and rocks of negligible internal gradients (g(int)), results are comparable, as expected, for all the studied protocols. For rocks of strong g(int), protocol-dependent artifacts are seen in the joint (D, T2) distributions, consistent with the effects of the internal fields. For laboratory petrophysics, the PFG methods offer several advantages: (a) significantly improved signal-to-noise ratio and acquisition times for repetitions over many samples; (b) freedom from heteronuclear contamination when fluorinated liquids are used in core holders; and (c) a palette of variants--one comparable with the FFG--for the study of rocks of significant g(int). Given suitable hardware, both PFG and FFG methods can be implemented in the same bench-top apparatus, providing a versatile test bed for application in a petrophysical laboratory. PMID:15833632
Chen, Li; Zhang, Lei; Kang, Qinjun; Viswanathan, Hari S.; Yao, Jun; Tao, Wenquan
2015-01-28
Here, 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. We find that 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.
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
NASA Astrophysics Data System (ADS)
Zhu, Jianting; Ogden, Fred L.; Lai, Wencong; Chen, Xiangfeng; Talbot, Cary A.
2016-04-01
Vadose zone flow problems are usually solved from the Richards equation. Solution to the Richards equation is generally challenging because the hydraulic conductivity and diffusivity in the equation are strongly non-linear functions of water content. The finite water-content method was proposed as an alternative general solution method of the vadose zone flow problem for infiltration, falling slugs, and vadose zone response to water table dynamics based on discretizing the water content domain into numerous bins instead of the traditional spatial discretization. In this study, we develop an improved approach to the original finite water-content method (referred to as TO method hereinafter) that better simulates diffusive effects but retains the robustness of the TO method. The approach treats advection and diffusion separately and considers diffusion on a bin by bin basis. After discretizing into water content bins, we treat the conductivity and diffusivity in individual bins as water content dependent constant evaluated at given water content corresponding to each bin. For each bin, we can solve the flow equations analytically since the hydraulic conductivity and diffusivity can be treated as a constant. We then develop solutions for each bin to determine the diffusive water amounts at each time step. The water amount ahead of the convective front for each bin is redistributed among water content bins to account for diffusive effects. The application of developed solution is straightforward only involving algebraic manipulations at each time step. The method can mainly improve water content profiles, but has no significant difference for the total infiltration rate and cumulative infiltration compared to the TO method. Although the method separately deals with advection and diffusion, it can account for the coupling effects of advection and diffusion reasonably well.
Absorption spectroscopy of powdered materials using time-resolved diffuse optical methods.
D'Andrea, Cosimo; Obraztsova, Ekaterina A; Farina, Andrea; Taroni, Paola; Lanzani, Guglielmo; Pifferi, Antonio
2012-11-10
In this paper a novel method, based on time-resolved diffuse optical spectroscopy, is proposed to measure the absorption of small amounts of nanostructured powder materials independent of scattering. Experimental validation, in the visible and near-infrared spectral range, has been carried out on India Ink^{particles. The effectiveness of the technique to measure scattering-free absorption is demonstrated on carbon nanotubes. The comparison between the absorption spectra acquired by the proposed method and conventional measurements performed with a commercial spectrophotometer is discussed. PMID:23142900}
Properties of alloy steel powders produced by the method of diffusion impregnation (review)
Napara-Volgina, S.G.
1985-06-01
In their review of research on the properties of alloy steel powders produced by the method of diffusion impregnation, the authors systematize their data into three charts, one on the characteristics of charges and the recommended areas of use of powders, one on the chemical and particle size compositions and technological properties of the powders, and one on the fine crystalline structure of alloy powders of different compositions. The authors recommend the use of such powders, especially powder metallurgy constructional steels, produced by hot stamping and other methods providing high density.
Diffusive Plasma Dechucking Method for Wafers to Reduce Falling Dust Particles
NASA Astrophysics Data System (ADS)
Jun, Hyun-Su
2013-06-01
A plasma dechucking method capable of effectively eliminating dust particles created during the plasma process was developed. Referred to as diffusive plasma dechucking (DPD), the method reduces the plasma potential and includes an argon gas purge to remove dust particles floating on top of the sheath after the main process. Experimental results indicate that DPD reduces the amount of falling dust particles after the process by approximately 50-80%. To analyze these results quantitatively, the Coulomb force and the neutral drag force exerted on the dust particles were considered. In addition, dust particle exhaust conditions were proposed with respect to dust particle size, plasma potential, and spatial electric field.
Effect of BiTek agar on lysostaphin susceptibility of staphylococci.
Langlois, B E; Dawson, K; Akers, K
1990-01-01
Staphylococci which were considered to be lysostaphin susceptible on P agar containing Bacto-Agar showed different degrees of resistance to lysostaphin when tested on P agar made with BiTek agar. As a result, lysostaphin-susceptible strains were misidentified as lysostaphin-resistant strains. Images PMID:2254432
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.
NASA Astrophysics Data System (ADS)
Kaźmierczak-Bałata, Anna; Bodzenta, Jerzy; Trefon-Radziejewska, Dominika
2010-01-01
The use of a typical measuring cryostat with a standard temperature controller was proposed for investigation of the temperature dependence of the thermal diffusivity of transparent samples. The basic idea is to use the cryostat heater to control the mean sample temperature and to generate the thermal wave in it, simultaneously. Because of the relatively high thermal inertia of the system, the measurements are carried out at frequencies not exceeding 50 mHz. The periodic temperature disturbance in the sample was detected optically by the use of the mirage effect. The proposed method was used for determination of the thermal diffusivity of yttrium aluminum garnet single crystals in a temperature range from 20 °C to 200 °C.
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.
GPU-Accelerated Finite Element Method for Modelling Light Transport in Diffuse Optical Tomography
Schweiger, Martin
2011-01-01
We introduce a GPU-accelerated finite element forward solver for the computation of light transport in scattering media. The forward model is the computationally most expensive component of iterative methods for image reconstruction in diffuse optical tomography, and performance optimisation of the forward solver is therefore crucial for improving the efficiency of the solution of the inverse problem. The GPU forward solver uses a CUDA implementation that evaluates on the graphics hardware the sparse linear system arising in the finite element formulation of the diffusion equation. We present solutions for both time-domain and frequency-domain problems. A comparison with a CPU-based implementation shows significant performance gains of the graphics accelerated solution, with improvements of approximately a factor of 10 for double-precision computations, and factors beyond 20 for single-precision computations. The gains are also shown to be dependent on the mesh complexity, where the largest gains are achieved for high mesh resolutions. PMID:22013431
NASA Astrophysics Data System (ADS)
Hirao, Akiko; Nishizawa, Hideyuki; Tsukamoto, Takayuki; Matsumoto, Kazuki
1999-10-01
A new easy method for obtaining a drift mobility and a diffusion coefficient from a nondispersive time-of-flight transient has been developed. Nondispersive transients are described well in the theoretical photocurrent equation (PTE) based on the fact that a carrier packet drifts at a constant velocity and is spread by diffusion, the top electrode acts as a reflecting and partially absorbing wall, and the counter electrode acts as an absorbing wall. The fitting of the PTE to photocurrent transients gives the mobility and the diffusion coefficient (D) simultaneously. These are suitable characteristic values for descriptions of carriers transport because they do not show the thickness dependence and the negative field dependence in a low electric field. The mobility that sometimes shows the thickness dependence and the negative field dependence in a low electric field, however, has usually been measured from the time of the intersection of the asymptotes to the plateau and trailing edge of the transients. In order to obtain (mu) a from photocurrent transients by a simple method, we have tried to describe t0 and tail-broadening parameter W as functions of (mu) a and D, where W is defined as (t1/2 - t0)/t1/2 and t1/2 is the time at which the current is a half of that in the plateau region. The dependences of calculated (mu) k and W on the electric field and the sample thickness agreed well with those of the experimental data. These results verify the PTE and suggest that (mu) a and D can be calculated from t0 and W. We also report that the diffusion coefficient is proportional to the power of 2 of the mobility. This result agrees with a theory based on the Langevin equation which describes motions of carriers in a fluctuated field.
Social diffusion of novel foraging methods in brown capuchin monkeys (Cebus apella)
Dindo, Marietta; Thierry, Bernard; Whiten, Andrew
2007-01-01
It has been reported that wild capuchin monkeys exhibit several group-specific behavioural traditions. By contrast, experiments have found little evidence for the social learning assumed necessary to support such traditions. The present study used a diffusion chain paradigm to investigate whether a novel foraging task could be observationally learned by capuchins (Cebus apella) and then transmitted along a chain of individuals. We used a two-action paradigm to control for independent learning. Either of two methods (lift or slide) could be used to open the door of a foraging apparatus to retrieve food. Two chains were tested (N1=4; N2=5), each beginning with an experimenter-trained model who demonstrated to a partner its group-specific method for opening the foraging apparatus. After the demonstration, if the observer was able to open the apparatus 20 times by either method, then it became the demonstrator for a new subject, thus simulating the spread of a foraging tradition among ‘generations’ of group members. Each method was transmitted along these respective chains with high fidelity, echoing similar results presently available only for chimpanzees and children. These results provide the first clear evidence for faithful diffusion of alternative foraging methods in monkeys, consistent with claims for capuchin traditions in the wild. PMID:17971322
NASA Astrophysics Data System (ADS)
Bodzenta, J.; Kaźmierczak-Bałata, A.; Łukasiewicz, T.; Pyka, M.
2008-01-01
Thermal diffusivities of pure YVO{4} single crystal and single crystals doped with Nd, Tm and Ca ions are measured using a modified Ångström's method. Measurements were carried out for main crystallographic directions ([100], [010] and [001]). Obtained results show that the thermal diffusivity in [001] direction is considerably higher than in (001) plane. Decrease of the thermal diffusivity is observed with growing concentration of dopants. For the heavier doped sample (5% at. of Tm + 0.4% at. of Ca) a drop of the thermal diffusivity is about 35%. The current investigation is a part of research project 3 T08A 035 29.
Özarslan, Evren; Westin, Carl-Fredrik; Mareci, Thomas H.
2016-01-01
The influence of Gaussian diffusion on the magnetic resonance signal is determined by the apparent diffusion coefficient (ADC) and tensor (ADT) of the diffusing fluid as well as the gradient waveform applied to sensitize the signal to diffusion. Estimations of ADC and ADT from diffusion-weighted acquisitions necessitate computations of, respectively, the b-value and b-matrix associated with the employed pulse sequence. We establish the relationship between these quantities and the gradient waveform by expressing the problem as a path integral and explicitly evaluating it. Further, we show that these important quantities can be conveniently computed for any gradient waveform using a simple algorithm that requires a few lines of code. With this representation, our technique complements the multiple correlation function (MCF) method commonly used to compute the effects of restricted diffusion, and provides a consistent and convenient framework for studies that aim to infer the microstructural features of the specimen. PMID:27182208
Studies on Aspirin Crystals Generated by a Modified Vapor Diffusion Method.
Mittal, Amit; Malhotra, Deepak; Jain, Preeti; Kalia, Anupama; Shunmugaperumal, Tamilvanan
2016-08-01
The objectives of the current investigation were (1) to study the influence of selected two different non-solvents (diethylether and dichloromethane) on the drug crystal formation of a model drug, aspirin (ASP-I) by the modified vapor diffusion method and (2) to characterize and compare the generated crystals (ASP-II and ASP-III) using different analytical techniques with that of unprocessed ASP-I. When compared to the classical vapor diffusion method which consumes about 15 days to generate drug crystals, the modified method needs only 12 h to get the same. Fourier transform-infrared spectroscopy (FT-IR) reveals that the internal structures of ASP-II and ASP-III crystals were identical when compared with ASP-I. Although the drug crystals showed a close similarity in X-ray diffraction patterns, the difference in the relative intensities of some of the diffraction peaks (especially at 2θ values of around 7.7 and 15.5) could be attributed to the crystal habit or crystal size modification. Similarly, the differential scanning calorimetry (DSC) study speculates that only the crystal habit modifications might occur but without involving any change in internal structure of the generated drug polymorphic form I. This is further substantiated from the scanning electron microscopy (SEM) pictures that indicated the formation of platy shape for the ASP-II crystals and needle shape for the ASP-III crystals. In addition, the observed slow dissolution of ASP crystals should indicate polymorph form I formation. Thus, the modified vapor diffusion method could routinely be used to screen and legally secure all possible forms of other drug entities too. PMID:26729528
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.
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...
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 §...
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, 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, 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 §...
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 §...
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...
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
2015-03-01
A coarse-grained simulation method to predict nuclear magnetic resonance (NMR) spectra of ions diffusing in porous carbons is proposed. The coarse-grained model uses input from molecular dynamics simulations such as the free-energy profile for ionic adsorption, and density-functional theory calculations are used to predict the NMR chemical shift of the diffusing ions. The approach is used to compute NMR spectra of ions in slit pores with pore widths ranging from 2 to 10 nm. As diffusion inside pores is fast, the NMR spectrum of an ion trapped in a single mesopore will be a sharp peak with a pore size dependent chemical shift. To account for the experimentally observed NMR line shapes, our simulations must model the relatively slow exchange between different pores. We show that the computed NMR line shapes depend on both the pore size distribution and the spatial arrangement of the pores. The technique presented in this work provides a tool to extract information about the spatial distribution of pore sizes from NMR spectra. Such information is difficult to obtain from other characterisation techniques. PMID:25747093
Diffusivity and porosity in rock matrix-laboratory methods using artificial and natural tracers
Valkiainen, M.; Olin, M.; Uusheimo, K.; Kumpulainen, H.; Lehikoinene, J.; Muurinen, A.
1993-12-31
The nature of diffusivity and porosity in crystalline rock was studied by electrical conductivity measurements, steady-state diffusion experiments, saturation-leaching of tracers with cylindrical rock samples and analysis of the concentrations of different elements from core samples or pore water near fractures. The phenomena of main interest were dead-end porosity, ion-exclusion, sorption, and the continuity of pore networks. The modelling of experimental results was based on a modified Fick`s second law for diffusion, which was solved either by analytical or numerical methods. The measured D{sub e} and {epsilon} were found to statistically follow an exponential presentation: Archie`s law. The existence of ion-exclusion for anions was confirmed. The connectivity of the pore network extended in the laboratory experiments at least six centimetres, in coarse of the pore network extended in the laboratory experiments at least six centimetres, in coarse-grained granite in nature several metres but in fine-grained rock samples of a uranium deposit the element mobilization effects could be seen only to the depth of 2-3 centimetres.
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.
Localized axial Green's function method for the convection-diffusion equations in arbitrary domains
NASA Astrophysics Data System (ADS)
Lee, Wanho; Kim, Do Wan
2014-10-01
A localized axial Green's function method (LAGM) is proposed for the convection-diffusion equation. The axial Green's function method (AGM) enables us to calculate the numerical solution of a multi-dimensional problem using only one-dimensional Green's functions for the axially split differential operators. This AGM has been developed not only for the elliptic boundary value problems but also for the steady Stokes flows, however, this paper is concerned with the localization of the AGM. This localization of the method is needed for practical purpose when computing the axial Green's function, specifically for the convection-diffusion equation on a line segment that we call the local axial line. Although our focus is mainly on the convection-dominated cases in arbitrary domains, this method can solve other cases in a unified way. Numerical results show that, despite irregular types of discretization on an arbitrary domain, we can calculate the numerical solutions using the LAGM without loss of accuracy even in cases of large convection. In particular, it is also shown that randomly distributed axial lines are available in our LAGM and complicated domains are not a burden.
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
Self-feeding MUSE: a robust method for high resolution diffusion imaging using interleaved EPI.
Zhang, Zhe; Huang, Feng; Ma, Xiaodong; Xie, Sheng; Guo, Hua
2015-01-15
Single-shot echo planar imaging (EPI) with parallel imaging techniques has been well established as the most popular method for clinical diffusion imaging, due to its fast acquisition and motion insensitivity. However, this approach is limited by the relatively low spatial resolution and image distortion. Interleaved EPI is able to break the limitations but the phase variations among different shots must be considered for artifact suppression. The introduction of multiplexed sensitivity-encoding (MUSE) can address the phase issue using sensitivity encoding (SENSE) for self-navigation of each interleave. However, MUSE has suboptimal results when the number of shots is high. To achieve higher spatial resolution and lower geometric distortion, we introduce two new schemes into the MUSE framework: 1) a self-feeding mechanism is adopted by using prior information regularized SENSE in order to obtain reliable phase estimation; and 2) retrospective motion detection and data rejection strategies are performed to exclude unusable data corrupted by severe pulsatile motions. The proposed method is named self-feeding MUSE (SF-MUSE). Experiments on healthy volunteers demonstrate that this new SF-MUSE approach provides more accurate motion-induced phase estimation and fewer artifacts caused by data corruption when compared with the original MUSE method. SF-MUSE is a robust method for high resolution diffusion imaging and suitable for practical applications with reasonable scan time. PMID:25451470
A Method for Studying Atomic Diffusion by STM Tip-Crash Induced Vacancy Island Coalescence
NASA Astrophysics Data System (ADS)
Lake, R. E.; Lange, A. P.; Ray, M. P.; Sosolik, C. E.
2007-11-01
The study of vacancy and adatom island motion on single crystal metals with the scanning tunneling microscope (STM) has explained many of the underlying atomic diffusion mechanisms responsible for movement of atoms on a surface. We present a new method for vacancy island creation at room temperature using a controlled mechanical tip-surface interaction. The method allows us to control the relative positions and initial sizes of vacancy islands with respect to one another and to surface defects. Complicated and closely spaced vacancy island configurations can also be engineered. This enhances our ability to collect statistics on the movement of the macro-scale vacancy islands and distinguish between mass transport channels. To demonstrate the technique, time series analysis of coalescence events on the surface of Ag(111) is presented. Diffusion coefficients of the Ag surface atoms obtained with this method are in general agreement with previous stochastic methods for creating vacancy islands such as low-dose sputtering [1]. [1] M. Eßer, K. Morgenstern, G. Rosenfeld, G. Comsa, Surf. Sci. 402-404, 341 (1998).
NASA Astrophysics Data System (ADS)
Yang, Zhi; Newling, Ben
2007-03-01
We present non-invasive, quantitative MRI wind-tunnel measurements in flowing gas (velocity > 10 m/s) at high Reynolds numbers (Re > 10^5). Our measurement method is three-dimensional and has the potential for saving time over traditional pointwise techniques. The method is suitable for liquids and for gases. We demonstrate the use of the technique on different test sections (bluff obstruction, clark Y-wing and cylinder). The mean velocity of gas flowing past those sections has been measured. We also investigate methods to measure flow correlation times by changing the acquisition interval between excitation of the sample and detection of the signal. This may be accomplished by making separate measurements or by using a multiple-point acquisition method. A measurement of correlation time allows us to map turbulent diffusivity. The MRI data are compared with computational fluid dynamics.
A diffuse-interface method for two-phase flows with soluble surfactants.
Teigen, Knut Erik; Song, Peng; Lowengrub, John; Voigt, Axel
2011-01-20
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
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
Fast non-overlapping Schwarz domain decomposition methods for solving the neutron diffusion equation
NASA Astrophysics Data System (ADS)
Jamelot, Erell; Ciarlet, Patrick
2013-05-01
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. APOLLO3 is a registered trademark in France.
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 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
Estimating Effective Vertical Diffusivity in Shallow Ponds by a Constrained Flux-Gradient Method
NASA Astrophysics Data System (ADS)
Bean, J. R.; Torgersen, T.
2004-12-01
Shallow ponds have been used to mitigate the deleterious effects of storm water run-off by acting as detention/retention basins that sequester run-off associated pollutants in sediments. Studies show that the retention efficiency of these systems can decrease over time as a result of the internal loading of nutrients/contaminants from the sediments back to the water column where they are available for export downstream. Quantifying the vertical transport of gases (down) and sediment derived materials (up) is vital to the modeling and understanding of the processes that contribute to the magnitude of internal loading. A critical parameter is the effective vertical diffusion coefficient: Kz=Dmolecular +Deddy (cm2 sec-1). The flux gradient method for estimating effective vertical thermal diffusivity has been applied with success in large lakes which undergo stratification cycles on seasonal or longer time scales. We offer a constrained version of the flux-gradient method that has been adapted for use in a shallow pond with a daily stratification cycle. The method employs heat as a tracer and assumes that transport in the face of a stable gradient is diffusive. By shrinking the spatial and temporal resolution of measurement to scales appropriate to the system of interest and carefully accounting for internal source and sink terms of heat (e.g solar radiation and sediment heat fluxes) we are able to calculate Kz as a function of time and depth during periods of stable stratification, i.e when the pond is not vertically well-mixed. Results show the magnitude of Kz varies from ca. 10-3 to 10-1 (cm2 sec-1) under stratified conditions depending primarily on the strength of stratification.
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.
Axial expansion methods for solution of the multi-dimensional neutron diffusion equation
Beaklini Filho, J.F.
1984-01-01
The feasibility and practical implementation of axial expansion methods for the solution of the multi-dimensional multigroup neutron diffusion (MGD) equations is investigated. The theoretical examination which is applicable to the general MGD equations in arbitrary geometry includes the derivation of a new weak (reduced) form of the MGD equations by expanding the axial component of the neutron flux in a series of known trial functions and utilizing the Galerkin weighting. A general two-group albedo boundary condition is included in the weak form as a natural boundary condition. The application of different types of trial functions is presented.
An Ion Diffusion Method for Visualising a Solid-like Water Nanofilm
Wang, Ya; Duan, Zhiguang; Fan, Daidi
2013-01-01
A nano-thick solid-like water film on solid surfaces plays an important role in various fields, including biology, materials science, atmospheric chemistry, catalysis and astrophysics. Visualising the water nanofilm has been a challenge due to its dynamic nature and nanoscale thickness. Here we report an ion diffusion method to address this problem using a membrane formed with a BSA-Na2CO3 (BSA, bovine serum albumin) mixture. After a solid-like water nanofilm deposits onto the membrane, Na+ and CO32− ions diffuse into the film to form a solid Na2CO3 phase in its place. Consequently, the morphology of the nanofilm can be visualised by the space filled by the Na2CO3. Using this method, we successfully observed polygon-like, ribbon-like and spot-like nanofilms at 193 K, 253 K and room temperature, respectively. Our method may provide a tool for characterising confined water films ranging from a few nanometres to hundreds of nanometres in thickness. PMID:24336341
Synthesis of metal-organic framework films by pore diffusion method
NASA Astrophysics Data System (ADS)
Murayama, Naohiro; Nishimura, Yuki; Kajiro, Hiroshi; Kishida, Satoru; Kinoshita, Kentaro; Tottori Univ Team; Nippon Steel; Sumitomo Metal Co. Collaboration; Tottori Integrated Frontier Resaerch Center (Tifrec) Collaboration; Tottori University Electronic Display Resaerch Center (Tedrec) Collaboration
Metal-organic frameworks (MOFs) presents high controllability in designing the nano-scale pore, and this enable molecular storages, catalysts, gas sensors, gas separation membranes, and electronic devices for next-generation. Therefore, a simple method for film synthesis of MOFs compared with conventional methods [1] is strongly required. In this paper, we provide pore diffusion method, in which a substrate containing constituent metals of MOF is inserted in solution that includes only linker molecules of MOF. As a result, 2D growth of MOF was effectively enhanced, and the formation of flat and dense MOF films was attained. The growth time, t, dependence of film thickness, d, can be expressed by the relation of d = Aln(t + 1) + B, where A and B are constants. It means that ionized coppers diffuse through the pores of MOFs and the synthesis reaction proceeds at the MOF/solvent interface. We demonstrated the fabrication of a HKUST-1/Cu-TPA hetero structure by synthesizing a Cu-TPA film continuously after the growth of a HKUST-1 film on the CuOx substrate.
3D modeling for solving forward model of no-contact fluorescence diffuse optical tomography method
NASA Astrophysics Data System (ADS)
Nouizi, F.; Chabrier, R.; Torregrossa, M.; Poulet, P.
2009-07-01
This paper presents detailed computational aspects of a new 3D modeling for solving the direct problem in a no-contact time-resolved Fluorescent Diffuse Optical Tomography (FDOT) method that rely on near-infrared scattered and fluorescent photons to image the optical properties and distribution of fluorescent probes in small laboratory animals. An optical scanner allowing performing in-vivo measurements in no-contact scheme was built in our laboratory and is presented. We use the three-dimensional Finite Element Method (FEM) to solve the coupled diffusion equations of excitation and fluorescence photons in highly scattering objects. The computed results allowed yielding photon density maps and the temporal profiles of photons on the surface of the small animal. Our 3D modeling of propagation of photons in the void space between the surface of the object and the detectors allows calculating the quantity of photons reaching the optodes. Simulations were carried-out on two test objects: a resin cylinder and a mouse phantom. The results demonstrate the potential applications of the method to pre-clinical imaging.
Advanced nodal neutron diffusion method with space-dependent cross sections: ILLICO-VX
Rajic, H.L.; Ougouag, A.M.
1987-01-01
Advanced transverse integrated nodal methods for neutron diffusion developed since the 1970s require that node- or assembly-homogenized cross sections be known. The underlying structural heterogeneity can be accurately accounted for in homogenization procedures by the use of heterogeneity or discontinuity factors. Other (milder) types of heterogeneity, burnup-induced or due to thermal-hydraulic feedback, can be resolved by explicitly accounting for the spatial variations of material properties. This can be done during the nodal computations via nonlinear iterations. The new method has been implemented in the code ILLICO-VX (ILLICO variable cross-section method). Numerous numerical tests were performed. As expected, the convergence rate of ILLICO-VX is lower than that of ILLICO, requiring approx. 30% more outer iterations per k/sub eff/ computation. The methodology has also been implemented as the NOMAD-VX option of the NOMAD, multicycle, multigroup, two- and three-dimensional nodal diffusion depletion code. The burnup-induced heterogeneities (space dependence of cross sections) are calculated during the burnup steps.
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
Sakai, Koji; Yamada, Kei; Sugimoto, Naozo
2012-02-01
A method for the measurement of temperature in the lateral ventricle using diffusion-weighted imaging (DWI) has been proposed recently. This method uses predetermined arbitrary thresholds, but a more objective method of calculation would be useful. We therefore compared four different calculation methods, two of which were newly created and did not require predetermined thresholds. A rectangular polyethylene terephthalate bottle (8 × 10 × 28 cm(3)) was filled with heated water (35.0-38.8 °C) and used as a water phantom. The DWI data of 23 healthy subjects (aged 26-75 years; mean ± standard deviation, 50.13 ± 19.1 years) were used for this study. The temperature was calculated using the following equation: T(°C) = 2256.74/ln(4.39221/D) - 273.15, where D is the diffusion coefficient. The mean ventricular temperature was calculated by four methods: two thresholding methods and two histogram curve-fitting methods. As a reference, we used the temperature measured at the tympanic membrane, which is known to be approximately 1 °C lower than the brain temperature. The averaged differences in temperature between mercury thermometry and classical predetermined thresholding methods for the water phantom were 0.10 ± 0.42 and 0.05 ± 0.41 °C, respectively. The histogram curve-fitting methods, however, yielded temperatures a little lower (averaged differences of -0.24 ± 0.32 and -0.14 ± 0.31 °C, respectively) than mercury thermometry. There was very little difference in temperature between tympanic thermometry and classical predetermined thresholding methods (+0.01 and -0.07 °C, respectively). In humans, however, the histogram curve-fitting methods yielded temperatures approximately 1 °C higher (+1.04 °C and +1.36 °C, respectively), suggesting that temperatures measured in this way more closely approximate the true brain temperature. The histogram curve-fitting methods were more objective and better
NASA Astrophysics Data System (ADS)
Mao, Bosi; Bentaleb, Ahmed; Louerat, Frédéric; Divoux, Thibaut; Snabre, Patrick
Numerous hydrogels are prepared by cooling down to ambient temperature, aqueous polymer solutions brought to a boil. Although the incubation time of the polymer solution at such a high temperature could be used as a tuning parameter, its impact on the subsequent gelation has been poorly investigated. Here we study the effect of prolonged heating at 80°C on a 1.5% wt solution of agar, a natural polysaccharide. The incubation time is varied from a few hours up to five days. We show that the agar sol. continuously degrades as the result of both the hydrolysis and the intermolecular oxidation of the polymer chains. Furthermore, electronic microscopy and X-ray diffraction experiments reveal that gels formed from older agar sols display an increasingly coarser microstructure composed of micron-sized aggregated pieces of polysaccharides, in contrast with the fibrous-like structure of gels made from fresh sols. Along with structural changes prolonged incubation time leads to weaker gels of lower shear elastic modulus. Finally, macro-indentation experiments coupled to direct visualization show that increasing the incubation time of the agar sol. decreases the yield strain of the gel by a factor of three, while the rupture scenario turns continuously from brittle to ductile-like. Acknowledging funding from BioMérieux & CNRS.
Bibi, Zainab; Shahid, Faiza; Ul Qader, Shah Ali; Aman, Afsheen
2015-04-01
Microbial xylanases, specially endo-β-1,4-xylanase catalyzes the hydrolysis of xylan, is considered one of the most significant hydrolases. It has numerous applications but most extensively is utilized in paper and pulp industry as a bio-bleaching agent. Immobilization technique is comprehensively studied with the expectation of modifying and improving enzyme stability and characteristics for commercial purposes. Currently, matrix entrapment technique is applied to immobilize endo-β-1,4-xylanase within agar-agar gel beads produced by Geobacillus stearothermophilus KIBGE-IB29. Maximal enzyme immobilization yield was achieved at 2.5% of agar-agar concentration. Optimized conditions demonstrated an increase in the optimal reaction time from 05 min to 30 min and incubation temperature from 50 °C to 60 °C with reference to free enzyme whereas; no effect was observed for optimum pH. Entrapment technique uniquely changed the kinetic parameters of immobilized endo-β-1,4-xylanase (Km: 0.5074 mg min(-1) to 0.5230 mg min(-1) and Vmax: 4773 U min(-1) to 968 U min(-1)) as compared to free enzyme. However, immobilized enzyme displayed broad thermal stability and retained 79.0% of its initial activity at 80 °C up to 30 min whereas; free enzyme completely lost its activity at this temperature. With respect to economic feasibility, the immobilized enzyme showed impressive recycling efficiency up to six reaction cycles. PMID:25603143
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.
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)
NASA Astrophysics Data System (ADS)
Lu, Bo; Song, Yicheng; Zhang, Junqian
2016-07-01
This article demonstrates the design of charging strategies for lithium ion batteries with considering the balance between diffusion induced stress and total charge time for two- and three-stage charge methods. For the two-stage galvanostatic-potentiostatic charge method the low mechanical stress can be achieved without increasing total charge time by switching the galvanostatic to the potentiostatic at the time moment when the lithium concentration at the surface of particles reaches the limit cbarsurf = 0 . A three-stage method, which consists of an initial galvanostatic stage of high current, a galvanostatic stage of low current and a potentiostatic ending stage, is suggested. Employing the initial galvanostatic stage of high current is helpful not only in accelerating the charge process, but also in controlling the mechanical stress once the electrical current and time duration of the initial galvanostatic stage are properly designed.
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.
Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.
2015-01-01
This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figure 1 is the evolution of the diffusion profiles of a containment granuloma over time.
Plimpton, Steven J.; Sershen, Cheryl L.; May, Elebeoba E.
2015-01-01
This paper describes a method for incorporating a diffusion field modeling oxygen usage and dispersion in a multi-scale model of Mycobacterium tuberculosis (Mtb) infection mediated granuloma formation. We implemented this method over a floating-point field to model oxygen dynamics in host tissue during chronic phase response and Mtb persistence. The method avoids the requirement of satisfying the Courant-Friedrichs-Lewy (CFL) condition, which is necessary in implementing the explicit version of the finite-difference method, but imposes an impractical bound on the time step. Instead, diffusion is modeled by a matrix-based, steady state approximate solution to the diffusion equation. Moreover, presented in figuremore » 1 is the evolution of the diffusion profiles of a containment granuloma over time.« less
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
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
Co-precipitation with PVP and Agar to Improve Physicomechanical Properties of Ibuprofen
Maghsoodi, Maryam; Kiafar, Farhad
2013-01-01
Objective(s) : Ibuprofen is a problematic drug in tableting due to its viscoelastic properties. Additionally its high cohesivity results in low flowability. In this study, co-precipitation of ibuprofen with varying concentration of agar and PVP to optimize properties of Ibuprofen was carried out. Materials and Methods: Co-precipitates of ibuprofen- PVP or agar were prepared by solvent evaporation technique under vacuum condition. Differential scanning calorimetry (DSC), X -ray diffraction of powder (XRDP) and FT-IR spectroscopy were used to investigate the solid state characteristics of the co-precipitates. The dissolution behavior, flowability, particle size and compaction properties of various batches were also studied. Results: Co-precipitation of drug with agar led to a change in habit from needle to plate shape crystals, while drug –PVP co-precipitates had agglomerated structure and consisted of numerous crystals which had been aggregated together. The co-precipitates showed improved flow properties compared with ibuprofen alone. Precipitation of ibuprofen with these additives led to modification in the dissolution of the drug. Agar in 1% w/w improved slightly the dissolution rate of drug while PVP had a negative impact and led to reduction in the dissolution rate of drug to less than that of pure drug. The all obtained co-precipitates exhibited significantly improved tableting behavior compared with drug crystals alone. This may be due to this fact that, the polymer covering the drug particles increases and changes the nature of the surface area available for interparticulate bonds between particles. DSC, XRDP and FT-IR experiments showed that drug particles, in co-precipitates samples, did not undergo polymorphic modifications. Conclusion: The study highlights the influence of polymeric additives on crystallization process leading to modified performance. PMID:24250942
Co-precipitation with PVP and Agar to Improve Physicomechanical Properties of Ibuprofen
Maghsoodi, Maryam; Kiafar, Farhad
2013-01-01
Objective(s) : Ibuprofen is a problematic drug in tableting due to its viscoelastic properties. Additionally its high cohesivity results in low flowability. In this study, co-precipitation of ibuprofen with varying concentration of agar and PVP to optimize properties of Ibuprofen was carried out. Materials and Methods: Co-precipitates of ibuprofen- PVP or agar were prepared by solvent evaporation technique under vacuum condition. Differential scanning calorimetry (DSC), X -ray diffraction of powder (XRDP) and FT-IR spectroscopy were used to investigate the solid state characteristics of the co-precipitates. The dissolution behavior, flowability, particle size and compaction properties of various batches were also studied. Results: Co-precipitation of drug with agar led to a change in habit from needle to plate shape crystals, while drug –PVP co-precipitates had agglomerated structure and consisted of numerous crystals which had been aggregated together. The co-precipitates showed improved flow properties compared with ibuprofen alone. Precipitation of ibuprofen with these additives led to modification in the dissolution of the drug. Agar in 1% w/w improved slightly the dissolution rate of drug while PVP had a negative impact and led to reduction in the dissolution rate of drug to less than that of pure drug. The all obtained co-precipitates exhibited significantly improved tableting behavior compared with drug crystals alone. This may be due to this fact that, the polymer covering the drug particles increases and changes the nature of the surface area available for interparticulate bonds between particles. DSC, XRDP and FT-IR experiments showed that drug particles, in co-precipitates samples, did not undergo polymorphic modifications. Conclusion: The study highlights the influence of polymeric additives on crystallization process leading to modified performance. PMID:24250936
Zhang, Guodong; Lampel, Keith A
2010-08-01
Shigella outbreaks are widely reported throughout the world. However, it remains a challenge to isolate Shigella spp. from foods by using conventional microbiological media. The main objective of this study was to determine the effectiveness of a novel chromogenic medium, Rainbow agar Shigella/Aeromonas (Rainbow agar), for the isolation and detection of Shigella spp. in foods. All four Shigella species, S. sonnei, S. flexneri, S. dysenteriae, and S. boydii, were studied. Rainbow agar was compared with tryptic soy agar, xylose lysine desoxycholate agar (XLD), and Salmonella Shigella agar (SSA) for enumeration of Shigella spp. in pure culture. This chromogenic agar and XLD were also used to isolate Shigella spp. in artificially contaminated foods (4.8 log CFU/g of food), including lettuce, parsley, cilantro, spinach, potato salad, and shrimp. The inhibitory effect on Shigella growth by Rainbow agar was between that of XLD and SSA. All vegetables studied showed a moderately high background microflora on XLD and Rainbow agar. With artificially inoculated produce, Rainbow agar recovered about 1 to 2 log CFU more S. sonnei, S. dysenteriae, and S. boydii per g of food than did XLD. For potato salad and shrimp, which had low background microflora on Rainbow agar, Rainbow agar was slightly better in recovering Shigella spp. than XLD was in most cases. However, we found that the addition of streptomycin (6.25 mg/liter) to Rainbow agar could facilitate the isolation of Shigella in vegetables tested. In conclusion, Rainbow agar was a much more effective medium than was XLD for the isolation of Shigella spp. from foods. PMID:20819355
Blood species identification using Near-Infrared diffuse transmitted spectra and PLS-DA method
NASA Astrophysics Data System (ADS)
Zhang, Linna; Zhang, Shengzhao; Sun, Meixiu; Wang, Zhennan; Li, Hongxiao; Li, Yingxin; Li, Gang; Lin, Ling
2016-05-01
Blood species identification is of great significance for blood supervision and wildlife investigations. The current methods used to identify the blood species are destructive. Near-Infrared spectroscopy method is known for its non-invasive properties. In this research, we combined Near-Infrared diffuse transmitted spectra and Partial Least Square Discrimination Analysis (PLS-DA) to identify three blood species, including macaque, human and mouse. Blind test and external test were used to assess the PLS-DA model. The model performed 100% accuracy in its identification between three blood species. This approach does not require a specific knowledge of biochemical features for each individual class but relies on a spectroscopic statistical differentiation of the whole components. This is the first time to demonstrate Near-Infrared diffuse transmitted spectra have the ability to identify the species of origin of blood samples. The results also support a good potential of absorption and scattering spectroscopy for species identification in practical applications for real-time detection.
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.
Method and apparatus for determining minority carrier diffusion length in semiconductors
Moore, Arnold R.
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.
Method and apparatus for determining minority carrier diffusion length in semiconductors
Moore, Arnold R.
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.
Application of a Particle Method to the Advection-Diffusion-Reaction Equation
NASA Astrophysics Data System (ADS)
Paster, A.; Bolster, D.; Benson, D. A.
2012-12-01
A reaction between two chemical species can only happen if molecules collide and react. Thus, the mixing of a system can become a limiting factor in the onset of reaction. Solving for reaction rate in a well-mixed system is typically a straightforward task. However, when incomplete mixing kicks in, obtaining a solution becomes more challenging. Since reaction can only happen in regions where both reactants co-exist, the incomplete mixing may slow down the reaction rate, when compared to a well-mixed system. The effect of incomplete mixing upon reaction is a highly important aspect of various processes in natural and engineered systems, ranging from mineral precipitation in geological formations to groundwater remediation in aquifers. We study a relatively simple system with a bi-molecular irreversible kinetic reaction A+B → Ø where the underlying transport of reactants is governed by an advection-diffusion equation, and the initial concentrations are given in terms of an average and a perturbation. Such a system does not have an analytical solution to date, even for the zero advection case. We model the system by a Monte Carlo particle tracking method, where particles represent some reactant mass. In this method, diffusion is modeled by a random walk of the particles, and reaction is modeled by annihilation of particles. The probability of the annihilation is proportional to the reaction rate constant and the probability density associated with particle co-location. We study the numerical method in depth, characterizing typical numerical errors and time step restrictions. In particular, we show that the numerical method converges to the advection-diffusion-reaction equation at the limit Δt →0. We also rigorously derive the relationship between the initial number of particles in the system and the initial concentrations perturbations represented by that number. We then use the particle simulations of zero-advection system to demonstrate the well
Kim, C J; Nagaraja, K V
1991-01-01
An agar gel enzyme assay (AGEA) was developed for the detection of antibodies to Salmonella enteritidis (SE). The assay was based on the ability of antibodies to diffuse through an agar gel and react with antigen coated on a polystyrene surface. The antigen-antibody reaction was then made visible by applying an enzyme-conjugated anti-immunoglobulin and the addition, subsequently, of a substrate-containing gel. The color change in circular zones was taken as the indication for the presence of antibodies. The present investigation reports identification of an antigen specific for SE and its use in the development of a relatively simple AGEA procedure. The results of AGEA were compared with those of conventional microagglutination (MA) test and serum plate (SP) test. The percentage agreement between MA and AGEA in positive serum sample was found to be 94.4%, and in negative serum samples it was found to be 88.8%. The present results suggest that the AGEA could be a very useful screening test for the detection of SE antibodies because the assay is inexpensive, specific and simple to perform without much equipment, and give results within a 3-hr period. PMID:1832368
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
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)
Oka, Chiemi; Ushimaru, Kazunori; Horiishi, Nanao; Tsuge, Takeharu; Kitamoto, Yoshitaka
2016-02-01
The present paper describes optimization of preparation conditions of a core-shell composite particle, and its heat generation by alternating magnetic fields. The composite particles are prepared with a modified emulsion solvent diffusion method, which is combined with Pickering emulsion stabilized by magnetic nanoparticles. In this method, the magnetic nanoparticles act as an emulsifier, and its amount and size are crucial to morphology of the composite particles. The magnetic nanoparticles of 8-9 nm would be strongly adsorbed at a liquid-liquid interface rather than the larger nanoparticles. At the optimized concentration of the magnetic nanoparticle’s suspension for the preparation, small and uniform composite particles are obtained since the amount of the nanoparticles is enough to prevent coalescence of droplets during the formation of the composites. The heat generation by alternating magnetic fields emerged certainly. This result suggests the composite particles have a property as a heat-generating carrier for hyperthermia treatment.
Varga, Agnes; Gyetvai, Gergely; Nagy, Lívia; Nagy, Géza
2009-08-01
The diffusion coefficient of glucose in different media is an important parameter in life sciences, as well as in biotechnology and microbiology. In this work a simple, fast method is proposed that is based on the electrochemical time of flight principle. In most of the earlier time of flight experiments performed, a constant flight distance was applied. In the present work a scanning electrochemical microscope (SECM) was applied as a measuring tool. With use of the SECM, the flying distance could be changed with high precision, making measurements with several flight distances more accurate and reliable values could be obtained for solutions as well as for gels. The conventional voltammetric methods are not applicable for glucose detection. In our work electrocatalytic copper oxide coated copper microelectrodes and micro-sized amperometric enzyme sensors were used as detectors, while microdroplet-ejecting pneumatically driven micropipettes were used as a source. PMID:19517100
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
NASA Astrophysics Data System (ADS)
Flegg, Mark B.; Hellander, Stefan; Erban, Radek
2015-05-01
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 called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (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: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h 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.
Mupirocin-mucin agar for selective enumeration of Bifidobacterium bifidum.
Pechar, Radko; Rada, Vojtech; Parafati, Lucia; Musilova, Sarka; Bunesova, Vera; Vlkova, Eva; Killer, Jiri; Mrazek, Jakub; Kmet, Vladimir; Svejstil, Roman
2014-11-17
Bifidobacterium bifidum is a bacterial species exclusively found in the human intestinal tract. This species is becoming increasingly popular as a probiotic organism added to lyophilized products. In this study, porcine mucin was used as the sole carbon source for the selective enumeration of B. bifidum in probiotic food additives. Thirty-six bifidobacterial strains were cultivated in broth with mucin. Only 13 strains of B. bifidum utilized the mucin to produce acids. B. bifidum was selectively enumerated in eight probiotic food supplements using agar (MM agar) containing mupirocin (100 mg/L) and mucin (20 g/L) as the sole carbon source. MM agar was fully selective if the B. bifidum species was presented together with Bifidobacterium animalis subsp. lactis, Bifidobacterium breve, and Bifidobacterium longum subsp. longum species and with lactic acid bacteria (lactobacilli, streptococci). Isolated strains of B. bifidum were identified using biochemical, PCR, MALDI-TOF procedures and 16S rRNA gene sequencing. The novel selective medium was also suitable for the isolation of B. bifidum strains from human fecal samples. PMID:25217723
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 80-100μm and 100-125μm 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% 1σ) 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% 1σ) ccSTP/g, yielding an age of 83 ka, again lower compared to that obtained by U-Th disequilibrium. The
NASA Astrophysics Data System (ADS)
Jackson, Bob; Silgram, Martyn; Quinton, John
2010-05-01
Recent UK government-funded research has shown that compacted, unvegetated tramlines wheelings can represent an important source and transport pathway, which can account for 80% of surface runoff, sediment and phosphorus losses to edge-of-field from cereals on moderate slopes. For example, recent research found 5.5-15.8% of rainfall lost as runoff, and losses of 0.8-2.9 kg TP/ha and 0.3-4.8 T/ha sediment from tramline wheelings. When compaction was released by shallow cultivation, runoff was reduced to 0.2-1.7% of rainfall with losses of 0.0-0.2 kg TP/ha and 0.003-0.3 T/ha sediment respectively i.e. close to reference losses from control areas without tramlines. Recent independent assessments using novel tracer techniques have also shown that tramline wheelings can represent important sediment sources at river catchment scale. In response to these latest findings, a new project is now underway investigating the most cost-effective and practical ways of operationalising methods for managing tramline wheelings in autumn-sown cereal systems to reduce the risk of soil compaction from the autumn spray operation and the associated risk of surface runoff and diffuse pollution loss of sediment, phosphorus and nitrogen to edge of field. Research is focusing on the over-winter period when soils are close to field capacity and the physical protection of the soil surface granted by growing crop is limited. This paper outlines this new multi-disciplinary project and associated methodologies, which include hillslope-scale event-based evaluations of the effectiveness of novel mitigation methods on surface runoff and diffuse pollution losses to edge of field, assessments of the economic and practical viability of mitigation methods, and modelling the impact on water quality of implementation of the most promising techniques at both farm and catchment scale. The study involves a large consortium with 20 partners, including many industrial organisations representing tractor, crop
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%.
Lattice Boltzmann method for convection-diffusion equations with general interfacial conditions
NASA Astrophysics Data System (ADS)
Hu, Zexi; Huang, Juntao; Yong, Wen-An
2016-04-01
In this work, we propose an interfacial scheme accompanying the lattice Boltzmann method for convection-diffusion equations with general interfacial conditions, including conjugate conditions with or without jumps in heat and mass transfer, continuity of macroscopic variables and normal fluxes in ion diffusion in porous media with different porosity, and the Kapitza resistance in heat transfer. The construction of this scheme is based on our boundary schemes [Huang and Yong, J. Comput. Phys. 300, 70 (2015), 10.1016/j.jcp.2015.07.045] for Robin boundary conditions on straight or curved boundaries. It gives second-order accuracy for straight interfaces and first-order accuracy for curved ones. In addition, the new scheme inherits the advantage of the boundary schemes in which only the current lattice nodes are involved. Such an interfacial scheme is highly desirable for problems with complex geometries or in porous media. The interfacial scheme is numerically validated with several examples. The results show the utility of the constructed scheme and very well support our theoretical predications.
NASA Astrophysics Data System (ADS)
Lagowski, J.; Aleynikov, A.; Savtchouk, A.; Edelman, P.
2004-07-01
The Ultimate surface photovoltage method of minority carrier diffusion length measurements reffered to as Ultimate SPV, replaces a sequential “one wavelength at a time” approach with simultaneous illumination with the entire set of wavelengths. In this multiwavelength beam, each monochromatic component is chopped with slightly different frequency. This enables simultaneous monitoring of all component SPV signals corresponding to different wavelengths using multi-frequency signal processing. The amplitude and phase of each component signals are then analyzed and used to calculate the diffusion length and surface lifetime. In-flight Ultimate SPV measurement, whereby the wafer continuously moves under SPV probe, is used for fast whole wafer mapping. In addition to speed advantages, Ultimate SPV offers a fundemental accuracy advantage due to elimination of differences in wafer condition during sequential illumination with individual wavelengths. High-speed measurements make it possible to add additional wafer treatments and perform multi-mapping required for separation of Fe and Cu in the silicon bulk. Wafer mapping in time of 2 minutes realized with Ultimate SPV is critical for monitoring of cobalt in silicon.
Campylobacter in broiler slaughter samples assessed by direct count on mCCDA and Campy-Cefex agar.
Gonsalves, Camila Cristina; Borsoi, Anderlise; Perdoncini, Gustavo; Rodrigues, Laura Beatriz; do Nascimento, Vladimir Pinheiro
2016-01-01
Campylobacter spp. cause foodborne illnesses in humans primarily through the consumption of contaminated chicken. The aim of this study was to evaluate the United States Department of Agriculture's (USDA) recommended methodology, protocol MLG 41.02, for the isolation, identification and direct plate counting of Campylobacter jejuni and C. coli samples from the broiler slaughtering process. A plating method using both mCCDA and Campy-Cefex agars is recommended to recover Campylobacter cells. It is also possible to use this method in different matrices (cloacal swabs and water samples). Cloacal swabs, samples from pre-chiller and post-chiller carcasses and samples of pre-chiller, chiller and direct supply water were collected each week for four weeks from the same flock at a slaughterhouse located in an abattoir in southern Brazil. Samples were analyzed to directly count Campylobacter spp., and the results showed a high frequency of Campylobacter spp. on Campy-Cefex agar. For the isolated species, 72% were identified as Campylobacter jejuni and 38% as Campylobacter coli. It was possible to count Campylobacter jejuni and Campylobacter coli from different samples, including the water supply samples, using the two-agar method. These results suggest that slaughterhouses can use direct counting methods with both agars and different matrices as a monitoring tool to assess the presence of Campylobacter bacteria in their products. PMID:27237112
Diffuse attenuation coefficient of downwelling irradiance: An evaluation of remote sensing methods
NASA Astrophysics Data System (ADS)
Lee, Zhong-Ping; Darecki, Miroslaw; Carder, Kendall L.; Davis, Curtiss O.; Stramski, Dariusz; Rhea, W. Joseph
2005-02-01
The propagation of downwelling irradiance at wavelength λ from surface to a depth (z) in the ocean is governed by the diffuse attenuation coefficient, ?(λ). There are two standard methods for the derivation of ?(λ) in remote sensing, which both are based on empirical relationships involving the blue-to-green ratio of ocean color. Recently, a semianalytical method to derive ?(λ) from reflectance has also been developed. In this study, using ?(490) and ?(443) as examples, we compare the ?(λ) values derived from the three methods using data collected in three different regions that cover oceanic and coastal waters, with ?(490) ranging from ˜0.04 to 4.0 m-1. The derived values are compared with the data calculated from in situ measurements of the vertical profiles of downwelling irradiance. The comparisons show that the two standard methods produced satisfactory estimates of ?(λ) in oceanic waters where attenuation is relatively low but resulted in significant errors in coastal waters. The newly developed semianalytical method appears to have no such limitation as it performed well for both oceanic and coastal waters. For all data in this study the average of absolute percentage difference between the in situ measured and the semianalytically derived ? is ˜14% for λ = 490 nm and ˜11% for λ = 443 nm.
Radiative transfer equation modeling by streamline diffusion modified continuous Galerkin method
NASA Astrophysics Data System (ADS)
Long, Feixiao; Li, Fengyan; Intes, Xavier; Kotha, Shiva P.
2016-03-01
Optical tomography has a wide range of biomedical applications. Accurate prediction of photon transport in media is critical, as it directly affects the accuracy of the reconstructions. The radiative transfer equation (RTE) is the most accurate deterministic forward model, yet it has not been widely employed in practice due to the challenges in robust and efficient numerical implementations in high dimensions. Herein, we propose a method that combines the discrete ordinate method (DOM) with a streamline diffusion modified continuous Galerkin method to numerically solve RTE. Additionally, a phase function normalization technique was employed to dramatically reduce the instability of the DOM with fewer discrete angular points. To illustrate the accuracy and robustness of our method, the computed solutions to RTE were compared with Monte Carlo (MC) simulations when two types of sources (ideal pencil beam and Gaussian beam) and multiple optical properties were tested. Results show that with standard optical properties of human tissue, photon densities obtained using RTE are, on average, around 5% of those predicted by MC simulations in the entire/deeper region. These results suggest that this implementation of the finite element method-RTE is an accurate forward model for optical tomography in human tissues.
A texture classification method for diffused liver diseases using Gabor wavelets.
Ahmadian, A; Mostafa, A; Abolhassani, M; Salimpour, Y
2005-01-01
We proposed an efficient method for classification of diffused liver diseases based on Gabor wavelet. It is well known that Gabor wavelets attain maximum joint space-frequency resolution which is highly significant in the process of texture extraction and presentation. This property has been explored here as the proposed method outperforms the classification rate obtained by using dyadic wavelets and methods based on statistical properties of textures. The feature vector is relatively small compared to other methods. This has a significant impact on the speed of retrieval process. In addition, the proposed algorithm is not sensitive to shift of the image contents. Since shifting the contents of an image will cause a circular shift of the Gabor filter coefficients in each sub-band. The proposed algorithm applied to discriminate ultrasonic liver images into three disease states that are normal liver, liver hepatitis and cirrhosis. In our experiment 45 liver sample images from each three disease states which already proven by needle biopsy were used. We achieved the sensitivity 85% in the distinction between normal and hepatitis liver images and 86% in the distinction between normal and cirrhosis liver images. Based on our experiments, the Gabor wavelet is more appropriate than dyadic wavelets and statistical based methods for texture classification as it leads to higher classification accuracy. PMID:17282503
Radiative transfer equation modeling by streamline diffusion modified continuous Galerkin method.
Long, Feixiao; Li, Fengyan; Intes, Xavier; Kotha, Shiva P
2016-03-01
Optical tomography has a wide range of biomedical applications. Accurate prediction of photon transport in media is critical, as it directly affects the accuracy of the reconstructions. The radiative transfer equation (RTE) is the most accurate deterministic forward model, yet it has not been widely employed in practice due to the challenges in robust and efficient numerical implementations in high dimensions. Herein, we propose a method that combines the discrete ordinate method (DOM) with a streamline diffusion modified continuous Galerkin method to numerically solve RTE. Additionally, a phase function normalization technique was employed to dramatically reduce the instability of the DOM with fewer discrete angular points. To illustrate the accuracy and robustness of our method, the computed solutions to RTE were compared with Monte Carlo (MC) simulations when two types of sources (ideal pencil beam and Gaussian beam) and multiple optical properties were tested. Results show that with standard optical properties of human tissue, photon densities obtained using RTE are, on average, around 5% of those predicted by MC simulations in the entire/deeper region. These results suggest that this implementation of the finite element method-RTE is an accurate forward model for optical tomography in human tissues. PMID:26953662
Comparison of EPI Distortion Correction Methods in Diffusion Tensor MRI Using a Novel Framework
Wu, M.; Chang, L.-C.; Walker, L.; Lemaitre, H.; Barnett, A.S.; Marenco, S.; Pierpaoli, C.
2016-01-01
Diffusion weighted images (DWIs) are commonly acquired with Echo-planar imaging (EPI). B0 inhomogeneities affect EPI by producing spatially nonlinear image distortions. Several strategies have been proposed to correct EPI distortions including B0 field mapping (B0M) and image registration. In this study, an experimental framework is proposed to evaluation the performance of different EPI distortion correction methods in improving DT-derived quantities. A deformable registration based method with mutual information metric and cubic B-spline modeled constrained deformation field (BSP) is proposed as an alternative when B0 mapping data are not available. BSP method is qualitatively and quantitatively compared to B0M method using the framework. Both methods can successful reduce EPI distortions and significantly improve the quality of DT-derived quantities. Overall, B0M was clearly superior in infratentorial regions including brainstem and cerebellum, as well as in the ventral areas of the temporal lobes while BSP was better in all rostral brain regions. PMID:18982621
Xu, Xiao-Quan; Hu, Hao; Su, Guo-Yi; Liu, Hu; Shi, Hai-Bin
2016-01-01
Objective To evaluate the differences in the apparent diffusion coefficient (ADC) measurements based on three different region of interest (ROI) selection methods, and compare their diagnostic performance in differentiating benign from malignant orbital tumors. Materials and Methods Diffusion-weighted imaging data of sixty-four patients with orbital tumors (33 benign and 31 malignant) were retrospectively analyzed. Two readers independently measured the ADC values using three different ROIs selection methods including whole-tumor (WT), single-slice (SS), and reader-defined small sample (RDSS). The differences of ADC values (ADC-ROIWT, ADC-ROISS, and ADC-ROIRDSS) between benign and malignant group were compared using unpaired t test. Receiver operating characteristic curve was used to determine and compare their diagnostic ability. The ADC measurement time was compared using ANOVA analysis and the measurement reproducibility was assessed using Bland-Altman method and intra-class correlation coefficient (ICC). Results Malignant group showed significantly lower ADC-ROIWT, ADC-ROISS, and ADC-ROIRDSS than benign group (all p < 0.05). The areas under the curve showed no significant difference when using ADC-ROIWT, ADC-ROISS, and ADC-ROIRDSS as differentiating index, respectively (all p > 0.05). The ROISS and ROIRDSS required comparable measurement time (p > 0.05), while significantly shorter than ROIWT (p < 0.05). The ROISS showed the best reproducibility (mean difference ± limits of agreement between two readers were 0.022 [-0.080–0.123] × 10-3 mm2/s; ICC, 0.997) among three ROI methods. Conclusion Apparent diffusion coefficient values based on the three different ROI selection methods can help to differentiate benign from malignant orbital tumors. The results of measurement time, reproducibility and diagnostic ability suggest that the ROISS method are potentially useful for clinical practice. PMID:27587953
Juozaitis, Arvydas; Willeke, Klaus; Grinshpun, Sergey A.; Donnelly, Jean
1994-01-01
To study impaction versus impingement for the collection and recovery of viable airborne microorganisms, three new bioaerosol samplers have been designed and built. They differ from each other by the medium onto which the bioaerosol particles are collected (glass, agar, and liquid) but have the same inlet and collection geometries and the same sampling flow rate. The bioaerosol concentrations recorded by three different collection techniques have been compared with each other: impaction onto a glass slide, impaction onto an agar medium, and impingement into a liquid. It was found that the particle collection efficiency of agar slide impaction depends on the concentration of agar in the collection medium and on the sampling time, when samples are collected on a nonmoving agar slide. Impingement into a liquid showed anomalous behavior with respect to the sampling flow rate. Optimal sampling conditions in which all three new samplers exhibit the same overall sampling efficiency for nonbiological particles have been established. Inlet and collection efficiencies of about 100% have been achieved for all three devices at a sampling flow rate of 10 liters/min. The new agar slide impactor and the new impinger were then used to study the biological factors affecting the overall sampling efficiency. Laboratory experiments on the total recovery of a typical environmental microorganism, Pseudomonas fluorescens ATCC 13525, showed that both sampling methods, impaction and impingement, provided essentially the same total recovery when relatively nonstressed microorganisms were sampled under optimal sampling conditions. Comparison tests of the newly developed bioaerosol samplers with those commercially available showed that the incorporation of our research findings into the design of the new samplers yields better performance data than data from currently available samplers. PMID:16349217
NASA Astrophysics Data System (ADS)
Huang, Juntao; Hu, Zexi; Yong, Wen-An
2016-04-01
In this paper, we present a kind of second-order curved boundary treatments for the lattice Boltzmann method solving two-dimensional convection-diffusion equations with general nonlinear Robin boundary conditions. The key idea is to derive approximate boundary values or normal derivatives on computational boundaries, with second-order accuracy, by using the prescribed boundary condition. Once the approximate information is known, the second-order bounce-back schemes can be perfectly adopted. Our boundary treatments are validated with a number of numerical examples. The results show the utility of our boundary treatments and very well support our theoretical predications on the second-order accuracy thereof. The idea is quite universal. It can be directly generalized to 3-dimensional problems, multiple-relaxation-time models, and the Navier-Stokes equations.
Boundary conditions of the lattice Boltzmann method for convection-diffusion equations
NASA Astrophysics Data System (ADS)
Huang, Juntao; Yong, Wen-An
2015-11-01
In this paper, we employ an asymptotic analysis technique and construct two boundary schemes accompanying the lattice Boltzmann method for convection-diffusion equations with general Robin boundary conditions. One scheme is for straight boundaries, with the boundary points locating at any distance from the lattice nodes, and has second-order accuracy. The other is for curved boundaries, has only first-order accuracy and is much simpler than the existing schemes. Unlike those in the literature, our schemes involve only the current lattice node. Such a "single-node" boundary schemes are highly desirable for problems with complex geometries. The two schemes are validated numerically with a number of examples. The numerical results show the utility of the constructed schemes and very well support our theoretical predications.
The Hirota Method for Reaction-Diffusion Equations with Three Distinct Roots
Tanoglu, Gamze; Pashaev, Oktay
2004-10-04
The Hirota Method, with modified background is applied to construct exact analytical solutions of nonlinear reaction-diffusion equations of two types. The first equation has only nonlinear reaction part, while the second one has in addition the nonlinear transport term. For both cases, the reaction part has the form of the third order polynomial with three distinct roots. We found analytic one-soliton solutions and the relationships between three simple roots and the wave speed of the soliton. For the first case, if one of the roots is the mean value of other two roots, the soliton is static. We show that the restriction on three distinct roots to obtain moving soliton is removed in the second case by, adding nonlinear transport term to the first equation.
Scalable implicit methods for reaction-diffusion equations in two and three space dimensions
Veronese, S.V.; Othmer, H.G.
1996-12-31
This paper describes the implementation of a solver for systems of semi-linear parabolic partial differential equations in two and three space dimensions. The solver is based on a parallel implementation of a non-linear Alternating Direction Implicit (ADI) scheme which uses a Cartesian grid in space and an implicit time-stepping algorithm. Various reordering strategies for the linearized equations are used to reduce the stride and improve the overall effectiveness of the parallel implementation. We have successfully used this solver for large-scale reaction-diffusion problems in computational biology and medicine in which the desired solution is a traveling wave that may contain rapid transitions. A number of examples that illustrate the efficiency and accuracy of the method are given here; the theoretical analysis will be presented.
Goodwin, C Rory; Xu, Risheng; Iyer, Rajiv; Sankey, Eric W; Liu, Ann; Abu-Bonsrah, Nancy; Sarabia-Estrada, Rachel; Frazier, James L; Sciubba, Daniel M; Jallo, George I
2016-03-01
Brainstem gliomas comprise 10-20% of all pediatric central nervous system (CNS) tumors and diffuse intrinsic pontine gliomas (DIPGs) account for the majority of these lesions. DIPG is a rapidly progressive disease with almost universally fatal outcomes and a median survival less than 12 months. Current standard-of-care treatment for DIPG includes radiation therapy, but its long-term survival effects are still under debate. Clinical trials investigating the efficacy of systemic administration of various therapeutic agents have been associated with disappointing outcomes. Recent efforts have focused on improvements in chemotherapeutic agents employed and in methods of localized and targeted drug delivery. This review provides an update on current preclinical and clinical studies investigating treatment options for brainstem gliomas. PMID:26849840
Hybrid Monte Carlo-Diffusion Method For Light Propagation in Tissue With a Low-Scattering Region
NASA Astrophysics Data System (ADS)
Hayashi, Toshiyuki; Kashio, Yoshihiko; Okada, Eiji
2003-06-01
The heterogeneity of the tissues in a head, especially the low-scattering cerebrospinal fluid (CSF) layer surrounding the brain has previously been shown to strongly affect light propagation in the brain. The radiosity-diffusion method, in which the light propagation in the CSF layer is assumed to obey the radiosity theory, has been employed to predict the light propagation in head models. Although the CSF layer is assumed to be a nonscattering region in the radiosity-diffusion method, fine arachnoid trabeculae cause faint scattering in the CSF layer in real heads. A novel approach, the hybrid Monte Carlo-diffusion method, is proposed to calculate the head models, including the low-scattering region in which the light propagation does not obey neither the diffusion approximation nor the radiosity theory. The light propagation in the high-scattering region is calculated by means of the diffusion approximation solved by the finite-element method and that in the low-scattering region is predicted by the Monte Carlo method. The intensity and mean time of flight of the detected light for the head model with a low-scattering CSF layer calculated by the hybrid method agreed well with those by the Monte Carlo method, whereas the results calculated by means of the diffusion approximation included considerable error caused by the effect of the CSF layer. In the hybrid method, the time-consuming Monte Carlo calculation is employed only for the thin CSF layer, and hence, the computation time of the hybrid method is dramatically shorter than that of the Monte Carlo method.
Hybrid Monte Carlo-diffusion method for light propagation in tissue with a low-scattering region.
Hayashi, Toshiyuki; Kashio, Yoshihiko; Okada, Eiji
2003-06-01
The heterogeneity of the tissues in a head, especially the low-scattering cerebrospinal fluid (CSF) layer surrounding the brain has previously been shown to strongly affect light propagation in the brain. The radiosity-diffusion method, in which the light propagation in the CSF layer is assumed to obey the radiosity theory, has been employed to predict the light propagation in head models. Although the CSF layer is assumed to be a nonscattering region in the radiosity-diffusion method, fine arachnoid trabeculae cause faint scattering in the CSF layer in real heads. A novel approach, the hybrid Monte Carlo-diffusion method, is proposed to calculate the head models, including the low-scattering region in which the light propagation does not obey neither the diffusion approximation nor the radiosity theory. The light propagation in the high-scattering region is calculated by means of the diffusion approximation solved by the finite-element method and that in the low-scattering region is predicted by the Monte Carlo method. The intensity and mean time of flight of the detected light for the head model with a low-scattering CSF layer calculated by the hybrid method agreed well with those by the Monte Carlo method, whereas the results calculated by means of the diffusion approximation included considerable error caused by the effect of the CSF layer. In the hybrid method, the time-consuming Monte Carlo calculation is employed only for the thin CSF layer, and hence, the computation time of the hybrid method is dramatically shorter than that of the Monte Carlo method. PMID:12790437
Fast optimization method based on the diffuser dot density for uniformity of the backlight module.
Huang, Bing-Le; Guo, Tai-Liang
2016-02-20
A fast optimization method based on the diffuser dot density (DDD) for uniformity of the backlight module (BLM) is proposed in the paper. First, the relationship between the efficiency of the light emerging and the DDD is analyzed, and then a simulation model that is employed to acquire a serial of simulating data is constructed. Second, a mathematic method to profit the relationship is adopted, and a polynomial relationship is derived. Finally, an algorithm to adjust the DDD and optimize the uniformity of the BLM based on the DDD is constructed. The simulation results prove that only by three times optimization, the uniformity of the BLM can reach 85.6%, and the experimental result indicates that the algorithm proposed in the paper can improve the uniformity rapidly. The final experimental result is that the uniformity of the third optimization reaches 77.4%, which satisfies the target 75% in the phase of designing the BLM. Compared to the conventional optimization method, the method can speed up the procedure and lower the expense of developing the BLM in fabricating the liquid-crystal display. PMID:26906605
Evaluation of rigid registration methods for whole head imaging in diffuse optical tomography.
Wu, Xue; Eggebrecht, Adam T; Ferradal, Silvina L; Culver, Joseph P; Dehghani, Hamid
2015-07-01
Functional brain imaging has become an important neuroimaging technique for the study of brain organization and development. Compared to other imaging techniques, diffuse optical tomography (DOT) is a portable and low-cost technique that can be applied to infants and hospitalized patients using an atlas-based light model. For DOT imaging, the accuracy of the forward model has a direct effect on the resulting recovered brain function within a field of view and so the accuracy of the spatially normalized atlas-based forward models must be evaluated. Herein, the accuracy of atlas-based DOT is evaluated on models that are spatially normalized via a number of different rigid registration methods on 24 subjects. A multileveled approach is developed to evaluate the correlation of the geometrical and sensitivity accuracies across the full field of view as well as within specific functional subregions. Results demonstrate that different registration methods are optimal for recovery of different sets of functional brain regions. However, the "nearest point to point" registration method, based on the EEG 19 landmark system, is shown to be the most appropriate registration method for image quality throughout the field of view of the high-density cap that covers the whole of the optically accessible cortex. PMID:26217675
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.
Dominé, F; Xueref, I
2001-09-01
Diffusion of gases in ice is involved in cloud, snow, and ice core chemistry, but few data exist on the relevant diffusion coefficients. A novel method to measure diffusion coefficients in ice has recently been proposed by Livingston et al. (Anal. Chem., 2000, 72, 5590-5599). It is based on depth profiling of doped ice crystals epitaxially grown on Ru(001) by laser resonant desorption (LRD). Using this method, Livingston et al. obtained a value of the diffusion coefficient of the HCl hydrate in ice at 190 K of about 5 x 10(-11) cm2/s. We argue here that this value is many orders of magnitude higher than what could be expected from literature values, which are not reported in sufficient detail by Livingston et al. We investigate the possibilities that their high value could be due to (1) diffusion in defects in the ice, which would be present in very high concentrations because of the ice growth method; and (2) the fact that diffusion of high concentrations of HCl in ice at 190 K forms an amorphous HCl:H2O solid mixture, where HCl diffusion is fast. We present new infrared spectroscopic data on solid HCl:H2O mixtures that confirm that such mixtures can indeed be formed in an amorphous state at 190 K. Our proposed interpretation is that by depositing large amounts of HCl on epitaxially grown ice, Livingston et al. created a superficial amorphous binary mixture and that fast diffusion of HCl in the ice, possibly accelerated by a high defect density, produced an amorphous HCl:H2O mixture. We conclude that the processes studied by Livingston et al. are different from those involved in the atmospheric and cryospheric sciences, and that their data, obtained by depth profiling using LRD, probably cannot be applied to those fields. PMID:11569830
NASA Astrophysics Data System (ADS)
Suzuki, Takuji; Terabe, Hiroki; Iida, Shimpei; Yamashita, Takashi; Nagashima, Yasuyuki
2014-09-01
We have developed a new method to study positron diffusion in metals. In this method, we observe positronium negative ions emitted from the sample surfaces after coating with alkali-metals to evaluate the yields of the positrons which return to the surfaces. γ-rays from the ions accelerated using an electric field are clearly distinguished from those emitted from pair-annihilation of positrons in the bulk or on the surface and self-annihilation of emitted positronium atoms. Reliable studies on positron diffusion in metals have been enabled by this method.
Differential recovery of Streptococcus mutans from various mitis-salivarius agar preparations.
Liljemark, W F; Okrent, D H; Bloomquist, C G
1976-01-01
Recoveries of Streptococcus mutans from human dental plaque were lower when plated on mitis-salivarius agar obtained from Baltimore Biological Laboratories as compared with mitis-salivarius agar obtained from Difco Laboratories. However, no difference in recoveries of established laboratory strains of S. mutans was observed between these two agar preparations. PMID:956358
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...
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
Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
Flegga, Mark B.; Hellander, Stefan; Erban, Radek
2015-01-01
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 called the ghost cell method (GCM), since it works by constructing a “ghost cell” in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (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) Δt → 0 and h is fixed; (ii) Δt → 0 and h → 0 such that √Δt/h 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. PMID:26568640
Khan, Ahmed Nawaz; Khar, Roop Krishen; Ajayakumar, P. V.
2016-01-01
Objective: The aim of present study was to establish near infrared-chemometric methods that could be effectively used for quality profiling through identification and quantification of amoxicillin (AMOX) in formulated capsule which were similar to commercial products. In order to evaluate a large number of market products easily and quickly, these methods were modeled. Materials and Methods: Thermo Scientific Antaris II near infrared analyzer with TQ Analyst Chemometric Software were used for the development and validation of the identification and quantification models. Several AMOX formulations were composed with four excipients microcrystalline cellulose, magnesium stearate, croscarmellose sodium and colloidal silicon dioxide. Development includes quadratic mixture formulation design, near infrared spectrum acquisition, spectral pretreatment and outlier detection. According to prescribed guidelines by International Conference on Harmonization (ICH) and European Medicine Agency (EMA) developed methods were validated in terms of specificity, accuracy, precision, linearity, and robustness. Results: On diffuse reflectance mode, an identification model based on discriminant analysis was successfully processed with 76 formulations; and same samples were also used for quantitative analysis using partial least square algorithm with four latent variables and 0.9937 correlation of coefficient followed by 2.17% root mean square error of calibration (RMSEC), 2.38% root mean square error of prediction (RMSEP), 2.43% root mean square error of cross-validation (RMSECV). Conclusion: Proposed model established a good relationship between the spectral information and AMOX identity as well as content. Resulted values show the performance of the proposed models which offers alternate choice for AMOX capsule evaluation, relative to that of well-established high-performance liquid chromatography method. Ultimately three commercial products were successfully evaluated using developed
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.
NASA Astrophysics Data System (ADS)
Baker, K. L.; Curtin, W. A.
2016-07-01
In many problems of interest to materials scientists and engineers, the evolution of crystalline extended defects (dislocations, cracks, grain boundaries, interfaces, voids, precipitates) is controlled by the flow of point defects (interstitial/substitutional atoms and/or vacancies) through the crystal into the extended defect. Precise modeling of this behavior requires fully atomistic methods in and around the extended defect, but the flow of point defects entering the defect region can be treated by coarse-grained methods. Here, a multiscale algorithm is presented to provide this coupling. Specifically, direct accelerated molecular dynamics (AMD) of extended defect evolution is coupled to a diffusing point defect concentration field that captures the long spatial and temporal scales of point defect motion in the presence of the internal stress fields generated by the evolving defect. The algorithm is applied to study vacancy absorption into an edge dislocation in aluminum where vacancy accumulation in the core leads to nucleation of a double-jog that then operates as a sink for additional vacancies; this corresponds to the initial stages of dislocation climb modeled with explicit atomistic resolution. The method is general and so can be applied to many other problems associated with nucleation, growth, and reaction due to accumulation of point defects in crystalline materials.
Inverse Monte Carlo method in a multilayered tissue model for diffuse reflectance spectroscopy.
Fredriksson, Ingemar; Larsson, Marcus; Strömberg, Tomas
2012-04-01
Model based data analysis of diffuse reflectance spectroscopy data enables the estimation of optical and structural tissue parameters. The aim of this study was to present an inverse Monte Carlo method based on spectra from two source-detector distances (0.4 and 1.2 mm), using a multilayered tissue model. The tissue model variables include geometrical properties, light scattering properties, tissue chromophores such as melanin and hemoglobin, oxygen saturation and average vessel diameter. The method utilizes a small set of presimulated Monte Carlo data for combinations of different levels of epidermal thickness and tissue scattering. The path length distributions in the different layers are stored and the effect of the other parameters is added in the post-processing. The accuracy of the method was evaluated using Monte Carlo simulations of tissue-like models containing discrete blood vessels, evaluating blood tissue fraction and oxygenation. It was also compared to a homogeneous model. The multilayer model performed better than the homogeneous model and all tissue parameters significantly improved spectral fitting. Recorded in vivo spectra were fitted well at both distances, which we previously found was not possible with a homogeneous model. No absolute intensity calibration is needed and the algorithm is fast enough for real-time processing. PMID:22559695
Diffusion processes in tumors: A nuclear medicine approach
NASA Astrophysics Data System (ADS)
Amaya, Helman
2016-07-01
The number of counts used in nuclear medicine imaging techniques, only provides physical information about the desintegration of the nucleus present in the the radiotracer molecules that were uptaken in a particular anatomical region, but that information is not a real metabolic information. For this reason a mathematical method was used to find a correlation between number of counts and 18F-FDG mass concentration. This correlation allows a better interpretation of the results obtained in the study of diffusive processes in an agar phantom, and based on it, an image from the PETCETIX DICOM sample image set from OsiriX-viewer software was processed. PET-CT gradient magnitude and Laplacian images could show direct information on diffusive processes for radiopharmaceuticals that enter into the cells by simple diffusion. In the case of the radiopharmaceutical 18F-FDG is necessary to include pharmacokinetic models, to make a correct interpretation of the gradient magnitude and Laplacian of counts images.
NASA Astrophysics Data System (ADS)
Endo, Takatsugu; Nemugaki, Shinya; Matsushita, Yuki; Sakai, Yasuhiro; Ozaki, Hiroaki; Hiejima, Yusuke; Kimura, Yoshifumi; Takahashi, Kenji
2016-06-01
To achieve ionic liquids (ILs) that show fast solute diffusivity independent of viscosity domination, sixteen ILs containing Si or Si-O-Si groups (SiILs) were synthesized. Diffusion coefficients of three solute molecules with different molecular sizes, i.e., CO, diphenylacetylene, and diphenylcyclopropenone, were determined in SiILs using the transient grating method and the results were compared to other solvent system. SiILs showed distinguishably faster diffusivity for the smallest solute, CO, than conventional ILs at the same viscosity, particularly in the high viscosity region. Based on previous results and our estimation, three plausible factors exists that contribute to the faster solute diffusivity in SiILs, i.e., the flexibility of the Si or Si-O-Si group, decreased interaction between the cation and the solute, and increased free volume because of the bulky structure.
Diffusion studies of Ra and Pb in GaAs by the alpha-particle energy loss method
NASA Astrophysics Data System (ADS)
Adamcyk, M.; Beaudoin, M.; Kelson, I.; Levy, Y.; Tiedje, T.
1998-12-01
The temperature dependence of the diffusion of lead in GaAs is determined by measuring the modification to the energy spectrum of emitted alpha particles from the decay chain of implanted 212Pb atoms. Diffusion rates are measured for temperatures up to 900 °C. Higher rates are observed for the diffusion in silicon-doped GaAs than in semi-insulating GaAs. An upper limit for the diffusion of radium in GaAs is similarly obtained from the decay of the 224Ra isotope. Implications for the use of implanted alpha sources for thickness monitoring during epitaxial film growth by the alpha-particle energy loss method are discussed.
Wang, Yangyang; Sun, Che-Nan; Fan, Fei; Sangoro, Joshua R; Berman, Marc B; Greenbaum, Steve G; Zawodzinski, Thomas A; Sokolov, Alexei P
2013-04-01
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 the Macdonald-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. PMID:23679415
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.
Bodzenta, Jerzy; Kaźmierczak-Bałata, Anna; Wokulska, Krystyna B; Kucytowski, Jacek; Łukasiewicz, Tadeusz; Hofman, Władysław
2009-03-01
Three crystals used in solid-state lasers, namely, yttrium aluminum garnet (YAG), yttrium orthovanadate (YVO(4)), and gadolinium calcium oxoborate (GdCOB), were investigated to determine the influence of dopants on their thermal diffusivity. The thermal diffusivity was measured by thermal wave method with a signal detection based on mirage effect. The YAG crystals were doped with Yb or V, the YVO(4) with Nd or Ca and Tm, and the GdCOB crystals contained Nd or Yb. In all cases, the doping caused a decrease in thermal diffusivity. The analysis of complementary measurements of ultrasound velocity changes caused by dopants leads to the conclusion that impurities create phonon scattering centers. This additional scattering reduces the phonon mean free path and accordingly results in the decrease of the thermal diffusivity of the crystal. The influence of doping on lattice parameters was investigated, additionally. PMID:19252616
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 ρd 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 ρd effects. Extrapolation to lower ρd suggests that m ≃4 -4.5 should be obtained from our PFC description at typical experimental ρd 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 ρd may nonetheless be relevant to systems in which comparable densities are obtained locally within heterogeneous defect domains such as dislocation cell walls or tangles.
Culture of Piscirickettsia salmonis on enriched blood agar.
Mauel, Michael J; Ware, Cynthia; Smith, Pedro A
2008-03-01
Piscirickettsia salmonis is the etiologic agent of piscirickettsiosis, an economically significant disease of fish. Isolation of P. salmonis by culturing on fish cell lines has been the standard technique since the initial isolation of the organism. The ability to grow P. salmonis on artificial media would relieve facilities of the cost of maintaining cell lines, permit isolation at fish culture sites with fewer contamination problems, and allow easier transport of isolates to diagnostic facilities for confirmation assays. This report describes the successful culture of P. salmonis on enriched blood agar. PMID:18319435
Sousa, Ana M M; Souza, Hiléia K S; Latona, Nicholas; Liu, Cheng-Kung; Gonçalves, Maria P; Liu, LinShu
2014-10-13
In the present paper, we test the suitability of ChCl/urea (DES-U) and ChCl/glycerol (DES-G) eutectic mixtures, each one prepared at 1:2 molar ratio, for the production of agar films. A three-step process is proposed: pre-solubilization of polymer in DES followed by compression-molding and subsequent drying. The mechanical properties, water resistance and microstructure of the films were evaluated at different polymer concentrations (i.e. 2-6%, w/w). DES-U showed by far, the best film forming ability. Agreeing with the diffusion and SEM data, films with the best mechanical properties were found at the lowest and highest agar concentrations (tensile strengths of 24.2-42 MPa and elongations of 15.4-38.9%). The water sorption and contact angle studies suggested increased hydrophilicity for the film containing the lowest concentration of agar. The use of choline chloride based ionic liquid analogues as solvent and plasticizer might be a promising tool for the development of new non-aqueous materials based on seaweed polysaccharides. PMID:25037344
Shibukawa, Atsushi; Okamoto, Atsushi; Takabayashi, Masanori; Tomita, Akihisa
2014-02-24
We propose a spatial cross modulation method using a random diffuser and a phase-only spatial light modulator (SLM), by which arbitrary complex-amplitude fields can be generated with higher spatial resolution and diffraction efficiency than off-axis and double-phase computer-generated holograms. Our method encodes the original complex object as a phase-only diffusion image by scattering the complex object using a random diffuser. In addition, all incoming light to the SLM is consumed for a single diffraction order, making a diffraction efficiency of more than 90% possible. This method can be applied for holographic data storage, three-dimensional displays, and other such applications. PMID:24663718
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.
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
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.
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…
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 γ 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.
A generalized diffusion model for growth of nanoparticles synthesized by colloidal methods.
Wen, Tianlong; Brush, Lucien N; Krishnan, Kannan M
2014-04-01
A nanoparticle growth model is developed to predict and guide the syntheses of monodisperse colloidal nanoparticles in the liquid phase. The model, without any a priori assumptions, is based on the Fick's law of diffusion, conservation of mass and the Gibbs-Thomson equation for crystal growth. In the limiting case, this model reduces to the same expression as the currently accepted model that requires the assumption of a diffusion layer around each nanoparticle. The present growth model bridges the two limiting cases of the previous model i.e. complete diffusion controlled and adsorption controlled growth of nanoparticles. Specifically, the results show that a monodispersion of nanoparticles can be obtained both with fast monomer diffusion and with surface reaction under conditions of small diffusivity to surface reaction constant ratio that results is growth 'focusing'. This comprehensive description of nanoparticle growth provides new insights and establishes the required conditions for fabricating monodisperse nanoparticles critical for a wide range of applications. PMID:24491334
Borelli's lactritmel agar induces conidiation in rare-macroconidia producing dermatophytic fungi.
Ilkit, Macit; Gümral, Ramazan; Döğen, Aylin
2012-10-01
Macroconidia are among the most important indicators used to identify dermatophytic fungi, but several do not usually sporulate and/or produce macroconidia on Sabouraud glucose agar. Specifically, Microsporum audouinii, M. ferrugineum, Trichophyton concentricum, T. schoenleinii, T. verrucosum, and T. violaceum (including T. soudanense and T. yaoundei) rarely form macroconidia and, therefore, cannot be easily identified. In this study, we investigated the production of macroconidia on nine common laboratory media, including Borelli's lactritmel agar (BLA), modified Borelli's lactritmel agar (MBLA), brain heart infusion agar (BHIA), Christensen's urease agar in Petri dishes (UPA), cornmeal dextrose agar (CMDA), Lowenstein-Jensen agar (LJA), malt extract agar (MEA), oatmeal agar (OA), and potato dextrose agar (PDA). The performance of these media was evaluated using 18 rare-macroconidia producing isolates, including representative of the six species mentioned above. All cultures in this study were incubated at 26°C on the bench, and conidia formation on each was investigated at 5, 10, 15, 20, 25, and 30 days of incubation. BLA apparently improved macroconidia production after 15 days and was the most useful nutrient agar medium to induce these phenotypic characters in daily practice, closely followed by OA, PDA, and MBLA. PMID:22563856