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Sample records for solute transport protein

  1. Solute carrier transporters: Pharmacogenomics research ...

    African Journals Online (AJOL)

    Aghogho

    2010-12-27

    Dec 27, 2010 ... This paper reviews the solute carrier transporters and highlights the fact that there is much to be learnt from .... transporters, drug targets, effect or proteins and meta- ... basolateral or apical plasma membrane of polarized cells,.

  2. A solute-binding protein for iron transport in Streptococcus iniae

    Directory of Open Access Journals (Sweden)

    Li Anxing

    2010-12-01

    Full Text Available Abstract Background Streptococcus iniae (S. iniae is a major pathogen that causes considerable morbidity and mortality in cultured fish worldwide. The pathogen's ability to adapt to the host affects the extent of infection, hence understanding the mechanisms by which S. iniae overcomes physiological stresses during infection will help to identify potential virulence determinants of streptococcal infection. Grow S. iniae under iron-restricted conditions is one approach for identifying host-specific protein expression. Iron plays an important role in many biological processes but it has low solubility under physiological condition. Many microorganisms have been shown to be able to circumvent this nutritional limitation by forming direct contacts with iron-containing proteins through ATP-binding cassette (ABC transporters. The ABC transporter superfamilies constitute many different systems that are widespread among living organisms with different functions, such as ligands translocation, mRNA translation, and DNA repair. Results An ABC transporter system, named as mtsABC (metal transport system was cloned from S. iniae HD-1, and was found to be involved in heme utilization. mtsABC is cotranscribed by three downstream genes, i.e., mtsA, mtsB, and mtsC. In this study, we cloned the first gene of the mtsABC transporter system (mtsA, and purified the corresponding recombinant protein MtsA. The analysis indicated that MtsA is a putative lipoprotein which binds to heme that can serve as an iron source for the microorganism, and is expressed in vivo during Kunming mice infection by S. iniae HD-1. Conclusions This is believed to be the first report on the cloning the ABC transporter lipoprotein from S. iniae genomic DNA. Together, our data suggested that MtsA is associated with heme, and is expressed in vivo during Kunming mice infection by S. iniae HD-1 which indicated that it can be a potential candidate for S. iniae subunit vaccine.

  3. Ion Transport in Confined Geometries below the Nanoscale: Access Resistance Dominates Protein Channel Conductance in Diluted Solutions.

    Science.gov (United States)

    Alcaraz, Antonio; López, M Lidón; Queralt-Martín, María; Aguilella, Vicente M

    2017-10-24

    Synthetic nanopores and mesoscopic protein channels have common traits like the importance of electrostatic interactions between the permeating ions and the nanochannel. Ion transport at the nanoscale occurs under confinement conditions so that the usual assumptions made in microfluidics are challenged, among others, by interfacial effects such as access resistance (AR). Here, we show that a sound interpretation of electrophysiological measurements in terms of channel ion selective properties requires the consideration of interfacial effects, up to the point that they dominate protein channel conductance in diluted solutions. We measure AR in a large ion channel, the bacterial porin OmpF, by means of single-channel conductance measurements in electrolyte solutions containing varying concentrations of high molecular weight PEG, sterically excluded from the pore. Comparison of experiments performed in charged and neutral planar membranes shows that lipid surface charges modify the ion distribution and determine the value of AR, indicating that lipid molecules are more than passive scaffolds even in the case of large transmembrane proteins. We also found that AR may reach up to 80% of the total channel conductance in diluted solutions, where electrophysiological recordings register essentially the AR of the system and depend marginally on the pore characteristics. These findings may have implications for several low aspect ratio biological channels that perform their physiological function in a low ionic strength and macromolecule crowded environment, just the two conditions enhancing the AR contribution.

  4. Solute transport in soil

    NARCIS (Netherlands)

    Zee, van der S.E.A.T.M.; Leijnse, A.

    2013-01-01

    Solute transport is of importance in view of the movement of nutrient elements, e.g. towards the plant root system, and because of a broad range of pollutants. Pollution is not necessarily man induced, but may be due to geological or geohydrological causes, e.g. in the cases of pollution with

  5. Effect of dialysate osmolarity on the transport of low-molecular weight solutes and proteins during CAPD

    NARCIS (Netherlands)

    Imholz, A. L.; Koomen, G. C.; Struijk, D. G.; Arisz, L.; Krediet, R. T.

    1993-01-01

    Osmotic-induced fluid and solute transport was studied in ten stable CAPD patients, who were examined twice within one week, using dialysate with 1.36% glucose on the first and 3.86% glucose on the second day. Peritoneal fluid kinetics were determined using intraperitoneally administered dextran 70

  6. Proteins in solution: Fractal surfaces in solutions

    Directory of Open Access Journals (Sweden)

    R. Tscheliessnig

    2016-02-01

    Full Text Available The concept of the surface of a protein in solution, as well of the interface between protein and 'bulk solution', is introduced. The experimental technique of small angle X-ray and neutron scattering is introduced and described briefly. Molecular dynamics simulation, as an appropriate computational tool for studying the hydration shell of proteins, is also discussed. The concept of protein surfaces with fractal dimensions is elaborated. We finish by exposing an experimental (using small angle X-ray scattering and a computer simulation case study, which are meant as demonstrations of the possibilities we have at hand for investigating the delicate interfaces that connect (and divide protein molecules and the neighboring electrolyte solution.

  7. Characterization of SLCO5A1/OATP5A1, a solute carrier transport protein with non-classical function.

    Directory of Open Access Journals (Sweden)

    Katrin Sebastian

    Full Text Available Organic anion transporting polypeptides (OATP/SLCO have been identified to mediate the uptake of a broad range of mainly amphipathic molecules. Human OATP5A1 was found to be expressed in the epithelium of many cancerous and non-cancerous tissues throughout the body but protein characterization and functional analysis have not yet been performed. This study focused on the biochemical characterization of OATP5A1 using Xenopus laevis oocytes and Flp-In T-REx-HeLa cells providing evidence regarding a possible OATP5A1 function. SLCO5A1 is highly expressed in mature dendritic cells compared to immature dendritic cells (∼6.5-fold and SLCO5A1 expression correlates with the differentiation status of primary blood cells. A core- and complex- N-glycosylated polypeptide monomer of ∼105 kDa and ∼130 kDa could be localized in intracellular membranes and on the plasma membrane, respectively. Inducible expression of SLCO5A1 in HeLa cells led to an inhibitory effect of ∼20% after 96 h on cell proliferation. Gene expression profiling with these cells identified immunologically relevant genes (e.g. CCL20 and genes implicated in developmental processes (e.g. TGM2. A single nucleotide polymorphism leading to the exchange of amino acid 33 (L→F revealed no differences regarding protein expression and function. In conclusion, we provide evidence that OATP5A1 might be a non-classical OATP family member which is involved in biological processes that require the reorganization of the cell shape, such as differentiation and migration.

  8. Rat organic solute carrier protein 1 (rOscp1) mediated the transport of organic solutes in Xenopus laevis oocytes: isolation and pharmacological characterization of rOscp1.

    Science.gov (United States)

    Izuno, Hisanori; Kobayashi, Yasuna; Sanada, Yutaka; Nihei, Daisuke; Suzuki, Masako; Kohyama, Noriko; Ohbayashi, Masayuki; Yamamoto, Toshinori

    2007-09-22

    Rat organic solute carrier protein 1 (rOscp1) was isolated from a rat testis cDNA library. Isolated rOscp1 cDNA consisted of 1089 base pairs that encoded a 363-amino acid protein, and the amino acid sequence was 88% and 93% identical to that of human OSCP1 (hOSCP1) and mouse Oscp1 (mOscp1), respectively. The message for rOscp1 is highly detected in rat testis. When expressed in X. oocytes, rOscp1 mediated the high affinity transport of p-aminohippurate (PAH) with a Km value of 15.7+/-1.9 microM, and rOscp1-mediated organic solutes were exhibited in time- and Na+-independent manners. rOscp1 also transported various structurally heterogenous compounds such as testosterone, dehydroepiandrosterone sulfate (DHEA-S), and taurocholate with some differences in substrate specificity compared with hOSCP1. Immunohistochemical analysis revealed that the rOscp1 protein is localized in the basal membrane side of Sertoli cells as observed in mouse testis [Kobayashi et al., 2007; Kobayashi, Y., Tsuchiya, A., Hayashi, T., Kohyama, N., Ohbayashi, M., Yamamoto, T., 2007. Isolation and characterization of polyspecific mouse organic solute carrier protein 1 (mOscp1). Drug Metabolism and Disposition 35 (7), 1239-1245]. Thus, the present results indicate that a newly isolated cDNA clone, rOscp1, is a polyspecific organic solute carrier protein with some differences in substrate specificity compared with human and mouse OSCP1.

  9. ATP-binding Cassette (ABC) Transport System Solute-binding Protein-guided Identification of Novel d-Altritol and Galactitol Catabolic Pathways in Agrobacterium tumefaciens C58*

    Science.gov (United States)

    Wichelecki, Daniel J.; Vetting, Matthew W.; Chou, Liyushang; Al-Obaidi, Nawar; Bouvier, Jason T.; Almo, Steven C.; Gerlt, John A.

    2015-01-01

    Innovations in the discovery of the functions of uncharacterized proteins/enzymes have become increasingly important as advances in sequencing technology flood protein databases with an exponentially growing number of open reading frames. This study documents one such innovation developed by the Enzyme Function Initiative (EFI; U54GM093342), the use of solute-binding proteins for transport systems to identify novel metabolic pathways. In a previous study, this strategy was applied to the tripartite ATP-independent periplasmic transporters. Here, we apply this strategy to the ATP-binding cassette transporters and report the discovery of novel catabolic pathways for d-altritol and galactitol in Agrobacterium tumefaciens C58. These efforts resulted in the description of three novel enzymatic reactions as follows: 1) oxidation of d-altritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) phosphorylation of d-tagatose to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and 3) epimerization of d-tagatose 6-phosphate C-4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction. The epimerization reaction catalyzed by a member of PF08013 is especially noteworthy, because the functions of members of PF08013 have been unknown. These discoveries were assisted by the following two synergistic bioinformatics web tools made available by the Enzyme Function Initiative: the EFI-Enzyme Similarity Tool and the EFI-Genome Neighborhood Tool. PMID:26472925

  10. Statistical mechanics of protein solutions

    NARCIS (Netherlands)

    Prinsen, P.

    2007-01-01

    We study theoretically thermodynamic properties of spherical globular proteins in aqueous solution with added monovalent salt. We show how one can determine an effective interaction potential between the proteins from experimental data as a function of salt concentration and we apply this to the

  11. Differences in the peritoneal transport of water, solutes and proteins between dialysis with two- and with three-litre exchanges

    NARCIS (Netherlands)

    Krediet, R. T.; Boeschoten, E. W.; Struijk, D. G.; Arisz, L.

    1988-01-01

    In eight, CAPD patients who either had insufficient results of dialysis treatment (six) or loss of ultrafiltration (two) on a normal scheme (4 X 2-1), the effects of a 3-1 dialysate exchange on the in situ intraperitoneal volume, solute mass transfer, and mass transfer area coefficients were

  12. Water-transporting proteins

    DEFF Research Database (Denmark)

    Zeuthen, Thomas

    2010-01-01

    . In the K(+)/Cl(-) and the Na(+)/K(+)/2Cl(-) cotransporters, water is entirely cotransported, while water transport in glucose uniporters and Na(+)-coupled transporters of nutrients and neurotransmitters takes place by both osmosis and cotransport. The molecular mechanism behind cotransport of water...... transport. Epithelial water transport is energized by the movements of ions, but how the coupling takes place is uncertain. All epithelia can transport water uphill against an osmotic gradient, which is hard to explain by simple osmosis. Furthermore, genetic removal of aquaporins has not given support...... to osmosis as the exclusive mode of transport. Water cotransport can explain the coupling between ion and water transport, a major fraction of transepithelial water transport and uphill water transport. Aquaporins enhance water transport by utilizing osmotic gradients and cause the osmolarity...

  13. Peritoneal solute transport and inflammation.

    Science.gov (United States)

    Davies, Simon J

    2014-12-01

    The speed with which small solutes cross the peritoneal membrane, termed peritoneal solute transport rate (PSTR), is a key measure of individual membrane performance. PSTR can be quantified easily by using the 4-hour dialysate to plasma creatinine ratio, which, although only an approximation to the diffusive characteristics of the membrane, has been well validated clinically in terms of its relationship to patient survival and changes in longitudinal membrane function. This has led to changes in peritoneal dialysis modality use and dialysis prescription. An important determinant of PSTR is intraperitoneal inflammation, as exemplified by local interleukin 6 production, which is largely independent of systemic inflammation and its relationship to comorbid conditions and increased mortality. There is no strong evidence to support the contention that the peritoneal membrane in some individuals with high PSTR is qualitatively different at the start of treatment; rather, it represents a spectrum that is determined in part by genetic factors. Both clinical and experimental evidence support the view that persistent intraperitoneal inflammation, detected as a continuously high or increasing PSTR, may predispose the membrane to progressive fibrosis. Copyright © 2014 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  14. Artificial oxygen transport protein

    Science.gov (United States)

    Dutton, P. Leslie

    2014-09-30

    This invention provides heme-containing peptides capable of binding molecular oxygen at room temperature. These compounds may be useful in the absorption of molecular oxygen from molecular oxygen-containing atmospheres. Also included in the invention are methods for treating an oxygen transport deficiency in a mammal.

  15. Urban Transportation: Issue and Solution

    Directory of Open Access Journals (Sweden)

    Haryati Shafii

    2011-10-01

    Full Text Available Generally, quality of life of urban population is heavily dependent on social facilities provided within the environment. One of the most important facilities is transportations. Study on transportation mode in an urban area is especially very important because for almost every individual living in a large and densely populated area, mobility is one of the most crucial issues in everyday life. Enhance mobility, faster journey to work and less pollution from petrol-propelled vehicles can increase the quality of life, which in turn lead to a sustainable urban living. The study present transportation mode usage issues faced by community related to quality of life in an urban area. This study identifies several issues of transportation mode in urban areas and its impact on the quality of life. The study areas are Putrajaya, Kuala Lumpur and Bandar Kajang, Selangor. The methodology used in this research is secondary and primary data. The questionnaires for the survey were distributed from May 2008 to Jun 2008. These researches were conducted on 144 respondents for to evaluate their perception of transportation mode correlated to the quality of life. The collected data were then analyzed using “Statistical Packages for the Social Science” (SPSS. The respondents comprise of 61 males and 84 females from the age group of 18 to 57 years. This study identifies the percentage of public transportation mode usage in urban area, such as buses (16.7%, train (ERL, monorail and commuter-6.4%; which is very low compared to owning personal car (45.8% and motorcycle (25.4%.The result shows owning personal car is the highest (45.8% in three study areas and monorail and taxi are the lowest (1.4%. The Chi Square Test shows that among the mode transportation with traffic jam is quite difference in Kuala Lumpur, Putrajaya and Kajang. Analysis of the Chi Square Test shows the result is 0.000 (two sides to respondent answering “yes” and analysis of Spearman

  16. Low-Protein Diet Supplemented with Keto Acids Is Associated with Suppression of Small-Solute Peritoneal Transport Rate in Peritoneal Dialysis Patients

    Directory of Open Access Journals (Sweden)

    Na Jiang

    2011-01-01

    Full Text Available Objective. We investigate whether low-protein diet would show benefits in suppressing peritoneal transport rate in peritoneal dialysis (PD patients. Methods. This is a supplemented analysis of our previously published trial, which randomized 60 PD patients to receive low- (LP: dietary protein intake of 0.6–0.8 g/kg/d, keto-acid-supplemented low- (sLP: 0.6–0.8 g/kg/d with 0.12 g/kg/d of keto acids, or high- (HP: 1.0–1.2 g/kg/d protein diet and lasted for one year. In this study, the variations of peritoneal transport rate were assessed. Results. While baseline D/Pcr (dialysate-to-plasma concentration ratio for creatinine at 4 hour and D/D0glu (dialysate glucose at 4 hour to baseline dialysate glucose concentration ratio were similar, D/Pcr in group sLP was lower, and D/D0glu was higher than those in the other two groups (P<0.05 at 12th month. D/D0glu increased (P<0.05, and D/Pcr tended to decrease, (P=0.071 in group sLP. Conclusions. Low-protein diet with keto acids may benefit PD patients by maintaining peritoneum at a lower transport rate.

  17. Low-protein diet supplemented with keto acids is associated with suppression of small-solute peritoneal transport rate in peritoneal dialysis patients.

    Science.gov (United States)

    Jiang, Na; Qian, Jiaqi; Lin, Aiwu; Fang, Wei; Zhang, Weiming; Cao, Liou; Wang, Qin; Ni, Zhaohui; Yao, Qiang

    2011-01-01

    Objective. We investigate whether low-protein diet would show benefits in suppressing peritoneal transport rate in peritoneal dialysis (PD) patients. Methods. This is a supplemented analysis of our previously published trial, which randomized 60 PD patients to receive low- (LP: dietary protein intake of 0.6-0.8 g/kg/d), keto-acid-supplemented low- (sLP: 0.6-0.8 g/kg/d with 0.12 g/kg/d of keto acids), or high- (HP: 1.0-1.2 g/kg/d) protein diet and lasted for one year. In this study, the variations of peritoneal transport rate were assessed. Results. While baseline D/P(cr) (dialysate-to-plasma concentration ratio for creatinine at 4 hour) and D/D0(glu) (dialysate glucose at 4 hour to baseline dialysate glucose concentration ratio) were similar, D/P(cr) in group sLP was lower, and D/D0(glu) was higher than those in the other two groups (P diet with keto acids may benefit PD patients by maintaining peritoneum at a lower transport rate.

  18. Low-Protein Diet Supplemented with Keto Acids Is Associated with Suppression of Small-Solute Peritoneal Transport Rate in Peritoneal Dialysis Patients

    OpenAIRE

    Jiang, Na; Qian, Jiaqi; Lin, Aiwu; Fang, Wei; Zhang, Weiming; Cao, Liou; Wang, Qin; Ni, Zhaohui; Yao, Qiang

    2011-01-01

    Objective. We investigate whether low-protein diet would show benefits in suppressing peritoneal transport rate in peritoneal dialysis (PD) patients. Methods. This is a supplemented analysis of our previously published trial, which randomized 60 PD patients to receive low- (LP: dietary protein intake of 0.6–0.8 g/kg/d), keto-acid-supplemented low- (sLP: 0.6–0.8 g/kg/d with 0.12 g/kg/d of keto acids), or high- (HP: 1.0–1.2 g/kg/d) protein diet and lasted for one year. In this study, the variat...

  19. Solute carrier transporters: potential targets for digestive system neoplasms.

    Science.gov (United States)

    Xie, Jing; Zhu, Xiao Yan; Liu, Lu Ming; Meng, Zhi Qiang

    2018-01-01

    Digestive system neoplasms are the leading causes of cancer-related death all over the world. Solute carrier (SLC) superfamily is composed of a series of transporters that are ubiquitously expressed in organs and tissues of digestive systems and mediate specific uptake of small molecule substrates in facilitative manner. Given the important role of SLC proteins in maintaining normal functions of digestive system, dysregulation of these protein in digestive system neoplasms may deliver biological and clinical significance that deserves systemic studies. In this review, we critically summarized the recent advances in understanding the role of SLC proteins in digestive system neoplasms. We highlighted that several SLC subfamilies, including metal ion transporters, transporters of glucose and other sugars, transporters of urea, neurotransmitters and biogenic amines, ammonium and choline, inorganic cation/anion transporters, transporters of nucleotide, amino acid and oligopeptide organic anion transporters, transporters of vitamins and cofactors and mitochondrial carrier, may play important roles in mediating the initiation, progression, metastasis, and chemoresistance of digestive system neoplasms. Proteins in these SLC subfamilies may also have diagnostic and prognostic values to particular cancer types. Differential expression of SLC proteins in tumors of digestive system was analyzed by extracting data from human cancer database, which revealed that the roles of SLC proteins may either be dependent on the substrates they transport or be tissue specific. In addition, small molecule modulators that pharmacologically regulate the functions of SLC proteins were discussed for their possible application in the treatment of digestive system neoplasms. This review highlighted the potential of SLC family proteins as drug target for the treatment of digestive system neoplasms.

  20. The solute carrier 6 family of transporters

    DEFF Research Database (Denmark)

    Bröer, Stefan; Gether, Ulrik

    2012-01-01

    of these transporters is associated with a variety of diseases. Pharmacological inhibition of the neurotransmitter transporters in this family is an important strategy in the management of neurological and psychiatric disorders. This review provides an overview of the biochemical and pharmacological properties......The solute carrier 6 (SLC6) family of the human genome comprises transporters for neurotransmitters, amino acids, osmolytes and energy metabolites. Members of this family play critical roles in neurotransmission, cellular and whole body homeostasis. Malfunction or altered expression...... of the SLC6 family transporters....

  1. Mass transport in polyelectrolyte solutions

    Science.gov (United States)

    Schipper, F. J. M.; Leyte, J. C.

    1999-02-01

    The self-diffusion coefficients of the three components of a salt-free heavy-water solution of polymethacrylic acid, completely neutralized with tetra-methylammonium hydroxide, were measured over a broad concentration range. Three concentration regions were observed for the self-diffusion of both the polyions and the counterions. At polyion concentrations below 0.01 mol monomer kg-1, the dilute concentration regime for the polymer, the polyion self-diffusion coefficient approaches the self-diffusion coefficient of a freely diffusing rod upon dilution. At polyelectrolyte concentrations above 0.1 mol monomer kg-1, the self-diffusion coefficients of the solvent, the counterions and the polymer decreased with concentration, suggesting that this decrease is due to a topological constraint on the motions of the components. In the intermediate-concentration region, the self-diffusion coefficients of the polyions and the counterions are independent of the concentration. The polyion dynamic behaviour is, in the intermediate- and high-concentration regions, reasonably well described by that of a hard sphere, with a radius of 3.7 nm. A correct prediction for the solvent dynamics is given by the obstruction effect of this hard sphere on the solvent. The relative counterion self-diffusion coefficient is predicted almost quantitatively over the entire concentration range with the Poisson-Boltzmann-Smoluchowski model for the spherical cell, provided that the sphere radius and the number of charges are chosen appropriately (approximately the number of charges in a persistence length). Using this model, the dependence of the counterion self-diffusion coefficient on the ionic strength, polyion concentration and counterion radius is calculated quantitatively over a large concentration range.

  2. Viscoelastic behavior and microstructure of protein solutions

    Science.gov (United States)

    Twenty percent solutions of calcium caseinate (CC), egg albumin (EA), fish protein isolate (FPI), soy protein isolate (SPI), wheat gluten (WG), and whey protein isolate (WPI) were examined during heating by small amplitude oscillatory shear measurements, which provided an indication of protein behav...

  3. A Mesoscopic Model for Protein-Protein Interactions in Solution

    OpenAIRE

    Lund, Mikael; Jönsson, Bo

    2003-01-01

    Protein self-association may be detrimental in biological systems, but can be utilized in a controlled fashion for protein crystallization. It is hence of considerable interest to understand how factors like solution conditions prevent or promote aggregation. Here we present a computational model describing interactions between protein molecules in solution. The calculations are based on a molecular description capturing the detailed structure of the protein molecule using x-ray or nuclear ma...

  4. Transporter taxonomy - a comparison of different transport protein classification schemes.

    Science.gov (United States)

    Viereck, Michael; Gaulton, Anna; Digles, Daniela; Ecker, Gerhard F

    2014-06-01

    Currently, there are more than 800 well characterized human membrane transport proteins (including channels and transporters) and there are estimates that about 10% (approx. 2000) of all human genes are related to transport. Membrane transport proteins are of interest as potential drug targets, for drug delivery, and as a cause of side effects and drug–drug interactions. In light of the development of Open PHACTS, which provides an open pharmacological space, we analyzed selected membrane transport protein classification schemes (Transporter Classification Database, ChEMBL, IUPHAR/BPS Guide to Pharmacology, and Gene Ontology) for their ability to serve as a basis for pharmacology driven protein classification. A comparison of these membrane transport protein classification schemes by using a set of clinically relevant transporters as use-case reveals the strengths and weaknesses of the different taxonomy approaches.

  5. Prediction of protein loop geometries in solution

    NARCIS (Netherlands)

    Rapp, Chaya S.; Strauss, Temima; Nederveen, Aart; Fuentes, Gloria

    2007-01-01

    The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the ability to reproduce protein loop geometries in

  6. Electrolyte solution transport in electropolar nanotubes

    International Nuclear Information System (INIS)

    Zhao Jianbing; Culligan, Patricia J; Chen Xi; Qiao Yu; Zhou Qulan; Li Yibing; Tak, Moonho; Park, Taehyo

    2010-01-01

    Electrolyte transport in nanochannels plays an important role in a number of emerging areas. Using non-equilibrium molecular dynamics (NEMD) simulations, the fundamental transport behavior of an electrolyte/water solution in a confined model nanoenvironment is systematically investigated by varying the nanochannel dimension, solid phase, electrolyte phase, ion concentration and transport rate. It is found that the shear resistance encountered by the nanofluid strongly depends on these material/system parameters; furthermore, several effects are coupled. The mechanisms of the nanofluidic transport characteristics are explained by considering the unique molecular/ion structure formed inside the nanochannel. The lower shear resistance observed in some of the systems studies could be beneficial for nanoconductors, while the higher shear resistance (or higher effective viscosity) observed in other systems might enhance the performance of energy dissipation devices.

  7. In Vitro Analysis of Metabolite Transport Proteins.

    Science.gov (United States)

    Roell, Marc-Sven; Kuhnert, Franziska; Zamani-Nour, Shirin; Weber, Andreas P M

    2017-01-01

    The photorespiratory cycle is distributed over four cellular compartments, the chloroplast, peroxisomes, cytoplasm, and mitochondria. Shuttling of photorespiratory intermediates between these compartments is essential to maintain the function of photorespiration. Specific transport proteins mediate the transport across biological membranes and represent important components of the cellular metabolism. Although significant progress was made in the last years on identifying and characterizing new transport proteins, the overall picture of intracellular metabolite transporters is still rather incomplete. The photorespiratory cycle requires at least 25 transmembrane transport steps; however to date only plastidic glycolate/glycerate transporter and the accessory 2-oxoglutarate/malate and glutamate/malate transporters as well as the mitochondrial transporter BOU1 have been identified. The characterization of transport proteins and defining their substrates and kinetics are still major challenges.Here we present a detailed set of protocols for the in vitro characterization of transport proteins. We provide protocols for the isolation of recombinant transport protein expressed in E. coli or Saccharomyces cerevisiae and the extraction of total leaf membrane protein for in vitro analysis of transporter proteins. Further we explain the process of reconstituting transport proteins in artificial lipid vesicles and elucidate the details of transport assays.

  8. Reexamining ultrafiltration and solute transport in groundwater

    Science.gov (United States)

    Neuzil, C. E.; Person, Mark

    2017-06-01

    Geologic ultrafiltration—slowing of solutes with respect to flowing groundwater—poses a conundrum: it is consistently observed experimentally in clay-rich lithologies, but has been difficult to identify in subsurface data. Resolving this could be important for clarifying clay and shale transport properties at large scales as well as interpreting solute and isotope patterns for applications ranging from nuclear waste repository siting to understanding fluid transport in tectonically active environments. Simulations of one-dimensional NaCl transport across ultrafiltering clay membrane strata constrained by emerging data on geologic membrane properties showed different ultrafiltration effects than have often been envisioned. In relatively high-permeability advection-dominated regimes, salinity increases occurred mostly within membrane units while their effluent salinity initially fell and then rose to match solute delivery. In relatively low-permeability diffusion-dominated regimes, salinity peaked at the membrane upstream boundary and effluent salinity remained low. In both scenarios, however, only modest salinity changes (up to ˜3 g L-1) occurred because of self-limiting tendencies; membrane efficiency declines as salinity rises, and although sediment compaction increases efficiency, it is also decreases permeability and allows diffusive transport to dominate. It appears difficult for ultrafiltration to generate brines as speculated, but widespread and less extreme ultrafiltration effects in the subsurface could be unrecognized. Conditions needed for ultrafiltration are present in settings that include topographically-driven flow systems, confined aquifer systems subjected to injection or withdrawal, compacting basins, and accretionary complexes.

  9. Pathogen transport in groundwater systems: contrasts with traditional solute transport

    Science.gov (United States)

    Hunt, Randall J.; Johnson, William P.

    2017-06-01

    Water quality affects many aspects of water availability, from precluding use to societal perceptions of fit-for-purpose. Pathogen source and transport processes are drivers of water quality because they have been responsible for numerous outbreaks resulting in large economic losses due to illness and, in some cases, loss of life. Outbreaks result from very small exposure (e.g., less than 20 viruses) from very strong sources (e.g., trillions of viruses shed by a single infected individual). Thus, unlike solute contaminants, an acute exposure to a very small amount of contaminated water can cause immediate adverse health effects. Similarly, pathogens are larger than solutes. Thus, interactions with surfaces and settling become important even as processes important for solutes such as diffusion become less important. These differences are articulated in "Colloid Filtration Theory", a separate branch of pore-scale transport. Consequently, understanding pathogen processes requires changes in how groundwater systems are typically characterized, where the focus is on the leading edges of plumes and preferential flow paths, even if such features move only a very small fraction of the aquifer flow. Moreover, the relatively short survival times of pathogens in the subsurface require greater attention to very fast (solute transport mechanisms discussed here, a more encompassing view of water quality and source water protection is attained. With this more holistic view and theoretical understanding, better evaluations can be made regarding drinking water vulnerability and the relation between groundwater and human health.

  10. Exact solution of the neutron transport equation in spherical geometry

    Energy Technology Data Exchange (ETDEWEB)

    Anli, Fikret; Akkurt, Abdullah; Yildirim, Hueseyin; Ates, Kemal [Kahramanmaras Suetcue Imam Univ. (Turkey). Faculty of Sciences and Letters

    2017-03-15

    Solution of the neutron transport equation in one dimensional slab geometry construct a basis for the solution of neutron transport equation in a curvilinear geometry. Therefore, in this work, we attempt to derive an exact analytical benchmark solution for both neutron transport equations in slab and spherical medium by using P{sub N} approximation which is widely used in neutron transport theory.

  11. Heterochiral Knottin Protein: Folding and Solution Structure.

    Science.gov (United States)

    Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L

    2017-10-31

    Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.

  12. Reactive solute transport in acidic streams

    Science.gov (United States)

    Broshears, R.E.

    1996-01-01

    Spatial and temporal profiles of Ph and concentrations of toxic metals in streams affected by acid mine drainage are the result of the interplay of physical and biogeochemical processes. This paper describes a reactive solute transport model that provides a physically and thermodynamically quantitative interpretation of these profiles. The model combines a transport module that includes advection-dispersion and transient storage with a geochemical speciation module based on MINTEQA2. Input to the model includes stream hydrologic properties derived from tracer-dilution experiments, headwater and lateral inflow concentrations analyzed in field samples, and a thermodynamic database. Simulations reproduced the general features of steady-state patterns of observed pH and concentrations of aluminum and sulfate in St. Kevin Gulch, an acid mine drainage stream near Leadville, Colorado. These patterns were altered temporarily by injection of sodium carbonate into the stream. A transient simulation reproduced the observed effects of the base injection.

  13. Numerical solution of the radionuclide transport equation

    International Nuclear Information System (INIS)

    Hadermann, J.; Roesel, F.

    1983-11-01

    A numerical solution of the one-dimensional geospheric radionuclide chain transport equation based on the pseudospectral method is developed. The advantages of this approach are flexibility in incorporating space and time dependent migration parameters, arbitrary boundary conditions and solute rock interactions as well as efficiency and reliability. As an application the authors investigate the impact of non-linear sorption isotherms on migration in crystalline rock. It is shown that non-linear sorption, in the present case a Freundlich isotherm, may reduce concentration at the geosphere outlet by orders of magnitude provided the migration time is comparable or larger than the half-life of the nuclide in question. The importance of fixing dispersivity within the continuum approach is stressed. (Auth.)

  14. Coupled geochemical and solute transport code development

    International Nuclear Information System (INIS)

    Morrey, J.R.; Hostetler, C.J.

    1985-01-01

    A number of coupled geochemical hydrologic codes have been reported in the literature. Some of these codes have directly coupled the source-sink term to the solute transport equation. The current consensus seems to be that directly coupling hydrologic transport and chemical models through a series of interdependent differential equations is not feasible for multicomponent problems with complex geochemical processes (e.g., precipitation/dissolution reactions). A two-step process appears to be the required method of coupling codes for problems where a large suite of chemical reactions must be monitored. Two-step structure requires that the source-sink term in the transport equation is supplied by a geochemical code rather than by an analytical expression. We have developed a one-dimensional two-step coupled model designed to calculate relatively complex geochemical equilibria (CTM1D). Our geochemical module implements a Newton-Raphson algorithm to solve heterogeneous geochemical equilibria, involving up to 40 chemical components and 400 aqueous species. The geochemical module was designed to be efficient and compact. A revised version of the MINTEQ Code is used as a parent geochemical code

  15. Transport of reactive and nonreactive solutes

    International Nuclear Information System (INIS)

    Garabedian, S.P.; Leblanc, D.R.

    1990-01-01

    A natural-gradient tracer test was conducted on Cape Cod, Massachusetts, to examine the transport and dispersion of solutes in a sand and gravel aquifer. A nonreactive tracer, bromide, and two reactive tracers, lithium and molybdate, were injected as a pulse in July 1985 and monitored in three dimensions for 3 years as they moved 280 meters downgradient through an array of multilevel samplers. The tracer transport was quantified using spatial moments. The calculated total mass of bromide for each sampling date varied from 86 to 105 percent of the injected mass, and the center of mass moved at a nearly constant horizontal velocity of 0.42 meters per day. The bromide cloud also moved downward about 4 meters, probably because of density-induced sinking and accretion of areal recharge from precipitation. After 200 meters of transport, the bromide cloud was more than 80 meters long but only 14 meters wide and 6 meters thick. The change in longitudinal dispersivity had reached a constant value (0.96 meters). The transverse horizontal and transverse vertical dispersivities were much smaller (1.8 centimeters and 1.5 millimeters, respectively) than the longitudinal value. The lithium and molybdate clouds followed the same path as the bromide cloud, but a significant amount of their mass was adsorbed onto the aquifer sediments, and their rates of movement were retarded about 50 percent relative to the bromide movement. (Author) (5 figs., 23 refs.)

  16. Solution NMR structure determination of proteins revisited

    International Nuclear Information System (INIS)

    Billeter, Martin; Wagner, Gerhard; Wuethrich, Kurt

    2008-01-01

    This 'Perspective' bears on the present state of protein structure determination by NMR in solution. The focus is on a comparison of the infrastructure available for NMR structure determination when compared to protein crystal structure determination by X-ray diffraction. The main conclusion emerges that the unique potential of NMR to generate high resolution data also on dynamics, interactions and conformational equilibria has contributed to a lack of standard procedures for structure determination which would be readily amenable to improved efficiency by automation. To spark renewed discussion on the topic of NMR structure determination of proteins, procedural steps with high potential for improvement are identified

  17. Water Transport Mediated by Other Membrane Proteins.

    Science.gov (United States)

    Huang, Boyue; Wang, Hongkai; Yang, Baoxue

    2017-01-01

    Water transport through membrane is so intricate that there are still some debates. (Aquaporins) AQPs are entirely accepted to allow water transmembrane movement depending on osmotic gradient. Cotransporters and uniporters , however, are also concerned in water homeotatsis. Urea transporter B (UT-B) has a single-channel water permeability that is similar to AQP1. Cystic fibrosis transmembrane conductance regulator (CFTR ) was initially thought as a water channel but now not believed to transport water directly. By cotranporters, water is transported by water osmosis coupling with substrates, which explains how water is transported across the isolated small intestine. This chapter provides information about water transport mediated by other membrane proteins except AQPs .

  18. Functional analysis of candidate ABC transporter proteins for sitosterol transport

    DEFF Research Database (Denmark)

    Albrecht, C; Elliott, J I; Sardini, A

    2002-01-01

    implicated in lipid movement and expressed in tissues with a role in sterol synthesis and absorption, might also be involved in sitosterol transport. Transport by the multidrug resistance P-glycoprotein (P-gp; Abcb1), the multidrug resistance-associated protein (Mrp1; Abcc1), the breast cancer resistance...

  19. One-dimensional spatially dependent solute transport in semi ...

    African Journals Online (AJOL)

    Initially porous domain is considered solute free and the input source condition is ... parameters for description of solute transport in porous media. ... flow assuming uniform initial concentration with first and third type boundary conditions. Aral.

  20. EHD proteins: Key conductors of endocytic transport

    Science.gov (United States)

    Naslavsky, Naava; Caplan, Steve

    2010-01-01

    Regulation of endocytic transport is controlled by an elaborate network of proteins. Rab GTP-binding proteins and their effectors have well-defined roles in mediating specific endocytic transport steps, but until recently, less was known about the four mammalian dynamin-like C-terminal Eps15 Homology Domain (EHD) proteins that also regulate endocytic events. In recent years, however, great strides have been made in understanding the structure and function of these unique proteins. Indeed, a growing body of literature addresses EHD protein structure, interactions with binding partners, functions in mammalian cells, and the generation of various new model systems. Accordingly, this is now an opportune time to pause and review the function and mechanisms of action of EHD proteins, and to highlight some of the challenges and future directions for the field. PMID:21067929

  1. A quasilinear model for solute transport under unsaturated flow

    International Nuclear Information System (INIS)

    Houseworth, J.E.; Leem, J.

    2009-01-01

    We developed an analytical solution for solute transport under steady-state, two-dimensional, unsaturated flow and transport conditions for the investigation of high-level radioactive waste disposal. The two-dimensional, unsaturated flow problem is treated using the quasilinear flow method for a system with homogeneous material properties. Dispersion is modeled as isotropic and is proportional to the effective hydraulic conductivity. This leads to a quasilinear form for the transport problem in terms of a scalar potential that is analogous to the Kirchhoff potential for quasilinear flow. The solutions for both flow and transport scalar potentials take the form of Fourier series. The particular solution given here is for two sources of flow, with one source containing a dissolved solute. The solution method may easily be extended, however, for any combination of flow and solute sources under steady-state conditions. The analytical results for multidimensional solute transport problems, which previously could only be solved numerically, also offer an additional way to benchmark numerical solutions. An analytical solution for two-dimensional, steady-state solute transport under unsaturated flow conditions is presented. A specific case with two sources is solved but may be generalized to any combination of sources. The analytical results complement numerical solutions, which were previously required to solve this class of problems.

  2. Stochastic dynamics modeling solute transport in porous media modeling solute transport in porous media

    CERN Document Server

    Kulasiri, Don

    2002-01-01

    Most of the natural and biological phenomena such as solute transport in porous media exhibit variability which can not be modeled by using deterministic approaches. There is evidence in natural phenomena to suggest that some of the observations can not be explained by using the models which give deterministic solutions. Stochastic processes have a rich repository of objects which can be used to express the randomness inherent in the system and the evolution of the system over time. The attractiveness of the stochastic differential equations (SDE) and stochastic partial differential equations (SPDE) come from the fact that we can integrate the variability of the system along with the scientific knowledge pertaining to the system. One of the aims of this book is to explaim some useufl concepts in stochastic dynamics so that the scientists and engineers with a background in undergraduate differential calculus could appreciate the applicability and appropriateness of these developments in mathematics. The ideas ...

  3. Peritoneal Fluid Transport rather than Peritoneal Solute Transport Associates with Dialysis Vintage and Age of Peritoneal Dialysis Patients

    Directory of Open Access Journals (Sweden)

    Jacek Waniewski

    2016-01-01

    Full Text Available During peritoneal dialysis (PD, the peritoneal membrane undergoes ageing processes that affect its function. Here we analyzed associations of patient age and dialysis vintage with parameters of peritoneal transport of fluid and solutes, directly measured and estimated based on the pore model, for individual patients. Thirty-three patients (15 females; age 60 (21–87 years; median time on PD 19 (3–100 months underwent sequential peritoneal equilibration test. Dialysis vintage and patient age did not correlate. Estimation of parameters of the two-pore model of peritoneal transport was performed. The estimated fluid transport parameters, including hydraulic permeability (LpS, fraction of ultrasmall pores (αu, osmotic conductance for glucose (OCG, and peritoneal absorption, were generally independent of solute transport parameters (diffusive mass transport parameters. Fluid transport parameters correlated whereas transport parameters for small solutes and proteins did not correlate with dialysis vintage and patient age. Although LpS and OCG were lower for older patients and those with long dialysis vintage, αu was higher. Thus, fluid transport parameters—rather than solute transport parameters—are linked to dialysis vintage and patient age and should therefore be included when monitoring processes linked to ageing of the peritoneal membrane.

  4. Peritoneal Fluid Transport rather than Peritoneal Solute Transport Associates with Dialysis Vintage and Age of Peritoneal Dialysis Patients

    Science.gov (United States)

    Waniewski, Jacek; Antosiewicz, Stefan; Baczynski, Daniel; Poleszczuk, Jan; Pietribiasi, Mauro; Lindholm, Bengt; Wankowicz, Zofia

    2016-01-01

    During peritoneal dialysis (PD), the peritoneal membrane undergoes ageing processes that affect its function. Here we analyzed associations of patient age and dialysis vintage with parameters of peritoneal transport of fluid and solutes, directly measured and estimated based on the pore model, for individual patients. Thirty-three patients (15 females; age 60 (21–87) years; median time on PD 19 (3–100) months) underwent sequential peritoneal equilibration test. Dialysis vintage and patient age did not correlate. Estimation of parameters of the two-pore model of peritoneal transport was performed. The estimated fluid transport parameters, including hydraulic permeability (LpS), fraction of ultrasmall pores (α u), osmotic conductance for glucose (OCG), and peritoneal absorption, were generally independent of solute transport parameters (diffusive mass transport parameters). Fluid transport parameters correlated whereas transport parameters for small solutes and proteins did not correlate with dialysis vintage and patient age. Although LpS and OCG were lower for older patients and those with long dialysis vintage, αu was higher. Thus, fluid transport parameters—rather than solute transport parameters—are linked to dialysis vintage and patient age and should therefore be included when monitoring processes linked to ageing of the peritoneal membrane. PMID:26989432

  5. Transport of Liquid Phase Organic Solutes in Liquid Crystalline Membranes

    OpenAIRE

    Han, Sangil

    2010-01-01

    Porous cellulose nitrate membranes were impregnated with 8CB and PCH5 LCs (liquid crystals) and separations of solutes dissolved in aqueous phases were performed while monitoring solute concentration via UV-VIS spectrometry. The diffusing organic solutes, which consist of one aromatic ring and various functional groups, were selected to exclude molecular size effects on the diffusion and sorption. We studied the effects on solute transport of solute intra-molecular hydrogen bonding and so...

  6. Protein aggregation in aqueous casein solution

    International Nuclear Information System (INIS)

    Yousri, R.M.

    1980-01-01

    From the vast amount of research efforts dealing with various aspects of radiation effects on foods and food components (11, 18, 5, 12, 19, 8, 9, 6, 13, 15, 17, 20), it is apparent up to now that much remains to be studied in depth, much may have to be added or corrected about radiation-induced physico-chemical changes in foods. A great many reactions that take place when foodstuffs are subjected to ionizing radiation are still not fully understood. The better understanding of some of the radiation-induced changes in pure proteins as such or in mixture with other food constituents could yield much data which could be meaningfully extrapolated to intact foods and consequently could help to improve the assessment of the wholesomeness of irradiated foods. It was the purpose of our investigations to elucidate some of the changes in the chemical structure of a pure protein (casein), irradiated as such or which added carbohydrate and/or lipid. The effect of subsequent storage of the irradiated solutions has been also examined. The formation of protein aggregates was studied by gel filtration technique. The application of thin-layer gel filtration, its speed and adaptability to very small samples facilitated the measurements of the extent of aggregation which occurred in protein molecules after irradiation. (orig.) [de

  7. Modelling multicomponent solute transport in structured soils

    NARCIS (Netherlands)

    Beinum, van G.W.

    2007-01-01

    The mobility of contaminants in soil is an important factor in determining their ability to spread into the wider environment. For non-volatile substances, transport within the soil is generally dominated by transport of dissolved fractions in the soil water phase, via either diffusion or

  8. Transport proteins promoting Escherichia coli pathogenesis

    Science.gov (United States)

    Tang, Fengyi; Saier, Milton H.

    2014-01-01

    Escherichia coli is a genetically diverse species infecting hundreds of millions of people worldwide annually. We examined seven well-characterized E. coli pathogens causing urinary tract infections, gastroenteritis, pyelonephritis and haemorrhagic colitis. Their transport proteins were identified and compared with each other and a non-pathogenic E. coli K12 strain to identify transport proteins related to pathogenesis. Each pathogen possesses a unique set of protein secretion systems for export to the cell surface or for injecting effector proteins into host cells. Pathogens have increased numbers of iron siderophore receptors and ABC iron uptake transporters, but the numbers and types of low-affinity secondary iron carriers were uniform in all strains. The presence of outer membrane iron complex receptors and high-affinity ABC iron uptake systems correlated, suggesting co-evolution. Each pathovar encodes a different set of pore-forming toxins and virulence-related outer membrane proteins lacking in K12. Intracellular pathogens proved to have a characteristically distinctive set of nutrient uptake porters, different from those of extracellular pathogens. The results presented in this report provide information about transport systems relevant to various types of E. coli pathogenesis that can be exploited in future basic and applied studies. PMID:24747185

  9. Transport proteins promoting Escherichia coli pathogenesis.

    Science.gov (United States)

    Tang, Fengyi; Saier, Milton H

    2014-01-01

    Escherichia coli is a genetically diverse species infecting hundreds of millions of people worldwide annually. We examined seven well-characterized E. coli pathogens causing urinary tract infections, gastroenteritis, pyelonephritis and haemorrhagic colitis. Their transport proteins were identified and compared with each other and a non-pathogenic E. coli K12 strain to identify transport proteins related to pathogenesis. Each pathogen possesses a unique set of protein secretion systems for export to the cell surface or for injecting effector proteins into host cells. Pathogens have increased numbers of iron siderophore receptors and ABC iron uptake transporters, but the numbers and types of low-affinity secondary iron carriers were uniform in all strains. The presence of outer membrane iron complex receptors and high-affinity ABC iron uptake systems correlated, suggesting co-evolution. Each pathovar encodes a different set of pore-forming toxins and virulence-related outer membrane proteins lacking in K12. Intracellular pathogens proved to have a characteristically distinctive set of nutrient uptake porters, different from those of extracellular pathogens. The results presented in this report provide information about transport systems relevant to various types of E. coli pathogenesis that can be exploited in future basic and applied studies. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Semantic role labeling for protein transport predicates

    Directory of Open Access Journals (Sweden)

    Martin James H

    2008-06-01

    Full Text Available Abstract Background Automatic semantic role labeling (SRL is a natural language processing (NLP technique that maps sentences to semantic representations. This technique has been widely studied in the recent years, but mostly with data in newswire domains. Here, we report on a SRL model for identifying the semantic roles of biomedical predicates describing protein transport in GeneRIFs – manually curated sentences focusing on gene functions. To avoid the computational cost of syntactic parsing, and because the boundaries of our protein transport roles often did not match up with syntactic phrase boundaries, we approached this problem with a word-chunking paradigm and trained support vector machine classifiers to classify words as being at the beginning, inside or outside of a protein transport role. Results We collected a set of 837 GeneRIFs describing movements of proteins between cellular components, whose predicates were annotated for the semantic roles AGENT, PATIENT, ORIGIN and DESTINATION. We trained these models with the features of previous word-chunking models, features adapted from phrase-chunking models, and features derived from an analysis of our data. Our models were able to label protein transport semantic roles with 87.6% precision and 79.0% recall when using manually annotated protein boundaries, and 87.0% precision and 74.5% recall when using automatically identified ones. Conclusion We successfully adapted the word-chunking classification paradigm to semantic role labeling, applying it to a new domain with predicates completely absent from any previous studies. By combining the traditional word and phrasal role labeling features with biomedical features like protein boundaries and MEDPOST part of speech tags, we were able to address the challenges posed by the new domain data and subsequently build robust models that achieved F-measures as high as 83.1. This system for extracting protein transport information from Gene

  11. A Mathematical Model of Solute Coupled Water Transport in Toad Intestine Incorporating Recirculation of the Actively Transported Solute

    DEFF Research Database (Denmark)

    Larsen, Erik Hviid; Sørensen, Jakob Balslev; Sørensen, Jens Nørkær

    2000-01-01

    those of tight junction and interspace basement membrane by convection-diffusion. With solute permeability of paracellular pathway large relative to paracellular water flow, the paracellular flux ratio of the solute (influx/outflux) is small (2-4) in agreement with experiments. The virtual solute......A mathematical model of an absorbing leaky epithelium is developed for analysis of solute coupled water transport. The non-charged driving solute diffuses into cells and is pumped from cells into the lateral intercellular space (lis). All membranes contain water channels with the solute passing...... increases with hydraulic conductance of the pathway carrying water from mucosal solution into lis. Uphill water transport is accomplished, but with high hydraulic conductance of cell membranes strength of transport is obscured by water flow through cells. Anomalous solvent drag occurs when back flux...

  12. Complement Activation by Ceramide Transporter Proteins

    NARCIS (Netherlands)

    Bode, G.H.; Losen, M.; Buurman, W.A.; Veerhuis, R.; Molenaar, P.C.; Steinbusch, H.W.M.; De Baets, M.H.; Daha, MR; Martinez-Martinez, P.

    2014-01-01

    C1q is the initiator of the classical complement pathway and, as such, is essential for efficient opsonization and clearance of pathogens, altered self-structures, and apoptotic cells. The ceramide transporter protein (CERT) and its longer splicing isoform CERTL are known to interact with

  13. Transport of Organic Solutes in Clay Formations

    Science.gov (United States)

    The research is a pilot investigation for the SERDP (Strategic Environmental Research and Development Program, DoD) founded project, Impact of Clay-DNAPL Interactions on Transport and Storage of Chlorinated Solvents in Low Permeability Zones, from 2010-2012. The report tries to s...

  14. A variational solution of transport equation based on spherical geometry

    International Nuclear Information System (INIS)

    Liu Hui; Zhang Ben'ai

    2002-01-01

    A variational method with differential forms gives better precision for numerical solution of transport critical problem based on spherical geometry, and its computation seems simple than other approximate methods

  15. Redox activity distinguishes solid-state electron transport from solution-based electron transfer in a natural and artificial protein: cytochrome C and hemin-doped human serum albumin.

    Science.gov (United States)

    Amdursky, Nadav; Ferber, Doron; Pecht, Israel; Sheves, Mordechai; Cahen, David

    2013-10-28

    Integrating proteins in molecular electronic devices requires control over their solid-state electronic transport behavior. Unlike "traditional" electron transfer (ET) measurements of proteins that involve liquid environments and a redox cycle, no redox cofactor is needed for solid-state electron transport (ETp) across the protein. Here we show the fundamental difference between these two approaches by macroscopic area measurements, which allow measuring ETp temperature dependence down to cryogenic temperatures, via cytochrome C (Cyt C), an ET protein with a heme (Fe-porphyrin) prosthetic group as a redox centre. We compare the ETp to electrochemical ET measurements, and do so also for the protein without the Fe (with metal-free porphyrin) and without porphyrin. As removing the porphyrin irreversibly alters the protein's conformation, we repeat these measurements with human serum albumin (HSA), 'doped' (by non-covalent binding) with a single hemin equivalent, i.e., these natural and artificial proteins share a common prosthetic group. ETp via Cyt C and HSA-hemin are very similar in terms of current magnitude and temperature dependence, which suggests similar ETp mechanisms via these two systems, thermally activated hopping (with ~0.1 eV activation energy) >190 K and tunneling by superexchange Fe(3+) + e(-)), measured by electrochemistry of HSA-hemin are only 4 times lower than those for Cyt C. However, while removing the Fe redox centre from the porphyrin ring markedly affects the ET rate, it hardly changes the ETp currents through these proteins, while removing the macrocycle (from HSA, which retains its conformation) significantly reduces ETp efficiency. These results show that solid-state ETp across proteins does not require the presence of a redox cofactor, and that while for ET the Fe ion is the main electron mediator, for ETp the porphyrin ring has this function.

  16. Mathematical modeling of fluid and solute transport in peritoneal dialysis

    OpenAIRE

    Waniewski, Jacek

    2001-01-01

    Optimization of peritoneal dialysis schedule and dialysis fluid composition needs, among others, methods for quantitative assessment of fluid and solute transport. Furthermore, an integrative quantitative description of physiological processes within the tissue, which contribute to the net transfer of fluid and solutes, is necessary for interpretation of the data and for predictions of the outcome of possible intervention into the peritoneal transport system. The current pro...

  17. Soy-dairy protein blend and whey protein ingestion after resistance exercise increases amino acid transport and transporter expression in human skeletal muscle

    Science.gov (United States)

    Reidy, P. T.; Walker, D. K.; Dickinson, J. M.; Gundermann, D. M.; Drummond, M. J.; Timmerman, K. L.; Cope, M. B.; Mukherjea, R.; Jennings, K.; Volpi, E.

    2014-01-01

    Increasing amino acid availability (via infusion or ingestion) at rest or postexercise enhances amino acid transport into human skeletal muscle. It is unknown whether alterations in amino acid availability, from ingesting different dietary proteins, can enhance amino acid transport rates and amino acid transporter (AAT) mRNA expression. We hypothesized that the prolonged hyperaminoacidemia from ingesting a blend of proteins with different digestion rates postexercise would enhance amino acid transport into muscle and AAT expression compared with the ingestion of a rapidly digested protein. In a double-blind, randomized clinical trial, we studied 16 young adults at rest and after acute resistance exercise coupled with postexercise (1 h) ingestion of either a (soy-dairy) protein blend or whey protein. Phenylalanine net balance and transport rate into skeletal muscle were measured using stable isotopic methods in combination with femoral arteriovenous blood sampling and muscle biopsies obtained at rest and 3 and 5 h postexercise. Phenylalanine transport into muscle and mRNA expression of select AATs [system L amino acid transporter 1/solute-linked carrier (SLC) 7A5, CD98/SLC3A2, system A amino acid transporter 2/SLC38A2, proton-assisted amino acid transporter 1/SLC36A1, cationic amino acid transporter 1/SLC7A1] increased to a similar extent in both groups (P protein blend resulted in a prolonged and positive net phenylalanine balance during postexercise recovery compared with whey protein (P protein synthesis increased similarly between groups. We conclude that, while both protein sources enhanced postexercise AAT expression, transport into muscle, and myofibrillar protein synthesis, postexercise ingestion of a protein blend results in a slightly prolonged net amino acid balance across the leg compared with whey protein. PMID:24699854

  18. Mathematical modeling of solute transport in the subsurface

    International Nuclear Information System (INIS)

    Naymik, T.G.

    1987-01-01

    A review of key works on solute transport models indicates that solute transport processes with the exception of advection are still poorly understood. Solute transport models generally do a good job when they are used to test scientific concepts and hypotheses, investigate natural processes, systematically store and manage data, and simulate mass balance of solutes under certain natural conditions. Solute transport models generally are not good for predicting future conditions with a high degree of certainty, or for determining concentrations precisely. The mathematical treatment of solute transport far surpasses their understanding of the process. Investigations of the extent of groundwater contamination and methods to remedy existing problems show the along-term nature of the hazard. Industrial organic compounds may be immiscible in water, highly volatile, or complexed with inorganic as well as other organic compounds; many remain stable in nature almost indefinitely. In the worst case, future disposal of hazardous waste may be restricted to deep burial, as is proposed for radioactive wastes. For investigations pertinent to transport of radionuclides from a geologic repository, the process cannot be fully understood without adequate thermodynamic and kinetic data bases

  19. Solute transport across the articular surface of injured cartilage.

    Science.gov (United States)

    Chin, Hooi Chuan; Moeini, Mohammad; Quinn, Thomas M

    2013-07-15

    Solute transport through extracellular matrix (ECM) is important to physiology and contrast agent-based clinical imaging of articular cartilage. Mechanical injury is likely to have important effects on solute transport since it involves alteration of ECM structure. Therefore it is of interest to characterize effects of mechanical injury on solute transport in cartilage. Using cartilage explants injured by an established mechanical compression protocol, effective partition coefficients and diffusivities of solutes for transport across the articular surface were measured. A range of fluorescent solutes (fluorescein isothiocyanate, 4 and 40kDa dextrans, insulin, and chondroitin sulfate) and an X-ray contrast agent (sodium iodide) were used. Mechanical injury was associated with a significant increase in effective diffusivity versus uninjured explants for all solutes studied. On the other hand, mechanical injury had no effects on effective partition coefficients for most solutes tested, except for 40kDa dextran and chondroitin sulfate where small but significant changes in effective partition coefficient were observed in injured explants. Findings highlight enhanced diffusive transport across the articular surface of injured cartilage, which may have important implications for injury and repair situations. Results also support development of non-equilibrium methods for identification of focal cartilage lesions by contrast agent-based clinical imaging. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. dispersion equation parameters of solute transport in agricultural

    African Journals Online (AJOL)

    Jane

    2011-08-31

    Aug 31, 2011 ... fields for predicting soil quality property. Key words: ... The classical approach of modeling solute transport in porous media uses the deterministic ... concentration of the solution in the liquid phase, u0 is the mean velocity and ...

  1. Temporal moment analysis of solute transport in a coupled fracture ...

    Indian Academy of Sciences (India)

    by considering an inlet boundary condition of constant continuous source in a single fracture. The effect of various fracture-skin parameters like porosity, thickness and ... Study on fluid flow and transport of solute through fractures has been an .... of solutes is happening normal to the direction of flow due to the free molecular.

  2. Sustainable freight transport in South Africa:Domestic intermodal solutions

    Directory of Open Access Journals (Sweden)

    Jan H. Havenga

    2011-11-01

    Full Text Available Due to the rapid deregulation of freight transport in South Africa two decades ago, and low historical investment in rail (with resultant poor service delivery, an integrated alternative to road and rail competition was never developed. High national freight logistics costs, significant road infrastructure challenges and environmental impact concerns of a road-dominated freight transport market have, however, fuelled renewed interest in intermodal transport solutions. In this article, a high-level business case for domestic intermodal solutions in South Africa is presented. The results demonstrate that building three intermodal terminals to connect the three major industrial hubs (i.e. Gauteng, Durban and Cape Town through an intermodal solution could reduce transport costs (including externalities for the identified 11.5 million tons of intermodalfriendly freight flows on the Cape and Natal corridors by 42% (including externalities.

  3. Determination of chemical solute transport parameters effecting radiostrontium interbed sediments

    International Nuclear Information System (INIS)

    Hemming, C.; Bunde, R.L.; Rosentreter, J.J.

    1993-01-01

    The extent to which radionuclides migrate in an aquifer system is a function of various physical, chemical, and biological processes. A measure of this migration rate is of primary concern when locating suitable storage sites for such species. Parameters including water-rock interactions, infiltration rates, chemical phase modification, and biochemical reactions all affect solute transport. While these different types of chemical reactions can influence solute transport in subsurface waters, distribution coefficients (Kd) can be send to effectively summarize the net chemical factors which dictate transport efficiency. This coefficient describes the partitioning of the solute between the solution and solid phase. Methodology used in determining and interpreting the distribution coefficient for radiostrontium in well characterized sediments will be presented

  4. Static light scattering to characterize membrane proteins in detergent solution

    NARCIS (Netherlands)

    Slotboom, Dirk Jan; Duurkens, Ria H.; Olieman, Kees; Erkens, Guus B.

    2008-01-01

    Determination of the oligomeric state or the subunit stoichiometry of integral membrane proteins in detergent solution is notoriously difficult, because the amount of detergent (and lipid) associated with the proteins is usually not known. Only two classical methods (sedimentation equilibrium

  5. Studies of Protein Solution Properties Using Osmotic Pressure Measurements

    Science.gov (United States)

    Agena, S.; Bogle, David; Pusey, Marc; Agena, S.

    1998-01-01

    Examination of the protein crystallization process involves investigation of the liquid and solid state and a protein's properties in these states. Liquid state studies such as protein self association in solution by light scattering methods or other methods have been used to examine a protein Is properties and therefore its crystallization process and conditions. Likewise can osmotic pressure data be used to examine protein properties and various published osmotic pressure studies were examined by us to correlate osmotic pressure to protein solution properties. The solution behavior of serum albumin, alpha - chymotrypsin, beta - lactoglobulin and ovalbumin was examined over a range of temperatures, pH values and different salt types and concentrations. Using virial expansion and a local composition model the non ideal solution behavior in form of the activity coefficients (thermodynamic) was described for the systems. This protein activity coefficient data was related to a protein's solubility behavior and this process and the results will be presented.

  6. Semianalytical Solutions of Radioactive or Reactive Transport in Variably-Fractured Layered Media: 1. Solutes

    International Nuclear Information System (INIS)

    George J. Moridis

    2001-01-01

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive solute tracers through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the non-flowing matrix account for (a) diffusion, (b) surface diffusion, (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first-order chemical reactions. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of 3 H, 237 Np and 239 Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity

  7. End-Member Formulation of Solid Solutions and Reactive Transport

    Energy Technology Data Exchange (ETDEWEB)

    Lichtner, Peter C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-09-01

    A model for incorporating solid solutions into reactive transport equations is presented based on an end-member representation. Reactive transport equations are solved directly for the composition and bulk concentration of the solid solution. Reactions of a solid solution with an aqueous solution are formulated in terms of an overall stoichiometric reaction corresponding to a time-varying composition and exchange reactions, equivalent to reaction end-members. Reaction rates are treated kinetically using a transition state rate law for the overall reaction and a pseudo-kinetic rate law for exchange reactions. The composition of the solid solution at the onset of precipitation is assumed to correspond to the least soluble composition, equivalent to the composition at equilibrium. The stoichiometric saturation determines if the solid solution is super-saturated with respect to the aqueous solution. The method is implemented for a simple prototype batch reactor using Mathematica for a binary solid solution. Finally, the sensitivity of the results on the kinetic rate constant for a binary solid solution is investigated for reaction of an initially stoichiometric solid phase with an undersaturated aqueous solution.

  8. Coupling between solute transport and chemical reactions models

    International Nuclear Information System (INIS)

    Samper, J.; Ajora, C.

    1993-01-01

    During subsurface transport, reactive solutes are subject to a variety of hydrodynamic and chemical processes. The major hydrodynamic processes include advection and convection, dispersion and diffusion. The key chemical processes are complexation including hydrolysis and acid-base reactions, dissolution-precipitation, reduction-oxidation, adsorption and ion exchange. The combined effects of all these processes on solute transport must satisfy the principle of conservation of mass. The statement of conservation of mass for N mobile species leads to N partial differential equations. Traditional solute transport models often incorporate the effects of hydrodynamic processes rigorously but oversimplify chemical interactions among aqueous species. Sophisticated chemical equilibrium models, on the other hand, incorporate a variety of chemical processes but generally assume no-flow systems. In the past decade, coupled models accounting for complex hydrological and chemical processes, with varying degrees of sophistication, have been developed. The existing models of reactive transport employ two basic sets of equations. The transport of solutes is described by a set of partial differential equations, and the chemical processes, under the assumption of equilibrium, are described by a set of nonlinear algebraic equations. An important consideration in any approach is the choice of primary dependent variables. Most existing models cannot account for the complete set of chemical processes, cannot be easily extended to include mixed chemical equilibria and kinetics, and cannot handle practical two and three dimensional problems. The difficulties arise mainly from improper selection of the primary variables in the transport equations. (Author) 38 refs

  9. Fluid transport with time on peritoneal dialysis: the contribution of free water transport and solute coupled water transport

    NARCIS (Netherlands)

    Coester, Annemieke M.; Smit, Watske; Struijk, Dirk G.; Krediet, Raymond T.

    2009-01-01

    Ultrafiltration in peritoneal dialysis occurs through endothelial water channels (free water transport) and together with solutes across small pores: solute coupled water transport. A review is given of cross-sectional studies and on the results of longitudinal follow-up

  10. Modelling Transcapillary Transport of Fluid and Proteins in Hemodialysis Patients.

    Directory of Open Access Journals (Sweden)

    Mauro Pietribiasi

    Full Text Available The kinetics of protein transport to and from the vascular compartment play a major role in the determination of fluid balance and plasma refilling during hemodialysis (HD sessions. In this study we propose a whole-body mathematical model describing water and protein shifts across the capillary membrane during HD and compare its output to clinical data while evaluating the impact of choosing specific values for selected parameters.The model follows a two-compartment structure (vascular and interstitial space and is based on balance equations of protein mass and water volume in each compartment. The capillary membrane was described according to the three-pore theory. Two transport parameters, the fractional contribution of large pores (αLP and the total hydraulic conductivity (LpS of the capillary membrane, were estimated from patient data. Changes in the intensity and direction of individual fluid and solute flows through each part of the transport system were analyzed in relation to the choice of different values of small pores radius and fractional conductivity, lymphatic sensitivity to hydraulic pressure, and steady-state interstitial-to-plasma protein concentration ratio.The estimated values of LpS and αLP were respectively 10.0 ± 8.4 mL/min/mmHg (mean ± standard deviation and 0.062 ± 0.041. The model was able to predict with good accuracy the profiles of plasma volume and serum total protein concentration in most of the patients (average root-mean-square deviation < 2% of the measured value.The applied model provides a mechanistic interpretation of fluid transport processes induced by ultrafiltration during HD, using a minimum of tuned parameters and assumptions. The simulated values of individual flows through each kind of pore and lymphatic absorption rate yielded by the model may suggest answers to unsolved questions on the relative impact of these not-measurable quantities on total vascular refilling and fluid balance.

  11. Analytical solution to the hybrid diffusion-transport equation

    International Nuclear Information System (INIS)

    Nanneh, M.M.; Williams, M.M.R.

    1986-01-01

    A special integral equation was derived in previous work using a hybrid diffusion-transport theory method for calculating the flux distribution in slab lattices. In this paper an analytical solution of this equation has been carried out on a finite reactor lattice. The analytical results of disadvantage factors are shown to be accurate in comparison with the numerical results and accurate transport theory calculations. (author)

  12. Complement activation by ceramide transporter proteins.

    Science.gov (United States)

    Bode, Gerard H; Losen, Mario; Buurman, Wim A; Veerhuis, Robert; Molenaar, Peter C; Steinbusch, Harry W M; De Baets, Marc H; Daha, Mohamed R; Martinez-Martinez, Pilar

    2014-02-01

    C1q is the initiator of the classical complement pathway and, as such, is essential for efficient opsonization and clearance of pathogens, altered self-structures, and apoptotic cells. The ceramide transporter protein (CERT) and its longer splicing isoform CERTL are known to interact with extracellular matrix components, such as type IV collagen, and with the innate immune protein serum amyloid P. In this article, we report a novel function of CERT in the innate immune response. Both CERT isoforms, when immobilized, were found to bind the globular head region of C1q and to initiate the classical complement pathway, leading to activation of C4 and C3, as well as generation of the membrane attack complex C5b-9. In addition, C1q was shown to bind to endogenous CERTL on the surface of apoptotic cells. These results demonstrate the role of CERTs in innate immunity, especially in the clearance of apoptotic cells.

  13. Composite Transport Model and Water and Solute Transport across Plant Roots: An Update

    Directory of Open Access Journals (Sweden)

    Yangmin X. Kim

    2018-02-01

    Full Text Available The present review examines recent experimental findings in root transport phenomena in terms of the composite transport model (CTM. It has been a well-accepted conceptual model to explain the complex water and solute flows across the root that has been related to the composite anatomical structure. There are three parallel pathways involved in the transport of water and solutes in roots – apoplast, symplast, and transcellular paths. The role of aquaporins (AQPs, which facilitate water flows through the transcellular path, and root apoplast is examined in terms of the CTM. The contribution of the plasma membrane bound AQPs for the overall water transport in the whole plant level was varying depending on the plant species, age of roots with varying developmental stages of apoplastic barriers, and driving forces (hydrostatic vs. osmotic. Many studies have demonstrated that the apoplastic barriers, such as Casparian bands in the primary anticlinal walls and suberin lamellae in the secondary cell walls, in the endo- and exodermis are not perfect barriers and unable to completely block the transport of water and some solute transport into the stele. Recent research on water and solute transport of roots with and without exodermis triggered the importance of the extension of conventional CTM adding resistances that arrange in series (epidermis, exodermis, mid-cortex, endodermis, and pericycle. The extension of the model may answer current questions about the applicability of CTM for composite water and solute transport of roots that contain complex anatomical structures with heterogeneous cell layers.

  14. Composite Transport Model and Water and Solute Transport across Plant Roots: An Update.

    Science.gov (United States)

    Kim, Yangmin X; Ranathunge, Kosala; Lee, Seulbi; Lee, Yejin; Lee, Deogbae; Sung, Jwakyung

    2018-01-01

    The present review examines recent experimental findings in root transport phenomena in terms of the composite transport model (CTM). It has been a well-accepted conceptual model to explain the complex water and solute flows across the root that has been related to the composite anatomical structure. There are three parallel pathways involved in the transport of water and solutes in roots - apoplast, symplast, and transcellular paths. The role of aquaporins (AQPs), which facilitate water flows through the transcellular path, and root apoplast is examined in terms of the CTM. The contribution of the plasma membrane bound AQPs for the overall water transport in the whole plant level was varying depending on the plant species, age of roots with varying developmental stages of apoplastic barriers, and driving forces (hydrostatic vs. osmotic). Many studies have demonstrated that the apoplastic barriers, such as Casparian bands in the primary anticlinal walls and suberin lamellae in the secondary cell walls, in the endo- and exodermis are not perfect barriers and unable to completely block the transport of water and some solute transport into the stele. Recent research on water and solute transport of roots with and without exodermis triggered the importance of the extension of conventional CTM adding resistances that arrange in series (epidermis, exodermis, mid-cortex, endodermis, and pericycle). The extension of the model may answer current questions about the applicability of CTM for composite water and solute transport of roots that contain complex anatomical structures with heterogeneous cell layers.

  15. Nonrelativistic grey Sn-transport radiative-shock solutions

    International Nuclear Information System (INIS)

    Ferguson, J. M.; Morel, J. E.; Lowrie, R. B.

    2017-01-01

    We present semi-analytic radiative-shock solutions in which grey Sn-transport is used to model the radiation, and we include both constant cross sections and cross sections that depend on temperature and density. These new solutions solve for a variable Eddington factor (VEF) across the shock domain, which allows for interesting physics not seen before in radiative-shock solutions. Comparisons are made with the grey nonequilibrium-diffusion radiative-shock solutions of Lowrie and Edwards [1], which assumed that the Eddington factor is constant across the shock domain. It is our experience that the local Mach number is monotonic when producing nonequilibrium-diffusion solutions, but that this monotonicity may disappear while integrating the precursor region to produce Sn-transport solutions. For temperature- and density-dependent cross sections we show evidence of a spike in the VEF in the far upstream portion of the radiative-shock precursor. We show evidence of an adaptation zone in the precursor region, adjacent to the embedded hydrodynamic shock, as conjectured by Drake [2, 3], and also confirm his expectation that the precursor temperatures adjacent to the Zel’dovich spike take values that are greater than the downstream post-shock equilibrium temperature. We also show evidence that the radiation energy density can be nonmonotonic under the Zel’dovich spike, which is indicative of anti-diffusive radiation flow as predicted by McClarren and Drake [4]. We compare the angle dependence of the radiation flow for the Sn-transport and nonequilibriumdiffusion radiation solutions, and show that there are considerable differences in the radiation flow between these models across the shock structure. Lastly, we analyze the radiation flow to understand the cause of the adaptation zone, as well as the structure of the Sn-transport radiation-intensity solutions across the shock structure.

  16. New numerical method for solving the solute transport equation

    International Nuclear Information System (INIS)

    Ross, B.; Koplik, C.M.

    1978-01-01

    The solute transport equation can be solved numerically by approximating the water flow field by a network of stream tubes and using a Green's function solution within each stream tube. Compared to previous methods, this approach permits greater computational efficiency and easier representation of small discontinuities, and the results are easier to interpret physically. The method has been used to study hypothetical sites for disposal of high-level radioactive waste

  17. Efficient solution of a multi objective fuzzy transportation problem

    Science.gov (United States)

    Vidhya, V.; Ganesan, K.

    2018-04-01

    In this paper we present a methodology for the solution of multi-objective fuzzy transportation problem when all the cost and time coefficients are trapezoidal fuzzy numbers and the supply and demand are crisp numbers. Using a new fuzzy arithmetic on parametric form of trapezoidal fuzzy numbers and a new ranking method all efficient solutions are obtained. The proposed method is illustrated with an example.

  18. Stable solutions of nonlocal electron heat transport equations

    International Nuclear Information System (INIS)

    Prasad, M.K.; Kershaw, D.S.

    1991-01-01

    Electron heat transport equations with a nonlocal heat flux are in general ill-posed and intrinsically unstable, as proved by the present authors [Phys. Fluids B 1, 2430 (1989)]. A straightforward numerical solution of these equations will therefore lead to absurd results. It is shown here that by imposing a minimal set of constraints on the problem it is possible to arrive at a globally stable, consistent, and energy conserving numerical solution

  19. Peritoneal fluid transport in CAPD patients with different transport rates of small solutes.

    Science.gov (United States)

    Sobiecka, Danuta; Waniewski, Jacek; Weryński, Andrzej; Lindholm, Bengt

    2004-01-01

    Continuous ambulatory peritoneal dialysis (CAPD) patients with high peritoneal solute transport rate often have inadequate peritoneal fluid transport. It is not known whether this inadequate fluid transport is due solely to a too rapid fall of osmotic pressure, or if the decreased effectiveness of fluid transport is also a contributing factor. To analyze fluid transport parameters and the effectiveness of dialysis fluid osmotic pressure in the induction of fluid flow in CAPD patients with different small solute transport rates. 44 CAPD patients were placed in low (n = 6), low-average (n = 13), high-average (n = 19), and high (n = 6) transport groups according to a modified peritoneal equilibration test (PET). The study involved a 6-hour peritoneal dialysis dwell with 2 L 3.86% glucose dialysis fluid for each patient. Radioisotopically labeled serum albumin was added as a volume marker.The fluid transport parameters (osmotic conductance and fluid absorption rate) were estimated using three mathematical models of fluid transport: (1) Pyle model (model P), which describes ultrafiltration rate as an exponential function of time; (2) model OS, which is based on the linear relationship of ultrafiltration rate and overall osmolality gradient between dialysis fluid and blood; and (3) model G, which is based on the linear relationship between ultrafiltration rate and glucose concentration gradient between dialysis fluid and blood. Diffusive mass transport coefficients (K(BD)) for glucose, urea, creatinine, potassium, and sodium were estimated using the modified Babb-Randerson-Farrell model. The high transport group had significantly lower dialysate volume and glucose and osmolality gradients between dialysate and blood, but significantly higher K(BD) for small solutes compared with the other transport groups. Osmotic conductance, fluid absorption rate, and initial ultrafiltration rate did not differ among the transport groups for model OS and model P. Model G yielded

  20. Green transportation logistics: the quest for win-win solutions

    DEFF Research Database (Denmark)

    measures and speed and route optimization; Sulphur emissions; Lifecycle emissions; Green rail transportation; Green air transportation; Green inland navigation and possible areas for further research. Throughout, the book pursues the goal of “win-win” solutions and analyzes the phenomenon of “push......This book examines the state of the art in green transportation logistics from the perspective of balancing environmental performance in the transportation supply chain while also satisfying traditional economic performance criteria. Part of the book is drawn from the recently completed European...... Union project Super Green, a three-year project intended to promote the development of European freight corridors in an environmentally friendly manner. Additional chapters cover both the methodological base and the application context of green transportation logistics. Individual chapters look...

  1. Solute transport in aggregated and layered porous media

    International Nuclear Information System (INIS)

    Koch, S.

    1993-01-01

    This work is a contribution to research in soil physics dealing with solute transport in porous media. The influence of structural inhomogeneities on solute transport is investigated. Detailed experiments at the laboratory scale are used to enlighten distinct processes which cannot be studied separately at field scale. Two main aspects are followed up: (i) to show the influence of aggregation of a porous medium on breakthrough time and spreading of an inert tracer and consequences on the estimation of parameter values of models describing solute transport in aggregated systems, (ii) to investigate the influences on the dispersion process when stratification is perpendicular to the direction of flow. Several concepts of modelling solute transport in soil are discussed. Models based on the convection-dispersion equation (CDE) are emphasized because they are used here to model solute transport experiments conducted with aggregated porous media. Stochastic concepts are introduced to show the limitations of the deterministic CDE approaches. Experiments are done in columns containing two kinds of solid phases and were saturated with water. The solid phases are porous and solid glass beads exhibiting a distinctly unimodal or bimodal pore size distribution. Experimental breakthrough curves (BTCs) are modelled with the CDE, a bicontinuum model with a phenomenological mass transfer rate and a bicontinuum spherical diffusion model. Experiments are also done in columns that are unsaturated containing porous materials that are layered. Flow is made at a steady rate. It is shown that layer boundaries have a severe influence on lateral mixing. They may force streamlines to converge or cause a lateral redistribution of solutes. (author) figs., tabs., 122 refs

  2. Quantifying the relative contributions of different solute carriers to aggregate substrate transport

    Science.gov (United States)

    Taslimifar, Mehdi; Oparija, Lalita; Verrey, Francois; Kurtcuoglu, Vartan; Olgac, Ufuk; Makrides, Victoria

    2017-01-01

    Determining the contributions of different transporter species to overall cellular transport is fundamental for understanding the physiological regulation of solutes. We calculated the relative activities of Solute Carrier (SLC) transporters using the Michaelis-Menten equation and global fitting to estimate the normalized maximum transport rate for each transporter (Vmax). Data input were the normalized measured uptake of the essential neutral amino acid (AA) L-leucine (Leu) from concentration-dependence assays performed using Xenopus laevis oocytes. Our methodology was verified by calculating Leu and L-phenylalanine (Phe) data in the presence of competitive substrates and/or inhibitors. Among 9 potentially expressed endogenous X. laevis oocyte Leu transporter species, activities of only the uniporters SLC43A2/LAT4 (and/or SLC43A1/LAT3) and the sodium symporter SLC6A19/B0AT1 were required to account for total uptake. Furthermore, Leu and Phe uptake by heterologously expressed human SLC6A14/ATB0,+ and SLC43A2/LAT4 was accurately calculated. This versatile systems biology approach is useful for analyses where the kinetics of each active protein species can be represented by the Hill equation. Furthermore, its applicable even in the absence of protein expression data. It could potentially be applied, for example, to quantify drug transporter activities in target cells to improve specificity. PMID:28091567

  3. The future of public transport in light of solutions for sustainable transport development

    Directory of Open Access Journals (Sweden)

    Kazimierz LEJDA

    2017-06-01

    Full Text Available The paper highlights possible directions in the development of sustainable public transport solutions. When appropriately identified and implemented, such solutions can contribute to improved quality of urban life by reducing the adverse effects of transport on human health and the natural environment. The paper also raises questions about implementing pedestrian traffic zones, expanding the level of cycling, and introducing a workable parking policy, congestion charges, electromobility and intelligent systems for road traffic management in conurbations.

  4. Transport-constrained extensions of collision and track length estimators for solutions of radiative transport problems

    International Nuclear Information System (INIS)

    Kong, Rong; Spanier, Jerome

    2013-01-01

    In this paper we develop novel extensions of collision and track length estimators for the complete space-angle solutions of radiative transport problems. We derive the relevant equations, prove that our new estimators are unbiased, and compare their performance with that of more conventional estimators. Such comparisons based on numerical solutions of simple one dimensional slab problems indicate the the potential superiority of the new estimators for a wide variety of more general transport problems

  5. Scaling and predicting solute transport processes in streams

    Science.gov (United States)

    R. González-Pinzón; R. Haggerty; M. Dentz

    2013-01-01

    We investigated scaling of conservative solute transport using temporal moment analysis of 98 tracer experiments (384 breakthrough curves) conducted in 44 streams located on five continents. The experiments span 7 orders of magnitude in discharge (10-3 to 103 m3/s), span 5 orders of magnitude in...

  6. GRRR. The EXPECT groundwater model for transport of solutes

    NARCIS (Netherlands)

    Meijers R; Sauter FJ; Veling EJM; van Grinsven JJM; Leijnse A; Uffink GJM; MTV; CWM; LBG

    1994-01-01

    In this report the design and first test results are presented of the EXPECT groundwater module for transport of solutes GRRR (GRoundwater source Receptor Relationships). This model is one of the abiotic compartment modules of the EXPECT model. The EXPECT model is a tool for scenario development

  7. Solute transport modelling with the variable temporally dependent ...

    Indian Academy of Sciences (India)

    Pintu Das

    2018-02-07

    Feb 7, 2018 ... in a finite domain with time-dependent sources and dis- tance-dependent dispersivities. Also, existing ... solute transport in multi-layered porous media using gen- eralized integral transform technique with .... methods for solving the fractional reaction-–sub-diffusion equation. To solve numerically the Eqs.

  8. Chlorovirus-mediated membrane depolarization of Chlorella alters secondary active transport of solutes.

    Science.gov (United States)

    Agarkova, Irina; Dunigan, David; Gurnon, James; Greiner, Timo; Barres, Julia; Thiel, Gerhard; Van Etten, James L

    2008-12-01

    Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of a family of large, double-stranded DNA, plaque-forming viruses that infect certain eukaryotic chlorella-like green algae from the genus Chlorovirus. PBCV-1 infection results in rapid host membrane depolarization and potassium ion release. One interesting feature of certain chloroviruses is that they code for functional potassium ion-selective channel proteins (Kcv) that are considered responsible for the host membrane depolarization and, as a consequence, the efflux of potassium ions. This report examines the relationship between cellular depolarization and solute uptake. Annotation of the virus host Chlorella strain NC64A genome revealed 482 putative transporter-encoding genes; 224 are secondary active transporters. Solute uptake experiments using seven radioactive compounds revealed that virus infection alters the transport of all the solutes. However, the degree of inhibition varied depending on the solute. Experiments with nystatin, a drug known to depolarize cell membranes, produced changes in solute uptake that are similar but not identical to those that occurred during virus infection. Therefore, these studies indicate that chlorovirus infection causes a rapid and sustained depolarization of the host plasma membrane and that this depolarization leads to the inhibition of secondary active transporters that changes solute uptake.

  9. Solute transport on the sub 100 ms scale across the lipid bilayer membrane of individual proteoliposomes.

    Science.gov (United States)

    Ohlsson, Gabriel; Tabaei, Seyed R; Beech, Jason; Kvassman, Jan; Johanson, Urban; Kjellbom, Per; Tegenfeldt, Jonas O; Höök, Fredrik

    2012-11-21

    Screening assays designed to probe ligand and drug-candidate regulation of membrane proteins responsible for ion-translocation across the cell membrane are wide spread, while efficient means to screen membrane-protein facilitated transport of uncharged solutes are sparse. We report on a microfluidic-based system to monitor transport of uncharged solutes across the membrane of multiple (>100) individually resolved surface-immobilized liposomes. This was accomplished by rapidly switching (solution above dye-containing liposomes immobilized on the floor of a microfluidic channel. With liposomes encapsulating the pH-sensitive dye carboxyfluorescein (CF), internal changes in pH induced by transport of a weak acid (acetic acid) could be measured at time scales down to 25 ms. The applicability of the set up to study biological transport reactions was demonstrated by examining the osmotic water permeability of human aquaporin (AQP5) reconstituted in proteoliposomes. In this case, the rate of osmotic-induced volume changes of individual proteoliposomes was time resolved by imaging the self quenching of encapsulated calcein in response to an osmotic gradient. Single-liposome analysis of both pure and AQP5-containing liposomes revealed a relatively large heterogeneity in osmotic permeability. Still, in the case of AQP5-containing liposomes, the single liposome data suggest that the membrane-protein incorporation efficiency depends on liposome size, with higher incorporation efficiency for larger liposomes. The benefit of low sample consumption and automated liquid handling is discussed in terms of pharmaceutical screening applications.

  10. Win-Win transportation solutions price reforms with multiple benefits

    International Nuclear Information System (INIS)

    Litman, T.

    2001-01-01

    Reform strategies in the transportation market, such as the Win-Win Transportation Solutions, can provide several economic, social and environmental benefits. The strategies are cost effective, technically feasible reforms based on market principles which help create a more equitable and efficient transportation system that supports sustainable economic development. The benefits they provide include reduced traffic congestion, road and parking facility savings, consumer savings, equity, safety and environmental protection. They also increase economic productivity. If fully implemented, they could reduce motor vehicle impacts by 15 to 30 per cent and could help achieve the Kyoto emission reduction targets. Examples of Win-Win strategies at the federal level include: (1) removal of subsidies to oil production and internalized costs, and (2) tax exempt employer provided transfer benefits. Examples of Win-Win strategies at the state/provincial level include: (1) distance-based vehicle insurance and registration fees, (2) least-coast transportation planning and funding, (3) revenue-neutral tax shifting, (4) road pricing, (5) reform motor carrier regulations for competition and efficiency, (6) local and regional transportation demand management programs, (7) more efficient land use, (8) more flexible zoning requirements, (9) parking cash out, (10) transportation management associations, (11) location-efficient housing and mortgages, (12) school and campus trip management, (13) car sharing, (14) non-motorized transport improvements, and (15) traffic calming. It was noted that any market reform that leads to more efficient use of existing transportation systems can provide better economic development benefits. 9 refs., 1 tab., 1 fig

  11. Light-driven solute transport in Halobacterium halobium

    Science.gov (United States)

    Lanyi, J. K.

    1979-01-01

    The cell membrane of Halobacterium halobium exhibits differential regions which contain crystalline arrays of a single kind of protein, termed bacteriorhodopsin. This bacterial retinal-protein complex resembles the visual pigment and, after the absorption of protons, translocates H(+) across the cell membrane, leading to an electrochemical gradient for protons between the inside and the outside of the cell. Thus, light is an alternate source of energy in these bacteria, in addition to terminal oxidation. The paper deals with work on light-driven transport in H. halobium with cell envelope vesicles. The discussion covers light-driven movements of H(+), Na(+), and K(+); light-driven amino acid transport; and apparent allosteric control of amino acid transport. The scheme of energy coupling in H. halobium vesicles appears simple, its quantitative details are quite complex and reveal regulatory phenomena. More knowledge is required of the way the coupling components are regulated by the ion gradients present.

  12. Numerical solution of the transport equation describing the radon transport from subsurface soil to buildings

    International Nuclear Information System (INIS)

    Savovic, S.; Djordjevich, A.; Ristic, G.

    2012-01-01

    A theoretical evaluation of the properties and processes affecting the radon transport from subsurface soil into buildings is presented in this work. The solution of the relevant transport equation is obtained using the explicit finite difference method (EFDM). Results are compared with analytical steady-state solution reported in the literature. Good agreement is found. It is shown that EFDM is effective and accurate for solving the equation that describes radon diffusion, advection and decay during its transport from subsurface to buildings, which is especially important when arbitrary initial and boundary conditions are required. (authors)

  13. Transport of organic solutes through amorphous teflon AF films.

    Science.gov (United States)

    Zhao, Hong; Zhang, Jie; Wu, Nianqiang; Zhang, Xu; Crowley, Katie; Weber, Stephen G

    2005-11-02

    Fluorous media have great potential for selective extraction (e.g., as applied to organic synthesis). Fluorous polymer films would have significant advantages in fluorous separations. Stable films of Teflon AF 2400 were cast from solution. Films appear defect-free (SEM; AFM). Rigid aromatic solutes are transported (from chloroform solution to chloroform receiving phase) in a size-dependent manner (log permeability is proportional to -0.0067 times critical volume). Benzene's permeability is about 2 orders of magnitude higher than in comparable gas-phase experiments. The films show selectivity for fluorinated solutes in comparison to the hydrogen-containing control. Transport rates are dependent on the solvent making up the source and receiving phases. The effect of solvent is, interestingly, not due to changes in partition ratio, but rather it is due to changes in the solute diffusion coefficient in the film. Solvents plasticize the films. A less volatile compound, -COOH-terminated poly(hexafluoropropylene oxide) (4), plasticizes the films (T(g) = -40 degrees C). Permeabilities are decreased in comparison to 4-free films apparently because of decreased diffusivity of solutes. The slope of dependence of log permeability on critical volume is not changed, however.

  14. Solute transport model for radioisotopes in layered soil

    International Nuclear Information System (INIS)

    Essel, P.

    2010-01-01

    The study considered the transport of a radioactive solute in solution from the surface of the earth down through the soil to the ground water when there is an accidental or intentional spillage of a radioactive material on the surface. The finite difference method was used to model the spatial and temporal profile of moisture content in a soil column using the θ-based Richard's equation leading to solution of the convective-dispersive equation for non-adsorbing solutes numerically. A matlab code has been generated to predict the transport of the radioactive contaminant, spilled on the surface of a vertically heterogeneous soil made up of two layers to determine the residence time of the solute in the unsaturated zone, the time it takes the contaminant to reach the groundwater and the amount of the solute entering the groundwater in various times and the levels of pollution in those times. The model predicted that, then there is a spillage of 7.2g of tritium, on the surface of the ground at the study area, it will take two years for the radionuclide to enter the groundwater and fifteen years to totally leave the unsaturated zone. There is therefore the need to try as much as possible to avoid intentional or accidental spillage of the radionuclide since it has long term effect. (au)

  15. Simulation of transportation of low enriched uranium solutions

    International Nuclear Information System (INIS)

    Hope, E.P.; Ades, M.J.

    1996-01-01

    A simulation of the transportation by truck of low enriched uranium solutions has been completed for NEPA purposes at the Savannah River Site. The analysis involves three distinct source terms, and establishes the radiological risks of shipment to three possible destinations. Additionally, loading accidents were analyzed to determine the radiological consequences of mishaps during handling and delivery. Source terms were developed from laboratory measurements of chemical samples from low enriched uranium feed materials being stored at SRS facilities, and from manufacturer data on transport containers. The transportation simulations were accomplished over the INTERNET using the DOE TRANSNET system at Sandia National Laboratory. The HIGHWAY 3.3 code was used to analyze routing scenarios, and the RADTRAN 4 code was used to analyze incident free and accident risks of transporting radiological materials. Loading accidents were assessed using the Savannah River Site AXAIR89Q and RELEASE 2 codes

  16. The secret to successful solute-transport modeling

    Science.gov (United States)

    Konikow, Leonard F.

    2011-01-01

    Modeling subsurface solute transport is difficult—more so than modeling heads and flows. The classical governing equation does not always adequately represent what we see at the field scale. In such cases, commonly used numerical models are solving the wrong equation. Also, the transport equation is hyperbolic where advection is dominant, and parabolic where hydrodynamic dispersion is dominant. No single numerical method works well for all conditions, and for any given complex field problem, where seepage velocity is highly variable, no one method will be optimal everywhere. Although we normally expect a numerically accurate solution to the governing groundwater-flow equation, errors in concentrations from numerical dispersion and/or oscillations may be large in some cases. The accuracy and efficiency of the numerical solution to the solute-transport equation are more sensitive to the numerical method chosen than for typical groundwater-flow problems. However, numerical errors can be kept within acceptable limits if sufficient computational effort is expended. But impractically long

  17. Water and solute transport across the peritoneal membrane.

    Science.gov (United States)

    Morelle, Johann; Devuyst, Olivier

    2015-09-01

    We review the molecular mechanisms of peritoneal transport and discuss how a better understanding of these mechanisms is relevant for dialysis therapy. Peritoneal dialysis involves diffusion and osmosis through the highly vascularized peritoneal membrane. Computer simulations, expression studies and functional analyses in Aqp1 knockout mice demonstrated the critical role of the water channel aquaporin-1 (AQP1) in water removal during peritoneal dialysis. Pharmacologic regulation of AQP1, either through increased expression or gating, is associated with increased water transport in rodent models of peritoneal dialysis. Water transport is impaired during acute peritonitis, despite unchanged expression of AQP1, resulting from the increased microvascular area that dissipates the osmotic gradient across the membrane. In long-term peritoneal dialysis patients, the fibrotic interstitium also impairs water transport, resulting in ultrafiltration failure. Recent data suggest that stroke and drug intoxications might benefit from peritoneal dialysis and could represent novel applications of peritoneal transport in the future. A better understanding of the regulation of osmotic water transport across the peritoneum offers novel insights into the role of water channels in microvascular endothelia, the functional importance of structural changes in the peritoneal interstitium and the transport of water and solutes across biological membranes in general.

  18. Stochastic analysis of transport of conservative solutes in caisson experiments

    International Nuclear Information System (INIS)

    Dagan, G.

    1995-01-01

    The Los Alamos National Laboratory has conducted in the past a series of experiments of transport of conservative and reactive solutes. The experimental setup and the experimental results are presented in a series of reports. The main aim of the experiments was to validate models of transport of solutes in unsaturated flow at the caisson intermediate scale, which is much larger than the one pertaining to laboratory columns. First attempts to analyze the experimental results were by one-dimensional convective-dispersion models. These models could not explain the observed solute breakthrough curves and particularly the large solute dispersion in the caisson effluent Since there were some question marks about the uniformity of water distribution at the caisson top, the transport experiments were repeated under conditions of saturated flow. In these experiments constant heads were applied at the top and the bottom of the caisson and the number of concentration monitoring stations was quadrupled. The analysis of the measurements by the same one-dimensional model indicated clearly that the fitted dispersivity is much larger than the pore-sole dispersivity and that it grows with the distance in an approximately linear fashion. This led to the conclusion, raised before, that transport in the caisson is dominated by heterogeneity effects, i.e. by spatial variability of the material Such effects cannot be captured by traditional one-dimensional models. In order to account for the effect of heterogeneity, the saturated flow experiments have been analyzed by using stochastic transport modeling. The apparent linear growth of dispersivity with distance suggested that the system behaves like a stratified one. Consequently, the model of Dagan and Bresier has been adopted in order to interpret concentration measurements. In this simple model the caisson is viewed as a bundle of columns of different permeabilities, which are characterized by a p.d.f. (probability denasity function)

  19. Proteins mediating intra- and intercellular transport of lipids and lipid-modified proteins

    NARCIS (Netherlands)

    Neumann, S.

    2008-01-01

    Proteins mediating intra- and intercellular transport of lipids and lipid-modified proteins In this thesis, I studied the intra- and intercellular transport of lipidic molecules, in particular glycosphingolipids and lipid-modified proteins. The first part focuses on the intracellular transport of

  20. Solution of the transport equation with account for inelastic collisions

    International Nuclear Information System (INIS)

    Kalashnikov, N.P.; Remizovich, V.S.; Ryazanov, M.I.

    1980-01-01

    The theory of charged particle scattering in a matter with account for inelastic collisions is considered. In ''directly-forward'' approximation the transport equation at the absence of elastic collisions is obtained. The solution of the transport equation is made without and with account for fluctuation of energy losses. Formulas for path-energy relation are given. Energy spectrum and distribution of fast charged particles with respect to paths are studied. The problem of quantum mechanical approach to the theory of multiple scattering of fast charged particles in a matter is discussed briefly

  1. From analytical solutions of solute transport equations to multidimensional time-domain random walk (TDRW) algorithms

    Science.gov (United States)

    Bodin, Jacques

    2015-03-01

    In this study, new multi-dimensional time-domain random walk (TDRW) algorithms are derived from approximate one-dimensional (1-D), two-dimensional (2-D), and three-dimensional (3-D) analytical solutions of the advection-dispersion equation and from exact 1-D, 2-D, and 3-D analytical solutions of the pure-diffusion equation. These algorithms enable the calculation of both the time required for a particle to travel a specified distance in a homogeneous medium and the mass recovery at the observation point, which may be incomplete due to 2-D or 3-D transverse dispersion or diffusion. The method is extended to heterogeneous media, represented as a piecewise collection of homogeneous media. The particle motion is then decomposed along a series of intermediate checkpoints located on the medium interface boundaries. The accuracy of the multi-dimensional TDRW method is verified against (i) exact analytical solutions of solute transport in homogeneous media and (ii) finite-difference simulations in a synthetic 2-D heterogeneous medium of simple geometry. The results demonstrate that the method is ideally suited to purely diffusive transport and to advection-dispersion transport problems dominated by advection. Conversely, the method is not recommended for highly dispersive transport problems because the accuracy of the advection-dispersion TDRW algorithms degrades rapidly for a low Péclet number, consistent with the accuracy limit of the approximate analytical solutions. The proposed approach provides a unified methodology for deriving multi-dimensional time-domain particle equations and may be applicable to other mathematical transport models, provided that appropriate analytical solutions are available.

  2. Sn approach applied to the solution of transport equation

    International Nuclear Information System (INIS)

    Lopes, J.P.

    1973-09-01

    In this work the origin of the Transport Theory is considered and the Transport Equation for the movement of the neutron in a system is established in its more general form, using the laws of nuclear physics. This equation is used as the starting point for development, under adequate assumptions, of simpler models that render the problem suitable for numerical solution. Representation of this model in different geometries is presented. The different processes of nuclear physics are introduced briefly and discussed. In addition, the boundary conditions for the different cases and a general procedure for the application of the Conservation Law are stated. The last chapter deals specifically with the S n method, its development, definitions and generalities. Computational schemes for obtaining the S n solution in spherical and cylindrical geometry, and convergence acceleration methods are also developed. (author)

  3. Geological entropy and solute transport in heterogeneous porous media

    Science.gov (United States)

    Bianchi, Marco; Pedretti, Daniele

    2017-06-01

    We propose a novel approach to link solute transport behavior to the physical heterogeneity of the aquifer, which we fully characterize with two measurable parameters: the variance of the log K values (σY2), and a new indicator (HR) that integrates multiple properties of the K field into a global measure of spatial disorder or geological entropy. From the results of a detailed numerical experiment considering solute transport in K fields representing realistic distributions of hydrofacies in alluvial aquifers, we identify empirical relationship between the two parameters and the first three central moments of the distributions of arrival times of solute particles at a selected control plane. The analysis of experimental data indicates that the mean and the variance of the solutes arrival times tend to increase with spatial disorder (i.e., HR increasing), while highly skewed distributions are observed in more orderly structures (i.e., HR decreasing) or at higher σY2. We found that simple closed-form empirical expressions of the bivariate dependency of skewness on HR and σY2 can be used to predict the emergence of non-Fickian transport in K fields considering a range of structures and heterogeneity levels, some of which based on documented real aquifers. The accuracy of these predictions and in general the results from this study indicate that a description of the global variability and structure of the K field in terms of variance and geological entropy offers a valid and broadly applicable approach for the interpretation and prediction of transport in heterogeneous porous media.

  4. Predictability of solute transport in diffusion-controlled hydrogeologic regimes

    International Nuclear Information System (INIS)

    Gillham, R.W.; Cherry, J.A.

    1983-01-01

    Hydrogeologic regimes that are favourable for the subsurface management of low-level radioactive wastes must have transport properties that will limit the migration velocity of contaminants to some acceptably low value. Of equal importance, for the purpose of impact assessment and licensing, is the need to be able to predict, with a reasonable degree of certainty and over long time periods, what the migration velocity of the various contaminants of interest will be. This paper presents arguments to show that in addition to having favourable velocity characteristics, transport in saturated, diffusion-controlled hydrogeologic regimes is considerably more predictable than in the most common alternatives. The classical transport models for unsaturated, saturated-advection-controlled and saturated-diffusion-controlled environments are compared, with particular consideration being given to the difficulties associated with the characterization of the respective transport parameters. Results are presented which show that the diffusion of non-reactive solutes and solutes that react according to a constant partitioning ratio (K/sub d/) are highly predictable under laboratory conditions and that the diffusion coefficients for the reactive solutes can be determined with a reasonable degree of accuracy from independent measurements of bulk density, porosity, distribution coefficient and tortuosity. Field evidence is presented which shows that the distribution of environmental isotopes and chloride in thick clayey deposits is consistent with a diffusion-type transport process in these media. These results are particularly important in that they not only demonstrate the occurrence of diffusion-controlled hydrogeologic regimes, but they also demonstrate the predictability of the migration characteristics over very long time periods

  5. A three-dimensional neutron transport benchmark solution

    International Nuclear Information System (INIS)

    Ganapol, B.D.; Kornreich, D.E.

    1993-01-01

    For one-group neutron transport theory in one dimension, several powerful analytical techniques have been developed to solve the neutron transport equation, including Caseology, Wiener-Hopf factorization, and Fourier and Laplace transform methods. In addition, after a Fourier transform in the transverse plane and formulation of a pseudo problem, two-dimensional (2-D) and three-dimensional (3-D) problems can be solved using the techniques specifically developed for the one-dimensional (1-D) case. Numerical evaluation of the resulting expressions requiring an inversion in the transverse plane have been successful for 2-D problems but becomes exceedingly difficult in the 3-D case. In this paper, we show that by using the symmetry along the beam direction, a 2-D problem can be transformed into a 3-D problem in an infinite medium. The numerical solution to the 3-D problem is then demonstrated. Thus, a true 3-D transport benchmark solution can be obtained from a well-established numerical solution to a 2-D problem

  6. A stochastic solution of the advective transport equation with uncertainty

    International Nuclear Information System (INIS)

    Williams, M.M.R.

    1991-01-01

    A model has been developed for calculating the transport of water-borne radionuclides through layers of porous materials, such as rock or clay. The model is based upon a purely advective transport equation, in which the fluid velocity is a random variable, thereby simulating dispersion in a more realistic manner than the ad hoc introduction of a dispersivity. In addition to a random velocity field, which is an observable physical phenomenon, allowance is made for uncertainty in our knowledge of the parameters which enter the equation, e.g. the retardation coefficient. This too, is assumed to be a random variable and contributes to the stochasticity of the resulting partial differential equation of transport. The stochastic differential equation can be solved analytically and then ensemble averages taken over the associated probability distribution of velocity and retardation coefficient. A method based upon a novel form of the central limit theorem of statistics is employed to obtain tractable solutions of a system consisting of many serial legs of varying properties. One interesting conclusion is that the total flux out of a medium is significantly underestimated by using the deterministic solution with an average transit time compared with that from the stochastically averaged solution. The theory is illustrated numerically for a number of physically relevant cases. (author) 8 figs., 4 tabs., 7 refs

  7. Small angle X-ray scattering from protein in solution

    International Nuclear Information System (INIS)

    Souza, C.F. de; Torriani, I.L.

    1988-01-01

    In this work we report experiments performed with giant respiratory proteins from annelids. X-ray scattering data were obtained both by the use of conventional rotating anod source and synchotron radiation. Data from solutions with several protein concentrations were analyzed. (A.C.A.S.) [pt

  8. Globular conformation of some ribosomal proteins in solution

    International Nuclear Information System (INIS)

    Serdyuk, I.N.; Spirin, A.S.

    1978-01-01

    The possibility that such RNA-binding proteins of the 30 S subparticle as S4, S7, S8 and S16 exist in the form of compact globules in solution has been explored experimentally. These proteins have been studied in D 2 O solution by neutron scattering to measure their radii of gyration. This type of radiation using D 2 O as a solvent provides the maximum 'contrast', that is the maximum difference between the scattering of the protein and the solvent. It allowed measurements to be made using protein at <= 1.5 mg/ml. The radii of gyration for the ribosomal proteins S4, S7, S8 and S16 were found to be relatively small corresponding to the radii of gyration of compact globular proteins of the same molecular weights. (Auth.)

  9. System for sampling active solutions in transport container; Systeme de prelevements de solutions actives sur les recipients de transport

    Energy Technology Data Exchange (ETDEWEB)

    Fradin, J.

    1958-12-03

    This report presents a system aimed at sampling active solution from a specific transport container (SCRGR model) while transferring this solution with a maximum safety. The sampling principle is described (a flexible tube connected to the receiving container, with a needle at the other end which goes through a rubber membrane and enters a plunger tube). Its benefits are outlined (operator protection, reduction of contamination risk; only the rubber membrane is removed and replaced). Some manufacturing details are described concerning the membrane and the cover.

  10. Transcellular movement of hydroxyurea is mediated by specific solute carrier transporters

    Science.gov (United States)

    Walker, Aisha L.; Franke, Ryan M.; Sparreboom, Alex; Ware, Russell E.

    2015-01-01

    Objective Hydroxyurea has proven laboratory and clinical therapeutic benefits for sickle cell anemia (SCA) and other diseases, yet many questions remain regarding its in vivo pharmacokinetic and pharmacodynamic profiles. Previous reports suggest that hydroxyurea passively diffuses across cells, but its observed rapid absorption and distribution are more consistent with facilitated or active transport. We investigated the potential role of solute carrier (SLC) transporters in cellular uptake and accumulation of hydroxyurea. Materials and Methods Passive diffusion of hydroxyurea across cell membranes was determined using the parallel artificial membrane permeability assay. SLC transporter screens were conducted using in vitro intracellular drug accumulation and transcellular transport assays in cell lines and oocytes overexpressing SLC transporters. Gene expression of SLC transporters was measured by real-time PCR in human tissues and cell lines. Results Hydroxyurea had minimal diffusion across a lipid bilayer but was a substrate for 5 different SLC transporters belonging to the OCTN and OATP families of transporters and urea transporters A and B. Further characterization of hydroxyurea transport revealed that cellular uptake by OATP1B3 is time and temperature dependent and inhibited by known substrates of OATP1B3. Urea transporters A and B are expressed differentially in human tissues and erythroid cells, and transport hydroxyurea bidirectionally via facilitated diffusion. Conclusions These studies provide new insight into drug transport proteins that may be involved in the in vivo absorption, cellular distribution, and elimination of hydroxyurea. Elucidation of hydroxyurea transcellular movement should improve our understanding of its pharmacokinetics and pharmacodynamics, and may help explain some of the inter-patient drug variability observed in patients with SCA. PMID:21256917

  11. Anomalous Protein-Protein Interactions in Multivalent Salt Solution

    Czech Academy of Sciences Publication Activity Database

    Pasquier, C.; Vazdar, M.; Forsman, J.; Jungwirth, Pavel; Lund, M.

    2017-01-01

    Roč. 121, č. 14 (2017), s. 3000-3006 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GA16-01074S Institutional support: RVO:61388963 Keywords : Monte Carlo * molecular dynamics * membranes * proteins * multivalent salts Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 3.177, year: 2016

  12. Hydrophilic solute transport across the rat blood-brain barrier

    International Nuclear Information System (INIS)

    Lucchesi, K.J.

    1987-01-01

    Brain capillary permeability-surface area products (PS) of hydrophilic solutes ranging in size from 180 to 5,500 Daltons were measured in rats according to the method of Ohno, Pettigrew and Rapoport. The distribution volume of 70 KD dextran at 10 minutes after i.v. injection was also measured to determine the residual volume of blood in brain tissue at the time of sacrifice. Small test solutes were injected in pairs in order to elucidate whether their transfer into the brain proceeds by diffusion through water- or lipid-filled channels or by vesicular transport. This issue was examined in rats whose blood-brain barrier (BBB) was presumed to be intact (untreated) and in rats that received intracarotid infusions to open the BBB (isosmotic salt (ISS) and hyperosmolar arabinose). Ohno PS values of 3 H-inulin and 14 C-L-glucose in untreated rats were found to decrease as the labelling time was lengthened. This was evidence that a rapidly equilibrating compartment exists between blood and brain that renders the Ohno two-compartment model inadequate for computing true transfer rate constants. When the data were reanalyzed using a multi-compartment graphical analysis, solutes with different molecular radii were found to enter the brain at approximately equal rates. Furthermore, unidirectional transport is likely to be initiated by solute adsorption to a glycocalyx coat on the luminal surface of brain capillary endothelium. Apparently, more inulin than L-glucose was adsorbed, which may account for its slightly faster transfer across the BBB. After rats were treated with intracarotid infusions of ISS or hyperosmolar arabinose, solute PS values were significantly increased, but the ratio of PS for each of the solute pairs approached that of their free-diffusion coefficients

  13. Artificial membranes with selective nanochannels for protein transport

    KAUST Repository

    Sutisna, Burhannudin

    2016-09-05

    A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

  14. Artificial membranes with selective nanochannels for protein transport

    KAUST Repository

    Sutisna, Burhannudin; Polymeropoulos, Georgios; Mygiakis, E.; Musteata, Valentina-Elena; Peinemann, Klaus-Viktor; Smilgies, D. M.; Hadjichristidis, Nikolaos; Nunes, Suzana Pereira

    2016-01-01

    A poly(styrene-b-tert-butoxystyrene-b-styrene) copolymer was synthesized by anionic polymerization and hydrolyzed to poly(styrene-b-4-hydroxystyrene-b-styrene). Lamellar morphology was confirmed in the bulk after annealing. Membranes were fabricated by self-assembly of the hydrolyzed copolymer in solution, followed by water induced phase separation. A high density of pores of 4 to 5 nm diameter led to a water permeance of 40 L m−2 h−1 bar−1 and molecular weight cut-off around 8 kg mol−1. The morphology was controlled by tuning the polymer concentration, evaporation time, and the addition of imidazole and pyridine to stabilize the terpolymer micelles in the casting solution via hydrogen bond complexes. Transmission electron microscopy of the membrane cross-sections confirmed the formation of channels with hydroxyl groups beneficial for hydrogen-bond forming sites. The morphology evolution was investigated by time-resolved grazing incidence small angle X-ray scattering experiments. The membrane channels reject polyethylene glycol with a molecular size of 10 kg mol−1, but are permeable to proteins, such as lysozyme (14.3 kg mol−1) and cytochrome c (12.4 kg mol−1), due to the right balance of hydrogen bond interactions along the channels, electrostatic attraction, as well as the right pore sizes. Our results demonstrate that artificial channels can be designed for protein transport via block copolymer self-assembly using classical methods of membrane preparation.

  15. Assessment of applications of transport models on regional scale solute transport

    Science.gov (United States)

    Guo, Z.; Fogg, G. E.; Henri, C.; Pauloo, R.

    2017-12-01

    Regional scale transport models are needed to support the long-term evaluation of groundwater quality and to develop management strategies aiming to prevent serious groundwater degradation. The purpose of this study is to evaluate the capacity of previously-developed upscaling approaches to accurately describe main solute transport processes including the capture of late-time tails under changing boundary conditions. Advective-dispersive contaminant transport in a 3D heterogeneous domain was simulated and used as a reference solution. Equivalent transport under homogeneous flow conditions were then evaluated applying the Multi-Rate Mass Transfer (MRMT) model. The random walk particle tracking method was used for both heterogeneous and homogeneous-MRMT scenarios under steady state and transient conditions. The results indicate that the MRMT model can capture the tails satisfactorily for plume transported with ambient steady-state flow field. However, when boundary conditions change, the mass transfer model calibrated for transport under steady-state conditions cannot accurately reproduce the tailing effect observed for the heterogeneous scenario. The deteriorating impact of transient boundary conditions on the upscaled model is more significant for regions where flow fields are dramatically affected, highlighting the poor applicability of the MRMT approach for complex field settings. Accurately simulating mass in both mobile and immobile zones is critical to represent the transport process under transient flow conditions and will be the future focus of our study.

  16. Quantifying solute transport processes: are chemically "conservative" tracers electrically conservative?

    Science.gov (United States)

    Singha, Kamini; Li, Li; Day-Lewis, Frederick D.; Regberg, Aaron B.

    2012-01-01

    The concept of a nonreactive or conservative tracer, commonly invoked in investigations of solute transport, requires additional study in the context of electrical geophysical monitoring. Tracers that are commonly considered conservative may undergo reactive processes, such as ion exchange, thus changing the aqueous composition of the system. As a result, the measured electrical conductivity may reflect not only solute transport but also reactive processes. We have evaluated the impacts of ion exchange reactions, rate-limited mass transfer, and surface conduction on quantifying tracer mass, mean arrival time, and temporal variance in laboratory-scale column experiments. Numerical examples showed that (1) ion exchange can lead to resistivity-estimated tracer mass, velocity, and dispersivity that may be inaccurate; (2) mass transfer leads to an overestimate in the mobile tracer mass and an underestimate in velocity when using electrical methods; and (3) surface conductance does not notably affect estimated moments when high-concentration tracers are used, although this phenomenon may be important at low concentrations or in sediments with high and/or spatially variable cation-exchange capacity. In all cases, colocated groundwater concentration measurements are of high importance for interpreting geophysical data with respect to the controlling transport processes of interest.

  17. Monte Carlo methods for flux expansion solutions of transport problems

    International Nuclear Information System (INIS)

    Spanier, J.

    1999-01-01

    Adaptive Monte Carlo methods, based on the use of either correlated sampling or importance sampling, to obtain global solutions to certain transport problems have recently been described. The resulting learning algorithms are capable of achieving geometric convergence when applied to the estimation of a finite number of coefficients in a flux expansion representation of the global solution. However, because of the nonphysical nature of the random walk simulations needed to perform importance sampling, conventional transport estimators and source sampling techniques require modification to be used successfully in conjunction with such flux expansion methods. It is shown how these problems can be overcome. First, the traditional path length estimators in wide use in particle transport simulations are generalized to include rather general detector functions (which, in this application, are the individual basis functions chosen for the flus expansion). Second, it is shown how to sample from the signed probabilities that arise as source density functions in these applications, without destroying the zero variance property needed to ensure geometric convergence to zero error

  18. A Finite-Difference Solution of Solute Transport through a Membrane Bioreactor

    Directory of Open Access Journals (Sweden)

    B. Godongwana

    2015-01-01

    Full Text Available The current paper presents a theoretical analysis of the transport of solutes through a fixed-film membrane bioreactor (MBR, immobilised with an active biocatalyst. The dimensionless convection-diffusion equation with variable coefficients was solved analytically and numerically for concentration profiles of the solutes through the MBR. The analytical solution makes use of regular perturbation and accounts for radial convective flow as well as axial diffusion of the substrate species. The Michaelis-Menten (or Monod rate equation was assumed for the sink term, and the perturbation was extended up to second-order. In the analytical solution only the first-order limit of the Michaelis-Menten equation was considered; hence the linearized equation was solved. In the numerical solution, however, this restriction was lifted. The solution of the nonlinear, elliptic, partial differential equation was based on an implicit finite-difference method (FDM. An upwind scheme was employed for numerical stability. The resulting algebraic equations were solved simultaneously using the multivariate Newton-Raphson iteration method. The solution allows for the evaluation of the effect on the concentration profiles of (i the radial and axial convective velocity, (ii the convective mass transfer rates, (iii the reaction rates, (iv the fraction retentate, and (v the aspect ratio.

  19. A finite element model for protein transport in vivo

    Directory of Open Access Journals (Sweden)

    Montas Hubert J

    2007-06-01

    Full Text Available Abstract Background Biological mass transport processes determine the behavior and function of cells, regulate interactions between synthetic agents and recipient targets, and are key elements in the design and use of biosensors. Accurately predicting the outcomes of such processes is crucial to both enhancing our understanding of how these systems function, enabling the design of effective strategies to control their function, and verifying that engineered solutions perform according to plan. Methods A Galerkin-based finite element model was developed and implemented to solve a system of two coupled partial differential equations governing biomolecule transport and reaction in live cells. The simulator was coupled, in the framework of an inverse modeling strategy, with an optimization algorithm and an experimental time series, obtained by the Fluorescence Recovery after Photobleaching (FRAP technique, to estimate biomolecule mass transport and reaction rate parameters. In the inverse algorithm, an adaptive method was implemented to calculate sensitivity matrix. A multi-criteria termination rule was developed to stop the inverse code at the solution. The applicability of the model was illustrated by simulating the mobility and binding of GFP-tagged glucocorticoid receptor in the nucleoplasm of mouse adenocarcinoma. Results The numerical simulator shows excellent agreement with the analytic solutions and experimental FRAP data. Detailed residual analysis indicates that residuals have zero mean and constant variance and are normally distributed and uncorrelated. Therefore, the necessary and sufficient criteria for least square parameter optimization, which was used in this study, were met. Conclusion The developed strategy is an efficient approach to extract as much physiochemical information from the FRAP protocol as possible. Well-posedness analysis of the inverse problem, however, indicates that the FRAP protocol provides insufficient

  20. Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems.

    Science.gov (United States)

    Cheng, Chi-Yuan; Han, Songi

    2013-01-01

    Membrane proteins regulate vital cellular processes, including signaling, ion transport, and vesicular trafficking. Obtaining experimental access to their structures, conformational fluctuations, orientations, locations, and hydration in membrane environments, as well as the lipid membrane properties, is critical to understanding their functions. Dynamic nuclear polarization (DNP) of frozen solids can dramatically boost the sensitivity of current solid-state nuclear magnetic resonance tools to enhance access to membrane protein structures in native membrane environments. Overhauser DNP in the solution state can map out the local and site-specific hydration dynamics landscape of membrane proteins and lipid membranes, critically complementing the structural and dynamics information obtained by electron paramagnetic resonance spectroscopy. Here, we provide an overview of how DNP methods in solids and solutions can significantly increase our understanding of membrane protein structures, dynamics, functions, and hydration in complex biological membrane environments.

  1. Engineering solutions of traffic safety problems of road transport

    Directory of Open Access Journals (Sweden)

    M. Bogdevičius

    2004-02-01

    Full Text Available The authors of this paper focus on the simulation of the motor vehicle movement (taking into consideration motor vehicle dynamics, motor vehicle hydraulic brake system influence on motor vehicle movement, interaction between its wheels with road pavements, road guardrail characteristics, interaction between motor vehicle and road guardrail on a certain road section and propose their specific solution of this problem. The presented results, illustrating the motor vehicle movement trajectories (motor vehicle braking and interaction between motor vehicle and road guardrail at various initial conditions and at various certain pavement surface of the road section under investigation and work of a motor vehicle hydraulic brake system. Taking into consideration the presented general mathematical model and computer aided test results it is possible to investigate various road transport traffic situations as well as to investigate various transport traffic safety problems.

  2. Solute transport in fractured rock - applications to radionuclide waste repositories

    International Nuclear Information System (INIS)

    Neretnieks, I.

    1990-12-01

    Flow and solute transport in fractured rocks has been intensively studied in the last decade. The increased interest is mainly due to the plans in many countries to site repositories for high level nuclear waste in deep geologic formations. All investigated crystalline rocks have been found to be fractured and most of the water flows in the fractures and fracture zones. The water transports dissolved species and radionuclides. It is thus of interest to be able to understand and to do predictive modelling of the flowrate of water, the flowpaths and the residence times of the water and of the nuclides. The dissolved species including the nuclides will interact with the surrounding rock in different ways and will in many cases be strongly retarded relative to the water velocity. Ionic species may be ion exchanged or sorbed in the mineral surfaces. Charges and neutral species may diffuse into the stagnant waters in the rock matrix and thus be withdrawn from the mobile water. These effects will be strongly dependent on how much rock surface is in contact with the flowing water. It has been found in a set of field experiments and by other observations that not all fractures conduct water. Furthermore it is found that conductive fractures only conduct the water in a small part of the fracture in what is called channels or preferential flowpaths. This report summarizes the present concepts of water flow and solute transport in fractured rocks. The data needs for predictive modelling are discussed and both field and laboratory measurement which have been used to obtain data are described. Several large scale field experiments which have been specially designed to study flow and tracer transport in crystalline rocks are described. In many of the field experients new techniques have been developed and used. (81 refs.) (author)

  3. Soil properties and preferential solute transport at the field scale

    DEFF Research Database (Denmark)

    Koestel, J K; Minh, Luong Nhat; Nørgaard, Trine

    An important fraction of water flow and solute transport through soil takes place through preferential flow paths. Although this had been already observed in the nineteenth century, it had been forgotten by the scientific community until it was rediscovered during the 1970s. The awareness...... of the relevance of preferential flow was broadly re-established in the community by the early 1990s. However, since then, the notion remains widespread among soil scientists that the occurrence and strength of preferential flow cannot be predicted from measurable proxy variables such as soil properties or land...

  4. Solute carrier transporters: potential targets for digestive system neoplasms

    OpenAIRE

    Xie, Jing; Zhu, Xiao Yan; Liu, Lu Ming; Meng, Zhi Qiang

    2018-01-01

    Jing Xie,1,2 Xiao Yan Zhu,1,2 Lu Ming Liu,1,2 Zhi Qiang Meng1,2 1Department of Integrative Oncology, Fudan University Shanghai Cancer Center, 2Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, People’s Republic of China Abstract: Digestive system neoplasms are the leading causes of cancer-related death all over the world. Solute carrier (SLC) superfamily is composed of a series of transporters that are ubiquitously expressed in organs and tissues o...

  5. On the Solution of the Neutron Transport Equation

    Energy Technology Data Exchange (ETDEWEB)

    Depken, S

    1962-12-15

    The neutron transport equation has occupied the attention of many authors since Placzek, Wick and others made their first attempts to solve it, Even in the simple case of energy independent cross-sections, and disregarding the motion of the scattering nucleons, it is difficult to find a solution in an analytical form which is easily surveyable and fitted for numerical calculations. In Part I of this paper some new viewpoints will be introduced which enable the solution to be presented in its simplest possible form. Part II is devoted to an investigation of some functions introduced in Part I. In Part III the results are applied to the case of large energy lethargy, and the validity of derived formulas is discussed.

  6. Applications of stochastic models to solute transport in fractured rocks

    International Nuclear Information System (INIS)

    Gelhar, L.W.

    1987-01-01

    A stochastic theory for flow and solute transport in a single variable aperture fracture bounded by sorbing porous matrix into which solutes may diffuse, is developed using a perturbation approximation and spectral solution techniques which assume local statistical homogeneity. The theory predicts that the effective aperture of the fracture for mean solute displacement will be larger than the aperture required to calculate the large-scale flow resistance of the fracture. This ratio of apertures is a function of the variance of the logarithm of the apertures. The theory also predicts the macrodispersion coefficient for large-scale transport in the fracture. The resulting macrodispersivity is proportional to the variance of the logaperture and to its correlation scale. When variable surface sorption is included, it is found that the macrodispersivity is increased significantly, in some cases more than an order of magnitude. It is also shown that the effective retardation coefficient for the sorptively heterogeneous fracture is found by simply taking the arithmetic mean of the local surface sorption coefficient. Matrix diffusion is also shown to increase the fracture macrodispesivity at very large times. A reexamination of the results of four different field tracer tests in crystalline rock in Sweden and Canada shows aperture ratios and dispersivities that are consistent with the stochastic theory. The variance of the natural logarithm of the aperture is found to be in the range of 3 to 6 and the correlation scales for logaperture ranges from .2 to 1.2 meters. Detailed recommendations for additional field investigations at scales ranging from a few meters up to a kilometer are presented. (orig.)

  7. The Effects of Silk Protein Solution on Quality of Mangosteen

    International Nuclear Information System (INIS)

    Phadvibulya, Valailak; Sudatis, Boonya; Panyarum, Kanyarat; Junsaithong, Mayuree; Kerdchoechuen, Orapin

    2011-06-01

    Full text: Sericin silk protein solution prepared from irradiated silk waste was applied as a wax coating on mangosteen fruits but was found not appropriate. Nonetheless, when the solution was sprayed onto fruits from the setting stage till maturity, it enhanced the fruit quality. Fruits showed a bigger stalk and greener, thicker and larger-angled calyx than untreated ones. They were edible after being kept at 25 C for 3 to 4 weeks. Fruits sprayed with the silk protein solution and untreated fruits were separately harvested and packed for export. A half of them were irradiated with gamma radiation for insect eradication and then kept at 10 C with 80 percents relative humidity. The unirradiated half was stored similarly. Results showed that rind color of irradiated fruits changed slower than unirradiated ones. However, silk protein solution spraying and irradiation did not affect fruit firmness and total soluble solids of mangosteen flesh. For sensory evaluation, it was found that sprayed and irradiated fruits showed no differences from the untreated ones in their physical properties, color, taste and odor. Fruits sprayed with the silk protein solution without irradiation had the longest shelf life of 6 weeks

  8. The Effects of Silk Protein Solution on Quality of Mangosteen

    Energy Technology Data Exchange (ETDEWEB)

    Phadvibulya, Valailak; Sudatis, Boonya; Panyarum, Kanyarat; Junsaithong, Mayuree [Thailand Institute of Nuclear Technology, Nakhon Nayok, (Thailand); Kerdchoechuen, Orapin [School of Bioresources and Technology, King Mongkuts University, Bangkok (Thailand)

    2011-06-15

    Full text: Sericin silk protein solution prepared from irradiated silk waste was applied as a wax coating on mangosteen fruits but was found not appropriate. Nonetheless, when the solution was sprayed onto fruits from the setting stage till maturity, it enhanced the fruit quality. Fruits showed a bigger stalk and greener, thicker and larger-angled calyx than untreated ones. They were edible after being kept at 25{sup C} for 3 to 4 weeks. Fruits sprayed with the silk protein solution and untreated fruits were separately harvested and packed for export. A half of them were irradiated with gamma radiation for insect eradication and then kept at 10{sup C} with 80 percents relative humidity. The unirradiated half was stored similarly. Results showed that rind color of irradiated fruits changed slower than unirradiated ones. However, silk protein solution spraying and irradiation did not affect fruit firmness and total soluble solids of mangosteen flesh. For sensory evaluation, it was found that sprayed and irradiated fruits showed no differences from the untreated ones in their physical properties, color, taste and odor. Fruits sprayed with the silk protein solution without irradiation had the longest shelf life of 6 weeks.

  9. [Changes induced by hypertonic solutions in the transportation of calcium by the cardiac reticular sarcoplasma].

    Science.gov (United States)

    Sierra, M; Holguín, J A

    1979-01-01

    In the sarcoplasmic reticulum of the myocardium, celular organell which function is to regulate the cytoplasmic concentration of calcium in contraction and relaxation, we have studied the effect of hypertonic solutions of sucrose between 1 and 6.96 times the normal tonicity in order to observe the behavior of the internal linked or free calcium of this structure, as well as to prove the hypothesis that hypertonic solutions encourage the calcium exit of the sarcoplasmatic reticulum with the resulting signs of contractures. The following results were obtained: 1. The ATP hydrolisis and calcium transport rate are 14% and 90% respectively of the maximum speeds of 10(-5) M in calcium, while for concentrations of 10(-7) M or ess of the said cation, the transport rates and the ATPase do not reach 5% of the maximum values. 2. Between 1 and 2.54 times of the normal tonicity the calcium uptake remains between 400 and 500 nmoles of calcium/mg protein/min, the transported amount of calcium varies between 14 and 16 nmoles/mg protein and the rate of the ATP hydrolysis increases a 37% to 0.4 M in sucrose. 3. Between 0.4 and 1.2 M in sucrose of 2.54 to 6.96 times the isotonicity, the calcium transport rate velocity as well as the ATP hydrolisis are strongly inhibited. The vesicles volume minimizes and the amount of linked calcium remains within the control values, proving that the capacity of linking this cathion is independent from sarcoplasmic reticulum volume. These results show that the sarcoplasmic reticulum is involved in the contractures induced by hypertonic solutions in intact cells, since the osmolarity increase produces changes of volume which results in a decrease of the calcium transportation velocity or in an increase of the exit of said cathion.

  10. Solution structure and dynamics of melanoma inhibitory activity protein

    International Nuclear Information System (INIS)

    Lougheed, Julie C.; Domaille, Peter J.; Handel, Tracy M.

    2002-01-01

    Melanoma inhibitory activity (MIA) is a small secreted protein that is implicated in cartilage cell maintenance and melanoma metastasis. It is representative of a recently discovered family of proteins that contain a Src Homologous 3 (SH3) subdomain. While SH3 domains are normally found in intracellular proteins and mediate protein-protein interactions via recognition of polyproline helices, MIA is single-domain extracellular protein, and it probably binds to a different class of ligands.Here we report the assignments, solution structure, and dynamics of human MIA determined by heteronuclear NMR methods. The structures were calculated in a semi-automated manner without manual assignment of NOE crosspeaks, and have a backbone rmsd of 0.38 A over the ordered regions of the protein. The structure consists of an SH3-like subdomain with N- and C-terminal extensions of approximately 20 amino acids each that together form a novel fold. The rmsd between the solution structure and our recently reported crystal structure is 0.86 A over the ordered regions of the backbone, and the main differences are localized to the most dynamic regions of the protein. The similarity between the NMR and crystal structures supports the use of automated NOE assignments and ambiguous restraints to accelerate the calculation of NMR structures

  11. TRANSPORT OF SOLUTES IN THE FIELD AS AFFECTED BY IRRIGATION

    Directory of Open Access Journals (Sweden)

    Alessandro Comegna

    2007-09-01

    Full Text Available This study documents and compares the transport of a conservative solute in near saturated soil profiles under flood and sprinkler irrigation. The experiments were carried out on a clay Vertic-Usthortens soil located near Potenza (Italy. Two 2x2 m2 plots were clipped of their native grass vegetation. After spraying on the surface a Cl- pulse as KCl salt; water was applied in five increments over two months as flood irrigation on the first plot and as sprinkler irrigation on the second one. Chloride resident concentration Cr, was sampled by soil coring at four different days after chemical application. Cr(z,t profiles were analyzed by spatial moment method. The recovered mass of Cl- and location of center of mass were comparable for the two types of irrigation. The spread around the center of mass, however, was higher for the flood-irrigated plot. In the flood-irrigated plot, more mass leached below the depth of 90 cm. The velocity of the center of mass was consistently 10-20% larger than the piston displacement velocity. To evaluate the nature of transport, the Cr(z,t distributions were modelled using quasi-steady solution of convection-dispersion equation(CDE. At the scale of our experiments the profiles of Cl- resident concentration are well-simulated.

  12. Solution-blown nanofiber mats from fish sarcoplasmic protein

    DEFF Research Database (Denmark)

    Sett, S.; Boutrup Stephansen, Karen; Yarin, A.L.

    2016-01-01

    In the present work, solution-blowing was adopted to form nanofibers from fish sarcoplasmic proteins (FSPs). Nanofiber mats containing different weight ratios (up to 90/10) of FSP in the FSP/nylon 6 blended nanofibers were formed from formic acid solutions, and compared to electrospun fibers made...... that the production rate of solution-blowing was increased 30-fold in relation to electrospinning. Overall, this study reveals FSP as an interesting biopolymeric alternative to synthetic polymers, and the introduction of FSP to nylon 6 provides a composite with controlled properties....

  13. Analysis of solute transport in plants using positron emission tomography

    International Nuclear Information System (INIS)

    Partelova, D.

    2016-01-01

    In the first part of the work, geometrically and radiochemically characterized standards (phantoms) imitating the plant tissues and allowing the exact quantification of visualised radioindicator in plant tissues were designed and prepared within the study of visual and analytical characteristics of used positron emission tomograph (microPET system) commercially developed for animal objects at visualization of thin objects. Individual experiments carried out by exposure of excised leaves of tobacco (Nicotiana tabacum L.) or radish (Raphanus sativus L.) in solutions of 2-deoxy-2-fluoro-D-glucose labelled with positron emitter 18 F (2-[ 18 F]FDG) containing 10-, 100-, or 1000-times higher concentrations of D-glucose (c glu ) in comparison with the original 2-[ 18 F]FDG solution showed that the significant changes in visualisation of 2-[ 18 F]FDG distribution as well as in chemical portion of 2-[ 18 F]FDG within the leaf blade were observed as result of increased c glu . In the experiments with the whole plants of tobacco or radish exposed in 2-[ 18 F]FDG solution through the root system, only minimal translocation of 18 F radioactivity into the above-ground parts of plants, also in the case of increased c glu , was observed, which suggest the role of root system as a selective barrier of 2-[ 18 F]FDG transport from roots to the above-ground parts. On the basis of mentioned knowledge and analytical approaches (application of prepared phantoms), the dynamic study of 2-[ 18 F]FDG uptake and transport within the excised leaf of tobacco or whole radish plant was carried out. The description of these processes was realized through the 3D PET images and through the quantification of 2-[ 18 F]FDG distribution within the chosen regions of interest from the point of view of accumulated 18 F radioactivity (in Bq) or amount of D-glucose (in μg) as well. Application of methods of multivariate analysis allows to found the similarities between studied objects mainly from the point

  14. Transport Visualization for Studying Mass Transfer and Solute Transport in Permeable Media

    International Nuclear Information System (INIS)

    Roy Haggerty

    2004-01-01

    Understanding and predicting mass transfer coupled with solute transport in permeable media is central to several energy-related programs at the US Department of Energy (e.g., CO 2 sequestration, nuclear waste disposal, hydrocarbon extraction, and groundwater remediation). Mass transfer is the set of processes that control movement of a chemical between mobile (advection-dominated) domains and immobile (diffusion- or sorption-dominated) domains within a permeable medium. Consequences of mass transfer on solute transport are numerous and may include (1) increased sequestration time within geologic formations; (2) reduction in average solute transport velocity by as much as several orders of magnitude; (3) long ''tails'' in concentration histories during removal of a solute from a permeable medium; (4) poor predictions of solute behavior over long time scales; and (5) changes in reaction rates due to mass transfer influences on pore-scale mixing of solutes. Our work produced four principle contributions: (1) the first comprehensive visualization of solute transport and mass transfer in heterogeneous porous media; (2) the beginnings of a theoretical framework that encompasses both macrodispersion and mass transfer within a single set of equations; (3) experimental and analytical tools necessary for understanding mixing and aqueous reaction in heterogeneous, granular porous media; (4) a clear experimental demonstration that reactive transport is often not accurately described by a simple coupling of the convection-dispersion equation with chemical reaction equations. The work shows that solute transport in heterogeneous media can be divided into 3 regimes--macrodispersion, advective mass transfer, and diffusive mass transfer--and that these regimes can be predicted quantitatively in binary media. We successfully predicted mass transfer in each of these regimes and verified the prediction by completing quantitative visualization experiments in each of the regimes, the

  15. Tunneling explains efficient electron transport via protein junctions.

    Science.gov (United States)

    Fereiro, Jerry A; Yu, Xi; Pecht, Israel; Sheves, Mordechai; Cuevas, Juan Carlos; Cahen, David

    2018-05-15

    Metalloproteins, proteins containing a transition metal ion cofactor, are electron transfer agents that perform key functions in cells. Inspired by this fact, electron transport across these proteins has been widely studied in solid-state settings, triggering the interest in examining potential use of proteins as building blocks in bioelectronic devices. Here, we report results of low-temperature (10 K) electron transport measurements via monolayer junctions based on the blue copper protein azurin (Az), which strongly suggest quantum tunneling of electrons as the dominant charge transport mechanism. Specifically, we show that, weakening the protein-electrode coupling by introducing a spacer, one can switch the electron transport from off-resonant to resonant tunneling. This is a consequence of reducing the electrode's perturbation of the Cu(II)-localized electronic state, a pattern that has not been observed before in protein-based junctions. Moreover, we identify vibronic features of the Cu(II) coordination sphere in transport characteristics that show directly the active role of the metal ion in resonance tunneling. Our results illustrate how quantum mechanical effects may dominate electron transport via protein-based junctions.

  16. Solutions to Improve Person Transport System in the Pitesti City by Analyzing Public Transport vs. Private Transport

    Science.gov (United States)

    Mihaela, Istrate; Alexandru, Boroiu; Viorel, Nicolae; Ionel, Vieru

    2017-10-01

    One of the major problems facing the Pitesti city is the road congestion that occurs in the central area of the city during the peak hours. With all the measures taken in recent years - the widening of road arteries, increasing the number of parking spaces, the creation of overground road passages - it is obvious that the problem can only be solved by a new philosophy regarding urban mobility: it is no longer possible to continue through solutions to increase the accessibility of the central area of the city, but it is necessary, on the contrary, to promote a policy of discouraging the penetration of vehicles in the city center, coupled with a policy of improving the connection between urban public transport and county public transport. This new approach is also proposed in the new Urban Mobility Plan of Pitesti city, under development. The most convincing argument for the necessity of this new orientation in the Pitesti city mobility plan is based on the analysis of the current situation of passenger transport on the territory of Pitesti city: the analysis of “public transport versus private transport” reveals a very low occupancy rate for cars and the fact that the road surface required for a passenger (the dynamic area) is much higher in the case of private transport than in the case of public transport. Measurements of passenger flows and vehicle flows on the 6 penetration ways in the city have been made and the calculations clearly demonstrate the benefits of an urban public transport system connected by “transshipment buses” to be made at the edge of the city, to the county public transport system. In terms of inter-county transport, it will continue to be connected to the urban public transport system by existing bus Station, within the city: South Bus Station and North Bus Station. The usefulness of the paper is that it identifies the solutions for sustainable mobility in Pitesti city and proposes concrete solutions for the development of the

  17. Approximate solutions for the two-dimensional integral transport equation. Solution of complex two-dimensional transport problems

    International Nuclear Information System (INIS)

    Sanchez, Richard.

    1980-11-01

    This work is divided into two parts: the first part deals with the solution of complex two-dimensional transport problems, the second one (note CEA-N-2166) treats the critically mixed methods of resolution. A set of approximate solutions for the isotropic two-dimensional neutron transport problem has been developed using the interface current formalism. The method has been applied to regular lattices of rectangular cells containing a fuel pin, cladding, and water, or homogenized structural material. The cells are divided into zones that are homogeneous. A zone-wise flux expansion is used to formulate a direct collision probability problem within a cell. The coupling of the cells is effected by making extra assumptions on the currents entering and leaving the interfaces. Two codes have been written: CALLIOPE uses a cylindrical cell model and one or three terms for the flux expansion, and NAUSICAA uses a two-dimensional flux representation and does a truly two-dimensional calculation inside each cell. In both codes, one or three terms can be used to make a space-independent expansion of the angular fluxes entering and leaving each side of the cell. The accuracies and computing times achieved with the different approximations are illustrated by numerical studies on two benchmark problems and by calculations performed in the APOLLO multigroup code [fr

  18. Molecular cell biology and physiology of solute transport

    Science.gov (United States)

    Caplan, Michael J.; Seo-Mayer, Patricia; Zhang, Li

    2010-01-01

    Purpose of review An enormous body of research has been focused on exploring the mechanisms through which epithelial cells establish their characteristic polarity. It is clear that under normal circumstances cell–cell contacts mediated by the calcium-dependent adhesion proteins of the intercellular adhesion junctions are required to initiate complete polarization. Furthermore, formation of the tight, or occluding, junctions that limit paracellular permeability has long been thought to help to establish polarity by preventing the diffusion of membrane proteins between the two plasmalemmal domains. This review will discuss several selected kinases and protein complexes and highlight their relevance to transporting epithelial cell polarization. Recent findings Recent work has shed new light on the roles of junctional complexes in establishing and maintaining epithelial cell polarity. In addition, work from several laboratories, suggests that the formation of these junctions is tied to processes that regulate cellular energy metabolism. Summary Junctional complexes and energy sensing kinases constitute a novel class of machinery whose capacity to generate and modulate epithelial cell polarity is likely to have wide ranging and important physiological ramifications. PMID:18695392

  19. Characterization of a novel organic solute transporter homologue from Clonorchis sinensis.

    Directory of Open Access Journals (Sweden)

    Yanyan Lu

    2018-04-01

    Full Text Available Clonorchis sinensis is a liver fluke that can dwell in the bile ducts of mammals. Bile acid transporters function to maintain the homeostasis of bile acids in C. sinensis, as they induce physiological changes or have harmful effects on C. sinensis survival. The organic solute transporter (OST transports mainly bile acid and belongs to the SLC51 subfamily of solute carrier transporters. OST plays a critical role in the recirculation of bile acids in higher animals. In this study, we cloned full-length cDNA of the 480-amino acid OST from C. sinensis (CsOST. Genomic analysis revealed 11 exons and nine introns. The CsOST protein had a 'Solute_trans_a' domain with 67% homology to Schistosoma japonicum OST. For further analysis, the CsOST protein sequence was split into the ordered domain (CsOST-N at the N-terminus and disordered domain (CsOST-C at the C-terminus. The tertiary structure of each domain was built using a threading-based method and determined by manual comparison. In a phylogenetic tree, the CsOST-N domain belonged to the OSTα and CsOST-C to the OSTβ clade. These two domains were more highly conserved with the OST α- and β-subunits at the structure level than at sequence level. These findings suggested that CsOST comprised the OST α- and β-subunits. CsOST was localized in the oral and ventral suckers and in the mesenchymal tissues abundant around the intestine, vitelline glands, uterus, and testes. This study provides fundamental data for the further understanding of homologues in other flukes.

  20. Characterization of a novel organic solute transporter homologue from Clonorchis sinensis

    Science.gov (United States)

    Dai, Fuhong; Lee, Ji-Yun; Pak, Jhang Ho; Sohn, Woon-Mok

    2018-01-01

    Clonorchis sinensis is a liver fluke that can dwell in the bile ducts of mammals. Bile acid transporters function to maintain the homeostasis of bile acids in C. sinensis, as they induce physiological changes or have harmful effects on C. sinensis survival. The organic solute transporter (OST) transports mainly bile acid and belongs to the SLC51 subfamily of solute carrier transporters. OST plays a critical role in the recirculation of bile acids in higher animals. In this study, we cloned full-length cDNA of the 480-amino acid OST from C. sinensis (CsOST). Genomic analysis revealed 11 exons and nine introns. The CsOST protein had a ‘Solute_trans_a’ domain with 67% homology to Schistosoma japonicum OST. For further analysis, the CsOST protein sequence was split into the ordered domain (CsOST-N) at the N-terminus and disordered domain (CsOST-C) at the C-terminus. The tertiary structure of each domain was built using a threading-based method and determined by manual comparison. In a phylogenetic tree, the CsOST-N domain belonged to the OSTα and CsOST-C to the OSTβ clade. These two domains were more highly conserved with the OST α- and β-subunits at the structure level than at sequence level. These findings suggested that CsOST comprised the OST α- and β-subunits. CsOST was localized in the oral and ventral suckers and in the mesenchymal tissues abundant around the intestine, vitelline glands, uterus, and testes. This study provides fundamental data for the further understanding of homologues in other flukes. PMID:29702646

  1. Fast Proton Titration Scheme for Multiscale Modeling of Protein Solutions.

    Science.gov (United States)

    Teixeira, Andre Azevedo Reis; Lund, Mikael; da Silva, Fernando Luís Barroso

    2010-10-12

    Proton exchange between titratable amino acid residues and the surrounding solution gives rise to exciting electric processes in proteins. We present a proton titration scheme for studying acid-base equilibria in Metropolis Monte Carlo simulations where salt is treated at the Debye-Hückel level. The method, rooted in the Kirkwood model of impenetrable spheres, is applied on the three milk proteins α-lactalbumin, β-lactoglobulin, and lactoferrin, for which we investigate the net-charge, molecular dipole moment, and charge capacitance. Over a wide range of pH and salt conditions, excellent agreement is found with more elaborate simulations where salt is explicitly included. The implicit salt scheme is orders of magnitude faster than the explicit analog and allows for transparent interpretation of physical mechanisms. It is shown how the method can be expanded to multiscale modeling of aqueous salt solutions of many biomolecules with nonstatic charge distributions. Important examples are protein-protein aggregation, protein-polyelectrolyte complexation, and protein-membrane association.

  2. Solution structure of the human signaling protein RACK1

    Directory of Open Access Journals (Sweden)

    Papa Priscila F

    2010-06-01

    Full Text Available Abstract Background The adaptor protein RACK1 (receptor of activated kinase 1 was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki-1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413 follows a stoichiometry of 1:1. The binding constant (KB observed for RACK1-Ki-1/57(122-413 interaction was of around (1.5 ± 0.2 × 106 M-1 and resulted in a dissociation constant (KD of (0.7 ± 0.1 × 10-6 M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413 interact strongly under the tested conditions.

  3. Multigroup adjoint transport solution using the method of cyclic characteristics

    International Nuclear Information System (INIS)

    Assawaroongruengchot, M.; Marleau, G.

    2005-01-01

    The adjoint transport solution algorithm based on the method of cyclic characteristics (MOCC) is developed for the heterogeneous 2-dimensional geometries. The adjoint characteristics equation associated with a cyclic tracking line is formulated, then a closed form for adjoint angular flux can be determined. The acceleration techniques are implemented using the group-reduction and group-splitting techniques. To demonstrate the efficacy of the algorithm, the calculations are performed on the 17*17 PWR and Watanabe-Maynard benchmark problems. Comparisons of adjoint flux and k eff results obtained by MOCC and collision probability (CP) methods are performed. The mathematical relationship between pseudo-adjoint flux obtained by CP method and adjoint flux by MOCC method is presented. It appears that the pseudo-adjoint flux by CP method is equivalent to the adjoint flux by MOCC method and that the MOCC method requires lower computing time than the CP method for a single adjoint flux calculation

  4. Multigroup adjoint transport solution using the method of cyclic characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Assawaroongruengchot, M.; Marleau, G. [Ecole Polytechnique de Montreal, Institut de Genie Nucleaire, Montreal, Quebec (Canada)

    2005-07-01

    The adjoint transport solution algorithm based on the method of cyclic characteristics (MOCC) is developed for the heterogeneous 2-dimensional geometries. The adjoint characteristics equation associated with a cyclic tracking line is formulated, then a closed form for adjoint angular flux can be determined. The acceleration techniques are implemented using the group-reduction and group-splitting techniques. To demonstrate the efficacy of the algorithm, the calculations are performed on the 17*17 PWR and Watanabe-Maynard benchmark problems. Comparisons of adjoint flux and k{sub eff} results obtained by MOCC and collision probability (CP) methods are performed. The mathematical relationship between pseudo-adjoint flux obtained by CP method and adjoint flux by MOCC method is presented. It appears that the pseudo-adjoint flux by CP method is equivalent to the adjoint flux by MOCC method and that the MOCC method requires lower computing time than the CP method for a single adjoint flux calculation.

  5. The quasi-diffusive approximation in transport theory: Local solutions

    International Nuclear Information System (INIS)

    Celaschi, M.; Montagnini, B.

    1995-01-01

    The one velocity, plane geometry integral neutron transport equation is transformed into a system of two equations, one of them being the equation of continuity and the other a generalized Fick's law, in which the usual diffusion coefficient is replaced by a self-adjoint integral operator. As the kernel of this operator is very close to the Green function of a diffusion equation, an approximate inversion by means of a second order differential operator allows to transform these equations into a purely differential system which is shown to be equivalent, in the simplest case, to a diffusion-like equation. The method, the principles of which have been exposed in a previous paper, is here extended and applied to a variety of problems. If the inversion is properly performed, the quasi-diffusive solutions turn out to be quite accurate, even in the vicinity of the interface between different material regions, where elementary diffusion theory usually fails. 16 refs., 3 tabs

  6. Approximate solution to neutron transport equation with linear anisotropic scattering

    International Nuclear Information System (INIS)

    Coppa, G.; Ravetto, P.; Sumini, M.

    1983-01-01

    A method to obtain an approximate solution to the transport equation, when both sources and collisions show a linearly anisotropic behavior, is outlined and the possible implications for numerical calculations in applied neutronics as well as shielding evaluations are investigated. The form of the differential system of equations taken by the method is quite handy and looks simpler and more manageable than any other today available technique. To go deeper into the efficiency of the method, some typical calculations concerning critical dimension of multiplying systems are then performed and the results are compared with the ones coming from the classical Ssub(N) approximations. The outcome of such calculations leads us to think of interesting developments of the method which could be quite useful in alternative to other today widespread approximate procedures, for any geometry, but especially for curved ones. (author)

  7. Engineering charge transport by heterostructuring solution-processed semiconductors

    Science.gov (United States)

    Voznyy, Oleksandr; Sutherland, Brandon R.; Ip, Alexander H.; Zhitomirsky, David; Sargent, Edward H.

    2017-06-01

    Solution-processed semiconductor devices are increasingly exploiting heterostructuring — an approach in which two or more materials with different energy landscapes are integrated into a composite system. Heterostructured materials offer an additional degree of freedom to control charge transport and recombination for more efficient optoelectronic devices. By exploiting energetic asymmetry, rationally engineered heterostructured materials can overcome weaknesses, augment strengths and introduce emergent physical phenomena that are otherwise inaccessible to single-material systems. These systems see benefit and application in two distinct branches of charge-carrier manipulation. First, they influence the balance between excitons and free charges to enhance electron extraction in solar cells and photodetectors. Second, they promote radiative recombination by spatially confining electrons and holes, which increases the quantum efficiency of light-emitting diodes. In this Review, we discuss advances in the design and composition of heterostructured materials, consider their implementation in semiconductor devices and examine unexplored paths for future advancement in the field.

  8. Coupling of solute transport and cell expansion in pea stems

    Science.gov (United States)

    Schmalstig, J. G.; Cosgrove, D. J.

    1990-01-01

    As cells expand and are displaced through the elongation zone of the epicotyl of etiolated pea (Pisum sativum L. var Alaska) seedlings, there is little net dilution of the cell sap, implying a coordination between cell expansion and solute uptake from the phloem. Using [14C] sucrose as a phloem tracer (applied to the hypogeous cotyledons), the pattern of label accumulation along the stem closely matched the growth rate pattern: high accumulation in the growing zone, little accumulation in nongrowing regions. Several results suggest that a major portion of phloem contents enters elongating cells through the symplast. We propose that the coordination between phloem transport and cell expansion is accomplished via regulatory pathways affecting both plasmodesmata conductivity and cell expansion.

  9. Biomimetic materials for protein storage and transport

    Science.gov (United States)

    Firestone, Millicent A [Elmhurst, IL; Laible, Philip D [Villa Park, IL

    2012-05-01

    The invention provides a method for the insertion of protein in storage vehicles and the recovery of the proteins from the vehicles, the method comprising supplying isolated protein; mixing the isolated protein with a fluid so as to form a mixture, the fluid comprising saturated phospholipids, lipopolymers, and a surfactant; cycling the mixture between a first temperature and a second temperature; maintaining the mixture as a solid for an indefinite period of time; diluting the mixture in detergent buffer so as to disrupt the composition of the mixture, and diluting to disrupt the fluid in its low viscosity state for removal of the guest molecules by, for example, dialysis, filtering or chromatography dialyzing/filtering the emulsified solid.

  10. Fluid and solute transport in a network of channels

    International Nuclear Information System (INIS)

    Moreno, L.; Neretnieks, I.

    1991-09-01

    A three-dimensional channel network model is presented. The fluid flow and solute transport are assumed to take place through a network of connected channels. The channels are generated assuming that the conductances are lognormally distributed. The flow is calculated resolving the pressure distribution and the sole transport is calculated by using a particle tracking technique. The model includes diffusion into the rock matrix and sorption within the matrix in addition to advection along the channel network. Different approaches are used to describe the channel volume and its relation to the conductivity. To quantify the diffusion into the rock matrix the size of the flow wetted surface (contact surface between the channel and the rock) is needed in addition to the diffusion properties and the sorption capacity of the rock. Two different geometries were simulated: regional parallel flow and convergent flow toward a tunnel. In the generation of the channel network, it is found that its connectivity is reduced when the standard deviation in conductances is increased. For large standard deviations, the water conducting channels are found to be few. Standard deviations for the distribution of the effluent channel flowrates were calculated. Comparisons were made with experimental data from drifts and tunnels as well as boreholes as a means to validate the model. (au) (31 refs.)

  11. Improved parallel solution techniques for the integral transport matrix method

    Energy Technology Data Exchange (ETDEWEB)

    Zerr, R. Joseph, E-mail: rjz116@psu.edu [Department of Mechanical and Nuclear Engineering, The Pennsylvania State University, University Park, PA (United States); Azmy, Yousry Y., E-mail: yyazmy@ncsu.edu [Department of Nuclear Engineering, North Carolina State University, Burlington Engineering Laboratories, Raleigh, NC (United States)

    2011-07-01

    Alternative solution strategies to the parallel block Jacobi (PBJ) method for the solution of the global problem with the integral transport matrix method operators have been designed and tested. The most straightforward improvement to the Jacobi iterative method is the Gauss-Seidel alternative. The parallel red-black Gauss-Seidel (PGS) algorithm can improve on the number of iterations and reduce work per iteration by applying an alternating red-black color-set to the subdomains and assigning multiple sub-domains per processor. A parallel GMRES(m) method was implemented as an alternative to stationary iterations. Computational results show that the PGS method can improve on the PBJ method execution time by up to 10´ when eight sub-domains per processor are used. However, compared to traditional source iterations with diffusion synthetic acceleration, it is still approximately an order of magnitude slower. The best-performing cases are optically thick because sub-domains decouple, yielding faster convergence. Further tests revealed that 64 sub-domains per processor was the best performing level of sub-domain division. An acceleration technique that improves the convergence rate would greatly improve the ITMM. The GMRES(m) method with a diagonal block pre conditioner consumes approximately the same time as the PBJ solver but could be improved by an as yet undeveloped, more efficient pre conditioner. (author)

  12. Improved parallel solution techniques for the integral transport matrix method

    International Nuclear Information System (INIS)

    Zerr, R. Joseph; Azmy, Yousry Y.

    2011-01-01

    Alternative solution strategies to the parallel block Jacobi (PBJ) method for the solution of the global problem with the integral transport matrix method operators have been designed and tested. The most straightforward improvement to the Jacobi iterative method is the Gauss-Seidel alternative. The parallel red-black Gauss-Seidel (PGS) algorithm can improve on the number of iterations and reduce work per iteration by applying an alternating red-black color-set to the subdomains and assigning multiple sub-domains per processor. A parallel GMRES(m) method was implemented as an alternative to stationary iterations. Computational results show that the PGS method can improve on the PBJ method execution time by up to 10´ when eight sub-domains per processor are used. However, compared to traditional source iterations with diffusion synthetic acceleration, it is still approximately an order of magnitude slower. The best-performing cases are optically thick because sub-domains decouple, yielding faster convergence. Further tests revealed that 64 sub-domains per processor was the best performing level of sub-domain division. An acceleration technique that improves the convergence rate would greatly improve the ITMM. The GMRES(m) method with a diagonal block pre conditioner consumes approximately the same time as the PBJ solver but could be improved by an as yet undeveloped, more efficient pre conditioner. (author)

  13. Placenta Copper Transport Proteins in Preeclampsia

    Science.gov (United States)

    Placental insufficiency underlying preeclampsia (PE) is associated with impaired placental angiogenesis. As copper (Cu) is essential to angiogenesis, we investigated differences in the expression of placental Cu transporters Menkes (ATP7A), Wilsons (ATP7B) and the Cu chaperone (CCS) for superoxide d...

  14. Transport of fluid and solutes in the body II. Model validation and implications.

    Science.gov (United States)

    Gyenge, C C; Bowen, B D; Reed, R K; Bert, J L

    1999-09-01

    A mathematical model of short-term whole body fluid, protein, and ion distribution and transport developed earlier [see companion paper: C. C. Gyenge, B. D. Bowen, R. K. Reed, and J. L. Bert. Am. J. Physiol. 277 (Heart Circ. Physiol. 46): H1215-H1227, 1999] is validated using experimental data available in the literature. The model was tested against data measured for the following three types of experimental infusions: 1) hyperosmolar saline solutions with an osmolarity in the range of 2,000-2,400 mosmol/l, 2) saline solutions with an osmolarity of approximately 270 mosmol/l and composition comparable with Ringer solution, and 3) an isosmotic NaCl solution with an osmolarity of approximately 300 mosmol/l. Good agreement between the model predictions and the experimental data was obtained with respect to the trends and magnitudes of fluid shifts between the intra- and extracellular compartments, extracellular ion and protein contents, and hematocrit values. The model is also able to yield information about inaccessible or difficult-to-measure system variables such as intracellular ion contents, cellular volumes, and fluid fluxes across the vascular capillary membrane, data that can be used to help interpret the behavior of the system.

  15. Small angle x-ray scattering from proteins in solution

    International Nuclear Information System (INIS)

    de Souza, C.F.; Torriani, I.L.; Bonafe, C.F.S.; Merrelles, N.C.; Vachette, P.

    1989-01-01

    In this work the authors report experiments performed with giant respiratory proteins from annelids (erythrocruorins), known to have a molecular weight in the order of four million Daltons. Preliminary x-ray scattering data was obtained using a conventional rotating anode source. High resolution small angle scattering curves were obtained with synchrotron radiation from the DCI storage ring at LURE. Data from solutions with several protein concentrations were analyzed in order to determine low resolution dimensional parameters, using Guinier plots from the smeared scattering curves and the inverse transformation method

  16. Radiation effects on viscosimetry of protein based solutions

    International Nuclear Information System (INIS)

    Sabato, S.F.; Lacroix, M.

    2002-01-01

    Due to their good functional properties allied to their excellent nutritional value, milk protein isolates and soy protein concentrates have gained a crescent interest. These proteins could have their structural properties improved when some treatments are applied, such as gamma irradiation, alone or in presence of other compounds, as a plasticizer. In this work, solutions of those proteins were mixed with a generally recognized as safe plasticizer, glycerol. These mixtures (8% protein (w/v) base) at two ratios 1:1 and 2:1 (protein:glycerol) were submitted to a gamma irradiation treatment ( 60 Co), at doses 0, 5, 15 and 25 kGy, and their rheological performance was studied. As irradiation dose increased viscosity measurements decayed significantly (p<0.05) for mixture soy/glycerol and calcium caseinate/glycerol. The mixture sodium caseinate/glycerol showed a trend to form aggregation of macromolecules with dose of 5 kGy, while the apparent viscosity for dispersions containing whey/glycerol remained almost constant as irradiation dose increases. In the case of soy protein isolate and sodium caseinate, a mixture of 2:1 showed a significant higher viscosity (p<0.05) than a mixture of 1:1

  17. Radiation effects on viscosimetry of protein based solutions

    Energy Technology Data Exchange (ETDEWEB)

    Sabato, S.F.; Lacroix, M. E-mail: monique.lacroix@inrs-iaf.uquebec.ca

    2002-03-01

    Due to their good functional properties allied to their excellent nutritional value, milk protein isolates and soy protein concentrates have gained a crescent interest. These proteins could have their structural properties improved when some treatments are applied, such as gamma irradiation, alone or in presence of other compounds, as a plasticizer. In this work, solutions of those proteins were mixed with a generally recognized as safe plasticizer, glycerol. These mixtures (8% protein (w/v) base) at two ratios 1:1 and 2:1 (protein:glycerol) were submitted to a gamma irradiation treatment ({sup 60}Co), at doses 0, 5, 15 and 25 kGy, and their rheological performance was studied. As irradiation dose increased viscosity measurements decayed significantly (p<0.05) for mixture soy/glycerol and calcium caseinate/glycerol. The mixture sodium caseinate/glycerol showed a trend to form aggregation of macromolecules with dose of 5 kGy, while the apparent viscosity for dispersions containing whey/glycerol remained almost constant as irradiation dose increases. In the case of soy protein isolate and sodium caseinate, a mixture of 2:1 showed a significant higher viscosity (p<0.05) than a mixture of 1:1.

  18. High-resolution neutron spectroscopy on protein solution samples

    International Nuclear Information System (INIS)

    Grimaldo, M.; Henning, M.; Roosen-Runge, F.; Seydel, T.; Jalarvo, N.; Zamponi, M.; Zanini, F.; Zhang, F.; Schreiber, F.

    2015-01-01

    Proteins in solution are subject to a complex superposition of global translational and rotational diffusion as well as internal relaxations covering a wide range of time scales. With the advent of new high-flux neutron spectrometers in combination with enhanced analysis frameworks it has become possible to separate these different contributions. We discuss new approaches to the analysis by presenting example spectra and fits from data recorded on the backscattering spectrometers IN16, IN16B, and BASIS on the same protein solution sample. We illustrate the separation of the rotational and translational diffusion contribution, the accurate treatment of the solvent contribution, and the extraction of information on internal fluctuations. We also highlight the progress made in passing from second- to third-generation backscattering spectrometers. (authors)

  19. Solution processed metal oxide thin film hole transport layers for high performance organic solar cells

    Science.gov (United States)

    Steirer, K. Xerxes; Berry, Joseph J.; Chesin, Jordan P.; Lloyd, Matthew T.; Widjonarko, Nicodemus Edwin; Miedaner, Alexander; Curtis, Calvin J.; Ginley, David S.; Olson, Dana C.

    2017-01-10

    A method for the application of solution processed metal oxide hole transport layers in organic photovoltaic devices and related organic electronics devices is disclosed. The metal oxide may be derived from a metal-organic precursor enabling solution processing of an amorphous, p-type metal oxide. An organic photovoltaic device having solution processed, metal oxide, thin-film hole transport layer.

  20. Mechanistic logic underlying the axonal transport of cytosolic proteins

    Science.gov (United States)

    Scott, David A.; Das, Utpal; Tang, Yong; Roy, Subhojit

    2011-01-01

    Proteins vital to presynaptic function are synthesized in the neuronal perikarya and delivered into synapses via two modes of axonal transport. While membrane-anchoring proteins are conveyed in fast axonal transport via motor-driven vesicles, cytosolic proteins travel in slow axonal transport; via mechanisms that are poorly understood. We found that in cultured axons, populations of cytosolic proteins tagged to photoactivable-GFP (PA-GFP) move with a slow motor-dependent anterograde bias; distinct from vesicular-trafficking or diffusion of untagged PA-GFP. The overall bias is likely generated by an intricate particle-kinetics involving transient assembly and short-range vectorial spurts. In-vivo biochemical studies reveal that cytosolic proteins are organized into higher-order structures within axon-enriched fractions that are largely segregated from vesicles. Data-driven biophysical modeling best predicts a scenario where soluble molecules dynamically assemble into mobile supra-molecular structures. We propose a model where cytosolic proteins are transported by dynamically assembling into multi-protein complexes that are directly/indirectly conveyed by motors. PMID:21555071

  1. Approximate and analytical solutions for solute transport from an injection well into a single fracture

    International Nuclear Information System (INIS)

    Chen, C.S.; Yates, S.R.

    1989-01-01

    In dealing with problems related to land-based nuclear waste management, a number of analytical and approximate solutions were developed to quantify radionuclide transport through fractures contained in the porous formation. It has been reported that by treating the radioactive decay constant as the appropriate first-order rate constant, these solutions can also be used to study injection problems of a similar nature subject to first-order chemical or biological reactions. The fracture is idealized by a pair of parallel, smooth plates separated by an aperture of constant thickness. Groundwater was assumed to be immobile in the underlying and overlying porous formations due to their low permeabilities. However, the injected radionuclides were able to move from the fracture into the porous matrix by molecular diffusion (the matrix diffusion) due to possible concentration gradients across the interface between the fracture and the porous matrix. Calculation of the transient solutions is not straightforward, and the paper documents a contained Fortran program, which computes the Stehfest inversion, the Airy functions, and gives the concentration distributions in the fracture as well as in the porous matrix for both transient and steady-state cases

  2. Direct observation of electrogenic NH4(+) transport in ammonium transport (Amt) proteins.

    Science.gov (United States)

    Wacker, Tobias; Garcia-Celma, Juan J; Lewe, Philipp; Andrade, Susana L A

    2014-07-08

    Ammonium transport (Amt) proteins form a ubiquitous family of integral membrane proteins that specifically shuttle ammonium across membranes. In prokaryotes, archaea, and plants, Amts are used as environmental NH4(+) scavengers for uptake and assimilation of nitrogen. In the eukaryotic homologs, the Rhesus proteins, NH4(+)/NH3 transport is used instead in acid-base and pH homeostasis in kidney or NH4(+)/NH3 (and eventually CO2) detoxification in erythrocytes. Crystal structures and variant proteins are available, but the inherent challenges associated with the unambiguous identification of substrate and monitoring of transport events severely inhibit further progress in the field. Here we report a reliable in vitro assay that allows us to quantify the electrogenic capacity of Amt proteins. Using solid-supported membrane (SSM)-based electrophysiology, we have investigated the three Amt orthologs from the euryarchaeon Archaeoglobus fulgidus. Af-Amt1 and Af-Amt3 are electrogenic and transport the ammonium and methylammonium cation with high specificity. Transport is pH-dependent, with a steep decline at pH values of ∼5.0. Despite significant sequence homologies, functional differences between the three proteins became apparent. SSM electrophysiology provides a long-sought-after functional assay for the ubiquitous ammonium transporters.

  3. Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers.

    Directory of Open Access Journals (Sweden)

    Curtiss P Schneider

    Full Text Available Much work has been performed on understanding the effects of additives on protein thermodynamics and degradation kinetics, in particular addressing the Hofmeister series and other broad empirical phenomena. Little attention, however, has been paid to the effect of additive-additive interactions on proteins. Our group and others have recently shown that such interactions can actually govern protein events, such as aggregation. Here we use dendrimers, which have the advantage that both size and surface chemical groups can be changed and therein studied independently. Dendrimers are a relatively new and broad class of materials which have been demonstrated useful in biological and therapeutic applications, such as drug delivery, perturbing amyloid formation, etc. Guanidinium modified dendrimers pose an interesting case given that guanidinium can form multiple attractive hydrogen bonds with either a protein surface or other components in solution, such as hydrogen bond accepting counterions. Here we present a study which shows that the behavior of such macromolecule species (modified PAMAM dendrimers is governed by intra-solvent interactions. Attractive guanidinium-anion interactions seem to cause clustering in solution, which inhibits cooperative binding to the protein surface but at the same time, significantly suppresses nonnative aggregation.

  4. Product Lifecycle Management and the Quest for Sustainable Space Transportation Solutions

    Science.gov (United States)

    Caruso, Pamela W.

    2009-01-01

    This viewgraph presentation reviews NASA Marshall's effort to sustain space transportation solutions through product lines that include: 1) Propulsion and Transportation Systems; 2) Life Support Systems; and 3) and Earth and Space Science Spacecraft Systems, and Operations.

  5. Finite element based composite solution for neutron transport problems

    International Nuclear Information System (INIS)

    Mirza, A.N.; Mirza, N.M.

    1995-01-01

    A finite element treatment for solving neutron transport problems is presented. The employs region-wise discontinuous finite elements for the spatial representation of the neutron angular flux, while spherical harmonics are used for directional dependence. Composite solutions has been obtained by using different orders of angular approximations in different parts of a system. The method has been successfully implemented for one dimensional slab and two dimensional rectangular geometry problems. An overall reduction in the number of nodal coefficients (more than 60% in some cases as compared to conventional schemes) has been achieved without loss of accuracy with better utilization of computational resources. The method also provides an efficient way of handling physically difficult situations such as treatment of voids in duct problems and sharply changing angular flux. It is observed that a great wealth of information about the spatial and directional dependence of the angular flux is obtained much more quickly as compared to Monte Carlo method, where most of the information in restricted to the locality of immediate interest. (author)

  6. New constructive solutions for building of transport construction facilities

    Directory of Open Access Journals (Sweden)

    Babayev Vladimir

    2017-01-01

    Full Text Available New structural systems for civil and transport engineering were examined. The basis for the formation of the proposed reinforced concrete structures is the ideology of reducing its dead weight, with a given bearing capacity, the realization of which is accomplished by burial during concreting large-sized liners of a given shape and manufactured from lightweight, inexpensive composite materials. The process of erecting these systems is presented in two forms: for flat structures - using self-tightening concrete, and for curvilinear ones - by using shotcrete technologies. The second direction is presented by steel-reinforced concrete structures. These structural systems were created on the basis of innovative component and methods of rationalization of parameters. The basis of the above methods is a compiler which includes the finite element method, adaptive evolution method and special iterative procedures. Experimental verification of structural solutions and formation procedures for suggested systems was performed. Comparison between theoretical and experimental data is given. Suggested systems were implemented in a number of building companies.

  7. Prediction of thermodynamic instabilities of protein solutions from simple protein–protein interactions

    International Nuclear Information System (INIS)

    D’Agostino, Tommaso; Solana, José Ramón; Emanuele, Antonio

    2013-01-01

    Highlights: ► We propose a model of effective protein–protein interaction embedding solvent effects. ► A previous square-well model is enhanced by giving to the interaction a free energy character. ► The temperature dependence of the interaction is due to entropic effects of the solvent. ► The validity of the original SW model is extended to entropy driven phase transitions. ► We get good fits for lysozyme and haemoglobin spinodal data taken from literature. - Abstract: Statistical thermodynamics of protein solutions is often studied in terms of simple, microscopic models of particles interacting via pairwise potentials. Such modelling can reproduce the short range structure of protein solutions at equilibrium and predict thermodynamics instabilities of these systems. We introduce a square well model of effective protein–protein interaction that embeds the solvent’s action. We modify an existing model [45] by considering a well depth having an explicit dependence on temperature, i.e. an explicit free energy character, thus encompassing the statistically relevant configurations of solvent molecules around proteins. We choose protein solutions exhibiting demixing upon temperature decrease (lysozyme, enthalpy driven) and upon temperature increase (haemoglobin, entropy driven). We obtain satisfactory fits of spinodal curves for both the two proteins without adding any mean field term, thus extending the validity of the original model. Our results underline the solvent role in modulating or stretching the interaction potential

  8. Control and optimization of solute transport in a thin porous tube

    KAUST Repository

    Griffiths, I. M.; Howell, P. D.; Shipley, R. J.

    2013-01-01

    differentials upon the dispersive solute behaviour are investigated. The model is used to explore the control of solute transport across the membrane walls via the membrane permeability, and a parametric expression for the permeability required to generate a

  9. Technology in rural transportation. Simple solution #6, traveler information on the internet

    Science.gov (United States)

    1997-01-01

    This application was identified as a promising rural Intelligent Transportation Systems (ITS) solution under a project sponsored by the Federal Highway Administration (FHWA) and the ENTERPRISE program. This summary describes the solution as well as o...

  10. Solute transport with periodic input point source in one-dimensional ...

    African Journals Online (AJOL)

    JOY

    groundwater flow velocity is considered proportional to multiple of temporal function and ζ th ... One-dimensional solute transport through porous media with or without .... solute free. ... the periodic concentration at source of the boundary i.e.,. 0.

  11. Supercharging Protein Complexes from Aqueous Solution Disrupts their Native Conformations

    Science.gov (United States)

    Sterling, Harry J.; Kintzer, Alexander F.; Feld, Geoffrey K.; Cassou, Catherine A.; Krantz, Bryan A.; Williams, Evan R.

    2012-02-01

    The effects of aqueous solution supercharging on the solution- and gas-phase structures of two protein complexes were investigated using traveling-wave ion mobility-mass spectrometry (TWIMS-MS). Low initial concentrations of m-nitrobenzyl alcohol ( m-NBA) in the electrospray ionization (ESI) solution can effectively increase the charge of concanavalin A dimers and tetramers, but at higher m-NBA concentrations, the increases in charge are accompanied by solution-phase dissociation of the dimers and up to a ~22% increase in the collision cross section (CCS) of the tetramers. With just 0.8% m-NBA added to the ESI solution of a ~630 kDa anthrax toxin octamer complex, the average charge is increased by only ~4% compared with the "native" complex, but it is sufficiently destabilized so that extensive gas-phase fragmentation occurs in the relatively high pressure regions of the TWIMS device. Anthrax toxin complexes exist in either a prechannel or a transmembrane channel state. With m-NBA, the prechannel state of the complex has the same CCS/charge ratio in the gas phase as the transmembrane channel state of the same complex formed without m-NBA, yet undergoes extensive dissociation, indicating that destabilization from supercharging occurs in the ESI droplet prior to ion formation and is not a result of Coulombic destabilization in the gas phase as a result of higher charging. These results demonstrate that the supercharging of large protein complexes is the result of conformational changes induced by the reagents in the ESI droplets, where enrichment of the supercharging reagent during droplet evaporation occurs.

  12. Semianalytical solutions of radioactive or reactive tracer transport in layered fractured media

    International Nuclear Information System (INIS)

    Moridis, G.J.; Bodvarsson, G.S.

    2001-01-01

    In this paper, semianalytical solutions are developed for the problem of transport of radioactive or reactive tracers (solutes or colloids) through a layered system of heterogeneous fractured media with misaligned fractures. The tracer transport equations in the matrix account for (a) diffusion, (b) surface diffusion (for solutes only), (c) mass transfer between the mobile and immobile water fractions, (d) linear kinetic or equilibrium physical, chemical, or combined solute sorption or colloid filtration, and (e) radioactive decay or first order chemical reactions. Any number of radioactive decay daughter products (or products of a linear, first-order reaction chain) can be tracked. The tracer-transport equations in the fractures account for the same processes, in addition to advection and hydrodynamic dispersion. Additionally, the colloid transport equations account for straining and velocity adjustments related to the colloidal size. The solutions, which are analytical in the Laplace space, are numerically inverted to provide the solution in time and can accommodate any number of fractured and/or porous layers. The solutions are verified using analytical solutions for limiting cases of solute and colloid transport through fractured and porous media. The effect of important parameters on the transport of 3 H, 237 Np and 239 Pu (and its daughters) is investigated in several test problems involving layered geological systems of varying complexity. 239 Pu colloid transport problems in multilayered systems indicate significant colloid accumulations at straining interfaces but much faster transport of the colloid than the corresponding strongly sorbing solute species

  13. Mathematical description of adsorption and transport of reactive solutes in soil: a review of selected literature

    International Nuclear Information System (INIS)

    Travis, C.C.

    1978-10-01

    This report reviews selected literature related to the mathematical description of the transport of reactive solutes through soil. The primary areas of the literature reviewed are (1) mathematical models in current use for description of the adsorption-desorption interaction between the soil solution and the soil matrix and (2) analytic solutions of the differential equations describing the convective-dispersive transport of reactive solutes through soil

  14. The effect of gamma irradiation on rice protein aqueous solution

    Science.gov (United States)

    Baccaro, Stefania; Bal, Oya; Cemmi, Alessia; Di Sarcina, Ilaria

    2018-05-01

    The use of proteins as natural biopolymers are sensibly increasing in several application fields such as food industry, packaging and environment protection. In particular, rice proteins (RP) present good nutritional, hypoallergenic and healthful properties very interesting for human consumption. Since ionizing radiation can be successfully applied on protein containing systems involved in different industrial processes, this work aims to determine the effect of gamma radiation on 5 wt%-7.5 wt% RP aqueous solutions in a wide range of absorbed doses up to around 40 kGy. The changes of RP secondary and tertiary structures and their chemical composition were followed by UV-VIS absorbance spectroscopy, luminescence analysis and pH measurements. The experimental data showed the occurrence of the unfolding of RP chains with the increase of the absorbed dose and the formation of new molecules, due to the reaction among tryptophane and tyrosine amino acids and the radical species induced by gamma radiation. The results are also confirmed by the modification of the pH values measured for the irradiated solutions.

  15. Position-dependent Effects of Polylysine on Sec Protein Transport*

    Science.gov (United States)

    Liang, Fu-Cheng; Bageshwar, Umesh K.; Musser, Siegfried M.

    2012-01-01

    The bacterial Sec protein translocation system catalyzes the transport of unfolded precursor proteins across the cytoplasmic membrane. Using a recently developed real time fluorescence-based transport assay, the effects of the number and distribution of positive charges on the transport time and transport efficiency of proOmpA were examined. As expected, an increase in the number of lysine residues generally increased transport time and decreased transport efficiency. However, the observed effects were highly dependent on the polylysine position in the mature domain. In addition, a string of consecutive positive charges generally had a more significant effect on transport time and efficiency than separating the charges into two or more charged segments. Thirty positive charges distributed throughout the mature domain resulted in effects similar to 10 consecutive charges near the N terminus of the mature domain. These data support a model in which the local effects of positive charge on the translocation kinetics dominate over total thermodynamic constraints. The rapid translocation kinetics of some highly charged proOmpA mutants suggest that the charge is partially shielded from the electric field gradient during transport, possibly by the co-migration of counter ions. The transport times of precursors with multiple positively charged sequences, or “pause sites,” were fairly well predicted by a local effect model. However, the kinetic profile predicted by this local effect model was not observed. Instead, the transport kinetics observed for precursors with multiple polylysine segments support a model in which translocation through the SecYEG pore is not the rate-limiting step of transport. PMID:22367204

  16. Position-dependent effects of polylysine on Sec protein transport.

    Science.gov (United States)

    Liang, Fu-Cheng; Bageshwar, Umesh K; Musser, Siegfried M

    2012-04-13

    The bacterial Sec protein translocation system catalyzes the transport of unfolded precursor proteins across the cytoplasmic membrane. Using a recently developed real time fluorescence-based transport assay, the effects of the number and distribution of positive charges on the transport time and transport efficiency of proOmpA were examined. As expected, an increase in the number of lysine residues generally increased transport time and decreased transport efficiency. However, the observed effects were highly dependent on the polylysine position in the mature domain. In addition, a string of consecutive positive charges generally had a more significant effect on transport time and efficiency than separating the charges into two or more charged segments. Thirty positive charges distributed throughout the mature domain resulted in effects similar to 10 consecutive charges near the N terminus of the mature domain. These data support a model in which the local effects of positive charge on the translocation kinetics dominate over total thermodynamic constraints. The rapid translocation kinetics of some highly charged proOmpA mutants suggest that the charge is partially shielded from the electric field gradient during transport, possibly by the co-migration of counter ions. The transport times of precursors with multiple positively charged sequences, or "pause sites," were fairly well predicted by a local effect model. However, the kinetic profile predicted by this local effect model was not observed. Instead, the transport kinetics observed for precursors with multiple polylysine segments support a model in which translocation through the SecYEG pore is not the rate-limiting step of transport.

  17. Hydrogeochemistry and simulated solute transport, Piceance Basin, northwestern Colorado

    Science.gov (United States)

    Robson, S.G.; Saulnier, G.J.

    1981-01-01

    Oil-shale mining activities in Piceance basin in northwestern Colorado could adversely affect the ground- and surface-water quality in the basin. This study of the hydrology and geochemistry of the area used ground-water solute-transport-modeling techniques to investigate the possible impact of the mines on water quality. Maps of the extent and structure of the aquifer were prepared and show that a saturated thickness of 2,000 feet occurs in the northeast part of the basin. Ground-water recharge in the upland areas in the east, south, and west parts of the basin moves down into deeper zones in the aquifer and laterally to the discharge areas along Piceance and Yellow Creeks. The saline zone and the unsaturated zone provide the majority of the dissolved solids found in the ground water. Precipitation, ion-exchange, and oxidation-reduction reactions are also occuring in the aquifer. Model simulations of ground-water pumpage in tracts C-a and C-b indicate that the altered direction of ground-water movement near the pumped mines will cause an improvement in ground-water quality near the mines and a degradation of water quality downgradient from the tracts. Model simulations of mine leaching in tract C-a and C-b indicate that equal rates of mine leaching in the tracts will produce much different effects on the water quality in the basin. Tract C-a, by virtue of its remote location from perennial streams, will primarily degrade the ground-water quality over a large area to the northeast of the tract. Tract C-b, by contrast, will primarily degrade the surface-water quality in Piceance Creek, with only localized effects on the ground-water quality. (USGS)

  18. Development of solute transport models in YMPYRÄ framework to simulate solute migration in military shooting and training areas

    Science.gov (United States)

    Warsta, L.; Karvonen, T.

    2017-12-01

    There are currently 25 shooting and training areas in Finland managed by The Finnish Defence Forces (FDF), where military activities can cause contamination of open waters and groundwater reservoirs. In the YMPYRÄ project, a computer software framework is being developed that combines existing open environmental data and proprietary information collected by FDF with computational models to investigate current and prevent future environmental problems. A data centric philosophy is followed in the development of the system, i.e. the models are updated and extended to handle available data from different areas. The results generated by the models are summarized as easily understandable flow and risk maps that can be opened in GIS programs and used in environmental assessments by experts. Substances investigated with the system include explosives and metals such as lead, and both surface and groundwater dominated areas can be simulated. The YMPYRÄ framework is composed of a three dimensional soil and groundwater flow model, several solute transport models and an uncertainty assessment system. Solute transport models in the framework include particle based, stream tube and finite volume based approaches. The models can be used to simulate solute dissolution from source area, transport in the unsaturated layers to groundwater and finally migration in groundwater to water extraction wells and springs. The models can be used to simulate advection, dispersion, equilibrium adsorption on soil particles, solubility and dissolution from solute phase and dendritic solute decay chains. Correct numerical solutions were confirmed by comparing results to analytical 1D and 2D solutions and by comparing the numerical solutions to each other. The particle based and stream tube type solute transport models were useful as they could complement the traditional finite volume based approach which in certain circumstances produced numerical dispersion due to piecewise solution of the

  19. Demonstrations in Solute Transport Using Dyes: Part II. Modeling.

    Science.gov (United States)

    Butters, Greg; Bandaranayake, Wije

    1993-01-01

    A solution of the convection-dispersion equation is used to describe the solute breakthrough curves generated in the demonstrations in the companion paper. Estimation of the best fit model parameters (solute velocity, dispersion, and retardation) is illustrated using the method of moments for an example data set. (Author/MDH)

  20. Multidrug and toxin extrusion proteins as transporters of antimicrobial drugs.

    Science.gov (United States)

    Nies, Anne T; Damme, Katja; Schaeffeler, Elke; Schwab, Matthias

    2012-12-01

    Antimicrobial drugs are essential in the treatment of infectious diseases. A better understanding of transport processes involved in drug disposition will improve the predictability of drug-drug interactions with consequences for drug response. Multidrug And Toxin Extrusion (MATE; SLC47A) proteins are efflux transporters mediating the excretion of several antimicrobial drugs as well as other organic compounds into bile and urine, thereby contributing to drug disposition. This review summarizes current knowledge of the structural and molecular features of human MATE transporters including their functional role in drug transport with a specific focus on antimicrobial drugs. The PubMed database was searched using the terms "MATE1," "MATE-2K," "MATE2," "SLC47A1," "SLC47A2," and "toxin extrusion protein" (up to June 2012). MATE proteins have been recognized as important transporters mediating the final excretion step of cationic drugs into bile and urine. These include the antiviral drugs acyclovir, amprenavir, and ganciclovir, the antibiotics cephalexin, cephradine and levofloxacin, as well as the antimalarial agents chloroquine and quinine. It is therefore important to enhance our understanding of the role of MATEs in drug extrusion with particular emphasis on the functional consequences of genetic variants on disposition of these antimicrobial drugs.

  1. A single continuum approximation of the solute transport in fractured porous media

    International Nuclear Information System (INIS)

    Jeong, J.T.; Lee, K.J.

    1992-01-01

    Solute transport in fractured porous media is described by the single continuum model, i.e., equivalent porous medium model. In this model, one-dimensional solute transport in the fracture and two-dimensional solute transport in the porous rock matrix is considered. The network of fractures embedded in the porous rock matrix is idealized as two orthogonally intersecting families of equally spaced, parallel fractures directed at 45 o to the regional groundwater flow direction. Governing equations are solved by the finite element method, and an upstream weighting technique is used in order to prevent the oscillation of the solution in the case of highly advection dominated transport. Breakthrough curves, similar to those of the one-dimensional solute transport problem in ordinary porous media, are obtained as a function of time according to volume or flux averaging of the concentration profile across the width of the flow region. The equivalent parameters, i.e., porosity and overall coefficient of longitudinal dispersivity, are obtained by a trial-and-error method. Analyses for the non-sorbing solute transport case show that within the range of considered parameters, and except for the region very close to the source, application of the single continuum model in the idealized fracture system is sufficient for modeling solute transport in fractured porous media. This numerical scheme is shown to be applicable to a sorbing solute and radionuclide transport. (author)

  2. New methods For Modeling Transport Of Water And Solutes In Soils

    DEFF Research Database (Denmark)

    Møldrup, Per

    Recent models for water and solute transport in unsaturated soils have been mechanistically based but numerically very involved. This dissertation concerns the development of mechanistically-based but numerically simple models for calculating and analyzing transport of water and solutes in soil...

  3. Solute transport by groundwater flow to wetland ecosystems : the environmental impact of human activities

    NARCIS (Netherlands)

    Schot, P.P.

    1991-01-01

    This thesis deals with solute transport by groundwater flow and the way in which solute transport is affected by human activities. This in relation to wetland ecosystems. Wetlands in the eastern part of the Vecht river plain in The Netherlands are historically renown for their great variety of

  4. Study of the transport of mercurial compounds by seric proteins

    International Nuclear Information System (INIS)

    Jullien-Saint Guily, Nicole

    1970-01-01

    A bond between the seric proteins and various mercurial compounds labeled with the radioisotopes 203 Hg and 197 Hg was demonstrated by means of research methods specific to radioactivity combined with protein separation techniques. In the course of this study it was shown how strongly the composition of the buffer during electrophoretic migration influences the transport of certain organo-mercurial compounds by the seric proteins. By means of a thioloprive: N - ethyl - maleimide, labeled with 14 C, it was proved that the bonding sites between the proteins and the mercurial compounds were the thiol groups of the proteins but that other bonding sites, in particular the amino groups, could also be involved. (author) [fr

  5. Rab proteins: The key regulators of intracellular vesicle transport

    International Nuclear Information System (INIS)

    Bhuin, Tanmay; Roy, Jagat Kumar

    2014-01-01

    Vesicular/membrane trafficking essentially regulates the compartmentalization and abundance of proteins within the cells and contributes in many signalling pathways. This membrane transport in eukaryotic cells is a complex process regulated by a large and diverse array of proteins. A large group of monomeric small GTPases; the Rabs are essential components of this membrane trafficking route. Most of the Rabs are ubiquitously expressed proteins and have been implicated in vesicle formation, vesicle motility/delivery along cytoskeleton elements and docking/fusion at target membranes through the recruitment of effectors. Functional impairments of Rabs affecting transport pathways manifest different diseases. Rab functions are accompanied by cyclical activation and inactivation of GTP-bound and GDP-bound forms between the cytosol and membranes which is regulated by upstream regulators. Rab proteins are characterized by their distinct sub-cellular localization and regulate a wide variety of endocytic, transcytic and exocytic transport pathways. Mutations of Rabs affect cell growth, motility and other biological processes. - Highlights: • Rab proteins regulate different signalling pathways. • Deregulation of Rabs is the fundamental causes of a variety of human diseases. • This paper gives potential directions in developing therapeutic targets. • This paper also gives ample directions for modulating pathways central to normal physiology. • These are the huge challenges for drug discovery and delivery in near future

  6. Rab proteins: The key regulators of intracellular vesicle transport

    Energy Technology Data Exchange (ETDEWEB)

    Bhuin, Tanmay [Cell and Developmental Biology Unit, Department of Zoology, The University of Burdwan, Golapbag 713104 (India); Roy, Jagat Kumar, E-mail: jkroy@bhu.ac.in [Cytogenetics Laboratory, Department of Zoology, Banaras Hindu University, Varanasi 221005 (India)

    2014-10-15

    Vesicular/membrane trafficking essentially regulates the compartmentalization and abundance of proteins within the cells and contributes in many signalling pathways. This membrane transport in eukaryotic cells is a complex process regulated by a large and diverse array of proteins. A large group of monomeric small GTPases; the Rabs are essential components of this membrane trafficking route. Most of the Rabs are ubiquitously expressed proteins and have been implicated in vesicle formation, vesicle motility/delivery along cytoskeleton elements and docking/fusion at target membranes through the recruitment of effectors. Functional impairments of Rabs affecting transport pathways manifest different diseases. Rab functions are accompanied by cyclical activation and inactivation of GTP-bound and GDP-bound forms between the cytosol and membranes which is regulated by upstream regulators. Rab proteins are characterized by their distinct sub-cellular localization and regulate a wide variety of endocytic, transcytic and exocytic transport pathways. Mutations of Rabs affect cell growth, motility and other biological processes. - Highlights: • Rab proteins regulate different signalling pathways. • Deregulation of Rabs is the fundamental causes of a variety of human diseases. • This paper gives potential directions in developing therapeutic targets. • This paper also gives ample directions for modulating pathways central to normal physiology. • These are the huge challenges for drug discovery and delivery in near future.

  7. Comparison of analytical transport and stochastic solutions for neutron slowing down in an infinite medium

    International Nuclear Information System (INIS)

    Jahshan, S.N.; Wemple, C.A.; Ganapol, B.D.

    1993-01-01

    A comparison of the numerical solutions of the transport equation describing the steady neutron slowing down in an infinite medium with constant cross sections is made with stochastic solutions obtained from tracking successive neutron histories in the same medium. The transport equation solution is obtained using a numerical Laplace transform inversion algorithm. The basis for the algorithm is an evaluation of the Bromwich integral without analytical continuation. Neither the transport nor the stochastic solution is limited in the number of scattering species allowed. The medium may contain an absorption component as well. (orig.)

  8. Isolated effects of external bath osmolality, solute concentration, and electrical charge on solute transport across articular cartilage.

    Science.gov (United States)

    Pouran, Behdad; Arbabi, Vahid; Zadpoor, Amir A; Weinans, Harrie

    2016-12-01

    The metabolic function of cartilage primarily depends on transport of solutes through diffusion mechanism. In the current study, we use contrast enhanced micro-computed tomography to determine equilibrium concentration of solutes through different cartilage zones and solute flux in the cartilage, using osteochondral plugs from equine femoral condyles. Diffusion experiments were performed with two solutes of different charge and approximately equal molecular weight, namely iodixanol (neutral) and ioxaglate (charge=-1) in order to isolate the effects of solute's charge on diffusion. Furthermore, solute concentrations as well as bath osmolality were changed to isolate the effects of steric hindrance on diffusion. Bath concentration and bath osmolality only had minor effects on the diffusion of the neutral solute through cartilage at the surface, middle and deep zones, indicating that the diffusion of the neutral solute was mainly Fickian. The negatively charged solute diffused considerably slower through cartilage than the neutral solute, indicating a large non-Fickian contribution in the diffusion of charged molecules. The numerical models determined maximum solute flux in the superficial zone up to a factor of 2.5 lower for the negatively charged solutes (charge=-1) as compared to the neutral solutes confirming the importance of charge-matrix interaction in diffusion of molecules across cartilage. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

  9. Structural basis for solute transport, nucleotide regulation, and immunological recognition of Neisseria meningitidis PorB

    Energy Technology Data Exchange (ETDEWEB)

    Tanabe, Mikio; Nimigean, Crina M.; Iverson, T.M. (Weill-Med); (Vanderbilt)

    2010-06-25

    PorB is the second most prevalent outer membrane protein in Neisseria meningitidis. PorB is required for neisserial pathogenesis and can elicit a Toll-like receptor mediated host immune response. Here, the x-ray crystal structure of PorB has been determined to 2.3 {angstrom} resolution. Structural analysis and cocrystallization studies identify three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one transports cations nonselectively, and one facilitates the specific uptake of sugars. During infection, PorB likely binds host mitochondrial ATP, and cocrystallization with the ATP analog AMP-PNP suggests that binding of nucleotides regulates these translocation pathways both by partial occlusion of the pore and by restricting the motion of a putative voltage gating loop. PorB is located on the surface of N. meningitidis and can be recognized by receptors of the host innate immune system. Features of PorB suggest that Toll-like receptor mediated recognition outer membrane proteins may be initiated with a nonspecific electrostatic attraction.

  10. Intracellular Transport and Kinesin Superfamily Proteins: Structure, Function and Dynamics

    Science.gov (United States)

    Hirokawa, N.; Takemura, R.

    Using various molecular cell biological and molecular genetic approaches, we identified kinesin superfamily proteins (KIFs) and characterized their significant functions in intracellular transport, which is fundamental for cellular morphogenesis, functioning, and survival. We showed that KIFs not only transport various membranous organelles, proteins complexes and mRNAs fundamental for cellular functions but also play significant roles in higher brain functions such as memory and learning, determination of important developmental processes such as left-right asymmetry formation and brain wiring. We also elucidated that KIFs recognize and bind to their specific cargoes using scaffolding or adaptor protein complexes. Concerning the mechanism of motility, we discovered the simplest unique monomeric motor KIF1A and determined by molecular biophysics, cryoelectron microscopy and X-ray crystallography that KIF1A can move on a microtubule processively as a monomer by biased Brownian motion and by hydolyzing ATP.

  11. Characterization of a novel sialic acid transporter of the sodium solute symporter (SSS) family and in vivo comparison with known bacterial sialic acid transporters.

    Science.gov (United States)

    Severi, Emmanuele; Hosie, Arthur H F; Hawkhead, Judith A; Thomas, Gavin H

    2010-03-01

    The function of sialic acids in the biology of bacterial pathogens is reflected by the diverse range of solute transporters that can recognize these sugar acids. Here, we use an Escherichia coliDeltananT strain to characterize the function of known and proposed bacterial sialic acid transporters. We discover that the STM1128 gene from Salmonella enterica serovar Typhimurium, which encodes a member of the sodium solute symporter family, is able to restore growth on sialic acid to the DeltananT strain and is able to transport [(14)C]-sialic acid. Using the DeltananT genetic background, we performed a direct in vivo comparison of the transport properties of the STM1128 protein with those of sialic acid transporters of the major facilitator superfamily and tripartite ATP-independent periplasmic families, E. coli NanT and Haemophilus influenzae SiaPQM, respectively. This revealed that both STM1128 and SiaPQM are sodium-dependent and, unlike SiaPQM, both STM1128 and NanT are reversible secondary carriers, demonstrating qualitative functional differences in the properties of sialic acid transporters used by bacteria that colonize humans.

  12. Effects of turbulent hyporheic mixing on reach-scale solute transport

    Science.gov (United States)

    Roche, K. R.; Li, A.; Packman, A. I.

    2017-12-01

    Turbulence rapidly mixes solutes and fine particles into coarse-grained streambeds. Both hyporheic exchange rates and spatial variability of hyporheic mixing are known to be controlled by turbulence, but it is unclear how turbulent mixing influences mass transport at the scale of stream reaches. We used a process-based particle-tracking model to simulate local- and reach-scale solute transport for a coarse-bed stream. Two vertical mixing profiles, one with a smooth transition from in-stream to hyporheic transport conditions and a second with enhanced turbulent transport at the sediment-water interface, were fit to steady-state subsurface concentration profiles observed in laboratory experiments. The mixing profile with enhanced interfacial transport better matched the observed concentration profiles and overall mass retention in the streambed. The best-fit mixing profiles were then used to simulate upscaled solute transport in a stream. Enhanced mixing coupled in-stream and hyporheic solute transport, causing solutes exchanged into the shallow subsurface to have travel times similar to the water column. This extended the exponential region of the in-stream solute breakthrough curve, and delayed the onset of the heavy power-law tailing induced by deeper and slower hyporheic porewater velocities. Slopes of observed power-law tails were greater than those predicted from stochastic transport theory, and also changed in time. In addition, rapid hyporheic transport velocities truncated the hyporheic residence time distribution by causing mass to exit the stream reach via subsurface advection, yielding strong exponential tempering in the in-stream breakthrough curves at the timescale of advective hyporheic transport through the reach. These results show that strong turbulent mixing across the sediment-water interface violates the conventional separation of surface and subsurface flows used in current models for solute transport in rivers. Instead, the full distribution of

  13. Affordable Freight Logistics Transport Information Management Optimisation and Asset Tracking Solution Using Smartphone GPS Capabilities

    Science.gov (United States)

    Muna, Joseph T.; Prescott, Kevin

    2011-08-01

    Traditionally, freight transport and telematics solutions that exploit the GPS capabilities of in- vehicle devices to provide innovative Location Based Services (LBS) including track and trace transport systems have been the preserve of a select cluster of transport operators and organisations with the financial resources to develop the requisite custom software and hardware on which they are deployed. The average cost of outfitting a typical transport vehicle or truck with the latest Intelligent Transport System (ITS) increases the cost of the vehicle by anything from a couple to several thousand Euros, depending on the complexity and completeness of the solution. Though this does not generally deter large fleet transport owners since they typically get Return on Investment (ROI) based on economies of scale, it presents a barrier for the smaller independent entities that constitute the majority of freight transport operators [1].The North Sea Freight Intelligent Transport Solution (NS FRITS), a project co-funded by the European Commission Interreg IVB North Sea Region Programme, aims to make acquisition of such transport solutions easier for those organisations that cannot afford the expensive, bespoke systems used by their larger competitors.The project addresses transport security threats by developing a system capable of informing major actors along the freight logistics supply chain, of changing circumstances within the region's major transport corridors and between transport modes. The project also addresses issues of freight volumes, inter-modality, congestion and eco-mobility [2].

  14. Fluid flow and convective transport of solutes within the intervertebral disc

    NARCIS (Netherlands)

    Ferguson, S.J.; Ito, K.; Nolte, L.P.

    2004-01-01

    Previous experimental and analytical studies of solute transport in the intervertebral disc have demonstrated that for small molecules diffusive transport alone fulfils the nutritional needs of disc cells. It has been often suggested that fluid flow into and within the disc may enhance the transport

  15. Water flow and solute transport in floating fen root mats

    Science.gov (United States)

    Stofberg, Sija F.; EATM van der Zee, Sjoerd

    2015-04-01

    be very similar and likely functionally related. Our experimental field data were used for modelling water flow and solute transport in floating fens, using HYDRUS 2D. Fluctuations of surface water and root mat, as well as geometry and unsaturated zone parameters can have a major influence on groundwater fluctuations and the exchange between rain and surface water and the water in the root mats. In combination with the duration of salt pulses in surface water, and sensitivity of fen plants to salinity (Stofberg et al. 2014, submitted), risks for rare plants can be anticipated.

  16. New diffusion-like solutions of one-speed transport equations in spherical geometry

    International Nuclear Information System (INIS)

    Sahni, D.C.

    1988-01-01

    Stationary, one-speed, spherically symmetric transport equations are considered in a conservative medium. Closed-form expressions are obtained for the angular flux ψ(r, μ) that yield a total flux varying as 1/r by using Sonine transforms. Properties of this solution are studied and it is shown that the solution can not be identified as a diffusion mode solution of the transport equation. Limitations of the Sonine transform technique are noted. (author)

  17. Myelin-associated proteins labelled by slow axonal transport

    International Nuclear Information System (INIS)

    Giorgi, P.P.; DuBois, H.

    1981-01-01

    This paper deals with the problem of protein metabolism and provides evidence that the neuronal contribution to myelin metabolism may be restricted to lipids only. On the other hand this line of research led to the partial characterization of a group of neuronal proteins probably involved in axo-glial interactions subserving the onset of myelination and the structural maintenance of the mature myelin sheath. Intraocular injection of radioactive amino acids allows the study of the anterograde transport of labelled proteins along retinofugal fibres which are well myelinated. Myelin extracted from the optic nerve and tract under these conditions also contains labelled proteins. Three hypotheses are available to explain this phenomenon. To offer an explanation for this phenomenon the work was planned as follows. a) Characterization of the spatio-temporal pattern of labelling of myelin, in order to define the experimental conditions (survival time and region of the optic pathway to be studied) necessary to obtain maximal labelling. b) Characterization (by gel electrophoresis) of the myelin-associated proteins which become labelled by axonal transport, in order to work on a consistent pattern of labelling. c) Investigation of the possible mechanism responsible for the labelling of myelin-associated proteins. (Auth.)

  18. A biomechanical triphasic approach to the transport of nondilute solutions in articular cartilage.

    Science.gov (United States)

    Abazari, Alireza; Elliott, Janet A W; Law, Garson K; McGann, Locksley E; Jomha, Nadr M

    2009-12-16

    Biomechanical models for biological tissues such as articular cartilage generally contain an ideal, dilute solution assumption. In this article, a biomechanical triphasic model of cartilage is described that includes nondilute treatment of concentrated solutions such as those applied in vitrification of biological tissues. The chemical potential equations of the triphasic model are modified and the transport equations are adjusted for the volume fraction and frictional coefficients of the solutes that are not negligible in such solutions. Four transport parameters, i.e., water permeability, solute permeability, diffusion coefficient of solute in solvent within the cartilage, and the cartilage stiffness modulus, are defined as four degrees of freedom for the model. Water and solute transport in cartilage were simulated using the model and predictions of average concentration increase and cartilage weight were fit to experimental data to obtain the values of the four transport parameters. As far as we know, this is the first study to formulate the solvent and solute transport equations of nondilute solutions in the cartilage matrix. It is shown that the values obtained for the transport parameters are within the ranges reported in the available literature, which confirms the proposed model approach.

  19. Prediction of arsenic and antimony transporter major intrinsic proteins from the genomes of crop plants.

    Science.gov (United States)

    Azad, Abul Kalam; Ahmed, Jahed; Alum, Md Asraful; Hasan, Md Mahbub; Ishikawa, Takahiro; Sawa, Yoshihiro

    2018-02-01

    Major intrinsic proteins (MIPs), commonly known as aquaporins, transport water and non-polar small solutes. Comparing the 3D models and the primary selectivity-related motifs (two Asn-Pro-Ala (NPA) regions, the aromatic/arginine (ar/R) selectivity filter, and Froger's positions (FPs)) of all plant MIPs that have been experimentally proven to transport arsenic (As) and antimony (Sb), some substrate-specific signature sequences (SSSS) or specificity determining sites (SDPs) have been predicted. These SSSS or SDPs were determined in 543 MIPs found in the genomes of 12 crop plants; the As and Sb transporters were predicted to be distributed in noduline-26 like intrinsic proteins (NIPs), and every plant had one or several As and Sb transporter NIPs. Phylogenetic grouping of the NIP subfamily based on the ar/R selectivity filter and FPs were linked to As and Sb transport. We further determined the group-wise substrate selectivity profiles of the NIPs in the 12 crop plants. In addition to two NPA regions, the ar/R filter, and FPs, certain amino acids especially in the pore line, loop D, and termini contribute to the functional distinctiveness of the NIP groups. Expression analysis of transcripts in different organs indicated that most of the As and Sb transporter NIPs were expressed in roots. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. One-dimensional spatially dependent solute transport in semi ...

    African Journals Online (AJOL)

    Space dependent retardation factor is also taken. The nature of porous media and solute pollutant are considered chemically non-reactive. Initially porous domain is considered solute free and the input source condition is considered uniformly continuous. A new transformation is introduced to solve the advection dispersion ...

  1. Yarrowia lipolytica vesicle-mediated protein transport pathways

    Directory of Open Access Journals (Sweden)

    Beckerich Jean-Marie

    2007-11-01

    transport shows that 40% of Y. lipolytica proteins are closer to animal ones, whereas they are only 13% in the case of S. cerevisiae. Conclusion These results provide further support for the idea, previously noted about the endoplasmic reticulum translocation pathway, that Y. lipolytica is more representative of vesicular secretion of animals and other fungi than is S. cerevisiae.

  2. UrbanTransport Solution An Experience From Prague

    African Journals Online (AJOL)

    unique firstlady

    Based on the result of the research ... associated with road transport like its impact on environment ..... Prague is utilizing a variety of marketing strategies used for many years in ... at strategic metro stations providing customers with maps , time ...

  3. A use of Ramachandran potentials in protein solution structure determinations

    International Nuclear Information System (INIS)

    Bertini, Ivano; Cavallaro, Gabriele; Luchinat, Claudio; Poli, Irene

    2003-01-01

    A strategy is developed to use database-derived φ-ψ constraints during simulated annealing procedures for protein solution structure determination in order to improve the Ramachandran plot statistics, while maintaining the agreement with the experimental constraints as the sole criterion for the selection of the family. The procedure, fully automated, consists of two consecutive simulated annealing runs. In the first run, the database-derived φ-ψ constraints are enforced for all aminoacids (but prolines and glycines). A family of structures is then selected on the ground of the lowest violations of the experimental constraints only, and the φ-ψ values for each residue are examined. In the second and final run, the database-derived φ-ψ constraints are enforced only for those residues which in the first run have ended in one and the same favored φ-ψ region. For residues which are either spread over different favored regions or concentrated in disallowed regions, the constraints are not enforced. The final family is then selected, after the second run, again only based on the agreement with the experimental constraints. This automated approach was implemented in DYANA and was tested on as many as 12 proteins, including some containing paramagnetic metals, whose structures had been previously solved in our laboratory. The quality of the structures, and of Ramachandran plot statistics in particular, was notably improved while preserving the agreement with the experimental constraints

  4. Application of Solution NMR Spectroscopy to Study Protein Dynamics

    Directory of Open Access Journals (Sweden)

    Christoph Göbl

    2012-03-01

    Full Text Available Recent advances in spectroscopic methods allow the identification of minute fluctuations in a protein structure. These dynamic properties have been identified as keys to some biological processes. The consequences of this structural flexibility can be far‑reaching and they add a new dimension to the structure-function relationship of biomolecules. Nuclear Magnetic Resonance (NMR spectroscopy allows the study of structure as well as dynamics of biomolecules in a very broad range of timescales at atomic level. A number of new NMR methods have been developed recently to allow the measurements of time scales and spatial fluctuations, which in turn provide the thermodynamics associated with the biological processes. Since NMR parameters reflect ensemble measurements, structural ensemble approaches in analyzing NMR data have also been developed. These new methods in some instances can even highlight previously hidden conformational features of the biomolecules. In this review we describe several solution NMR methods to study protein dynamics and discuss their impact on important biological processes.

  5. The nucleobase cation symporter 1 of Chlamydomonas reinhardtii and that of the evolutionarily distant Arabidopsis thaliana display parallel function and establish a plant-specific solute transport profile.

    Science.gov (United States)

    Schein, Jessica R; Hunt, Kevin A; Minton, Janet A; Schultes, Neil P; Mourad, George S

    2013-09-01

    The single cell alga Chlamydomonas reinhardtii is capable of importing purines as nitrogen sources. An analysis of the annotated C. reinhardtii genome reveals at least three distinct gene families encoding for known nucleobase transporters. In this study the solute transport and binding properties for the lone C. reinhardtii nucleobase cation symporter 1 (CrNCS1) are determined through heterologous expression in Saccharomyces cerevisiae. CrNCS1 acts as a transporter of adenine, guanine, uracil and allantoin, sharing similar - but not identical - solute recognition specificity with the evolutionary distant NCS1 from Arabidopsis thaliana. The results suggest that the solute specificity for plant NCS1 occurred early in plant evolution and are distinct from solute transport specificities of single cell fungal NCS1 proteins. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

  6. Influence of multidrug resistance and drug transport proteins on chemotherapy drug metabolism.

    Science.gov (United States)

    Joyce, Helena; McCann, Andrew; Clynes, Martin; Larkin, Annemarie

    2015-05-01

    Chemotherapy involving the use of anticancer drugs remains an important strategy in the overall management of patients with metastatic cancer. Acquisition of multidrug resistance remains a major impediment to successful chemotherapy. Drug transporters in cell membranes and intracellular drug metabolizing enzymes contribute to the resistance phenotype and determine the pharmacokinetics of anticancer drugs in the body. ATP-binding cassette (ABC) transporters mediate the transport of endogenous metabolites and xenobiotics including cytotoxic drugs out of cells. Solute carrier (SLC) transporters mediate the influx of cytotoxic drugs into cells. This review focuses on the substrate interaction of these transporters, on their biology and what role they play together with drug metabolizing enzymes in eliminating therapeutic drugs from cells. The majority of anticancer drugs are substrates for the ABC transporter and SLC transporter families. Together, these proteins have the ability to control the influx and the efflux of structurally unrelated chemotherapeutic drugs, thereby modulating the intracellular drug concentration. These interactions have important clinical implications for chemotherapy because ultimately they determine therapeutic efficacy, disease progression/relapse and the success or failure of patient treatment.

  7. Pharmaceutical excipients influence the function of human uptake transporting proteins.

    Science.gov (United States)

    Engel, Anett; Oswald, Stefan; Siegmund, Werner; Keiser, Markus

    2012-09-04

    Although pharmaceutical excipients are supposed to be pharmacologically inactive, solubilizing agents like Cremophor EL have been shown to interact with cytochrome P450 (CYP)-dependent drug metabolism as well as efflux transporters such as P-glycoprotein (ABCB1) and multidrug resistance associated protein 2 (ABCC2). However, knowledge about their influence on the function of uptake transporters important in drug disposition is very limited. In this study we investigated the in vitro influence of polyethylene glycol 400 (PEG), hydroxypropyl-β-cyclodextrin (HPCD), Solutol HS 15 (SOL), and Cremophor EL (CrEL) on the organic anion transporting polypeptides (OATP) 1A2, OATP2B1, OATP1B1, and OATP1B3 and the Na(+)/taurocholate cotransporting polypeptide (NTCP). In stably transfected human embryonic kidney cells we analyzed the competition of the excipients with the uptake of bromosulfophthalein in OATP1B1, OATP1B3, OATP2B1, and NTCP, estrone-3-sulfate (E(3)S) in OATP1A2, OATP1B1, and OATP2B1, estradiol-17β-glucuronide in OATP1B3, and taurocholate (TA) in OATP1A2 and NTCP cells. SOL and CrEL were the most potent inhibitors of all transporters with the strongest effect on OATP1A2, OATP1B3, and OATP2B1 (IC(50) < 0.01%). HPCD also strongly inhibited all transport proteins but only for substrates containing a sterane-backbone. Finally, PEG seems to be a selective and potent modulator of OATP1A2 with IC(50) values of 0.05% (TA) and 0.14% (E(3)S). In conclusion, frequently used solubilizing agents were shown to interact substantially with intestinal and hepatic uptake transporters which should be considered in drug development. However, the clinical relevance of these findings needs to be evaluated in further in vivo studies.

  8. Effect of protein solution components in the adsorption of Herbaspirillum seropedicae GlnB protein on mica.

    Science.gov (United States)

    Ferreira, Cecília F G; Benelli, Elaine M; Klein, Jorge J; Schreiner, Wido; Camargo, Paulo C

    2009-10-15

    The adsorption of proteins and its buffer solution on mica surfaces was investigated by atomic force microscopy (AFM). Different salt concentration of the Herbaspirillum seropedicae GlnB protein (GlnB-Hs) solution deposited on mica was investigated. This protein is a globular, soluble homotrimer (36kDa), member of PII-like proteins family involved in signal transducing in prokaryote. Supramolecular structures were formed when this protein was deposited onto bare mica surface. The topographic AFM images of the GlnB-Hs films showed that at high salt concentration the supramolecular structures are spherical-like, instead of the typical doughnut-like shape for low salt concentration. AFM images of NaCl and Tris from the buffer solution showed structures with the same pattern as those observed for high salt protein solution, misleading the image interpretation. XPS experiments showed that GlnB protein film covers the mica surface without chemical reaction.

  9. Brine transport in porous media self-similar solutions

    NARCIS (Netherlands)

    C.J. van Duijn (Hans); L.A. Peletier (Bert); R.J. Schotting (Ruud)

    1996-01-01

    textabstractIn this paper we analyze a model for brine transport in porous media, which includes a mass balance for the fluid, a mass balance for salt, Darcy's law and an equation of state, which relates the fluid density to the salt mass fraction. This model incorporates the effect of local volume

  10. UrbanTransport Solution An Experience From Prague | Jeremiah ...

    African Journals Online (AJOL)

    This paper examines the urban transport problems in Prague in Czech Republic. Based on the result of the research conducted, it was found that with the collapsed of Communism in Czech Republic, there was an upsurge in the use of private cars which was not possible during communism because the law does not ...

  11. Solute transport through porous media using asymptotic dispersivity

    Indian Academy of Sciences (India)

    ber of processes and porous media properties including convective transport .... existence of regions within the porous medium in which there is minimum advective flow. .... concentration at x = L. The initial and the exit boundary conditions can be .... rial was cleaned, washed and dried to ensure that the material free from ...

  12. Reactive solute transport in an asymmetrical fracture-rock matrix system

    Science.gov (United States)

    Zhou, Renjie; Zhan, Hongbin

    2018-02-01

    The understanding of reactive solute transport in a single fracture-rock matrix system is the foundation of studying transport behavior in the complex fractured porous media. When transport properties are asymmetrically distributed in the adjacent rock matrixes, reactive solute transport has to be considered as a coupled three-domain problem, which is more complex than the symmetric case with identical transport properties in the adjacent rock matrixes. This study deals with the transport problem in a single fracture-rock matrix system with asymmetrical distribution of transport properties in the rock matrixes. Mathematical models are developed for such a problem under the first-type and the third-type boundary conditions to analyze the spatio-temporal concentration and mass distribution in the fracture and rock matrix with the help of Laplace transform technique and de Hoog numerical inverse Laplace algorithm. The newly acquired solutions are then tested extensively against previous analytical and numerical solutions and are proven to be robust and accurate. Furthermore, a water flushing phase is imposed on the left boundary of system after a certain time. The diffusive mass exchange along the fracture/rock matrixes interfaces and the relative masses stored in each of three domains (fracture, upper rock matrix, and lower rock matrix) after the water flushing provide great insights of transport with asymmetric distribution of transport properties. This study has the following findings: 1) Asymmetric distribution of transport properties imposes greater controls on solute transport in the rock matrixes. However, transport in the fracture is mildly influenced. 2) The mass stored in the fracture responses quickly to water flushing, while the mass stored in the rock matrix is much less sensitive to the water flushing. 3) The diffusive mass exchange during the water flushing phase has similar patterns under symmetric and asymmetric cases. 4) The characteristic distance

  13. The effect of low-GDP solution on ultrafiltration and solute transport in continuous ambulatory peritoneal dialysis patients.

    Science.gov (United States)

    Cho, Kyu-Hyang; Do, Jun-Young; Park, Jong-Won; Yoon, Kyung-Woo; Kim, Yong-Lim

    2013-01-01

    Several studies have reported benefits for human peritoneal mesothelial cell function of a neutral-pH dialysate low in glucose degradation products (GDPs). However, the effects of low-GDP solution on ultrafiltration (UF), transport of solutes, and control of body water remain elusive. We therefore investigated the effect of low-GDP solution on UF, solute transport, and control of body water. Among 79 new continuous ambulatory peritoneal dialysis (CAPD) patients, 60 completed a 12-month protocol (28 in a lactate-based high-GDP solution group, 32 in a lactate-based low-GDP solution group). Clinical indices--including 24-hour UF volume (UFV), 24-hour urine volume (UV), residual renal function, and dialysis adequacy--were measured at months 1, 6, and 12. At months 1, 6, and 12, UFV, glucose absorption, 4-hour dialysate-to-plasma (D/P) creatinine, and 1-hour D/P Na(+) were assessed during a modified 4.25% peritoneal equilibration test (PET). Body composition by bioelectric impedance analysis was measured at months 1 and 12 in 26 CAPD patients. Daily UFV was lower in the low-GDP group. Despite similar solute transport and aquaporin function, the low-GDP group also showed lower UFV and higher glucose absorption during the PET. Factors associated with UFV during the PET were lactate-based high-GDP solution and 1-hour D/P Na(+). No differences in volume status and obesity at month 12 were observed, and improvements in hypervolemia were equal in both groups. Compared with the high-GDP group, the low-GDP group had a lower UFV during a PET and a lower daily UFV during the first year after peritoneal dialysis initiation. Although the low-GDP group had a lower daily UFV, no difficulties in controlling edema were encountered.

  14. Nuclear transport of heat shock proteins in stressed cells

    International Nuclear Information System (INIS)

    Chughtai, Zahoor Saeed

    2001-01-01

    Nuclear import of proteins that are too large to passively enter the nucleus requires soluble factors, energy , and a nuclear localization signal (NLS). Nuclear protein transport can be regulated, and different forms of stress affect nucleocytoplasmic trafficking. As such, import of proteins containing a classical NLS is inhibited in starving yeast cells. In contrast, the heat shock protein hsp70 Ssa4p concentrates in nuclei upon starvation. Nuclear concentration of Ssa4p in starving cells is reversible, and transfer of nutrient-depleted cells to fresh medium induces Ssa4p nuclear export. This export reaction represents an active process that is sensitive to oxidative stress. Upon starvation, the N-terminal domain of Ssa4p mediates Ssa4p nuclear accumulation, and a short hydrophobic sequence, termed Star (for starvation), is sufficient to localize the reporter proteins green fluorescent protein or β-gaIactosidase to nuclei. To determine whether nuclear accumulation of Star-β-galactosidase depends on a specific nuclear carrier, I have analyzed its distribution in mutant yeast strains that carry a deletion of a single β-importin gene. With this assay I have identified Nmd5p as a β-importin required to concentrate Star-β-galactosidase in nuclei of stationary phase cells. (author)

  15. Nuclear transport of heat shock proteins in stressed cells

    Energy Technology Data Exchange (ETDEWEB)

    Chughtai, Zahoor Saeed

    2001-07-01

    Nuclear import of proteins that are too large to passively enter the nucleus requires soluble factors, energy , and a nuclear localization signal (NLS). Nuclear protein transport can be regulated, and different forms of stress affect nucleocytoplasmic trafficking. As such, import of proteins containing a classical NLS is inhibited in starving yeast cells. In contrast, the heat shock protein hsp70 Ssa4p concentrates in nuclei upon starvation. Nuclear concentration of Ssa4p in starving cells is reversible, and transfer of nutrient-depleted cells to fresh medium induces Ssa4p nuclear export. This export reaction represents an active process that is sensitive to oxidative stress. Upon starvation, the N-terminal domain of Ssa4p mediates Ssa4p nuclear accumulation, and a short hydrophobic sequence, termed Star (for starvation), is sufficient to localize the reporter proteins green fluorescent protein or {beta}-gaIactosidase to nuclei. To determine whether nuclear accumulation of Star-{beta}-galactosidase depends on a specific nuclear carrier, I have analyzed its distribution in mutant yeast strains that carry a deletion of a single {beta}-importin gene. With this assay I have identified Nmd5p as a {beta}-importin required to concentrate Star-{beta}-galactosidase in nuclei of stationary phase cells. (author)

  16. Diverging diamond interchange, results from the right transportation solution survey : staff summary, January 2010.

    Science.gov (United States)

    2010-01-01

    Based on the results from this research, MoDOT can confidently state that the diverging diamond was the right transportation solution for the Interstate 44 and Route 13 intersection. The overall results show: Most Springfield area residents were ...

  17. Exact and Numerical Solutions of a Spatially-Distributed Mathematical Model for Fluid and Solute Transport in Peritoneal Dialysis

    Directory of Open Access Journals (Sweden)

    Roman Cherniha

    2016-06-01

    Full Text Available The nonlinear mathematical model for solute and fluid transport induced by the osmotic pressure of glucose and albumin with the dependence of several parameters on the hydrostatic pressure is described. In particular, the fractional space available for macromolecules (albumin was used as a typical example and fractional fluid void volume were assumed to be different functions of hydrostatic pressure. In order to find non-uniform steady-state solutions analytically, some mathematical restrictions on the model parameters were applied. Exact formulae (involving hypergeometric functions for the density of fluid flux from blood to tissue and the fluid flux across tissues were constructed. In order to justify the applicability of the analytical results obtained, a wide range of numerical simulations were performed. It was found that the analytical formulae can describe with good approximation the fluid and solute transport (especially the rate of ultrafiltration for a wide range of values of the model parameters.

  18. Analysis of the Sodium Recirculation Theory of Solute Coupled Water Transport in Small Intestine

    DEFF Research Database (Denmark)

    Larsen, E. H.; Sørensen, Jens Nørkær; Sørensen, J. B.

    2002-01-01

    Our previous mathematical model of solute-coupled water transport through the intestinal epithelium is extended for dealing with electrolytes rather than electroneutral solutes. A 3Na+-2K+ pump in the lateral membranes provides the energy-requiring step for driving transjunctional and translateral......, computations predict that the concentration differences between lis and bathing solutions are small for all three ions. Nevertheless, the diffusion fluxes of the ions out of lis significantly exceed their mass transports. It is concluded that isotonic transport requires recirculation of all three ions....... The computed sodium recirculation flux that is required for isotonic transport corresponds to that estimated in experiments on toad small intestine. This result is shown to be robust and independent of whether the apical entrance mechanism for the sodium ion is a channel, a SGLT1 transporter driving inward...

  19. Brain washing : Transport of cerebral extracellular fluids and solutes

    NARCIS (Netherlands)

    Bedussi, B.

    2017-01-01

    Regulation of extracellular volume and fluid composition provides a robust microenvironment for brain cells. In peripheral tissue, fluid surplus and solutes are removed from the interstitium via drainage into lymphatic channels. Since the central nervous system lacks a proper lymphatic vasculature,

  20. Preliminary model of fluid and solute distribution and transport during hemorrhage.

    Science.gov (United States)

    Gyenge, C C; Bowen, B D; Reed, R K; Bert, J L

    2003-01-01

    The distribution and transport of fluid, ions, and other solutes (plasma proteins and glucose) are described in a mathematical model of unresuscitated hemorrhage. The model is based on balances of each material in both the circulation and its red blood cells, as well as in a whole-body tissue compartment along with its cells. Exchange between these four compartments occurs by a number of different mechanisms. The hemorrhage model has as its basis a validated model, due to Gyenge et al., of fluid and solute exchange in the whole body of a standard human. Hypothetical but physiologically based features such as glucose and small ion releases along with cell membrane changes are incorporated into the hemorrhage model to describe the system behavior, particularly during larger hemorrhages. Moderate (10%-30% blood volume loss) and large (> 30% blood loss) hemorrhage dynamics are simulated and compared with available data. The model predictions compare well with the available information for both types of hemorrhages and provide a reasonable description of the progression of a large hemorrhage from the compensatory phase through vascular collapse.

  1. A compartmentalized solute transport model for redox zones in contaminated aquifers: 1. Theory and development

    Science.gov (United States)

    Abrams , Robert H.; Loague, Keith

    2000-01-01

    This paper, the first of two parts [see Abrams and Loague, this issue], takes the compartmentalized approach for the geochemical evolution of redox zones presented by Abrams et al. [1998] and embeds it within a solute transport framework. In this paper the compartmentalized approach is generalized to facilitate the description of its incorporation into a solute transport simulator. An equivalent formulation is developed which removes any discontinuities that may occur when switching compartments. Rate‐limited redox reactions are modeled with a modified Monod relationship that allows either the organic substrate or the electron acceptor to be the rate‐limiting reactant. Thermodynamic constraints are used to inhibit lower‐energy redox reactions from occurring under infeasible geochemical conditions without imposing equilibrium on the lower‐energy reactions. The procedure used allows any redox reaction to be simulated as being kinetically limited or thermodynamically limited, depending on local geochemical conditions. Empirical reaction inhibition methods are not needed. The sequential iteration approach (SIA), a technique which allows the number of solute transport equations to be reduced, is adopted to solve the coupled geochemical/solute transport problem. When the compartmentalized approach is embedded within the SIA, with the total analytical concentration of each component as the dependent variable in the transport equation, it is possible to reduce the number of transport equations even further than with the unmodified SIA. A one‐dimensional, coupled geochemical/solute transport simulation is presented in which redox zones evolve dynamically in time and space. The compartmentalized solute transport (COMPTRAN) model described in this paper enables the development of redox zones to be simulated under both kinetic and thermodynamic constraints. The modular design of COMPTRAN facilitates the use of many different, preexisting solute transport and

  2. Fluid flow and convective transport of solutes within the intervertebral disc.

    Science.gov (United States)

    Ferguson, Stephen J; Ito, Keita; Nolte, Lutz P

    2004-02-01

    Previous experimental and analytical studies of solute transport in the intervertebral disc have demonstrated that for small molecules diffusive transport alone fulfils the nutritional needs of disc cells. It has been often suggested that fluid flow into and within the disc may enhance the transport of larger molecules. The goal of the study was to predict the influence of load-induced interstitial fluid flow on mass transport in the intervertebral disc. An iterative procedure was used to predict the convective transport of physiologically relevant molecules within the disc. An axisymmetric, poroelastic finite-element structural model of the disc was developed. The diurnal loading was divided into discrete time steps. At each time step, the fluid flow within the disc due to compression or swelling was calculated. A sequentially coupled diffusion/convection model was then employed to calculate solute transport, with a constant concentration of solute being provided at the vascularised endplates and outer annulus. Loading was simulated for a complete diurnal cycle, and the relative convective and diffusive transport was compared for solutes with molecular weights ranging from 400 Da to 40 kDa. Consistent with previous studies, fluid flow did not enhance the transport of low-weight solutes. During swelling, interstitial fluid flow increased the unidirectional penetration of large solutes by approximately 100%. Due to the bi-directional temporal nature of disc loading, however, the net effect of convective transport over a full diurnal cycle was more limited (30% increase). Further study is required to determine the significance of large solutes and the timing of their delivery for disc physiology.

  3. TLC scheme for numerical solution of the transport equation on equilateral triangular meshes

    International Nuclear Information System (INIS)

    Walters, W.F.

    1983-01-01

    A new triangular linear characteristic TLC scheme for numerically solving the transport equation on equilateral triangular meshes has been developed. This scheme uses the analytic solution of the transport equation in the triangle as its basis. The data on edges of the triangle are assumed linear as is the source representation. A characteristic approach or nodal approach is used to obtain the analytic solution. Test problems indicate that the new TLC is superior to the widely used DITRI scheme for accuracy

  4. Water flow and solute transport through fractured rock

    International Nuclear Information System (INIS)

    Bolt, J.E.; Bourke, P.J.; Pascoe, D.M.; Watkins, V.M.B.; Kingdon, R.D.

    1990-09-01

    In densely fractured slate at the Nirex research site in Cornwall, the positions, orientations and hydraulic conductivities of the 380 fractures intersecting a drill hole between 9 and 50 m depth have been individually measured. These data have been used: to determine the dimensions of statistically representative volumes of the network of fractures and to predict, using discrete flow path modelling and the NAPSAC code, the total flows into the fractures when large numbers are simultaneously pressurised along various lengths of the hole. Corresponding measurements, which validated the NAPSAC code to factor of two accuracy for the Cornish site, are reported. Possibilities accounting for this factor are noted for experimental investigation, and continuing, more extensive, inter hole flow and transport measurements are outlined. The application of this experimental and theoretical approach for calculating radionuclide transport in less densely fractured rock suitable for waste disposal is discussed. (Author)

  5. Water flow and solute transport through fractured rock

    International Nuclear Information System (INIS)

    Bourke, P.J.; Kingdon, R.D.; Bolt, J.E.; Pascoe, D.M.; Watkins, V.M.B.

    1991-01-01

    In densely fractured slate at the Nirex research site in Cornwall, the positions, orientations and hydraulic conductivities of the 380 fractures intersecting a drill hole between 9 and 50 m depths have been individually measured. These data have been used: - to determine the dimensions of statistically representative volumes of the sheetwork of fractures; - to predict; using discrete flowpath modelling and the NAPSAC code; the total flows into the fractures when large numbers are simultaneously pressurised along various lengths of the hole; Corresponding measurements, which proved the modelling and validated the code to factor of two accuracy, are reported. Possibilities accounting for this factor are noted for experimental investigation, and continuing, more extensive inter-hole flow and transport measurements are outlined. The application of this experimental and theoretical approach for calculating radionuclide transport in less densely fractured rock suitable for waste disposal is discussed. 7 figs., 9 refs

  6. A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain.

    Science.gov (United States)

    Wu, R; Wilton, R; Cuff, M E; Endres, M; Babnigg, G; Edirisinghe, J N; Henry, C S; Joachimiak, A; Schiffer, M; Pokkuluri, P R

    2017-04-01

    We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from Lake Retba, in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously, and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport. © 2017 The Protein Society.

  7. A transportronic solution to the problem of interorbital transportation

    Science.gov (United States)

    Brown, William C.

    1992-01-01

    An all-electronic transportation system described by the term 'transportronics' is examined as a means of solving the current problem of the high cost of transporting material from low-Earth orbit (LEO) to geostationary orbit (GEO). In this transportation system, low cost electric energy at the surface of the Earth is efficiently converted into microwave power which is then efficiently formed into a narrow beam which is kept incident upon the orbital transfer vehicles (OTV's) by electronic tracking. The incident beam is efficiently captured and converted into DC power by a device which has a very high ratio of DC power output to its mass. Because the mass of the electric thruster is also low, the resulting acceleration is unprecedented for electric-propelled vehicles. However, the performance of the system in terms of transit times from LEO to GEO is penalized by the short time of contact between the beam and the vehicle in low-Earth orbits. This makes it necessary to place the Earth based transmitters and the vehicles in the equatorial plane thus introducing many geopolitical factors. Technically, however, such a system as described in the report may out-perform any other approach to transportation in the LEO to GEO regime. The report describes and analyzes all portions of the beamed microwave power transmission system in considerable detail. An economic analysis of the operating and capital costs is made with the aid of a reference system capable of placing about 130,000 kilograms of payload into GEO each year. More mature states of the system are then examined, to a level in which 60,000 metric tons per year could be placed into GEO.

  8. Numerical fluid solutions for nonlocal electron transport in hot plasmas: Equivalent diffusion versus nonlocal source

    International Nuclear Information System (INIS)

    Colombant, Denis; Manheimer, Wallace

    2010-01-01

    Flux limitation and preheat are important processes in electron transport occurring in laser produced plasmas. The proper calculation of both of these has been a subject receiving much attention over the entire lifetime of the laser fusion project. Where nonlocal transport (instead of simple single flux limit) has been modeled, it has always been with what we denote the equivalent diffusion solution, namely treating the transport as only a diffusion process. We introduce here a new approach called the nonlocal source solution and show it is numerically viable for laser produced plasmas. It turns out that the equivalent diffusion solution generally underestimates preheat. Furthermore, the advance of the temperature front, and especially the preheat, can be held up by artificial 'thermal barriers'. The nonlocal source method of solution, on the other hand more accurately describes preheat and can stably calculate the solution for the temperature even if the heat flux is up the gradient.

  9. Effects of Temperature on Solute Transport Parameters in Differently-Textured Soils at Saturated Condition

    Science.gov (United States)

    Hamamoto, S.; Arihara, M.; Kawamoto, K.; Nishimura, T.; Komatsu, T.; Moldrup, P.

    2014-12-01

    Subsurface warming driven by global warming, urban heat islands, and increasing use of shallow geothermal heating and cooling systems such as the ground source heat pump, potentially causes changes in subsurface mass transport. Therefore, understanding temperature dependency of the solute transport characteristics is essential to accurately assess environmental risks due to increased subsurface temperature. In this study, one-dimensional solute transport experiments were conducted in soil columns under temperature control to investigate effects of temperature on solute transport parameters, such as solute dispersion and diffusion coefficients, hydraulic conductivity, and retardation factor. Toyoura sand, Kaolin clay, and intact loamy soils were used in the experiments. Intact loamy soils were taken during a deep well boring at the Arakawa Lowland in Saitama Prefecture, Japan. In the transport experiments, the core sample with 5-cm diameter and 4-cm height was first isotropically consolidated, whereafter 0.01M KCl solution was injected to the sample from the bottom. The concentrations of K+ and Cl- in the effluents were analyzed by an ion chromatograph to obtain solute breakthrough curves. The solute transport parameters were calculated from the breakthrough curves. The experiments were conducted under different temperature conditions (15, 25, and 40 oC). The retardation factor for the intact loamy soils decreased with increasing temperature, while water permeability increased due to reduced viscosity of water at higher temperature. Opposite, the effect of temperature on solute dispersivity for the intact loamy soils was insignificant. The effects of soil texture on the temperature dependency of the solute transport characteristics will be further investigated from comparison of results from differently-textured samples.

  10. A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain: Periplasmic Ligand Binding Protein Dret_0059

    Energy Technology Data Exchange (ETDEWEB)

    Wu, R. [Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne Illinois 60439; Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Wilton, R. [Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Cuff, M. E. [Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne Illinois 60439; Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Structural Biology Center, Argonne National Laboratory, Argonne Illinois 60439; Endres, M. [Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne Illinois 60439; Babnigg, G. [Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne Illinois 60439; Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Edirisinghe, J. N. [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne Illinois 60439; Computation Institute, University of Chicago, Chicago Illinois 60637; Henry, C. S. [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne Illinois 60439; Computation Institute, University of Chicago, Chicago Illinois 60637; Joachimiak, A. [Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne Illinois 60439; Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Structural Biology Center, Argonne National Laboratory, Argonne Illinois 60439; Department of Biochemistry and Molecular Biology, University of Chicago, Chicago Illinois 60637; Schiffer, M. [Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439; Pokkuluri, P. R. [Biosciences Division, Argonne National Laboratory, Argonne Illinois 60439

    2017-03-06

    We report the structural and biochemical characterization of a novel periplasmic ligand-binding protein, Dret_0059, from Desulfohalobium retbaense DSM 5692, an organism isolated from the Salt Lake Retba in Senegal. The structure of the protein consists of a unique combination of a periplasmic solute binding protein (SBP) domain at the N-terminal and a tandem PAS-like sensor domain at the C-terminal region. SBP domains are found ubiquitously and their best known function is in solute transport across membranes. PAS-like sensor domains are commonly found in signal transduction proteins. These domains are widely observed as parts of many protein architectures and complexes but have not been observed previously within the same polypeptide chain. In the structure of Dret_0059, a ketoleucine moiety is bound to the SBP, whereas a cytosine molecule is bound in the distal PAS-like domain of the tandem PAS-like domain. Differential scanning flourimetry support the binding of ligands observed in the crystal structure. There is significant interaction between the SBP and tandem PAS-like domains, and it is possible that the binding of one ligand could have an effect on the binding of the other. We uncovered three other proteins with this structural architecture in the non-redundant sequence data base, and predict that they too bind the same substrates. The genomic context of this protein did not offer any clues for its function. We did not find any biological process in which the two observed ligands are coupled. The protein Dret_0059 could be involved in either signal transduction or solute transport.

  11. Chloroplast Iron Transport Proteins - Function and Impact on Plant Physiology.

    Science.gov (United States)

    López-Millán, Ana F; Duy, Daniela; Philippar, Katrin

    2016-01-01

    Chloroplasts originated about three billion years ago by endosymbiosis of an ancestor of today's cyanobacteria with a mitochondria-containing host cell. During evolution chloroplasts of higher plants established as the site for photosynthesis and thus became the basis for all life dependent on oxygen and carbohydrate supply. To fulfill this task, plastid organelles are loaded with the transition metals iron, copper, and manganese, which due to their redox properties are essential for photosynthetic electron transport. In consequence, chloroplasts for example represent the iron-richest system in plant cells. However, improvement of oxygenic photosynthesis in turn required adaptation of metal transport and homeostasis since metal-catalyzed generation of reactive oxygen species (ROS) causes oxidative damage. This is most acute in chloroplasts, where radicals and transition metals are side by side and ROS-production is a usual feature of photosynthetic electron transport. Thus, on the one hand when bound by proteins, chloroplast-intrinsic metals are a prerequisite for photoautotrophic life, but on the other hand become toxic when present in their highly reactive, radical generating, free ionic forms. In consequence, transport, storage and cofactor-assembly of metal ions in plastids have to be tightly controlled and are crucial throughout plant growth and development. In the recent years, proteins for iron transport have been isolated from chloroplast envelope membranes. Here, we discuss their putative functions and impact on cellular metal homeostasis as well as photosynthetic performance and plant metabolism. We further consider the potential of proteomic analyses to identify new players in the field.

  12. Regulation of dopamine transporter function by protein-protein interactions: new discoveries and methodological challenges

    DEFF Research Database (Denmark)

    Eriksen, Jacob; Jørgensen, Trine Nygaard; Gether, Ulrik

    2010-01-01

    -synaptic neurons. This has led to the identification of a plethora of different kinases, receptors and scaffolding proteins that interact with DAT and hereby either modulate the catalytic activity of the transporter or regulate its trafficking and degradation. Several new tools for studying DAT regulation in live...

  13. The Governor's Challenge: "Building a Stronger Virginia Today": Transportation Visions and Solutions

    Science.gov (United States)

    Baker, Susan

    2008-01-01

    Using STM(Science, Technology, Engineering, Math) education, this emerging workforce will have the chance to creatively solve one of Virginia's biggest challenges: TRANSPORTATION. - Students will be asked to develop alternative transportation systems for the state. This competition will enable teams to work with business mentors to design creative solutions for regional gridlocks and develop other transportation systems to more easily and expediently reach all parts of the Commonwealth.

  14. Protein Kinases C-Mediated Regulations of Drug Transporter Activity, Localization and Expression

    Directory of Open Access Journals (Sweden)

    Abdullah Mayati

    2017-04-01

    Full Text Available Drug transporters are now recognized as major actors in pharmacokinetics, involved notably in drug–drug interactions and drug adverse effects. Factors that govern their activity, localization and expression are therefore important to consider. In the present review, the implications of protein kinases C (PKCs in transporter regulations are summarized and discussed. Both solute carrier (SLC and ATP-binding cassette (ABC drug transporters can be regulated by PKCs-related signaling pathways. PKCs thus target activity, membrane localization and/or expression level of major influx and efflux drug transporters, in various normal and pathological types of cells and tissues, often in a PKC isoform-specific manner. PKCs are notably implicated in membrane insertion of bile acid transporters in liver and, in this way, are thought to contribute to cholestatic or choleretic effects of endogenous compounds or drugs. The exact clinical relevance of PKCs-related regulation of drug transporters in terms of drug resistance, pharmacokinetics, drug–drug interactions and drug toxicity remains however to be precisely determined. This issue is likely important to consider in the context of the development of new drugs targeting PKCs-mediated signaling pathways, for treating notably cancers, diabetes or psychiatric disorders.

  15. New solution for transport and industrial noise protection through reflective noise barriers

    Directory of Open Access Journals (Sweden)

    Kralov Ivan

    2017-01-01

    Full Text Available A new solution for protection of transportation and industrial noise through reflective noise barriers is proposed and investigated in this study. The new solution combines the advantages of the known barriers and has its own advantages in addition. The preliminary results show a very good level of noise reduction for this type of barriers.

  16. Large time behaviour of oscillatory nonlinear solute transport in porous media

    NARCIS (Netherlands)

    Duijn, van C.J.; Zee, van der S.E.A.T.M.

    2018-01-01

    Oscillations in flow occur under many different situations in natural porous media, due to tidal, daily or seasonal patterns. In this paper, we investigate how such oscillations in flow affect the transport of an initially sharp solute front, if the solute undergoes nonlinear sorption and,

  17. Reactive silica transport in fractured porous media: Analytical solutions for a system of parallel fractures

    Science.gov (United States)

    Yang, Jianwen

    2012-04-01

    A general analytical solution is derived by using the Laplace transformation to describe transient reactive silica transport in a conceptualized 2-D system involving a set of parallel fractures embedded in an impermeable host rock matrix, taking into account of hydrodynamic dispersion and advection of silica transport along the fractures, molecular diffusion from each fracture to the intervening rock matrix, and dissolution of quartz. A special analytical solution is also developed by ignoring the longitudinal hydrodynamic dispersion term but remaining other conditions the same. The general and special solutions are in the form of a double infinite integral and a single infinite integral, respectively, and can be evaluated using Gauss-Legendre quadrature technique. A simple criterion is developed to determine under what conditions the general analytical solution can be approximated by the special analytical solution. It is proved analytically that the general solution always lags behind the special solution, unless a dimensionless parameter is less than a critical value. Several illustrative calculations are undertaken to demonstrate the effect of fracture spacing, fracture aperture and fluid flow rate on silica transport. The analytical solutions developed here can serve as a benchmark to validate numerical models that simulate reactive mass transport in fractured porous media.

  18. Aquaporin-11: A channel protein lacking apparent transport function expressed in brain

    Directory of Open Access Journals (Sweden)

    Tsunenari Takashi

    2006-05-01

    Full Text Available Abstract Background The aquaporins are a family of integral membrane proteins composed of two subfamilies: the orthodox aquaporins, which transport only water, and the aquaglyceroporins, which transport glycerol, urea, or other small solutes. Two recently described aquaporins, numbers 11 and 12, appear to be more distantly related to the other mammalian aquaporins and aquaglyceroporins. Results We report on the characterization of Aquaporin-11 (AQP11. AQP11 RNA and protein is found in multiple rat tissues, including kidney, liver, testes and brain. AQP11 has a unique distribution in brain, appearing in Purkinje cell dendrites, hippocampal neurons of CA1 and CA2, and cerebral cortical neurons. Immunofluorescent staining of Purkinje cells indicates that AQP11 is intracellular. Unlike other aquaporins, Xenopus oocytes expressing AQP11 in the plasma membrane failed to transport water, glycerol, urea, or ions. Conclusion AQP11 is functionally distinct from other proteins of the aquaporin superfamily and could represent a new aquaporin subfamily. Further studies are necessary to elucidate the role of AQP11 in the brain.

  19. Prolonged river water pollution due to variable-density flow and solute transport in the riverbed

    Science.gov (United States)

    Jin, Guangqiu; Tang, Hongwu; Li, Ling; Barry, D. A.

    2015-04-01

    A laboratory experiment and numerical modeling were used to examine effects of density gradients on hyporheic flow and solute transport under the condition of a solute pulse input to a river with regular bed forms. Relatively low-density gradients due to an initial salt pulse concentration of 1.55 kg m-3 applied in the experiment were found to modulate significantly the pore-water flow and solute transport in the riverbed. Such density gradients increased downward flow and solute transport in the riverbed by factors up to 1.6. This resulted in a 12.2% increase in the total salt transfer from the water column to the riverbed over the salt pulse period. As the solute pulse passed, the effect of the density gradients reversed, slowing down the release of the solute back to the river water by a factor of 3.7. Numerical modeling indicated that these density effects intensified as salt concentrations in the water column increased. Simulations further showed that the density gradients might even lead to unstable flow and result in solute fingers in the bed of large bed forms. The slow release of solute from the bed back to the river led to a long tail of solute concentration in the river water. These findings have implications for assessment of impact of pollution events on river systems, in particular, long-term effects on both the river water and riverbed due to the hyporheic exchange.

  20. Integrated compartmental model for describing the transport of solute in a fractured porous medium. [FRACPORT

    Energy Technology Data Exchange (ETDEWEB)

    DeAngelis, D.L.; Yeh, G.T.; Huff, D.D.

    1984-10-01

    This report documents a model, FRACPORT, that simulates the transport of a solute through a fractured porous matrix. The model should be useful in analyzing the possible transport of radionuclides from shallow-land burial sites in humid environments. The use of the model is restricted to transport through saturated zones. The report first discusses the general modeling approach used, which is based on the Integrated Compartmental Method. The basic equations of solute transport are then presented. The model, which assumes a known water velocity field, solves these equations on two different time scales; one related to rapid transport of solute along fractures and the other related to slower transport through the porous matrix. FRACPORT is validated by application to a simple example of fractured porous medium transport that has previously been analyzed by other methods. Then its utility is demonstrated in analyzing more complex cases of pulses of solute into a fractured matrix. The report serves as a user's guide to FRACPORT. A detailed description of data input, along with a listing of input for a sample problem, is provided. 16 references, 18 figures, 3 tables.

  1. Membrane proteins involved in transport, vesicle traffic and Ca(2+) signaling increase in beetroots grown in saline soils.

    Science.gov (United States)

    Lino, Bárbara; Chagolla, Alicia; E González de la Vara, Luis

    2016-07-01

    By separating plasma membrane proteins according to their hydropathy from beetroots grown in saline soils, several proteins probably involved in salt tolerance were identified by mass spectrometry. Beetroots, as a salt-tolerant crop, have developed mechanisms to cope with stresses associated with saline soils. To observe which plasma membrane (PM) proteins were more abundant in beet roots grown in saline soils, beet root plants were irrigated with water or 0.2 M NaCl. PM-enriched membrane preparations were obtained from these plants, and their proteins were separated according to their hydropathy by serial phase partitioning with Triton X-114. Some proteins whose abundance increased visibly in membranes from salt-grown beetroots were identified by mass spectrometry. Among them, there was a V-type H(+)-ATPase (probably from contaminating vacuolar membranes), which increased with salt at all stages of beetroots' development. Proteins involved in solute transport (an H(+)-transporting PPase and annexins), vesicle traffic (clathrin and synaptotagmins), signal perception and transduction (protein kinases and phospholipases, mostly involved in calcium signaling) and metabolism, appeared to increase in salt-grown beetroot PM-enriched membranes. These results suggest that PM and vacuolar proteins involved in transport, metabolism and signal transduction increase in beet roots adapted to saline soils. In addition, these results show that serial phase partitioning with Triton X-114 is a useful method to separate membrane proteins for their identification by mass spectrometry.

  2. The Human Gene SLC25A29, of Solute Carrier Family 25, Encodes a Mitochondrial Transporter of Basic Amino Acids*

    Science.gov (United States)

    Porcelli, Vito; Fiermonte, Giuseppe; Longo, Antonella; Palmieri, Ferdinando

    2014-01-01

    The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport carboxylates, amino acids, nucleotides, and cofactors across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. In this work, a member of this family, SLC25A29, previously reported to be a mitochondrial carnitine/acylcarnitine- or ornithine-like carrier, has been thoroughly characterized biochemically. The SLC25A29 gene was overexpressed in Escherichia coli, and the gene product was purified and reconstituted in phospholipid vesicles. Its transport properties and kinetic parameters demonstrate that SLC25A29 transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Carnitine and acylcarnitines were not transported by SLC25A29. This carrier catalyzed substantial uniport besides a counter-exchange transport, exhibited a high transport affinity for arginine and lysine, and was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation. PMID:24652292

  3. The human gene SLC25A29, of solute carrier family 25, encodes a mitochondrial transporter of basic amino acids.

    Science.gov (United States)

    Porcelli, Vito; Fiermonte, Giuseppe; Longo, Antonella; Palmieri, Ferdinando

    2014-05-09

    The human genome encodes 53 members of the solute carrier family 25 (SLC25), also called the mitochondrial carrier family, many of which have been shown to transport carboxylates, amino acids, nucleotides, and cofactors across the inner mitochondrial membrane, thereby connecting cytosolic and matrix functions. In this work, a member of this family, SLC25A29, previously reported to be a mitochondrial carnitine/acylcarnitine- or ornithine-like carrier, has been thoroughly characterized biochemically. The SLC25A29 gene was overexpressed in Escherichia coli, and the gene product was purified and reconstituted in phospholipid vesicles. Its transport properties and kinetic parameters demonstrate that SLC25A29 transports arginine, lysine, homoarginine, methylarginine and, to a much lesser extent, ornithine and histidine. Carnitine and acylcarnitines were not transported by SLC25A29. This carrier catalyzed substantial uniport besides a counter-exchange transport, exhibited a high transport affinity for arginine and lysine, and was saturable and inhibited by mercurial compounds and other inhibitors of mitochondrial carriers to various degrees. The main physiological role of SLC25A29 is to import basic amino acids into mitochondria for mitochondrial protein synthesis and amino acid degradation.

  4. Mass transfer processes and field-scale transport of organic solutes

    International Nuclear Information System (INIS)

    Brusseau, M.L.

    1990-01-01

    The influence of mass transfer processes, such as sorption/desorption and mass transfer between immiscible liquids and water, on the transport of organic solutes is discussed. Rate-limited sorption of organic solutes caused by a diffusion-constrained mechanism is shown to be significant under laboratory conditions. The significance of the impact of nonequilibrium sorption on field-scale transport is scale dependent. The impact of organic liquids on mass transfer and transport of organic solutes depends upon the nature of the solute and the nature and form of the organic liquid. For example, while retardation of nonionic solutes is decreased in mixed-solvent systems, (i.e. systems comprised of water and a miscible organic liquid or an immiscible liquid present in concentrations below phase separation), the retardation of organic acids may, in some cases, increase with addition of a cosolvent. While the presence of an immiscible liquid existing as a mobile phase will reduce retention of organic solutes, the presence of residual saturation of an immiscible liquid can significantly increase retention. A model is presented that incorporates the effects of retention resulting from residual saturation, as well as nonequilibrium sorption, on the transport of organic solutes. (Author) (70 refs., 3 figs.)

  5. The separation of radionuclide migration by solution and particle transport in LLRW repository buffer material

    International Nuclear Information System (INIS)

    Torok, J.; Buckley, L.P.; Woods, B.L.

    1989-01-01

    Laboratory-scale lysimeter experiments were performed with simulated waste forms placed in candidate buffer materials which have been chosen for a low-level radioactive waste repository. Radionuclide releases into the effluent water and radionuclide capture by the buffer material were determined. The results could not be explained by traditional solution transport mechanisms, and transport by particles released from the waste form and/or transport by buffer particles were suspected as the dominant mechanism for radionuclide release from the lysimeters. To elucidate the relative contribution of particle and solution transport, the waste forms were replaced by a wafer of neutron-activated buffer soaked with selected soluble isotopes. Particle transport was determined by the movement of gamma-emitting neutron-activation products through the lysimeter. Solution transport was quantified by comparing the migration of soluble radionuclides relative to the transport of neutron activation products. The new approach for monitoring radionuclide migration in soil is presented. It facilitates the determination of most of the fundamental coefficients required to model the transport process

  6. VS2DRTI: Simulating Heat and Reactive Solute Transport in Variably Saturated Porous Media.

    Science.gov (United States)

    Healy, Richard W; Haile, Sosina S; Parkhurst, David L; Charlton, Scott R

    2018-01-29

    Variably saturated groundwater flow, heat transport, and solute transport are important processes in environmental phenomena, such as the natural evolution of water chemistry of aquifers and streams, the storage of radioactive waste in a geologic repository, the contamination of water resources from acid-rock drainage, and the geologic sequestration of carbon dioxide. Up to now, our ability to simulate these processes simultaneously with fully coupled reactive transport models has been limited to complex and often difficult-to-use models. To address the need for a simple and easy-to-use model, the VS2DRTI software package has been developed for simulating water flow, heat transport, and reactive solute transport through variably saturated porous media. The underlying numerical model, VS2DRT, was created by coupling the flow and transport capabilities of the VS2DT and VS2DH models with the equilibrium and kinetic reaction capabilities of PhreeqcRM. Flow capabilities include two-dimensional, constant-density, variably saturated flow; transport capabilities include both heat and multicomponent solute transport; and the reaction capabilities are a complete implementation of geochemical reactions of PHREEQC. The graphical user interface includes a preprocessor for building simulations and a postprocessor for visual display of simulation results. To demonstrate the simulation of multiple processes, the model is applied to a hypothetical example of injection of heated waste water to an aquifer with temperature-dependent cation exchange. VS2DRTI is freely available public domain software. © 2018, National Ground Water Association.

  7. Optimal solution of full fuzzy transportation problems using total integral ranking

    Science.gov (United States)

    Sam’an, M.; Farikhin; Hariyanto, S.; Surarso, B.

    2018-03-01

    Full fuzzy transportation problem (FFTP) is a transportation problem where transport costs, demand, supply and decision variables are expressed in form of fuzzy numbers. To solve fuzzy transportation problem, fuzzy number parameter must be converted to a crisp number called defuzzyfication method. In this new total integral ranking method with fuzzy numbers from conversion of trapezoidal fuzzy numbers to hexagonal fuzzy numbers obtained result of consistency defuzzyfication on symmetrical fuzzy hexagonal and non symmetrical type 2 numbers with fuzzy triangular numbers. To calculate of optimum solution FTP used fuzzy transportation algorithm with least cost method. From this optimum solution, it is found that use of fuzzy number form total integral ranking with index of optimism gives different optimum value. In addition, total integral ranking value using hexagonal fuzzy numbers has an optimal value better than the total integral ranking value using trapezoidal fuzzy numbers.

  8. Global stability and exact solution of an arbitrary-solute nonlinear cellular mass transport system.

    Science.gov (United States)

    Benson, James D

    2014-12-01

    The prediction of the cellular state as a function of extracellular concentrations and temperatures has been of interest to physiologists for nearly a century. One of the most widely used models in the field is one where mass flux is linearly proportional to the concentration difference across the membrane. These fluxes define a nonlinear differential equation system for the intracellular state, which when coupled with appropriate initial conditions, define the intracellular state as a function of the extracellular concentrations of both permeating and nonpermeating solutes. Here we take advantage of a reparametrization scheme to extend existing stability results to a more general setting and to a develop analytical solutions to this model for an arbitrary number of extracellular solutes. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Approximate solution of the transport equation by methods of Galerkin type

    International Nuclear Information System (INIS)

    Pitkaranta, J.

    1977-01-01

    Questions of the existence, uniqueness, and convergence of approximate solutions of transport equations by methods of the Galerkin type (where trial and weighting functions are the same) are discussed. The results presented do not exclude the infinite-dimensional case. Two strategies can be followed in the variational approximation of the transport operator: one proceeds from the original form of the transport equation, while the other is based on the partially symmetrized equation. Both principles are discussed in this paper. The transport equation is assumed in a discretized multigroup form

  10. SOLUTIONS AND MEANS OF ALTERNATIVE TRANSPORT IN THE CONCEPT OF SUSTAINABLE DEVELOPMENT

    Directory of Open Access Journals (Sweden)

    CATALIN POPESCU

    2017-12-01

    Full Text Available The paper aims to achieve an overview of innovative initiatives on alternative transport in recent years in the context of increasing emissions of greenhouse gases. In this context are presented the main problems caused by motorized traffic in the urban agglomerations. Also, there are mentioned measures that could be implemented in busy urban areas. On this occasion are mentioned both new technical solutions and new means of alternative transport type. Additional, specific projects and programs are highlighted using bicycle transportation. There are mentioned initiatives regarding urban transportation completed in European projects such as: CIVITAS, EFFECTS etc. The examples and figures are mainly focused on Romania.

  11. Co-solute assistance in refolding of recombinant proteins | Gerami ...

    African Journals Online (AJOL)

    Prokaryotic expression system is the most widely used host for the production of recombinant proteins but inclusion body formation is a major bottleneck in the production of recombinant proteins in prokaryotic cells, especially in Escherichia coli. In vitro refolding of inclusion body into the the proteins with native ...

  12. Stochastic models of solute transport in highly heterogeneous geologic media

    Energy Technology Data Exchange (ETDEWEB)

    Semenov, V.N.; Korotkin, I.A.; Pruess, K.; Goloviznin, V.M.; Sorokovikova, O.S.

    2009-09-15

    A stochastic model of anomalous diffusion was developed in which transport occurs by random motion of Brownian particles, described by distribution functions of random displacements with heavy (power-law) tails. One variant of an effective algorithm for random function generation with a power-law asymptotic and arbitrary factor of asymmetry is proposed that is based on the Gnedenko-Levy limit theorem and makes it possible to reproduce all known Levy {alpha}-stable fractal processes. A two-dimensional stochastic random walk algorithm has been developed that approximates anomalous diffusion with streamline-dependent and space-dependent parameters. The motivation for introducing such a type of dispersion model is the observed fact that tracers in natural aquifers spread at different super-Fickian rates in different directions. For this and other important cases, stochastic random walk models are the only known way to solve the so-called multiscaling fractional order diffusion equation with space-dependent parameters. Some comparisons of model results and field experiments are presented.

  13. ORGANIZATIONAL STRESS SOURCES AND SOLUTION PROPOSALS IN PUBLIC TRANSPORT

    Directory of Open Access Journals (Sweden)

    Mehmet Zennur GÜRBÜZ

    2017-09-01

    Full Text Available Organizational stress is a concept which can have negative effects for both the workers and the organizations. The purpose of this study is to determine and classify the organizational stress sources that public transportation are exposed to, and to provide suggestions for managing these stress factors. A comprehensive literature survey is made in organizational stress factors and the following classes are identified: work structure, organizational structure, organizational policy, within-company relations and physical conditions. A questionnaire is developed forAnkara EGO General Directorate; applied to 2.137 drivers in Ankara in 2016 with a meaningful return of 1.554 data sets, representing 72% of the population and results are statistically analysed. Descriptive statistics, factor analysis and related validity and regional variance analyses are performed by SPSS (22.0 software. The study revealed that: drivers are exposed to mid-level stess; and most critical stress causes are “injustice and/or insufficiency of salaries”, “aggresive, violent behavior and verbal abuse of passengers towards drivers”, “fear of losing jobs or renewal of the contract”. A significant level of variation in stres levels are identified with respect to different regions of Ankara where drivers are assigned.  Suggestions are made in relation to different stres causes to lower the stress levels exposed.

  14. Generalizing Source Geometry of Site Contamination by Simulating and Analyzing Analytical Solution of Three-Dimensional Solute Transport Model

    Directory of Open Access Journals (Sweden)

    Xingwei Wang

    2014-01-01

    Full Text Available Due to the uneven distribution of pollutions and blur edge of pollutant area, there will exist uncertainty of source term shape in advective-diffusion equation model of contaminant transport. How to generalize those irregular source terms and deal with those uncertainties is very critical but rarely studied in previous research. In this study, the fate and transport of contaminant from rectangular and elliptic source geometry were simulated based on a three-dimensional analytical solute transport model, and the source geometry generalization guideline was developed by comparing the migration of contaminant. The result indicated that the variation of source area size had no effect on pollution plume migration when the plume migrated as far as five times of source side length. The migration of pollution plume became slower with the increase of aquifer thickness. The contaminant concentration was decreasing with scale factor rising, and the differences among various scale factors became smaller with the distance to field increasing.

  15. Urea transporter proteins as targets for small-molecule diuretics.

    Science.gov (United States)

    Esteva-Font, Cristina; Anderson, Marc O; Verkman, Alan S

    2015-02-01

    Conventional diuretics such as furosemide and thiazides target salt transporters in kidney tubules, but urea transporters (UTs) have emerged as alternative targets. UTs are a family of transmembrane channels expressed in a variety of mammalian tissues, in particular the kidney. UT knockout mice and humans with UT mutations exhibit reduced maximal urinary osmolality, demonstrating that UTs are necessary for the concentration of urine. Small-molecule screening has identified potent and selective inhibitors of UT-A, the UT protein expressed in renal tubule epithelial cells, and UT-B, the UT protein expressed in vasa recta endothelial cells. Data from UT knockout mice and from rodents administered UT inhibitors support the diuretic action of UT inhibition. The kidney-specific expression of UT-A1, together with high selectivity of the small-molecule inhibitors, means that off-target effects of such small-molecule drugs should be minimal. This Review summarizes the structure, expression and function of UTs, and looks at the evidence supporting the validity of UTs as targets for the development of salt-sparing diuretics with a unique mechanism of action. UT-targeted inhibitors may be useful alone or in combination with conventional diuretics for therapy of various oedemas and hyponatraemias, potentially including those refractory to treatment with current diuretics.

  16. Parallel computing solution of Boltzmann neutron transport equation

    International Nuclear Information System (INIS)

    Ansah-Narh, T.

    2010-01-01

    The focus of the research was on developing parallel computing algorithm for solving Eigen-values of the Boltzmam Neutron Transport Equation (BNTE) in a slab geometry using multi-grid approach. In response to the problem of slow execution of serial computing when solving large problems, such as BNTE, the study was focused on the design of parallel computing systems which was an evolution of serial computing that used multiple processing elements simultaneously to solve complex physical and mathematical problems. Finite element method (FEM) was used for the spatial discretization scheme, while angular discretization was accomplished by expanding the angular dependence in terms of Legendre polynomials. The eigenvalues representing the multiplication factors in the BNTE were determined by the power method. MATLAB Compiler Version 4.1 (R2009a) was used to compile the MATLAB codes of BNTE. The implemented parallel algorithms were enabled with matlabpool, a Parallel Computing Toolbox function. The option UseParallel was set to 'always' and the default value of the option was 'never'. When those conditions held, the solvers computed estimated gradients in parallel. The parallel computing system was used to handle all the bottlenecks in the matrix generated from the finite element scheme and each domain of the power method generated. The parallel algorithm was implemented on a Symmetric Multi Processor (SMP) cluster machine, which had Intel 32 bit quad-core x 86 processors. Convergence rates and timings for the algorithm on the SMP cluster machine were obtained. Numerical experiments indicated the designed parallel algorithm could reach perfect speedup and had good stability and scalability. (au)

  17. Explicit finite-difference solution of two-dimensional solute transport with periodic flow in homogenous porous media

    Directory of Open Access Journals (Sweden)

    Djordjevich Alexandar

    2017-12-01

    Full Text Available The two-dimensional advection-diffusion equation with variable coefficients is solved by the explicit finitedifference method for the transport of solutes through a homogenous two-dimensional domain that is finite and porous. Retardation by adsorption, periodic seepage velocity, and a dispersion coefficient proportional to this velocity are permitted. The transport is from a pulse-type point source (that ceases after a period of activity. Included are the firstorder decay and zero-order production parameters proportional to the seepage velocity, and periodic boundary conditions at the origin and at the end of the domain. Results agree well with analytical solutions that were reported in the literature for special cases. It is shown that the solute concentration profile is influenced strongly by periodic velocity fluctuations. Solutions for a variety of combinations of unsteadiness of the coefficients in the advection-diffusion equation are obtainable as particular cases of the one demonstrated here. This further attests to the effectiveness of the explicit finite difference method for solving two-dimensional advection-diffusion equation with variable coefficients in finite media, which is especially important when arbitrary initial and boundary conditions are required.

  18. Export of recombinant proteins in Escherichia coli using ABC transporter with an attached lipase ABC transporter recognition domain (LARD

    Directory of Open Access Journals (Sweden)

    Moon Yuseok

    2009-01-01

    Full Text Available Abstract Background ATP binding cassette (ABC transporter secretes the protein through inner and outer membranes simultaneously in gram negative bacteria. Thermostable lipase (TliA of Pseudomonas fluorescens SIK W1 is secreted through the ABC transporter. TliA has four glycine-rich repeats (GGXGXD in its C-terminus, which appear in many ABC transporter-secreted proteins. From a homology model of TliA derived from the structure of P. aeruginosa alkaline protease (AprA, lipase ABC transporter domains (LARDs were designed for the secretion of fusion proteins. Results The LARDs included four glycine-rich repeats comprising a β-roll structure, and were added to the C-terminus of test proteins. Either Pro-Gly linker or Factor Xa site was added between fusion proteins and LARDs. We attached different length of LARDs such as LARD0, LARD1 or whole TliA (the longest LARD to three types of proteins; green fluorescent protein (GFP, epidermal growth factor (EGF and cytoplasmic transduction peptide (CTP. These fusion proteins were expressed in Escherichia coli together with ABC transporter of either P. fluorescens or Erwinia chrysanthemi. Export of fusion proteins with the whole TliA through the ABC transporter was evident on the basis of lipase enzymatic activity. Upon supplementation of E. coli with ABC transporter, GFP-LARDs and EGF-LARDs were excreted into the culture supernatant. Conclusion The LARDs or whole TliA were attached to C-termini of model proteins and enabled the export of the model proteins such as GFP and EGF in E. coli supplemented with ABC transporter. These results open the possibility for the extracellular production of recombinant proteins in Pseudomonas using LARDs or TliA as a C-terminal signal sequence.

  19. Efflux of drugs and solutes from brain: the interactive roles of diffusional transcapillary transport, bulk flow and capillary transporters.

    Science.gov (United States)

    Groothuis, Dennis R; Vavra, Michael W; Schlageter, Kurt E; Kang, Eric W-Y; Itskovich, Andrea C; Hertzler, Shannon; Allen, Cathleen V; Lipton, Howard L

    2007-01-01

    We examined the roles of diffusion, convection and capillary transporters in solute removal from extracellular space (ECS) of the brain. Radiolabeled solutes (eight with passive distribution and four with capillary or cell transporters) were injected into the brains of rats (n=497) and multiple-time point experiments measured the amount remaining in brain as a function of time. For passively distributed compounds, there was a relationship between lipid:water solubility and total brain efflux:diffusional efflux, which dominated when k(p), the transcapillary efflux rate constant, was >10(0) h(-1); when 10(-1)transporters. The total efflux rate constant, k(eff), was the sum of a passive component (k(p)=0.0018 h(-1)), a convective component (k(csf)=0.2 h(-1)), and a variable, concentration-dependent component (k(x)=0 to 0.45 h(-1)). Compounds with cell membrane transporters had longer clearance half times as did an oligonucleotide, which interacted with cell surface receptors. Manipulation of physiologic state (n=35) did not affect efflux, but sucrose efflux half time was longer with pentobarbital anesthesia (24 h) than with no anesthesia or ketamine-xylazine anesthesia (2 to 3 h). These results show that solute clearance from normal brain ECS may involve multiple physiologic pathways, may be affected by anesthesia, and suggests that convection-mediated efflux may be manipulated to increase or decrease drug clearance from brain.

  20. Semianalytical solutions for contaminant transport under variable velocity field in a coastal aquifer

    Science.gov (United States)

    Koohbor, Behshad; Fahs, Marwan; Ataie-Ashtiani, Behzad; Simmons, Craig T.; Younes, Anis

    2018-05-01

    Existing closed-form solutions of contaminant transport problems are limited by the mathematically convenient assumption of uniform flow. These solutions cannot be used to investigate contaminant transport in coastal aquifers where seawater intrusion induces a variable velocity field. An adaptation of the Fourier-Galerkin method is introduced to obtain semi-analytical solutions for contaminant transport in a confined coastal aquifer in which the saltwater wedge is in equilibrium with a freshwater discharge flow. Two scenarios dealing with contaminant leakage from the aquifer top surface and contaminant migration from a source at the landward boundary are considered. Robust implementation of the Fourier-Galerkin method is developed to efficiently solve the coupled flow, salt and contaminant transport equations. Various illustrative examples are generated and the semi-analytical solutions are compared against an in-house numerical code. The Fourier series are used to evaluate relevant metrics characterizing contaminant transport such as the discharge flux to the sea, amount of contaminant persisting in the groundwater and solute flux from the source. These metrics represent quantitative data for numerical code validation and are relevant to understand the effect of seawater intrusion on contaminant transport. It is observed that, for the surface contamination scenario, seawater intrusion limits the spread of the contaminant but intensifies the contaminant discharge to the sea. For the landward contamination scenario, moderate seawater intrusion affects only the spatial distribution of the contaminant plume while extreme seawater intrusion can increase the contaminant discharge to the sea. The developed semi-analytical solution presents an efficient tool for the verification of numerical models. It provides a clear interpretation of the contaminant transport processes in coastal aquifers subject to seawater intrusion. For practical usage in further studies, the full

  1. Water flow and solute transport using environmental isotopes and modeling

    International Nuclear Information System (INIS)

    Hussein, M.F.

    2001-01-01

    The deep unsaturated zone may be a useful hydrological archive in desert environments characterized by scant or sporadic rainfall and slow percolation of rainwater over decades or even centuries. This moisture archive provides a useful way to distinguish the net downward flow of recharge water, whereas the isotopic composition and concentration of the conservative solutes of the preserved moisture could be used to reconstruct the history of recharge under the prevailing deficient water balance. The major advantage of such coupled approach is to obtain independent estimates of groundwater recharge rates which are normally difficult to evaluate using the hydrological methods applied in the temperate zones. The study was conducted in the Shiekh-Zoweid/Raffa area in the northeastern coastal strip of Sinai Peninsula. Bore-holes were dry-drilled in a line perpendicular to the sea shoreline (using an 8-inch diameter hand-operated rotary rig) for the unsaturated sediment collection from successive 0.5m thick layers down to a depth of 20m. Samples were investigated for the moisture contents and the chemical and isotope composition of this moisture was determined. Physical parameters were also assessed including porosity and volumetric moisture content. Chloride mass-balance was used to calculate recharge rates through the unsaturated zone by predicting the position of the 1963-Tritium peak in the unsaturated column. Analysis of moisture, chloride and deuterium profiles showed three principle peaks (along with minor ones) in Karafin site indicating few major recharge events that have taken place during the last few decades. Adjustment of these episodes has also been attempted using two historical major rainfall events (known from nearby meteorological stations). Application of the methodology in water resources management in arid regions is discussed. (author)

  2. Continuous time random walk analysis of solute transport in fractured porous media

    Energy Technology Data Exchange (ETDEWEB)

    Cortis, Andrea; Cortis, Andrea; Birkholzer, Jens

    2008-06-01

    The objective of this work is to discuss solute transport phenomena in fractured porous media, where the macroscopic transport of contaminants in the highly permeable interconnected fractures can be strongly affected by solute exchange with the porous rock matrix. We are interested in a wide range of rock types, with matrix hydraulic conductivities varying from almost impermeable (e.g., granites) to somewhat permeable (e.g., porous sandstones). In the first case, molecular diffusion is the only transport process causing the transfer of contaminants between the fractures and the matrix blocks. In the second case, additional solute transfer occurs as a result of a combination of advective and dispersive transport mechanisms, with considerable impact on the macroscopic transport behavior. We start our study by conducting numerical tracer experiments employing a discrete (microscopic) representation of fractures and matrix. Using the discrete simulations as a surrogate for the 'correct' transport behavior, we then evaluate the accuracy of macroscopic (continuum) approaches in comparison with the discrete results. However, instead of using dual-continuum models, which are quite often used to account for this type of heterogeneity, we develop a macroscopic model based on the Continuous Time Random Walk (CTRW) framework, which characterizes the interaction between the fractured and porous rock domains by using a probability distribution function of residence times. A parametric study of how CTRW parameters evolve is presented, describing transport as a function of the hydraulic conductivity ratio between fractured and porous domains.

  3. Pore connectivity effects on solute transport in rocks

    International Nuclear Information System (INIS)

    Hu, Qinhong; Ewing, Robert P.

    2001-01-01

    Retardation of nuclear contaminants in rock matrices can lead to long retention times, allowing substantial radionuclide decay prior to eventual release. Imbibition and diffusion into the rock matrix can move contaminants away from an active fracture, thereby contributing to their retardation. However, diffusive transport in some rocks may behave anomalously because of their sparsely connected porespace, in contrast to diffusion in rocks with denser pore connections. We examined imbibition of weakly sorbing tracers into welded tuff and Indiana sandstone, and water imbibition into metagraywacke and Berea sandstone. Tuff samples were initially equilibrated to 12% and 76% water (v/v) within controlled humidity chambers, while the other rocks were air-dried. For imbibition, one face was exposed to water, with or without tracer, and uptake was measured over time. Following imbibition, tracer concentration measurements were made at fine (1 mm) increments. Three anomalous results were observed: (1) Indiana sandstone and metagraywacke showed mass of imbibed water scaling as time 0.26 , while tuff and Berea sandstone showed the more classical scaling with time 0.5 ; (2) tracer movement into dry (2% initial saturation) Indiana sandstone showed a dispersion pattern similar to that expected during tracer movement into moist (76% initial saturation) tuff; and (3) tracer concentrations at the inlet face of the tuff sample were approximately twice those deeper inside the sample. The experiment was then modeled using random walk methods on a 3-D lattice with different values of pore coordination. Network model simulations that used a pore coordination of 1.49 for Indiana sandstone and 1.56 for metagraywacke showed similar temporal scaling, a result of their porespace being close to the percolation threshold. Tracer concentration profiles in Indiana sandstone and tuff were closely matched by simulations that used pore coordinations of 1.49 and 1.68, respectively, because of how low

  4. Pore Connectivity Effects on Solute Transport in Rocks

    International Nuclear Information System (INIS)

    Oinhong Hu

    2001-01-01

    Retardation of nuclear contaminants in rock matrices can lead to long retention times, allowing substantial radionuclide decay prior to eventual release. Imbibition and diffusion into the rock matrix can move contaminants away from an active fracture, thereby contributing to their retardation. However, diffusive transport in some rocks may behave anomalously because of their sparsely connected porespace, in contrast to diffusion in rocks with denser pore connections. We examined imbibition of weakly sorbing tracers into welded tuff and Indiana sandstone, and water imbibition into metagraywacke and Berea sandstone. Tuff samples were initially equilibrated to 12% and 76% water (v/v) within controlled humidity chambers, while the other rocks were air-dried. For imbibition, one face was exposed to water, with or without tracer, and uptake was measured over time. Following imbibition, tracer concentration measurements were made at fine (1 mm) increments. Three anomalous results were observed: (1) Indiana sandstone and metagraywacke showed mass of imbibed water scaling as time 0.26 , while tuff and Berea sandstone showed the more classical scaling with time 0.05 ; (2) tracer movement into dry (2% initial saturation) Indiana sandstone showed a dispersion pattern similar to that expected during tracer movement into moist (76% initial saturation) tuft and (3) tracer concentrations at the inlet face of the tuff sample were approximately twice those deeper inside the sample. The experiment was then modeled using random walk methods on a 3-D lattice with different values of pore coordination. Network model simulations that used a pore coordination of 1.49 for Indiana sandstone and 1.56 for metagraywacke showed similar temporal scaling, a result of their porespace being close to the percolation threshold. Tracer concentration profiles in Indiana sandstone and tuff were closely matched by simulations that used pore coordinations of 1.49 and 1.68, respectively, because of how low

  5. Pharmaceutical Perspective on Opalescence and Liquid-Liquid Phase Separation in Protein Solutions.

    Science.gov (United States)

    Raut, Ashlesha S; Kalonia, Devendra S

    2016-05-02

    Opalescence in protein solutions reduces aesthetic appeal of a formulation and can be an indicator of the presence of aggregates or precursor to phase separation in solution signifying reduced product stability. Liquid-liquid phase separation of a protein solution into a protein-rich and a protein-poor phase has been well-documented for globular proteins and recently observed for monoclonal antibody solutions, resulting in physical instability of the formulation. The present review discusses opalescence and liquid-liquid phase separation (LLPS) for therapeutic protein formulations. A brief discussion on theoretical concepts based on thermodynamics, kinetics, and light scattering is presented. This review also discusses theoretical concepts behind intense light scattering in the vicinity of the critical point termed as "critical opalescence". Both opalescence and LLPS are affected by the formulation factors including pH, ionic strength, protein concentration, temperature, and excipients. Literature reports for the effect of these formulation factors on attractive protein-protein interactions in solution as assessed by the second virial coefficient (B2) and the cloud-point temperature (Tcloud) measurements are also presented. The review also highlights pharmaceutical implications of LLPS in protein solutions.

  6. Solution structure of human intestinal fatty acid binding protein: Implications for ligand entry and exit

    International Nuclear Information System (INIS)

    Zhang Fengli; Luecke, Christian; Baier, Leslie J.; Sacchettini, James C.; Hamilton, James A.

    1997-01-01

    The human intestinal fatty acid binding protein (I-FABP) is a small (131 amino acids) protein which binds dietary long-chain fatty acids in the cytosol of enterocytes. Recently, an alanine to threonine substitution at position 54 in I-FABP has been identified which affects fatty acid binding and transport, and is associated with the development of insulin resistance in several populations including Mexican-Americans and Pima Indians. To investigate the molecular basis of the binding properties of I-FABP, the 3D solution structure of the more common form of human I-FABP (Ala54) was studied by multidimensional NMR spectroscopy.Recombinant I-FABP was expressed from E. coli in the presence and absence of 15N-enriched media. The sequential assignments for non-delipidated I-FABP were completed by using 2D homonuclear spectra (COSY, TOCSY and NOESY) and 3D heteronuclear spectra(NOESY-HMQC and TOCSY-HMQC). The tertiary structure of human I-FABP was calculated by using the distance geometry program DIANA based on 2519 distance constraints obtained from the NMR data. Subsequent energy minimization was carried out by using the program SYBYL in the presence of distance constraints. The conformation of human I-FABP consists of 10 antiparallel β-strands which form two nearly orthogonal β-sheets of five strands each, and two short α-helices that connect the β-strands A and B. The interior of the protein consists of a water-filled cavity between the two β-sheets. The NMR solution structure of human I-FABP is similar to the crystal structure of rat I-FABP.The NMR results show significant conformational variability of certain backbone segments around the postulated portal region for the entry and exit of fatty acid ligand

  7. Solution structure of human intestinal fatty acid binding protein: Implications for ligand entry and exit

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Fengli [Boston University School of Medicine, Department of Biophysics (United States); Luecke, Christian [Johann Wolfgang Goethe-Universitaet (Germany); Baier, Leslie J. [NIDDK, NIH, Phoenix Epidemiology and Clinical Research Branch (United States); Sacchettini, James C. [Texas A and M University, Department of Biochemistry and Biophysics (United States); Hamilton, James A. [Boston University School of Medicine, Department of Biophysics (United States)

    1997-04-15

    The human intestinal fatty acid binding protein (I-FABP) is a small (131 amino acids) protein which binds dietary long-chain fatty acids in the cytosol of enterocytes. Recently, an alanine to threonine substitution at position 54 in I-FABP has been identified which affects fatty acid binding and transport, and is associated with the development of insulin resistance in several populations including Mexican-Americans and Pima Indians. To investigate the molecular basis of the binding properties of I-FABP, the 3D solution structure of the more common form of human I-FABP (Ala54) was studied by multidimensional NMR spectroscopy.Recombinant I-FABP was expressed from E. coli in the presence and absence of 15N-enriched media. The sequential assignments for non-delipidated I-FABP were completed by using 2D homonuclear spectra (COSY, TOCSY and NOESY) and 3D heteronuclear spectra(NOESY-HMQC and TOCSY-HMQC). The tertiary structure of human I-FABP was calculated by using the distance geometry program DIANA based on 2519 distance constraints obtained from the NMR data. Subsequent energy minimization was carried out by using the program SYBYL in the presence of distance constraints. The conformation of human I-FABP consists of 10 antiparallel {beta}-strands which form two nearly orthogonal {beta}-sheets of five strands each, and two short {alpha}-helices that connect the {beta}-strands A and B. The interior of the protein consists of a water-filled cavity between the two {beta}-sheets. The NMR solution structure of human I-FABP is similar to the crystal structure of rat I-FABP.The NMR results show significant conformational variability of certain backbone segments around the postulated portal region for the entry and exit of fatty acid ligand.

  8. Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

    2017-05-01

    The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Multidrug and toxin extrusion proteins mediate cellular transport of cadmium

    International Nuclear Information System (INIS)

    Yang, Hong; Guo, Dong; Obianom, Obinna N.; Su, Tong; Polli, James E.; Shu, Yan

    2017-01-01

    Cadmium (Cd) is an environmentally prevalent toxicant posing increasing risk to human health worldwide. As compared to the extensive research in Cd tissue accumulation, little was known about the elimination of Cd, particularly its toxic form, Cd ion (Cd 2+ ). In this study, we aimed to examine whether Cd 2+ is a substrate of multidrug and toxin extrusion proteins (MATEs) that are important in renal xenobiotic elimination. HEK-293 cells overexpressing the human MATE1 (HEK-hMATE1), human MATE2-K (HEK-hMATE2-K) and mouse Mate1 (HEK-mMate1) were used to study the cellular transport and toxicity of Cd 2+ . The cells overexpressing MATEs showed a 2–4 fold increase of Cd 2+ uptake that could be blocked by the MATE inhibitor cimetidine. A saturable transport profile was observed with the Michaelis-Menten constant (K m ) of 130 ± 15.8 μM for HEK-hMATE1; 139 ± 21.3 μM for HEK-hMATE2-K; and 88.7 ± 13.5 μM for HEK-mMate1, respectively. Cd 2+ could inhibit the uptake of metformin, a substrate of MATE transporters, with the half maximal inhibitory concentration (IC 50 ) of 97.5 ± 6.0 μM, 20.2 ± 2.6 μM, and 49.9 ± 6.9 μM in HEK-hMATE1, HEK-hMATE2-K, and HEK-mMate1 cells, respectively. In addition, hMATE1 could transport preloaded Cd 2+ out of the HEK-hMATE1 cells, thus resulting in a significant decrease of Cd 2+ -induced cytotoxicity. The present study has provided the first evidence supporting that MATEs transport Cd 2+ and may function as cellular elimination machinery in Cd intoxication. - Highlights: • Cadmium is an environmentally prevalent toxicant. • Little was known regarding the elimination and detoxification of cadmium. • Cadmium ion is here demonstrated as a substrate of MATE transporters. • MATEs may function as cellular elimination machinery in cadmium detoxification.

  10. Multidrug and toxin extrusion proteins mediate cellular transport of cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Hong; Guo, Dong; Obianom, Obinna N. [Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, MD (United States); Su, Tong [Department of Oral Maxillofacial Surgery, the First Affiliated Hospital, Xiangya Medical School, Central South University, Hunan 410007 (China); Polli, James E. [Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, MD (United States); Shu, Yan, E-mail: yshu@rx.umaryland.edu [Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland at Baltimore, MD (United States)

    2017-01-01

    Cadmium (Cd) is an environmentally prevalent toxicant posing increasing risk to human health worldwide. As compared to the extensive research in Cd tissue accumulation, little was known about the elimination of Cd, particularly its toxic form, Cd ion (Cd{sup 2+}). In this study, we aimed to examine whether Cd{sup 2+} is a substrate of multidrug and toxin extrusion proteins (MATEs) that are important in renal xenobiotic elimination. HEK-293 cells overexpressing the human MATE1 (HEK-hMATE1), human MATE2-K (HEK-hMATE2-K) and mouse Mate1 (HEK-mMate1) were used to study the cellular transport and toxicity of Cd{sup 2+}. The cells overexpressing MATEs showed a 2–4 fold increase of Cd{sup 2+} uptake that could be blocked by the MATE inhibitor cimetidine. A saturable transport profile was observed with the Michaelis-Menten constant (K{sub m}) of 130 ± 15.8 μM for HEK-hMATE1; 139 ± 21.3 μM for HEK-hMATE2-K; and 88.7 ± 13.5 μM for HEK-mMate1, respectively. Cd{sup 2+} could inhibit the uptake of metformin, a substrate of MATE transporters, with the half maximal inhibitory concentration (IC{sub 50}) of 97.5 ± 6.0 μM, 20.2 ± 2.6 μM, and 49.9 ± 6.9 μM in HEK-hMATE1, HEK-hMATE2-K, and HEK-mMate1 cells, respectively. In addition, hMATE1 could transport preloaded Cd{sup 2+} out of the HEK-hMATE1 cells, thus resulting in a significant decrease of Cd{sup 2+}-induced cytotoxicity. The present study has provided the first evidence supporting that MATEs transport Cd{sup 2+} and may function as cellular elimination machinery in Cd intoxication. - Highlights: • Cadmium is an environmentally prevalent toxicant. • Little was known regarding the elimination and detoxification of cadmium. • Cadmium ion is here demonstrated as a substrate of MATE transporters. • MATEs may function as cellular elimination machinery in cadmium detoxification.

  11. Analytical solutions of a fractional diffusion-advection equation for solar cosmic-ray transport

    International Nuclear Information System (INIS)

    Litvinenko, Yuri E.; Effenberger, Frederic

    2014-01-01

    Motivated by recent applications of superdiffusive transport models to shock-accelerated particle distributions in the heliosphere, we analytically solve a one-dimensional fractional diffusion-advection equation for the particle density. We derive an exact Fourier transform solution, simplify it in a weak diffusion approximation, and compare the new solution with previously available analytical results and with a semi-numerical solution based on a Fourier series expansion. We apply the results to the problem of describing the transport of energetic particles, accelerated at a traveling heliospheric shock. Our analysis shows that significant errors may result from assuming an infinite initial distance between the shock and the observer. We argue that the shock travel time should be a parameter of a realistic superdiffusive transport model.

  12. Effects of sorption and temperature on solute transport in unsaturated steady flow

    International Nuclear Information System (INIS)

    Fuentes, H.R.; Polzer, W.L.; Essington, E.H.

    1986-01-01

    It is known that temperature affects physical and chemical processes and that these processes may alter the transport of solutes in the environment. Laboratory column studies were performed in unsaturated flow conditions with a composite pulse containing iodide, cobalt, cesium and strontium each at 10 -3 M. The experiments were performed with Bandelier Tuff and produced breakthrough curves that indicate significant changes in transport due to a temperature change from 25 0 C to 5 0 C for nonconservative solutes. Also, the interpretation of the temperature and sorption data suggest that the differences in transport between 5 0 C and 25 0 C for nonconservative solutes may be predicted in a qualitative manner from batch equilibrium and nonequilibrium sorption data and the theory of sorption used in deriving the modified Freundlich isotherm equation. These effects should be of concern in modeling and management of spills and waste disposal within this range of environmental temperatures

  13. [Adsorption characteristics of proteins on membrane surface and effect of protein solution environment on permeation behavior of berberine].

    Science.gov (United States)

    Li, Yi-Qun; Xu, Li; Zhu, Hua-Xu; Tang, Zhi-Shu; Li, Bo; Pan, Yong-Lan; Yao, Wei-Wei; Fu, Ting-Ming; Guo, Li-Wei

    2017-10-01

    In order to explore the adsorption characteristics of proteins on the membrane surface and the effect of protein solution environment on the permeation behavior of berberine, berberine and proteins were used as the research object to prepare simulated solution. Low field NMR, static adsorption experiment and membrane separation experiment were used to study the interaction between the proteins and ceramic membrane or between the proteins and berberine. The static adsorption capacity of proteins, membrane relative flux, rejection rate of proteins, transmittance rate of berberine and the adsorption rate of proteins and berberine were used as the evaluation index. Meanwhile, the membrane resistance distribution, the particle size distribution and the scanning electron microscope (SEM) were determined to investigate the adsorption characteristics of proteins on ceramic membrane and the effect on membrane separation process of berberine. The results showed that the ceramic membrane could adsorb the proteins and the adsorption model was consistent with Langmuir adsorption model. In simulating the membrane separation process, proteins were the main factor to cause membrane fouling. However, when the concentration of proteins was 1 g•L⁻¹, the proteins had no significant effect on membrane separation process of berberine. Copyright© by the Chinese Pharmaceutical Association.

  14. Imaging transport phenomena during lysozyme protein crystal growth by the hanging drop technique

    Science.gov (United States)

    Sethia Gupta, Anamika; Gupta, Rajive; Panigrahi, P. K.; Muralidhar, K.

    2013-06-01

    The present study reports the transport process that occurs during the growth of lysozyme protein crystals by the hanging drop technique. A rainbow schlieren technique has been employed for imaging changes in salt concentration. A one dimensional color filter is used to record the deflection of the light beam. An optical microscope and an X-ray crystallography unit are used to characterize the size, tetragonal shape and Bravais lattice constants of the grown crystals. A parametric study on the effect of drop composition, drop size, reservoir height and number of drops on the crystal size and quality is reported. Changes in refractive index are not large enough to create a meaningful schlieren image in the air gap between the drop and the reservoir. However, condensation of fresh water over the reservoir solution creates large changes in the concentration of NaCl, giving rise to clear color patterns in the schlieren images. These have been analyzed to obtain salt concentration profiles near the free surface of the reservoir solution as a function of time. The diffusion of fresh water into the reservoir solution at the early stages of crystal growth followed by the mass flux of salt from the bulk solution towards the free surface has been recorded. The overall crystal growth process can be classified into two regimes, as demarcated by the changes in slope of salt concentration within the reservoir. The salt concentration in the reservoir equilibrates at long times when the crystallization process is complete. Thus, transport processes in the reservoir emerge as the route to monitor protein crystal growth in the hanging drop configuration. Results show that crystal growth rate is faster for a higher lysozyme concentration, smaller drops, and larger reservoir heights.

  15. Numerical modelling of coupled fluid, heat, and solute transport in deformable fractured rock

    International Nuclear Information System (INIS)

    Chan, T.; Reid, J.A.K.

    1987-01-01

    This paper reports on a three-dimensional (3D) finite-element code, MOTIF (model of transport in fractured/porous media), developed to model the coupled processes of groundwater flow, heat transport, brine transport, and one-species radionuclide transport in geological media. Three types of elements are available: a 3D continuum element, a planar fracture element that can be oriented in any arbitrary direction in 3D space or pipe flow in 3D space, and a line element for simulating fracture flow in 2D space or pipe flow in 3D space. As a quality-assurance measure, the MOTIF code was verified by comparison of its results with analytical solutions and other published numerical solutions

  16. Fluctuation theorem for channel-facilitated membrane transport of interacting and noninteracting solutes.

    Science.gov (United States)

    Berezhkovskii, Alexander M; Bezrukov, Sergey M

    2008-05-15

    In this paper, we discuss the fluctuation theorem for channel-facilitated transport of solutes through a membrane separating two reservoirs. The transport is characterized by the probability, P(n)(t), that n solute particles have been transported from one reservoir to the other in time t. The fluctuation theorem establishes a relation between P(n)(t) and P-(n)(t): The ratio P(n)(t)/P-(n)(t) is independent of time and equal to exp(nbetaA), where betaA is the affinity measured in the thermal energy units. We show that the same fluctuation theorem is true for both single- and multichannel transport of noninteracting particles and particles which strongly repel each other.

  17. Identification of key target markets for intermodal freight transport solutions in South Africa

    Directory of Open Access Journals (Sweden)

    Joubert van Eeden

    2010-11-01

    Full Text Available The Accelerated and Shared Growth Initiative for South Africa (AsgiSA identified South Africa's freight logistics challenges as among the key binding constraints on the country's growth aspirations. The research presented here points to the structural imbalance between road and rail freight transport as one of the key contributors to this state of affairs. Most long-distance corridor transport has been captured by road. However, long-distance transport is a market segment that is very suitable for intermodal transportation : rail is utilised for the high-density, long-distance component and road for the feeder and distribution services at the corridor end points. A market segmentation approach is developed to identify the corridors and industries that are natural candidates for such solutions, thereby paving the way for role-players and stakeholders to initiate a dialogue on the development of appropriate solutions.

  18. Modeling of water and solute transport under variably saturated conditions: state of the art

    International Nuclear Information System (INIS)

    Lappala, E.G.

    1980-01-01

    This paper reviews the equations used in deterministic models of mass and energy transport in variably saturated porous media. Analytic, quasi-analytic, and numerical solution methods to the nonlinear forms of transport equations are discussed with respect to their advantages and limitations. The factors that influence the selection of a modeling method are discussed in this paper; they include the following: (1) the degree of coupling required among the equations describing the transport of liquids, gases, solutes, and energy; (2) the inclusion of an advection term in the equations; (3) the existence of sharp fronts; (4) the degree of nonlinearity and hysteresis in the transport coefficients and boundary conditions; (5) the existence of complex boundaries; and (6) the availability and reliability of data required by the models

  19. Simulation of unsaturated flow and nonreactive solute transport in a heterogeneous soil at the field scale

    International Nuclear Information System (INIS)

    Rockhold, M.L.

    1993-02-01

    A field-scale, unsaturated flow and solute transport experiment at the Las Cruces trench site in New Mexico was simulated as part of a ''blind'' modeling exercise to demonstrate the ability or inability of uncalibrated models to predict unsaturated flow and solute transport in spatially variable porous media. Simulations were conducted using a recently developed multiphase flow and transport simulator. Uniform and heterogeneous soil models were tested, and data from a previous experiment at the site were used with an inverse procedure to estimate water retention parameters. A spatial moment analysis was used to provide a quantitative basis for comparing the mean observed and simulated flow and transport behavior. The results of this study suggest that defensible predictions of waste migration and fate at low-level waste sites will ultimately require site-specific data for model calibration

  20. Oxalic acid complexes: Promising draw solutes for forward osmosis (FO) in protein enrichment

    KAUST Repository

    Ge, Qingchun; Chung, Neal Tai-Shung

    2015-01-01

    Highly soluble oxalic acid complexes (OACs) were synthesized through a one-pot reaction. The OACs exhibit excellent performance as draw solutes in FO processes with high water fluxes and negligible reverse solute fluxes. Efficient protein enrichment was achieved. The diluted OACs can be recycled via nanofiltration and are promising as draw solutes.

  1. Container transport direct call – logistic solution to container transport via Estonia

    Directory of Open Access Journals (Sweden)

    A. Tolli

    2007-12-01

    Full Text Available Container transport in the world grows up to 12 % every year. Chinese container transport contributes majority of container flows in international container transport. Many world seaports compete for Chinese container flows and make eff orts to get investments and direct calls from China to their ports. Estonia has a possibility to decrease its large dependence and risks due to the transit of oil and oil products and coal with the help of container flows from China. In addition to a favorable geographical location Estonia has several other important arguments, like suffi cient land in the harbours for developing a container terminal to launch extensive container transport transit from China. Port of St. Petersburg, container transport port closest to Estonia by the Baltic Sea, is overloaded. Estonia can compete for container flows directed to Moscow, Nizhniy Novgorod, Kazan and Kaluga. Construction of an international high-tech container terminal in Port of Tallinn serves as one important precondition for directing Russian transit container flows through Estonia. Such a container terminal could service also larger vessels and container flows from China. Container lines and container terminals operating as alliances are jointly able to substantially increase container flows through countries.

  2. Spatial model of convective solute transport in brain extracellular space does not support a "glymphatic" mechanism.

    Science.gov (United States)

    Jin, Byung-Ju; Smith, Alex J; Verkman, Alan S

    2016-12-01

    A "glymphatic system," which involves convective fluid transport from para-arterial to paravenous cerebrospinal fluid through brain extracellular space (ECS), has been proposed to account for solute clearance in brain, and aquaporin-4 water channels in astrocyte endfeet may have a role in this process. Here, we investigate the major predictions of the glymphatic mechanism by modeling diffusive and convective transport in brain ECS and by solving the Navier-Stokes and convection-diffusion equations, using realistic ECS geometry for short-range transport between para-arterial and paravenous spaces. Major model parameters include para-arterial and paravenous pressures, ECS volume fraction, solute diffusion coefficient, and astrocyte foot-process water permeability. The model predicts solute accumulation and clearance from the ECS after a step change in solute concentration in para-arterial fluid. The principal and robust conclusions of the model are as follows: (a) significant convective transport requires a sustained pressure difference of several mmHg between the para-arterial and paravenous fluid and is not affected by pulsatile pressure fluctuations; (b) astrocyte endfoot water permeability does not substantially alter the rate of convective transport in ECS as the resistance to flow across endfeet is far greater than in the gaps surrounding them; and (c) diffusion (without convection) in the ECS is adequate to account for experimental transport studies in brain parenchyma. Therefore, our modeling results do not support a physiologically important role for local parenchymal convective flow in solute transport through brain ECS. © 2016 Jin et al.

  3. TRACKING AND TRACING SOLUTION FOR DANGEROUS GOODS CARRIED BY INTERMODAL TRANSPORT

    Directory of Open Access Journals (Sweden)

    Marek Kvet

    2014-03-01

    Full Text Available This paper deals with the problem of designing a complex tracking and tracing solution for dangerous goods transportation with the support of modern information technologies. This research activity presents a part of the “ChemLogTT” [2] project solved at the University of Žilina. The main goal of our contribution is to present basic conception of a complex developed software tool for monitoring and analyzing mentioned dangerous goods transportation.

  4. Influence of pore structure on solute transport in degraded and undegraded fen peat soils

    Directory of Open Access Journals (Sweden)

    C. Kleimeier

    2017-10-01

    Full Text Available In peat soils, decomposition and degradation reduce the proportion of large pores by breaking down plant debris into smaller fragments and infilling inter-particle pore spaces. This affects water flow and solute migration which, in turn, influence reactive transport processes and biogeochemical functions. In this study we conducted flow-through reactor experiments to investigate the interplay between pore structure and solute transport in samples of undegraded and degraded peat collected in Canada and Germany, respectively. The pore size distributions and transport parameters were characterised using the breakthrough curve and two-region non-equilibrium transport model analyses for a non-reactive solute. The results of transport characterisation showed a higher fraction of immobile pores in the degraded peat with higher diffusive exchanges of solutes between the mobile and immobile pores associated with the dual-porosity structure. The rates of steady-state potential nitrate reduction were compared with pore fractions and exchange coefficients to investigate the influence of pore structure on the rates of nitrate reduction. The results indicated that the degraded peat has potential to provide the necessary boundary conditions to support nitrate removal and serves as a favourable substrate for denitrification, due to the nature of its pore structure and its lower organic carbon content compared to undegraded peat.

  5. Ion Transport in Organic Electrolyte Solution through the Pore Channels of Anodic Nanoporous Alumina Membranes

    International Nuclear Information System (INIS)

    Fukutsuka, Tomokazu; Koyamada, Kohei; Maruyama, Shohei; Miyazaki, Kohei; Abe, Takeshi

    2016-01-01

    Highlights: • Ion transport in organic electrolyte solution in macro- and meso-pores was focused. • Anodic nanoporous alumina membrane was used as a porous material. • The specific ion conductivities drastically decreased in macro- and meso-pores. - Abstract: For the development of high energy density lithium-ion batteries with the high rate performance, the enhancement of the ion transport in the electrolyte solutions impregnated in the porous electrodes is a key. To study the ion transport in porous electrodes, anodic nanoporous alumina (APA) self-standing membranes with macro- or meso-pores were used as model porous materials. These membranes had nearly spherical pore channels of discrete 20–68 nm in diameters. By using the geometric shape of the pores, we attempted to evaluate the specific ion conductivities of the organic electrolyte solution dissolving lithium salt simply. AC impedance spectroscopy measurement of a four-electrode cell with membranes showed one depressed semi-circle in the Nyquist plots and this semi-circle can be assigned as the ion transport resistance in the pores. The specific ion conductivities evaluated from the ion transport resistances and the geometric parameters showed very small values, even in the macro-pores, as compared with that of the bulk electrolyte solution.

  6. The simulation of solute transport: An approach free of numerical dispersion

    International Nuclear Information System (INIS)

    Carrera, J.; Melloni, G.

    1987-01-01

    The applicability of most algorithms for simulation of solute transport is limited either by instability or by numerical dispersion, as seen by a review of existing methods. A new approach is proposed that is free of these two problems. The method is based on the mixed Eulerian-Lagrangian formulation of the mass-transport problem, thus ensuring stability. Advection is simulated by a variation of reverse-particle tracking that avoids the accumulation of interpolation errors, thus preventing numerical dispersion. The algorithm has been implemented in a one-dimensional code. Excellent results are obtained, in comparison with an analytical solution. 36 refs., 14 figs., 1 tab

  7. Verification of T2VOC using an analytical solution for VOC transport in vadose zone

    Energy Technology Data Exchange (ETDEWEB)

    Shan, C. [Lawrence Berkeley Laboratory, Berkeley, CA (United States)

    1995-03-01

    T2VOC represents an adaption of the STMVOC to the TOUGH2 environment. In may contaminated sites, transport of volatile organic chemicals (VOC) is a serious problem which can be simulated by T2VOC. To demonstrate the accuracy and robustness of the code, we chose a practical problem of VOC transport as the test case, conducted T2VOC simulations, and compared the results of T2VOC with those of an analytical solution. The agreements between T2VOC and the analytical solutions are excellent. In addition, the numerical results of T2VOC are less sensitive to grid size and time step to a certain extent.

  8. Expression of solute carrier 7A4 (SLC7A4) in the plasma membrane is not sufficient to mediate amino acid transport activity.

    OpenAIRE

    Wolf, Sabine; Janzen, Annette; Vékony, Nicole; Martiné, Ursula; Strand, Dennis; Closs, Ellen I

    2002-01-01

    Member 4 of human solute carrier family 7 (SLC7A4) exhibits significant sequence homology with the SLC7 subfamily of human cationic amino acid transporters (hCATs) [Sperandeo, Borsani, Incerti, Zollo, Rossi, Zuffardi, Castaldo, Taglialatela, Andria and Sebastio (1998) Genomics 49, 230-236]. It is therefore often referred to as hCAT-4 even though no convincing transport activity has been shown for this protein. We expressed SLC7A4 in Xenopus laevis oocytes, but could not detect any transport a...

  9. Preliminary modeling for solute transport in a fractured zone at the Korea underground research tunnel (KURT)

    Energy Technology Data Exchange (ETDEWEB)

    Park, Chung Kyun; Lee, Jaek Wang; Baik, Min Hoon; Jeong, Jong Tae [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2012-02-15

    Migration tests were performed with conservative tracers in a fractured zone that had a single fracture of about 2.5 m distance at the KURT. To interpret the migration of the tracers in the fractured rock, a solute transport model was developed. A two dimensional variable aperture channel model was adopted to describe the fractured path and hydrology, and a particle tracking method was used for solute transport. The simulation tried not only to develop a migration model of solutes for open flow environments but also to produce ideas for a better understanding of solute behaviours in indefinable fracture zones by comparing them to experimental results. The results of our simulations and experiments are described as elution and breakthrough curves, and are quantified by momentum analysis. The main retardation mechanism of nonsorbing tracers, including matrixdiffusion, was investigated.

  10. Limit Theorems and Their Relation to Solute Transport in Simulated Fractured Media

    Science.gov (United States)

    Reeves, D. M.; Benson, D. A.; Meerschaert, M. M.

    2003-12-01

    Solute particles that travel through fracture networks are subject to wide velocity variations along a restricted set of directions. This may result in super-Fickian dispersion along a few primary scaling directions. The fractional advection-dispersion equation (FADE), a modification of the original advection-dispersion equation in which a fractional derivative replaces the integer-order dispersion term, has the ability to model rapid, non-Gaussian solute transport. The FADE assumes that solute particle motions converge to either α -stable or operator stable densities, which are modeled by spatial fractional derivatives. In multiple dimensions, the multi-fractional dispersion derivative dictates the order and weight of differentiation in all directions, which correspond to the statistics of large particle motions in all directions. This study numerically investigates the presence of super- Fickian solute transport through simulated two-dimensional fracture networks. An ensemble of networks is gen

  11. Analytical solution of electrohydrodynamic flow and transport in rectangular channels: inclusion of double layer effects

    KAUST Repository

    Joekar-Niasar, V.

    2013-01-25

    Upscaling electroosmosis in porous media is a challenge due to the complexity and scale-dependent nonlinearities of this coupled phenomenon. "Pore-network modeling" for upscaling electroosmosis from pore scale to Darcy scale can be considered as a promising approach. However, this method requires analytical solutions for flow and transport at pore scale. This study concentrates on the development of analytical solutions of flow and transport in a single rectangular channel under combined effects of electrohydrodynamic forces. These relations will be used in future works for pore-network modeling. The analytical solutions are valid for all regimes of overlapping electrical double layers and have the potential to be extended to nonlinear Boltzmann distribution. The innovative aspects of this study are (a) contribution of overlapping of electrical double layers to the Stokes flow as well as Nernst-Planck transport has been carefully included in the analytical solutions. (b) All important transport mechanisms including advection, diffusion, and electromigration have been included in the analytical solutions. (c) Fully algebraic relations developed in this study can be easily employed to upscale electroosmosis to Darcy scale using pore-network modeling. © 2013 Springer Science+Business Media Dordrecht.

  12. Analytical solution of electrohydrodynamic flow and transport in rectangular channels: inclusion of double layer effects

    KAUST Repository

    Joekar-Niasar, V.; Schotting, R.; Leijnse, A.

    2013-01-01

    Upscaling electroosmosis in porous media is a challenge due to the complexity and scale-dependent nonlinearities of this coupled phenomenon. "Pore-network modeling" for upscaling electroosmosis from pore scale to Darcy scale can be considered as a promising approach. However, this method requires analytical solutions for flow and transport at pore scale. This study concentrates on the development of analytical solutions of flow and transport in a single rectangular channel under combined effects of electrohydrodynamic forces. These relations will be used in future works for pore-network modeling. The analytical solutions are valid for all regimes of overlapping electrical double layers and have the potential to be extended to nonlinear Boltzmann distribution. The innovative aspects of this study are (a) contribution of overlapping of electrical double layers to the Stokes flow as well as Nernst-Planck transport has been carefully included in the analytical solutions. (b) All important transport mechanisms including advection, diffusion, and electromigration have been included in the analytical solutions. (c) Fully algebraic relations developed in this study can be easily employed to upscale electroosmosis to Darcy scale using pore-network modeling. © 2013 Springer Science+Business Media Dordrecht.

  13. Used Fuel Logistics: Decades of Experience with transportation and Interim storage solutions

    Energy Technology Data Exchange (ETDEWEB)

    Orban, G.; Shelton, C.

    2015-07-01

    Used fuel inventories are growing worldwide. While some countries have opted for a closed cycle with recycling, numerous countries must expand their interim storage solutions as implementation of permanent repositories is taking more time than foreseen. In both cases transportation capabilities will have to be developed. AREVA TN has an unparalleled expertise with transportation of used fuel. For more than 50 years AREVA TN has safely shipped more than 7,000 used fuel transport casks. The transportation model that was initially developed in the 1970s has been adapted and enhanced over the years to meet more restrictive regulatory requirements and evolving customer needs, and to address public concerns. The numerous “lessons learned” have offered data and guidance that have allowed for also efficient and consistent improvement over the decades. AREVA TN has also an extensive experience with interim dry storage solutions in many countries on-site but also is working with partners to developed consolidated interim storage facility. Both expertise with storage and transportation contribute to safe, secure and smooth continuity of the operations. This paper will describe decades of experience with a very successful transportation program as well as interim storage solutions. (Author)

  14. Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate.

    Science.gov (United States)

    Bosdriesz, Evert; Magnúsdóttir, Stefanía; Bruggeman, Frank J; Teusink, Bas; Molenaar, Douwe

    2015-06-01

    Microorganisms rely on binding-protein assisted, active transport systems to scavenge for scarce nutrients. Several advantages of using binding proteins in such uptake systems have been proposed. However, a systematic, rigorous and quantitative analysis of the function of binding proteins is lacking. By combining knowledge of selection pressure and physiochemical constraints, we derive kinetic, thermodynamic, and stoichiometric properties of binding-protein dependent transport systems that enable a maximal import activity per amount of transporter. Under the hypothesis that this maximal specific activity of the transport complex is the selection objective, binding protein concentrations should exceed the concentration of both the scarce nutrient and the transporter. This increases the encounter rate of transporter with loaded binding protein at low substrate concentrations, thereby enhancing the affinity and specific uptake rate. These predictions are experimentally testable, and a number of observations confirm them. © 2015 FEBS.

  15. Anomalous solute transport in saturated porous media: Relating transport model parameters to electrical and nuclear magnetic resonance properties

    Science.gov (United States)

    Swanson, Ryan D; Binley, Andrew; Keating, Kristina; France, Samantha; Osterman, Gordon; Day-Lewis, Frederick D.; Singha, Kamini

    2015-01-01

    The advection-dispersion equation (ADE) fails to describe commonly observed non-Fickian solute transport in saturated porous media, necessitating the use of other models such as the dual-domain mass-transfer (DDMT) model. DDMT model parameters are commonly calibrated via curve fitting, providing little insight into the relation between effective parameters and physical properties of the medium. There is a clear need for material characterization techniques that can provide insight into the geometry and connectedness of pore spaces related to transport model parameters. Here, we consider proton nuclear magnetic resonance (NMR), direct-current (DC) resistivity, and complex conductivity (CC) measurements for this purpose, and assess these methods using glass beads as a control and two different samples of the zeolite clinoptilolite, a material that demonstrates non-Fickian transport due to intragranular porosity. We estimate DDMT parameters via calibration of a transport model to column-scale solute tracer tests, and compare NMR, DC resistivity, CC results, which reveal that grain size alone does not control transport properties and measured geophysical parameters; rather, volume and arrangement of the pore space play important roles. NMR cannot provide estimates of more-mobile and less-mobile pore volumes in the absence of tracer tests because these estimates depend critically on the selection of a material-dependent and flow-dependent cutoff time. Increased electrical connectedness from DC resistivity measurements are associated with greater mobile pore space determined from transport model calibration. CC was hypothesized to be related to length scales of mass transfer, but the CC response is unrelated to DDMT.

  16. Regional distribution of serotonin transporter protein in postmortem human brain

    Energy Technology Data Exchange (ETDEWEB)

    Kish, Stephen J. [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada)]. E-mail: Stephen_Kish@CAMH.net; Furukawa, Yoshiaki [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Chang Lijan [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Tong Junchao [Human Neurochemical Pathology Laboratory, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Ginovart, Nathalie [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Wilson, Alan [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Houle, Sylvain [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada); Meyer, Jeffrey H. [PET Centre, Centre for Addiction and Mental Health, Toronto, ON, M5T 1R8 (Canada)

    2005-02-01

    Introduction: The primary approach in assessing the status of brain serotonin neurons in human conditions such as major depression and exposure to the illicit drug ecstasy has been the use of neuroimaging procedures involving radiotracers that bind to the serotonin transporter (SERT). However, there has been no consistency in the selection of a 'SERT-free' reference region for the estimation of free and nonspecific binding, as occipital cortex, cerebellum and white matter have all been employed. Objective and Methods: To identify areas of human brain that might have very low SERT levels, we measured, by a semiquantitative Western blotting procedure, SERT protein immunoreactivity throughout the postmortem brain of seven normal adult subjects. Results: Serotonin transporter could be quantitated in all examined brain areas. However, the SERT concentration in cerebellar cortex and white matter were only at trace values, being approximately 20% of average cerebral cortex and 5% of average striatum values. Conclusion: Although none of the examined brain areas are completely free of SERT, human cerebellar cortex has low SERT binding as compared to other examined brain regions, with the exception of white matter. Since the cerebellar cortical SERT binding is not zero, this region will not be a suitable reference region for SERT radioligands with very low free and nonspecific binding. For SERT radioligands with reasonably high free and nonspecific binding, the cerebellar cortex should be a useful reference region, provided other necessary radioligand assumptions are met.

  17. Regional distribution of serotonin transporter protein in postmortem human brain

    International Nuclear Information System (INIS)

    Kish, Stephen J.; Furukawa, Yoshiaki; Chang Lijan; Tong Junchao; Ginovart, Nathalie; Wilson, Alan; Houle, Sylvain; Meyer, Jeffrey H.

    2005-01-01

    Introduction: The primary approach in assessing the status of brain serotonin neurons in human conditions such as major depression and exposure to the illicit drug ecstasy has been the use of neuroimaging procedures involving radiotracers that bind to the serotonin transporter (SERT). However, there has been no consistency in the selection of a 'SERT-free' reference region for the estimation of free and nonspecific binding, as occipital cortex, cerebellum and white matter have all been employed. Objective and Methods: To identify areas of human brain that might have very low SERT levels, we measured, by a semiquantitative Western blotting procedure, SERT protein immunoreactivity throughout the postmortem brain of seven normal adult subjects. Results: Serotonin transporter could be quantitated in all examined brain areas. However, the SERT concentration in cerebellar cortex and white matter were only at trace values, being approximately 20% of average cerebral cortex and 5% of average striatum values. Conclusion: Although none of the examined brain areas are completely free of SERT, human cerebellar cortex has low SERT binding as compared to other examined brain regions, with the exception of white matter. Since the cerebellar cortical SERT binding is not zero, this region will not be a suitable reference region for SERT radioligands with very low free and nonspecific binding. For SERT radioligands with reasonably high free and nonspecific binding, the cerebellar cortex should be a useful reference region, provided other necessary radioligand assumptions are met

  18. An Experimental Study on Solute Transport in One-Dimensional Clay Soil Columns

    Directory of Open Access Journals (Sweden)

    Muhammad Zaheer

    2017-01-01

    Full Text Available Solute transport in low-permeability media such as clay has not been studied carefully up to present, and we are often unclear what the proper governing law is for describing the transport process in such media. In this study, we composed and analyzed the breakthrough curve (BTC data and the development of leaching in one-dimensional solute transport experiments in low-permeability homogeneous and saturated media at small scale, to identify key parameters controlling the transport process. Sodium chloride (NaCl was chosen to be the tracer. A number of tracer tests were conducted to inspect the transport process under different conditions. The observed velocity-time behavior for different columns indicated the decline of soil permeability when switching from tracer introducing to tracer flushing. The modeling approaches considered were the Advection-Dispersion Equation (ADE, Two-Region Model (TRM, Continuous Time Random Walk (CTRW, and Fractional Advection-Dispersion Equation (FADE. It was found that all the models can fit the transport process very well; however, ADE and TRM were somewhat unable to characterize the transport behavior in leaching. The CTRW and FADE models were better in capturing the full evaluation of tracer-breakthrough curve and late-time tailing in leaching.

  19. Test of the 'glymphatic' hypothesis demonstrates diffusive and aquaporin-4-independent solute transport in rodent brain parenchyma.

    Science.gov (United States)

    Smith, Alex J; Yao, Xiaoming; Dix, James A; Jin, Byung-Ju; Verkman, Alan S

    2017-08-21

    Transport of solutes through brain involves diffusion and convection. The importance of convective flow in the subarachnoid and paravascular spaces has long been recognized; a recently proposed 'glymphatic' clearance mechanism additionally suggests that aquaporin-4 (AQP4) water channels facilitate convective transport through brain parenchyma. Here, the major experimental underpinnings of the glymphatic mechanism were re-examined by measurements of solute movement in mouse brain following intracisternal or intraparenchymal solute injection. We found that: (i) transport of fluorescent dextrans in brain parenchyma depended on dextran size in a manner consistent with diffusive rather than convective transport; (ii) transport of dextrans in the parenchymal extracellular space, measured by 2-photon fluorescence recovery after photobleaching, was not affected just after cardiorespiratory arrest; and (iii) Aqp4 gene deletion did not impair transport of fluorescent solutes from sub-arachnoid space to brain in mice or rats. Our results do not support the proposed glymphatic mechanism of convective solute transport in brain parenchyma.

  20. Modeling variably saturated subsurface solute transport with MODFLOW-UZF and MT3DMS

    Science.gov (United States)

    Morway, Eric D.; Niswonger, Richard G.; Langevin, Christian D.; Bailey, Ryan T.; Healy, Richard W.

    2013-01-01

    The MT3DMS groundwater solute transport model was modified to simulate solute transport in the unsaturated zone by incorporating the unsaturated-zone flow (UZF1) package developed for MODFLOW. The modified MT3DMS code uses a volume-averaged approach in which Lagrangian-based UZF1 fluid fluxes and storage changes are mapped onto a fixed grid. Referred to as UZF-MT3DMS, the linked model was tested against published benchmarks solved analytically as well as against other published codes, most frequently the U.S. Geological Survey's Variably-Saturated Two-Dimensional Flow and Transport Model. Results from a suite of test cases demonstrate that the modified code accurately simulates solute advection, dispersion, and reaction in the unsaturated zone. Two- and three-dimensional simulations also were investigated to ensure unsaturated-saturated zone interaction was simulated correctly. Because the UZF1 solution is analytical, large-scale flow and transport investigations can be performed free from the computational and data burdens required by numerical solutions to Richards' equation. Results demonstrate that significant simulation runtime savings can be achieved with UZF-MT3DMS, an important development when hundreds or thousands of model runs are required during parameter estimation and uncertainty analysis. Three-dimensional variably saturated flow and transport simulations revealed UZF-MT3DMS to have runtimes that are less than one tenth of the time required by models that rely on Richards' equation. Given its accuracy and efficiency, and the wide-spread use of both MODFLOW and MT3DMS, the added capability of unsaturated-zone transport in this familiar modeling framework stands to benefit a broad user-ship.

  1. Solution of the neutron transport problem with anisotropic scattering in cylindrical geometry by the decomposition method

    International Nuclear Information System (INIS)

    Goncalves, G.A.; Bogado Leite, S.Q.; Vilhena, M.T. de

    2009-01-01

    An analytical solution has been obtained for the one-speed stationary neutron transport problem, in an infinitely long cylinder with anisotropic scattering by the decomposition method. Series expansions of the angular flux distribution are proposed in terms of suitably constructed functions, recursively obtainable from the isotropic solution, to take into account anisotropy. As for the isotropic problem, an accurate closed-form solution was chosen for the problem with internal source and constant incident radiation, obtained from an integral transformation technique and the F N method

  2. Numerical Solution of the Electron Transport Equation in the Upper Atmosphere

    Energy Technology Data Exchange (ETDEWEB)

    Woods, Mark Christopher [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Holmes, Mark [Rensselaer Polytechnic Inst., Troy, NY (United States); Sailor, William C [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-07-01

    A new approach for solving the electron transport equation in the upper atmosphere is derived. The problem is a very stiff boundary value problem, and to obtain an accurate numerical solution, matrix factorizations are used to decouple the fast and slow modes. A stable finite difference method is applied to each mode. This solver is applied to a simplifieed problem for which an exact solution exists using various versions of the boundary conditions that might arise in a natural auroral display. The numerical and exact solutions are found to agree with each other to at least two significant digits.

  3. Two endoplasmic reticulum (ER) membrane proteins that facilitate ER-to-Golgi transport of glycosylphosphatidylinositol-anchored proteins.

    Science.gov (United States)

    Barz, W P; Walter, P

    1999-04-01

    Many eukaryotic cell surface proteins are anchored in the lipid bilayer through glycosylphosphatidylinositol (GPI). GPI anchors are covalently attached in the endoplasmic reticulum (ER). The modified proteins are then transported through the secretory pathway to the cell surface. We have identified two genes in Saccharomyces cerevisiae, LAG1 and a novel gene termed DGT1 (for "delayed GPI-anchored protein transport"), encoding structurally related proteins with multiple membrane-spanning domains. Both proteins are localized to the ER, as demonstrated by immunofluorescence microscopy. Deletion of either gene caused no detectable phenotype, whereas lag1Delta dgt1Delta cells displayed growth defects and a significant delay in ER-to-Golgi transport of GPI-anchored proteins, suggesting that LAG1 and DGT1 encode functionally redundant or overlapping proteins. The rate of GPI anchor attachment was not affected, nor was the transport rate of several non-GPI-anchored proteins. Consistent with a role of Lag1p and Dgt1p in GPI-anchored protein transport, lag1Delta dgt1Delta cells deposit abnormal, multilayered cell walls. Both proteins have significant sequence similarity to TRAM, a mammalian membrane protein thought to be involved in protein translocation across the ER membrane. In vivo translocation studies, however, did not detect any defects in protein translocation in lag1Delta dgt1Delta cells, suggesting that neither yeast gene plays a role in this process. Instead, we propose that Lag1p and Dgt1p facilitate efficient ER-to-Golgi transport of GPI-anchored proteins.

  4. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

    Science.gov (United States)

    Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

    2017-09-05

    In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  5. Analytic solutions for colloid transport with time- or depth-dependent retention in porous media

    Science.gov (United States)

    Elucidating and quantifying the transport of industrial nanoparticles (e.g. silver, carbon nanotubes, and graphene oxide) and other colloid-size particles such as viruses and bacteria is important to safeguard and manage the quality of the subsurface environment. Analytic solutions were derived for...

  6. Ground-water solute transport modeling using a three-dimensional scaled model

    International Nuclear Information System (INIS)

    Crider, S.S.

    1987-01-01

    Scaled models are used extensively in current hydraulic research on sediment transport and solute dispersion in free surface flows (rivers, estuaries), but are neglected in current ground-water model research. Thus, an investigation was conducted to test the efficacy of a three-dimensional scaled model of solute transport in ground water. No previous results from such a model have been reported. Experiments performed on uniform scaled models indicated that some historical problems (e.g., construction and scaling difficulties; disproportionate capillary rise in model) were partly overcome by using simple model materials (sand, cement and water), by restricting model application to selective classes of problems, and by physically controlling the effect of the model capillary zone. Results from these tests were compared with mathematical models. Model scaling laws were derived for ground-water solute transport and used to build a three-dimensional scaled model of a ground-water tritium plume in a prototype aquifer on the Savannah River Plant near Aiken, South Carolina. Model results compared favorably with field data and with a numerical model. Scaled models are recommended as a useful additional tool for prediction of ground-water solute transport

  7. Semianalytical Solutions for Transport in Aquifer and Fractured Clay Matrix System

    Science.gov (United States)

    A three-dimensional mathematical model that describes transport of contaminant in a horizontal aquifer with simultaneous diffusion into a fractured clay formation is proposed. A group of analytical solutions is derived based on specific initial and boundary conditions as well as ...

  8. Determination of a closed-form solution for the multidimensional transport equation using a fractional derivative

    International Nuclear Information System (INIS)

    Zabadal, J.; Vilhena, M.T.; Segatto, C.F.; Pazos, R.P.Ruben Panta.

    2002-01-01

    In this work we construct a closed-form solution for the multidimensional transport equation rewritten in integral form which is expressed in terms of a fractional derivative of the angular flux. We determine the unknown order of the fractional derivative comparing the kernel of the integral equation with the one of the Riemann-Liouville definition of fractional derivative. We report numerical simulations

  9. Determination of a closed-form solution for the multidimensional transport equation using a fractional derivative

    Energy Technology Data Exchange (ETDEWEB)

    Zabadal, J. E-mail: jorge.zabadal@ufrgs.br; Vilhena, M.T. E-mail: vilhena@mat.ufrgs.br; Segatto, C.F. E-mail: cynthia@mat.ufrgs.br; Pazos, R.P.Ruben Panta. E-mail: rpp@mat.pucrgs.br

    2002-07-01

    In this work we construct a closed-form solution for the multidimensional transport equation rewritten in integral form which is expressed in terms of a fractional derivative of the angular flux. We determine the unknown order of the fractional derivative comparing the kernel of the integral equation with the one of the Riemann-Liouville definition of fractional derivative. We report numerical simulations.

  10. Positive solution of a time and energy dependent neutron transport problem

    International Nuclear Information System (INIS)

    Pao, C.V.

    1975-01-01

    A constructive method is given for the determination of a solution and an existence--uniqueness theorem for some nonlinear time and energy dependent neutron transport problems, including the linear transport system. The geometry of the medium under consideration is allowed to be either bounded or unbounded which includes the geometry of a finite or infinite cylinder, a half-space and the whole space R/subm/ (m=1,2,center-dotcenter-dotcenter-dot). Our approach to the problem is by successive approximation which leads to various recursion formulas for the approximations in terms of explicit integrations. It is shown under some Lipschitz conditions on the nonlinear functions, which describe the process of neutrons absorption, fission, and scattering, that the sequence of approximations converges to a unique positive solution. Since these conditions are satisfied by the linear transport equation, all the results for the nonlinear system are valid for the linear transport problem. In the general nonlinear problem, the existence of both local and global solutions are discussed, and an iterative process for the construction of the solution is given

  11. Relationship between application scale and maximum time latency in intelligent transport solutions

    NARCIS (Netherlands)

    Knoop, V.; Lint, J. van; Vries, J.; Kester, L.J.H.M.; Passchier, I.

    2013-01-01

    Congestion is a major problem in large, urbanized areas. Intelligent transport solutions aim to reduce this problem. In general, traffic is monitored with the use of sensors, the resulting data are processed, a traffic state is estimated, and a control measure is computed and implemented. The

  12. Direct interaction between linear electron transfer chains and solute transport systems in bacteria

    NARCIS (Netherlands)

    Elferink, Marieke G.L.; Hellingwerf, Klaas J.; Belkum, Marco J. van; Poolman, Bert; Konings, Wil N.

    1984-01-01

    In studies on alanine and lactose transport in Rhodopseudomonas sphaeroides we have demonstrated that the rate of solute uptake in this phototrophic bacterium is regulated by the rate of light-induced cyclic electron transfer. In the present paper the interaction between linear electron transfer

  13. Application of finite element method in the solution of transport equation

    International Nuclear Information System (INIS)

    Maiorino, J.R.; Vieira, W.J.

    1985-01-01

    It is presented the application of finite element method in the solution of second order transport equation (self-adjoint) for the even parity flux. The angular component is treated by expansion in Legendre polinomials uncoupled of the spatial component, which is approached by an expansion in base functions, interpolated in each spatial element. (M.C.K.) [pt

  14. MaSTiS, microorganism and solute transport in streams, model documentation and user manual

    Science.gov (United States)

    In-stream fate and transport of solutes and microorganisms need to be understood to evaluate suitability of waters for agricultural, recreational, and household uses and eventually minimize surface water contamination. Concerns over safety of this water resulted in development of predictive models f...

  15. Field-scale water flow and solute transport : SWAP model concepts, parameter estimation and case studies = [Waterstroming en transport van opgeloste stoffen op veldschaal

    NARCIS (Netherlands)

    Dam, van J.C.

    2000-01-01

    Water flow and solute transport in top soils are important elements in many environmental studies. The agro- and ecohydrological model SWAP (Soil-Water-Plant-Atmosphere) has been developed to simulate simultaneously water flow, solute transport, heat flow and crop growth at field scale

  16. Automatic protein structure solution from weak X-ray data

    Science.gov (United States)

    Skubák, Pavol; Pannu, Navraj S.

    2013-11-01

    Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

  17. Modeling study of solute transport in the unsaturated zone. Information and data sets. Volume 1

    International Nuclear Information System (INIS)

    Polzer, W.L.; Fuentes, H.R.; Springer, E.P.; Nyhan, J.W.

    1986-05-01

    The Environmental Science Group (HSE-12) is conducting a study to compare various approaches of modeling water and solute transport in porous media. Various groups representing different approaches will model a common set of transport data so that the state of the art in modeling and field experimentation can be discussed in a positive framework with an assessment of current capabilities and future needs in this area of research. This paper provides information and sets of data that will be useful to the modelers in meeting the objectives of the modeling study. The information and data sets include: (1) a description of the experimental design and methods used in obtaining solute transport data, (2) supporting data that may be useful in modeling the data set of interest, and (3) the data set to be modeled

  18. Solution to the monoenergetic time-dependent neutron transport equation with a time-varying source

    International Nuclear Information System (INIS)

    Ganapol, B.D.

    1986-01-01

    Even though fundamental time-dependent neutron transport problems have existed since the inception of neutron transport theory, it has only been recently that a reliable numerical solution to one of the basic problems has been obtained. Experience in generating numerical solutions to time-dependent transport equations has indicated that the multiple collision formulation is the most versatile numerical technique for model problems. The formulation coupled with a moment reconstruction of each collided flux component has led to benchmark-quality (four- to five-digit accuracy) numerical evaluation of the neutron flux in plane infinite geometry for any degree of scattering anisotropy and for both pulsed isotropic and beam sources. As will be shown in this presentation, this solution can serve as a Green's function, thus extending the previous results to more complicated source situations. Here we will be concerned with a time-varying source at the center of an infinite medium. If accurate, such solutions have both pedagogical and practical uses as benchmarks against which other more approximate solutions designed for a wider class of problems can be compared

  19. A nonequilibrium model for reactive contaminant transport through fractured porous media: Model development and semianalytical solution

    Science.gov (United States)

    Joshi, Nitin; Ojha, C. S. P.; Sharma, P. K.

    2012-10-01

    In this study a conceptual model that accounts for the effects of nonequilibrium contaminant transport in a fractured porous media is developed. Present model accounts for both physical and sorption nonequilibrium. Analytical solution was developed using the Laplace transform technique, which was then numerically inverted to obtain solute concentration in the fracture matrix system. The semianalytical solution developed here can incorporate both semi-infinite and finite fracture matrix extent. In addition, the model can account for flexible boundary conditions and nonzero initial condition in the fracture matrix system. The present semianalytical solution was validated against the existing analytical solutions for the fracture matrix system. In order to differentiate between various sorption/transport mechanism different cases of sorption and mass transfer were analyzed by comparing the breakthrough curves and temporal moments. It was found that significant differences in the signature of sorption and mass transfer exists. Applicability of the developed model was evaluated by simulating the published experimental data of Calcium and Strontium transport in a single fracture. The present model simulated the experimental data reasonably well in comparison to the model based on equilibrium sorption assumption in fracture matrix system, and multi rate mass transfer model.

  20. Lateral transport of solutes in microfluidic channels using electrochemically generated gradients in redox-active surfactants.

    Science.gov (United States)

    Liu, Xiaoyang; Abbott, Nicholas L

    2011-04-15

    We report principles for a continuous flow process that can separate solutes based on a driving force for selective transport that is generated by a lateral concentration gradient of a redox-active surfactant across a microfluidic channel. Microfluidic channels fabricated with gold electrodes lining each vertical wall were used to electrochemically generate concentration gradients of the redox-active surfactant 11-ferrocenylundecyl-trimethylammonium bromide (FTMA) in a direction perpendicular to the flow. The interactions of three solutes (a hydrophobic dye, 1-phenylazo-2-naphthylamine (yellow AB), an amphiphilic molecule, 2-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-pentanoyl)-1-hexadecanoyl-sn-glycero-3-phosphocholine (BODIPY C(5)-HPC), and an organic salt, 1-methylpyridinium-3-sulfonate (MPS)) with the lateral gradients in surfactant/micelle concentration were shown to drive the formation of solute-specific concentration gradients. Two distinct physical mechanisms were identified to lead to the solute concentration gradients: solubilization of solutes by micelles and differential adsorption of the solutes onto the walls of the microchannels in the presence of the surfactant concentration gradient. These two mechanisms were used to demonstrate delipidation of a mixture of BODIPY C(5)-HPC (lipid) and MPS and purification of BODIPY C(5)-HPC from a mixture of BODIPY C(5)-HPC and yellow AB. Overall, the results of this study demonstrate that lateral concentration gradients of redox-active surfactants formed within microfluidic channels can be used to transport solutes across the microfluidic channels in a solute-dependent manner. The approach employs electrical potentials (solutions having high ionic strength (>0.1M), and offers the basis of continuous processes for the purification or separation of solutes in microscale systems. © 2011 American Chemical Society

  1. A numerical solution of the coupled proton-H atom transport equations for the proton aurora

    International Nuclear Information System (INIS)

    Basu, B.; Jasperse, J.R.; Grossbard, N.J.

    1990-01-01

    A numerical code has been developed to solve the coupled proton-H atom linear transport equations for the proton aurora. The transport equations have been simplified by using plane-parallel geometry and the forward-scattering approximations only. Otherwise, the equations and their numerical solutions are exact. Results are presented for the particle fluxes and the energy deposition rates, and they are compared with the previous analytical results that were obtained by using additional simplifying approximations. It is found that although the analytical solutions for the particle fluxes differ somewhat from the numerical solutions, the energy deposition rates calculated by the two methods agree to within a few percent. The accurate particle fluxes given by the numerical code are useful for accurate calculation of the characteristic quantities of the proton aurora, such as the ionization rates and the emission rates

  2. A Review of Darcy's Law: Limitations and Alternatives for Predicting Solute Transport

    Science.gov (United States)

    Steenhuis, Tammo; Kung, K.-J. Sam; Jaynes, Dan; Helling, Charles S.; Gish, Tim; Kladivko, Eileen

    2016-04-01

    Darcy's Law that was derived originally empirically 160 years ago, has been used successfully in calculating the (Darcy) flux in porous media throughout the world. However, field and laboratory experiments have demonstrated that the Darcy flux employed in the convective disperse equation could only successfully predict solute transport under two conditions: (1) uniformly or densely packed porous media; and (2) field soils under relatively dry condition. Employing the Darcy flux for solute transport in porous media with preferential flow pathways was problematic. In this paper we examine the theoretical background behind these field and laboratory observations and then provide an alternative to predict solute movement. By examining the characteristics of the momentum conservation principles on which Darcy's law is based, we show under what conditions Darcy flux can predict solute transport in porous media of various complexity. We find that, based on several case studies with capillary pores, Darcy's Law inherently merges momentum and in that way erases information on pore-scale velocities. For that reason the Darcy flux cannot predict flow in media with preferential flow conduits where individual pore velocities are essential in predicting the shape of the breakthrough curve and especially "the early arrival" of solutes. To overcome the limitations of the assumption in Darcy's law, we use Jury's conceptualization and employ the measured chemical breakthrough curve as input to characterize the impact of individual preferential flow pathways on chemical transport. Specifically, we discuss how best to take advantage of Jury's conceptualization to extract the pore-scale flow velocity to accurately predict chemical transport through soils with preferential flow pathways.

  3. Modeling water flow and solute transport in unsaturated zone inside NSRAWD project

    International Nuclear Information System (INIS)

    Constantin, A.; Diaconu, D.; Bucur, C.; Genty, A.

    2015-01-01

    The NSRAWD project (2010-2013) - Numerical Simulations for Radioactive Waste Disposal was initiated under a collaboration agreement between the Institute for Nuclear Research and the French Alternative Energies and Atomic Energy Commission (CEA). The context of the project was favorable to combine the modeling activities with an experimental part in order to improve and validate the numerical models used so far to simulate water flow and solute transport at Saligny site, Romania. The numerical models developed in the project were refined and validated on new hydrological data gathered between 2010-2012 by a monitoring station existent on site which performs automatic determination of soil water content and matrix potential, as well as several climate parameters (wind, temperature and precipitations). Water flow and solute transport was modeled in transient conditions, by taking into consideration, as well as neglecting the evapotranspiration phenomenon, on the basis of a tracer test launched on site. The determination of dispersivities for solute transport was targeted from the solute plume. The paper presents the main results achieved in the NSRAWD project related to water flow and solute transport in the unsaturated area of the Saligny site. The results indicated satisfactory predictions for the simulation of water flow in the unsaturated area, in steady state and transient conditions. In the case of tracer transport modeling, dispersivity coefficients could not be finally well fitted for the data measured on site and in order to obtain a realistic preview over the values of these parameters, further investigations are recommended. The article is followed by the slides of the presentation

  4. A complete NUHOMS {sup registered} solution for storage and transport of high burnup spent fuel

    Energy Technology Data Exchange (ETDEWEB)

    Bondre, J. [Transnuclear, Inc. (AREVA Group), Fremont, CA (United States)

    2004-07-01

    The discharge burnups of spent fuel from nuclear power plants keep increasing with plants discharging or planning to discharge fuel with burnups in excess of 60,000 MWD/MTU. Due to limited capacity of spent fuel pools, transfer of older cooler spent fuel from fuel pool to dry storage, and very limited options for transport of spent fuel, there is a critical need for dry storage of high burnup, higher heat load spent fuel so that plants could maintain their full core offload reserve capability. A typical NUHOMS {sup registered} solution for dry spent fuel storage is shown in the Figure 1. Transnuclear, Inc. offers two advanced NUHOMS {sup registered} solutions for the storage and transportation of high burnup fuel. One includes the NUHOMS {sup registered} 24PTH system for plants with 90.7 Metric Ton (MT) crane capacity; the other offers the higher capacity NUHOMS {sup registered} 32PTH system for higher crane capacity. These systems include NUHOMS {sup registered} - 24PTH and -32PTH Transportable Canisters stored in a concrete storage overpack (HSM-H). These canisters are designed to meet all the requirements of both storage and transport regulations. They are designed to be transported off-site either directly from the spent fuel pool or from the storage overpack in a suitable transport cask.

  5. Optimized Baxter model of protein solutions : Electrostatics versus adhesion

    NARCIS (Netherlands)

    Prinsen, P.; Odijk, T.

    2004-01-01

    A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the second virial coefficient is first outlined by balancing the

  6. Analytical solution and simplified analysis of coupled parent-daughter steady-state transport with multirate mass transfer

    Science.gov (United States)

    R. Haggerty

    2013-01-01

    In this technical note, a steady-state analytical solution of concentrations of a parent solute reacting to a daughter solute, both of which are undergoing transport and multirate mass transfer, is presented. Although the governing equations are complicated, the resulting solution can be expressed in simple terms. A function of the ratio of concentrations, In (daughter...

  7. Volumetric interpretation of protein adsorption: interfacial packing of protein adsorbed to hydrophobic surfaces from surface-saturating solution concentrations.

    Science.gov (United States)

    Kao, Ping; Parhi, Purnendu; Krishnan, Anandi; Noh, Hyeran; Haider, Waseem; Tadigadapa, Srinivas; Allara, David L; Vogler, Erwin A

    2011-02-01

    The maximum capacity of a hydrophobic adsorbent is interpreted in terms of square or hexagonal (cubic and face-centered-cubic, FCC) interfacial packing models of adsorbed blood proteins in a way that accommodates experimental measurements by the solution-depletion method and quartz-crystal-microbalance (QCM) for the human proteins serum albumin (HSA, 66 kDa), immunoglobulin G (IgG, 160 kDa), fibrinogen (Fib, 341 kDa), and immunoglobulin M (IgM, 1000 kDa). A simple analysis shows that adsorbent capacity is capped by a fixed mass/volume (e.g. mg/mL) surface-region (interphase) concentration and not molar concentration. Nearly analytical agreement between the packing models and experiment suggests that, at surface saturation, above-mentioned proteins assemble within the interphase in a manner that approximates a well-ordered array. HSA saturates a hydrophobic adsorbent with the equivalent of a single square or hexagonally-packed layer of hydrated molecules whereas the larger proteins occupy two-or-more layers, depending on the specific protein under consideration and analytical method used to measure adsorbate mass (solution depletion or QCM). Square or hexagonal (cubic and FCC) packing models cannot be clearly distinguished by comparison to experimental data. QCM measurement of adsorbent capacity is shown to be significantly different than that measured by solution depletion for similar hydrophobic adsorbents. The underlying reason is traced to the fact that QCM measures contribution of both core protein, water of hydration, and interphase water whereas solution depletion measures only the contribution of core protein. It is further shown that thickness of the interphase directly measured by QCM systematically exceeds that inferred from solution-depletion measurements, presumably because the static model used to interpret solution depletion does not accurately capture the complexities of the viscoelastic interfacial environment probed by QCM. Copyright © 2010

  8. Control and optimization of solute transport in a thin porous tube

    KAUST Repository

    Griffiths, I. M.

    2013-03-01

    Predicting the distribution of solutes or particles in flows within porous-walled tubes is essential to inform the design of devices that rely on cross-flow filtration, such as those used in water purification, irrigation devices, field-flow fractionation, and hollow-fibre bioreactors for tissue-engineering applications. Motivated by these applications, a radially averaged model for fluid and solute transport in a tube with thin porous walls is derived by developing the classical ideas of Taylor dispersion. The model includes solute diffusion and advection via both radial and axial flow components, and the advection, diffusion, and uptake coefficients in the averaged equation are explicitly derived. The effect of wall permeability, slip, and pressure differentials upon the dispersive solute behaviour are investigated. The model is used to explore the control of solute transport across the membrane walls via the membrane permeability, and a parametric expression for the permeability required to generate a given solute distribution is derived. The theory is applied to the specific example of a hollow-fibre membrane bioreactor, where a uniform delivery of nutrient across the membrane walls to the extra-capillary space is required to promote spatially uniform cell growth. © 2013 American Institute of Physics.

  9. Non-cooperative and cooperative solutions of government subsidy on public transportation

    Directory of Open Access Journals (Sweden)

    Husniah Hennie

    2018-01-01

    Full Text Available The paper deals with two models of government subsidy given to a public transport operator: (i the subsidy for buying bus from an appointed public transport manufacturer, and (ii the subsidy for reimbursing reduced ticket price for passengers. The models are developed to determine the maximum profit for both the public transport operator and the manufacturer. Since we consider two parties – the public transport operator and the manufacturer of the bus, then we use game theoretical approach by considering non-cooperative and cooperative solutions. Furthermore, since the bus is repairable we consider virtual age to model the preventive maintenance and we consider minimal repair to model the corrective maintenance. We analyse both type of subsidy models and give some numerical examples which show the effects of different subsidies to the profit of operator and manufacturer. The result of the numerical examples indicates that reducing ticket price would give a higher profit both to the operator and the manufacturer.

  10. Modeling of water flow and solute transport in unsaturated heterogeneous fields

    International Nuclear Information System (INIS)

    Bresler, E.; Dagan, G.

    1982-01-01

    A comprehensive model which considers dispersive solute transport, nonsteady moisture flow regimes and complex boundary conditions is described. The main assumptions are: vertical flow; spatial variability which is associated with the saturated hydraulic conductivity K/sub s/ occurs in the horizontal plane, but is constant in the profile, and has a lognormal probability distribution function (PDF); deterministic recharge and solute concentration are applied during infiltration; the soil is at uniform water content and salt concentration prior to infiltration. The problem is to solve, for arbitrary K/sub s/, the Richards' equation of flow simultaneously with the diffusion-convection equation for salt transport, with the boundary and initial conditions appropriate to infiltration-redistribution. Once this is achieved, the expectation and variance of various quantities of interest (solute concentration, moisture content) are obtained by using the statistical averaging procedure and the given PDF of K/sub s/. Since the solution of Richards' equation for the infiltration-redistribution cycle is extremely difficult (for a given K/sub s/), an approxiate solution is derived by using the concept of piston flow type wetting fronts. Similarly, accurate numerical solutions are used as input for the same statistical averaging procedure. The stochastic model is applied to two spatially variable soils by using both accurate numerical solutions and the simplified water and salt transport models. A comparison between the results shows that the approximate simplified models lead to quite accurate values of the expectations and variances of the flow variables for the entire field. It is suggested that in spatially variable fields, stochastic modeling represents the actual flow phenomena realistically, and provides the main statistical moments by using simplified flow models which can be used with confidence in applications

  11. EDM-DEDM and protein crystal structure solution.

    Science.gov (United States)

    Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Anna Maria; Siliqi, Dritan

    2009-05-01

    Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249-256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM-DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed.

  12. Laboratory experiments on solute transport in bimodal porous media under cyclic precipitation-evaporation boundary conditions

    Science.gov (United States)

    Cremer, Clemens; Neuweiler, Insa

    2016-04-01

    Flow and solute transport in the shallow subsurface is strongly governed by atmospheric boundary conditions. Erratically varying infiltration and evaporation cycles lead to alternating upward and downward flow, as well as spatially and temporally varying water contents and associated hydraulic conductivity of the prevailing materials. Thus presenting a highly complicated, dynamic system. Knowledge of subsurface solute transport processes is vital to assess e.g. the entry of, potentially hazardous, solutes to the groundwater and nutrient uptake by plant roots and can be gained in many ways. Besides field measurements and numerical simulations, physical laboratory experiments represent a way to establish process understanding and furthermore validate numerical schemes. With the aim to gain a better understanding and to quantify solute transport in the unsaturated shallow subsurface under natural precipitation conditions in heterogeneous media, we conduct physical laboratory experiments in a 22 cm x 8 cm x 1 cm flow cell that is filled with two types of sand and apply cyclic infiltration-evaporation phases at the soil surface. Pressure at the bottom of the domain is kept constant. Following recent studies (Lehmann and Or, 2009; Bechtold et al., 2011a), heterogeneity is introduced by a sharp vertical interface between coarse and fine sand. Fluorescent tracers are used to i) qualitatively visualize transport paths within the domain and ii) quantify solute leaching at the bottom of the domain. Temporal and spatial variations in water content during the experiment are derived from x-ray radiographic images. Monitored water contents between infiltration and evaporation considerably changed in the coarse sand while the fine sand remained saturated throughout the experiments. Lateral solute transport through the interface in both directions at different depths of the investigated soil columns were observed. This depended on the flow rate applied at the soil surface and

  13. The Influence of the Addition of Polyacrylic Hydrogel on the Content of Proteins, Minerals and Trace Elements in Milk Protein Solutions

    Directory of Open Access Journals (Sweden)

    Aleksandar Ž. Kostić

    2014-01-01

    Full Text Available Solutions of milk protein concentrate, whey protein concentrate and bovine serum albumin (BSA were treated with polyacrylic hydrogel to establish whether the hydrogel could be used for decontamination of heavy metal ions from milk protein-based products. The obtained results indicated that swelling of hydrogel in these solutions had different effects on their mineral, trace element and total protein content. Total protein and phosphorus content increased in milk protein concentrate and whey protein concentrate solutions after swelling of hydrogel without changes in their protein compositions. On the other hand, the protein content in BSA solution decreased after swelling. The content of Na did not change in milk protein concentrate solution, whereas it significantly increased in whey protein concentrate solution after hydrogel swelling. The content of Ca and Mg was reduced after the swelling in milk protein concentrate and whey protein concentrate solutions for 20.3–63.4 %, depending on the analysed sample and the mineral. The content of Zn did not change during swelling, whereas the content of Fe, Cu, Mn, Ni and Pb significantly decreased after hydrogel swelling in all analysed samples. According to the obtained results, the addition of polyacrylic hydrogel to milk and whey protein concentrate solutions can significantly decrease the content of heavy metal ions without affecting their protein composition. Therefore, this work could be useful in developing a new technological process for heavy metal purification of milk protein-based products.

  14. Analytical solution for the transport equation for neutral particles in cylindrical and Cartesian geometry

    International Nuclear Information System (INIS)

    Goncalves, Glenio Aguiar

    2003-01-01

    In this work, we are reported analytical solutions for the transport equation for neutral particles in cylindrical and cartesian geometry. For the cylindrical geometry, it is applied the Hankel transform of order zero in the S N approximation of the one-dimensional cylindrical transport equation, assuming azimuthal symmetry and isotropic scattering. This procedure is coined HTSN method. The anisotropic problem is handled using the decomposition method, generating a recursive approach, which the HTSN solution is used as initial condition. For cartesian geometry, the one and two dimensional transport equation is derived in the angular variable as many time as the degree of the anisotropic scattering. This procedure leads to set of integro-differential plus one differential equation that can be really solved by the variable separation method. Following this procedure, it was possible to come out with the Case solution for the one-dimensional problem. Numerical simulations are reported for the cylindrical transport problem both isotropic and anisotropic case of quadratic degree. (author)

  15. Visualization of protein interaction networks: problems and solutions

    Directory of Open Access Journals (Sweden)

    Agapito Giuseppe

    2013-01-01

    Full Text Available Abstract Background Visualization concerns the representation of data visually and is an important task in scientific research. Protein-protein interactions (PPI are discovered using either wet lab techniques, such mass spectrometry, or in silico predictions tools, resulting in large collections of interactions stored in specialized databases. The set of all interactions of an organism forms a protein-protein interaction network (PIN and is an important tool for studying the behaviour of the cell machinery. Since graphic representation of PINs may highlight important substructures, e.g. protein complexes, visualization is more and more used to study the underlying graph structure of PINs. Although graphs are well known data structures, there are different open problems regarding PINs visualization: the high number of nodes and connections, the heterogeneity of nodes (proteins and edges (interactions, the possibility to annotate proteins and interactions with biological information extracted by ontologies (e.g. Gene Ontology that enriches the PINs with semantic information, but complicates their visualization. Methods In these last years many software tools for the visualization of PINs have been developed. Initially thought for visualization only, some of them have been successively enriched with new functions for PPI data management and PIN analysis. The paper analyzes the main software tools for PINs visualization considering four main criteria: (i technology, i.e. availability/license of the software and supported OS (Operating System platforms; (ii interoperability, i.e. ability to import/export networks in various formats, ability to export data in a graphic format, extensibility of the system, e.g. through plug-ins; (iii visualization, i.e. supported layout and rendering algorithms and availability of parallel implementation; (iv analysis, i.e. availability of network analysis functions, such as clustering or mining of the graph, and the

  16. Evidence of a gustatory-vestibular pathway for protein transport.

    Science.gov (United States)

    Gacek, Richard; Lyon, Michael J

    2010-02-01

    To demonstrate anatomically a pathway for protein transport from the palate to the vestibular system. The vestibulofacial anastomosis and associated ganglion cells were identified in a collection of 160 horizontally sectioned human temporal bones that had been stained with hematoxylin and eosin. Wheat germ agglutinin-horseradish peroxidase (HRP) was applied to the greater superficial petrosal nerve in 4 Sprague-Dawley rats. After 30 hours, the rats were killed by intracardiac perfusion, and the seventh and eighth nerves with adjacent brainstem removed. Frozen sections cut at 30 mum through this block were then reacted for HRP, counterstained with neutral red, and mounted on slides for examination in the light microscope. Thirty-two of the 160 human temporal bones contained sections through the vestibulofacial anastomosis and its ganglion. In all cases, the ganglion was incorporated into the vestibular ganglion (VG) adjacent to the nervus intermedius. In all 4 experimental rats, HRP reaction product labeled a small number of ganglion cells in the VG adjacent to the nervus intermedius and facial nerve. These observations support the presence of a pathway from receptors in the palate to the VG.

  17. Training-induced changes in membrane transport proteins of human skeletal muscle

    DEFF Research Database (Denmark)

    Juel, C.

    2006-01-01

    Training improves human physical performance by inducing structural and cardiovascular changes, metabolic changes, and changes in the density of membrane transport proteins. This review focuses on the training-induced changes in proteins involved in sarcolemmal membrane transport. It is concluded...

  18. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  19. Mathematical model formulation and validation of water and solute transport in whole hamster pancreatic islets.

    Science.gov (United States)

    Benson, James D; Benson, Charles T; Critser, John K

    2014-08-01

    Optimization of cryopreservation protocols for cells and tissues requires accurate models of heat and mass transport. Model selection often depends on the configuration of the tissue. Here, a mathematical and conceptual model of water and solute transport for whole hamster pancreatic islets has been developed and experimentally validated incorporating fundamental biophysical data from previous studies on individual hamster islet cells while retaining whole-islet structural information. It describes coupled transport of water and solutes through the islet by three methods: intracellularly, intercellularly, and in combination. In particular we use domain decomposition techniques to couple a transmembrane flux model with an interstitial mass transfer model. The only significant undetermined variable is the cellular surface area which is in contact with the intercellularly transported solutes, Ais. The model was validated and Ais determined using a 3×3 factorial experimental design blocked for experimental day. Whole islet physical experiments were compared with model predictions at three temperatures, three perfusing solutions, and three islet size groups. A mean of 4.4 islets were compared at each of the 27 experimental conditions and found to correlate with a coefficient of determination of 0.87±0.06 (mean ± SD). Only the treatment variable of perfusing solution was found to be significant (p<0.05). We have devised a model that retains much of the intrinsic geometric configuration of the system, and thus fewer laboratory experiments are needed to determine model parameters and thus to develop new optimized cryopreservation protocols. Additionally, extensions to ovarian follicles and other concentric tissue structures may be made. Copyright © 2014 Elsevier Inc. All rights reserved.

  20. THE IMPORTANCE OF LIMIT SOLUTIONS & TEMPORAL AND SPATIAL SCALES IN THE TEACHING OF TRANSPORT PHENOMENA

    Directory of Open Access Journals (Sweden)

    SÁVIO LEANDRO BERTOLI

    2016-07-01

    Full Text Available In the engineering courses the field of Transport Phenomena is of significant importance and it is in several disciplines relating to Fluid Mechanics, Heat and Mass Transfer. In these disciplines, problems involving these phenomena are mathematically formulated and analytical solutions are obtained whenever possible. The aim of this paper is to emphasize the possibility of extending aspects of the teaching-learning in this area by a method based on time scales and limit solutions. Thus, aspects relative to the phenomenology naturally arise during the definition of the scales and / or by determining the limit solutions. Aspects concerning the phenomenology of the limit problems are easily incorporated into the proposed development, which contributes significantly to the understanding of physics inherent in the mathematical modeling of each limiting case studied. Finally the study aims to disseminate the use of the limit solutions and of the time scales in the general fields of engineering.

  1. Exact solutions of Fisher and Burgers equations with finite transport memory

    International Nuclear Information System (INIS)

    Kar, Sandip; Banik, Suman Kumar; Ray, Deb Shankar

    2003-01-01

    The Fisher and Burgers equations with finite memory transport, describing reaction-diffusion and convection-diffusion processes, respectively have recently attracted a lot of attention in the context of chemical kinetics, mathematical biology and turbulence. We show here that they admit exact solutions. While the speed of the travelling wavefront is dependent on the relaxation time in the Fisher equation, memory effects significantly smoothen out the shock wave nature of the Burgers solution, without any influence on the corresponding wave speed. We numerically analyse the ansatz for the exact solution and show that for the reaction-diffusion system the strength of the reaction term must be moderate enough not to exceed a critical limit to allow a travelling wave solution to exist for appreciable finite memory effect

  2. Exact solutions of Fisher and Burgers equations with finite transport memory

    CERN Document Server

    Kar, S; Ray, D S

    2003-01-01

    The Fisher and Burgers equations with finite memory transport, describing reaction-diffusion and convection-diffusion processes, respectively have recently attracted a lot of attention in the context of chemical kinetics, mathematical biology and turbulence. We show here that they admit exact solutions. While the speed of the travelling wavefront is dependent on the relaxation time in the Fisher equation, memory effects significantly smoothen out the shock wave nature of the Burgers solution, without any influence on the corresponding wave speed. We numerically analyse the ansatz for the exact solution and show that for the reaction-diffusion system the strength of the reaction term must be moderate enough not to exceed a critical limit to allow a travelling wave solution to exist for appreciable finite memory effect.

  3. Exact solutions of the population balance equation including particle transport, using group analysis

    Science.gov (United States)

    Lin, Fubiao; Meleshko, Sergey V.; Flood, Adrian E.

    2018-06-01

    The population balance equation (PBE) has received an unprecedented amount of attention in recent years from both academics and industrial practitioners because of its long history, widespread use in engineering, and applicability to a wide variety of particulate and discrete-phase processes. However it is typically impossible to obtain analytical solutions, although in almost every case a numerical solution of the PBEs can be obtained. In this article, the symmetries of PBEs with homogeneous coagulation kernels involving aggregation, breakage and growth processes and particle transport in one dimension are found by direct solving the determining equations. Using the optimal system of one and two-dimensional subalgebras, all invariant solutions and reduced equations are obtained. In particular, an explicit analytical physical solution is also presented.

  4. Examination and Manipulation of Protein Surface Charge in Solution with Electrospray Ionization Mass Spectrometry

    Science.gov (United States)

    Gross, Deborah S.; Van Ryswyk, Hal

    2014-01-01

    Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool for examining the charge of proteins in solution. The charge can be manipulated through choice of solvent and pH. Furthermore, solution-accessible, protonated lysine side chains can be specifically tagged with 18-crown-6 ether to form noncovalent adducts. Chemical derivatization…

  5. A direct comparison of protein structure in the gas and solution phase: the Trp-cage

    DEFF Research Database (Denmark)

    Patriksson, Alexandra; Adams, Christopher M; Kjeldsen, Frank

    2007-01-01

    Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location...

  6. Water and Solute Transport in Arid Vadose Zones: Innovations in Measurement and Analysis

    International Nuclear Information System (INIS)

    Tyler, S W.; Scanlon, Bridget R.; Gee, Glendon W.; Allison, G B.; Parlange, M. B.; Hopmans, J. W.

    1999-01-01

    Understanding the physics of flow and transport through the vadose zone has advanced significantly in the last three decades. These advances have been made primarily in humid regions or in irrigated agricultural settings. While some of the techniques are useful, many are not suited to arid regions. The fluxes of water and solutes typically found in arid regions are often orders of magnitude smaller than those found in agricultural settings, while the time scales for transport can be orders of magnitude larger. The depth over which transport must be characterized is also often much greater than in humid regions. Rather than relying on advances in applied tracers, arid-zone researchers have developed natural tracer techniques that are capable of quantifying transport over tens to thousands of years. Techniques have been developed to measure the hydraulic properties of sediments at all water contents, including the very dry range and at far greater depths. As arid and semiarid regions come under increased development pressures for such activities as hazardous- and radioactive-waste disposal, the development of techniques and the understanding of water and solute transport have become crucial components in defining the environmental impacts of activities at the landsurface

  7. CFEST Coupled Flow, Energy & Solute Transport Version CFEST005 User’s Guide

    Energy Technology Data Exchange (ETDEWEB)

    Freedman, Vicky L.; Chen, Yousu; Gilca, Alex; Cole, Charles R.; Gupta, Sumant K.

    2006-07-20

    The CFEST (Coupled Flow, Energy, and Solute Transport) simulator described in this User’s Guide is a three-dimensional finite-element model used to evaluate groundwater flow and solute mass transport. Confined and unconfined aquifer systems, as well as constant and variable density fluid flows can be represented with CFEST. For unconfined aquifers, the model uses a moving boundary for the water table, deforming the numerical mesh so that the uppermost nodes are always at the water table. For solute transport, changes in concentra¬tion of a single dissolved chemical constituent are computed for advective and hydrodynamic transport, linear sorption represented by a retardation factor, and radioactive decay. Although several thermal parameters described in this User’s Guide are required inputs, thermal transport has not yet been fully implemented in the simulator. Once fully implemented, transport of thermal energy in the groundwater and solid matrix of the aquifer can also be used to model aquifer thermal regimes. The CFEST simulator is written in the FORTRAN 77 language, following American National Standards Institute (ANSI) standards. Execution of the CFEST simulator is controlled through three required text input files. These input file use a structured format of associated groups of input data. Example input data lines are presented for each file type, as well as a description of the structured FORTRAN data format. Detailed descriptions of all input requirements, output options, and program structure and execution are provided in this User’s Guide. Required inputs for auxillary CFEST utilities that aide in post-processing data are also described. Global variables are defined for those with access to the source code. Although CFEST is a proprietary code (CFEST, Inc., Irvine, CA), the Pacific Northwest National Laboratory retains permission to maintain its own source, and to distribute executables to Hanford subcontractors.

  8. Multiscale Roughness Influencing on Transport Behavior of Passive Solute through a Single Self-affine Fracture

    Science.gov (United States)

    Dou, Z.

    2017-12-01

    In this study, the influence of multi-scale roughness on transport behavior of the passive solute through the self-affine fracture was investigated. The single self-affine fracture was constructed by the successive random additions (SRA) and the fracture roughness was decomposed into two different scales (i.e. large-scale primary roughness and small-scale secondary roughness) by the Wavelet analysis technique. The fluid flow in fractures, which was characterized by the Forchheimer's law, showed the non-linear flow behaviors such as eddies and tortuous streamlines. The results indicated that the small-scale secondary roughness was primarily responsible for the non-linear flow behaviors. The direct simulations of asymptotic passive solute transport represented the Non-Fickian transport characteristics (i.e. early arrivals and long tails) in breakthrough curves (BTCs) and residence time distributions (RTDs) with and without consideration of the secondary roughness. Analysis of multiscale BTCs and RTDs showed that the small-scale secondary roughness played a significant role in enhancing the Non-Fickian transport characteristics. We found that removing small-scale secondary roughness led to the lengthening arrival and shortening tail. The peak concentration in BTCs decreased as the secondary roughness was removed, implying that the secondary could also enhance the solute dilution. The estimated BTCs by the Fickian advection-dispersion equation (ADE) yielded errors which decreased with the small-scale secondary roughness being removed. The mobile-immobile model (MIM) was alternatively implemented to characterize the Non-Fickian transport. We found that the MIM was more capable of estimating Non-Fickian BTCs. The small-scale secondary roughness resulted in the decreasing mobile domain fraction and the increasing mass exchange rate between immobile and mobile domains. The estimated parameters from the MIM could provide insight into the inherent mechanism of roughness

  9. Implementation of Solute Transport in the Vadose Zone into the `HYDRUS Package for MODFLOW'

    Science.gov (United States)

    Simunek, J.; Beegum, S.; Szymkiewicz, A.; Sudheer, K. P.

    2017-12-01

    The 'HYDRUS package for MODFLOW' was developed by Seo et al. (2007) and Twarakavi et al. (2008) to simultaneously evaluate transient water flow in both unsaturated and saturated zones. The package, which is based on the HYDRUS-1D model (Šimůnek et al., 2016) simulating unsaturated water flow in the vadose zone, was incorporated into MODFLOW (Harbaugh et al., 2000) simulating saturated groundwater flow. The HYDRUS package in the coupled model can be used to represent the effects of various unsaturated zone processes, including infiltration, evaporation, root water uptake, capillary rise, and recharge in homogeneous or layered soil profiles. The coupled model is effective in addressing spatially-variable saturated-unsaturated hydrological processes at the regional scale, allowing for complex layering in the unsaturated zone, spatially and temporarily variable water fluxes at the soil surface and in the root zone, and with alternating recharge and discharge fluxes (Twarakavi et al., 2008). One of the major limitations of the coupled model was that it could not be used to simulate at the same time solute transport. However, solute transport is highly dependent on water table fluctuations due to temporal and spatial variations in groundwater recharge. This is an important concern when the coupled model is used for analyzing groundwater contamination due to transport through the unsaturated zone. The objective of this study is to integrate the solute transport model (the solute transport part of HYDRUS-1D for the unsaturated zone and MT3DMS (Zheng and Wang, 1999; Zheng, 2009) for the saturated zone) into an existing coupled water flow model. The unsaturated zone component of the coupled model can consider solute transport involving many biogeochemical processes and reactions, including first-order degradation, volatilization, linear or nonlinear sorption, one-site kinetic sorption, two-site sorption, and two-kinetic sites sorption (Šimůnek and van Genuchten, 2008

  10. Transport of fluid and solutes in the body I. Formulation of a mathematical model.

    Science.gov (United States)

    Gyenge, C C; Bowen, B D; Reed, R K; Bert, J L

    1999-09-01

    A compartmental model of short-term whole body fluid, protein, and ion distribution and transport is formulated. The model comprises four compartments: a vascular and an interstitial compartment, each with an embedded cellular compartment. The present paper discusses the assumptions on which the model is based and describes the equations that make up the model. Fluid and protein transport parameters from a previously validated model as well as ionic exchange parameters from the literature or from statistical estimation [see companion paper: C. C. Gyenge, B. D. Bowen, R. K. Reed, and J. L. Bert. Am. J. Physiol. 277 (Heart Circ. Physiol. 46): H1228-H1240, 1999] are used in formulating the model. The dynamic model has the ability to simulate 1) transport across the capillary membrane of fluid, proteins, and small ions and their distribution between the vascular and interstitial compartments; 2) the changes in extracellular osmolarity; 3) the distribution and transport of water and ions associated with each of the cellular compartments; 4) the cellular transmembrane potential; and 5) the changes of volume in the four fluid compartments. The validation and testing of the proposed model against available experimental data are presented in the companion paper.

  11. Selective labeling of pulmonary surfactant protein SP-C in organic solution

    DEFF Research Database (Denmark)

    Plasencia, I; Cruz, A; López-Lacomba, J L

    2001-01-01

    Pulmonary surfactant protein SP-C has been isolated from porcine lungs and treated with dansyl isothiocyanate in chloroform:methanol 2:1 (v/v) solutions,under conditions optimized to introduce a single dansyl group covalently attached to the N-terminalamine group of the protein without loss of its...

  12. Solution scattering studies on a virus capsid protein as a building block for nanoscale assemblies

    NARCIS (Netherlands)

    Comellas Aragones, M.; Comellas-Aragones, Marta; Sikkema, Friso D.; Delaittre, Guillaume; Terry, Ann E.; King, Stephen M.; Visser, Dirk; Heenan, Richard K.; Nolte, Roeland J.M.; Cornelissen, Jeroen Johannes Lambertus Maria; Feiters, Martin C.

    2011-01-01

    Self-assembled protein cages are versatile building blocks in the construction of biomolecular nanostructures. Because of the defined assembly behaviour the cowpea chlorotic mottle virus (CCMV) protein is often used for such applications. Here we report a detailed solution scattering study of the

  13. Evaluation of back scatter interferometry, a method for detecting protein binding in solution

    DEFF Research Database (Denmark)

    Jepsen, S. T.; Jørgensen, Thomas Martini; Zong, Weiyong

    2015-01-01

    Back Scatter Interferometry (BSI) has been proposed to be a highly sensitive and versatile refractive index sensor usable for analytical detection of biomarker and protein interactions in solution. However the existing literature on BSI lacks a physical explanation of why protein interactions in ...

  14. The use of non-dimensional representation of the solute transport equations

    International Nuclear Information System (INIS)

    Laurens, J.-M.

    1988-07-01

    This report presents the results obtained in a pilot investigation into the use of non-dimensional representations of the solute transport equations, so as to improve the efficiency of the PRA codes used by the DoE and its contractors. A reduced set of parameters was obtained for a single layer transport model. As expected, the response was shown to be highly sensitive on the new parameters. A faster convergence of the system was observed when the sampling technique used was changed to take into account the properties of the new parameters, such that uniform coverage of the reduced parameter hyperspace was achieved. (author)

  15. Approximate solutions for the two-dimensional integral transport equation. The critically mixed methods of resolution

    International Nuclear Information System (INIS)

    Sanchez, Richard.

    1980-11-01

    This work is divided into two part the first part (note CEA-N-2165) deals with the solution of complex two-dimensional transport problems, the second one treats the critically mixed methods of resolution. These methods are applied for one-dimensional geometries with highly anisotropic scattering. In order to simplify the set of integral equation provided by the integral transport equation, the integro-differential equation is used to obtain relations that allow to lower the number of integral equation to solve; a general mathematical and numerical study is presented [fr

  16. Modeling particle-facilitated solute transport using the C-Ride module of HYDRUS

    Science.gov (United States)

    Simunek, Jiri; Bradford, Scott A.

    2017-04-01

    Strongly sorbing chemicals (e.g., heavy metals, radionuclides, pharmaceuticals, and/or explosives) in soils are associated predominantly with the solid phase, which is commonly assumed to be stationary. However, recent field- and laboratory-scale observations have shown that, in the presence of mobile colloidal particles (e.g., microbes, humic substances, clays and metal oxides), the colloids could act as pollutant carriers and thus provide a rapid transport pathway for strongly sorbing contaminants. Such transport can be further accelerated since these colloidal particles may travel through interconnected larger pores where the water velocity is relatively high. Additionally, colloidal particles have a considerable adsorption capacity for other species present in water because of their large specific surface areas and their high concentrations in soil-water and groundwater. As a result, the transport of contaminants can be significantly, sometimes dramatically, enhanced when they are adsorbed to mobile colloids. To address this problem, we have developed the C-Ride module for HYDRUS-1D. This one-dimensional numerical module is based on the HYDRUS-1D software package and incorporates mechanisms associated with colloid and colloid-facilitated solute transport in variably saturated porous media. This numerical model accounts for both colloid and solute movement due to convection, diffusion, and dispersion in variably-saturated soils, as well as for solute movement facilitated by colloid transport. The colloids transport module additionally considers processes of attachment/detachment to/from the solid phase, straining, and/or size exclusion. Various blocking and depth dependent functions can be used to modify the attachment and straining coefficients. The module additionally considers the effects of changes in the water content on colloid/bacteria transport and attachment/detachment to/from solid-water and air-water interfaces. For example, when the air

  17. Spatially distributed characterization of hyporheic solute transport during baseflow recession in a headwater mountain stream using electrical geophysical imaging

    Science.gov (United States)

    Adam S. Ward; Michael N. Gooseff; Michael Fitzgerald; Thomas J. Voltz; Kamini Singha

    2014-01-01

    The transport of solutes along hyporheic flowpaths is recognized as central to numerous biogeochemical cycles, yet our understanding of how this transport changes with baseflow recession, particularly in a spatially distributed manner, is limited. We conducted four steady-state solute tracer injections and collected electrical resistivity data to characterize hyporheic...

  18. Molecular theory for nuclear magnetic relaxation in protein solutions and tissue

    International Nuclear Information System (INIS)

    Kimmich, R.; Nusser, W.; Gneiting, T.

    1990-01-01

    A model theory is presented explaining a series of striking phenomena observed with nuclear magnetic relaxation in protein systems such as solutions or tissue. The frequency, concentration and temperature dependences of proton or deuteron relaxation times of protein solutions and tissue are explained. It is concluded that the translational diffusion of water molecules along the rugged surfaces of proteins and, to a minor degree, protein backbone fluctuations are crucial processes. The rate limiting factor of macromolecular tumbling is assumed to be given by the free water content in a certain analogy to the free-volume model of Cohen ad Turnbull. There are two characteristic water mass fractions indicating the saturation of the hydration shells and the onset of protein tumbling. A closed and relatively simple set of relaxation formulas is presented. The potentially fractal nature of the diffusion of water molecules on the protein surface is discussed. (author). 43 refs.; 4 figs

  19. Analysis of Nanobody-Epitope Interactions in Living Cells via Quantitative Protein Transport Assays.

    Science.gov (United States)

    Früholz, Simone; Pimpl, Peter

    2017-01-01

    Over the past few decades, quantitative protein transport analyses have been used to elucidate the sorting and transport of proteins in the endomembrane system of plants. Here, we have applied our knowledge about transport routes and the corresponding sorting signals to establish an in vivo system for testing specific interactions between soluble proteins.Here, we describe the use of quantitative protein transport assays in tobacco mesophyll protoplasts to test for interactions occurring between a GFP-binding nanobody and its GFP epitope. For this, we use a secreted GFP-tagged α-amylase as a reporter together with a vacuolar-targeted RFP-tagged nanobody. The interaction between these proteins is then revealed by a transport alteration of the secretory reporter due to the interaction-triggered attachment of the vacuolar sorting signal.

  20. A multi scale approximation solution for the time dependent Boltzmann-transport equation

    International Nuclear Information System (INIS)

    Merk, B.

    2004-03-01

    The basis of all transient simulations for nuclear reactor cores is the reliable calculation of the power production. The local power distribution is generally calculated by solving the space, time, energy and angle dependent neutron transport equation known as Boltzmann equation. The computation of exact solutions of the Boltzmann equation is very time consuming. For practical numerical simulations approximated solutions are usually unavoidable. The objective of this work is development of an effective multi scale approximation solution for the Boltzmann equation. Most of the existing methods are based on separation of space and time. The new suggested method is performed without space-time separation. This effective approximation solution is developed on the basis of an expansion for the time derivative of different approximations to the Boltzmann equation. The method of multiple scale expansion is used for the expansion of the time derivative, because the problem of the stiff time behaviour can't be expressed by standard expansion methods. This multiple scale expansion is used in this work to develop approximation solutions for different approximations of the Boltzmann equation, starting from the expansion of the point kinetics equations. The resulting analytic functions are used for testing the applicability and accuracy of the multiple scale expansion method for an approximation solution with 2 delayed neutron groups. The results are tested versus the exact analytical results for the point kinetics equations. Very good agreement between both solutions is obtained. The validity of the solution with 2 delayed neutron groups to approximate the behaviour of the system with 6 delayed neutron groups is demonstrated in an additional analysis. A strategy for a solution with 4 delayed neutron groups is described. A multiple scale expansion is performed for the space-time dependent diffusion equation for one homogenized cell with 2 delayed neutron groups. The result is

  1. The substrate-binding protein imposes directionality on an electrochemical sodium gradient-driven TRAP transporter

    NARCIS (Netherlands)

    Mulligan, Christopher; Geertsma, Eric R.; Severi, Emmanuele; Kelly, David J.; Poolman, Bert; Thomas, Gavin H.

    2009-01-01

    Substrate-binding protein-dependent secondary transporters are widespread in prokaryotes and are represented most frequently by members of the tripartite ATP-independent periplasmic (TRAP) transporter family. Here, we report the membrane reconstitution of a TRAP transporter, the sialic acid-specific

  2. Eutectic fusion used for the survey of transport of mass in metallic solutions

    International Nuclear Information System (INIS)

    Savane, Y.S.; Katty, S.; Balde, M.L.; Cisse, S.; Rogov, V.I.

    1997-09-01

    The phenomenon of eutectic fusion could be used for the survey of transport of mass in metallic solutions, which allows to determine the part of the ionic conductibility in the solutions. The survey done in the system In 2 Bi Bi-In at a temperature of 72 deg. C with a current of 4A allowed to find a ionic current of 2,6.10 -3 which constitutes about 0,07% of the total current. So the part of ionic conductibility in the eutectic fusion of the system In 2 Bi Bi-In is of 0,07%. (author)

  3. Solution of charged particle transport equation by Monte-Carlo method in the BRANDZ code system

    International Nuclear Information System (INIS)

    Artamonov, S.N.; Androsenko, P.A.; Androsenko, A.A.

    1992-01-01

    Consideration is given to the issues of Monte-Carlo employment for the solution of charged particle transport equation and its implementation in the BRANDZ code system under the conditions of real 3D geometry and all the data available on radiation-to-matter interaction in multicomponent and multilayer targets. For the solution of implantation problem the results of BRANDZ data comparison with the experiments and calculations by other codes in complexes systems are presented. The results of direct nuclear pumping process simulation for laser-active media by a proton beam are also included. 4 refs.; 7 figs

  4. Structural Basis for a Ribofuranosyl Binding Protein: Insights into the Furanose Specific Transport

    Energy Technology Data Exchange (ETDEWEB)

    Bagaria, A.; Swaminathan, S.; Kumaran, D.; Burley, S. K.

    2011-04-01

    The ATP-binding cassette transporters (ABC-transporters) are members of one of the largest protein superfamilies, with representatives in all extant phyla. These integral membrane proteins utilize the energy of ATP hydrolysis to carry out certain biological processes, including translocation of various substrates across membranes and non-transport related processes such as translation of RNA and DNA repair. Typically, such transport systems in bacteria consist of an ATP binding component, a transmembrane permease, and a periplasmic receptor or binding protein. Soluble proteins found in the periplasm of gram-negative bacteria serve as the primary receptors for transport of many compounds, such as sugars, small peptides, and some ions. Ligand binding activates these periplasmic components, permitting recognition by the membrane spanning domain, which supports for transport and, in some cases, chemotaxis. Transport and chemotaxis processes appear to be independent of one another, and a few mutants of bifunctional periplasmic components reveal the absence of one or the other function. Previously published high-resolution X-ray structures of various periplasmic ligand binding proteins include Arabinose binding protein (ABP), Allose binding protein (ALBP), Glucose-galactose binding protein (GBP) and Ribose binding protein (RBP). Each of these proteins consists of two structurally similar domains connected by a three-stranded hinge region, with ligand buried between the domains. Upon ligand binding and release, various conformational changes have been observed. For RBP, open (apo) and closed (ligand bound) conformations have been reported and so for MBP. The closed/active form of the protein interacts with the integral membrane component of the system in both transport and chemotaxis. Herein, we report 1.9{angstrom} resolution X-ray structure of the R{sub f}BP periplasmic component of an ABC-type sugar transport system from Hahella chejuensis (UniProt Id Q2S7D2) bound to

  5. Molecular Effects of Concentrated Solutes on Protein Hydration, Dynamics, and Electrostatics.

    Science.gov (United States)

    Abriata, Luciano A; Spiga, Enrico; Peraro, Matteo Dal

    2016-08-23

    Most studies of protein structure and function are performed in dilute conditions, but proteins typically experience high solute concentrations in their physiological scenarios and biotechnological applications. High solute concentrations have well-known effects on coarse protein traits like stability, diffusion, and shape, but likely also perturb other traits through finer effects pertinent at the residue and atomic levels. Here, NMR and molecular dynamics investigations on ubiquitin disclose variable interactions with concentrated solutes that lead to localized perturbations of the protein's surface, hydration, electrostatics, and dynamics, all dependent on solute size and chemical properties. Most strikingly, small polar uncharged molecules are sticky on the protein surface, whereas charged small molecules are not, but the latter still perturb the internal protein electrostatics as they diffuse nearby. Meanwhile, interactions with macromolecular crowders are favored mainly through hydrophobic, but not through polar, surface patches. All the tested small solutes strongly slow down water exchange at the protein surface, whereas macromolecular crowders do not exert such strong perturbation. Finally, molecular dynamics simulations predict that unspecific interactions slow down microsecond- to millisecond-timescale protein dynamics despite having only mild effects on pico- to nanosecond fluctuations as corroborated by NMR. We discuss our results in the light of recent advances in understanding proteins inside living cells, focusing on the physical chemistry of quinary structure and cellular organization, and we reinforce the idea that proteins should be studied in native-like media to achieve a faithful description of their function. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Solution Properties of Murine Leukemia Virus Gag Protein: Differences from HIV-1 Gag▿

    Science.gov (United States)

    Datta, Siddhartha A. K.; Zuo, Xiaobing; Clark, Patrick K.; Campbell, Stephen J.; Wang, Yun-Xing; Rein, Alan

    2011-01-01

    Immature retrovirus particles are assembled from the multidomain Gag protein. In these particles, the Gag proteins are arranged radially as elongated rods. We have previously characterized the properties of HIV-1 Gag in solution. In the absence of nucleic acid, HIV-1 Gag displays moderately weak interprotein interactions, existing in monomer-dimer equilibrium. Neutron scattering and hydrodynamic studies suggest that the protein is compact, and biochemical studies indicate that the two ends can approach close in three-dimensional space, implying the need for a significant conformational change during assembly. We now describe the properties of the Gag protein of Moloney murine leukemia virus (MLV), a gammaretrovirus. We found that this protein is very different from HIV-1 Gag: it has much weaker protein-protein interaction and is predominantly monomeric in solution. This has allowed us to study the protein by small-angle X-ray scattering and to build a low-resolution molecular envelope for the protein. We found that MLV Gag is extended in solution, with an axial ratio of ∼7, comparable to its dimensions in immature particles. Mutational analysis suggests that runs of prolines in its matrix and p12 domains and the highly charged stretch at the C terminus of its capsid domain all contribute to this extended conformation. These differences between MLV Gag and HIV-1 Gag and their implications for retroviral assembly are discussed. PMID:21917964

  7. Interactions between globular proteins and F-actin in isotonic saline solution.

    Science.gov (United States)

    Lakatos, S; Minton, A P

    1991-10-05

    Solutions of each of three different globular proteins (cytochrome c, chromophorically labeled serum albumin, and chromophorically labeled aldolase), mixed with another unlabeled globular protein or with fibrous actin, were prepared in pH 8.0 Tris-HCl buffer containing 0.15 M NaCl. Each solution was centrifuged at low speed, at 5 degrees C, until unassociated globular protein in solution achieved sedimentation equilibrium. Individual absorbance gradients of both macrosolutes in the mixtures subsequent to centrifugation were obtained via optical scans of the centrifuge tubes at two wavelengths. The gradients of each macrosolute in mixtures of two globular proteins revealed no association of globular proteins under the conditions of these experiments, but perturbation of the gradients of serum albumin, aldolase, and cytochrome c in the presence of F-actin indicated association of all three globular proteins with F-actin. Perturbation of actin gradients in the presence of serum albumin and aldolase suggested partial depolymerization of the F-actin by the globular protein. Analysis of the data with a simple phenomenological model relating free globular protein, bound globular protein, and total actin concentration provided estimates of the respective equilibrium constants for association of serum albumin and aldolase with F-actin, under the conditions of these experiments, of the order of 0.1 microM-1.

  8. Solution of stochastic media transport problems using a numerical quadrature-based method

    International Nuclear Information System (INIS)

    Pautz, S. D.; Franke, B. C.; Prinja, A. K.; Olson, A. J.

    2013-01-01

    We present a new conceptual framework for analyzing transport problems in random media. We decompose such problems into stratified subproblems according to the number of material pseudo-interfaces within realizations. For a given subproblem we assign pseudo-interface locations in each realization according to product quadrature rules, which allows us to deterministically generate a fixed number of realizations. Quadrature integration of the solutions of these realizations thus approximately solves each subproblem; the weighted superposition of solutions of the subproblems approximately solves the general stochastic media transport problem. We revisit some benchmark problems to determine the accuracy and efficiency of this approach in comparison to randomly generated realizations. We find that this method is very accurate and fast when the number of pseudo-interfaces in a problem is generally low, but that these advantages quickly degrade as the number of pseudo-interfaces increases. (authors)

  9. Chain segmentation for the Monte Carlo solution of particle transport problems

    International Nuclear Information System (INIS)

    Ragheb, M.M.H.

    1984-01-01

    A Monte Carlo approach is proposed where the random walk chains generated in particle transport simulations are segmented. Forward and adjoint-mode estimators are then used in conjunction with the firstevent source density on the segmented chains to obtain multiple estimates of the individual terms of the Neumann series solution at each collision point. The solution is then constructed by summation of the series. The approach is compared to the exact analytical and to the Monte Carlo nonabsorption weighting method results for two representative slowing down and deep penetration problems. Application of the proposed approach leads to unbiased estimates for limited numbers of particle simulations and is useful in suppressing an effective bias problem observed in some cases of deep penetration particle transport problems

  10. Three-dimensional transport theory: An analytical solution of an internal beam searchlight problem-I

    International Nuclear Information System (INIS)

    Williams, M.M.R.

    2009-01-01

    We describe a number of methods for obtaining analytical solutions and numerical results for three-dimensional one-speed neutron transport problems in a half-space containing a variety of source shapes which emit neutrons mono-directionally. For example, we consider an off-centre point source, a ring source and a disk source, or any combination of these, and calculate the surface scalar flux as a function of the radial and angular co-ordinates. Fourier transforms in the transverse directions are used and a Laplace transform in the axial direction. This enables the Wiener-Hopf method to be employed, followed by an inverse Fourier-Hankel transform. Some additional transformations are introduced which enable the inverse Hankel transforms involving Bessel functions to be evaluated numerically more efficiently. A hybrid diffusion theory method is also described which is shown to be a useful guide to the general behaviour of the solutions of the transport equation.

  11. DRAGON solutions to the 3D transport benchmark over a range in parameter space

    International Nuclear Information System (INIS)

    Martin, Nicolas; Hebert, Alain; Marleau, Guy

    2010-01-01

    DRAGON solutions to the 'NEA suite of benchmarks for 3D transport methods and codes over a range in parameter space' are discussed in this paper. A description of the benchmark is first provided, followed by a detailed review of the different computational models used in the lattice code DRAGON. Two numerical methods were selected for generating the required quantities for the 729 configurations of this benchmark. First, S N calculations were performed using fully symmetric angular quadratures and high-order diamond differencing for spatial discretization. To compare S N results with those of another deterministic method, the method of characteristics (MoC) was also considered for this benchmark. Comparisons between reference solutions, S N and MoC results illustrate the advantages and drawbacks of each methods for this 3-D transport problem.

  12. Compilation of field-scale caisson data on solute transport in the unsaturated zone

    International Nuclear Information System (INIS)

    Polzer, W.L.; Essington, E.H.; Fuentes, H.R.; Nyhan, J.W.

    1986-11-01

    Los Alamos National Laboratory has conducted technical support studies to assess siting requirements mandated by Nuclear Regulatory Commission in 10 CFR Part 61. Field-scale transport studies were conducted under unsaturated moisture conditions and under steady and unsteady flow conditions in large caissons located and operated in a natural (field) environment. Moisture content, temperature, flow rate, base-line chemical, tracer influent, and tracer breakthrough data collected during tracer migration studies in the caisson are compiled in tables and graphs. Data suggest that the imposition of a period of drainage (influent solution flow was stopped) may cause an increase in tracer concentration in the soil solution at various sampling points in the caisson. Evaporation during drainage and diffusion of the tracers from immobile to mobile water are two phenomena that could explain the increase. Data also suggest that heterogeneity of sorption sites may increase the variability in transport of sorbing tracers compared with nonsorbing tracers

  13. Presentation of some methods for the solution of the monoenergetic neutrons transport equation

    International Nuclear Information System (INIS)

    Valle G, E. del.

    1978-01-01

    The neutrons transport theory problems whose solution has been reached were collected in order to show that the transport equation is so complicated that different techniques were developed so as to give approximative numerical solutions to problems concerning the practical application. Such a technique, which had not been investigated in the literature dealing with these problems, is described here. The results which were obtained through this technique in undimensional problems of criticity are satisfactory and speaking in a conceptual way this method is extremely simple because it times. There is no limitation to deal with problems related neutrons sources with an arbitrary distribution and in principle the application of this technique can be extended to unhomogeneous environments. (author)

  14. Study of reactive solutes transport and PAH migration in unsaturated soils

    International Nuclear Information System (INIS)

    Gujisaite, V.; Simonnot, M.O.; Gujisaite, V.; Morel, J.L.; Ouvrard, S.; Simonnot, M.O.; Gaudet, J.P.

    2005-01-01

    Experimental studies about solute transport in soil have most of the time been conducted under saturated conditions, whereas studies with unsaturated media are usually limited to hydrodynamic analysis. Those are mainly concerning the prediction of water flow, which is the main vector for the transport of contaminants in soil. Only a few studies have made the link between unsaturated flow and physical, chemical and biological interactions, which are controlling the availability of pollutants. However, the presence of a gaseous phase in soil can modify not only the movement of soil solution, but also chemical interactions and exchanges between soil aggregates and solution. Study of reactive solute transport in the vadose zone seems thus to be a necessary stage to predict contaminant fate in natural soils, for risk assessment as well as for the design of effective processes for the remediation of contaminated soils. This question is the main objective of the present work developed in the frame of our French Scientific Interest Group Industrial Wastelands called 'GISFI' (www.gisfi.prd.fr), based around a scientific and technological project dedicated to acquisition of knowledge for sustainable requalification of degraded sites polluted by past industrial activities. We will focus here on Polycyclic Aromatic Hydrocarbons (PAH), which are among the most widely discussed environmental contaminants because of their toxicity for human health and ecosystems. They are present in large quantities in soils polluted by former industrial activities, especially in relation to the coal extraction, exploitation and treatment. An experimental system has been specifically designed at the laboratory scale to carry out experiments under controlled conditions, with an unsaturated steady-state flow. The first experiments are performed on model soils, in order to investigate unsaturated steady-state flow in relation to interactions mechanisms. We have thus chosen to use a sandy

  15. Hydro-dynamic Solute Transport under Two-Phase Flow Conditions.

    Science.gov (United States)

    Karadimitriou, Nikolaos K; Joekar-Niasar, Vahid; Brizuela, Omar Godinez

    2017-07-26

    There are abundant examples of natural, engineering and industrial applications, in which "solute transport" and "mixing" in porous media occur under multiphase flow conditions. Current state-of-the-art understanding and modelling of such processes are established based on flawed and non-representative models. Moreover, there is no direct experimental result to show the true hydrodynamics of transport and mixing under multiphase flow conditions while the saturation topology is being kept constant for a number of flow rates. With the use of a custom-made microscope, and under well-controlled flow boundary conditions, we visualized directly the transport of a tracer in a Reservoir-on-Chip (RoC) micromodel filled with two immiscible fluids. This study provides novel insights into the saturation-dependency of transport and mixing in porous media. To our knowledge, this is the first reported pore-scale experiment in which the saturation topology, relative permeability, and tortuosity were kept constant and transport was studied under different dynamic conditions in a wide range of saturation. The critical role of two-phase hydrodynamic properties on non-Fickian transport and saturation-dependency of dispersion are discussed, which highlight the major flaws in parametrization of existing models.

  16. Low Resolution Structure of RAR1-GST-Tag Fusion Protein in Solution

    International Nuclear Information System (INIS)

    Taube, M.; Kozak, M.; Jarmolowski, A.

    2010-01-01

    RAR1 is a protein required for resistance mediated by many R genes and function upstream of signaling pathways leading to H 2 O 2 accumulation. The structure and conformation of RAR1-GST-Tag fusion protein from barley (Hordeum vulgare) in solution was studied by the small angle scattering of synchrotron radiation. It was found that the dimer of RAR1-GST-Tag protein is characterized in solution by radius of gyration R G = 6.19 nm and maximal intramolecular vector D max = 23 nm. On the basis of the small angle scattering of synchrotron radiation SAXS data two bead models obtained by ab initio modeling are proposed. Both models show elongated conformations. We also concluded that molecules of fusion protein form: dimers in solution via interaction of GST domains. (authors)

  17. Coupled Spatio-Temporal Patterns of Solute Transport, Metabolism and Nutrient Uptake in Streams

    Science.gov (United States)

    Kurz, M. J.; Schmidt, C.

    2017-12-01

    Slower flow velocities and longer residence times within stream transient storage (TS) zones facilitate interaction between solutes and microbial communities, potentially increasing local rates of metabolic activity. Multiple factors, including channel morphology and substrate, variable hydrology, and seasonal changes in biological and physical parameters, result in changes in the solute transport dynamics and reactivity of TS zones over time and space. These changes would be expected to, in turn, influence rates of whole-stream ecosystem functions such as metabolism and nutrient uptake. However, the linkages between solute transport and ecosystem functioning within TS zones, and the contribution of TS zones to whole-stream functioning, are not always so straight forward. This may be due, in part, to methodological challenges. In this study we investigated the influence of stream channel hydro-morphology and substrate type on reach (103 m) and sub-reach (102 m) scale TS and ecosystem functioning. Patterns in solute transport, metabolism and nitrate uptake were tracked from April through October in two contrasting upland streams using several methods. The two streams, located in the Harz Mountains, Germany, are characterized by differing size (0.02 vs. 0.3 m3/s), dominant stream channel substrate (bedrock vs. alluvium) and sub-reach morphology (predominance of pools, riffles and glides). Solute transport parameters and respiration rates at the reach and sub-reach scale were estimated monthly from coupled pulse injections of the reactive tracer resazurin (Raz) and conservative tracers uranine and salt. Raz, a weakly fluorescent dye, irreversibly transforms to resorufin (Rru) under mildly reducing conditions, providing a proxy for aerobic respiration. Daily rates of primary productivity, respiration and nitrate retention at the reach scale were estimated using the diel cycles in dissolved oxygen and nitrate concentrations measured by in-situ sensors. Preliminary

  18. Magnetic Modulation of the Transport of Organophilic Solutes through Supported Magnetic Ionic Liquid Membranes.

    Czech Academy of Sciences Publication Activity Database

    Daniel, C.L.; Rubio, A.M.; Sebastião, P.J.; Afonso, C.A.M.; Storch, Jan; Izák, Pavel; Portugal, C.A.M.; Crespo, J.G.

    2016-01-01

    Roč. 505, MAY 1 (2016), s. 36-43 ISSN 0376-7388 R&D Projects: GA ČR(CZ) GAP106/12/0569 Grant - others:ERANET(PT) ERA-CHEM/0001/2008; EUI(ES) 2008- 03857; FCT-MCTES(PT) SFRH/BD/81552/2011 Institutional support: RVO:67985858 Keywords : magnetic ionic liquids (MILs) * solute transport modulation * magnetic field Subject RIV: CI - Industrial Chemistry, Chemical Engineering Impact factor: 6.035, year: 2016

  19. Bounds and maximum principles for the solution of the linear transport equation

    International Nuclear Information System (INIS)

    Larsen, E.W.

    1981-01-01

    Pointwise bounds are derived for the solution of time-independent linear transport problems with surface sources in convex spatial domains. Under specified conditions, upper bounds are derived which, as a function of position, decrease with distance from the boundary. Also, sufficient conditions are obtained for the existence of maximum and minimum principles, and a counterexample is given which shows that such principles do not always exist

  20. Diffusion Dominant Solute Transport Modelling In Deep Repository Under The Effect of Emplacement Media Degradation - 13285

    International Nuclear Information System (INIS)

    Kwong, S.; Jivkov, A.P.

    2013-01-01

    Deep geologic disposal of high activity and long-lived radioactive waste is being actively considered and pursued in many countries, where low permeability geological formations are used to provide long term waste contaminant with minimum impact to the environment and risk to the biosphere. A multi-barrier approach that makes use of both engineered and natural barriers (i.e. geological formations) is often used to further enhance the containment performance of the repository. As the deep repository system subjects to a variety of thermo-hydro-chemo-mechanical (THCM) effects over its long 'operational' lifespan (e.g. 0.1 to 1.0 million years, the integrity of the barrier system will decrease over time (e.g. fracturing in rock or clay)). This is broadly referred as media degradation in the present study. This modelling study examines the effects of media degradation on diffusion dominant solute transport in fractured media that are typical of deep geological environment. In particular, reactive solute transport through fractured media is studied using a 2-D model, that considers advection and diffusion, to explore the coupled effects of kinetic and equilibrium chemical processes, while the effects of degradation is studied using a pore network model that considers the media diffusivity and network changes. Model results are presented to demonstrate the use of a 3D pore-network model, using a novel architecture, to calculate macroscopic properties of the medium such as diffusivity, subject to pore space changes as the media degrade. Results from a reactive transport model of a representative geological waste disposal package are also presented to demonstrate the effect of media property change on the solute migration behaviour, illustrating the complex interplay between kinetic biogeochemical processes and diffusion dominant transport. The initial modelling results demonstrate the feasibility of a coupled modelling approach (using pore-network model and reactive

  1. Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids.

    Science.gov (United States)

    Tan, Kemin; Chang, Changsoo; Cuff, Marianne; Osipiuk, Jerzy; Landorf, Elizabeth; Mack, Jamey C; Zerbs, Sarah; Joachimiak, Andrzej; Collart, Frank R

    2013-10-01

    Lignin comprises 15-25% of plant biomass and represents a major environmental carbon source for utilization by soil microorganisms. Access to this energy resource requires the action of fungal and bacterial enzymes to break down the lignin polymer into a complex assortment of aromatic compounds that can be transported into the cells. To improve our understanding of the utilization of lignin by microorganisms, we characterized the molecular properties of solute binding proteins of ATP-binding cassette transporter proteins that interact with these compounds. A combination of functional screens and structural studies characterized the binding specificity of the solute binding proteins for aromatic compounds derived from lignin such as p-coumarate, 3-phenylpropionic acid and compounds with more complex ring substitutions. A ligand screen based on thermal stabilization identified several binding protein clusters that exhibit preferences based on the size or number of aromatic ring substituents. Multiple X-ray crystal structures of protein-ligand complexes for these clusters identified the molecular basis of the binding specificity for the lignin-derived aromatic compounds. The screens and structural data provide new functional assignments for these solute-binding proteins which can be used to infer their transport specificity. This knowledge of the functional roles and molecular binding specificity of these proteins will support the identification of the specific enzymes and regulatory proteins of peripheral pathways that funnel these compounds to central metabolic pathways and will improve the predictive power of sequence-based functional annotation methods for this family of proteins. Copyright © 2013 Wiley Periodicals, Inc.

  2. Upscaling solute transport in naturally fractured porous media with the continuous time random walk method

    Energy Technology Data Exchange (ETDEWEB)

    Geiger, S.; Cortis, A.; Birkholzer, J.T.

    2010-04-01

    Solute transport in fractured porous media is typically 'non-Fickian'; that is, it is characterized by early breakthrough and long tailing and by nonlinear growth of the Green function-centered second moment. This behavior is due to the effects of (1) multirate diffusion occurring between the highly permeable fracture network and the low-permeability rock matrix, (2) a wide range of advection rates in the fractures and, possibly, the matrix as well, and (3) a range of path lengths. As a consequence, prediction of solute transport processes at the macroscale represents a formidable challenge. Classical dual-porosity (or mobile-immobile) approaches in conjunction with an advection-dispersion equation and macroscopic dispersivity commonly fail to predict breakthrough of fractured porous media accurately. It was recently demonstrated that the continuous time random walk (CTRW) method can be used as a generalized upscaling approach. Here we extend this work and use results from high-resolution finite element-finite volume-based simulations of solute transport in an outcrop analogue of a naturally fractured reservoir to calibrate the CTRW method by extracting a distribution of retention times. This procedure allows us to predict breakthrough at other model locations accurately and to gain significant insight into the nature of the fracture-matrix interaction in naturally fractured porous reservoirs with geologically realistic fracture geometries.

  3. An Overview of Problems and Solutions for Urban Freight Transport in Brazilian Cities

    Directory of Open Access Journals (Sweden)

    Leise K. Oliveira

    2018-04-01

    Full Text Available Urban freight transport is a challenge for Brazilian cities due to the lack of adequate planning for freight flow movement. Public managers also show negligence and a lack of awareness when dealing with urban logistics. Decision-support data on urban freight transport are still scarce, despite being of fundamental value to economic development. With this in mind, this paper presents problems and solutions regarding urban freight transport in Brazilian cities. Data were obtained through a survey conducted in nine cities and analysed by means of descriptive statistics and the successive intervals method. Additionally, a cluster analysis was performed to identify patterns regarding the typical characteristics of each city in order to compare and generalise the perception of retailers regarding problems and solutions at the national level. The results indicate divergent opinions among retailers from different cities, even from cities with similar socioeconomic profiles and urban dynamics. The municipalities which demonstrated the most similarities were (i Betim and Niteroi, in the Southeast of Brazil; (ii Palmas and Quixada, in the North and Northeast, respectively; and (iii Palmas and Caruaru, also in the North and Northeast. The results reinforce the importance of studying the local context and involving stakeholders in the process of planning urban logistics solutions.

  4. Transport of titanium dioxide nanoparticles in saturated porous media under various solution chemistry conditions

    International Nuclear Information System (INIS)

    Wang Yu; Gao Bin; Morales, Verónica L.; Tian Yuan; Wu Lei; Gao Jie; Bai Wei; Yang Liuyan

    2012-01-01

    Because of its wide applications, nanosized titanium dioxide may become a potential environmental risk to soil and groundwater system. It is therefore important to improve current understanding of the environmental fate and transport of titanium oxides nanoparticles (TONPs). In this work, the effect of solution chemistry (i.e., pH, ionic strength, and natural organic matter (NOM) concentration) on the deposition and transport of TONPs in saturated porous media was examined in detail. Laboratory columns packed with acid-cleaned quartz sand were used in the experiment as porous media. Transport experiments were conducted with various chemistry combinations, including four ionic strengths, three pH levels, and two NOM concentrations. The results showed that TONP mobility increased with increasing solution pH, but decreased with increasing solution ionic strength. It is also found that the presence of NOM in the system enhanced the mobility of TONPs in the saturated porous media. The Derjaguin–Landau–Verwey–Overbeek (DLVO) theory was used to justify the mobility trends observed in the experimental data. Predictions from the theory agreed excellently with the experimental data.

  5. Regional flow and solute transport modeling for site suitability. Part I

    International Nuclear Information System (INIS)

    Rowe, J.; Miller, I.

    1979-12-01

    The nature of regional flow systems in large sedimentary basins will largely determine the effectiveness of regional flow as a barrier to radionuclide escape from deep geologic repositories. The purpose of the work reported herein and the proposed future work is to develop a methodology for evaluating regional flow barriers by using numerical models. The Williston Basin was chosen as an archetype case for the regional modeling study. However, due to the simplified nature of the study, the results are not meant to represent the behavior of a repository actually placed within the Williston Basin. The major components of this Phase I study are: (1) assembly and reduction of available data; (2) formulation of a simplified geohydrologic model; (3) computer simulation of fluid flow; and (4) computer simulation of solute transport. As of this report, the first two items are essentially completed. Computer simulation of fluid flow will require some revision and further study, which will be done in the second phase of this study. Computer simulation of solute transport has been considered only on a very preliminary basis. Important conclusions of this Phase I study are as follows. Assembly and reduction of data require an extensive work effort. Generally, the parameters describing fluid flow are poorly known on a regional basis and those describing solute transport are unknown

  6. Solutes transport in unsaturated double-porosity medium. Modelling by homogenization and applications

    International Nuclear Information System (INIS)

    Tran Ngoc, T.D.

    2008-07-01

    This Ph.D thesis presents the development of the solute transport models in unsaturated double-porosity medium, by using the asymptotic homogenization method. The obtained macroscopic models concern diffusion, diffusion-convection and dispersion-convection, according to the transport regime which is characterized by the non-dimensional numbers. The models consist of two coupled equations that show the local non-equilibrium of concentrations. The double-porosity transport models were numerically implemented using the code COMSOL Multiphysics (finite elements method), and compared with the solution of the same problem at the fine scale. The implementation allows solving the coupled equations in the macro- and micro-porosity domains (two-scale computations). The calculations of the dispersion tensor as a solution of the local boundary value problems, were also conducted. It was shown that the dispersivity depends on the saturation, the physical properties of the macro-porosity domain and the internal structure of the double-porosity medium. Finally, two series of experiments were performed on a physical model of double-porosity that is composed of a periodic assemblage of sintered clay spheres in Hostun sand HN38. The first experiment was a drainage experiment, which was conducted in order to validate the unsaturated flow model. The second series was a dispersion experiment in permanent unsaturated water flow condition (water content measured by gamma ray attenuation technique). A good agreement between the numerical simulations and the experimental observations allows the validation of the developed models. (author)

  7. Regional flow and solute transport modeling for site suitability. Part I

    Energy Technology Data Exchange (ETDEWEB)

    Rowe, J.; Miller, I.

    1979-12-01

    The nature of regional flow systems in large sedimentary basins will largely determine the effectiveness of regional flow as a barrier to radionuclide escape from deep geologic repositories. The purpose of the work reported herein and the proposed future work is to develop a methodology for evaluating regional flow barriers by using numerical models. The Williston Basin was chosen as an archetype case for the regional modeling study. However, due to the simplified nature of the study, the results are not meant to represent the behavior of a repository actually placed within the Williston Basin. The major components of this Phase I study are: (1) assembly and reduction of available data; (2) formulation of a simplified geohydrologic model; (3) computer simulation of fluid flow; and (4) computer simulation of solute transport. As of this report, the first two items are essentially completed. Computer simulation of fluid flow will require some revision and further study, which will be done in the second phase of this study. Computer simulation of solute transport has been considered only on a very preliminary basis. Important conclusions of this Phase I study are as follows. Assembly and reduction of data require an extensive work effort. Generally, the parameters describing fluid flow are poorly known on a regional basis and those describing solute transport are unknown.

  8. Solution and study of nodal neutron transport equation applying the LTSN-DiagExp method

    International Nuclear Information System (INIS)

    Hauser, Eliete Biasotto; Pazos, Ruben Panta; Vilhena, Marco Tullio de; Barros, Ricardo Carvalho de

    2003-01-01

    In this paper we report advances about the three-dimensional nodal discrete-ordinates approximations of neutron transport equation for Cartesian geometry. We use the combined collocation method of the angular variables and nodal approach for the spatial variables. By nodal approach we mean the iterated transverse integration of the S N equations. This procedure leads to the set of one-dimensional averages angular fluxes in each spatial variable. The resulting system of equations is solved with the LTS N method, first applying the Laplace transform to the set of the nodal S N equations and then obtained the solution by symbolic computation. We include the LTS N method by diagonalization to solve the nodal neutron transport equation and then we outline the convergence of these nodal-LTS N approximations with the help of a norm associated to the quadrature formula used to approximate the integral term of the neutron transport equation. (author)

  9. Application of multiphysics models to efficient design of experiments of solute transport across articular cartilage.

    Science.gov (United States)

    Pouran, Behdad; Arbabi, Vahid; Weinans, Harrie; Zadpoor, Amir A

    2016-11-01

    Transport of solutes helps to regulate normal physiology and proper function of cartilage in diarthrodial joints. Multiple studies have shown the effects of characteristic parameters such as concentration of proteoglycans and collagens and the orientation of collagen fibrils on the diffusion process. However, not much quantitative information and accurate models are available to help understand how the characteristics of the fluid surrounding articular cartilage influence the diffusion process. In this study, we used a combination of micro-computed tomography experiments and biphasic-solute finite element models to study the effects of three parameters of the overlying bath on the diffusion of neutral solutes across cartilage zones. Those parameters include bath size, degree of stirring of the bath, and the size and concentration of the stagnant layer that forms at the interface of cartilage and bath. Parametric studies determined the minimum of the finite bath size for which the diffusion behavior reduces to that of an infinite bath. Stirring of the bath proved to remarkably influence neutral solute transport across cartilage zones. The well-stirred condition was achieved only when the ratio of the diffusivity of bath to that of cartilage was greater than ≈1000. While the thickness of the stagnant layer at the cartilage-bath interface did not significantly influence the diffusion behavior, increase in its concentration substantially elevated solute concentration in cartilage. Sufficient stirring attenuated the effects of the stagnant layer. Our findings could be used for efficient design of experimental protocols aimed at understanding the transport of molecules across articular cartilage. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Solution Structure of an Antifreeze Protein CfAFP-501 from Choristoneura fumiferana

    International Nuclear Information System (INIS)

    Li Congmin; Guo Xianrong; Jia Zongchao; Xia Bin; Jin Changwen

    2005-01-01

    Antifreeze proteins (AFPs) are widely employed by various organisms as part of their overwintering survival strategy. AFPs have the unique ability to suppress the freezing point of aqueous solution and inhibit ice recrystallization through binding to the ice seed crystals and restricting their growth. The solution structure of CfAFP-501 from spruce budworm has been determined by NMR spectroscopy. Our result demonstrates that CfAFP-501 retains its rigid and highly regular structure in solution. Overall, the solution structure is similar to the crystal structure except the N- and C-terminal regions. NMR spin-relaxation experiments further indicate the overall rigidity of the protein and identify a collection of residues with greater flexibilities. Furthermore, Pro91 shows a cis conformation in solution instead of the trans conformation determined in the crystal structure

  11. Thermally Cross-Linkable Hole Transport Materials for Solution Processed Phosphorescent OLEDs

    Science.gov (United States)

    Kim, Beom Seok; Kim, Ohyoung; Chin, Byung Doo; Lee, Chil Won

    2018-04-01

    Materials for unique fabrication of a solution-processed, multi-layered organic light-emitting diode (OLED) were developed. Preparation of a hole transport layer with a thermally cross-linkable chemical structure, which can be processed to form a thin film and then transformed into an insoluble film by using an amine-alcohol condensation reaction with heat treatment, was investigated. Functional groups, such as triplenylamine linked with phenylcarbazole or biphenyl, were employed in the chemical structure of the hole transport layer in order to maintain high triplet energy properties. When phenylcarbazole or biphenyl compounds continuously react with triphenylamine under acid catalysis, a chemically stable thin film material with desirable energy-level properties for a blue OLED could be obtained. The prepared hole transport materials showed excellent surface roughness and thermal stability in comparison with the commercial reference material. On the solution-processed model hole transport layer, we fabricated a device with a blue phosphorescent OLED by using sequential vacuum deposition. The maximum external quantum, 19.3%, was improved by more than 40% over devices with the commercial reference material (11.4%).

  12. Finite element simulation of moisture movement and solute transport in a large caisson

    International Nuclear Information System (INIS)

    Huyakorn, P.S.; Jones, B.G.; Parker, J.C.; Wadsworth, T.D.; White, H.O. Jr.

    1987-01-01

    The results of the solute transport experiments performed on compacted, crushed Bandelier Tuff in caisson B of the experimental cluster described by DePoorter (1981) are simulated. Both one- and three-dimensional simulations of solute transport have been performed using two selected finite element codes. Results of bromide and iodide tracer experiments conducted during near-steady flow conditions have been analyzed for pulse additions made on December 6, 1984, and followed over a period of up to 60 days. In addition, a pulse addition of nonconservative strontium tracer on September 28, 1984, during questionably steady flow conditions has been analyzed over a period of 240 days. One-dimensional finite element flow and transport simulations were carried out assuming the porous medium to be homogeneous and the injection source uniformly distributed. To evaluate effects of the nonuniform source distribution and also to investigate effects of inhomogeneous porous medium properties, three dimensional finite element analyses of transport were carried out. Implications of the three-dimensional effects for the design and analysis of future tracer studies are discussed

  13. Numerical investigations of solute transport in bimodal porous media under dynamic boundary conditions

    Science.gov (United States)

    Cremer, Clemens; Neuweiler, Insa; Bechtold, Michel; Vanderborght, Jan

    2016-04-01

    Quantification of flow and solute transport in the shallow subsurface adjacent to the atmosphere is decisive to prevent groundwater pollution and conserve groundwater quality, to develop successful remediation strategies and to understand nutrient cycling. In nature, due to erratic precipitation-evaporation patterns, soil moisture content and related hydraulic conductivity in the vadose zone are not only variable in space but also in time. Flow directions and flow paths locally change between precipitation and evaporation periods. This makes the identification and description of solute transport processes in the vadose zone a complex problem. Recent studies (Lehmann and Or, 2009; Bechtold et al., 2011a) focused on the investigation of upward transport of solutes during evaporation in heterogeneous soil columns, where heterogeneity was introduced by a sharp vertical material interface between two types of sand. Lateral solute transport through the interface in both (lateral) directions was observed at different depths of the investigated soil columns. Following recent approaches, we conduct two-dimensional numerical simulations in a similar setup which is composed of two sands with a sharp vertical material interface. The investigation is broadened from the sole evaporation to combined precipitation-evaporation cycles in order to quantify transport processes resulting from the combined effects of heterogeneous soil structure and dynamic flow conditions. Simulations are performed with a coupled finite volume and random walk particle tracking algorithm (Ippisch et al., 2006; Bechtold et al., 2011b). By comparing scenarios with cyclic boundary conditions and stationary counterparts with the same net flow rate, we found that duration and intensity of precipitation and evaporation periods potentially have an influence on lateral redistribution of solutes and thus leaching rates. Whether or not dynamic boundary conditions lead to significant deviations in the transport

  14. Representing solute transport through the multi-barrier disposal system by simplified concepts

    International Nuclear Information System (INIS)

    Poteri, A.; Nordman, H.; Pulkkanen, V-M.; Kekaelaeinen, P.; Hautojaervi, A.

    2012-02-01

    The repository system chosen in Finland for spent nuclear fuel is composed of multiple successive transport barriers. If a waste canister is leaking, this multi-barrier system retards and limits the release rates of radionuclides into the biosphere. Analysis of radionuclide migration in the previous performance assessments has largely been based on numerical modelling of the repository system. The simplified analytical approach introduced here provides a tool to analyse the performance of the whole system using simplified representations of the individual transport barriers. This approach is based on the main characteristics of the individual barriers and on the generic nature of the coupling between successive barriers. In the case of underground repository the mass transfer between successive transport barriers is strongly restricted by the interfaces between barriers leading to well-mixed conditions in these barriers. The approach here simplifies the barrier system so that it can be described with a very simple compartment model, where each barrier is represented by a single, or in the case of buffer, by not more than two compartments. This system of compartments could be solved in analogy with a radioactive decay chain. The model of well mixed compartments lends itself to a very descriptive way to represent and analyse the barrier system because the relative efficiency of the different barriers in hindering transport of solutes can be parameterised by the solutes half-times in the corresponding compartments. In a real repository system there will also be a delay between the start of the inflow and the start of the outflow from the barrier. This delay can be important for the release rates of the short lived and sorbing radionuclides, and it was also included in the simplified representation of the barrier system. In a geological multi-barrier system, spreading of the outflowing release pulse is often governed by the typical behaviour of one transport barrier

  15. Representing solute transport through the multi-barrier disposal system by simplified concepts

    Energy Technology Data Exchange (ETDEWEB)

    Poteri, A.; Nordman, H.; Pulkkanen, V-M. [VTT Technical Research Centre of Finland, Espoo (Finland); Kekaelaeinen, P. [Jyvaeskylae Univ. (Finland). Dept. pf Physics; Hautojaervi, A.

    2012-02-15

    The repository system chosen in Finland for spent nuclear fuel is composed of multiple successive transport barriers. If a waste canister is leaking, this multi-barrier system retards and limits the release rates of radionuclides into the biosphere. Analysis of radionuclide migration in the previous performance assessments has largely been based on numerical modelling of the repository system. The simplified analytical approach introduced here provides a tool to analyse the performance of the whole system using simplified representations of the individual transport barriers. This approach is based on the main characteristics of the individual barriers and on the generic nature of the coupling between successive barriers. In the case of underground repository the mass transfer between successive transport barriers is strongly restricted by the interfaces between barriers leading to well-mixed conditions in these barriers. The approach here simplifies the barrier system so that it can be described with a very simple compartment model, where each barrier is represented by a single, or in the case of buffer, by not more than two compartments. This system of compartments could be solved in analogy with a radioactive decay chain. The model of well mixed compartments lends itself to a very descriptive way to represent and analyse the barrier system because the relative efficiency of the different barriers in hindering transport of solutes can be parameterised by the solutes half-times in the corresponding compartments. In a real repository system there will also be a delay between the start of the inflow and the start of the outflow from the barrier. This delay can be important for the release rates of the short lived and sorbing radionuclides, and it was also included in the simplified representation of the barrier system. In a geological multi-barrier system, spreading of the outflowing release pulse is often governed by the typical behaviour of one transport barrier

  16. The Method of Manufactured Solutions for RattleSnake A SN Radiation Transport Solver Inside the MOOSE Framework

    International Nuclear Information System (INIS)

    Wang, Yaqi

    2012-01-01

    The Method of Manufactured Solutions (MMS) is an accepted technique to verify that a numerical discretization for the radiation transport equation has been implemented correctly. This technique offers a few advantages over other methods such as benchmark problems or analytical solutions. The solution can be manufactured such that properties for the angular flux are either stressed or preserved. For radiation transport, these properties can include desired smoothness, positiveness and arbitrary order of anisotropy in angle. Another advantage is that the angular flux solution can be manufactured for multidimensional problems where analytical solutions are difficult to obtain in general.

  17. Electrostatics promotes molecular crowding and selects the aggregation pathway in fibril-forming protein solutions

    International Nuclear Information System (INIS)

    Raccosta, S.; Martorana, V.; Manno, M.; Blanco, M.; Roberts, C.J.

    2016-01-01

    The role of intermolecular interaction in fibril-forming protein solutions and its relation with molecular conformation are crucial aspects for the control and inhibition of amyloid structures. Here, we study the fibril formation and the protein-protein interactions for two proteins at acidic ph, lysozyme and α-chymotrypsinogen. By using light scattering experiments and the Kirkwood-Buff integral approach, we show how concentration fluctuations are damped even at moderate protein concentrations by the dominant long-ranged electrostatic repulsion, which determines an effective crowded environment. In denaturing conditions, electrostatic repulsion keeps the monomeric solution in a thermodynamically metastable state, which is escaped through kinetically populated conformational sub-states. This explains how electrostatics acts as a gatekeeper in selecting a specific aggregation pathway.

  18. Mechanisms to explain the reverse perivascular transport of solutes out of the brain.

    Science.gov (United States)

    Schley, D; Carare-Nnadi, R; Please, C P; Perry, V H; Weller, R O

    2006-02-21

    Experimental studies and observations in the human brain indicate that interstitial fluid and solutes, such as amyloid-beta (Abeta), are eliminated from grey matter of the brain along pericapillary and periarterial pathways. It is unclear, however, what constitutes the motive force for such transport within blood vessel walls, which is in the opposite direction to blood flow. In this paper the potential for global pressure differences to achieve such transport are considered. A mathematical model is constructed in order to test the hypothesis that perivascular drainage of interstitial fluid and solutes out of brain tissue is driven by pulsations of the blood vessel walls. Here it is assumed that drainage occurs through a thin layer between astrocytes and endothelial cells or between smooth muscle cells. The model suggests that, during each pulse cycle, there are periods when fluid and solutes are driven along perivascular spaces in the reverse direction to the flow of blood. It is shown that successful drainage may depend upon some attachment of solutes to the lining of the perivascular space, in order to produce a valve-like effect, although an alternative without this requirement is also postulated. Reduction in pulse amplitude, as in ageing cerebral vessels, would prolong the attachment time, encourage precipitation of Abeta peptides in vessel walls, and impair elimination of Abeta from the brain. These factors may play a role in the pathogenesis of cerebral amyloid angiopathy and in the accumulation of Abeta in the brain in Alzheimer's disease.

  19. A lattice Boltzmann model for solute transport in open channel flow

    Science.gov (United States)

    Wang, Hongda; Cater, John; Liu, Haifei; Ding, Xiangyi; Huang, Wei

    2018-01-01

    A lattice Boltzmann model of advection-dispersion problems in one-dimensional (1D) open channel flows is developed for simulation of solute transport and pollutant concentration. The hydrodynamics are calculated based on a previous lattice Boltzmann approach to solving the 1D Saint-Venant equations (LABSVE). The advection-dispersion model is coupled with the LABSVE using the lattice Boltzmann method. Our research recovers the advection-dispersion equations through the Chapman-Enskog expansion of the lattice Boltzmann equation. The model differs from the existing schemes in two points: (1) the lattice Boltzmann numerical method is adopted to solve the advection-dispersion problem by meso-scopic particle distribution; (2) and the model describes the relation between discharge, cross section area and solute concentration, which increases the applicability of the water quality model in practical engineering. The model is verified using three benchmark tests: (1) instantaneous solute transport within a short distance; (2) 1D point source pollution with constant velocity; (3) 1D point source pollution in a dam break flow. The model is then applied to a 50-year flood point source pollution accident on the Yongding River, which showed good agreement with a MIKE 11 solution and gauging data.

  20. Benchmarking the invariant embedding method against analytical solutions in model transport problems

    International Nuclear Information System (INIS)

    Malin, Wahlberg; Imre, Pazsit

    2005-01-01

    The purpose of this paper is to demonstrate the use of the invariant embedding method in a series of model transport problems, for which it is also possible to obtain an analytical solution. Due to the non-linear character of the embedding equations, their solution can only be obtained numerically. However, this can be done via a robust and effective iteration scheme. In return, the domain of applicability is far wider than the model problems investigated in this paper. The use of the invariant embedding method is demonstrated in three different areas. The first is the calculation of the energy spectrum of reflected (sputtered) particles from a multiplying medium, where the multiplication arises from recoil production. Both constant and energy dependent cross sections with a power law dependence were used in the calculations. The second application concerns the calculation of the path length distribution of reflected particles from a medium without multiplication. This is a relatively novel and unexpected application, since the embedding equations do not resolve the depth variable. The third application concerns the demonstration that solutions in an infinite medium and a half-space are interrelated through embedding-like integral equations, by the solution of which the reflected flux from a half-space can be reconstructed from solutions in an infinite medium or vice versa. In all cases the invariant embedding method proved to be robust, fast and monotonically converging to the exact solutions. (authors)

  1. On the spectral analysis of iterative solutions of the discretized one-group transport equation

    International Nuclear Information System (INIS)

    Sanchez, Richard

    2004-01-01

    We analyze the Fourier-mode technique used for the spectral analysis of iterative solutions of the one-group discretized transport equation. We introduce a direct spectral analysis for the iterative solution of finite difference approximations for finite slabs composed of identical layers, providing thus a complementary analysis that is more appropriate for reactor applications. Numerical calculations for the method of characteristics and with the diamond difference approximation show the appearance of antisymmetric modes generated by the iteration on boundary data. We have also utilized the discrete Fourier transform to compute the spectrum for a periodic slab containing N identical layers and shown that at the limit N → ∞ one obtains the familiar Fourier-mode solution

  2. Effects of reservoir heterogeneity on scaling of effective mass transfer coefficient for solute transport

    Science.gov (United States)

    Leung, Juliana Y.; Srinivasan, Sanjay

    2016-09-01

    Modeling transport process at large scale requires proper scale-up of subsurface heterogeneity and an understanding of its interaction with the underlying transport mechanisms. A technique based on volume averaging is applied to quantitatively assess the scaling characteristics of effective mass transfer coefficient in heterogeneous reservoir models. The effective mass transfer coefficient represents the combined contribution from diffusion and dispersion to the transport of non-reactive solute particles within a fluid phase. Although treatment of transport problems with the volume averaging technique has been published in the past, application to geological systems exhibiting realistic spatial variability remains a challenge. Previously, the authors developed a new procedure where results from a fine-scale numerical flow simulation reflecting the full physics of the transport process albeit over a sub-volume of the reservoir are integrated with the volume averaging technique to provide effective description of transport properties. The procedure is extended such that spatial averaging is performed at the local-heterogeneity scale. In this paper, the transport of a passive (non-reactive) solute is simulated on multiple reservoir models exhibiting different patterns of heterogeneities, and the scaling behavior of effective mass transfer coefficient (Keff) is examined and compared. One such set of models exhibit power-law (fractal) characteristics, and the variability of dispersion and Keff with scale is in good agreement with analytical expressions described in the literature. This work offers an insight into the impacts of heterogeneity on the scaling of effective transport parameters. A key finding is that spatial heterogeneity models with similar univariate and bivariate statistics may exhibit different scaling characteristics because of the influence of higher order statistics. More mixing is observed in the channelized models with higher-order continuity. It

  3. Fast axonal transport of labeled proteins in motoneurons of exercise-trained rats

    International Nuclear Information System (INIS)

    Jasmin, B.J.; Lavoie, P.A.; Gardiner, P.F.

    1988-01-01

    In this study, the fast orthograde axonal transport of radiolabeled proteins was measured to determine the effects of endurance-running training on transport velocity and amounts of transported proteins in rat sciatic motoneurons. Female rats were subjected to a progressive running-training program for 10-12 wk. Twenty-four hours after the last training session, rats underwent right L4-L5 dorsal root ganglionectomy. The next day, 20 microCi of [3H]leucine was injected bilaterally in the vicinity of the motoneuronal cell bodies supplying the sciatic nerve, to study axonal transport parameters. Results showed that peak and average transport velocities of labeled proteins were significantly (P less than 0.05) increased by 22 and 29%, respectively, in the deafferented nerves of the runners as compared with controls. Moreover, the amount of total transported protein-bound radioactivity was increased in both left (40%) and right (37%) sciatic nerves of the runners. An exhaustive exercise session reduced (P less than 0.05) peak displacement (8%) and total transported protein-bound radioactivity (36%) in the sciatic nerves of control rats, whereas no changes were noticed in trained animals. The data suggest that chronic endurance running induces significant adaptations in the fast axonal transport of labeled proteins

  4. The composite water and solute transport of barley (Hordeum vulgare) roots: effect of suberized barriers.

    Science.gov (United States)

    Ranathunge, Kosala; Kim, Yangmin X; Wassmann, Friedrich; Kreszies, Tino; Zeisler, Viktoria; Schreiber, Lukas

    2017-03-01

    Roots have complex anatomical structures, and certain localized cell layers develop suberized apoplastic barriers. The size and tightness of these barriers depend on the growth conditions and on the age of the root. Such complex anatomical structures result in a composite water and solute transport in roots. Development of apoplastic barriers along barley seminal roots was detected using various staining methods, and the suberin amounts in the apical and basal zones were analysed using gas chromatography-mass spectometry (GC-MS). The hydraulic conductivity of roots ( Lp r ) and of cortical cells ( Lp c ) was measured using root and cell pressure probes. When grown in hydroponics, barley roots did not form an exodermis, even at their basal zones. However, they developed an endodermis. Endodermal Casparian bands first appeared as 'dots' as early as at 20 mm from the apex, whereas a patchy suberin lamellae appeared at 60 mm. The endodermal suberin accounted for the total suberin of the roots. The absolute amount in the basal zone was significantly higher than in the apical zone, which was inversely proportional to the Lp r . Comparison of Lp r and Lp c suggested that cell to cell pathways dominate for water transport in roots. However, the calculation of Lp r from Lp c showed that at least 26 % of water transport occurs through the apoplast. Roots had different solute permeabilities ( P sr ) and reflection coefficients ( σ sr ) for the solutes used. The σ sr was below unity for the solutes, which have virtually zero permeability for semi-permeable membranes. Suberized endodermis significantly reduces Lp r of seminal roots. The water and solute transport across barley roots is composite in nature and they do not behave like ideal osmometers. The composite transport model should be extended by adding components arranged in series (cortex, endodermis) in addition to the currently included components arranged in parallel (apoplastic, cell to cell pathways). © The

  5. Colloid transport in porous media: impact of hyper-saline solutions.

    Science.gov (United States)

    Magal, Einat; Weisbrod, Noam; Yechieli, Yoseph; Walker, Sharon L; Yakirevich, Alexander

    2011-05-01

    The transport of colloids suspended in natural saline solutions with a wide range of ionic strengths, up to that of Dead Sea brines (10(0.9) M) was explored. Migration of microspheres through saturated sand columns of different sizes was studied in laboratory experiments and simulated with mathematical models. Colloid transport was found to be related to the solution salinity as expected. The relative concentration of colloids at the columns outlet decreased (after 2-3 pore volumes) as the solution ionic strength increased until a critical value was reached (ionic strength > 10(-1.8) M) and then remained constant above this level of salinity. The colloids were found to be mobile even in the extremely saline brines of the Dead Sea. At such high ionic strength no energetic barrier to colloid attachment was presumed to exist and colloid deposition was expected to be a favorable process. However, even at these salinity levels, colloid attachment was not complete and the transport of ∼ 30% of the colloids through the 30-cm long columns was detected. To further explore the deposition of colloids on sand surfaces in Dead Sea brines, transport was studied using 7-cm long columns through which hundreds of pore volumes were introduced. The resulting breakthrough curves exhibited a bimodal shape whereby the relative concentration (C/C(0)) of colloids at the outlet rose to a value of 0.8, and it remained relatively constant (for the ∼ 18 pore volumes during which the colloid suspension was flushed through the column) and then the relative concentration increased to a value of one. The bimodal nature of the breakthrough suggests different rates of colloid attachment. Colloid transport processes were successfully modeled using the limited entrapment model, which assumes that the colloid attachment rate is dependent on the concentration of the attached colloids. Application of this model provided confirmation of the colloid aggregation and their accelerated attachment during

  6. Cadmium uptake from solution by plants and its transport from roots to shoots

    Energy Technology Data Exchange (ETDEWEB)

    Jarvis, S.C.; Jones, L.H.P.; Hopper, M.J.

    1976-02-01

    The uptake of cadmium by the roots of plants, and its transport to shoots was examined using solution culture. Uptake by the roots of perennial ryegrass over a period of 4 hours from an aqueous solution containing 0.25 ppm cadmium as CdCl/sub 2/ was (i) enhanced by killing the roots and (ii) depressed when Ca/sup 2 +/, Mn/sup 2 +/ or Zn/sup 2 +/ were added to the solution. The distribution of cadmium between the roots and shoots of 23 species was examined at 4 days after a single, 3-day exposure to a nutrient solution containing 0.01 ppm added Cd. In all except 3 species, i.e. kale, lettuce and watercress, more than 50% of that taken up was retained in the shoot, and in fibrous roots of fodder beet, parsnip, carrot and radish it was greater than in the swollen storage roots. When perennial ryegrass was similarly exposed to solutions containing 0.01, 0.05, and 0.25 ppm added cadmium, uptake, as measured at 3 days after adding cadmium, increased with increasing rates of addition, but the proportion retained in the roots was constant (approximately 88%). There was no further transport from roots to shoots during the next 21 days, with the result that the concentration in the shoots decreased progressively with increasing growth. It is concluded that although the roots of several species can take up large quantities of cadmium from solution there are mechanisms which may restrict the movement of cadmium through plants, and thus to animals. 21 references, 7 tables.

  7. Fibrin structural and diffusional analysis suggests that fibers are permeable to solute transport.

    Science.gov (United States)

    Leonidakis, Kimon Alexandros; Bhattacharya, Pinaki; Patterson, Jennifer; Vos, Bart E; Koenderink, Gijsje H; Vermant, Jan; Lambrechts, Dennis; Roeffaers, Maarten; Van Oosterwyck, Hans

    2017-01-01

    Fibrin hydrogels are promising carrier materials in tissue engineering. They are biocompatible and easy to prepare, they can bind growth factors and they can be prepared from a patient's own blood. While fibrin structure and mechanics have been extensively studied, not much is known about the relation between structure and diffusivity of solutes within the network. This is particularly relevant for solutes with a size similar to that of growth factors. A novel methodological approach has been used in this study to retrieve quantitative structural characteristics of fibrin hydrogels, by combining two complementary techniques, namely confocal fluorescence microscopy with a fiber extraction algorithm and turbidity measurements. Bulk rheological measurements were conducted to determine the impact of fibrin hydrogel structure on mechanical properties. From these measurements it can be concluded that variations in the fibrin hydrogel structure have a large impact on the rheological response of the hydrogels (up to two orders of magnitude difference in storage modulus) but only a moderate influence on the diffusivity of dextran solutes (up to 25% difference). By analyzing the diffusivity measurements by means of the Ogston diffusion model we further provide evidence that individual fibrin fibers can be semi-permeable to solute transport, depending on the average distance between individual protofibrils. This can be important for reducing mass transport limitations, for modulating fibrinolysis and for growth factor binding, which are all relevant for tissue engineering. Fibrin is a natural biopolymer that has drawn much interest as a biomimetic carrier in tissue engineering applications. We hereby use a novel combined approach for the structural characterization of fibrin networks based on optical microscopy and light scattering methods that can also be applied to other fibrillar hydrogels, like collagen. Furthermore, our findings on the relation between solute transport

  8. Influence of DNA-methylation on zinc homeostasis in myeloid cells: Regulation of zinc transporters and zinc binding proteins.

    Science.gov (United States)

    Kessels, Jana Elena; Wessels, Inga; Haase, Hajo; Rink, Lothar; Uciechowski, Peter

    2016-09-01

    The distribution of intracellular zinc, predominantly regulated through zinc transporters and zinc binding proteins, is required to support an efficient immune response. Epigenetic mechanisms such as DNA methylation are involved in the expression of these genes. In demethylation experiments using 5-Aza-2'-deoxycytidine (AZA) increased intracellular (after 24 and 48h) and total cellular zinc levels (after 48h) were observed in the myeloid cell line HL-60. To uncover the mechanisms that cause the disturbed zinc homeostasis after DNA demethylation, the expression of human zinc transporters and zinc binding proteins were investigated. Real time PCR analyses of 14 ZIP (solute-linked carrier (SLC) SLC39A; Zrt/IRT-like protein), and 9 ZnT (SLC30A) zinc transporters revealed significantly enhanced mRNA expression of the zinc importer ZIP1 after AZA treatment. Because ZIP1 protein was also enhanced after AZA treatment, ZIP1 up-regulation might be the mediator of enhanced intracellular zinc levels. The mRNA expression of ZIP14 was decreased, whereas zinc exporter ZnT3 mRNA was also significantly increased; which might be a cellular reaction to compensate elevated zinc levels. An enhanced but not significant chromatin accessibility of ZIP1 promoter region I was detected by chromatin accessibility by real-time PCR (CHART) assays after demethylation. Additionally, DNA demethylation resulted in increased mRNA accumulation of zinc binding proteins metallothionein (MT) and S100A8/S100A9 after 48h. MT mRNA was significantly enhanced after 24h of AZA treatment also suggesting a reaction of the cell to restore zinc homeostasis. These data indicate that DNA methylation is an important epigenetic mechanism affecting zinc binding proteins and transporters, and, therefore, regulating zinc homeostasis in myeloid cells. Copyright © 2016 Elsevier GmbH. All rights reserved.

  9. Modelling transport of water and solutes in future wetlands in Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Vikstroem, Maria; Gustafsson, Lars-Goeran [DHI Water and Environment AB, Vaexjoe (Sweden)

    2006-03-15

    been analyzed. Results from the transport modelling show that a solute in the bedrock is transported quickly towards the peat surface in discharge areas for Bolundsfjaerden. After around 10 years, a stationary condition is reached. For the recharge area that develops in large parts of the mire, the solute is transported through horizontal dispersion, which results in much lower concentrations. The solute concentration is at the lowest where the overland water pressure is at the highest close to the south western inlet. Puttan has a vertical flow pattern that differs from Bolundsfjaerden. The pressure from water on the peat surface is considerably lower and for a major part of the year Puttan is a discharge area with an upwards flow direction. The spatial distribution of solutes is more even over the surface than for Bolundsfjaerden, but higher concentrations are found around today's shoreline. A solute reaching the wetland through surface runoff is transported relatively slow through the mire at Bolundsfjaerden. Due to the recharge conditions, the solute is spread to the underlying soil layers. The vertical solute transport follows the discharge and recharge areas, where high concentrations, up to the source strength, are reached in major parts of the formation, while lower concentrations are reached in the discharge areas and underneath clay sediment.

  10. Modelling transport of water and solutes in future wetlands in Forsmark

    International Nuclear Information System (INIS)

    Vikstroem, Maria; Gustafsson, Lars-Goeran

    2006-03-01

    analyzed. Results from the transport modelling show that a solute in the bedrock is transported quickly towards the peat surface in discharge areas for Bolundsfjaerden. After around 10 years, a stationary condition is reached. For the recharge area that develops in large parts of the mire, the solute is transported through horizontal dispersion, which results in much lower concentrations. The solute concentration is at the lowest where the overland water pressure is at the highest close to the south western inlet. Puttan has a vertical flow pattern that differs from Bolundsfjaerden. The pressure from water on the peat surface is considerably lower and for a major part of the year Puttan is a discharge area with an upwards flow direction. The spatial distribution of solutes is more even over the surface than for Bolundsfjaerden, but higher concentrations are found around today's shoreline. A solute reaching the wetland through surface runoff is transported relatively slow through the mire at Bolundsfjaerden. Due to the recharge conditions, the solute is spread to the underlying soil layers. The vertical solute transport follows the discharge and recharge areas, where high concentrations, up to the source strength, are reached in major parts of the formation, while lower concentrations are reached in the discharge areas and underneath clay sediment

  11. Groundwater and solute transport modeling at Hyporheic zone of upper part Citarum River

    Science.gov (United States)

    Iskandar, Irwan; Farazi, Hendy; Fadhilah, Rahmat; Purnandi, Cipto; Notosiswoyo, Sudarto

    2017-06-01

    Groundwater and surface water interaction is an interesting topic to be studied related to the water resources and environmental studies. The study of interaction between groundwater and river water at the Upper Part Citarum River aims to know the contribution of groundwater to the river or reversely and also solute transport of dissolved ions between them. Analysis of drill logs, vertical electrical sounding at the selected sections, measurement of dissolved ions, and groundwater modeling were applied to determine the flow and solute transport phenomena at the hyporheic zone. It showed the hyporheic zone dominated by silt and clay with hydraulic conductivity range from 10-4∼10-8 m/s. The groundwater flowing into the river with very low gradient and it shows that the Citarum River is a gaining stream. The groundwater modeling shows direct seepage of groundwater into the Citarum River is only 186 l/s, very small compared to the total discharge of the river. Total dissolved ions of the groundwater ranged from 200 to 480 ppm while the river water range from 200 to 2,000 ppm. Based on solute transport modeling it indicates dissolved ions dispersion of the Citarum River into groundwater may occur in some areas such as Bojongsoang-Dayeuh Kolot and Nanjung. This situation would increase the dissolved ions in groundwater in the region due to the contribution of the Citarum River. The results of the research can be a reference for further studies related to the mechanism of transport of the pollutants in the groundwater around the Citarum River.

  12. Capillary-Driven Solute Transport and Precipitation in Porous Media during Dry-Out

    Science.gov (United States)

    Ott, Holger; Andrew, Matthew; Blunt, Martin; Snippe, Jeroen

    2014-05-01

    The injection of dry or under-saturated gases or supercritical (SC) fluids into water bearing formations might lead to a formation dry-out in the vicinity of the injection well. The dry-out is caused by the evaporation/dissolution of formation water into the injected fluid and the subsequent transport of dissolved water in the injected fluid away from the injection well. Dry-out results in precipitation from solutes of the formation brine and consequently leads to a reduction of the rock's pore space (porosity) and eventually to a reduction of permeability near the injection well, or even to the loss of injectivity. Recently evidence has been found that the complexity of the pore space and the respective capillary driven solute transport plays a key role. While no effective-permeability (Keff) reduction was observed in a single-porosity sandstone, multi porosity carbonate rocks responded to precipitation with a strong reduction of Keff. The reason for the different response of Keff to salt precipitation is suspected to be in the exact location of the precipitate (solid salt) in the pore space. In this study, we investigate dry-out and salt precipitation due to supercritical CO2 injection in single and multi-porosity systems under near well-bore conditions. We image fluid saturation changes by means of μCT scanning during desaturation. We are able to observe capillary driven transport of the brine phase and the respective transport of solutes on the rock's pore scale. Finally we have access to the precipitated solid-salt phase and their distribution. The results can proof the thought models behind permeability porosity relationships K(φ) for injectivity modeling. The topic and the mechanisms we show are of general interest for drying processes in porous material such as soils and paper.

  13. Diffusion Dominant Solute Transport Modelling in Fractured Media Under Deep Geological Environment - 12211

    Energy Technology Data Exchange (ETDEWEB)

    Kwong, S. [National Nuclear Laboratory (United Kingdom); Jivkov, A.P. [Research Centre for Radwaste and Decommissioning and Modelling and Simulation Centre, University of Manchester (United Kingdom)

    2012-07-01

    Deep geologic disposal of high activity and long-lived radioactive waste is gaining increasing support in many countries, where suitable low permeability geological formation in combination with engineered barriers are used to provide long term waste contaminant and minimise the impacts to the environment and risk to the biosphere. This modelling study examines the solute transport in fractured media under low flow velocities that are relevant to a deep geological environment. In particular, reactive solute transport through fractured media is studied using a 2-D model, that considers advection and diffusion, to explore the coupled effects of kinetic and equilibrium chemical processes. The effects of water velocity in the fracture, matrix porosity and diffusion on solute transport are investigated and discussed. Some illustrative modelled results are presented to demonstrate the use of the model to examine the effects of media degradation on solute transport, under the influences of hydrogeological (diffusion dominant) and microbially mediated chemical processes. The challenges facing the prediction of long term degradation such as cracks evolution, interaction and coalescence are highlighted. The potential of a novel microstructure informed modelling approach to account for these effects is discussed, particularly with respect to investigating multiple phenomena impact on material performance. The GRM code is used to examine the effects of media degradation for a geological waste disposal package, under the combined hydrogeological (diffusion dominant) and chemical effects in low groundwater flow conditions that are typical of deep geological disposal systems. An illustrative reactive transport modelling application demonstrates the use of the code to examine the interplay of kinetic controlled biogeochemical reactive processes with advective and diffusive transport, under the influence of media degradation. The initial model results are encouraging which show the

  14. Hyporheic less-mobile porosity and solute transport in porous media

    Science.gov (United States)

    MahmoodPoorDehkordy, F.; Briggs, M. A.; Day-Lewis, F. D.; Scruggs, C.; Singha, K.; Zarnetske, J. P.; Lane, J. W., Jr.; Bagtzoglou, A. C.

    2017-12-01

    Solute transport and reactive processes are strongly influenced by hydrodynamic exchange with the hyporheic zone. Contaminant transport and redox zonation in the hyporheic zone and near-stream aquifer can be impacted by the exchange between mobile and less-mobile porosity zones in heterogeneous porous media. Less-mobile porosity zones can be created by fine materials with tight pore throats (e.g. clay, organics) and in larger, well-connected pores down gradient of flow obstructions (e.g. sand behind cobbles). Whereas fluid sampling is primarily responsive to the more-mobile domain, tracking solute tracer dynamics by geoelectrical methods provides direct information about both more- and less-mobile zones. During tracer injection through porous media of varied pore connectivity, a lag between fluid and bulk electrical conductivity is observed, creating a hysteresis loop when plotted in conductivity space. Thus, the combination of simultaneous fluid and bulk electrical conductivity measurements enables a much improved quantification of less-mobile solute dynamics compared to traditional fluid-only sampling approaches. We have demonstrated the less-mobile porosity exchange in laboratory-scale column experiments verified by simulation models. The experimental approach has also been applied to streambed sediments in column and reach-scale field experiments and verified using numerical simulation. Properties of the resultant hysteresis loops can be used to estimate exchange parameters of less-mobile porosity. Our integrated approach combining field experiments, laboratory experiments, and numerical modeling provides new insights into the effect of less-mobile porosity on solute transport in the hyporheic zone.

  15. Solute transport in aquifers: The comeback of the advection dispersion equation and the First Order Approximation

    Science.gov (United States)

    Fiori, A.; Zarlenga, A.; Jankovic, I.; Dagan, G.

    2017-12-01

    Natural gradient steady flow of mean velocity U takes place in heterogeneous aquifers of random logconductivity Y = lnK , characterized by the normal univariate PDF f(Y) and autocorrelation ρY, of variance σY2 and horizontal integral scale I. Solute transport is quantified by the Breakthrough Curve (BTC) M at planes at distance x from the injection plane. The study builds on the extensive 3D numerical simulations of flow and transport of Jankovic et al. (2017) for different conductivity structures. The present study further explores the predictive capabilities of the Advection Dispersion Equation (ADE), with macrodispersivity αL given by the First Order Approximation (FOA), by checking in a quantitative manner its applicability. After a discussion on the suitable boundary conditions for ADE, we find that the ADE-FOA solution is a sufficiently accurate predictor for applications, the many other sources of uncertainty prevailing in practice notwithstanding. We checked by least squares and by comparison of travel time of quantiles of M that indeed the analytical Inverse Gaussian M with αL =σY2 I , is able to fit well the bulk of the simulated BTCs. It tends to underestimate the late arrival time of the thin and persistent tail. The tail is better reproduced by the semi-analytical MIMSCA model, which also allows for a physical explanation of the success of the Inverse Gaussian solution. Examination of the pertinent longitudinal mass distribution shows that it is different from the commonly used Gaussian one in the analysis of field experiments, and it captures the main features of the plume measurements of the MADE experiment. The results strengthen the confidence in the applicability of the ADE and the FOA to predicting longitudinal spreading in solute transport through heterogeneous aquifers of stationary random structure.

  16. Immunohistochemical expression profiles of solute carrier transporters in alpha-fetoprotein-producing gastric cancer.

    Science.gov (United States)

    Shimakata, Takaaki; Kamoshida, Shingo; Kawamura, Jumpei; Ogane, Naoki; Kameda, Yoichi; Yanagita, Emmy; Itoh, Tomoo; Takeda, Risa; Naka, Ayano; Sakamaki, Kuniko; Hayashi, Yurie; Kuwao, Sadahito

    2016-11-01

    Alpha-fetoprotein (AFP)-producing gastric cancer (GC) is an aggressive tumour with high rates of liver metastasis and poor prognosis, and for which a validated chemotherapy regimen has not been established. Drug uptake by solute carrier (SLC) transporters is proposed as one of the mechanisms involved in sensitivity to chemotherapy. In this study, we aimed to develop important insights into effective chemotherapeutic regimens for AFP-producing GC. We evaluated immunohistochemically the expression levels of a panel of SLC transporters in 20 AFP-producing GCs and 130 conventional GCs. SLC transporters examined were human equilibrative nucleoside transporter 1 (hENT1), organic anion transporter 2 (OAT2), organic cation transporter (OCT) 2, OCT6 and organic anion-transporting polypeptide 1B3 (OATP1B3). The rates of high expression levels of hENT1 (hENT1 high ) and OAT2 (OAT2 high ) were statistically higher in AFP-producing GC, compared with conventional GC. When analysing hENT1 and OAT2 in combination, hENT1 high /OAT2 high was the most particular expression profile for AFP-producing GC, with a greater significance than hENT1 or OAT2 alone. However, no significant differences in OCT2, OCT6 or OATP1B3 levels were detected between AFP-producing and conventional GCs. However, immunoreactivity for hENT1, OAT2 and OCT6 tended to be increased in GC tissues compared with non-neoplastic epithelia. Because hENT1 and OAT2 are crucial for the uptake of gemcitabine and 5-fluorouracil, respectively, our results suggest that patients with AFP-producing GC could potentially benefit from gemcitabine/fluoropyrimidine combination chemotherapy. Increased expression of hENT1, OAT2 and OCT6 may also be associated with the progression of GC. © 2016 John Wiley & Sons Ltd.

  17. Modeling variably saturated multispecies reactive groundwater solute transport with MODFLOW-UZF and RT3D

    Science.gov (United States)

    Bailey, Ryan T.; Morway, Eric D.; Niswonger, Richard G.; Gates, Timothy K.

    2013-01-01

    A numerical model was developed that is capable of simulating multispecies reactive solute transport in variably saturated porous media. This model consists of a modified version of the reactive transport model RT3D (Reactive Transport in 3 Dimensions) that is linked to the Unsaturated-Zone Flow (UZF1) package and MODFLOW. Referred to as UZF-RT3D, the model is tested against published analytical benchmarks as well as other published contaminant transport models, including HYDRUS-1D, VS2DT, and SUTRA, and the coupled flow and transport modeling system of CATHY and TRAN3D. Comparisons in one-dimensional, two-dimensional, and three-dimensional variably saturated systems are explored. While several test cases are included to verify the correct implementation of variably saturated transport in UZF-RT3D, other cases are included to demonstrate the usefulness of the code in terms of model run-time and handling the reaction kinetics of multiple interacting species in variably saturated subsurface systems. As UZF1 relies on a kinematic-wave approximation for unsaturated flow that neglects the diffusive terms in Richards equation, UZF-RT3D can be used for large-scale aquifer systems for which the UZF1 formulation is reasonable, that is, capillary-pressure gradients can be neglected and soil parameters can be treated as homogeneous. Decreased model run-time and the ability to include site-specific chemical species and chemical reactions make UZF-RT3D an attractive model for efficient simulation of multispecies reactive transport in variably saturated large-scale subsurface systems.

  18. A computational model for simulating solute transport and oxygen consumption along the nephrons

    Science.gov (United States)

    Vallon, Volker; Edwards, Aurélie

    2016-01-01

    The goal of this study was to investigate water and solute transport, with a focus on sodium transport (TNa) and metabolism along individual nephron segments under differing physiological and pathophysiological conditions. To accomplish this goal, we developed a computational model of solute transport and oxygen consumption (QO2) along different nephron populations of a rat kidney. The model represents detailed epithelial and paracellular transport processes along both the superficial and juxtamedullary nephrons, with the loop of Henle of each model nephron extending to differing depths of the inner medulla. We used the model to assess how changes in TNa may alter QO2 in different nephron segments and how shifting the TNa sites alters overall kidney QO2. Under baseline conditions, the model predicted a whole kidney TNa/QO2, which denotes the number of moles of Na+ reabsorbed per moles of O2 consumed, of ∼15, with TNa efficiency predicted to be significantly greater in cortical nephron segments than in medullary segments. The TNa/QO2 ratio was generally similar among the superficial and juxtamedullary nephron segments, except for the proximal tubule, where TNa/QO2 was ∼20% higher in superficial nephrons, due to the larger luminal flow along the juxtamedullary proximal tubules and the resulting higher, flow-induced transcellular transport. Moreover, the model predicted that an increase in single-nephron glomerular filtration rate does not significantly affect TNa/QO2 in the proximal tubules but generally increases TNa/QO2 along downstream segments. The latter result can be attributed to the generally higher luminal [Na+], which raises paracellular TNa. Consequently, vulnerable medullary segments, such as the S3 segment and medullary thick ascending limb, may be relatively protected from flow-induced increases in QO2 under pathophysiological conditions. PMID:27707705

  19. Anisotropic surface hole-transport property of triphenylamine-derivative single crystal prepared by solution method

    Energy Technology Data Exchange (ETDEWEB)

    Umeda, Minoru, E-mail: mumeda@vos.nagaokaut.ac.jp [Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188 (Japan); Katagiri, Mitsuhiko; Shironita, Sayoko [Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188 (Japan); Nagayama, Norio [Nagaoka University of Technology, Kamitomioka, Nagaoka, Niigata 940-2188 (Japan); Ricoh Company, Ltd., Nishisawada, Numazu, Shizuoka 410-0007 (Japan)

    2016-12-01

    Highlights: • A hole transport molecule was investigated based on its electrochemical redox characteristics. • The solubility and supersolubility curves of the molecule were measured in order to prepare a large crystal. • The polarization micrograph and XRD results revealed that a single crystal was obtained. • An anisotropic surface conduction, in which the long-axis direction exceeds that of the amorphous layer, was observed. • The anisotropic surface conduction was well explained by the molecular stacked structure. - Abstract: This paper reports the anisotropic hole transport at the triphenylamine-derivative single crystal surface prepared by a solution method. Triphenylamine derivatives are commonly used in a hole-transport material for organic photoconductors of laser-beam printers, in which the materials are used as an amorphous form. For developing organic photovoltaics using the photoconductor’s technology, preparation of a single crystal seems to be a specific way by realizing the high mobility of an organic semiconductor. In this study, a single crystal of 4-(2,2-diphenylethenyl)-N,N-bis(4-methylphenyl)-benzenamine (TPA) was prepared and its anisotropic hole-transport property measured. First, the hole-transport property of the TPA was investigated based on its chemical structure and electrochemical redox characteristics. Next, a large-scale single crystal formation at a high rate was developed by employing a solution method based on its solubility and supersolubility curves. The grown TPA was found to be a single crystal based on the polarization micrograph observation and crystallographic analysis. For the TPA single crystal, an anisotropic surface conduction was found, which was well explained by its molecular stack structure. The measured current in the long-axis direction is one order of magnitude greater than that of amorphous TPA.

  20. All-solution processed composite hole transport layer for quantum dot light emitting diode

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiaoli [Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Science, Tianjin University, Tianjin 300072 (China); Synergetic Innovation Center of Chemical Science and Engineering, Tianjin (China); Dai, Haitao, E-mail: htdai@tju.edu.cn [Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Science, Tianjin University, Tianjin 300072 (China); Zhao, Junliang; Wang, Shuguo [Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, School of Science, Tianjin University, Tianjin 300072 (China); Sun, Xiaowei [Department of Electrical & Electronic Engineering, South University of Science and Technology of China, Tangchang Road 1088, Shenzhen, Guangdong 518055 (China)

    2016-03-31

    In the present work, poly-TPD and TCTA composite hole transport layer (HTL) was employed in solution processed CdSe/ZnS quantum dot light emitting diodes (QLEDs). As the doping level of TCTA can determine the carriers transport efficiency of HTL, the proper mixing ratio of TCTA and poly-TPD should be found to optimize the performance of composite HTL for QLEDs. The doping of poly-TPD by low TCTA content can make its HOMO level lower and then reduce the energy barrier height from HTL to quantum dots (QDs), whereas the doping of poly-TPD by the concentrated TCTA results in the degraded performance of QLEDs due to its decreased hole transport mobility. By using the optimized composition with poly-TPD:TCTA (3:1) as the hole transport layer, the luminescence of the device exhibits about double enhancement compared with that of poly-TPD based device. The improvement of luminescence is mainly attributed to the lower energy barrier of hole injection. The Förster resonant energy transfer (FRET) mechanism in the devices was investigated through theoretical and experimental analysis and the results indicate that the TCTA doping makes no difference on FRET. Therefore, the charge injection mechanism dominates the improved performance of the devices. - Highlights: • Quantum dot light emitting diodes (QLEDs) were fabricated by all solution method. • The performance of QLEDs was optimized by varying the composite hole transport layer. • The blend HTL could promote hole injection by optimizing HOMO levels. • The energy transfer mechanism was analyzed by studying Förster resonant energy transfer process.

  1. Reactive solute transport in streams: A surface complexation approach for trace metal sorption

    Science.gov (United States)

    Runkel, Robert L.; Kimball, Briant A.; McKnight, Diane M.; Bencala, Kenneth E.

    1999-01-01

    A model for trace metals that considers in-stream transport, metal oxide precipitation-dissolution, and pH-dependent sorption is presented. Linkage between a surface complexation submodel and the stream transport equations provides a framework for modeling sorption onto static and/or dynamic surfaces. A static surface (e.g., an iron- oxide-coated streambed) is defined as a surface with a temporally constant solid concentration. Limited contact between solutes in the water column and the static surface is considered using a pseudokinetic approach. A dynamic surface (e.g., freshly precipitated metal oxides) has a temporally variable solid concentration and is in equilibrium with the water column. Transport and deposition of solute mass sorbed to the dynamic surface is represented in the stream transport equations that include precipitate settling. The model is applied to a pH-modification experiment in an acid mine drainage stream. Dissolved copper concentrations were depressed for a 3 hour period in response to the experimentally elevated pH. After passage of the pH front, copper was desorbed, and dissolved concentrations returned to ambient levels. Copper sorption is modeled by considering sorption to aged hydrous ferric oxide (HFO) on the streambed (static surface) and freshly precipitated HFO in the water column (dynamic surface). Comparison of parameter estimates with reported values suggests that naturally formed iron oxides may be more effective in removing trace metals than synthetic oxides used in laboratory studies. The model's ability to simulate pH, metal oxide precipitation-dissolution, and pH-dependent sorption provides a means of evaluating the complex interactions between trace metal chemistry and hydrologic transport at the field scale.

  2. Indirect estimation of the Convective Lognormal Transfer function model parameters for describing solute transport in unsaturated and undisturbed soil.

    Science.gov (United States)

    Mohammadi, Mohammad Hossein; Vanclooster, Marnik

    2012-05-01

    Solute transport in partially saturated soils is largely affected by fluid velocity distribution and pore size distribution within the solute transport domain. Hence, it is possible to describe the solute transport process in terms of the pore size distribution of the soil, and indirectly in terms of the soil hydraulic properties. In this paper, we present a conceptual approach that allows predicting the parameters of the Convective Lognormal Transfer model from knowledge of soil moisture and the Soil Moisture Characteristic (SMC), parameterized by means of the closed-form model of Kosugi (1996). It is assumed that in partially saturated conditions, the air filled pore volume act as an inert solid phase, allowing the use of the Arya et al. (1999) pragmatic approach to estimate solute travel time statistics from the saturation degree and SMC parameters. The approach is evaluated using a set of partially saturated transport experiments as presented by Mohammadi and Vanclooster (2011). Experimental results showed that the mean solute travel time, μ(t), increases proportionally with the depth (travel distance) and decreases with flow rate. The variance of solute travel time σ²(t) first decreases with flow rate up to 0.4-0.6 Ks and subsequently increases. For all tested BTCs predicted solute transport with μ(t) estimated from the conceptual model performed much better as compared to predictions with μ(t) and σ²(t) estimated from calibration of solute transport at shallow soil depths. The use of μ(t) estimated from the conceptual model therefore increases the robustness of the CLT model in predicting solute transport in heterogeneous soils at larger depths. In view of the fact that reasonable indirect estimates of the SMC can be made from basic soil properties using pedotransfer functions, the presented approach may be useful for predicting solute transport at field or watershed scales. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. A cell transportation solution that preserves live circulating tumor cells in patient blood samples.

    Science.gov (United States)

    Stefansson, Steingrimur; Adams, Daniel L; Ershler, William B; Le, Huyen; Ho, David H

    2016-05-06

    Circulating tumor cells (CTCs) are typically collected into CellSave fixative tubes, which kills the cells, but preserves their morphology. Currently, the clinical utility of CTCs is mostly limited to their enumeration. More detailed investigation of CTC biology can be performed on live cells, but obtaining live CTCs is technically challenging, requiring blood collection into biocompatible solutions and rapid isolation which limits transportation options. To overcome the instability of CTCs, we formulated a sugar based cell transportation solution (SBTS) that stabilizes cell viability at ambient temperature. In this study we examined the long term viability of human cancer cell lines, primary cells and CTCs in human blood samples in the SBTS for transportation purposes. Four cell lines, 5 primary human cells and purified human PBMCs were tested to determine the viability of cells stored in the transportation solution at ambient temperature for up to 7 days. We then demonstrated viability of MCF-7 cells spiked into normal blood with SBTS and stored for up to 7 days. A pilot study was then run on blood samples from 3 patients with metastatic malignancies stored with or without SBTS for 6 days. CTCs were then purified by Ficoll separation/microfilter isolation and identified using CTC markers. Cell viability was assessed using trypan blue or CellTracker™ live cell stain. Our results suggest that primary/immortalized cell lines stored in SBTS remain ~90% viable for > 72 h. Further, MCF-7 cells spiked into whole blood remain viable when stored with SBTS for up to 7 days. Finally, live CTCs were isolated from cancer patient blood samples kept in SBTS at ambient temperature for 6 days. No CTCs were isolated from blood samples stored without SBTS. In this proof of principle pilot study we show that viability of cell lines is preserved for days using SBTS. Further, this solution can be used to store patient derived blood samples for eventual isolation of viable CTCs after

  4. A cell transportation solution that preserves live circulating tumor cells in patient blood samples

    International Nuclear Information System (INIS)

    Stefansson, Steingrimur; Adams, Daniel L.; Ershler, William B.; Le, Huyen; Ho, David H.

    2016-01-01

    Circulating tumor cells (CTCs) are typically collected into CellSave fixative tubes, which kills the cells, but preserves their morphology. Currently, the clinical utility of CTCs is mostly limited to their enumeration. More detailed investigation of CTC biology can be performed on live cells, but obtaining live CTCs is technically challenging, requiring blood collection into biocompatible solutions and rapid isolation which limits transportation options. To overcome the instability of CTCs, we formulated a sugar based cell transportation solution (SBTS) that stabilizes cell viability at ambient temperature. In this study we examined the long term viability of human cancer cell lines, primary cells and CTCs in human blood samples in the SBTS for transportation purposes. Four cell lines, 5 primary human cells and purified human PBMCs were tested to determine the viability of cells stored in the transportation solution at ambient temperature for up to 7 days. We then demonstrated viability of MCF-7 cells spiked into normal blood with SBTS and stored for up to 7 days. A pilot study was then run on blood samples from 3 patients with metastatic malignancies stored with or without SBTS for 6 days. CTCs were then purified by Ficoll separation/microfilter isolation and identified using CTC markers. Cell viability was assessed using trypan blue or CellTracker™ live cell stain. Our results suggest that primary/immortalized cell lines stored in SBTS remain ~90 % viable for > 72 h. Further, MCF-7 cells spiked into whole blood remain viable when stored with SBTS for up to 7 days. Finally, live CTCs were isolated from cancer patient blood samples kept in SBTS at ambient temperature for 6 days. No CTCs were isolated from blood samples stored without SBTS. In this proof of principle pilot study we show that viability of cell lines is preserved for days using SBTS. Further, this solution can be used to store patient derived blood samples for eventual isolation of viable CTCs

  5. PHAST--a program for simulating ground-water flow, solute transport, and multicomponent geochemical reactions

    Science.gov (United States)

    Parkhurst, David L.; Kipp, Kenneth L.; Engesgaard, Peter; Charlton, Scott R.

    2004-01-01

    The computer program PHAST simulates multi-component, reactive solute transport in three-dimensional saturated ground-water flow systems. PHAST is a versatile ground-water flow and solute-transport simulator with capabilities to model a wide range of equilibrium and kinetic geochemical reactions. The flow and transport calculations are based on a modified version of HST3D that is restricted to constant fluid density and constant temperature. The geochemical reactions are simulated with the geochemical model PHREEQC, which is embedded in PHAST. PHAST is applicable to the study of natural and contaminated ground-water systems at a variety of scales ranging from laboratory experiments to local and regional field scales. PHAST can be used in studies of migration of nutrients, inorganic and organic contaminants, and radionuclides; in projects such as aquifer storage and recovery or engineered remediation; and in investigations of the natural rock-water interactions in aquifers. PHAST is not appropriate for unsaturated-zone flow, multiphase flow, density-dependent flow, or waters with high ionic strengths. A variety of boundary conditions are available in PHAST to simulate flow and transport, including specified-head, flux, and leaky conditions, as well as the special cases of rivers and wells. Chemical reactions in PHAST include (1) homogeneous equilibria using an ion-association thermodynamic model; (2) heterogeneous equilibria between the aqueous solution and minerals, gases, surface complexation sites, ion exchange sites, and solid solutions; and (3) kinetic reactions with rates that are a function of solution composition. The aqueous model (elements, chemical reactions, and equilibrium constants), minerals, gases, exchangers, surfaces, and rate expressions may be defined or modified by the user. A number of options are available to save results of simulations to output files. The data may be saved in three formats: a format suitable for viewing with a text editor; a

  6. Heterogeneous nucleation promotes carrier transport in solution-processed organic field-effect transistors

    KAUST Repository

    Li, Ruipeng

    2012-09-04

    A new way to investigate and control the growth of solution-cast thin films is presented. The combination of in situ quartz crystal microbalance measurements with dissipation capabilities (QCM-D) and in situ grazing-incidence wide-angle X-ray scattering (GIWAXS) in an environmental chamber provides unique quantitative insights into the time-evolution of the concentration of the solution, the onset of nucleation, and the mode of growth of the organic semiconductor under varied drying conditions. It is demonstrated that careful control over the kinetics of solution drying enhances carrier transport significantly by promoting phase transformation predominantly via heterogeneous nucleation and sustained surface growth of a highly lamellar structure at the solid-liquid interface at the expense of homogeneous nucleation. A new way to investigate and control the growth of drop-cast thin films is presented. The solution-processing of small-molecule thin films of TIPS-pentacene is investigated using time-resolved techniques to reveal the mechanisms of nucleation and growth leading to solid film formation. By tuning the drying speed of the solution, the balance between surface and bulk growth modes is altered, thereby controlling the lamellar formation and tuning the carrier mobility in organic field-effect transistors Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. PHAST Version 2-A Program for Simulating Groundwater Flow, Solute Transport, and Multicomponent Geochemical Reactions

    Science.gov (United States)

    Parkhurst, David L.; Kipp, Kenneth L.; Charlton, Scott R.

    2010-01-01

    The computer program PHAST (PHREEQC And HST3D) simulates multicomponent, reactive solute transport in three-dimensional saturated groundwater flow systems. PHAST is a versatile groundwater flow and solute-transport simulator with capabilities to model a wide range of equilibrium and kinetic geochemical reactions. The flow and transport calculations are based on a modified version of HST3D that is restricted to constant fluid density and constant temperature. The geochemical reactions are simulated with the geochemical model PHREEQC, which is embedded in PHAST. Major enhancements in PHAST Version 2 allow spatial data to be defined in a combination of map and grid coordinate systems, independent of a specific model grid (without node-by-node input). At run time, aquifer properties are interpolated from the spatial data to the model grid; regridding requires only redefinition of the grid without modification of the spatial data. PHAST is applicable to the study of natural and contaminated groundwater systems at a variety of scales ranging from laboratory experiments to local and regional field scales. PHAST can be used in studies of migration of nutrients, inorganic and organic contaminants, and radionuclides; in projects such as aquifer storage and recovery or engineered remediation; and in investigations of the natural rock/water interactions in aquifers. PHAST is not appropriate for unsaturated-zone flow, multiphase flow, or density-dependent flow. A variety of boundary conditions are available in PHAST to simulate flow and transport, including specified-head, flux (specified-flux), and leaky (head-dependent) conditions, as well as the special cases of rivers, drains, and wells. Chemical reactions in PHAST include (1) homogeneous equilibria using an ion-association or Pitzer specific interaction thermodynamic model; (2) heterogeneous equilibria between the aqueous solution and minerals, ion exchange sites, surface complexation sites, solid solutions, and gases; and

  8. Solute transport and storage mechanisms in wetlands of the Everglades, south Florida

    Science.gov (United States)

    Harvey, Judson W.; Saiers, James E.; Newlin, Jessica T.

    2005-01-01

    Solute transport and storage processes in wetlands play an important role in biogeochemical cycling and in wetland water quality functions. In the wetlands of the Everglades, there are few data or guidelines to characterize transport through the heterogeneous flow environment. Our goal was to conduct a tracer study to help quantify solute exchange between the relatively fast flowing water in the open part of the water column and much more slowly moving water in thick floating vegetation and in the pore water of the underlying peat. We performed a tracer experiment that consisted of a constant‐rate injection of a sodium bromide (NaBr) solution for 22 hours into a 3 m wide, open‐ended flume channel in Everglades National Park. Arrival of the bromide tracer was monitored at an array of surface water and subsurface samplers for 48 hours at a distance of 6.8 m downstream of the injection. A one‐dimensional transport model was used in combination with an optimization code to identify the values of transport parameters that best explained the tracer observations. Parameters included dimensions and mass transfer coefficients describing exchange with both short (hours) and longer (tens of hours) storage zones as well as the average rates of advection and longitudinal dispersion in the open part of the water column (referred to as the “main flow zone”). Comparison with a more detailed set of tracer measurements tested how well the model's storage zones approximated the average characteristics of tracer movement into and out of the layer of thick floating vegetation and the pore water in the underlying peat. The rate at which the relatively fast moving water in the open water column was exchanged with slowly moving water in the layer of floating vegetation and in sediment pore water amounted to 50 and 3% h−1, respectively. Storage processes decreased the depth‐averaged velocity of surface water by 50% relative to the water velocity in the open part of the water

  9. Active zone proteins are transported via distinct mechanisms regulated by Par-1 kinase.

    Directory of Open Access Journals (Sweden)

    Kara R Barber

    2017-02-01

    Full Text Available Disruption of synapses underlies a plethora of neurodevelopmental and neurodegenerative disease. Presynaptic specialization called the active zone plays a critical role in the communication with postsynaptic neuron. While the role of many proteins at the active zones in synaptic communication is relatively well studied, very little is known about how these proteins are transported to the synapses. For example, are there distinct mechanisms for the transport of active zone components or are they all transported in the same transport vesicle? Is active zone protein transport regulated? In this report we show that overexpression of Par-1/MARK kinase, a protein whose misregulation has been implicated in Autism spectrum disorders (ASDs and neurodegenerative disorders, lead to a specific block in the transport of an active zone protein component- Bruchpilot at Drosophila neuromuscular junctions. Consistent with a block in axonal transport, we find a decrease in number of active zones and reduced neurotransmission in flies overexpressing Par-1 kinase. Interestingly, we find that Par-1 acts independently of Tau-one of the most well studied substrates of Par-1, revealing a presynaptic function for Par-1 that is independent of Tau. Thus, our study strongly suggests that there are distinct mechanisms that transport components of active zones and that they are tightly regulated.

  10. Effects of Pisha sandstone content on solute transport in a sandy soil.

    Science.gov (United States)

    Zhen, Qing; Zheng, Jiyong; He, Honghua; Han, Fengpeng; Zhang, Xingchang

    2016-02-01

    In sandy soil, water, nutrients and even pollutants are easily leaching to deeper layers. The objective of this study was to assess the effects of Pisha sandstone on soil solute transport in a sandy soil. The miscible displacement technique was used to obtain breakthrough curves (BTCs) of Br(-) as an inert non-adsorbed tracer and Na(+) as an adsorbed tracer. The incorporation of Pisha sandstone into sandy soil was able to prevent the early breakthrough of both tracers by decreasing the saturated hydraulic conductivity compared to the controlled sandy soil column, and the impeding effects increased with Pisha sandstone content. The BTCs of Br(-) were accurately described by both the convection-dispersion equation (CDE) and the two-region model (T-R), and the T-R model fitted the experimental data slightly better than the CDE. The two-site nonequilibrium model (T-S) accurately fit the Na(+) transport data. Pisha sandstone impeded the breakthrough of Na(+) not only by decreasing the saturated hydraulic conductivity but also by increasing the adsorption capacity of the soil. The measured CEC values of Pisha sandstone were up to 11 times larger than those of the sandy soil. The retardation factors (R) determined by the T-S model increased with increasing Pisha sandstone content, and the partition coefficient (K(d)) showed a similar trend to R. According to the results of this study, Pisha sandstone can successfully impede solute transport in a sandy soil column. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. External intermittency prediction using AMR solutions of RANS turbulence and transported PDF models

    Science.gov (United States)

    Olivieri, D. A.; Fairweather, M.; Falle, S. A. E. G.

    2011-12-01

    External intermittency in turbulent round jets is predicted using a Reynolds-averaged Navier-Stokes modelling approach coupled to solutions of the transported probability density function (pdf) equation for scalar variables. Solutions to the descriptive equations are obtained using a finite-volume method, combined with an adaptive mesh refinement algorithm, applied in both physical and compositional space. This method contrasts with conventional approaches to solving the transported pdf equation which generally employ Monte Carlo techniques. Intermittency-modified eddy viscosity and second-moment turbulence closures are used to accommodate the effects of intermittency on the flow field, with the influence of intermittency also included, through modifications to the mixing model, in the transported pdf equation. Predictions of the overall model are compared with experimental data on the velocity and scalar fields in a round jet, as well as against measurements of intermittency profiles and scalar pdfs in a number of flows, with good agreement obtained. For the cases considered, predictions based on the second-moment turbulence closure are clearly superior, although both turbulence models give realistic predictions of the bimodal scalar pdfs observed experimentally.

  12. Nonpoint source solute transport normal to aquifer bedding in heterogeneous, Markov chain random fields

    Science.gov (United States)

    Zhang, Hua; Harter, Thomas; Sivakumar, Bellie

    2006-06-01

    Facies-based geostatistical models have become important tools for analyzing flow and mass transport processes in heterogeneous aquifers. Yet little is known about the relationship between these latter processes and the parameters of facies-based geostatistical models. In this study, we examine the transport of a nonpoint source solute normal (perpendicular) to the major bedding plane of an alluvial aquifer medium that contains multiple geologic facies, including interconnected, high-conductivity (coarse textured) facies. We also evaluate the dependence of the transport behavior on the parameters of the constitutive facies model. A facies-based Markov chain geostatistical model is used to quantify the spatial variability of the aquifer system's hydrostratigraphy. It is integrated with a groundwater flow model and a random walk particle transport model to estimate the solute traveltime probability density function (pdf) for solute flux from the water table to the bottom boundary (the production horizon) of the aquifer. The cases examined include two-, three-, and four-facies models, with mean length anisotropy ratios for horizontal to vertical facies, ek, from 25:1 to 300:1 and with a wide range of facies volume proportions (e.g., from 5 to 95% coarse-textured facies). Predictions of traveltime pdfs are found to be significantly affected by the number of hydrostratigraphic facies identified in the aquifer. Those predictions of traveltime pdfs also are affected by the proportions of coarse-textured sediments, the mean length of the facies (particularly the ratio of length to thickness of coarse materials), and, to a lesser degree, the juxtapositional preference among the hydrostratigraphic facies. In transport normal to the sedimentary bedding plane, traveltime is not lognormally distributed as is often assumed. Also, macrodispersive behavior (variance of the traveltime) is found not to be a unique function of the conductivity variance. For the parameter range

  13. Solute transport in coupled inland-coastal water systems. General conceptualisation and application to Forsmark

    International Nuclear Information System (INIS)

    Jarsjoe, Jerker; Destouni, Georgia; Persson, Klas; Prieto, Carmen

    2007-12-01

    We formulate a general theoretical conceptualisation of solute transport from inland sources to downstream recipients, considering main recipient load contributions from all different nutrient and pollutant sources that may exist within any catchment. Since the conceptualisation is model independent, its main hydrological factors and mass delivery factors can be quantified on the basis of inputs to and outputs from any considered analytical or numerical model. Some of the conceptually considered source contribution and transport pathway combinations are however commonly neglected in catchment-scale solute transport and attenuation modelling, in particular those related to subsurface sources, diffuse sources at the land surface and direct groundwater transport into the recipient. The conceptual framework provides a possible tool for clarification of underlying and often implicit model assumptions, which can be useful for e.g. inter-model comparisons. In order to further clarify and explain research questions that may be of particular importance for transport pathways from deep groundwater surrounding a repository, we concretise and interpret some selected transport scenarios for model conditions in the Forsmark area. Possible uncertainties in coastal discharge predictions, related to uncertain spatial variation of evapotranspiration within the catchment, were shown to be small for the relatively large, focused surface water discharges from land to sea, because local differences were averaged out along the length of the main water flow paths. In contrast, local flux values within the diffuse groundwater flow field from land to sea are more uncertain, although estimates of mean values and total sums of submarine groundwater discharge (SGD) along some considerable coastline length may be robust. The present results show that 80% to 90% of the total coastal discharge of Forsmark occurred through focused flows in visible streams, whereas the remaining 10% to 20% was

  14. Improved performance of organic solar cells with solution processed hole transport layer

    Science.gov (United States)

    Bhargav, Ranoo; Gairola, S. P.; Patra, Asit; Naqvi, Samya; Dhawan, S. K.

    2018-06-01

    This work is based on Cobalt Oxide as solution processed, inexpensive and effective hole transport layer (HTL) for efficient organic photovoltaic applications (OPVs). In Organic solar cell (OSC) devices ITO coated glass substrate used as a transparent anode electrode for light incident, HTL material Co3O4 dissolve in DMF solvent deposited on anode electrode, after that active layer material (donor/acceptor) deposited on to HTL and finally Al were deposited by thermal evaporation used as cathode electrode. These devices were fabricated with PCDTBT well known low band gap donor material in OSCs and blended with PC71BM as an acceptor material using simplest device structure ITO/Co3O4/active layer/Al at ambient conditions. The power conversion efficiencies (PCEs) based on Co3O4 and PEDOT:PSS have been achieved to up to 3.21% and 1.47% with PCDTBT respectively. In this study we reported that the devices fabricated with Co3O4 showed better performance as compare to the devices fabricated with well known and most studied solution processed HTL material PEDOT:PSS under identical environmental conditions. The surface morphology of the HTL film was characterized by (AFM). Lastly, we have provided Co3O4 as an efficient hole transport material HTL for solution processed organic photovoltaic applications.

  15. Assessment of assembly homogenized two-steps core dynamic calculations using direct whole core transport solutions

    International Nuclear Information System (INIS)

    Hursin, Mathieu; Downar, Thomas J.; Yoon, Joo Il; Joo, Han Gyu

    2016-01-01

    Highlights: • Reactivity initiated accident analysis with direct whole core transient transport code. • Comparison with usual “two steps” procedure. • Effect of effective delayed neutron fraction definition on energy deposition in the fuel. • Effect of homogenized few-group cross sections generation at the assembly level on energy deposition in the fuel. • Effect of effective fuel temperature definition on energy deposition in the fuel. - Abstract: The impact of the approximations in the “two-steps” procedure used in the current generation of nodal simulators for core transient calculations is assessed by using a higher order solution obtained from a direct, whole core, transient transport calculation. A control rod ejection accident in an idealized minicore is analyzed with PARCS, which uses the two-steps procedure and DeCART which provides the higher order solution. DeCART is used as lattice code to provide the homogenized cross sections and kinetics parameters to PARCS. The approximations made by using (1) the homogenized few-group cross sections and kinetic parameters generated at the assembly level, (2) an effective delayed neutrons fraction, (3) an effective fuel temperature and (4) the few-group formulation are investigated in terms of global and local core power behavior. The results presented in the paper show that the current two-steps procedure produces sufficiently accurate transient results with respect to the direct whole core calculation solution, provided that its parameters are carefully generated using the prescriptions described in the present article.

  16. High-Pressure-High-Temperature Processing Reduces Maillard Reaction and Viscosity in Whey Protein-Sugar Solutions

    NARCIS (Netherlands)

    Avila Ruiz, Geraldine; Xi, Bingyan; Minor, Marcel; Sala, Guido; Boekel, van Tiny; Fogliano, Vincenzo; Stieger, Markus

    2016-01-01

    The aim of the study was to determine the influence of pressure in high-pressure-high-temperature (HPHT) processing on Maillard reactions and protein aggregation of whey protein-sugar solutions. Solutions of whey protein isolate containing either glucose or trehalose at pH 6, 7, and 9 were

  17. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution

    OpenAIRE

    Hammel, Michal; Němeček, Daniel; Keightley, J. Andrew; Thomas, George J.; Geisbrecht, Brian V.

    2007-01-01

    The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein–protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data r...

  18. Residual dipolar couplings : a new technique for structure determination of proteins in solution

    NARCIS (Netherlands)

    van Lune, Frouktje Sapke

    2004-01-01

    The aim of the work described in this thesis was to investigate how residual dipolar couplings can be used to resolve or refine the three-dimensional structure of one of the proteins of the phosphoenol-pyruvate phosphotransferase system (PTS), the main transport system for carbohydrates in

  19. FASTREACT – An efficient numerical framework for the solution of reactive transport problems

    International Nuclear Information System (INIS)

    Trinchero, Paolo; Molinero, Jorge; Román-Ross, Gabriela; Berglund, Sten; Selroos, Jan-Olof

    2014-01-01

    Highlights: • We present a tool for the efficient solution of reactive transport problems. • The tool is used to simulate radionuclide transport in a two-dimensional medium. • The results are successfully compared with those obtained using an Eulerian approach. • A large-scale application example is also solved. • The results show that the proposed tool can efficiently solve large-scale models. - Abstract: In the framework of safety assessment studies for geological disposal, large scale reactive transport models are powerful inter-disciplinary tools aiming at supporting regulatory decision making as well as providing input to repository engineering activities. Important aspects of these kinds of models are their often very large temporal and spatial modelling scales and the need to integrate different non-linear processes (e.g., mineral dissolution and precipitation, adsorption and desorption, microbial reactions and redox transformations). It turns out that these types of models may be computationally highly demanding. In this work, we present a Lagrangian-based framework, denoted as FASTREACT, that aims at solving multi-component-reactive transport problems with a computationally efficient approach allowing complex modelling problems to be solved in large spatial and temporal scales. The tool has been applied to simulate radionuclide migration in a synthetic heterogeneous transmissivity field and the results have been successfully compared with those obtained using a standard Eulerian approach. Finally, the same geochemical model has been coupled to an ensemble of realistic three-dimensional transport pathways to simulate the migration of a set of radionuclides from a hypothetical repository for spent nuclear fuel to the surface. The results of this modelling exercise, which includes key processes such as the exchange of mass between the conductive fractures and the matrix, show that FASTREACT can efficiently solve large-scale reactive transport models

  20. Transport of soluble proteins through the Golgi occurs by diffusion via continuities across cisternae

    Science.gov (United States)

    Beznoussenko, Galina V; Parashuraman, Seetharaman; Rizzo, Riccardo; Polishchuk, Roman; Martella, Oliviano; Di Giandomenico, Daniele; Fusella, Aurora; Spaar, Alexander; Sallese, Michele; Capestrano, Maria Grazia; Pavelka, Margit; Vos, Matthijn R; Rikers, Yuri GM; Helms, Volkhard; Mironov, Alexandre A; Luini, Alberto

    2014-01-01

    The mechanism of transport through the Golgi complex is not completely understood, insofar as no single transport mechanism appears to account for all of the observations. Here, we compare the transport of soluble secretory proteins (albumin and α1-antitrypsin) with that of supramolecular cargoes (e.g., procollagen) that are proposed to traverse the Golgi by compartment progression–maturation. We show that these soluble proteins traverse the Golgi much faster than procollagen while moving through the same stack. Moreover, we present kinetic and morphological observations that indicate that albumin transport occurs by diffusion via intercisternal continuities. These data provide evidence for a transport mechanism that applies to a major class of secretory proteins and indicate the co-existence of multiple intra-Golgi trafficking modes. DOI: http://dx.doi.org/10.7554/eLife.02009.001 PMID:24867214

  1. Testosterone increases urinary calcium excretion and inhibits expression of renal calcium transport proteins.

    NARCIS (Netherlands)

    Hsu, Y.J.; Dimke, H.; Schoeber, J.P.H.; Hsu, S.C.; Lin, S.H.; Chu, P.; Hoenderop, J.G.J.; Bindels, R.J.M.

    2010-01-01

    Although gender differences in the renal handling of calcium have been reported, the overall contribution of androgens to these differences remains uncertain. We determined here whether testosterone affects active renal calcium reabsorption by regulating calcium transport proteins. Male mice had

  2. Application of preconditioned GMRES to the numerical solution of the neutron transport equation

    International Nuclear Information System (INIS)

    Patton, B.W.; Holloway, J.P.

    2002-01-01

    The generalized minimal residual (GMRES) method with right preconditioning is examined as an alternative to both standard and accelerated transport sweeps for the iterative solution of the diamond differenced discrete ordinates neutron transport equation. Incomplete factorization (ILU) type preconditioners are used to determine their effectiveness in accelerating GMRES for this application. ILU(τ), which requires the specification of a dropping criteria τ, proves to be a good choice for the types of problems examined in this paper. The combination of ILU(τ) and GMRES is compared with both DSA and unaccelerated transport sweeps for several model problems. It is found that the computational workload of the ILU(τ)-GMRES combination scales nonlinearly with the number of energy groups and quadrature order, making this technique most effective for problems with a small number of groups and discrete ordinates. However, the cost of preconditioner construction can be amortized over several calculations with different source and/or boundary values. Preconditioners built upon standard transport sweep algorithms are also evaluated as to their effectiveness in accelerating the convergence of GMRES. These preconditioners show better scaling with such problem parameters as the scattering ratio, the number of discrete ordinates, and the number of spatial meshes. These sweeps based preconditioners can also be cast in a matrix free form that greatly reduces storage requirements

  3. Modeling study of solute transport in the unsaturated zone: Workshop proceedings

    International Nuclear Information System (INIS)

    Springer, E.P.; Fuentes, H.R.

    1987-04-01

    Issues addressed were the adequacy of the data for the various models, effectiveness of the models to represent the data, particular information provided by the models, the role of caisson experiments in providing fundamental knowledge of porous-media water flow and solute transport, and the importance of geochemistry to the transport of nonconservative tracers. These proceedings include the presentations made by each of the modelers; the summary document written by the panel; and a transcript of the discussions, both the discussions that followed individual presentations and the general discussion held on the second day. This publication completes the series on the workshop. Volume I in the series (NUREG/CR-4615, Vol. I) contains background information and the data sets provided each modeler

  4. PARTRACK - A particle tracking algorithm for transport and dispersion of solutes in a sparsely fractured rock

    International Nuclear Information System (INIS)

    Svensson, Urban

    2001-04-01

    A particle tracking algorithm, PARTRACK, that simulates transport and dispersion in a sparsely fractured rock is described. The main novel feature of the algorithm is the introduction of multiple particle states. It is demonstrated that the introduction of this feature allows for the simultaneous simulation of Taylor dispersion, sorption and matrix diffusion. A number of test cases are used to verify and demonstrate the features of PARTRACK. It is shown that PARTRACK can simulate the following processes, believed to be important for the problem addressed: the split up of a tracer cloud at a fracture intersection, channeling in a fracture plane, Taylor dispersion and matrix diffusion and sorption. From the results of the test cases, it is concluded that PARTRACK is an adequate framework for simulation of transport and dispersion of a solute in a sparsely fractured rock

  5. Modeling of amorphous pocket formation in silicon by numerical solution of the heat transport equation

    International Nuclear Information System (INIS)

    Kovac, D.; Otto, G.; Hobler, G.

    2005-01-01

    In this paper we present a model of amorphous pocket formation that is based on binary collision simulations to generate the distribution of deposited energy, and on numerical solution of the heat transport equation to describe the quenching process. The heat transport equation is modified to consider the heat of melting when the melting temperature is crossed at any point in space. It is discretized with finite differences on grid points that coincide with the crystallographic lattice sites, which allows easy determination of molten atoms. Atoms are considered molten if the average of their energy and the energy of their neighbors meets the melting criterion. The results obtained with this model are in good overall agreement with published experimental data on P, As, Te and Tl implantations in Si and with data on the polyatomic effect at cryogenic temperature

  6. Transport and dosimetric solutions for the ELIMED laser-driven beam line

    Energy Technology Data Exchange (ETDEWEB)

    Cirrone, G.A.P. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Romano, F. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Medical Physics School, University of Catania, Via S. Sofia 64 - 95125 Catania (Italy); Scuderi, V. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Institute of Physics ASCR, v.v.i. (FZU), ELI-Beamlines Project, Na Slovance 2, 182 21 Prague (Czech Republic); Amato, A. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Candiano, G. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Medical Physics School, University of Catania, Via S. Sofia 64 - 95125 Catania (Italy); Cuttone, G. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Giove, D. [INFN Sezione di Milano, Via Celoria 16, Milano (Italy); Korn, G.; Krasa, J. [Institute of Physics ASCR, v.v.i. (FZU), ELI-Beamlines Project, Na Slovance 2, 182 21 Prague (Czech Republic); Leanza, R. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Universitá degli Studi di Catania, Dipartimento di Fisica e Astronomia, Via S. Sofia 64, Catania (Italy); Manna, R. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Maggiore, M. [INFN-LNL, Viale dell' Universitá 2 - 35020 Legnaro (PD) (Italy); Marchese, V. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Margarone, D. [Institute of Physics ASCR, v.v.i. (FZU), ELI-Beamlines Project, Na Slovance 2, 182 21 Prague (Czech Republic); Milluzzo, G. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Universitá degli Studi di Catania, Dipartimento di Fisica e Astronomia, Via S. Sofia 64, Catania (Italy); Petringa, G. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Sabini, M.G. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Azienda Ospedaliera Cannizzaro, Via Messina 829 - 95100 Catania (Italy); Schillaci, F. [INFN-LNS, Via S. Sofia 62 - 95125 Catania (Italy); Medical Physics School, University of Catania, Via S. Sofia 64 - 95125 Catania (Italy); and others

    2015-10-01

    Within 2017, the ELIMED (ELI-Beamlines MEDical applications) transport beam-line and dosimetric systems for laser-generated beams will be installed at the ELI-Beamlines facility in Prague (CZ), inside the ELIMAIA (ELI Multidisciplinary Applications of laser–Ion Acceleration) interaction room. The beam-line will be composed of two sections: one in vacuum, devoted to the collecting, focusing and energy selection of the primary beam and the second in air, where the ELIMED beam-line dosimetric devices will be located. This paper briefly describes the transport solutions that will be adopted together with the main dosimetric approaches. In particular, the description of an innovative Faraday Cup detector with its preliminary experimental tests will be reported.

  7. Method of model reduction and multifidelity models for solute transport in random layered porous media

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Zhijie; Tartakovsky, Alexandre M.

    2017-09-01

    This work presents a hierarchical model for solute transport in bounded layered porous media with random permeability. The model generalizes the Taylor-Aris dispersion theory to stochastic transport in random layered porous media with a known velocity covariance function. In the hierarchical model, we represent (random) concentration in terms of its cross-sectional average and a variation function. We derive a one-dimensional stochastic advection-dispersion-type equation for the average concentration and a stochastic Poisson equation for the variation function, as well as expressions for the effective velocity and dispersion coefficient. We observe that velocity fluctuations enhance dispersion in a non-monotonic fashion: the dispersion initially increases with correlation length λ, reaches a maximum, and decreases to zero at infinity. Maximum enhancement can be obtained at the correlation length about 0.25 the size of the porous media perpendicular to flow.

  8. Solute transport in a well under slow-purge and no-purge conditions

    Science.gov (United States)

    Plummer, M. A.; Britt, S. L.; Martin-Hayden, J. M.

    2010-12-01

    Non-purge sampling techniques, such as diffusion bags and in-situ sealed samplers, offer reliable and cost-effective groundwater monitoring methods that are a step closer to the goal of real-time monitoring without pumping or sample collection. Non-purge methods are, however, not yet completely accepted because questions remain about how solute concentrations in an unpurged well relate to concentrations in the adjacent formation. To answer questions about how undisturbed well water samples compare to formation concentrations, and to provide the information necessary to interpret results from non-purge monitoring systems, we have conducted a variety of physical experiments and numerical simulations of flow and transport in and through monitoring wells under low-flow and ambient flow conditions. Previous studies of flow and transport in wells used a Darcy’s law - based continuity equation for flow, which is often justified under the strong, forced-convection flow caused by pumping or large vertical hydraulic potential gradients. In our study, we focus on systems with weakly forced convection, where density-driven free convection may be of similar strength. We therefore solved Darcy’s law for porous media domains and the Navier Stokes equations for flow in the well, and coupled solution of the flow equations to that of solute transport. To illustrate expected in-well transport behavior under low-flow conditions, we present results of three particular studies: (1) time-dependent effluent concentrations from a well purged at low-flow pumping rates, (2) solute-driven density effects in a well under ambient horizontal flow and (3) temperature-driven mixing in a shallow well subject to seasonal temperature variations. Results of the first study illustrate that assumptions about the nature of in-well flow have a significant impact on effluent concentration curves even during pumping, with Poiseuille-type flow producing more rapid removal of concentration differences

  9. Nuclear transport factor directs localization of protein synthesis during mitosis

    NARCIS (Netherlands)

    Bogaart, Geert van den; Meinema, Anne C.; Krasnikov, Viktor; Veenhoff, Liesbeth M.; Poolman, Bert

    Export of messenger RNA from the transcription site in the nucleus and mRNA targeting to the translation site in the cytoplasm are key regulatory processes in protein synthesis. In yeast, the mRNA-binding proteins Nab2p and Nab4p/Hrp1p accompany transcripts to their translation site, where the

  10. Communication Maps: Exploring Energy Transport through Proteins and Water

    Czech Academy of Sciences Publication Activity Database

    Agbo, J. K.; Gnanasekaran, Ramachandran; Leitner, D. M.

    2014-01-01

    Roč. 54, 8/9 (2014), s. 1065-1073 ISSN 0021-2148 Institutional support: RVO:61388963 Keywords : energy transfer * heme proteins * hydrogen bonds * molecular modeling * protein models Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.221, year: 2014

  11. Protein-bound solute removal during extended multipass versus standard hemodialysis

    DEFF Research Database (Denmark)

    Eloot, Sunny; Van Biesen, Wim; Axelsen, Mette

    2015-01-01

    and middle molecules compared to standard hemodialysis (SHD). Since protein-bound solutes (PBS) exert important pathophysiological effects, we investigated whether MPHD results in improved removal of PBS as well. METHODS: A cross-over study (Clinical Trial NCT01267760) was performed in nine stable HD......), hippuric acid (HA), indole acetic acid (IAA), indoxyl sulfate (IS), and p-cresylsulfate (PCS). Dialyser extraction ratio, reduction ratio, and solute removal were calculated for these solutes. RESULTS: Already at 60 min after dialysis start, the extraction ratio in the hemodialyser was a factor 1.4-4 lower...

  12. Solution-grown organic single-crystalline p-n junctions with ambipolar charge transport.

    Science.gov (United States)

    Fan, Congcheng; Zoombelt, Arjan P; Jiang, Hao; Fu, Weifei; Wu, Jiake; Yuan, Wentao; Wang, Yong; Li, Hanying; Chen, Hongzheng; Bao, Zhenan

    2013-10-25

    Organic single-crystalline p-n junctions are grown from mixed solutions. First, C60 crystals (n-type) form and, subsequently, C8-BTBT crystals (p-type) nucleate heterogeneously on the C60 crystals. Both crystals continue to grow simultaneously into single-crystalline p-n junctions that exhibit ambipolar charge transport characteristics. This work provides a platform to study organic single-crystalline p-n junctions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Global existence of weak solutions to dissipative transport equations with nonlocal velocity

    Science.gov (United States)

    Bae, Hantaek; Granero-Belinchón, Rafael; Lazar, Omar

    2018-04-01

    We consider 1D dissipative transport equations with nonlocal velocity field: where is a nonlocal operator given by a Fourier multiplier. We especially consider two types of nonlocal operators: (1) , the Hilbert transform, (2) . In this paper, we show several global existence of weak solutions depending on the range of γ, δ and α. When , we take initial data having finite energy, while we take initial data in weighted function spaces (in the real variables or in the Fourier variables), which have infinite energy, when .

  14. Solution methods for compartment models of transport through the environment using numerical inversion of Laplace transforms

    International Nuclear Information System (INIS)

    Garratt, T.J.

    1989-05-01

    Compartment models for the transport of radionuclides in the biosphere are conventionally solved using a numerical time-stepping procedure. This report examines an alternative method based on the numerical inversion of Laplace transforms, which is potentially more efficient and accurate for some classes of problem. The central problem considered is the most efficient and robust technique for solving the Laplace-transformed rate equations. The conclusion is that Gaussian elimination is the most efficient and robust solution method. A general compartment model has been implemented on a personal computer and used to solve a realistic case including radionuclide decay chains. (author)

  15. Less is More: Membrane Protein Digestion Beyond Urea–Trypsin Solution for Next-level Proteomics*

    Science.gov (United States)

    Zhang, Xi

    2015-01-01

    The goal of next-level bottom-up membrane proteomics is protein function investigation, via high-coverage high-throughput peptide-centric quantitation of expression, modifications and dynamic structures at systems scale. Yet efficient digestion of mammalian membrane proteins presents a daunting barrier, and prevalent day-long urea–trypsin in-solution digestion proved insufficient to reach this goal. Many efforts contributed incremental advances over past years, but involved protein denaturation that disconnected measurement from functional states. Beyond denaturation, the recent discovery of structure/proteomics omni-compatible detergent n-dodecyl-β-d-maltopyranoside, combined with pepsin and PNGase F columns, enabled breakthroughs in membrane protein digestion: a 2010 DDM-low-TCEP (DLT) method for H/D-exchange (HDX) using human G protein-coupled receptor, and a 2015 flow/detergent-facilitated protease and de-PTM digestions (FDD) for integrative deep sequencing and quantitation using full-length human ion channel complex. Distinguishing protein solubilization from denaturation, protease digestion reliability from theoretical specificity, and reduction from alkylation, these methods shifted day(s)-long paradigms into minutes, and afforded fully automatable (HDX)-protein-peptide-(tandem mass tag)-HPLC pipelines to instantly measure functional proteins at deep coverage, high peptide reproducibility, low artifacts and minimal leakage. Promoting—not destroying—structures and activities harnessed membrane proteins for the next-level streamlined functional proteomics. This review analyzes recent advances in membrane protein digestion methods and highlights critical discoveries for future proteomics. PMID:26081834

  16. The Staphylococcus aureus extracellular adherence protein (Eap) adopts an elongated but structured conformation in solution.

    Science.gov (United States)

    Hammel, Michal; Nemecek, Daniel; Keightley, J Andrew; Thomas, George J; Geisbrecht, Brian V

    2007-12-01

    The extracellular adherence protein (Eap) of Staphylococcus aureus participates in a wide range of protein-protein interactions that facilitate the initiation and dissemination of Staphylococcal disease. In this report, we describe the use of a multidisciplinary approach to characterize the solution structure of full-length Eap. In contrast to previous reports suggesting that a six-domain isoform of Eap undergoes multimerization, sedimentation equilibrium analytical ultracentrifugation data revealed that a four-domain isoform of Eap is a monomer in solution. In vitro proteolysis and solution small angle X-ray scattering studies both indicate that Eap adopts an extended conformation in solution, where the linkers connecting sequential EAP modules are solvent exposed. Construction of a low-resolution model of full-length Eap using a combination of ab initio deconvolution of the SAXS data and rigid body modeling of the EAP domain crystal structure suggests that full-length Eap may present several unique concave surfaces capable of participating in ligand binding. These results also raise the possibility that such surfaces may be held together by additional interactions between adjacent EAP modules. This hypothesis is supported by a comparative Raman spectroscopic analysis of full-length Eap and a stoichiometric solution of the individual EAP modules, which indicates the presence of additional secondary structure and a greater extent of hydrogen/deuterium exchange protection in full-length Eap. Our results provide the first insight into the solution structure of full-length Eap and an experimental basis for interpreting the EAP domain crystal structures within the context of the full-length molecule. They also lay a foundation for future studies into the structural and molecular bases of Eap-mediated protein-protein interactions with its many ligands.

  17. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

    Energy Technology Data Exchange (ETDEWEB)

    Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

    2014-06-01

    The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain α-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

  18. WAP Based An Alternative Solution for Traffic Transportation Problem in Sidoarjo Surrounding Area Using AHP

    Directory of Open Access Journals (Sweden)

    Arna Fariza

    2009-08-01

    Full Text Available In line with the increasing interest on Lapindo mud disaster which causes several roadway covered by mud, there is a need to give an alternative solution for traffic transportation problem in surrounding area. The possible criteria for the solution of this road way are length, surface, traffic, and width of the road. Types of vehicle across the road also give a contribution to the criteria. By using Geography Information System (GIS, it is easy to all drivers to take decision which way has to be chosen based on the real condition. GIS is used to visualize the alternative road, which is possible to take. Analytic Hierarchy Processing (AHP is a decision method which is based on many criteria and alternatives. The input of AHP can be a preference or real value. Applied AHP to decide value of each alternative is based on application of Wireless Application Protocol (WAP assessment.

  19. Water and solute transport in agricultural soils predicted by volumetric clay and silt contents

    DEFF Research Database (Denmark)

    Karup, Dan; Møldrup, Per; Paradelo Pérez, Marcos

    2016-01-01

    tracer mass could be well fitted to an analytical solution to the classical convection-dispersion equation. Both cumulative tracer mass and concentration as a function of time were hereby reasonable well predicted from the simple inputs of bulk density, clay and silt contents, and applied tracer mass......Solute transport through the soil matrix is heterogeneous and greatly affected by soil texture, soil structure, and macropore networks. This study examined the relationship between tracer breakthrough characteristics, soil hydraulic properties, and basic soil properties. Hundred...... of the soil structure rather than the actual formation of macropores causing preferential flow. The arrival times of 5 % and up to 50 % of the tracer mass were found to be strongly correlated with volumetric fines content. The hereby predicted tracer concentration breakthrough points up to 50% of applied...

  20. The solution of the multigroup neutron transport equation using spherical harmonics

    International Nuclear Information System (INIS)

    Fletcher, K.

    1981-01-01

    A solution of the multi-group neutron transport equation in up to three space dimensions is presented. The flux is expanded in a series of unnormalised spherical harmonics. Using the various recurrence formulae a linked set of first order differential equations is obtained for the moments psisup(g)sub(lm)(r), γsup(g)sub(lm)(r). Terms with odd l are eliminated resulting in a second order system which is solved by two methods. The first is a finite difference formulation using an iterative procedure, secondly, in XYZ and XY geometry a finite element solution is given. Results for a test problem using both methods are exhibited and compared. (orig./RW) [de

  1. Matrix-oriented implementation for the numerical solution of the partial differential equations governing flows and transport in porous media

    KAUST Repository

    Sun, Shuyu; Salama, Amgad; El-Amin, Mohamed

    2012-01-01

    In this paper we introduce a new technique for the numerical solution of the various partial differential equations governing flow and transport phenomena in porous media. This method is proposed to be used in high level programming languages like

  2. Transport proteins of parasitic protists and their role in nutrient salvage.

    Science.gov (United States)

    Dean, Paul; Major, Peter; Nakjang, Sirintra; Hirt, Robert P; Embley, T Martin

    2014-01-01

    The loss of key biosynthetic pathways is a common feature of important parasitic protists, making them heavily dependent on scavenging nutrients from their hosts. This is often mediated by specialized transporter proteins that ensure the nutritional requirements of the parasite are met. Over the past decade, the completion of several parasite genome projects has facilitated the identification of parasite transporter proteins. This has been complemented by functional characterization of individual transporters along with investigations into their importance for parasite survival. In this review, we summarize the current knowledge on transporters from parasitic protists and highlight commonalities and differences in the transporter repertoires of different parasitic species, with particular focus on characterized transporters that act at the host-pathogen interface.

  3. Correlation of Aquaporins and Transmembrane Solute Transporters Revealed by Genome-Wide Analysis in Developing Maize Leaf

    Directory of Open Access Journals (Sweden)

    Xun Yue

    2012-01-01

    Full Text Available Aquaporins are multifunctional membrane channels that facilitate the transmembrane transport of water and solutes. When transmembrane mineral nutrient transporters exhibit the same expression patterns as aquaporins under diverse temporal and physiological conditions, there is a greater probability that they interact. In this study, genome-wide temporal profiling of transcripts analysis and coexpression network-based approaches are used to examine the significant specificity correlation of aquaporins and transmembrane solute transporters in developing maize leaf. The results indicate that specific maize aquaporins are related to specific transmembrane solute transporters. The analysis demonstrates a systems-level correlation between aquaporins, nutrient transporters, and the homeostasis of mineral nutrients in developing maize leaf. Our results provide a resource for further studies into the physiological function of these aquaporins.

  4. Transport of neutral solute across articular cartilage: the role of zonal diffusivities.

    Science.gov (United States)

    Arbabi, V; Pouran, B; Weinans, H; Zadpoor, A A

    2015-07-01

    Transport of solutes through diffusion is an important metabolic mechanism for the avascular cartilage tissue. Three types of interconnected physical phenomena, namely mechanical, electrical, and chemical, are all involved in the physics of transport in cartilage. In this study, we use a carefully designed experimental-computational setup to separate the effects of mechanical and chemical factors from those of electrical charges. Axial diffusion of a neutral solute Iodixanol into cartilage was monitored using calibrated microcomputed tomography micro-CT images for up to 48 hr. A biphasic-solute computational model was fitted to the experimental data to determine the diffusion coefficients of cartilage. Cartilage was modeled either using one single diffusion coefficient (single-zone model) or using three diffusion coefficients corresponding to superficial, middle, and deep cartilage zones (multizone model). It was observed that the single-zone model cannot capture the entire concentration-time curve and under-predicts the near-equilibrium concentration values, whereas the multizone model could very well match the experimental data. The diffusion coefficient of the superficial zone was found to be at least one order of magnitude larger than that of the middle zone. Since neutral solutes were used, glycosaminoglycan (GAG) content cannot be the primary reason behind such large differences between the diffusion coefficients of the different cartilage zones. It is therefore concluded that other features of the different cartilage zones such as water content and the organization (orientation) of collagen fibers may be enough to cause large differences in diffusion coefficients through the cartilage thickness.

  5. Cytoplasmic electric fields and electroosmosis: possible solution for the paradoxes of the intracellular transport of biomolecules.

    Science.gov (United States)

    Andreev, Victor P

    2013-01-01

    The objective of the paper is to show that electroosmotic flow might play an important role in the intracellular transport of biomolecules. The paper presents two mathematical models describing the role of electroosmosis in the transport of the negatively charged messenger proteins to the negatively charged nucleus and in the recovery of the fluorescence after photobleaching. The parameters of the models were derived from the extensive review of the literature data. Computer simulations were performed within the COMSOL 4.2a software environment. The first model demonstrated that the presence of electroosmosis might intensify the flux of messenger proteins to the nucleus and allow the efficient transport of the negatively charged phosphorylated messenger proteins against the electrostatic repulsion of the negatively charged nucleus. The second model revealed that the presence of the electroosmotic flow made the time of fluorescence recovery dependent on the position of the bleaching spot relative to cellular membrane. The magnitude of the electroosmotic flow effect was shown to be quite substantial, i.e. increasing the flux of the messengers onto the nucleus up to 4-fold relative to pure diffusion and resulting in the up to 3-fold change in the values of fluorescence recovery time, and therefore the apparent diffusion coefficient determined from the fluorescence recovery after photobleaching experiments. Based on the results of the modeling and on the universal nature of the electroosmotic flow, the potential wider implications of electroosmotic flow in the intracellular and extracellular biological processes are discussed. Both models are available for download at ModelDB.

  6. Water, solute and heat transport in the soil: the Australian connection

    Science.gov (United States)

    Knight, John

    2016-04-01

    The interest of Peter Raats in water, solute and heat transport in the soil has led to scientific and/or personal interactions with several Australian scientists such as John Philip, David Smiles, Greg Davis and John Knight. Along with John Philip and Robin Wooding, Peter was an early user of the Gardner (1958) linearised model of soil water flow, which brought him into competition with John Philip. I will discuss some of Peter's solutions relevant to infiltration from line and point sources, cavities and basins. A visit to Canberra, Australia in the early 1980s led to joint work on soil water flow, and on combined water and solute movement with David Smiles and others. In 1983 Peter was on the PhD committee for Greg Davis at the University of Wollongong, and some of the methods in his thesis 'Mathematical modelling of rate-limiting mechanisms of pyritic oxidation in overburden dumps' were later used by Peter's student Sjoerd van der Zee. David Smiles and Peter wrote a survey article 'Hydrology of swelling clay soils' in 2005. In the last decade Peter has been investigating the history of groundwater and vadose zone hydrology, and recently he and I have been bringing to light the largely forgotten work of Lewis Fry Richardson on finite difference solution of the heat equation, drainage theory, soil physics, and the soil-plant-atmosphere continuum.

  7. Effect of surface charge of immortalized mouse cerebral endothelial cell monolayer on transport of charged solutes.

    Science.gov (United States)

    Yuan, Wei; Li, Guanglei; Gil, Eun Seok; Lowe, Tao Lu; Fu, Bingmei M

    2010-04-01

    Charge carried by the surface glycocalyx layer (SGL) of the cerebral endothelium has been shown to significantly modulate the permeability of the blood-brain barrier (BBB) to charged solutes in vivo. The cultured monolayer of bEnd3, an immortalized mouse cerebral endothelial cell line, is becoming a popular in vitro BBB model due to its easy growth and maintenance of many BBB characteristics over repeated passages. To test whether the SGL of bEnd3 monolayer carries similar charge as that in the intact BBB and quantify this charge, which can be characterized by the SGL thickness (L(f)) and charge density (C(mf)), we measured the solute permeability of bEnd3 monolayer to neutral solutes and to solutes with similar size but opposite charges: negatively charged alpha-lactalbumin (-11) and positively charged ribonuclease (+3). Combining the measured permeability data with a transport model across the cell monolayer, we predicted the L(f) and the C(mf) of bEnd3 monolayer, which is approximately 160 nm and approximately 25 mEq/L, respectively. We also investigated whether orosomucoid, a plasma glycoprotein modulating the charge of the intact BBB, alters the charge of bEnd3 monolayer. We found that 1 mg/mL orosomucoid would increase SGL charge density of bEnd3 monolayer to approximately 2-fold of its control value.

  8. Solute transport in coupled inland-coastal water systems. General conceptualisation and application to Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    Jarsjoe, Jerker; Destouni, Georgia; Persson, Klas; Prieto, Carmen (Dept. of Physical Geography, Quaternary Geology, Stockholm Univ., Stockholm (Sweden))

    2007-12-15

    We formulate a general theoretical conceptualisation of solute transport from inland sources to downstream recipients, considering main recipient load contributions from all different nutrient and pollutant sources that may exist within any catchment. Since the conceptualisation is model independent, its main hydrological factors and mass delivery factors can be quantified on the basis of inputs to and outputs from any considered analytical or numerical model. Some of the conceptually considered source contribution and transport pathway combinations are however commonly neglected in catchment-scale solute transport and attenuation modelling, in particular those related to subsurface sources, diffuse sources at the land surface and direct groundwater transport into the recipient. The conceptual framework provides a possible tool for clarification of underlying and often implicit model assumptions, which can be useful for e.g. inter-model comparisons. In order to further clarify and explain research questions that may be of particular importance for transport pathways from deep groundwater surrounding a repository, we concretise and interpret some selected transport scenarios for model conditions in the Forsmark area. Possible uncertainties in coastal discharge predictions, related to uncertain spatial variation of evapotranspiration within the catchment, were shown to be small for the relatively large, focused surface water discharges from land to sea, because local differences were averaged out along the length of the main water flow paths. In contrast, local flux values within the diffuse groundwater flow field from land to sea are more uncertain, although estimates of mean values and total sums of submarine groundwater discharge (SGD) along some considerable coastline length may be robust. The present results show that 80% to 90% of the total coastal discharge of Forsmark occurred through focused flows in visible streams, whereas the remaining 10% to 20% was

  9. Effect of physical training on glucose transporter protein and mRNA levels in rat adipocytes

    DEFF Research Database (Denmark)

    Stallknecht, B; Andersen, P H; Vinten, J

    1993-01-01

    Physical training increases insulin-stimulated glucose transport and the number of glucose transporters in adipocytes measured by cytochalasin B binding. In the present study we used immunoblotting to measure the abundance of two glucose transporters (GLUT-4, GLUT-1) in white adipocytes from....../or intrinsic activity). GLUT-1 protein and mRNA levels/adipocyte volume did not change with age or training....

  10. Solution structure of the cold-shock-like protein from Rickettsia rickettsii

    International Nuclear Information System (INIS)

    Gerarden, Kyle P.; Fuchs, Andrew M.; Koch, Jonathan M.; Mueller, Melissa M.; Graupner, David R.; O’Rorke, Justin T.; Frost, Caleb D.; Heinen, Heather A.; Lackner, Emily R.; Schoeller, Scott J.; House, Paul G.; Peterson, Francis C.; Veldkamp, Christopher T.

    2012-01-01

    The solution structure of the cold-shock-like protein from R. rickettsii, the causative agent of Rocky Mountain spotted fever, is reported. Rocky Mountain spotted fever is caused by Rickettsia rickettsii infection. R. rickettsii can be transmitted to mammals, including humans, through the bite of an infected hard-bodied tick of the family Ixodidae. Since the R. rickettsii genome contains only one cold-shock-like protein and given the essential nature of cold-shock proteins in other bacteria, the structure of the cold-shock-like protein from R. rickettsii was investigated. With the exception of a short α-helix found between β-strands 3 and 4, the solution structure of the R. rickettsii cold-shock-like protein has the typical Greek-key five-stranded β-barrel structure found in most cold-shock domains. Additionally, the R. rickettsii cold-shock-like protein, with a ΔG of unfolding of 18.4 kJ mol −1 , has a similar stability when compared with other bacterial cold-shock proteins

  11. Identification and Quantitative Assessment of Uremic Solutes as Inhibitors of Renal Organic Anion Transporters, OAT1 and OAT3.

    Science.gov (United States)

    Hsueh, Chia-Hsiang; Yoshida, Kenta; Zhao, Ping; Meyer, Timothy W; Zhang, Lei; Huang, Shiew-Mei; Giacomini, Kathleen M

    2016-09-06

    One of the characteristics of chronic kidney disease (CKD) is the accumulation of uremic solutes in the plasma. Less is known about the effects of uremic solutes on transporters that may play critical roles in pharmacokinetics. We evaluated the effect of 72 uremic solutes on organic anion transporter 1 and 3 (OAT1 and OAT3) using a fluorescent probe substrate, 6-carboxyfluorescein. A total of 12 and 13 solutes were identified as inhibitors of OAT1 and OAT3, respectively. Several of them inhibited OAT1 or OAT3 at clinically relevant concentrations and reduced the transport of other OAT1/3 substrates in vitro. Review of clinical studies showed that the active secretion of most drugs that are known substrates of OAT1/3 deteriorated faster than the renal filtration in CKD. Collectively, these data suggest that through inhibition of OAT1 and OAT3, uremic solutes contribute to the decline in renal drug clearance in patients with CKD.

  12. Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Gronenborn, A.M.; Clore, G.M. [National Institutes of Health, Bethesda, MD (United States)

    1994-12-01

    Complete understanding of a protein`s function and mechanism of action can only be achieved with a knowledge of its three-dimensional structure at atomic resolution. At present, there are two methods available for determining such structures. The first method, which has been established for many years, is x-ray diffraction of protein single crystals. The second method has blossomed only in the last 5 years and is based on the application of nuclear magnetic resonance (NMR) spectroscopy to proteins in solution. This review paper describes three- and four-dimensional NMR methods applied to protein structure determination and was adapted from Clore and Gronenborn. The review focuses on the underlying principals and practice of multidimensional NMR and the structural information obtained.

  13. Ultrafast excited and ground-state dynamics of the green fluorescent protein chromophore in solution

    NARCIS (Netherlands)

    Vengris, M.; van Stokkum, I.H.M.; He, X.; Bell, A.F.; Tonge, P.J.; van Grondelle, R.; Larsen, D.S.

    2004-01-01

    Ultrafast dispersed pump-dump-probe spectroscopy was applied to HBDI (4′-hydroxybenzylidene-2,3-dimethylimidazolinone), a model green fluorescent protein (GFP) chromophore in solution with different protonation states. The measured three-dimensional data was analyzed using a global analysis method

  14. Evaluations of cellulose accessibilities of lignocelluloses by solute exclusion and protein adsorption techniques

    Science.gov (United States)

    Q.Q. Wang; Z. He; Z. Zhu; Y.-H.P. Zhang; Y. Ni; X.L. Luo; J.Y. Zhu

    2012-01-01

    Cellulose accessibilities of a set of hornified lignocellulosic substrates derived by drying the never dried pretreated sample and a set of differently pretreated lodgepople pine substrates, were evaluated using solute exclusion and protein adsorption methods. Direct measurements of cellulase adsorption onto cellulose surface of the set of pretreated substrates were...

  15. Protein Carbamylation in Peritoneal Dialysis and the Effect of Low Glucose Plus Amino Acid Solutions.

    Science.gov (United States)

    Trottier, Caitlin; Perl, Jeffrey; Freeman, Megan; Thadhani, Ravi; Berg, Anders; Kalim, Sahir

    2018-01-01

    Protein carbamylation is a post-translational urea-driven protein modification associated with mortality. Free amino acids (AAs) competitively inhibit protein carbamylation and parenteral AA therapy reduces carbamylation in hemodialysis (HD) patients. Peritoneal dialysis (PD) yields differences in urea clearance and AA balance compared with HD, but the influence of PD and intraperitoneal AA solutions on carbamylation is unclear. Thus, we first measured carbamylated albumin (C-Alb; a marker of carbamylation load) in 100 diabetic HD patients frequency-matched by age, sex, and race to 98 diabetic PD subjects from the IMPENDIA trial, which originally compared the metabolic effects of low-glucose PD solutions (incorporating icodextrin and AAs) to a control group (dextrose-only solutions). We then determined the effects of the AA-enriched PD solutions by measuring the 6-month change in C-Alb within the IMPENDIA cohort by treatment allocation (48 treated vs 50 controls). Peritoneal dialysis patients, when compared with HD patients, had higher baseline urea and higher C-Alb. Among IMPENDIA participants, there was no difference in C-Alb change in either arm, but treated subjects showed a trend towards increased carbamylation. Treated subjects also demonstrated an increase in urea, possibly explaining the carbamylation trend. In summary, carbamylation levels in PD patients appeared higher than in matched HD patients. A regimen of AA and low-glucose PD solutions did not reduce C-Alb in IMPENDIA subjects. Copyright © 2018 International Society for Peritoneal Dialysis.

  16. Flow and solute transport in backfilled tunnel and collapsed backfill - possible extension of Comp32

    International Nuclear Information System (INIS)

    Neretnieks, Ivars

    2006-09-01

    In the Swedish deep geological final repository for spent fuel the tunnels will be filled with a backfill with low permeability. However, some flow may take place in the backfill. Nuclides released from a leaking canister could diffuse up to the flowing water in the backfill and be transported downstream in the tunnel. At an intersection of the tunnel with a fracture zone the contaminated water might flow out into the zone.This report addresses the transport mechanisms and rate of transport from a leaking canister up through the buffer and backfill in the deposition hole, further into the backfill in the tunnel and the transport along the tunnel. Spreading by diffusion in the buffer and backfill as well as retardation of sorbing nuclides is accounted for.The transport mechanisms and rates of transport are described and some simple models with analytical solutions are used to quantify the processes. These simple solutions are used to gain insights into when different transport mechanisms are important. The simple solutions are used to simulate a base case example where a non-sorbing nuclide (iodide) and a sorbing nuclide (radium) move in the backfill by diffusion and by advective flow. The simple sample calculations show that it would take thousands of years for iodide to move 20 m along the tunnel and that a release pulse would spread out considerably over time. The sorbing nuclide 226 Ra with a half life of 1,600 years would be strongly retarded by sorption and would decay to insignificance during its migration along the tunnel. The consequences of a collapse of backfill leaving a channel above the backfill is also studied by a simple analytical model that accounts for water flowing in the collapsed part of the backfill at the ceiling of the tunnel. A nuclide that diffuses up to the flowing channel will flow with the ('rapidly' flowing) water but will be retarded by diffusion down into the backfill again. This down diffusion retards the nuclide migration

  17. Flow and solute transport in backfilled tunnel and collapsed backfill - possible extension of Comp32

    Energy Technology Data Exchange (ETDEWEB)

    Neretnieks, Ivars [Royal Inst. of Technology, Stockholm (Sweden). Dept. of Chemical Engineering and Technology

    2006-09-15

    In the Swedish deep geological final repository for spent fuel the tunnels will be filled with a backfill with low permeability. However, some flow may take place in the backfill. Nuclides released from a leaking canister could diffuse up to the flowing water in the backfill and be transported downstream in the tunnel. At an intersection of the tunnel with a fracture zone the contaminated water might flow out into the zone.This report addresses the transport mechanisms and rate of transport from a leaking canister up through the buffer and backfill in the deposition hole, further into the backfill in the tunnel and the transport along the tunnel. Spreading by diffusion in the buffer and backfill as well as retardation of sorbing nuclides is accounted for.The transport mechanisms and rates of transport are described and some simple models with analytical solutions are used to quantify the processes. These simple solutions are used to gain insights into when different transport mechanisms are important. The simple solutions are used to simulate a base case example where a non-sorbing nuclide (iodide) and a sorbing nuclide (radium) move in the backfill by diffusion and by advective flow. The simple sample calculations show that it would take thousands of years for iodide to move 20 m along the tunnel and that a release pulse would spread out considerably over time. The sorbing nuclide {sup 226}Ra with a half life of 1,600 years would be strongly retarded by sorption and would decay to insignificance during its migration along the tunnel. The consequences of a collapse of backfill leaving a channel above the backfill is also studied by a simple analytical model that accounts for water flowing in the collapsed part of the backfill at the ceiling of the tunnel. A nuclide that diffuses up to the flowing channel will flow with the ('rapidly' flowing) water but will be retarded by diffusion down into the backfill again. This down diffusion retards the nuclide

  18. Finite medium Green's function solutions to nuclide transport in porous media

    International Nuclear Information System (INIS)

    Oston, S.G.

    1979-01-01

    Current analytical techniques for predicting the transport of nuclides in porous materials center on the Green's function approach - i.e., determining the response characteristics of a geologic pathway to an impulse function input. To data, the analyses all have set the boundary conditions needed to solve the 1-D transport equation as though each pathway were infinite in length. The purpose of this work is to critically examine the effect that this infinite pathway assumption has on Green's function models of nuclide transport in porous media. The work described herein has directly attacked the more difficult problem of obtaining suitable Green's functions for finite pathways whose dimensions, in fact, may not be much greater than the diffusion length. Two different finite media Green's functions describing the nuclide mass flux have been determined, depending on whether the pathway is terminated by a high or a low flow resistance at the outlet end. Pulse shapes and peak amplitudes have been computed for each Green's function over a wide range of geohydrologic parameters. These results have been compared to both infinite and semi-infinite medium solutions. It was found that predicted pulse shapes are quite sensitive to selection of a Green's function model for short pathways only. For long pathways all models tend toward a symmetric Gaussian flux-time history at the outlet. Thus, the results of our previous waste transport studies using the infinite pathway assumption are still generally valid because they always included at least one long pathway. It was also found that finite medium models offer some unique computational advantages for evaluating nuclide transport in a series of connecting pathways

  19. Ultrafiltration of protein solutions; the role of protein association in rejection and osmotic pressure

    NARCIS (Netherlands)

    van den Berg, G.B.; Hanemaaijer, J.H.; Smolders, C.A.

    1987-01-01

    The monomer-dimer equilibrium of the protein β-lactoglobulin under neutral conditions appears to influence the rejection and the osmotic pressure build-up, both phenomena closely related to ultrafiltration. Rejection measurements indicate different rejections for the β-lactoglobulin monomers and

  20. Continuous desalting of refolded protein solution improves capturing in ion exchange chromatography: A seamless process.

    Science.gov (United States)

    Walch, Nicole; Jungbauer, Alois

    2017-06-01

    Truly continuous biomanufacturing processes enable an uninterrupted feed stream throughout the whole production without the need for holding tanks. We have utilized microporous anion and cation exchangers into which only salts, but not proteins, can penetrate into the pores for desalting of protein solutions, while diafiltration or dilution is usually employed for feed adjustments. Anion exchange and cation exchange chromatography columns were connected in series to remove both anions and cations. To increase operation performance, a continuous process was developed comprised of four columns. Continuous mode was achieved by staggered cycle operation, where one set of columns, consisting of one anion exchange and one cation exchange column, was loaded during the regeneration of the second set. Refolding, desalting and subsequent ion exchange capturing with a scFv as the model protein was demonstrated. The refolding solution was successfully desalted resulting in a consistent conductivity below 0.5 mS/cm from initial values of 10 to 11 mS/cm. With continuous operation process time could be reduced by 39% while productivity was increased to 163% compared to batch operation. Desalting of the protein solution resulted in up to 7-fold higher binding capacities in the subsequent ion exchange capture step with conventional protein binding resins. © 2017 The Authors. Biotechnology Journal published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Transportation Problems in Special Education Programs in Rural Areas - A Specific Solution and Some Suggestions for Delivery System Development.

    Science.gov (United States)

    Brody, Z. H.

    The paper describes transportation problems encountered and solutions employed in delivering systems of comprehensive services to handicapped children in Anderson County, Tennessee, a predominantly rural area with considerable mountain area. Detailed are methods of transportation utilized in the four different program areas of the county special…

  2. Detergent-associated solution conformations of helical and beta-barrel membrane proteins.

    Science.gov (United States)

    Mo, Yiming; Lee, Byung-Kwon; Ankner, John F; Becker, Jeffrey M; Heller, William T

    2008-10-23

    Membrane proteins present major challenges for structural biology. In particular, the production of suitable crystals for high-resolution structural determination continues to be a significant roadblock for developing an atomic-level understanding of these vital cellular systems. The use of detergents for extracting membrane proteins from the native membrane for either crystallization or reconstitution into model lipid membranes for further study is assumed to leave the protein with the proper fold with a belt of detergent encompassing the membrane-spanning segments of the structure. Small-angle X-ray scattering was used to probe the detergent-associated solution conformations of three membrane proteins, namely bacteriorhodopsin (BR), the Ste2p G-protein coupled receptor from Saccharomyces cerevisiae, and the Escherichia coli porin OmpF. The results demonstrate that, contrary to the traditional model of a detergent-associated membrane protein, the helical proteins BR and Ste2p are not in the expected, compact conformation and associated with detergent micelles, while the beta-barrel OmpF is indeed embedded in a disk-like micelle in a properly folded state. The comparison provided by the BR and Ste2p, both members of the 7TM family of helical membrane proteins, further suggests that the interhelical interactions between the transmembrane helices of the two proteins differ, such that BR, like other rhodopsins, can properly refold to crystallize, while Ste2p continues to prove resistant to crystallization from an initially detergent-associated state.

  3. Theoretical aspects of pressure and solute denaturation of proteins: A Kirkwood-buff-theory approach

    Science.gov (United States)

    Ben-Naim, Arieh

    2012-12-01

    A new approach to the problem of pressure-denaturation (PD) and solute-denaturation (SD) of proteins is presented. The problem is formulated in terms of Le Chatelier principle, and a solution is sought in terms of the Kirkwood-Buff theory of solutions. It is found that both problems have one factor in common; the excluded volumes of the folded and the unfolded forms with respect to the solvent molecules. It is shown that solvent-induced effects operating on hydrophilic groups along the protein are probably the main reason for PD. On the other hand, the SD depends on the preferential solvation of the folded and the unfolded forms with respect to solvent and co-solvent molecules.

  4. Effect of electric charge on the transperitoneal transport of plasma proteins during CAPD

    NARCIS (Netherlands)

    Buis, B.; Koomen, G. C.; Imholz, A. L.; Struijk, D. G.; Reddingius, R. E.; Arisz, L.; Krediet, R. T.

    1996-01-01

    BACKGROUND: Controversy exists as to whether electric charges of plasma proteins influence their transport across the peritoneal membrane during CAPD. Fixed negative charges in the peritoneal membrane are diminished during peritonitis in rats. METHODS: Peritoneal clearances of 10 proteins and their

  5. Coupled Fluid, Energy, and Solute Transport (CFEST) model: Formulation and user's manual

    International Nuclear Information System (INIS)

    Gupta, S.K.; Cole, C.R.; Kincaid, C.T.; Monti, A.M.

    1987-10-01

    The CFEST (Coupled Fluid, Energy, and Solute Transport) code has been developed to analyze coupled hydrologic, thermal, and solute transport processes. It treats single-pahse Darcy ground-water flow in a horizontal or vertical plane, or in fully three-dimensional space under nonisothermal conditions. The code has the capability to model discontinuous and continuous layering, time-dependent and constant sources/sinks, and transient as well as steady-stae ground-water flow. The code offers a wide choice of boundary conditions such as precsribed heads, nodal injection or withdrawal, constant or spatially varying infiltration rates, and welemental source/sink. Initial conditions for the flow analysis can be prescribed pressure or hydraulic head. The heterogeneity in aquifer permeability and porosity can be described by geologic unit or explicity for given elements. Three-dimensional elelments are generated from user-defined well logs at each surface node. To facilitate interaction between disciplines, support programs are provided to plot the finite element grid, well logs, contour maps of input and output parameters, and vertical cross sections. Ground-water travel paths and times and volumetric rates from a specified point can be determined from support programs. This report includes governing partial differential equations, finite element formulation, a use's manual, verification test examples, sample problems, and source listings. 36 refs., 121 figs., 36 tabs

  6. Sediment and solute transport in a mountainous watershed in Valle del Cauca, Colombia

    Science.gov (United States)

    Guzman, Christian; Hoyos Villada, Fanny; Morales Vargas, Amalia; Rivera, Baudelino; Da Silva, Mayesse; Moreno Padilla, Pedro; Steenhuis, Tammo

    2015-04-01

    Sediment samples and solute concentrations were measured from the La Vega micro watershed in the southwestern region of the Colombian Andes. A main goal of this study was to improve prediction of soil surface and soil nutrient changes, based on field measurements, within small basin of the Aguaclara watershed network receiving different types of conservation measures. Two modeling approaches for stream discharge and sediment transport predictions were used with one of these based on infiltration-excess and the other on saturation-excess runoff. These streams are a part of a recent initiative from a water fund established by Asobolo, Asocaña, and Cenicaña in collaboration with the Natural Capital Project to improve conservation efforts and monitor their effects. On-site soil depth changes, groundwater depth measurements, and soil nutrient concentrations were also monitored to provide more information about changes within this mountainous watershed during one part of the yearly rainy season. This information is being coupled closely with the outlet sediment concentration and solute concentration patterns to discern correlations between scales. Lateral transects in the upper, middle, and lower part of the hillsides in the La Vega micro watershed showed differences in soil nutrient status and soil surface depth changes. The model based on saturation-excess, semi-distributed hydrology was able to reproduce discharge and sediment transport rates as well as the initially used infiltration excess model indicating available options for comparison of conservation changes in the future.

  7. Solution and Study of the Two-Dimensional Nodal Neutron Transport Equation

    International Nuclear Information System (INIS)

    Panta Pazos, Ruben; Biasotto Hauser, Eliete; Tullio de Vilhena, Marco

    2002-01-01

    In the last decade Vilhena and coworkers reported an analytical solution to the two-dimensional nodal discrete-ordinates approximations of the neutron transport equation in a convex domain. The key feature of these works was the application of the combined collocation method of the angular variable and nodal approach in the spatial variables. By nodal approach we mean the transverse integration of the SN equations. This procedure leads to a set of one-dimensional S N equations for the average angular fluxes in the variables x