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Sample records for intraflagellar transport particle

  1. Intraflagellar transport: keeping the motors coordinated.

    PubMed

    Cole, Douglas G

    2005-10-11

    Intraflagellar transport is a conserved delivery system that services eukaryotic cilia and flagella. Recent work in the nematode Caenorhabditis elegans has identified proteins required for the functional coordination of intraflagellar transport motors and their cargoes. PMID:16213810

  2. Dissecting the Sequential Assembly and Localization of Intraflagellar Transport Particle Complex B in Chlamydomonas

    PubMed Central

    Richey, Elizabeth A.; Qin, Hongmin

    2012-01-01

    Intraflagellar transport (IFT), the key mechanism for ciliogenesis, involves large protein particles moving bi-directionally along the entire ciliary length. IFT particles contain two large protein complexes, A and B, which are constructed with proteins in a core and several peripheral proteins. Prior studies have shown that in Chlamydomonas reinhardtii, IFT46, IFT52, and IFT88 directly interact with each other and are in a subcomplex of the IFT B core. However, ift46, bld1, and ift88 mutants differ in phenotype as ift46 mutants are able to form short flagella, while the other two lack flagella completely. In this study, we investigated the functional differences of these individual IFT proteins contributing to complex B assembly, stability, and basal body localization. We found that complex B is completely disrupted in bld1 mutant, indicating an essential role of IFT52 for complex B core assembly. Ift46 mutant cells are capable of assembling a relatively intact complex B, but such complex is highly unstable and prone to degradation. In contrast, in ift88 mutant cells the complex B core still assembles and remains stable, but the peripheral proteins no longer attach to the B core. Moreover, in ift88 mutant cells, while complex A and the anterograde IFT motor FLA10 are localized normally to the transition fibers, complex B proteins instead are accumulated at the proximal ends of the basal bodies. In addition, in bld2 mutant, the IFT complex B proteins still localize to the proximal ends of defective centrioles which completely lack transition fibers. Taken together, these results revealed a step-wise assembly process for complex B, and showed that the complex first localizes to the proximal end of the centrioles and then translocates onto the transition fibers via an IFT88-dependent mechanism. PMID:22900094

  3. Single-particle imaging reveals intraflagellar transport-independent transport and accumulation of EB1 in Chlamydomonas flagella.

    PubMed

    Harris, J Aaron; Liu, Yi; Yang, Pinfen; Kner, Peter; Lechtreck, Karl F

    2016-01-15

    The microtubule (MT) plus-end tracking protein EB1 is present at the tips of cilia and flagella; end-binding protein 1 (EB1) remains at the tip during flagellar shortening and in the absence of intraflagellar transport (IFT), the predominant protein transport system in flagella. To investigate how EB1 accumulates at the flagellar tip, we used in vivo imaging of fluorescent protein-tagged EB1 (EB1-FP) in Chlamydomonas reinhardtii. After photobleaching, the EB1 signal at the flagellar tip recovered within minutes, indicating an exchange with unbleached EB1 entering the flagella from the cell body. EB1 moved independent of IFT trains, and EB1-FP recovery did not require the IFT pathway. Single-particle imaging showed that EB1-FP is highly mobile along the flagellar shaft and displays a markedly reduced mobility near the flagellar tip. Individual EB1-FP particles dwelled for several seconds near the flagellar tip, suggesting the presence of stable EB1 binding sites. In simulations, the two distinct phases of EB1 mobility are sufficient to explain its accumulation at the tip. We propose that proteins uniformly distributed throughout the cytoplasm like EB1 accumulate locally by diffusion and capture; IFT, in contrast, might be required to transport proteins against cellular concentration gradients into or out of cilia. PMID:26631555

  4. Single-particle imaging reveals intraflagellar transport–independent transport and accumulation of EB1 in Chlamydomonas flagella

    PubMed Central

    Harris, J. Aaron; Liu, Yi; Yang, Pinfen; Kner, Peter; Lechtreck, Karl F.

    2016-01-01

    The microtubule (MT) plus-end tracking protein EB1 is present at the tips of cilia and flagella; end-binding protein 1 (EB1) remains at the tip during flagellar shortening and in the absence of intraflagellar transport (IFT), the predominant protein transport system in flagella. To investigate how EB1 accumulates at the flagellar tip, we used in vivo imaging of fluorescent protein–tagged EB1 (EB1-FP) in Chlamydomonas reinhardtii. After photobleaching, the EB1 signal at the flagellar tip recovered within minutes, indicating an exchange with unbleached EB1 entering the flagella from the cell body. EB1 moved independent of IFT trains, and EB1-FP recovery did not require the IFT pathway. Single-particle imaging showed that EB1-FP is highly mobile along the flagellar shaft and displays a markedly reduced mobility near the flagellar tip. Individual EB1-FP particles dwelled for several seconds near the flagellar tip, suggesting the presence of stable EB1 binding sites. In simulations, the two distinct phases of EB1 mobility are sufficient to explain its accumulation at the tip. We propose that proteins uniformly distributed throughout the cytoplasm like EB1 accumulate locally by diffusion and capture; IFT, in contrast, might be required to transport proteins against cellular concentration gradients into or out of cilia. PMID:26631555

  5. Functional coordination of intraflagellar transport motors.

    PubMed

    Ou, Guangshuo; Blacque, Oliver E; Snow, Joshua J; Leroux, Michel R; Scholey, Jonathan M

    2005-07-28

    Cilia have diverse roles in motility and sensory reception, and defects in cilia function contribute to ciliary diseases such as Bardet-Biedl syndrome (BBS). Intraflagellar transport (IFT) motors assemble and maintain cilia by transporting ciliary precursors, bound to protein complexes called IFT particles, from the base of the cilium to their site of incorporation at the distal tip. In Caenorhabditis elegans, this is accomplished by two IFT motors, kinesin-II and osmotic avoidance defective (OSM)-3 kinesin, which cooperate to form two sequential anterograde IFT pathways that build distinct parts of cilia. By observing the movement of fluorescent IFT motors and IFT particles along the cilia of numerous ciliary mutants, we identified three genes whose protein products mediate the functional coordination of these motors. The BBS proteins BBS-7 and BBS-8 are required to stabilize complexes of IFT particles containing both of the IFT motors, because IFT particles in bbs-7 and bbs-8 mutants break down into two subcomplexes, IFT-A and IFT-B, which are moved separately by kinesin-II and OSM-3 kinesin, respectively. A conserved ciliary protein, DYF-1, is specifically required for OSM-3 kinesin to dock onto and move IFT particles, because OSM-3 kinesin is inactive and intact IFT particles are moved by kinesin-II alone in dyf-1 mutants. These findings implicate BBS ciliary disease proteins and an OSM-3 kinesin activator in the formation of two IFT pathways that build functional cilia. PMID:16049494

  6. Intraflagellar transport complex structure and cargo interactions

    PubMed Central

    2013-01-01

    Intraflagellar transport (IFT) is required for the assembly and maintenance of cilia, as well as the proper function of ciliary motility and signaling. IFT is powered by molecular motors that move along the axonemal microtubules, carrying large complexes of IFT proteins that travel together as so-called trains. IFT complexes likely function as adaptors that mediate interactions between anterograde/retrograde motors and ciliary cargoes, facilitating cargo transport between the base and tip of the cilium. Here, we provide an up-to-date review of IFT complex structure and architecture, and discuss how interactions with cargoes and motors may be achieved. PMID:23945166

  7. Spatial Distribution of Intraflagellar Transport Proteins in Vertebrate Photoreceptors

    PubMed Central

    Luby-Phelps, Katharine; Fogerty, Joseph; Baker, Sheila A.; Pazour, Gregory J.; Besharse, Joseph C.

    2008-01-01

    Intraflagellar transport (IFT) of a ∼17S particle containing at least 16 distinct polypeptides is required for the assembly and maintenance of cilia and flagella. Although both genetic and biochemical evidence suggest a role for IFT in vertebrate photoreceptors, the spatial distribution of IFT proteins within photoreceptors remains poorly defined. We have evaluated the distribution of 4 IFT proteins using a combination of immunocytochemistry and rod-specific over-expression of GFP tagged IFT proteins. Endogenous IFT proteins are most highly concentrated within the inner segment, around the basal body, and within the outer segment IFT proteins are localized in discrete particles along the entire length of the axoneme. IFT52-GFP and IFT57-GFP mimicked this pattern in transgenic Xenopus. PMID:17931679

  8. Unexpected Roles for Ciliary Kinesins and Intraflagellar Transport Proteins.

    PubMed

    Pooranachandran, Niedharsan; Malicki, Jarema J

    2016-06-01

    Transport of proteins in the ciliary shaft is driven by microtubule-dependent motors, kinesins. Prior studies suggested that the heterotrimeric ciliary kinesin may be dispensable for certain aspects of transport in specialized cilia of vertebrate photoreceptor cells. To test this possibility further, we analyzed the mutant phenotype of the zebrafish kif3a gene, which encodes the common motor subunit of heterotrimeric ciliary kinesins. Cilia are absent in all organs examined, leading to the conclusion that kif3a is indispensable for ciliogenesis in all cells, including photoreceptors. Unexpectedly, kif3a function precedes ciliogenesis as ciliary basal bodies are mispositioned in mutant photoreceptors. This phenotype is much less pronounced in intraflagellar transport (IFT) mutants and reveals that kif3a has a much broader role than previously assumed. Despite the severity of their basal body phenotype, kif3a mutant photoreceptors survive longer compared to those in IFT mutants, which display much weaker basal body mispositioning. This effect is absent in kif3a;IFT double mutants, indicating that IFT proteins have ciliary transport-independent roles, which add to the severity of their photoreceptor phenotype. kif3a is dispensable for basal body docking in otic vesicle sensory epithelia and, surprisingly, short cilia form in mechanosensory cristae even in the absence of kif3a In contrast to Kif3a, the functions of the Kif3c-related protein, encoded by the kif3c-like (kif3cl) gene, and the homodimeric ciliary kinesin, kif17, are dispensable for photoreceptor morphogenesis. These studies demonstrate unexpected new roles for both ciliary heterotrimeric kinesins and IFT particle genes and clarify the function of kif17, the homodimeric ciliary kinesin gene. PMID:27038111

  9. Prostaglandin signaling regulates ciliogenesis by modulating intraflagellar transport

    PubMed Central

    Jin, Daqing; Ni, Terri T.; Sun, Jianjian; Wan, Haiyan; Amack, Jeffrey D.; Yu, Guangju; Fleming, Jonathan; Chiang, Chin; Li, Wenyan; Papierniak, Anna; Cheepala, Satish; Conseil, Gwenaëlle; Cole, Susan P.C.; Zhou, Bin; Drummond, Iain A.; Schuetz, John D.; Malicki, Jarema; Zhong, Tao P.

    2014-01-01

    Cilia are microtubule-based organelles that mediate signal transduction in a variety of tissues. Despite their importance, the signaling cascades that regulate cilia formation remain incompletely understood. Here we report that prostaglandin signaling affects ciliogenesis by regulating anterograde intraflagellar transport (IFT). Zebrafish leakytail (lkt) mutants display ciliogenesis defects, and lkt locus encodes an ATP-binding cassette transporter (ABCC4). We show that Lkt/ABCC4 localizes to the cell membrane and exports prostaglandin E2 (PGE2), a function that is abrogated by the Lkt/ABCC4T804M mutant. PGE2 synthesis enzyme Cyclooxygenase-1 and its receptor, EP4, which localizes to the cilium and activates cAMP-mediated signaling cascade, are required for cilia formation and elongation. Importantly, PGE2 signaling increases anterograde but not retrograde velocity of IFT and promotes ciliogenesis in mammalian cells. These findings lead us to propose that Lkt/ABCC4-mediated PGE2 signaling acts through a ciliary G-protein-coupled receptor, EP4, to upregulate cAMP synthesis and increase anterograde IFT, thereby promoting ciliogenesis. PMID:25173977

  10. Transition fibre protein FBF1 is required for the ciliary entry of assembled intraflagellar transport complexes.

    PubMed

    Wei, Qing; Xu, Qingwen; Zhang, Yuxia; Li, Yujie; Zhang, Qing; Hu, Zeng; Harris, Peter C; Torres, Vicente E; Ling, Kun; Hu, Jinghua

    2013-01-01

    Sensory organelle cilia have critical roles in mammalian embryonic development and tissue homeostasis. Intraflagellar transport (IFT) machinery is required for the assembly and maintenance of cilia. Yet, how this large complex passes through the size-dependent barrier at the ciliary base remains enigmatic. Here we report that FBF1, a highly conserved transition fibre protein, is required for the ciliary import of assembled IFT particles at the ciliary base. We cloned dyf-19, the Caenorhabditis elegans homologue of human FBF1, in a whole-genome screen for ciliogenesis mutants. DYF-19 localizes specifically to transition fibres and interacts directly with the IFT-B component DYF-11/IFT54. Although not a structural component of transition fibres, DYF-19 is required for the transit of assembled IFT particles through the ciliary base. Furthermore, we found that human FBF1 shares conserved localization and function with its worm counterpart. We conclude that FBF1 is a key functional transition fibre component that actively facilitates the ciliary entry of assembled IFT machinery. PMID:24231678

  11. The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery.

    PubMed

    Toriyama, Michinori; Lee, Chanjae; Taylor, S Paige; Duran, Ivan; Cohn, Daniel H; Bruel, Ange-Line; Tabler, Jacqueline M; Drew, Kevin; Kelly, Marcus R; Kim, Sukyoung; Park, Tae Joo; Braun, Daniela A; Pierquin, Ghislaine; Biver, Armand; Wagner, Kerstin; Malfroot, Anne; Panigrahi, Inusha; Franco, Brunella; Al-Lami, Hadeel Adel; Yeung, Yvonne; Choi, Yeon Ja; Duffourd, Yannis; Faivre, Laurence; Rivière, Jean-Baptiste; Chen, Jiang; Liu, Karen J; Marcotte, Edward M; Hildebrandt, Friedhelm; Thauvin-Robinet, Christel; Krakow, Deborah; Jackson, Peter K; Wallingford, John B

    2016-06-01

    Cilia use microtubule-based intraflagellar transport (IFT) to organize intercellular signaling. Ciliopathies are a spectrum of human diseases resulting from defects in cilia structure or function. The mechanisms regulating the assembly of ciliary multiprotein complexes and the transport of these complexes to the base of cilia remain largely unknown. Combining proteomics, in vivo imaging and genetic analysis of proteins linked to planar cell polarity (Inturned, Fuzzy and Wdpcp), we identified and characterized a new genetic module, which we term CPLANE (ciliogenesis and planar polarity effector), and an extensive associated protein network. CPLANE proteins physically and functionally interact with the poorly understood ciliopathy-associated protein Jbts17 at basal bodies, where they act to recruit a specific subset of IFT-A proteins. In the absence of CPLANE, defective IFT-A particles enter the axoneme and IFT-B trafficking is severely perturbed. Accordingly, mutation of CPLANE genes elicits specific ciliopathy phenotypes in mouse models and is associated with ciliopathies in human patients. PMID:27158779

  12. Direct evidence for BBSome-associated intraflagellar transport reveals distinct properties of native mammalian cilia

    PubMed Central

    Williams, Corey L.; McIntyre, Jeremy C.; Norris, Stephen R.; Jenkins, Paul M.; Zhang, Lian; Pei, Qinglin; Verhey, Kristen; Martens, Jeffrey R.

    2014-01-01

    Cilia dysfunction underlies a class of human diseases with variable penetrance in different organ systems. Across eukaryotes, intraflagellar transport (IFT) facilitates cilia biogenesis and cargo trafficking, but our understanding of mammalian IFT is insufficient. Here we perform live analysis of cilia ultrastructure, composition and cargo transport in native mammalian tissue using olfactory sensory neurons. Proximal and distal axonemes of these neurons show no bias towards IFT kinesin-2 choice, and Kif17 homodimer is dispensable for distal segment IFT. We identify Bardet–Biedl syndrome proteins (BBSome) as bona fide constituents of IFT in olfactory sensory neurons, and show that they exist in 1:1 stoichiometry with IFT particles. Conversely, subpopulations of peripheral membrane proteins, as well as transmembrane olfactory signalling pathway components, are capable of IFT but with significantly less frequency and/or duration. Our results yield a model for IFT and cargo trafficking in native mammalian cilia and may explain the penetrance of specific ciliopathy phenotypes in olfactory neurons. PMID:25504142

  13. Subunit Interactions and Organization of the Chlamydomonas reinhardtii Intraflagellar Transport Complex A Proteins*

    PubMed Central

    Behal, Robert H.; Miller, Mark S.; Qin, Hongmin; Lucker, Ben F.; Jones, Alexis; Cole, Douglas G.

    2012-01-01

    Chlamydomonas reinhardtii intraflagellar transport (IFT) particles can be biochemically resolved into two smaller assemblies, complexes A and B, that contain up to six and 15 protein subunits, respectively. We provide here the proteomic and immunological analyses that verify the identity of all six Chlamydomonas A proteins. Using sucrose density gradient centrifugation and antibody pulldowns, we show that all six A subunits are associated in a 16 S complex in both the cell bodies and flagella. A significant fraction of the cell body IFT43, however, exhibits a much slower sedimentation of ∼2 S and is not associated with the IFT A complex. To identify interactions between the six A proteins, we combined exhaustive yeast-based two-hybrid analysis, heterologous recombinant protein expression in Escherichia coli, and analysis of the newly identified complex A mutants, ift121 and ift122. We show that IFT121 and IFT43 interact directly and provide evidence for additional interactions between IFT121 and IFT139, IFT121 and IFT122, IFT140 and IFT122, and IFT140 and IFT144. The mutant analysis further allows us to propose that a subset of complex A proteins, IFT144/140/122, can form a stable 12 S subcomplex that we refer to as the IFT A core. Based on these results, we propose a model for the spatial arrangement of the six IFT A components. PMID:22170070

  14. An essential role for DYF-11/MIP-T3 in assembling functional intraflagellar transport complexes.

    PubMed

    Li, Chunmei; Inglis, Peter N; Leitch, Carmen C; Efimenko, Evgeni; Zaghloul, Norann A; Mok, Calvin A; Davis, Erica E; Bialas, Nathan J; Healey, Michael P; Héon, Elise; Zhen, Mei; Swoboda, Peter; Katsanis, Nicholas; Leroux, Michel R

    2008-03-01

    MIP-T3 is a human protein found previously to associate with microtubules and the kinesin-interacting neuronal protein DISC1 (Disrupted-in-Schizophrenia 1), but whose cellular function(s) remains unknown. Here we demonstrate that the C. elegans MIP-T3 ortholog DYF-11 is an intraflagellar transport (IFT) protein that plays a critical role in assembling functional kinesin motor-IFT particle complexes. We have cloned a loss of function dyf-11 mutant in which several key components of the IFT machinery, including Kinesin-II, as well as IFT subcomplex A and B proteins, fail to enter ciliary axonemes and/or mislocalize, resulting in compromised ciliary structures and sensory functions, and abnormal lipid accumulation. Analyses in different mutant backgrounds further suggest that DYF-11 functions as a novel component of IFT subcomplex B. Consistent with an evolutionarily conserved cilia-associated role, mammalian MIP-T3 localizes to basal bodies and cilia, and zebrafish mipt3 functions synergistically with the Bardet-Biedl syndrome protein Bbs4 to ensure proper gastrulation, a key cilium- and basal body-dependent developmental process. Our findings therefore implicate MIP-T3 in a previously unknown but critical role in cilium biogenesis and further highlight the emerging role of this organelle in vertebrate development. PMID:18369462

  15. WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia.

    PubMed

    Patel-King, Ramila S; Gilberti, Renée M; Hom, Erik F Y; King, Stephen M

    2013-09-01

    Retrograde intraflagellar transport (IFT) is required for assembly of cilia. We identify a Chlamydomonas flagellar protein (flagellar-associated protein 163 [FAP163]) as being closely related to the D1bIC(FAP133) intermediate chain (IC) of the dynein that powers this movement. Biochemical analysis revealed that FAP163 is present in the flagellar matrix and is actively trafficked by IFT. Furthermore, FAP163 copurified with D1bIC(FAP133) and the LC8 dynein light chain, indicating that it is an integral component of the retrograde IFT dynein. To assess the functional role of FAP163, we generated an RNA interference knockdown of the orthologous protein (WD60) in planaria. The Smed-wd60(RNAi) animals had a severe ciliary assembly defect that dramatically compromised whole-organism motility. Most cilia were present as short stubs that had accumulated large quantities of IFT particle-like material between the doublet microtubules and the membrane. The few remaining approximately full-length cilia had a chaotic beat with a frequency reduced from 24 to ∼10 Hz. Thus WD60/FAP163 is a dynein IC that is absolutely required for retrograde IFT and ciliary assembly. PMID:23864713

  16. Intraflagellar transport is essential for mammalian spermiogenesis but is absent in mature sperm

    PubMed Central

    San Agustin, Jovenal T.; Pazour, Gregory J.; Witman, George B.

    2015-01-01

    Drosophila sperm are unusual in that they do not require the intraflagellar transport (IFT) system for assembly of their flagella. In the mouse, the IFT proteins are very abundant in testis, but we here show that mature sperm are completely devoid of them, making the importance of IFT to mammalian sperm development unclear. To address this question, we characterized spermiogenesis and fertility in the Ift88Tg737Rpw mouse. This mouse has a hypomorphic mutation in the gene encoding the IFT88 subunit of the IFT particle. This mutation is highly disruptive to ciliary assembly in other organs. Ift88−/− mice are completely sterile. They produce ∼350-fold fewer sperm than wild-type mice, and the remaining sperm completely lack or have very short flagella. The short flagella rarely have axonemes but assemble ectopic microtubules and outer dense fibers and accumulate improperly assembled fibrous sheath proteins. Thus IFT is essential for the formation but not the maintenance of mammalian sperm flagella. PMID:26424803

  17. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.

    PubMed

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R; Mans, Dorus A; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E C; Yap, Zhi Min; Letteboer, Stef J F; Taylor, S Paige; Herridge, Warren; Johnson, Colin A; Scambler, Peter J; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M; Beales, Philip L; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M; Witman, George B

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  18. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport

    PubMed Central

    Schmidts, Miriam; Hou, Yuqing; Cortés, Claudio R.; Mans, Dorus A.; Huber, Celine; Boldt, Karsten; Patel, Mitali; van Reeuwijk, Jeroen; Plaza, Jean-Marc; van Beersum, Sylvia E. C.; Yap, Zhi Min; Letteboer, Stef J. F.; Taylor, S. Paige; Herridge, Warren; Johnson, Colin A.; Scambler, Peter J.; Ueffing, Marius; Kayserili, Hulya; Krakow, Deborah; King, Stephen M.; Beales, Philip L.; Al-Gazali, Lihadh; Wicking, Carol; Cormier-Daire, Valerie; Roepman, Ronald; Mitchison, Hannah M.; Witman, George B.; Al-Turki, Saeed; Anderson, Carl; Anney, Richard; Antony, Dinu; Asimit, Jennifer; Ayub, Mohammad; Barrett, Jeff; Barroso, Inês; Bentham, Jamie; Bhattacharya, Shoumo; Blackwood, Douglas; Bobrow, Martin; Bochukova, Elena; Bolton, Patrick; Boustred, Chris; Breen, Gerome; Brion, Marie-Jo; Brown, Andrew; Calissano, Mattia; Carss, Keren; Chatterjee, Krishna; Chen, Lu; Cirak, Sebhattin; Clapham, Peter; Clement, Gail; Coates, Guy; Collier, David; Cosgrove, Catherine; Cox, Tony; Craddock, Nick; Crooks, Lucy; Curran, Sarah; Daly, Allan; Danecek, Petr; Smith, George Davey; Day-Williams, Aaron; Day, Ian; Durbin, Richard; Edkins, Sarah; Ellis, Peter; Evans, David; Farooqi, I. Sadaf; Fatemifar, Ghazaleh; Fitzpatrick, David; Flicek, Paul; Floyd, Jamie; Foley, A. Reghan; Franklin, Chris; Futema, Marta; Gallagher, Louise; Gaunt, Tom; Geschwind, Daniel; Greenwood, Celia; Grozeva, Detelina; Guo, Xiaosen; Gurling, Hugh; Hart, Deborah; Hendricks, Audrey; Holmans, Peter; Huang, Jie; Humphries, Steve E.; Hurles, Matt; Hysi, Pirro; Jackson, David; Jamshidi, Yalda; Jewell, David; Chris, Joyce; Kaye, Jane; Keane, Thomas; Kemp, John; Kennedy, Karen; Kent, Alastair; Kolb-Kokocinski, Anja; Lachance, Genevieve; Langford, Cordelia; Lee, Irene; Li, Rui; Li, Yingrui; Ryan, Liu; Lönnqvist, Jouko; Lopes, Margarida; MacArthur, Daniel G.; Massimo, Mangino; Marchini, Jonathan; Maslen, John; McCarthy, Shane; McGuffin, Peter; McIntosh, Andrew; McKechanie, Andrew; McQuillin, Andrew; Memari, Yasin; Metrustry, Sarah; Min, Josine; Moayyeri, Alireza; Morris, James; Muddyman, Dawn; Muntoni, Francesco; Northstone, Kate; O'Donovan, Michael; O'Rahilly, Stephen; Onoufriadis, Alexandros; Oualkacha, Karim; Owen, Michael; Palotie, Aarno; Panoutsopoulou, Kalliope; Parker, Victoria; Parr, Jeremy; Paternoster, Lavinia; Paunio, Tiina; Payne, Felicity; Perry, John; Pietilainen, Olli; Plagnol, Vincent; Quail, Michael A.; Quaye, Lydia; Raymond, Lucy; Rehnström, Karola; Brent Richards, J.; Ring, Sue; Ritchie, Graham R S; Savage, David B.; Schoenmakers, Nadia; Semple, Robert K.; Serra, Eva; Shihab, Hashem; Shin, So-Youn; Skuse, David; Small, Kerrin; Smee, Carol; Soler, Artigas María; Soranzo, Nicole; Southam, Lorraine; Spector, Tim; St Pourcain, Beate; St. Clair, David; Stalker, Jim; Surdulescu, Gabriela; Suvisaari, Jaana; Tachmazidou, Ioanna; Tian, Jing; Timpson, Nic; Tobin, Martin; Valdes, Ana; van Kogelenberg, Margriet; Vijayarangakannan, Parthiban; Wain, Louise; Walter, Klaudia; Wang, Jun; Ward, Kirsten; Wheeler, Ellie; Whittall, Ros; Williams, Hywel; Williamson, Kathy; Wilson, Scott G.; Wong, Kim; Whyte, Tamieka; ChangJiang, Xu; Zeggini, Eleftheria; Zhang, Feng; Zheng, Hou-Feng

    2015-01-01

    The analysis of individuals with ciliary chondrodysplasias can shed light on sensitive mechanisms controlling ciliogenesis and cell signalling that are essential to embryonic development and survival. Here we identify TCTEX1D2 mutations causing Jeune asphyxiating thoracic dystrophy with partially penetrant inheritance. Loss of TCTEX1D2 impairs retrograde intraflagellar transport (IFT) in humans and the protist Chlamydomonas, accompanied by destabilization of the retrograde IFT dynein motor. We thus define TCTEX1D2 as an integral component of the evolutionarily conserved retrograde IFT machinery. In complex with several IFT dynein light chains, it is required for correct vertebrate skeletal formation but may be functionally redundant under certain conditions. PMID:26044572

  19. TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella

    PubMed Central

    Ishikawa, Hiroaki; Ide, Takahiro; Yagi, Toshiki; Jiang, Xue; Hirono, Masafumi; Sasaki, Hiroyuki; Yanagisawa, Haruaki; Wemmer, Kimberly A; Stainier, Didier YR; Qin, Hongmin; Kamiya, Ritsu; Marshall, Wallace F

    2014-01-01

    Cilia/flagella are assembled and maintained by the process of intraflagellar transport (IFT), a highly conserved mechanism involving more than 20 IFT proteins. However, the functions of individual IFT proteins are mostly unclear. To help address this issue, we focused on a putative IFT protein TTC26/DYF13. Using live imaging and biochemical approaches we show that TTC26/DYF13 is an IFT complex B protein in mammalian cells and Chlamydomonas reinhardtii. Knockdown of TTC26/DYF13 in zebrafish embryos or mutation of TTC26/DYF13 in C. reinhardtii, produced short cilia with abnormal motility. Surprisingly, IFT particle assembly and speed were normal in dyf13 mutant flagella, unlike in other IFT complex B mutants. Proteomic and biochemical analyses indicated a particular set of proteins involved in motility was specifically depleted in the dyf13 mutant. These results support the concept that different IFT proteins are responsible for different cargo subsets, providing a possible explanation for the complexity of the IFT machinery. DOI: http://dx.doi.org/10.7554/eLife.01566.001 PMID:24596149

  20. Intraflagellar Transport/Hedgehog-Related Signaling Components Couple Sensory Cilium Morphology and Serotonin Biosynthesis in Caenorhabditis elegans

    PubMed Central

    Moussaif, Mustapha; Sze, Ji Ying

    2009-01-01

    Intraflagellar transport in cilia has been proposed as a crucial mediator of Hedgehog signal transduction during embryonic pattern formation in both vertebrates and invertebrates. Here, we show that the Hh receptor Patched-related factor DAF-6 and intraflagellar transport modulate serotonin production in Caenorhabditis elegans animals, by remodeling the architecture of dendritic cilia of a pair of ADF serotonergic chemosensory neurons. Wild-type animals under aversive environment drastically reduce DAF-6 expression in glia-like cells surrounding the cilia of chemosensory neurons, resulting in cilium structural remodeling and upregulation of the serotonin-biosynthesis enzyme tryptophan hydroxylase tph-1 in the ADF neurons. These cellular and molecular modifications are reversed when the environment improves. Mutants of daf-6 or intraflagellar transport constitutively upregulate tph-1 expression. Epistasis analyses indicate that DAF-6/intraflagellar transport and the OCR-2/OSM-9 TRPV channel act in concert, regulating two layers of activation of tph-1 in the ADF neurons. The TRPV signaling turns on tph-1 expression under favorable and aversive conditions, whereas inactivation of DAF-6 by stress results in further upregulation of tph-1 independently of OCR-2/OSM-9 activity. Behavioral analyses suggest that serotonin facilitates larval animals resuming development when the environment improves. Our study revealed the cilium structure of serotonergic neurons as a trigger of regulated serotonin production, and demonstrated that a Hedgehog-related signaling component is dynamically regulated by environment and underscores neuroplasticity of serotonergic neurons in C. elegans under stress and stress recovery. PMID:19339602

  1. Microtubule doublets are double-track railways for intraflagellar transport trains.

    PubMed

    Stepanek, Ludek; Pigino, Gaia

    2016-05-01

    The cilium is a large macromolecular machine that is vital for motility, signaling, and sensing in most eukaryotic cells. Its conserved core structure, the axoneme, contains nine microtubule doublets, each comprising a full A-microtubule and an incomplete B-microtubule. However, thus far, the function of this doublet geometry has not been understood. We developed a time-resolved correlative fluorescence and three-dimensional electron microscopy approach to investigate the dynamics of intraflagellar transport (IFT) trains, which carry ciliary building blocks along microtubules during the assembly and disassembly of the cilium. Using this method, we showed that each microtubule doublet is used as a bidirectional double-track railway: Anterograde IFT trains move along B-microtubules, and retrograde trains move along A-microtubules. Thus, the microtubule doublet geometry provides direction-specific rails to coordinate bidirectional transport of ciliary components. PMID:27151870

  2. Retrograde Intraflagellar Transport Mutants Identify Complex A Proteins With Multiple Genetic Interactions in Chlamydomonas reinhardtii

    PubMed Central

    Iomini, Carlo; Li, Linya; Esparza, Jessica M.; Dutcher, Susan K.

    2009-01-01

    The intraflagellar transport machinery is required for the assembly of cilia. It has been investigated by biochemical, genetic, and computational methods that have identified at least 21 proteins that assemble into two subcomplexes. It has been hypothesized that complex A is required for retrograde transport. Temperature-sensitive mutations in FLA15 and FLA17 show defects in retrograde intraflagellar transport (IFT) in Chlamydomonas. We show that IFT144 and IFT139, two complex A proteins, are encoded by FLA15 and FLA17, respectively. The fla15 allele is a missense mutation in a conserved cysteine and the fla17 allele is an in-frame deletion of three exons. The flagellar assembly defect of each mutant is rescued by the respective transgenes. In fla15 and fla17 mutants, bulges form in the distal one-third of the flagella at the permissive temperature and this phenotype is also rescued by the transgenes. These bulges contain the complex B component IFT74/72, but not α-tubulin or p28, a component of an inner dynein arm, which suggests specificity with respect to the proteins that accumulate in these bulges. IFT144 and IFT139 are likely to interact with each other and other proteins on the basis of three distinct genetic tests: (1) Double mutants display synthetic flagellar assembly defects at the permissive temperature, (2) heterozygous diploid strains exhibit second-site noncomplemention, and (3) transgenes confer two-copy suppression. Since these tests show different levels of phenotypic sensitivity, we propose they illustrate different gradations of gene interaction between complex A proteins themselves and with a complex B protein (IFT172). PMID:19720863

  3. Function and regulation of primary cilia and intraflagellar transport proteins in the skeleton

    PubMed Central

    Yuan, Xue; Serra, Rosa A.; Yang, Shuying

    2014-01-01

    Primary cilia are microtubule-based organelles that project from the cell surface to enable transduction of various developmental signaling pathways. The process of intraflagellar transport (IFT) is crucial for the building and maintenance of primary cilia. Ciliary dysfunction has been found in a range of disorders called ciliopathies, some of which display severe skeletal dysplasias. In recent years, interest has grown in uncovering the function of primary cilia/IFT proteins in bone development, mechanotransduction, and cellular regulation. We summarize recent advances in understanding the function of cilia and IFT proteins in the regulation of cell differentiation in osteoblasts, osteocytes, chondrocytes, and mesenchymal stem cells (MSCs). We also discuss the mechanosensory function of cilia and IFT proteins in bone cells, cilia orientation, and other functions of cilia in chondrocytes. PMID:24961486

  4. The GTPase IFT27 is involved in both anterograde and retrograde intraflagellar transport

    PubMed Central

    Huet, Diego; Blisnick, Thierry; Perrot, Sylvie; Bastin, Philippe

    2014-01-01

    The construction of cilia and flagella depends on intraflagellar transport (IFT), the bidirectional movement of two protein complexes (IFT-A and IFT-B) driven by specific kinesin and dynein motors. IFT-B and kinesin are associated to anterograde transport whereas IFT-A and dynein participate to retrograde transport. Surprisingly, the small GTPase IFT27, a member of the IFT-B complex, turns out to be essential for retrograde cargo transport in Trypanosoma brucei. We reveal that this is due to failure to import both the IFT-A complex and the IFT dynein into the flagellar compartment. To get further molecular insight about the role of IFT27, GDP- or GTP-locked versions were expressed in presence or absence of endogenous IFT27. The GDP-locked version is unable to enter the flagellum and to interact with other IFT-B proteins and its sole expression prevents flagellum formation. These findings demonstrate that a GTPase-competent IFT27 is required for association to the IFT complex and that IFT27 plays a role in the cargo loading of the retrograde transport machinery. DOI: http://dx.doi.org/10.7554/eLife.02419.001 PMID:24843028

  5. Two classes of short intraflagellar transport train with different 3D structures are present in Chlamydomonas flagella.

    PubMed

    Vannuccini, Elisa; Paccagnini, Eugenio; Cantele, Francesca; Gentile, Mariangela; Dini, Daniele; Fino, Federica; Diener, Dennis; Mencarelli, Caterina; Lupetti, Pietro

    2016-05-15

    Intraflagellar transport (IFT) is responsible for the bidirectional trafficking of molecular components required for the elongation and maintenance of eukaryotic cilia and flagella. Cargo is transported by IFT 'trains', linear rows of multiprotein particles moved by molecular motors along the axonemal doublets. We have previously described two structurally distinct categories of 'long' and 'short' trains. Here, we analyse the relative number of these trains throughout flagellar regeneration and show that long trains are most abundant at the beginning of flagellar growth whereas short trains gradually increase in number as flagella elongate. These observations are incompatible with the previous hypothesis that short trains are derived solely from the reorganization of long trains at the flagellar tip. We demonstrate with electron tomography the existence of two distinct ultrastructural organizations for the short trains, we name these 'narrow' and 'wide', and provide the first 3D model of the narrow short trains. These trains are characterized by tri-lobed units, which repeat longitudinally every 16 nm and contact protofilament 7 of the B-tubule. Functional implications of the new structural evidence are discussed. PMID:27044756

  6. The molecular identities of the Caenorhabditis elegans intraflagellar transport genes dyf-6, daf-10 and osm-1.

    PubMed

    Bell, Leslie R; Stone, Steven; Yochem, John; Shaw, Jocelyn E; Herman, Robert K

    2006-07-01

    The Caenorhabditis elegans genes dyf-6, daf-10, and osm-1 are among the set of genes that affect chemotaxis and the ability of certain sensory neurons to take up fluorescent dyes from the environment. Some genes in this category are known to be required for intraflagellar transport (IFT), which is the bidirectional movement of raft-like particles along the axonemes of cilia and flagella. The cloning of dyf-6, daf-10, and osm-1 are described here. The daf-10 and osm-1 gene products resemble each other and contain WD and WAA repeats. DYF-6, the product of a complex locus, lacks known motifs, but orthologs are present in flies and mammals. Phenotypic analysis of dyf-6 mutants expressing an OSM-6::GFP reporter indicates that the cilia of the amphid and phasmid dendritic endings are foreshortened. Consistent with genetic mosaic analysis, which indicates that dyf-6 functions in neurons of the amphid sensilla, DYF-6::GFP is expressed in amphid and phasmid neurons. Movement of DYF-6::GFP within the ciliated endings of the neurons indicates that DYF-6 is involved in IFT. In addition, IFT can be observed in dauer larvae. PMID:16648645

  7. The intraflagellar transport protein IFT80 is required for cilia formation and osteogenesis

    PubMed Central

    Yang, Shuying; Wang, Changdong

    2012-01-01

    Intraflagellar transport (IFT) proteins are essential for the assembly and maintenance of cilia, which play important roles in development and homeostasis. IFT80 is a newly defined IFT protein. Partial mutation of IFT80 in humans causes diseases such as Jeune asphyxiating thoracic dystrophy (JATD) and short rib polydactyly (SRP) type III with abnormal skeletal development. However, the role and mechanism of IFT80 in osteogenesis is unknown. Here, we first detected IFT80 expression pattern and found that IFT80 was highly expressed in mouse long bone, skull, and during osteoblast differentiation. By using lentivirus-mediated RNA interference (RNAi) technology to silence IFT80 in murine mesenchymal progenitor cell line-C3H10T1/2 and bone marrow derived stromal cells, we found that silencing IFT80 led to either shortening or loss of cilia and the decrease of Arl13b expression - a small GTPase that is localized in cilia. Additionally, silencing IFT80 blocked the expression of osteoblast markers and significantly inhibited ALP activity and cell mineralization. We further found that IFT80 silencing inhibited the expression of Gli2, a critical transcriptional factor in the hedgehog signaling pathway. Overexpression of Gli2 rescued the deficiency of osteoblast differentiation from IFT80-silenced cells, and dramatically promoted osteoblast differentiation. Moreover, introduction of Smo agonist (SAG) promotes osteoblast differentiation, which was partially inhibited by IFT80 silencing. Thus, these results suggested that IFT80 plays an important role in osteogenesis through regulating Hedgehog/Gli signal pathways. PMID:22771375

  8. Intraflagellar transport is required for the maintenance of the trypanosome flagellum composition but not its length.

    PubMed

    Fort, Cécile; Bonnefoy, Serge; Kohl, Linda; Bastin, Philippe

    2016-08-01

    Intraflagellar transport (IFT) is required for construction of most cilia and flagella. Here, we used electron microscopy, immunofluorescence and live video microscopy to show that IFT is absent or arrested in the mature flagellum of Trypanosoma brucei upon RNA interference (RNAi)-mediated knockdown of IFT88 and IFT140, respectively. Flagella assembled prior to RNAi did not shorten, showing that IFT is not essential for the maintenance of flagella length. Although the ultrastructure of the axoneme was not visibly affected, flagellar beating was strongly reduced and the distribution of several flagellar components was drastically modified. The R subunit of the protein kinase A was no longer concentrated in the flagellum but was largely found in the cell body whereas the kinesin 9B motor was accumulating at the distal tip of the flagellum. In contrast, the distal tip protein FLAM8 was dispersed along the flagellum. This reveals that IFT also functions in maintaining the distribution of some flagellar proteins after construction of the organelle is completed. PMID:27343245

  9. Functional genomics of intraflagellar transport-associated proteins in C. elegans.

    PubMed

    Inglis, Peter N; Blacque, Oliver E; Leroux, Michel R

    2009-01-01

    The nematode Caenorhabditis elegans presents numerous advantages for the identification and molecular analysis of intraflagellar transport (IFT)-associated proteins, which play a critical role in the formation of cilia. Many proteins were first described as participating in IFT in this organism, including IFTA-1 (IFT121), DYF-1 (fleer/IFT70), DYF-2 (IFT144), DYF-3 (Qilin), DYF-11 (MIP-T3/IFT54), DYF-13, XBX-1 (dynein light intermediate chain), XBX-2 (dynein light chain), CHE-13 (IFT57/HIPPI), orthologs of Bardet-Biedl syndrome proteins, and potential regulatory protein, IFTA-2 (RABL5/IFT22). Transgenic animals bearing green fluorescent protein (GFP)-tagged proteins can be generated with ease, and in vivo imaging of IFT in both wild-type and cilia mutant strains can be performed quickly. The analyses permit detailed information on the localization and dynamic properties (velocities along the ciliary axoneme) of the relevant proteins, providing insights into their potential functions in processes such as anterograde and retrograde transport and cilium formation, as well as association with distinct modules of the IFT machinery (e.g., IFT subcomplexes A or B). Behavioral studies of the corresponding IFT-associated gene mutants further enable an understanding of the ciliary role of the proteins-e.g., in chemosensation, lipid homeostasis, lifespan control, and signaling-in a multicellular animal. In this chapter, we discuss how C. elegans can be used for the identification and characterization of IFT-associated proteins, focusing on methods for the generation of GFP-tagged IFT reporter strains, time-lapse microscopy, and IFT rate measurements. PMID:20409822

  10. Why motor proteins team up - Intraflagellar transport in C. elegans cilia

    PubMed Central

    Mijalkovic, Jona; Prevo, Bram; Peterman, Erwin J. G.

    2016-01-01

    ABSTRACT Inside the cell, vital processes such as cell division and intracellular transport are driven by the concerted action of different molecular motor proteins. In C. elegans chemosensory cilia, 2 kinesin-2 family motor proteins, kinesin-II and OSM-3, team up to drive intraflagellar transport (IFT) in the anterograde direction, from base to tip, whereas IFT dynein hitchhikes toward the tip and subsequently drives IFT in the opposite, retrograde direction, thereby recycling both kinesins. While it is evident that at least a retrograde and an anterograde motor are necessary to drive IFT, it has remained puzzling why 2 same-polarity kinesins are employed. Recently, we addressed this question by combining advanced genome-engineering tools with ultrasensitive, quantitative fluorescence microscopy to study IFT with single-molecule sensitivity.1,2 Using this combination of approaches, we uncovered a differentiation in kinesin-2 function, in which the slower kinesin-II operates as an ‘importer’, loading IFT trains into the cilium before gradually handing them over to the faster OSM-3. OSM-3 subsequently acts as a long-range ‘transporter’, driving the IFT trains toward the tip. The two kinesin-2 motors combine their unique motility properties to achieve something neither motor can achieve on its own; that is to optimize the amount of cargo inside the cilium. In this commentary, we provide detailed insight into the rationale behind our research approach and comment on our recent findings. Moreover, we discuss the role of IFT dynein and provide an outlook on future studies. PMID:27384150

  11. Intraflagellar transport 27 is essential for hedgehog signaling but dispensable for ciliogenesis during hair follicle morphogenesis.

    PubMed

    Yang, Ning; Li, Li; Eguether, Thibaut; Sundberg, John P; Pazour, Gregory J; Chen, Jiang

    2015-06-15

    Hair follicle morphogenesis requires precisely controlled reciprocal communications, including hedgehog (Hh) signaling. Activation of the Hh signaling pathway relies on the primary cilium. Disrupting ciliogenesis results in hair follicle morphogenesis defects due to attenuated Hh signaling; however, the loss of cilia makes it impossible to determine whether hair follicle phenotypes in these cilia mutants are caused by the loss of cilia, disruption of Hh signaling, or a combination of these events. In this study, we characterized the function of Ift27, which encodes a subunit of intraflagellar transport (IFT) complex B. Hair follicle morphogenesis of Ift27-null mice was severely impaired, reminiscent of phenotypes observed in cilia and Hh mutants. Furthermore, the Hh signaling pathway was attenuated in Ift27 mutants, which was in association with abnormal ciliary trafficking of SMO and GLI2, and impaired processing of Gli transcription factors; however, formation of the ciliary axoneme was unaffected. The ciliary localization of IFT25 (HSPB11), the binding partner of IFT27, was disrupted in Ift27 mutant cells, and Ift25-null mice displayed hair follicle phenotypes similar to those of Ift27 mutants. These data suggest that Ift27 and Ift25 operate in a genetically and functionally dependent manner during hair follicle morphogenesis. This study suggests that the molecular trafficking machineries underlying ciliogenesis and Hh signaling can be segregated, thereby providing important insights into new avenues of inhibiting Hh signaling, which might be adopted in the development of targeted therapies for Hh-dependent cancers, such as basal cell carcinoma. PMID:26023097

  12. Dysfunction of intraflagellar transport-A causes hyperphagia-induced obesity and metabolic syndrome

    PubMed Central

    Jacobs, Damon T.; Silva, Luciane M.; Allard, Bailey A.; Schonfeld, Michael P.; Chatterjee, Anindita; Talbott, George C.

    2016-01-01

    ABSTRACT Primary cilia extend from the plasma membrane of most vertebrate cells and mediate signaling pathways. Ciliary dysfunction underlies ciliopathies, which are genetic syndromes that manifest multiple clinical features, including renal cystic disease and obesity. THM1 (also termed TTC21B or IFT139) encodes a component of the intraflagellar transport-A complex and mutations in THM1 have been identified in 5% of individuals with ciliopathies. Consistent with this, deletion of murine Thm1 during late embryonic development results in cystic kidney disease. Here, we report that deletion of murine Thm1 during adulthood results in obesity, diabetes, hypertension and fatty liver disease, with gender differences in susceptibility to weight gain and metabolic dysfunction. Pair-feeding of Thm1 conditional knock-out mice relative to control littermates prevented the obesity and related disorders, indicating that hyperphagia caused the obese phenotype. Thm1 ablation resulted in increased localization of adenylyl cyclase III in primary cilia that were shortened, with bulbous distal tips on neurons of the hypothalamic arcuate nucleus, an integrative center for signals that regulate feeding and activity. In pre-obese Thm1 conditional knock-out mice, expression of anorexogenic pro-opiomelanocortin (Pomc) was decreased by 50% in the arcuate nucleus, which likely caused the hyperphagia. Fasting of Thm1 conditional knock-out mice did not alter Pomc nor orexogenic agouti-related neuropeptide (Agrp) expression, suggesting impaired sensing of changes in peripheral signals. Together, these data indicate that the Thm1-mutant ciliary defect diminishes sensitivity to feeding signals, which alters appetite regulation and leads to hyperphagia, obesity and metabolic disease. PMID:27482817

  13. Intraflagellar transport 27 is essential for hedgehog signaling but dispensable for ciliogenesis during hair follicle morphogenesis

    PubMed Central

    Yang, Ning; Li, Li; Eguether, Thibaut; Sundberg, John P.; Pazour, Gregory J.; Chen, Jiang

    2015-01-01

    Hair follicle morphogenesis requires precisely controlled reciprocal communications, including hedgehog (Hh) signaling. Activation of the Hh signaling pathway relies on the primary cilium. Disrupting ciliogenesis results in hair follicle morphogenesis defects due to attenuated Hh signaling; however, the loss of cilia makes it impossible to determine whether hair follicle phenotypes in these cilia mutants are caused by the loss of cilia, disruption of Hh signaling, or a combination of these events. In this study, we characterized the function of Ift27, which encodes a subunit of intraflagellar transport (IFT) complex B. Hair follicle morphogenesis of Ift27-null mice was severely impaired, reminiscent of phenotypes observed in cilia and Hh mutants. Furthermore, the Hh signaling pathway was attenuated in Ift27 mutants, which was in association with abnormal ciliary trafficking of SMO and GLI2, and impaired processing of Gli transcription factors; however, formation of the ciliary axoneme was unaffected. The ciliary localization of IFT25 (HSPB11), the binding partner of IFT27, was disrupted in Ift27 mutant cells, and Ift25-null mice displayed hair follicle phenotypes similar to those of Ift27 mutants. These data suggest that Ift27 and Ift25 operate in a genetically and functionally dependent manner during hair follicle morphogenesis. This study suggests that the molecular trafficking machineries underlying ciliogenesis and Hh signaling can be segregated, thereby providing important insights into new avenues of inhibiting Hh signaling, which might be adopted in the development of targeted therapies for Hh-dependent cancers, such as basal cell carcinoma. PMID:26023097

  14. The FLA3 KAP Subunit Is Required for Localization of Kinesin-2 to the Site of Flagellar Assembly and Processive Anterograde Intraflagellar TransportV⃞

    PubMed Central

    Mueller, Joshua; Perrone, Catherine A.; Bower, Raqual; Cole, Douglas G.; Porter, Mary E.

    2005-01-01

    Intraflagellar transport (IFT) is a bidirectional process required for assembly and maintenance of cilia and flagella. Kinesin-2 is the anterograde IFT motor, and Dhc1b/Dhc2 drives retrograde IFT. To understand how either motor interacts with the IFT particle or how their activities might be coordinated, we characterized a ts mutation in the Chlamydomonas gene encoding KAP, the nonmotor subunit of Kinesin-2. The fla3-1 mutation is an amino acid substitution in a conserved C-terminal domain. fla3-1 strains assemble flagella at 21°C, but cannot maintain them at 33°C. Although the Kinesin-2 complex is present at both 21 and 33°C, the fla3-1 Kinesin-2 complex is not efficiently targeted to or retained in the basal body region or flagella. Video-enhanced DIC microscopy of fla3-1 cells shows that the frequency of anterograde IFT particles is significantly reduced. Anterograde particles move at near wild-type velocities, but appear larger and pause more frequently in fla3-1. Transformation with an epitope-tagged KAP gene rescues all of the fla3-1 defects and results in preferential incorporation of tagged KAP complexes into flagella. KAP is therefore required for the localization of Kinesin-2 at the site of flagellar assembly and the efficient transport of anterograde IFT particles within flagella. PMID:15616187

  15. The intraflagellar transport dynein complex of trypanosomes is made of a heterodimer of dynein heavy chains and of light and intermediate chains of distinct functions

    PubMed Central

    Blisnick, Thierry; Buisson, Johanna; Absalon, Sabrina; Marie, Alexandra; Cayet, Nadège; Bastin, Philippe

    2014-01-01

    Cilia and flagella are assembled by intraflagellar transport (IFT) of protein complexes that bring tubulin and other precursors to the incorporation site at their distal tip. Anterograde transport is driven by kinesin, whereas retrograde transport is ensured by a specific dynein. In the protist Trypanosoma brucei, two distinct genes encode fairly different dynein heavy chains (DHCs; ∼40% identity) termed DHC2.1 and DHC2.2, which form a heterodimer and are both essential for retrograde IFT. The stability of each heavy chain relies on the presence of a dynein light intermediate chain (DLI1; also known as XBX-1/D1bLIC). The presence of both heavy chains and of DLI1 at the base of the flagellum depends on the intermediate dynein chain DIC5 (FAP133/WDR34). In the IFT140RNAi mutant, an IFT-A protein essential for retrograde transport, the IFT dynein components are found at high concentration at the flagellar base but fail to penetrate the flagellar compartment. We propose a model by which the IFT dynein particle is assembled in the cytoplasm, reaches the base of the flagellum, and associates with the IFT machinery in a manner dependent on the IFT-A complex. PMID:24989795

  16. The intraflagellar transport dynein complex of trypanosomes is made of a heterodimer of dynein heavy chains and of light and intermediate chains of distinct functions.

    PubMed

    Blisnick, Thierry; Buisson, Johanna; Absalon, Sabrina; Marie, Alexandra; Cayet, Nadège; Bastin, Philippe

    2014-09-01

    Cilia and flagella are assembled by intraflagellar transport (IFT) of protein complexes that bring tubulin and other precursors to the incorporation site at their distal tip. Anterograde transport is driven by kinesin, whereas retrograde transport is ensured by a specific dynein. In the protist Trypanosoma brucei, two distinct genes encode fairly different dynein heavy chains (DHCs; ∼40% identity) termed DHC2.1 and DHC2.2, which form a heterodimer and are both essential for retrograde IFT. The stability of each heavy chain relies on the presence of a dynein light intermediate chain (DLI1; also known as XBX-1/D1bLIC). The presence of both heavy chains and of DLI1 at the base of the flagellum depends on the intermediate dynein chain DIC5 (FAP133/WDR34). In the IFT140(RNAi) mutant, an IFT-A protein essential for retrograde transport, the IFT dynein components are found at high concentration at the flagellar base but fail to penetrate the flagellar compartment. We propose a model by which the IFT dynein particle is assembled in the cytoplasm, reaches the base of the flagellum, and associates with the IFT machinery in a manner dependent on the IFT-A complex. PMID:24989795

  17. Caenorhabditis elegans DYF-2, an orthologue of human WDR19, is a component of the intraflagellar transport machinery in sensory cilia.

    PubMed

    Efimenko, Evgeni; Blacque, Oliver E; Ou, Guangshuo; Haycraft, Courtney J; Yoder, Bradley K; Scholey, Jonathan M; Leroux, Michel R; Swoboda, Peter

    2006-11-01

    The intraflagellar transport (IFT) machinery required to build functional cilia consists of a multisubunit complex whose molecular composition, organization, and function are poorly understood. Here, we describe a novel tryptophan-aspartic acid (WD) repeat (WDR) containing IFT protein from Caenorhabditis elegans, DYF-2, that plays a critical role in maintaining the structural and functional integrity of the IFT machinery. We determined the identity of the dyf-2 gene by transgenic rescue of mutant phenotypes and by sequencing of mutant alleles. Loss of DYF-2 function selectively affects the assembly and motility of different IFT components and leads to defects in cilia structure and chemosensation in the nematode. Based on these observations, and the analysis of DYF-2 movement in a Bardet-Biedl syndrome mutant with partially disrupted IFT particles, we conclude that DYF-2 can associate with IFT particle complex B. At the same time, mutations in dyf-2 can interfere with the function of complex A components, suggesting an important role of this protein in the assembly of the IFT particle as a whole. Importantly, the mouse orthologue of DYF-2, WDR19, also localizes to cilia, pointing to an important evolutionarily conserved role for this WDR protein in cilia development and function. PMID:16957054

  18. The Intraflagellar Transport Protein IFT27 Promotes BBSome Exit from Cilia through the GTPase ARL6/BBS3

    PubMed Central

    Liew, Gerald M.; Ye, Fan; Nager, Andrew R.; Murphy, J. Patrick; Lee, Jaclyn S.; Aguiar, Mike; Breslow, David K.; Gygi, Steven P.; Nachury, Maxence V.

    2014-01-01

    SUMMARY The sorting of signaling receptors into and out of cilia relies on the BBSome, a complex of Bardet-Biedl syndrome (BBS) proteins, and on the intraflagellar transport (IFT) machinery. GTP loading onto the Arf-like GTPase ARL6/BBS3 drives assembly of a membrane-apposed BBSome coat that promotes cargo entry into cilia, yet how and where ARL6 is activated remains elusive. Here, we show that the Rab-like GTPase IFT27/RABL4, a known component of IFT complex B, promotes the exit of BBSome and associated cargoes from cilia. Unbiased proteomics and biochemical reconstitution assays show that, upon disengagement from the rest of IFT-B, IFT27 directly interacts with the nucleotide-free form of ARL6. Furthermore, IFT27 prevents aggregation of nucleotide-free ARL6 in solution. Thus, we propose that IFT27 separates from IFT-B inside cilia to promote ARL6 activation, BBSome coat assembly and subsequent ciliary exit, mirroring the process by which BBSome mediates cargo entry into cilia. PMID:25443296

  19. Getting to the heart of intraflagellar transport using Trypanosoma and Chlamydomonas models: the strength is in their differences

    PubMed Central

    2013-01-01

    Cilia and flagella perform diverse roles in motility and sensory perception, and defects in their construction or their function are responsible for human genetic diseases termed ciliopathies. Cilia and flagella construction relies on intraflagellar transport (IFT), the bi-directional movement of ‘trains’ composed of protein complexes found between axoneme microtubules and the flagellum membrane. Although extensive information about IFT components and their mode of action were discovered in the green algae Chlamydomonas reinhardtii, other model organisms have revealed further insights about IFT. This is the case of Trypanosoma brucei, a flagellated protist responsible for sleeping sickness that is turning out to be an emerging model for studying IFT. In this article, we review different aspects of IFT, based on studies of Chlamydomonas and Trypanosoma. Data available from both models are examined to ask challenging questions about IFT such as the initiation of flagellum construction, the setting-up of IFT and the mode of formation of IFT trains, and their remodeling at the tip as well as their recycling at the base. Another outstanding question is the individual role played by the multiple IFT proteins. The use of different models, bringing their specific biological and experimental advantages, will be invaluable in order to obtain a global understanding of IFT. PMID:24289478

  20. Components of Intraflagellar Transport Complex A Function Independently of the Cilium to Regulate Canonical Wnt Signaling in Drosophila.

    PubMed

    Balmer, Sophie; Dussert, Aurore; Collu, Giovanna M; Benitez, Elvira; Iomini, Carlo; Mlodzik, Marek

    2015-09-28

    The development of multicellular organisms requires the precisely coordinated regulation of an evolutionarily conserved group of signaling pathways. Temporal and spatial control of these signaling cascades is achieved through networks of regulatory proteins, segregation of pathway components in specific subcellular compartments, or both. In vertebrates, dysregulation of primary cilia function has been strongly linked to developmental signaling defects, yet it remains unclear whether cilia sequester pathway components to regulate their activation or cilia-associated proteins directly modulate developmental signaling events. To elucidate this question, we conducted an RNAi-based screen in Drosophila non-ciliated cells to test for cilium-independent loss-of-function phenotypes of ciliary proteins in developmental signaling pathways. Our results show no effect on Hedgehog signaling. In contrast, our screen identified several cilia-associated proteins as functioning in canonical Wnt signaling. Further characterization of specific components of Intraflagellar Transport complex A uncovered a cilia-independent function in potentiating Wnt signals by promoting β-catenin/Armadillo activity. PMID:26364750

  1. Gli2 and Gli3 Localize to Cilia and Require the Intraflagellar Transport Protein Polaris for Processing and Function

    SciTech Connect

    Michaud III, Edward J; Haycraft, Courtney J; Aydin Son, Yesim; Zhang, Qihong; Yoder, Bradley

    2005-01-01

    Intraflagellar transport (IFT) proteins are essential for cilia assembly and have recently been associated with a number of developmental processes, such as left-right axis specification and limb and neural tube patterning. Genetic studies indicate that IFT proteins are required for Sonic hedgehog (Shh)signaling downstream of the Smoothened and Patched membrane proteins but upstream of the Glioma (Gli) transcription factors. However, the role that IFT proteins play in transduction of Shh signaling and the importance of cilia in this process remain unknown. Here we provide insights into the mechanism by which defects in an IFT protein, Tg737/Polaris, affect Shh signaling in the murine limb bud. Our data show that loss of Tg737 results in altered Gli3 processing that abrogates Gli3-mediated repression of Gli1 transcriptional activity. In contrast to the conclusions drawn from genetic analysis, the activity of Gli1 and truncated forms of Gli3 (Gli3R) are unaffected in Tg737 mutants at the molecular level, indicating that Tg737/Polaris is differentially involved in specific activities of the Gli proteins. Most important, a negative regulator of Shh signaling, Suppressor of fused, and the three full-length Gli transcription factors localize to the distal tip of cilia in addition to the nucleus. Thus, our data support a model where cilia have a direct role in Gli processing and Shh signal transduction.

  2. Regulation of Cilium Length and Intraflagellar Transport by the RCK-Kinases ICK and MOK in Renal Epithelial Cells

    PubMed Central

    Broekhuis, Joost R.; Verhey, Kristen J.; Jansen, Gert

    2014-01-01

    Primary cilia are important sensory organelles. They exist in a wide variety of lengths, which could reflect different cell-specific functions. How cilium length is regulated is unclear, but it probably involves intraflagellar transport (IFT), which transports protein complexes along the ciliary axoneme. Studies in various organisms have identified the small, conserved family of ros-cross hybridizing kinases (RCK) as regulators of cilium length. Here we show that Intestinal Cell Kinase (ICK) and MAPK/MAK/MRK overlapping kinase (MOK), two members of this family, localize to cilia of mouse renal epithelial (IMCD-3) cells and negatively regulate cilium length. To analyze the effects of ICK and MOK on the IFT machinery, we set up live imaging of five fluorescently tagged IFT proteins: KIF3B, a subunit of kinesin-II, the main anterograde IFT motor, complex A protein IFT43, complex B protein IFT20, BBSome protein BBS8 and homodimeric kinesin KIF17, whose function in mammalian cilia is unclear. Interestingly, all five proteins moved at ∼0.45 µm/s in anterograde and retrograde direction, suggesting they are all transported by the same machinery. Moreover, GFP tagged ICK and MOK moved at similar velocities as the IFT proteins, suggesting they are part of, or transported by the IFT machinery. Indeed, loss- or gain-of-function of ICK affected IFT speeds: knockdown increased anterograde velocities, whereas overexpression reduced retrograde speed. In contrast, MOK knockdown or overexpression did not affect IFT speeds. Finally, we found that the effects of ICK or MOK knockdown on cilium length and IFT are suppressed by rapamycin treatment, suggesting that these effects require the mTORC1 pathway. Our results confirm the importance of RCK kinases as regulators of cilium length and IFT. However, whereas some of our results suggest a direct correlation between cilium length and IFT speed, other results indicate that cilium length can be modulated independent of IFT speed. PMID

  3. Interaction of mouse TTC30/DYF-1 with multiple intraflagellar transport complex B proteins and KIF17.

    PubMed

    Howard, Paul W; Jue, Shall F; Maurer, Richard A

    2013-08-15

    Intraflagellar transport (IFT) is a microtubule based system that supports the assembly and maintenance of cilia. Genetic and biochemical studies have identified two distinct complexes containing multiple proteins that are part of the IFT machinery. In this study we prepared mouse pituitary cells that expressed an epitope-tagged IFT protein and immuno-purified the IFT B complex from these cells. Mass spectrometry analysis of the isolated complex led to identification of a number of well known components of the IFT B complex. In addition, peptides corresponding to mouse tetratricopeptide repeat proteins, TTC30A1, TTC30A2 and TTC30B were identified. The mouse Ttc30A1, Ttc30A2, Ttc30B genes are orthologs of Caenorhabditis elegans dyf-1, which is required for assembly of the distal segment of the cilia. We used co-immunoprecipitation studies to provide evidence that, TTC30A1, TTC30A2 or TTC30B can be incorporated into a complex with a known IFT B protein, IFT52. We also found that TTC30B can interact with mouse KIF17, a kinesin which participates in IFT. In vitro expression in a cell-free system followed by co-immunoprecipitation also provided evidence that TTC30B can directly interact with several different IFT B complex proteins. The findings support the view that mouse TTC30A1, TTC30A2 and TTC30B can contribute to the IFT B complex, likely through interactions with multiple IFT proteins and also suggest a possible link to the molecular motor, KIF17 to support transport of cargo during IFT. PMID:23810713

  4. Interaction of mouse TTC30/DYF-1 with multiple intraflagellar transport complex B proteins and KIF17

    PubMed Central

    Howard, Paul W.; Jue, Shall F.; Maurer, Richard A.

    2013-01-01

    Intraflagellar transport (IFT) is a microtubule based system that supports the assembly and maintenance of cilia. Genetic and biochemical studies have identified two distinct complexes containing multiple proteins that are part of the IFT machinery. In this study we prepared mouse pituitary cells that expressed an epitope-tagged IFT protein and immuno-purified the IFT B complex from these cells. Mass spectrometry analysis of the isolated complex led to identification of a number of well known components of the IFT B complex. In addition, peptides corresponding to mouse tetratricopeptide repeat proteins, TTC30A1, TTC30A2 and TTC30B were identified. The mouse Ttc30A1, Ttc30A2, Ttc30B genes are orthologs of Caenorhabditis elegans dyf-1, which is required for assembly of the distal segment of the cilia. We used co-immunoprecipitation studies to provide evidence that, TTC30A1, TTC30A2 or TTC30B can be incorporated into a complex with a known IFT B protein, IFT52. We also found that TTC30B can interact with mouse KIF17, a kinesin which participates in IFT. In vitro expression in a cell-free system followed by co-immunoprecipitation also provided evidence that TTC30B can directly interact with several different IFT B complex proteins. The findings support the view that mouse TTC30A1, TTC30A2 and TTC30B can contribute to the IFT B complex, likely through interactions with multiple IFT proteins and also suggest a possible link to the molecular motor, KIF17 to support transport of cargo during IFT. PMID:23810713

  5. Biochemical analysis of PIFTC3, the Trypanosoma brucei orthologue of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components.

    PubMed

    Franklin, Joseph B; Ullu, Elisabetta

    2010-10-01

    DYF-13, originally identified in Caenorhabditis elegans within a collection of dye-filling chemosensory mutants, is one of several proteins that have been classified as putatively involved in intraflagellar transport (IFT), the bidirectional movement of protein complexes along cilia and flagella and specifically in anterograde IFT. Although genetic studies have highlighted a fundamental role of DYF-13 in nematode sensory cilium and trypanosome flagellum biogenesis, biochemical studies on DYF-13 have lagged behind. Here, we show that in Trypanosoma brucei the orthologue to DYF-13, PIFTC3, participates in a macromolecular complex of approximately 660 kDa. Mass spectroscopy of affinity-purified PIFTC3 revealed several components of IFT complex B as well as orthologues of putative IFT factors DYF-1, DYF-3, DYF-11/Elipsa and IFTA-2. DYF-11 was further analysed and shown to be concentrated near the basal bodies and in the flagellum, and to be required for flagellum elongation. In addition, by coimmunoprecipitation we detected an interaction between DYF-13 and IFT122, a component of IFT complex A, which is required for retrograde transport. Thus, our biochemical analysis supports the model, proposed by genetic analysis in C. elegans, that the trypanosome orthologue of DYF-13 plays a central role in the IFT mechanism. PMID:20923419

  6. Overall Architecture of the Intraflagellar Transport (IFT)-B Complex Containing Cluap1/IFT38 as an Essential Component of the IFT-B Peripheral Subcomplex.

    PubMed

    Katoh, Yohei; Terada, Masaya; Nishijima, Yuya; Takei, Ryota; Nozaki, Shohei; Hamada, Hiroshi; Nakayama, Kazuhisa

    2016-05-20

    Intraflagellar transport (IFT) is essential for assembly and maintenance of cilia and flagella as well as ciliary motility and signaling. IFT is mediated by multisubunit complexes, including IFT-A, IFT-B, and the BBSome, in concert with kinesin and dynein motors. Under high salt conditions, purified IFT-B complex dissociates into a core subcomplex composed of at least nine subunits and at least five peripherally associated proteins. Using the visible immunoprecipitation assay, which we recently developed as a convenient protein-protein interaction assay, we determined the overall architecture of the IFT-B complex, which can be divided into core and peripheral subcomplexes composed of 10 and 6 subunits, respectively. In particular, we identified TTC26/IFT56 and Cluap1/IFT38, neither of which was included with certainty in previous models of the IFT-B complex, as integral components of the core and peripheral subcomplexes, respectively. Consistent with this, a ciliogenesis defect of Cluap1-deficient mouse embryonic fibroblasts was rescued by exogenous expression of wild-type Cluap1 but not by mutant Cluap1 lacking the binding ability to other IFT-B components. The detailed interaction map as well as comparison of subcellular localization of IFT-B components between wild-type and Cluap1-deficient cells provides insights into the functional relevance of the architecture of the IFT-B complex. PMID:26980730

  7. Crystal structures of IFT70/52 and IFT52/46 provide insight into intraflagellar transport B core complex assembly

    PubMed Central

    Taschner, Michael; Kotsis, Fruzsina; Braeuer, Philipp; Kuehn, E. Wolfgang

    2014-01-01

    Cilia are microtubule-based organelles that assemble via intraflagellar transport (IFT) and function as signaling hubs on eukaryotic cells. IFT relies on molecular motors and IFT complexes that mediate the contacts with ciliary cargo. To elucidate the architecture of the IFT-B complex, we reconstituted and purified the nonameric IFT-B core from Chlamydomonas reinhardtii and determined the crystal structures of C. reinhardtii IFT70/52 and Tetrahymena IFT52/46 subcomplexes. The 2.5-Å resolution IFT70/52 structure shows that IFT52330–370 is buried deeply within the IFT70 tetratricopeptide repeat superhelix. Furthermore, the polycystic kidney disease protein IFT88 binds IFT52281–329 in a complex that interacts directly with IFT70/IFT52330–381 in trans. The structure of IFT52C/IFT46C was solved at 2.3 Å resolution, and we show that it is essential for IFT-B core integrity by mediating interaction between IFT88/70/52/46 and IFT81/74/27/25/22 subcomplexes. Consistent with this, overexpression of mammalian IFT52C in MDCK cells is dominant-negative and causes IFT protein mislocalization and disrupted ciliogenesis. These data further rationalize several ciliogenesis phenotypes of IFT mutant strains. PMID:25349261

  8. Intraflagellar transport proteins 172, 80, 57, 54, 38, and 20 form a stable tubulin-binding IFT-B2 complex.

    PubMed

    Taschner, Michael; Weber, Kristina; Mourão, André; Vetter, Melanie; Awasthi, Mayanka; Stiegler, Marc; Bhogaraju, Sagar; Lorentzen, Esben

    2016-04-01

    Intraflagellar transport (IFT) relies on the IFT complex and is required for ciliogenesis. The IFT-B complex consists of 9-10 stably associated core subunits and six "peripheral" subunits that were shown to dissociate from the core structure at moderate salt concentration. We purified the six "peripheral"IFT-B subunits of Chlamydomonas reinhardtiias recombinant proteins and show that they form a stable complex independently of the IFT-B core. We suggest a nomenclature of IFT-B1 (core) and IFT-B2 (peripheral) for the two IFT-B subcomplexes. We demonstrate that IFT88, together with the N-terminal domain of IFT52, is necessary to bridge the interaction between IFT-B1 and B2. The crystal structure of IFT52N reveals highly conserved residues critical for IFT-B1/IFT-B2 complex formation. Furthermore, we show that of the three IFT-B2 subunits containing a calponin homology (CH) domain (IFT38, 54, and 57), only IFT54 binds αβ-tubulin as a potential IFT cargo, whereas the CH domains of IFT38 and IFT57 mediate the interaction with IFT80 and IFT172, respectively. Crystal structures of IFT54 CH domains reveal that tubulin binding is mediated by basic surface-exposed residues. PMID:26912722

  9. Defective ciliogenesis, embryonic lethality and severe impairment of the Sonic Hedgehog pathway caused by inactivation of the mouse complex A intraflagellar transport gene Ift122/Wdr10, partially overlapping with the DNA repair gene Med1/Mbd4

    PubMed Central

    Cortellino, Salvatore; Wang, Chengbing; Wang, Baolin; Bassi, Maria Rosaria; Caretti, Elena; Champeval, Delphine; Calmont, Amelie; Jarnik, Michal; Burch, John; Zaret, Kenneth; Larue, Lionel; Bellacosa, Alfonso

    2009-01-01

    Primary cilia are assembled and maintained by evolutionarily conserved intraflagellar transport (IFT) proteins that are involved in the coordinated movement of macromolecular cargo from the basal body to the cilium tip and back. The IFT machinery is organized in two structural complexes named complex A and complex B. Recently, inactivation in the mouse germline of Ift genes belonging to complex B revealed a requirement of ciliogenesis, or proteins involved in ciliogenesis, for Sonic Hedgehog (Shh) signaling in mammals. Here we report on a complex A mutant mouse, defective for the Ift122 gene. Ift122-null embryos show multiple developmental defects (exencephaly, situs viscerum inversus, delay in turning, hemorrhage and defects in limb development) that result in lethality. In the node, primary cilia were absent or malformed in homozygous mutant and heterozygous embryos, respectively. Impairment of the Shh pathway was apparent in both neural tube patterning (expansion of motoneurons and rostro-caudal level-dependent contraction or expansion of the dorso-lateral interneurons), and limb patterning (ectrosyndactyly). These phenotypes are distinct from both complex B IFT mutant embryos and embryos defective for the ciliary protein hennin/Arl13b, and suggest reduced levels of both Gli2/Gli3 activator and Gli3 repressor functions. We conclude that complex A and complex B factors play similar but distinct roles in ciliogenesis and Shh/Gli3 signaling. PMID:19000668

  10. Summary of Alpha Particle Transport

    SciTech Connect

    Medley, S.S.; White, R.B.; Zweben, S.J.

    1998-08-19

    This paper summarizes the talks on alpha particle transport which were presented at the 5th International Atomic Energy Agency's Technical Committee Meeting on "Alpha Particles in Fusion Research" held at the Joint European Torus, England in September 1997.

  11. Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

    PubMed

    Phirke, Prasad; Efimenko, Evgeni; Mohan, Swetha; Burghoorn, Jan; Crona, Filip; Bakhoum, Mathieu W; Trieb, Maria; Schuske, Kim; Jorgensen, Erik M; Piasecki, Brian P; Leroux, Michel R; Swoboda, Peter

    2011-09-01

    Cilia are ubiquitous cell surface projections that mediate various sensory- and motility-based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. To identify new components required for cilium biogenesis and function, we sought to further define and validate the transcriptional targets of DAF-19, the ciliogenic C. elegans RFX transcription factor. Transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using embryos staged to when the cell types developing cilia in the worm, the ciliated sensory neurons (CSNs), still differentiate. Comparisons between the two populations revealed 881 differentially regulated genes with greater than a 1.5-fold increase or decrease in expression. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional GFP fusions revealed CSN-specific expression patterns for 11 of 14 candidate genes. We show that two uncharacterized candidate genes, termed dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK7/CCRK/LF2p-related serine/threonine kinase that is necessary for the proper function of intraflagellar transport, a process critical for cilium biogenesis. Together, our microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover-in addition to DYF-17 and DYF-18-cellular components important for cilium formation and function. PMID:21740898

  12. Particle transport in plasma reactors

    SciTech Connect

    Rader, D.J.; Geller, A.S.; Choi, Seung J.; Kushner, M.J.

    1995-01-01

    SEMATECH and the Department of Energy have established a Contamination Free Manufacturing Research Center (CFMRC) located at Sandia National Laboratories. One of the programs underway at the CFMRC is directed towards defect reduction in semiconductor process reactors by the application of computational modeling. The goal is to use fluid, thermal, plasma, and particle transport models to identify process conditions and tool designs that reduce the deposition rate of particles on wafers. The program is directed toward defect reduction in specific manufacturing tools, although some model development is undertaken when needed. The need to produce quantifiable improvements in tool defect performance requires the close cooperation among Sandia, universities, SEMATECH, SEMATECH member companies, and equipment manufacturers. Currently, both plasma (e.g., etch, PECVD) and nonplasma tools (e.g., LPCVD, rinse tanks) are being worked on under this program. In this paper the authors summarize their recent efforts to reduce particle deposition on wafers during plasma-based semiconductor manufacturing.

  13. Transport of sputtered neutral particles

    SciTech Connect

    Parker, G.J.; Hitchon, W.N.G.; Koch, D.J. ||

    1995-04-01

    The initial deposition rate of sputtered material along the walls of a trench is calculated numerically. The numerical scheme is a nonstatistical description of long-mean-free-path transport in the gas phase. Gas-phase collisions are included by using a ``transition matrix`` to describe the particle motion, which in the present work is from the source through a cylindrical chamber and into a rectangular trench. The method is much faster and somewhat more accurate than Monte Carlo methods. Initial deposition rates of sputtered material along the walls of the trench are presented for various physical and geometrical situations, and the deposition rates are compared to other computational and experimental results.

  14. Ordered transport and identification of particles

    DOEpatents

    Shera, E. Brooks

    1993-01-01

    A method and apparatus are provided for application of electrical field gradients to induce particle velocities to enable particle sequence and identification information to be obtained. Particle sequence is maintained by providing electroosmotic flow for an electrolytic solution in a particle transport tube. The transport tube and electrolytic solution are selected to provide an electroosmotic radius of >100 so that a plug flow profile is obtained for the electrolytic solution in the transport tube. Thus, particles are maintained in the same order in which they are introduced in the transport tube. When the particles also have known electrophoretic velocities, the field gradients introduce an electrophoretic velocity component onto the electroosmotic velocity. The time that the particles pass selected locations along the transport tube may then be detected and the electrophoretic velocity component calculated for particle identification. One particular application is the ordered transport and identification of labeled nucleotides sequentially cleaved from a strand of DNA.

  15. Ordered transport and identification of particles

    DOEpatents

    Shera, E.B.

    1993-05-11

    A method and apparatus are provided for application of electrical field gradients to induce particle velocities to enable particle sequence and identification information to be obtained. Particle sequence is maintained by providing electroosmotic flow for an electrolytic solution in a particle transport tube. The transport tube and electrolytic solution are selected to provide an electroosmotic radius of >100 so that a plug flow profile is obtained for the electrolytic solution in the transport tube. Thus, particles are maintained in the same order in which they are introduced in the transport tube. When the particles also have known electrophoretic velocities, the field gradients introduce an electrophoretic velocity component onto the electroosmotic velocity. The time that the particles pass selected locations along the transport tube may then be detected and the electrophoretic velocity component calculated for particle identification. One particular application is the ordered transport and identification of labeled nucleotides sequentially cleaved from a strand of DNA.

  16. Quadrupole Induced Resonant Particle Transport

    NASA Astrophysics Data System (ADS)

    Gilson, Erik; Fajans, Joel

    1999-11-01

    We have performed experiments that explore the effects of a magnetic quadrupole field on a pure electron plasma confined in a Malmberg-Penning trap. A model that we have developed describes the shape of the plasma and shows that a certain class of resonant particles follows trajectories that take them out of the plasma. Even though the quadrupole field destroys the cylindrical symmetry of the system, our theory predicts that if the electrons are off resonance, then the lifetime of the plasma will not be greatly affected by the quadrupole field. Our preliminary experimental results show that the shape of the plasma and the plasma lifetime agree with our model. We are investigating the scaling of this behavior with various experimental parameters such as the plasma length, density, and strength of the quadrupole field. In addition to being an example of resonant particle transport, this effect may find practical applications in experiments that plan to use magnetic quadrupole neutral atom traps to confine anti-hydrogen created in double-well positron/anti-proton Malmberg-Penning traps. (ATHENA Collaboration.)

  17. Quadrupole Induced Resonant Particle Transport

    NASA Astrophysics Data System (ADS)

    Gilson, Erik; Fajans, Joel

    1998-11-01

    We have performed experiments that explore the effects of a magnetic quadrupole field on a pure electron plasma confined in a Penning-Malmberg trap. A model that we have developed describes the shape of the plasma and shows that a certain class of resonant particles follows trajectories that take them out of the plasma. Even though the quadrupole field destroys the cylindrical symmetry of the system, our theory predicts that if the electrons are off resonance, then the lifetime of the plasma will not be greatly affected by the quadrupole field. Our preliminary experimental results show that the shape of the plasma and the plasma lifetime agree with our model. We are investigating the scaling of this behavior with various experimental parameters such as the plasma length, density, and strength of the quadrupole field. In addition to being an example of resonant particle transport, this effect may find practical applications in experiments that plan to use magnetic quadrupole neutral atom traps to confine anti-hydrogen created in double-well positron/anti-proton Penning-Malmberg traps. (ATHENA Collaboration.)

  18. Particle transport induced by electrostatic wave fluctuations

    NASA Astrophysics Data System (ADS)

    Rosalem, K. C.; Roberto, M.; Caldas, I. L.

    2015-10-01

    Particle transport driven by electrostatic waves at the plasma edge is numerically investigated, for large aspect ratio tokamaks, by considering a kinetic model derived from guiding-center equations of motion. Initially, the transport is estimated for trajectories obtained from differential equations for a wave spectrum generated by a dominant spatial mode and three time modes. Then, in case of infinite time modes, the differential equations of motion are used to introduce a symplectic map that allows to analyze the particle transport. The particle transport barriers are observed for spatial localized dominant perturbation and infinite modes. In presence of infinite spatial modes, periodic islands arise in between chaotic trajectories at the plasma edge.

  19. Ratchet transport powered by chiral active particles

    NASA Astrophysics Data System (ADS)

    Ai, Bao-Quan

    2016-01-01

    We numerically investigate the ratchet transport of mixtures of active and passive particles in a transversal asymmetric channel. A big passive particle is immersed in a ‘sea’ of active particles. Due to the chirality of active particles, the longitudinal directed transport is induced by the transversal asymmetry. For the active particles, the chirality completely determines the direction of the ratchet transport, the counterclockwise and clockwise particles move to the opposite directions and can be separated. However, for the passive particle, the transport behavior becomes complicated, the direction is determined by competitions among the chirality, the self-propulsion speed, and the packing fraction. Interestingly, within certain parameters, the passive particle moves to the left, while active particles move to the right. In addition, there exist optimal parameters (the chirality, the height of the barrier, the self-propulsion speed and the packing fraction) at which the rectified efficiency takes its maximal value. Our findings could be used for the experimental pursuit of the ratchet transport powered by chiral active particles.

  20. Ratchet transport powered by chiral active particles.

    PubMed

    Ai, Bao-quan

    2016-01-01

    We numerically investigate the ratchet transport of mixtures of active and passive particles in a transversal asymmetric channel. A big passive particle is immersed in a 'sea' of active particles. Due to the chirality of active particles, the longitudinal directed transport is induced by the transversal asymmetry. For the active particles, the chirality completely determines the direction of the ratchet transport, the counterclockwise and clockwise particles move to the opposite directions and can be separated. However, for the passive particle, the transport behavior becomes complicated, the direction is determined by competitions among the chirality, the self-propulsion speed, and the packing fraction. Interestingly, within certain parameters, the passive particle moves to the left, while active particles move to the right. In addition, there exist optimal parameters (the chirality, the height of the barrier, the self-propulsion speed and the packing fraction) at which the rectified efficiency takes its maximal value. Our findings could be used for the experimental pursuit of the ratchet transport powered by chiral active particles. PMID:26795952

  1. Ratchet transport powered by chiral active particles

    PubMed Central

    Ai, Bao-quan

    2016-01-01

    We numerically investigate the ratchet transport of mixtures of active and passive particles in a transversal asymmetric channel. A big passive particle is immersed in a ‘sea’ of active particles. Due to the chirality of active particles, the longitudinal directed transport is induced by the transversal asymmetry. For the active particles, the chirality completely determines the direction of the ratchet transport, the counterclockwise and clockwise particles move to the opposite directions and can be separated. However, for the passive particle, the transport behavior becomes complicated, the direction is determined by competitions among the chirality, the self-propulsion speed, and the packing fraction. Interestingly, within certain parameters, the passive particle moves to the left, while active particles move to the right. In addition, there exist optimal parameters (the chirality, the height of the barrier, the self-propulsion speed and the packing fraction) at which the rectified efficiency takes its maximal value. Our findings could be used for the experimental pursuit of the ratchet transport powered by chiral active particles. PMID:26795952

  2. Lattice Boltzmann Simulations of Peristaltic Particle Transport

    NASA Astrophysics Data System (ADS)

    Connington, Kevin; Kang, Qinjun; Viswanathan, Hari; Chen, Shiyi; Abdel-Fattah, Amr

    2008-11-01

    A peristaltic flow occurs when a tube or channel with flexible walls transports the contained fluid by progressing a series of contraction or expansion waves along the length of those walls. It is a mechanism used to transport fluid and immersed solid particles when it is ineffective or impossible to impose a favorable pressure gradient or desirous to avoid contact between the transported mixture and mechanical moving parts. Peristaltic transport occurs in many physiological situations and has myriad industrial applications. We focus our study on the peristaltic transport of a macroscopic particle in a two dimensional channel using the Lattice Boltzmann Method (LBM). We systematically investigate the effect of variation of the relevant non-dimensional parameters of the system on the particle transport. We examine the particle behavior when the system exhibits the peculiar phenomenon of fluid ``trapping.'' Finally, we analyze how the particle presence affects stress, pressure, and dissipation in the fluid in hopes of determining preferred working conditions for peristaltic transport of shear-sensitive particles.

  3. Particle transport in planetary magnetospheres

    SciTech Connect

    Birmingham, T.J.

    1984-11-01

    Particle energization in Earth's and Jupiter's magnetospheres is discussed. Understanding of the large scale magnetic and electric fields in which charged particles move is reviewed. Orbit theory in the adiabatic approximation is sketched. General conditions for adiabatic breakdown at each of three levels of periodicity are presented. High energy losses and lower energy sources argue for the existence of magnetospheric accelerations. Nonadiabatic acceleration processes are mentioned. Slow diffusive energization by particle interactions with electromagnetic fluctuations is outlined. This mechanism seems adequate at Earth but, operating alone, is unconvincing for Jupiter. Adding spatial diffusion in the radially distended Jovian magnetodisk may resolve the difficulty. (ESA)

  4. Particle Transport in Parallel-Plate Reactors

    SciTech Connect

    Rader, D.J.; Geller, A.S.

    1999-08-01

    A major cause of semiconductor yield degradation is contaminant particles that deposit on wafers while they reside in processing tools during integrated circuit manufacturing. This report presents numerical models for assessing particle transport and deposition in a parallel-plate geometry characteristic of a wide range of single-wafer processing tools: uniform downward flow exiting a perforated-plate showerhead separated by a gap from a circular wafer resting on a parallel susceptor. Particles are assumed to originate either upstream of the showerhead or from a specified position between the plates. The physical mechanisms controlling particle deposition and transport (inertia, diffusion, fluid drag, and external forces) are reviewed, with an emphasis on conditions encountered in semiconductor process tools (i.e., sub-atmospheric pressures and submicron particles). Isothermal flow is assumed, although small temperature differences are allowed to drive particle thermophoresis. Numerical solutions of the flow field are presented which agree with an analytic, creeping-flow expression for Re < 4. Deposition is quantified by use of a particle collection efficiency, which is defined as the fraction of particles in the reactor that deposit on the wafer. Analytic expressions for collection efficiency are presented for the limiting case where external forces control deposition (i.e., neglecting particle diffusion and inertia). Deposition from simultaneous particle diffusion and external forces is analyzed by an Eulerian formulation; for creeping flow and particles released from a planar trap, the analysis yields an analytic, integral expression for particle deposition based on process and particle properties. Deposition from simultaneous particle inertia and external forces is analyzed by a Lagrangian formulation, which can describe inertia-enhanced deposition resulting from particle acceleration in the showerhead. An approximate analytic expression is derived for particle

  5. Magnetotail particle dynamics and transport

    NASA Technical Reports Server (NTRS)

    Speiser, Theodore W.

    1995-01-01

    The main thrust of our research is to study the consequences of particle dynamics in the current sheet region of the magnetotail. The importance of understanding particle dynamics, in and near current sheets, cannot be over estimated, especially in light of NASA's recent interest in developing global circulation models to predict space weather. We have embarked on a long-term study to investigate the electrical resistance due to chaotic behavior, compare this resistance to inertial effects, and relate it to that resistance required in MHD modeling for reconnection to proceed. Using a single-particle model and observations, we have also found that a neutral line region can be remotely sensed. We plan to evaluate other cases of satellite observations near times of substorm onset to elucidate the relationship between the temporal development of a near-Earth neutral line and onset.

  6. Magnetotail particle dynamics and transport

    NASA Astrophysics Data System (ADS)

    Speiser, Theodore W.

    1995-06-01

    The main thrust of our research is to study the consequences of particle dynamics in the current sheet region of the magnetotail. The importance of understanding particle dynamics, in and near current sheets, cannot be over estimated, especially in light of NASA's recent interest in developing global circulation models to predict space weather. We have embarked on a long-term study to investigate the electrical resistance due to chaotic behavior, compare this resistance to inertial effects, and relate it to that resistance required in MHD modeling for reconnection to proceed. Using a single-particle model and observations, we have also found that a neutral line region can be remotely sensed. We plan to evaluate other cases of satellite observations near times of substorm onset to elucidate the relationship between the temporal development of a near-Earth neutral line and onset.

  7. Particle transport in a moving corner

    NASA Astrophysics Data System (ADS)

    Laine-Pearson, F. E.; Hydon, P. E.

    2006-07-01

    This paper describes particle transport in Stokes flow in a two-dimensional corner whose walls oscillate, which is a simple model for particle transport in the pulmonary alveoli. Formally speaking, the wall motion produces a perturbation to the well-known Moffatt corner eddies. However, this ‘perturbation’ is dominant as the corner is approached. The motion of particles is regular near to the corner. Far from the corner, chaotic motion within the main part of the flow is restricted to very small regions. We deduce that there is competition between the far-field motion that generates eddies and the wall motion. The relative strengths of these two motions determines whether a given particle moves regularly or chaotically. Consequently, there is an intermediate region in which chaotic transport is maximized.

  8. Particle transport and deposition: basic physics of particle kinetics

    PubMed Central

    Tsuda, Akira; Henry, Frank S.; Butler, James P.

    2015-01-01

    The human body interacts with the environment in many different ways. The lungs interact with the external environment through breathing. The enormously large surface area of the lung with its extremely thin air-blood barrier is exposed to particles suspended in the inhaled air. Whereas the particle-lung interaction may cause deleterious effects on health if the inhaled pollutant aerosols are toxic, this interaction can be beneficial for disease treatment if the inhaled particles are therapeutic aerosolized drug. In either case, an accurate estimation of dose and sites of deposition in the respiratory tract is fundamental to understanding subsequent biological response, and the basic physics of particle motion and engineering knowledge needed to understand these subjects is the topic of this chapter. A large portion of this chapter deals with three fundamental areas necessary to the understanding of particle transport and deposition in the respiratory tract. These are: 1) the physical characteristics of particles, 2) particle behavior in gas flow, and 3) gas flow patterns in the respiratory tract. Other areas, such as particle transport in the developing lung and in the diseased lung are also considered. The chapter concludes with a summary and a brief discussion of areas of future research. PMID:24265235

  9. Turbulence driven particle transport in Texas Helimak

    SciTech Connect

    Toufen, D. L.; Guimaraes-Filho, Z. O.; Marcus, F. A.; Caldas, I. L.; Gentle, K. W.

    2012-01-15

    We analyze the turbulence driven particle transport in Texas Helimak [K. W. Gentle and H. He, Plasma Sci. Technol. 10, 284 (2008)], a toroidal plasma device with a one-dimensional equilibrium with magnetic curvature and shear. Alterations on the radial electric field, through an external voltage bias, change the spectral plasma characteristics inducing a dominant frequency for negative bias values and a broad band frequency spectrum for positive bias values. When applying a negative bias, the transport is high where the waves propagate with phase velocities near the plasma flow velocity, an indication that the transport is strongly affected by a wave particle resonant interaction. On the other hand, for positive bias values, the plasma has a reversed shear flow, and we observe that the transport is almost zero in the shearless radial region, an evidence of a transport barrier in this region.

  10. Kinetic transport simulation of energetic particles

    NASA Astrophysics Data System (ADS)

    Sheng, He; Waltz, R. E.

    2016-05-01

    A kinetic transport code (EPtran) is developed for the transport of the energetic particles (EPs). The EPtran code evolves the EP distribution function in radius, energy, and pitch angle phase space (r, E, λ) to steady state with classical slowing down, pitch angle scattering, as well as radial and energy transport of the injected EPs (neutral beam injection (NBI) or fusion alpha). The EPtran code is illustrated by treating the transport of NBI fast ions from high-n ITG/TEM micro-turbulence and EP driven unstable low-n Alfvén eigenmodes (AEs) in a well-studied DIII-D NBI heated discharge with significant AE central core loss. The kinetic transport code results for this discharge are compared with previous study using a simple EP density moment transport code ALPHA (R.E. Waltz and E.M. Bass 2014 Nucl. Fusion 54 104006). The dominant EP-AE transport is treated with a local stiff critical EP density (or equivalent pressure) gradient radial transport model modified to include energy-dependence and the nonlocal effects EP drift orbits. All previous EP transport models assume that the EP velocity space distribution function is not significantly distorted from the classical ‘no transport’ slowing down distribution. Important transport distortions away from the slowing down EP spectrum are illustrated by a focus on the coefficient of convection: EP energy flux divided by the product of EP average energy and EP particle flux.

  11. Transport of particles across continental shelves

    SciTech Connect

    Nittrouer, C.A. ); Wright, L.D. College of William and Mary, Gloucester Point, VA )

    1994-02-01

    Transport of particulate material across continental shelves is well demonstrated by the distributions on the seabed and in the water column of geological, chemical, or biological components, whose sources are found farther landward or farther seaward. This paper addresses passive (incapable of swimming) particles and their transport across (not necessarily off) continental shelves during high stands of sea level. Among the general factors that influence across-shelf transport are shelf geometry, latitudinal constraints, and the timescale of interest. Research studies have investigated the physical mechanisms of transport and have made quantitative estimates of mass flux across continental shelves. Important mechanisms include wind-driven flows, internal wave, wave-orbital flows, infragravity phenomena, buoyant plumes, and surf zone processes. Most particulate transport occurs in the portion of the water column closest to the seabed. Therefore physical processes are effective where and when they influence the bottom boundary layer, causing shear stresses sufficient to erode and transport particulate material. Biological and geological processes at the seabed play important roles within the boundary layer. The coupling of hydrodynamic forces from currents and surface gravity waves has a particularly strong influence on across-shelf transport; during storm events, the combined effect can transport particles tens of kilometers seaward. Several important mechanisms can cause bidirectional (seaward and landward) transport, and estimates of the net flux are difficult to obtain. Also, measurements of across-shelf transport are made difficult by the dominance of along-shelf transport. Geological parameters are often the best indicators of net across-shelf transport integrated over time scales longer than a month. For example, fluvially discharged particles with distinct composition commonly accumulate in the midshelf region. 47 refs., 16 figs.

  12. Deterministic particle transport in a ratchet flow

    NASA Astrophysics Data System (ADS)

    Beltrame, Philippe; Makhoul, Mounia; Joelson, Maminirina

    2016-01-01

    This study is motivated by the issue of the pumping of particle through a periodic modulated channel. We focus on a simplified deterministic model of small inertia particles within the Stokes flow framework that we call "ratchet flow." A path-following method is employed in the parameter space in order to retrace the scenario which from bounded periodic solutions leads to particle transport. Depending on whether the magnitude of the particle drag is moderate or large, two main transport mechanisms are identified in which the role of the parity symmetry of the flow differs. For large drag, transport is induced by flow asymmetry, while for moderate drag, since the full transport solution bifurcation structure already exists for symmetric settings, flow asymmetry only makes the transport effective. We analyzed the scenarios of current reversals for each mechanism as well as the role of synchronization. In particular we show that, for large drag, the particle drift is similar to phase slip in a synchronization problem.

  13. Aeolian particle flux profiles and transport unsteadiness

    NASA Astrophysics Data System (ADS)

    Bauer, Bernard O.; Davidson-Arnott, Robin G. D.

    2014-07-01

    Vertical profiles of aeolian sediment flux are commonly modeled as an exponential decay of particle (mass) transport with height above the surface. Data from field and wind-tunnel studies provide empirical support for this parameterization, although a large degree of variation in the precise shape of the vertical flux profile has been reported. This paper explores the potential influence of wind unsteadiness and time-varying intensity of transport on the geometry (slope, curvature) of aeolian particle flux profiles. Field evidence from a complex foredune environment demonstrates that (i) the time series of wind and sediment particle flux are often extremely variable with periods of intense transport (referred to herein as sediment "flurries") separated by periods of weak or no transport; (ii) sediment flurries contribute the majority of transport in a minority of the time; (iii) the structure of a flurry includes a "ramp-up" phase lasting a few seconds, a "core" phase lasting a few seconds to many tens of seconds, and a "ramp-down" phase lasting a few seconds during which the system relaxes to a background, low-intensity transport state; and (iv) conditional averaging of flux profiles for flurry and nonflurry periods reveals differences between the geometry of the mean profiles and hence the transport states that produce them. These results caution against the indiscriminate reliance on regression statistics derived from time-averaged sediment flux profiles, especially those with significant flurry and nonflurry periods, when calibrating or assessing the validity of steady state models of aeolian saltation.

  14. Modeling Particle Acceleration and Transport at CIRs

    NASA Astrophysics Data System (ADS)

    Li, G.; Zhao, L.; Ebert, R. W.; Desai, M. I.; Dayeh, M. A.; Mason, G. M.; Chen, Y.; Wu, Z.

    2014-12-01

    CIRs are a major site for particle acceleration during solar minimum. Earlier Ulysses observations have found that particles can be accelerated at both the forward and the reverse shocks that often form at a few AUs. The accelerated particles then propagate back to the Earth along Parker's field line. Theoretical calculations predicted a modulation of the spectrum at low energies, qualitatively agreed with obsevations at 1 AU. However, this picture was recently challenged by STEREO observations, where local accelerations near 1 AU were inferred in many events. In this work, we perform a detailed numerical calculation to study particle acceleration and transport in one CIR event which was observed by both ACE and STEREO spacecraft. We obtain particle currents at different heliocentric distances and different longitudes, as well as particle anisotropy. These values are compared with observations and the implication on the acceleration site and the interplanetary turbulence spectrum is discussed.

  15. Scalable Domain Decomposed Monte Carlo Particle Transport

    NASA Astrophysics Data System (ADS)

    O'Brien, Matthew Joseph

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation. The main algorithms we consider are: • Domain decomposition of constructive solid geometry: enables extremely large calculations in which the background geometry is too large to fit in the memory of a single computational node. • Load Balancing: keeps the workload per processor as even as possible so the calculation runs efficiently. • Global Particle Find: if particles are on the wrong processor, globally resolve their locations to the correct processor based on particle coordinate and background domain. • Visualizing constructive solid geometry, sourcing particles, deciding that particle streaming communication is completed and spatial redecomposition. These algorithms are some of the most important parallel algorithms required for domain decomposed Monte Carlo particle transport. We demonstrate that our previous algorithms were not scalable, prove that our new algorithms are scalable, and run some of the algorithms up to 2 million MPI processes on the Sequoia supercomputer.

  16. Axonal transport of ribonucleoprotein particles (vaults).

    PubMed

    Li, J Y; Volknandt, W; Dahlstrom, A; Herrmann, C; Blasi, J; Das, B; Zimmermann, H

    1999-01-01

    RNA was previously shown to be transported into both dendritic and axonal compartments of nerve cells, presumably involving a ribonucleoprotein particle. In order to reveal potential mechanisms of transport we investigated the axonal transport of the major vault protein of the electric ray Torpedo marmorata. This protein is the major protein component of a ribonucleoprotein particle (vault) carrying a non-translatable RNA and has a wide distribution in the animal kingdom. It is highly enriched in the cholinergic electromotor neurons and similar in size to synaptic vesicles. The axonal transport of vaults was investigated by immunofluorescence, using the anti-vault protein antibody as marker, and cytofluorimetric scanning, and was compared to that of the synaptic vesicle membrane protein SV2 and of the beta-subunit of the F1-ATPase as a marker for mitochondria. Following a crush significant axonal accumulation of SV2 proximal to the crush could first be observed after 1 h, that of mitochondria after 3 h and that of vaults after 6 h, although weekly fluorescent traces of accumulations of vault protein were observed in the confocal microscope as early as 3 h. Within the time-period investigated (up to 72 h) the accumulation of all markers increased continuously. Retrograde accumulations also occurred, and the immunofluorescence for the retrograde component, indicating recycling, was weaker than that for the anterograde component, suggesting that more than half of the vaults are degraded within the nerve terminal. High resolution immunofluorescence revealed a granular structure-in accordance with the biochemical characteristics of vaults. Of interest was the observation that the increase of vault immunoreactivity proximal to the crush accelerated with time after crushing, while that of SV2-containing particles appeared to decelerate, indicating that the crush procedure with time may have induced perikaryal alterations in the production and subsequent export to the axon

  17. FLUKA: A Multi-Particle Transport Code

    SciTech Connect

    Ferrari, A.; Sala, P.R.; Fasso, A.; Ranft, J.; /Siegen U.

    2005-12-14

    This report describes the 2005 version of the Fluka particle transport code. The first part introduces the basic notions, describes the modular structure of the system, and contains an installation and beginner's guide. The second part complements this initial information with details about the various components of Fluka and how to use them. It concludes with a detailed history and bibliography.

  18. PROJECT 4 -- TRANSPORT AND FATE PARTICLES

    EPA Science Inventory

    These experiments use size and surface-fixed charge defined ultrafine particulates to provide baseline information on the time course and extent of their systemic absorption. Understanding the nature of particle transport in blood will be important for recognizing the likeliho...

  19. Scalable Domain Decomposed Monte Carlo Particle Transport

    SciTech Connect

    O'Brien, Matthew Joseph

    2013-12-05

    In this dissertation, we present the parallel algorithms necessary to run domain decomposed Monte Carlo particle transport on large numbers of processors (millions of processors). Previous algorithms were not scalable, and the parallel overhead became more computationally costly than the numerical simulation.

  20. Particle simulation of transport in fusion devices

    SciTech Connect

    Procassini, R.J.; Birdsall, C.K.; Morse, E.C. . Electronics Research Lab.); Cohen, B.I. )

    1989-10-17

    Our research in the area of transport processes in fusion devices has recently been centered on the development of particle simulation models of transport in the scrape-off layer (SOL) of a diverted tokamak. As part of this research, we have been involved in the development of a suitable boundary condition for the plasma current at a floating plate that allows use of long time- and space-scale implicit simulation techniques. We have also been involved in a comparison of results from our particle-in-cell (PIC) code and a bounce-averaged Fokker-Planck (FP) code for the study of particle confinement in an auxiliary heated mirror plasma. 3 refs., 1 fig.

  1. Heavy particle transport in sputtering systems

    NASA Astrophysics Data System (ADS)

    Trieschmann, Jan

    2015-09-01

    This contribution aims to discuss the theoretical background of heavy particle transport in plasma sputtering systems such as direct current magnetron sputtering (dcMS), high power impulse magnetron sputtering (HiPIMS), or multi frequency capacitively coupled plasmas (MFCCP). Due to inherently low process pressures below one Pa only kinetic simulation models are suitable. In this work a model appropriate for the description of the transport of film forming particles sputtered of a target material has been devised within the frame of the OpenFOAM software (specifically dsmcFoam). The three dimensional model comprises of ejection of sputtered particles into the reactor chamber, their collisional transport through the volume, as well as deposition of the latter onto the surrounding surfaces (i.e. substrates, walls). An angular dependent Thompson energy distribution fitted to results from Monte-Carlo simulations is assumed initially. Binary collisions are treated via the M1 collision model, a modified variable hard sphere (VHS) model. The dynamics of sputtered and background gas species can be resolved self-consistently following the direct simulation Monte-Carlo (DSMC) approach or, whenever possible, simplified based on the test particle method (TPM) with the assumption of a constant, non-stationary background at a given temperature. At the example of an MFCCP research reactor the transport of sputtered aluminum is specifically discussed. For the peculiar configuration and under typical process conditions with argon as process gas the transport of aluminum sputtered of a circular target is shown to be governed by a one dimensional interaction of the imposed and backscattered particle fluxes. The results are analyzed and discussed on the basis of the obtained velocity distribution functions (VDF). This work is supported by the German Research Foundation (DFG) in the frame of the Collaborative Research Centre TRR 87.

  2. Particle Swarm Transport in Fracture Networks

    NASA Astrophysics Data System (ADS)

    Pyrak-Nolte, L. J.; Mackin, T.; Boomsma, E.

    2012-12-01

    Colloidal particles of many types occur in fractures in the subsurface as a result of both natural and industrial processes (e.g., environmental influences, synthetic nano- & micro-particles from consumer products, chemical and mechanical erosion of geologic material, proppants used in gas and oil extraction, etc.). The degree of localization and speed of transport of such particles depends on the transport mechanisms, the chemical and physical properties of the particles and the surrounding rock, and the flow path geometry through the fracture. In this study, we investigated the transport of particle swarms through artificial fracture networks. A synthetic fracture network was created using an Objet Eden 350V 3D printer to build a network of fractures. Each fracture in the network had a rectangular cross-sectional area with a constant depth of 7 mm but with widths that ranged from 2 mm to 11 mm. The overall dimensions of the network were 132 mm by 166 mm. The fracture network had 7 ports that were used either as the inlet or outlet for fluid flow through the sample or for introducing a particle swarm. Water flow rates through the fracture were controlled with a syringe pump, and ranged from zero flow to 6 ml/min. Swarms were composed of a dilute suspension (2% by mass) of 3 μm fluorescent polystyrene beads in water. Swarms with volumes of 5, 10, 20, 30 and 60 μl were used and delivered into the network using a second syringe pump. The swarm behavior was imaged using an optical fluorescent imaging system illuminated by green (525 nm) LED arrays and captured by a CCD camera. For fracture networks with quiescent fluids, particle swarms fell under gravity and remained localized within the network. Large swarms (30-60 μl) were observed to bifurcate at shallower depths resulting in a broader dispersal of the particles than for smaller swarm volumes. For all swarm volumes studied, particle swarms tended to bifurcate at the intersection between fractures. These

  3. Particle transport inferences from density sawteeth

    SciTech Connect

    Chen, J.; Li, Q.; Zhuang, G.; Liao, K.; Gentle, K. W.

    2014-05-15

    Sawtooth oscillations in tokamaks are defined by their effect on electron temperature: a rapid flattening of the core profile followed by an outward heat pulse and a slow core recovery caused by central heating. Recent high-resolution, multi-chord interferometer measurements on JTEXT extend these studies to particle transport. Sawteeth only partially flatten the core density profile, but enhanced particle diffusion on the time scale of the thermal crash occurs over much of the profile, relevant for impurities. Recovery between crashes implies an inward pinch velocity extending to the center.

  4. Solar energetic particle transport in the heliosphere

    NASA Astrophysics Data System (ADS)

    Pei, Chunsheng

    2007-08-01

    The transport of solar energetic particles (SEPs) in the inner heliosphere is a very important issue which can affect our daily life. For example, large SEP events can lead to the failure of power grids, interrupt communications, and may participate in global climate change. The SEPS also can harm humans in space and destroy the instruments on board spacecraft. Studying the transport of SEPs also helps us understand remote regions of space which are not visible to us because there are not enough photons in those places. The interplanetary magnetic field is the medium in which solar energetic particles travel. The Parker Model of the solar wind and its successor, the Weber and Davis model, have been the dominant models of the solar wind and the interplanetary magnetic field since 1960s. In this thesis, I have reviewed these models and applied an important correction to the Weber and Davis model Various solar wind models and their limitations are presented. Different models can affect the calculation of magnetic field direction at 1 AU by as much as about 30%. Analysis of the onset of SEP events could be used to infer the release time of solar energetic particles and to differentiate between models of particle acceleration near the Sun. It is demonstrated that because of the nature of the stochastic heliospheric magnetic field, the path length measured along the line of force can be shorter than that of the nominal Parker spiral. These results help to explain recent observations. A two dimensional model and a fully three dimensional numerical model for the transport of SEPs has been developed based on Parker's transport equation for the first time. ''Reservoir'' phenomenon, which means the inner heliosphere works like a reservoir for SEPs during large SEP events, and multi-spacecraft observation of peak intensities are explained by this numerical model.

  5. Gyrokinetic particle simulation of neoclassical transport

    SciTech Connect

    Lin, Z.; Tang, W.M.; Lee, W.W.

    1995-02-01

    A time varying weighting ({delta} f) scheme for gyrokinetic particle simulation is applied to a steady state, multi-species simulation of neoclassical transport. Accurate collision operators conserving momentum and energy are developed and implemented. Simulation results using these operators are found to agree very well with neoclassical theory. For example, it is dynamically demonstrated in these multispecies simulations that like-particle collisions produce no particle flux and that the neoclassical fluxes are ambipolar for an ion-electron plasma. An important physics feature of the present scheme is the introduction of toroidal sheared flow to the simulations. Simulation results are in agreement with the existing analytical neoclassical theory of Hinton and Wong. The poloidal electric field associated with toroidal mass flow is found to enhance density gradient driven electron particle flux and the bootstrap current while reducing temperature gradient driven flux and current. Finally, neoclassical theory in steep gradient profile relevant to the edge regime is examined by taking into account finite banana width effects. In general, the present work demonstrates a valuable new capability for studying important aspects of neoclassical transport inaccessible by conventional analytical calculation processes.

  6. Gyrokinetic particle simulation of neoclassical transport

    SciTech Connect

    Lin, Z.; Tang, W.M.; Lee, W.W.

    1995-08-01

    A time varying weighting ({delta}{ital f} ) scheme for gyrokinetic particle simulation is applied to a steady-state, multispecies simulation of neoclassical transport. Accurate collision operators conserving momentum and energy are developed and implemented. Simulation results using these operators are found to agree very well with neoclassical theory. For example, it is dynamically demonstrated that like-particle collisions produce no particle flux and that the neoclassical fluxes are ambipolar for an ion--electron plasma. An important physics feature of the present scheme is the introduction of toroidal flow to the simulations. Simulation results are in agreement with the existing analytical neoclassical theory. The poloidal electric field associated with toroidal mass flow is found to enhance density gradient-driven electron particle flux and the bootstrap current while reducing temperature gradient-driven flux and current. Finally, neoclassical theory in steep gradient profile relevant to the edge regime is examined by taking into account finite banana width effects. In general, in the present work a valuable new capability for studying important aspects of neoclassical transport inaccessible by conventional analytical calculation processes is demonstrated. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.

  7. Solar energetic particle anisotropies and insights into particle transport

    NASA Astrophysics Data System (ADS)

    Leske, R. A.; Cummings, A. C.; Cohen, C. M. S.; Mewaldt, R. A.; Labrador, A. W.; Stone, E. C.; Wiedenbeck, M. E.; Christian, E. R.; Rosenvinge, T. T. von

    2016-03-01

    As solar energetic particles (SEPs) travel through interplanetary space, their pitch-angle distributions are shaped by the competing effects of magnetic focusing and scattering. Measurements of SEP anisotropies can therefore reveal information about interplanetary conditions such as magnetic field strength, topology, and turbulence levels at remote locations from the observer. Onboard each of the two STEREO spacecraft, the Low Energy Telescope (LET) measures pitch-angle distributions for protons and heavier ions up to iron at energies of about 2-12 MeV/nucleon. Anisotropies observed using LET include bidirectional flows within interplanetary coronal mass ejections, sunward-flowing particles when STEREO was magnetically connected to the back side of a shock, and loss-cone distributions in which particles with large pitch angles underwent magnetic mirroring at an interplanetary field enhancement that was too weak to reflect particles with the smallest pitch angles. Unusual oscillations in the width of a beamed distribution at the onset of the 23 July 2012 SEP event were also observed and remain puzzling. We report LET anisotropy observations at both STEREO spacecraft and discuss their implications for SEP transport, focusing exclusively on the extreme event of 23 July 2012 in which a large variety of anisotropies were present at various times during the event.

  8. Particle Transport through Hydrogels Is Charge Asymmetric

    PubMed Central

    Zhang, Xiaolu; Hansing, Johann; Netz, Roland R.; DeRouchey, Jason E.

    2015-01-01

    Transport processes within biological polymer networks, including mucus and the extracellular matrix, play an important role in the human body, where they serve as a filter for the exchange of molecules and nanoparticles. Such polymer networks are complex and heterogeneous hydrogel environments that regulate diffusive processes through finely tuned particle-network interactions. In this work, we present experimental and theoretical studies to examine the role of electrostatics on the basic mechanisms governing the diffusion of charged probe molecules inside model polymer networks. Translational diffusion coefficients are determined by fluorescence correlation spectroscopy measurements for probe molecules in uncharged as well as cationic and anionic polymer solutions. We show that particle transport in the charged hydrogels is highly asymmetric, with diffusion slowed down much more by electrostatic attraction than by repulsion, and that the filtering capability of the gel is sensitive to the solution ionic strength. Brownian dynamics simulations of a simple model are used to examine key parameters, including interaction strength and interaction range within the model networks. Simulations, which are in quantitative agreement with our experiments, reveal the charge asymmetry to be due to the sticking of particles at the vertices of the oppositely charged polymer networks. PMID:25650921

  9. Transport of Particle Swarms Through Fractures

    NASA Astrophysics Data System (ADS)

    Boomsma, E.; Pyrak-Nolte, L. J.

    2011-12-01

    The transport of engineered micro- and nano-scale particles through fractured rock is often assumed to occur as dispersions or emulsions. Another potential transport mechanism is the release of particle swarms from natural or industrial processes where small liquid drops, containing thousands to millions of colloidal-size particles, are released over time from seepage or leaks. Swarms have higher velocities than any individual colloid because the interactions among the particles maintain the cohesiveness of the swarm as it falls under gravity. Thus particle swarms give rise to the possibility that engineered particles may be transported farther and faster in fractures than predicted by traditional dispersion models. In this study, the effect of fractures on colloidal swarm cohesiveness and evolution was studied as a swarm falls under gravity and interacts with fracture walls. Transparent acrylic was used to fabricate synthetic fracture samples with either (1) a uniform aperture or (2) a converging aperture followed by a uniform aperture (funnel-shaped). The samples consisted of two blocks that measured 100 x 100 x 50 mm. The separation between these blocks determined the aperture (0.5 mm to 50 mm). During experiments, a fracture was fully submerged in water and swarms were released into it. The swarms consisted of dilute suspensions of either 25 micron soda-lime glass beads (2% by mass) or 3 micron polystyrene fluorescent beads (1% by mass) with an initial volume of 5μL. The swarms were illuminated with a green (525 nm) LED array and imaged optically with a CCD camera. In the uniform aperture fracture, the speed of the swarm prior to bifurcation increased with aperture up to a maximum at a fracture width of approximately 10 mm. For apertures greater than ~15 mm, the velocity was essentially constant with fracture width (but less than at 10 mm). This peak suggests that two competing mechanisms affect swarm velocity in fractures. The wall provides both drag, which

  10. High Energy Particle Transport Code System.

    Energy Science and Technology Software Center (ESTSC)

    2003-12-17

    Version 00 NMTC/JAM is an upgraded version of the code CCC-694/NMTC-JAERI97, which was developed in 1982 at JAERI and is based on the CCC-161/NMTC code system. NMTC/JAM simulates high energy nuclear reactions and nuclear meson transport processes. The applicable energy range of NMTC/JAM was extended in principle up to 200 GeV for nucleons and mesons by introducing the high energy nuclear reaction code Jet-Aa Microscopic (JAM) for the intra-nuclear cascade part. For the evaporation andmore » fission process, a new model, GEM, can be used to describe the light nucleus production from the excited residual nucleus. According to the extension of the applicable energy, the nucleon-nucleus non-elastic, elastic and differential elastic cross section data were upgraded. In addition, the particle transport in a magnetic field was implemented for beam transport calculations. Some new tally functions were added, and the format of input and output of data is more user friendly. These new calculation functions and utilities provide a tool to carry out reliable neutronics study of a large scale target system with complex geometry more accurately and easily than with the previous model. It implements an intranuclear cascade model taking account of the in-medium nuclear effects and the preequilibrium calculation model based on the exciton one. For treating the nucleon transport process, the nucleon-nucleus cross sections are revised to those derived by the systematics of Pearlstein. Moreover, the level density parameter derived by Ignatyuk is included as a new option for particle evaporation calculation. A geometry package based on the Combinatorial Geometry with multi-array system and the importance sampling technique is implemented in the code. Tally function is also employed for obtaining such physical quantities as neutron energy spectra, heat deposition and nuclide yield without editing a history file. The code can simulate both the primary spallation reaction and the

  11. Particle transport due to magnetic fluctuations

    SciTech Connect

    Stoneking, M.R.; Hokin, S.A.; Prager, S.C.; Fiksel, G.; Ji, H.; Den Hartog, D.J.

    1994-01-01

    Electron current fluctuations are measured with an electrostatic energy analyzer at the edge of the MST reversed-field pinch plasma. The radial flux of fast electrons (E>T{sub e}) due to parallel streaming along a fluctuating magnetic field is determined locally by measuring the correlated product <{tilde J}{sub e}{tilde B}{sub r}>. Particle transport is small just inside the last closed flux surface ({Gamma}{sub e,mag} < 0.1 {Gamma}{sub e,total}), but can account for all observed particle losses inside r/a=0.8. Electron diffusion is found to increase with parallel velocity, as expected for diffusion in a region of field stochasticity.

  12. Nonambipolar transport by trapped particles in tokamaks.

    PubMed

    Park, Jong-Kyu; Boozer, Allen H; Menard, Jonathan E

    2009-02-13

    Small nonaxisymmetric perturbations of the magnetic field can greatly change the performance of tokamaks through nonambipolar transport. A number of theories have been developed, but the predictions were not consistent with experimental observations in tokamaks. This Letter provides a resolution, with a generalized analytic treatment of the nonambipolar transport. It is shown that the discrepancy between theory and experiment can be greatly reduced by two effects: (1) the small fraction of trapped particles for which the bounce and precession rates resonate; (2) the nonaxisymmetric variation in the field strength along the perturbed magnetic field lines rather than along the unperturbed magnetic field lines. The expected sensitivity of the International Thermonuclear Experimental Reactor to nonaxisymmetries is also discussed. PMID:19257595

  13. Experimental Test of Resonant Particle Transport Theory

    NASA Astrophysics Data System (ADS)

    Eggleston, D. L.

    1999-11-01

    It has long been suggested that the single-particle resonant transport theory developed for tandem mirrors might be able to explain asymmetry-induced transport in Malmberg-Penning traps.(C.F. Driscoll and J.H. Malmberg, Phys. Rev. Lett. 50), 167 (1983). We have recently adapted this theory to non-neutral plasmas(D.L. Eggleston and T.M. O'Neil, Phys. Plasmas 6), 2699 (1999). and are attempting an experimental test under the simplest possible conditions. The experiment(D.L. Eggleston, Phys. Plasmas 4), 1196 (1997). employs forty wall sectors in order to apply an asymmetry consisting of a single Fourier mode: φ1 =φ _nlωexp [ i( fracnπ Lz+lθ -ω t) ] . The electron density is kept low enough to avoid complications due to collective effects (shielding and waves) while the usual azimuthal E× B drift is maintained by a negatively biased central wire. We have confirmed the dominant role played by resonant particlesfootnote D.L. Eggleston, Bull. Am. Phys. Soc. 43, 1805 (1998). and here report on an absolute comparison between experimental and theoretical values for the radial particle flux. Interestingly, our initial results indicate that the experimental flux is forty times smaller than the theoretical value.

  14. PARTICLE TRANSPORT IN YOUNG PULSAR WIND NEBULAE

    SciTech Connect

    Tang Xiaping; Chevalier, Roger A. E-mail: rac5x@virginia.edu

    2012-06-20

    The model for pulsar wind nebulae (PWNe) as a result of the magnetohydrodynamic (MHD) downstream flow from a shocked, relativistic pulsar wind has been successful in reproducing many features of the nebulae observed close to central pulsars. However, observations of well-studied young nebulae like the Crab Nebula, 3C 58, and G21.5-0.9 do not show the toroidal magnetic field on a larger scale that might be expected in the MHD flow model; in addition, the radial variation of spectral index due to synchrotron losses is smoother than expected in the MHD flow model. We find that pure diffusion models can reproduce the basic data on nebular size and spectral index variation for the Crab, 3C 58, and G21.5-0.9. Most of our models use an energy-independent diffusion coefficient; power-law variations of the coefficient with energy are degenerate with variation in the input particle energy distribution index in the steady state, transmitting boundary case. Energy-dependent diffusion is a possible reason for the smaller diffusion coefficient inferred for the Crab. Monte Carlo simulations of the particle transport allowing for advection and diffusion of particles suggest that diffusion dominates over much of the total nebular volume of the Crab. Advection dominates close to the pulsar and is likely to play a role in the X-ray half-light radius. The source of diffusion and mixing of particles is uncertain, but may be related to the Rayleigh-Taylor instability at the outer boundary of a young PWN or to instabilities in the toroidal magnetic field structure.

  15. Modeling pollutant transport using a meshless-lagrangian particle model

    SciTech Connect

    Carrington, D. B.; Pepper, D. W.

    2002-01-01

    A combined meshless-Lagrangian particle transport model is used to predict pollutant transport over irregular terrain. The numerical model for initializing the velocity field is based on a meshless approach utilizing multiquadrics established by Kansa. The Lagrangian particle transport technique uses a random walk procedure to depict the advection and dispersion of pollutants over any type of surface, including street and city canyons

  16. Transport of airborne particles within a room.

    PubMed

    Richmond-Bryant, J; Eisner, A D; Brixey, L A; Wiener, R W

    2006-02-01

    The objective of this study is to test a technique used to analyze contaminant transport in the wake of a bluff body under controlled experimental conditions for application to aerosol transport in a complex furnished room. Specifically, the hypothesis tested by our work is that the dispersion of contaminants in a room is related to the turbulence kinetic energy and length scale. This turbulence is, in turn, determined by the size and shape of furnishings within the room and by the ventilation characteristics. This approach was tested for indoor dispersion through computational fluid dynamics simulations and laboratory experiments. In each, 3 mum aerosols were released in a furnished room with varied contaminant release locations (at the inlet vent or under a desk). The realizable k approximately epsilon model was employed in the simulations, followed by a Lagrangian particle trajectory simulation used as input for an in-house FORTRAN code to compute aerosol concentration. For the experiments, concentrations were measured simultaneously at seven locations by laser photometry, and air velocity was measured using laser Doppler velocimetry. The results suggest that turbulent diffusion is a significant factor in contaminant residence time in a furnished room. This procedure was then expanded to develop a simplified correlation between contaminant residence time and the number of enclosing surfaces around a point containing the contaminant. Practical Implications The work presented here provides a methodology for relating local aerosol residence time to properties of room ventilation and furniture arrangement. This technique may be used to assess probable locations of high concentration by knowing only the particle release location, furniture configuration, inlet and outlet locations, and air speeds, which are all observable features. Applications of this method include development of 'rules of thumb' for first responders entering a room where an agent has been released

  17. Peristaltic particle transport using the Lattice Boltzmann method

    SciTech Connect

    Connington, Kevin William; Kang, Qinjun; Viswanathan, Hari S; Abdel-fattah, Amr; Chen, Shiyi

    2009-01-01

    Peristaltic transport refers to a class of internal fluid flows where the periodic deformation of flexible containing walls elicits a non-negligible fluid motion. It is a mechanism used to transport fluid and immersed solid particles in a tube or channel when it is ineffective or impossible to impose a favorable pressure gradient or desirous to avoid contact between the transported mixture and mechanical moving parts. Peristaltic transport occurs in many physiological situations and has myriad industrial applications. We focus our study on the peristaltic transport of a macroscopic particle in a two-dimensional channel using the lattice Boltzmann method. We systematically investigate the effect of variation of the relevant dimensionless parameters of the system on the particle transport. We find, among other results, a case where an increase in Reynolds number can actually lead to a slight increase in particle transport, and a case where, as the wall deformation increases, the motion of the particle becomes non-negative only. We examine the particle behavior when the system exhibits the peculiar phenomenon of fluid trapping. Under these circumstances, the particle may itself become trapped where it is subsequently transported at the wave speed, which is the maximum possible transport in the absence of a favorable pressure gradient. Finally, we analyze how the particle presence affects stress, pressure, and dissipation in the fluid in hopes of determining preferred working conditions for peristaltic transport of shear-sensitive particles. We find that the levels of shear stress are most hazardous near the throat of the channel. We advise that shear-sensitive particles should be transported under conditions where trapping occurs as the particle is typically situated in a region of innocuous shear stress levels.

  18. The telegraph equation in charged particle transport

    NASA Technical Reports Server (NTRS)

    Gombosi, T. I.; Jokipii, J. R.; Kota, J.; Lorencz, K.; Williams, L. L.

    1993-01-01

    We present a new derivation of the telegraph equation which modifies its coefficients. First, an infinite order partial differential equation is obtained for the velocity space solid angle-averaged phase-space distribution of particles which underwent at least a few collisions. It is shown that, in the lowest order asymptotic expansion, this equation simplifies to the well-known diffusion equation. The second-order asymptotic expansion for isotropic small-angle scattering results in a modified telegraph equation with a signal propagation speed of v(5/11) exp 1/2 instead of the usual v/3 exp 1/2. Our derivation of a modified telegraph equation follows from an expansion of the Boltzmann equation in the relevant smallness parameters and not from a truncation of an eigenfunction expansion. This equation is consistent with causality. It is shown that, under steady state conditions in a convecting plasma, the telegraph equation may be regarded as a diffusion equation with a modified transport coefficient, which describes a combination of diffusion and cosmic-ray inertia.

  19. Transport of active ellipsoidal particles in ratchet potentials

    SciTech Connect

    Ai, Bao-Quan Wu, Jian-Chun

    2014-03-07

    Rectified transport of active ellipsoidal particles is numerically investigated in a two-dimensional asymmetric potential. The out-of-equilibrium condition for the active particle is an intrinsic property, which can break thermodynamical equilibrium and induce the directed transport. It is found that the perfect sphere particle can facilitate the rectification, while the needlelike particle destroys the directed transport. There exist optimized values of the parameters (the self-propelled velocity, the torque acting on the body) at which the average velocity takes its maximal value. For the ellipsoidal particle with not large asymmetric parameter, the average velocity decreases with increasing the rotational diffusion rate, while for the needlelike particle (very large asymmetric parameter), the average velocity is a peaked function of the rotational diffusion rate. By introducing a finite load, particles with different shapes (or different self-propelled velocities) will move to the opposite directions, which is able to separate particles of different shapes (or different self-propelled velocities)

  20. Entropic Ratchet transport of interacting active Brownian particles

    SciTech Connect

    Ai, Bao-Quan; He, Ya-Feng; Zhong, Wei-Rong

    2014-11-21

    Directed transport of interacting active (self-propelled) Brownian particles is numerically investigated in confined geometries (entropic barriers). The self-propelled velocity can break thermodynamical equilibrium and induce the directed transport. It is found that the interaction between active particles can greatly affect the ratchet transport. For attractive particles, on increasing the interaction strength, the average velocity first decreases to its minima, then increases, and finally decreases to zero. For repulsive particles, when the interaction is very weak, there exists a critical interaction at which the average velocity is minimal, nearly tends to zero, however, for the strong interaction, the average velocity is independent of the interaction.

  1. Transport of anisotropic chiral particles in a confined structure

    NASA Astrophysics Data System (ADS)

    Hu, Cai-tian; Ou, Ya-li; Wu, Jian-chun; Ai, Bao-quan

    2016-03-01

    Directed transport of anisotropic chiral particles is numerically investigated in the presence of the regular arrays of rigid half-circle obstacles. It is found that due to the rotational-translational coupling, the transport of anisotropic particles is considerably more complicated compared to the isotropic case. For isotropic chiral particles, the transport direction is completely determined by the chirality of particles. However, for anisotropic chiral particles, the competition between the chirality and the anisotropic degree determines the transport direction. For a given chirality, by suitably tailoring parameters (the anisotropic degree and the self-propulsion speed), particles with different anisotropic degrees (or self-propulsion speed) can move in different directions and can be separated.

  2. Transport and capture of colloidal particles in single fractures

    SciTech Connect

    Bonano, E.J.; Beyeler, W.E.

    1984-01-01

    In this study, the transport and capture rates of colloidal particles were calculated for a parallel-plate channel simulating a single fracture. The steady-state convective diffusion equation was solved with the particle velocity normal to the walls of the channel being the sum of the external forces acting on the particles. The forces considered were the gravitational, London-van der Waals and electric-double layer forces. The effects of parameters governing these forces and particle production mechanism on the rates of particle capture and transport are determined. The dynamic balance between particle production and capture has a significant effect on the concentration of particles leaving the fracture. The average particle velocity, though higher than the average fluid velocity, seems to be insensitive to phenomena governing particle capture. 8 references, 5 figures.

  3. Two Dimensional Particle Transport in the Cct Tokamak Edge Plasma

    NASA Astrophysics Data System (ADS)

    Tynan, George Robert

    The physics of particle transport in the CCT tokamak plasma edge is studied experimentally in this dissertation. A full poloidal array of Langmuir probes is used to measure the equilibrium plasma and transport properties of the CCT edge plasma during Ohmic and H-mode discharges. During Ohmic L-mode, the equilibrium plasma density and electron temperature are found to vary on a magnetic flux surface. The equilibrium plasma distribution coincides with the distribution of particle transport. Inside the last closed flux surface, convective processes dominate particle transport. Several large convective cells are observed near the limiter radius. At and beyond the limiter radius, turbulent transport is significant. The turbulence appears to be driven by the convective plasma flows. In Ohmic L-mode-like discharges, plasma transport occurs predominantly through the low-field region of the tokamak with local bad curvature. The convective cells are destroyed at the L-H transition and replaced with a more poloidally symmetric, radially narrow jet of plasma flow at the limiter radius. The jet effectively isolates the plasma core from the scrape -off layer. The turbulence associated with the convective cells is reduced across the edge region. Radial particle transport across the limiter radius is thus inhibited and the global particle confinement is increased. The available data suggest that the residual H-mode particle transport is more poloidally symmetric.

  4. The effects of realistic pancake solenoids on particle transport

    SciTech Connect

    Gu, X.; Okamura, M.; Pikin, A.; Fischer, W.; Luo, Y.

    2011-02-01

    Solenoids are widely used to transport or focus particle beams. Usually, they are assumed as being ideal solenoids with a high axial-symmetry magnetic field. Using the Vector Field Opera program, we modeled asymmetrical solenoids with realistic geometry defects, caused by finite conductor and current jumpers. Their multipole magnetic components were analyzed with the Fourier fit method; we present some possible optimized methods for them. We also discuss the effects of 'realistic' solenoids on low energy particle transport. The finding in this paper may be applicable to some lower energy particle transport system design.

  5. Transport of Energetic Particles by Microturbulence in Magnetized Plasmas

    SciTech Connect

    Zhang Wenlu; Lin Zhihong; Chen Liu

    2008-08-29

    Transport of energetic particles by the microturbulence in magnetized plasmas is studied in gyrokinetic simulations of the ion temperature gradient turbulence. The probability density function of the ion radial excursion is found to be very close to a Gaussian, indicating a diffusive transport process. The particle diffusivity can thus be calculated from a random walk model. The diffusivity is found to decrease drastically for high energy particles due to the averaging effects of the large gyroradius and orbit width, and the fast decorrelation of the energetic particles with the waves.

  6. Electrokinetic transport of heterogeneous particles in suspensions

    NASA Technical Reports Server (NTRS)

    Anderson, John L.

    1993-01-01

    The focus of research over the past nine months had been on a theory for the electrophoresis of slender particles and on trajectory analysis of colloidal doublets rotating in electric fields. Brief summaries of the research are given.

  7. Moisture Transport in Silica Gel Particle Beds: I. Theoretical Study

    SciTech Connect

    Pesaran, A. A.; Mills, A. F.

    1986-08-01

    Diffusion mechanisms of moisture within silica gel particles are investigated. It is found that for microporous silica gel surface diffusion is the dominant mechanism of moisture transport, while for macroporous silica gel both Knudsen and surface diffusion are important.

  8. Energetic particle transport and acceleration within the interplanetary medium

    NASA Astrophysics Data System (ADS)

    Dalla, Silvia

    2016-07-01

    The propagation through space of energetic particles accelerated at the Sun and in the inner heliosphere is governed by the characteristics of the interplanetary magnetic field. At large scales, the average Parker spiral configuration, on which transient magnetic structures may be superimposed, dominates the transport, while at smaller scales turbulence scatters the particles and produces field line meandering. This talk will review the classical 1D approach to interplanetary transport, mainly applied to Solar Energetic Particles (SEPs), as well as alternative models which allow for effects such as scattering perpendicular to the average magnetic field and field line meandering. The recently emphasized role of drifts in the propagation of SEPs will be discussed. The presentation will also review processes by which particle acceleration takes place within the interplanetary medium and the overall way in which acceleration and transport shape in-situ observations of energetic particles.

  9. Transport and harvesting of suspended particles using modulated ultrasound.

    PubMed

    Whitworth, G; Grundy, M A; Coakley, W T

    1991-11-01

    Polystyrene particles of 9 microns diameter were acoustically concentrated along the axis of a water-filled cylindrical waveguide containing a 3 MHz standing wave field. Modulation of the acoustic field enabled transport of the concentrated particles in the axial direction. Four modulations were investigated: 1, a fixed frequency difference introduced between two transducers; 2, ramping the transducer frequency; 3, tone burst, i.e. sound that is pulsed on and off, allowing intermittent sedimentation under gravity; and 4, switching the sound off to allow continuous sedimentation. The most efficient transport (leaving the fewest particles in suspension) of clumps to one end of the container was achieved with method 1 above. In this system the maximum speed of transport of the axial clumps was 24 mm s-1. A theory developed here for the transport of particles in a pseudo (i.e. slowly moving) standing wave field predicts an upper limit, which increases with particle size, for the speed of an entrained body. For a single 9 microns diameter particle in a field with a spatial peak pressure amplitude of 0.4 MPa this speed would be 0.5 mm s-1. The higher experimental speeds observed here emphasize the value of acoustically concentrating particles into relatively large clumps prior to initiating transport. PMID:1949343

  10. Scalings of energetic particle transport by ion temperature gradient microturbulence

    SciTech Connect

    Zhang Wenlu; Decyk, Viktor; Holod, Ihor; Xiao Yong; Lin Zhihong; Chen Liu

    2010-05-15

    Transport scaling of energetic particles by ion temperature gradient microturbulence in magnetized plasmas is studied in massively paralleled gyrokinetic particle-in-cell simulations. It is found that the diffusivity decreases drastically at high particles energy (E) to plasma temperature (T) ratio because of the averaging effects of the large gyroradius and drift-orbit width, and the fast wave-particle decorrelation. At high energy, the diffusivity follows a (E/T){sup -1} scaling for purely passing particles, a (E/T){sup -2} scaling for deeply trapped particles and a (E/T){sup -1} scaling for particles with an isotropic velocity distribution since the diffusivity therein is contributed mostly by the passing particles.

  11. Efficiency of a statistical transport model for turbulent particle dispersion

    NASA Astrophysics Data System (ADS)

    Litchford, Ron J.; Jeng, San-Mou

    1992-05-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains.

  12. Efficiency of a statistical transport model for turbulent particle dispersion

    SciTech Connect

    Litchford, R.J.; Jeng, San-Mou )

    1992-05-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains. 2 refs.

  13. Efficiency of a statistical transport model for turbulent particle dispersion

    NASA Technical Reports Server (NTRS)

    Litchford, Ron J.; Jeng, San-Mou

    1992-01-01

    In developing its theory for turbulent dispersion transport, the Litchford and Jeng (1991) statistical transport model for turbulent particle dispersion took a generalized approach in which the perturbing influence of each turbulent eddy on consequent interactions was transported through all subsequent eddies. Nevertheless, examinations of this transport relation shows it to be able to decay rapidly: this implies that additional computational efficiency may be obtained via truncation of unneccessary transport terms. Attention is here given to the criterion for truncation, as well as to expected efficiency gains.

  14. Fluid enhancement of particle transport in nanochannels

    NASA Astrophysics Data System (ADS)

    Li, Zhigang; Drazer, German

    2006-11-01

    We investigate the effect that fluid density has on the mobility of a spherical nanoparticle moving through a cylindrical nanochannel. The solid nanoparticle, the channel wall, and the fluid are described at the molecular level, and we use molecular dynamics simulations to study their behavior. We consider densities ranging from a few fluid molecules to a relatively dense fluid inside the channel. The inhomogeneous distribution of the fluid molecules inside the channel results in the competition of two effects as the fluid density is increased. The fluid molecules adsorb on the channel surface, and thus reduce the friction with the wall and enhance the mobility of the particle. On the other hand, the addition of fluid molecules increases the viscous drag on the particle and thus reduces its mobility. The outcome of these competing effects depends on the strength of the interaction between the atoms in the particle and those in the wall. We examine three different cases, i.e., intermediate, strong, and weak interaction energies. For an intermediate interaction, two distinct peaks are observed in the mobility of the particle as the first two adsorbed fluid layers form. On the other hand, a monotonously increasing mobility is found for a strong interaction energy, and a nearly constant mobility is observed for a weak interaction.

  15. Sandia Computational Engine for Particle Transport for Radiation Effects.

    Energy Science and Technology Software Center (ESTSC)

    2014-09-01

    Version 00 The SCEPTRE code solves the linear Boltzmann transport equation for one-, two- and three-dimensional geometries. SCEPTRE is capable of handling any particle type for which multigroup-Legendre cross sections are available. However, the code is designed primarily to model the transport of photons, electrons, and positrons through matter. For efficiency and flexibility, SCEPTRE contains capability for both the first- and second-order forms of the Boltzmann transport equation.

  16. Parameterization of Submesoscale Particle Transport in the Gulf of Mexico

    NASA Astrophysics Data System (ADS)

    Haza, A. C.; Ozgokmen, T. M.; Griffa, A.; Poje, A. C.; Hogan, P. J.; Jacobs, G. A.

    2014-12-01

    Submesoscale flows have a significant impact on the transport at their own scales, yet require extensive data sets and numerical computations, making them challenging to approach deterministically. A recent Lagrangian parametrization to correct particle transport at the submesoscales is implemented to an eddy permitting ocean model at 1/25 degree grid for the surface circulation of the Gulf of Mexico. It combines mesoscale transport from the deterministic Lagrangian Coherent Structures (LCS) and statistical Lagrangian subgridscale (LSGS) models over the submesoscale range. Comparison to a 1km submesoscale-permitting ocean model shows a significant improvement of the scale-dependent relative dispersion and particle distribution.

  17. Colloidal particle transport with simultaneous birth, growth, and capture

    SciTech Connect

    Bonano, E.J.; Beyeler, W.E.

    1985-01-01

    The simultaneous transport, birth, growth, and capture of colloidal particles suspended in a fluid within a parallel-plate channel was investigated. Growth and dispersion along the size axis were treated in the same fashion as convection and diffusion along a space coordinate axis. The capture and transport rates were given in terms of an average Sherwood number and average overall particle velocity relative to the fluid's velocity, respectively. The effects of changes in size dispersivity and fluid velocity on the capture and transport rates were significant. The opposite was the case for changes in the particle growth rate. Under all conditions considered here, the particle front had a higher average velocity than the fluid. 9 refs., 8 figs.

  18. Dissipative particle dynamics model for colloid transport in porous media

    SciTech Connect

    Pan, W.; Tartakovsky, A. M.

    2013-08-01

    We present that the transport of colloidal particles in porous media can be effectively modeled with a new formulation of dissipative particle dynamics, which augments standard DPD with non-central dissipative shear forces between particles while preserving angular momentum. Our previous studies have demonstrated that the new formulation is able to capture accurately the drag forces as well as the drag torques on colloidal particles that result from the hydrodynamic retardation effect. In the present work, we use the new formulation to study the contact efficiency in colloid filtration in saturated porous media. Note that the present model include all transport mechanisms simultaneously, including gravitational sedimentation, interception and Brownian diffusion. Our results of contact efficiency show a good agreement with the predictions of the correlation equation proposed by Tufenkji and EliMelech, which also incorporate all transport mechanisms simultaneously without the additivity assumption.

  19. Isotope effects on particle transport in the Compact Helical System

    NASA Astrophysics Data System (ADS)

    Tanaka, K.; Okamura, S.; Minami, T.; Ida, K.; Mikkelsen, D. R.; Osakabe, M.; Yoshimura, Y.; Isobe, M.; Morita, S.; Matsuoka, K.

    2016-05-01

    The hydrogen isotope effects of particle transport were studied in the hydrogen and deuterium dominant plasmas of the Compact Helical System (CHS). Longer decay time of electron density after the turning-off of the gas puffing was observed in the deuterium dominant plasma suggesting that the recycling was higher and/or the particle confinement was better in the deuterium dominant plasma. Density modulation experiments showed the quantitative difference of the particle transport coefficients. Density was scanned from 0.8  ×  1019 m-3 to 4  ×  1019 m-3 under the same magnetic field and almost the same heating power. In the low density regime (line averaged density  <  2.5  ×  1019 m-3), the lower particle diffusivity and the larger inwardly directed core convection velocity was observed in the deuterium dominant plasma, while in the high density regime (line averaged density  >2.5  ×  1019 m-3) no clear difference was observed. This result indicates that the isotope effects of particle transport exist only in the low density regime. Comparison with neoclassical transport coefficients showed that the difference of particle transport is likely to be due to the difference of turbulence driven anomalous transport. Linear character of the ion scale turbulence was studied. The smaller linear growth rate qualitatively agreed with the reduced particle transport in the deuterium dominant plasma of the low density regime.

  20. An Integrated Radiation Transport Particle-in-Cell Method

    NASA Astrophysics Data System (ADS)

    Lee, H. J.; Verboncoeur, J. P.; Smith, H. B.; Parker, G. J.; Birdsall, C. K.

    2000-10-01

    The study of radiation transport is important to understand the basic physics and to calculate the efficiency in a lamp discharge or laser induced plasma. Many models neglect radiation transport effects in evolving the steady state. In this study, we established a basic model to calculate radiation transport, including the effects of nonuniform ground state density and atomic collisions in one dimensional cylindrical and planar geometries. We coupled radiation transport with the self-consistent kinetic particle-in-cell codes, XPDP1 and XPDC1[1]. We treat electrons and ions with a particle-in-cell method, and the neutral ground and excited states with a fluid model to calculate radiation transport and atomic collisions. The steady state result of this model compares well with the solution of Holstein equation[2]. [1] J. P. Verboncoeur, M. V. Alves, V. Vahedi, and C. K. Birdsall, Journal of Computational Physics 104, 321 (1993). [2] T. Holstein, Phys. Rev. 72, 1213 (1947).

  1. Monte Carlo Particle Transport Capability for Inertial Confinement Fusion Applications

    SciTech Connect

    Brantley, P S; Stuart, L M

    2006-11-06

    A time-dependent massively-parallel Monte Carlo particle transport calculational module (ParticleMC) for inertial confinement fusion (ICF) applications is described. The ParticleMC package is designed with the long-term goal of transporting neutrons, charged particles, and gamma rays created during the simulation of ICF targets and surrounding materials, although currently the package treats neutrons and gamma rays. Neutrons created during thermonuclear burn provide a source of neutrons to the ParticleMC package. Other user-defined sources of particles are also available. The module is used within the context of a hydrodynamics client code, and the particle tracking is performed on the same computational mesh as used in the broader simulation. The module uses domain-decomposition and the MPI message passing interface to achieve parallel scaling for large numbers of computational cells. The Doppler effects of bulk hydrodynamic motion and the thermal effects due to the high temperatures encountered in ICF plasmas are directly included in the simulation. Numerical results for a three-dimensional benchmark test problem are presented in 3D XYZ geometry as a verification of the basic transport capability. In the full paper, additional numerical results including a prototype ICF simulation will be presented.

  2. Airflow and Particle Transport in the Human Respiratory System

    NASA Astrophysics Data System (ADS)

    Kleinstreuer, C.; Zhang, Z.

    2010-01-01

    Airflows in the nasal cavities and oral airways are rather complex, possibly featuring a transition to turbulent jet-like flow, recirculating flow, Dean's flow, vortical flows, large pressure drops, prevailing secondary flows, and merging streams in the case of exhalation. Such complex flows propagate subsequently into the tracheobronchial airways. The underlying assumptions for particle transport and deposition are that the aerosols are spherical, noninteracting, and monodisperse and deposit upon contact with the airway surface. Such dilute particle suspensions are typically modeled with the Euler-Lagrange approach for micron particles and in the Euler-Euler framework for nanoparticles. Micron particles deposit nonuniformly with very high concentrations at some local sites (e.g., carinal ridges of large bronchial airways). In contrast, nanomaterial almost coats the airway surfaces, which has implications of detrimental health effects in the case of inhaled toxic nanoparticles. Geometric airway features, as well as histories of airflow fields and particle distributions, may significantly affect particle deposition.

  3. Discrete elements method of neutral particle transport

    SciTech Connect

    Mathews, K.A.

    1983-01-01

    A new discrete elements (L/sub N/) transport method is derived and compared to the discrete ordinates S/sub N/ method, theoretically and by numerical experimentation. The discrete elements method is more accurate than discrete ordinates and strongly ameliorates ray effects for the practical problems studied. The discrete elements method is shown to be more cost effective, in terms of execution time with comparable storage to attain the same accuracy, for a one-dimensional test case using linear characteristic spatial quadrature. In a two-dimensional test case, a vacuum duct in a shield, L/sub N/ is more consistently convergent toward a Monte Carlo benchmark solution than S/sub N/, using step characteristic spatial quadrature. An analysis of the interaction of angular and spatial quadrature in xy-geometry indicates the desirability of using linear characteristic spatial quadrature with the L/sub N/ method.

  4. Particle transport in macropores of undisturbed soil columns

    NASA Astrophysics Data System (ADS)

    Jacobsen, O. H.; Moldrup, P.; Larsen, C.; Konnerup, L.; Petersen, L. W.

    1997-09-01

    Particle-facilitated transport may be an important process in the leaching of contaminants such as pesticides, phosphorus and heavy metals. In this work particle transport in macropores through intact soil columns was quantified. Irrigation intensities corresponding to naturally occurring storm events were used. Intact soil columns (18.3 cm inner diameter, 20 cm length) were sampled at two different depths (2-22 cm and 42-62 cm) from a structured sandy loam. Infiltration experiments, consisting of leaching of naturally occurring particles and infiltration with two types of colloidal suspensions were performed on each column. The active macroporosity was estimated in a dye experiment. A significant transport of particles (especially clay and silt) through macropores was observed at both depths. The total amount of mobilized particles at a certain amount of water outflow was found to be higher at depth 42-62 cm than at depth 2-22 cm, but unaffected by irrigation intensity. The particle size in the effluent was found to decrease over time during both the leaching of naturally occurring particles and during the subsequent leaching of colloids from the infiltration with colloidal suspensions, but seemed to stabilize at a particle size <10 μm. The decreasing particle size may be explained by differences in both the adsorption capacity and in the exposure to hydraulic forces of the different particle sizes and by mechanical entrapment of large particles in the macropores. No significant differences were found between the infiltration of the two different types of colloid suspension, probably due to their relatively small differences in zeta potential and particle size. The mass recovery of the infiltrated colloids was found to be significantly larger at depth 42-62 cm than at depth 2-22 cm, probably due to the larger size of the macropores at depth 42-62 cm. A simple advection-reaction model, which takes two different particle size fractions (< and >10 μm) into account

  5. Controlled particle transport in a plasma chamber with striped electrode

    SciTech Connect

    Jiang Ke; Li Yangfang; Shimizu, T.; Konopka, U.; Thomas, H. M.; Morfill, G. E.

    2009-12-15

    The controlled transport of micrometer size dust particles in a parallel-plate radio frequency discharge has been investigated. The lower stainless steel electrode consisted of 100 independently controllable electrical metal stripes. The voltage signals on these stripes were modulated, causing traveling plasma sheath distortions. Because the particles trapped in local potential wells moved according to the direction of the distortion, the transport velocity could be actively controlled by adjusting frequencies and phase shifts of the applied periodic voltage signals. To investigate the detailed principle of this transport, molecular dynamic simulations was performed to reproduce the observations with the plasma background conditions calculated by separated particle-in-cell simulations for the experimental parameters. The findings will help develop novel technologies for investigating large-scale complex plasma systems and techniques for achieving clean environments in plasma processing reactors.

  6. Incipient Motion and Particle Transport in Gravel - Streams

    NASA Astrophysics Data System (ADS)

    Matin, Habib

    The incipient motion of sediment particles in gravel-bed rivers is a very important process. It represents the difference between bed stability and bed mobility. A field study was conducted in Oak Creek, Oregon to investigate incipient motion of individual particles in gravel-bed streams. Investigation was also made of the incipient motion of individual gravel particles in the armor layer, using painted gravel placed on the bed of the stream and recovered after successive high flows. The effect of gravel particle shape was examined for a wide range of flow conditions to determine its significance on incipient motion. The result of analysis indicates a wide variation in particle shapes present. Incipient motion and general transport were found to be generally independent of particle shape regardless of particle sizes. A sample of bed material may contain a mixture of shapes such as well-rounded, oval, flat, disc-like, pencil-shaped, angular, and block-like. These are not likely to move in identical manners during transport nor to start motion at the same flow condition. This leads to questions about the role of shape in predicting incipient motion and equal mobility in gravel-bed streams. The study suggests that gravel particles initiate motion in a manner that is independent of particle shape. One explanation may be that for a natural bed surface many particles rest in orientations that give them the best protection against disturbance, probably a result of their coming to rest gradually during a period of decreasing flows, rather than being randomly dumped. But even when tracer particles were placed randomly in the bed surface there was no evident selectively for initiation of motion on the basis of particle shape. It can be concluded from analysis based on the methods of Parker et al. and Komar that there is room for both equal mobility and flow-competence evaluations. However, the equal mobility concept is best applied for conditions near incipient motion and

  7. Optimization of magnetic switches for single particle and cell transport

    NASA Astrophysics Data System (ADS)

    Abedini-Nassab, Roozbeh; Murdoch, David M.; Kim, CheolGi; Yellen, Benjamin B.

    2014-06-01

    The ability to manipulate an ensemble of single particles and cells is a key aim of lab-on-a-chip research; however, the control mechanisms must be optimized for minimal power consumption to enable future large-scale implementation. Recently, we demonstrated a matter transport platform, which uses overlaid patterns of magnetic films and metallic current lines to control magnetic particles and magnetic-nanoparticle-labeled cells; however, we have made no prior attempts to optimize the device geometry and power consumption. Here, we provide an optimization analysis of particle-switching devices based on stochastic variation in the particle's size and magnetic content. These results are immediately applicable to the design of robust, multiplexed platforms capable of transporting, sorting, and storing single cells in large arrays with low power and high efficiency.

  8. Optimization of magnetic switches for single particle and cell transport

    SciTech Connect

    Abedini-Nassab, Roozbeh; Yellen, Benjamin B.; Murdoch, David M.; Kim, CheolGi

    2014-06-28

    The ability to manipulate an ensemble of single particles and cells is a key aim of lab-on-a-chip research; however, the control mechanisms must be optimized for minimal power consumption to enable future large-scale implementation. Recently, we demonstrated a matter transport platform, which uses overlaid patterns of magnetic films and metallic current lines to control magnetic particles and magnetic-nanoparticle-labeled cells; however, we have made no prior attempts to optimize the device geometry and power consumption. Here, we provide an optimization analysis of particle-switching devices based on stochastic variation in the particle's size and magnetic content. These results are immediately applicable to the design of robust, multiplexed platforms capable of transporting, sorting, and storing single cells in large arrays with low power and high efficiency.

  9. Transport of Fusion Alpha Particles in ITER Scenarios

    NASA Astrophysics Data System (ADS)

    Bass, E. M.; Waltz, R. E.

    2014-10-01

    We predict the fusion-born alpha particle density in steady-state and hybrid (reverse shear) ITER scenarios with an integrated 1D transport model. The model combines ``stiff'' critical gradient alpha-driven Alfvén eigenmode (AE) transport with a quasilinear approximation of microturbulent transport. In an ITER baseline case, AE transport is found to redistribute alphas within the core but not propagate to the loss boundary. The remaining microturbulence at the edge causes negligible alpha-channel energy flux there (neglecting ripple loss). We set the AE stiff transport critical gradient threshold at gAE =gITG , below which microturbulence can nonlinearly suppress AE transport, and the more stringent condition gAE = 0 . Work supported in part by the US DOE under GA-Grant No. DE-FG02-95ER54309 and SciDAC-GSEP Grant No DE-FC02-08ER54977.

  10. Transport and diffusion of overdamped Brownian particles in random potentials

    NASA Astrophysics Data System (ADS)

    Simon, Marc Suñé; Sancho, J. M.; Lindenberg, Katja

    2013-12-01

    We present a numerical study of the anomalies in transport and diffusion of overdamped Brownian particles in totally disordered potential landscapes in one and in two dimensions. We characterize and analyze the effects of three different disordered potentials. The anomalous regimes are characterized by the time exponents that exhibit the statistical moments of the ensemble of particle trajectories. The anomaly in the transport is always of the subtransport type, but diffusion presents a greater variety of anomalies: Both subdiffusion and superdiffusion are possible. In two dimensions we present a mixed anomaly: subdiffusion in the direction perpendicular to the force and superdiffusion in the parallel direction.

  11. Particle Tracking Model and Abstraction of Transport Processes

    SciTech Connect

    B. Robinson

    2000-04-07

    The purpose of the transport methodology and component analysis is to provide the numerical methods for simulating radionuclide transport and model setup for transport in the unsaturated zone (UZ) site-scale model. The particle-tracking method of simulating radionuclide transport is incorporated into the FEHM computer code and the resulting changes in the FEHM code are to be submitted to the software configuration management system. This Analysis and Model Report (AMR) outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the unsaturated zone at Yucca Mountain. In addition, methods for determining colloid-facilitated transport parameters are outlined for use in the Total System Performance Assessment (TSPA) analyses. Concurrently, process-level flow model calculations are being carrier out in a PMR for the unsaturated zone. The computer code TOUGH2 is being used to generate three-dimensional, dual-permeability flow fields, that are supplied to the Performance Assessment group for subsequent transport simulations. These flow fields are converted to input files compatible with the FEHM code, which for this application simulates radionuclide transport using the particle-tracking algorithm outlined in this AMR. Therefore, this AMR establishes the numerical method and demonstrates the use of the model, but the specific breakthrough curves presented do not necessarily represent the behavior of the Yucca Mountain unsaturated zone.

  12. Recent advances in the Mercury Monte Carlo particle transport code

    SciTech Connect

    Brantley, P. S.; Dawson, S. A.; McKinley, M. S.; O'Brien, M. J.; Stevens, D. E.; Beck, B. R.; Jurgenson, E. D.; Ebbers, C. A.; Hall, J. M.

    2013-07-01

    We review recent physics and computational science advances in the Mercury Monte Carlo particle transport code under development at Lawrence Livermore National Laboratory. We describe recent efforts to enable a nuclear resonance fluorescence capability in the Mercury photon transport. We also describe recent work to implement a probability of extinction capability into Mercury. We review the results of current parallel scaling and threading efforts that enable the code to run on millions of MPI processes. (authors)

  13. Experimental investigation of suspended particles transport through porous media: particle and grain size effect.

    PubMed

    Liu, Quansheng; Cui, Xianze; Zhang, Chengyuan; Huang, Shibing

    2016-01-01

    Particle and grain size may influence the transportation and deposition characteristics of particles within pollutant transport and within granular filters that are typically used in wastewater treatment. We conducted two-dimensional sandbox experiments using quartz powder as the particles and quartz sand as the porous medium to study the response of transportation and deposition formation to changes in particle diameter (ds, with median diameter 18, 41, and 82 μm) and grain diameter (dp, with median diameter 0.36, 1.25, and 2.82 mm) considering a wide range of diameter ratios (ds/dp) from 0.0064 to 0.228. Particles were suspended in deionized water, and quartz sand was used as the porous medium, which was meticulously cleaned to minimize any physicochemical and impurities effects that could result in indeterminate results. After the experiments, the particle concentration of the effluent and particle mass per gram of dry sands were measured to explore changes in transportation and deposition characteristics under different conditions. In addition, a micro-analysis was conducted to better analyse the results on a mesoscopic scale. The experimental observation analyses indicate that different diameter ratios (ds/dp) may lead to different deposit formations. As ds/dp increased, the deposit formation changed from 'Random Deposition Type' to 'Gradient Deposition Type', and eventually became 'Inlet Deposition Type'. PMID:26323505

  14. Transport and diffusion of underdamped Brownian particles in random potentials

    NASA Astrophysics Data System (ADS)

    Suñé Simon, Marc; Sancho, J. M.; Lindenberg, Katja

    2014-09-01

    We present numerical results for the transport and diffusion of underdamped Brownian particles in one-dimensional disordered potentials. We compare the anomalies observed with those found in the overdamped regime and with results for a periodic potential. We relate these anomalies to the time dependent probability distributions for the position and velocity of the particles. The anomalies are caused by the random character of the barrier crossing events between locked and running states which is manifested in the spatial distributions. The role of the velocities is small because the particles quickly thermalize into locked or running states.

  15. 950809 Charged particle transport updated multi-group diffusion

    SciTech Connect

    Corman, E.G.; Perkins, S.T.; Dairiki, N.T.

    1995-09-01

    In 1974, a charged particle transport scheme was introduced which utilized a multi-group diffusion method for the spatial transport and slowing down of energetic ions in a hot plasma. In this treatment a diffusion coefficient was used which was flux-limited to provide, hopefully, some degree of accuracy when the slowing down of an energetic charged particle is dominated by Coulomb collisions with thermal ions and electrons in a plasma medium. An advantage of this method was a very fast, memory-contained program for calculating the behavior of energetic charged particles which resulted in smoothly varying particle number densities and energy depositions. The main limitation of the original multi-group charged particle diffusion scheme is its constraint to a basic ten group structure; the same ten group structure for each of the five energetic ions tracked. This is regarded as a severe limitation, inasmuch as more groups would be desired to simulate more accurately the corresponding Monte Carlo results of energies deposited over spatial zones from a charged particle source. More generally, it seems preferable to have a different group structure for each particle type since they are created at inherently different energies. In this paper, the basic theory and multi-group description will be given. This is followed by the specific techniques that were used to solve the resultant equations. Finally, the modifications that were made to the cross section data as well as the methods used for energy and momentum deposition are described.

  16. [alpha]-particle transport-driven current in tokamaks

    SciTech Connect

    Heikkinen, J.A. ); Sipilae, S.K. )

    1995-03-01

    It is shown that the radial transport of fusion-born energetic [alpha] particles, induced by electrostatic waves traveling in one poloidal direction, is directly connected to a net momentum of [alpha] particles in the toroidal direction in tokamaks. Because the momentum change is almost independent of toroidal velocity, the energy required for the momentum generation remains small on an [alpha]-particle population sustained by an isotropic time-independent source. By numerical toroidal Monte Carlo calculations it is shown that the current carried by [alpha] particles in the presence of intense well penetrated waves can reach several mega-amperes in reactor-sized tokamaks. The current obtained can greatly exceed the neoclassical bootstrap current of the [alpha] particles.

  17. Estimates of Lagrangian particle transport by wave groups: forward transport by Stokes drift and backward transport by the return flow

    NASA Astrophysics Data System (ADS)

    van den Bremer, Ton S.; Taylor, Paul H.

    2014-11-01

    Although the literature has examined Stokes drift, the net Lagrangian transport by particles due to of surface gravity waves, in great detail, the motion of fluid particles transported by surface gravity wave groups has received considerably less attention. In practice nevertheless, the wave field on the open sea often has a group-like structure. The motion of particles is different, as particles at sufficient depth are transported backwards by the Eulerian return current that was first described by Longuet-Higgins & Stewart (1962) and forms an inseparable counterpart of Stokes drift for wave groups ensuring the (irrotational) mass balance holds. We use WKB theory to study the variation of the Lagrangian transport by the return current with depth distinguishing two-dimensional seas, three-dimensional seas, infinite depth and finite depth. We then provide dimensional estimates of the net horizontal Lagrangian transport by the Stokes drift on the one hand and the return flow on the other hand for realistic sea states in all four cases. Finally we propose a simple scaling relationship for the transition depth: the depth above which Lagrangian particles are transported forwards by the Stokes drift and below which such particles are transported backwards by the return current.

  18. MATHEMATICAL ANALYSIS OF PARTICLE TRANSPORT AND DEPOSITION IN HUMAN LUNGS

    EPA Science Inventory

    MATHEMATICAL ANALYSIS OF PARTICLE TRANSPORT AND DEPOSITION IN HUMAN LUNGS. Jung-il Choi*, Center for Environmental Medicine, University of North Carolina, Chapel Hill, NC 27599; C. S. Kim, USEPA National Health and Environmental Effects Research Lab. RTP, NC 27711

    Partic...

  19. Probing cytoskeleton dynamics by intracellular particle transport analysis

    NASA Astrophysics Data System (ADS)

    Götz, M.; Hodeck, K. F.; Witzel, P.; Nandi, A.; Lindner, B.; Heinrich, D.

    2015-07-01

    All cellular functions arise from the transport of molecules through a heterogeneous, highly dynamic cell interior for intracellular signaling. Here, the impact of intracellular architecture and cytoskeleton dynamics on transport processes is revealed by high-resolution single particle tracking within living cells, in combination with time-resolved local mean squared displacement (I-MSD) analysis. We apply the I-MSD analysis to trajectories of 200 nm silica particles within living cells of Dictyostelium discoideum obtained by high resolution spinning disc confocal microscopy with a frame rate of 100 fps and imaging in one fixed focal plane. We investigate phases of motor-driven active transport and subdiffusion, normal diffusion, as well as superdiffusion with high spatial and temporal resolution. Active directed intracellular motion is attributed to microtubule associated molecular motor driven transport with average absolute velocities of 2.8 μm s-1 for 200 nm diameter particles. Diffusion processes of these particles within wild-type cells are found to exhibit diffusion constants ranging across two orders of magnitude from subdiffusive to superdiffusive behavior. This type of analysis might prove of ample importance for medical applications, like targeted drug treatment of cells by nano-sized carriers or innovative diagnostic assays.

  20. Linear kinetic theory and particle transport in stochastic mixtures

    SciTech Connect

    Pomraning, G.C.

    1995-12-31

    We consider the formulation of linear transport and kinetic theory describing energy and particle flow in a random mixture of two or more immiscible materials. Following an introduction, we summarize early and fundamental work in this area, and we conclude with a brief discussion of recent results.

  1. The Effect of Particle Density on Aeolian Transport

    NASA Technical Reports Server (NTRS)

    Williams, S. H.; Greeley, R.

    1985-01-01

    A set of experiments using a wide range of particle densities was performed in an open-circuit, terrestrial-atmospheric-pressure wind tunnel at Arizona State University. The results show that saltation flux equations derived for typical geologic material overpredict the flux of low-density particles. Walnut shells (approximately 1.1 g/cc) were used in the experiment and correspond to volcanic ash or ice. Less mass is transported by the wind in the case of low particle density because the style of transport is different. There is a direct, counter-intuitive relationship between particle density and transport height. Measurements of the vertical distribution of material show that the low-density walnut shells travel in a zone within 10 cm of the surface while high-density (approximately 4.5 g/cc) chromite particles travel as 50 cm. Furthermore, the overall saltation rate of the chromite is approximately four times greater than the walnut shells at the same freestream wind speed, even though the wind is much further above threshold for the walnut shells.

  2. Transport of biochar particles in saturated granular media: effects of pyrolysis temperature and particle size.

    PubMed

    Wang, Dengjun; Zhang, Wei; Hao, Xiuzhen; Zhou, Dongmei

    2013-01-15

    Land application of biochar is increasingly being considered for potential agronomic and environmental benefits, e.g., enhancing carbon sequestration, nutrient retention, water holding capacity, and crop productivity; and reducing greenhouse gas emissions and bioavailability of environmental contaminants. However, little is known about the transport of biochar particles in the aqueous environment, which represents a critical knowledge gap because biochar particles can facilitate the transport of adsorbed contaminants. In this study, column experiments were conducted to investigate biochar particle transport and retention in water-saturated quartz sand. Specific factors considered included biochar feedstocks (wheat straw and pine needle), pyrolysis temperature (350 and 550 °C), and particle size (micrometer-particle (MP) and nanoparticle (NP)). Greater mobility was observed for the biochars of lower pyrolysis temperatures and smaller particle sizes. Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) calculations that considered measured zeta potentials and Lewis acid-base interactions were used to better understand the influence of pyrolysis temperature on biochars particle transport. Most biochars exhibited attractive acid-base interactions that impeded their transport, whereas the biochar with the greatest mobility had repulsive acid-base interaction. Nonetheless, greater retention of the MPs than that of the NPs was in contrast with the XDLVO predictions. Straining and biochar surface charge heterogeneity were found to enhance the retention of biochar MPs, but played an insignificant role in the biochar NP retention. Experimental breakthrough curves and retention profiles were well-described using a two-site kinetic retention model that accounted for depth-dependent retention at one site. Modeled first-order retention coefficients on both sites 1 and 2 increased with increasing pyrolysis temperature and particle size. PMID:23249307

  3. Origin and transport of high energy particles in the galaxy

    NASA Technical Reports Server (NTRS)

    Wefel, John P.

    1987-01-01

    The origin, confinement, and transport of cosmic ray nuclei in the galaxy was studied. The work involves interpretations of the existing cosmic ray physics database derived from both balloon and satellite measurements, combined with an effort directed towards defining the next generation of instruments for the study of cosmic radiation. The shape and the energy dependence of the cosmic ray pathlength distribution in the galaxy was studied, demonstrating that the leaky box model is not a good representation of the detailed particle transport over the energy range covered by the database. Alternative confinement methods were investigated, analyzing the confinement lifetime in these models based upon the available data for radioactive secondary isotopes. The source abundances of several isotopes were studied using compiled nuclear physics data and the detailed transport calculations. The effects of distributed particle acceleration on the secondary to primary ratios were investigated.

  4. Experiments on Particle Sorting and Partial Bed-load Transport

    NASA Astrophysics Data System (ADS)

    Chen, D.; Sun, H.; Zhang, Y.; Chen, L.

    2014-12-01

    This study explore the complex dynamics of partial bed-load transport in a series of well-controlled laboratory experiments. Observations show that moving particles may experience bimodal transport (i.e., coexistence of long trapping time and large jump length) related to bed coarsening and the formation of clusters on a heterogeneous gravel-bed, which is distinguished from the traditional theory of hiding-exposing interactions among mixed-size particles. A fractional derivative model is finally applied to characterize the overall behavior of partial bed-load transport, including the coexistence of the sub-diffusion and non-local feature caused by turbulence and the micro-relief within an armor layer.

  5. Applying dispersive changes to Lagrangian particles in groundwater transport models

    USGS Publications Warehouse

    Konikow, Leonard F.

    2010-01-01

    Method-of-characteristics groundwater transport models require that changes in concentrations computed within an Eulerian framework to account for dispersion be transferred to moving particles used to simulate advective transport. A new algorithm was developed to accomplish this transfer between nodal values and advecting particles more precisely and realistically compared to currently used methods. The new method scales the changes and adjustments of particle concentrations relative to limiting bounds of concentration values determined from the population of adjacent nodal values. The method precludes unrealistic undershoot or overshoot for concentrations of individual particles. In the new method, if dispersion causes cell concentrations to decrease during a time step, those particles in the cell having the highest concentration will decrease the most, and those with the lowest concentration will decrease the least. The converse is true if dispersion is causing concentrations to increase. Furthermore, if the initial concentration on a particle is outside the range of the adjacent nodal values, it will automatically be adjusted in the direction of the acceptable range of values. The new method is inherently mass conservative.

  6. Applying Dispersive Changes to Lagrangian Particles in Groundwater Transport Models

    USGS Publications Warehouse

    Konikow, L.F.

    2010-01-01

    Method-of-characteristics groundwater transport models require that changes in concentrations computed within an Eulerian framework to account for dispersion be transferred to moving particles used to simulate advective transport. A new algorithm was developed to accomplish this transfer between nodal values and advecting particles more precisely and realistically compared to currently used methods. The new method scales the changes and adjustments of particle concentrations relative to limiting bounds of concentration values determined from the population of adjacent nodal values. The method precludes unrealistic undershoot or overshoot for concentrations of individual particles. In the new method, if dispersion causes cell concentrations to decrease during a time step, those particles in the cell having the highest concentration will decrease the most, and those with the lowest concentration will decrease the least. The converse is true if dispersion is causing concentrations to increase. Furthermore, if the initial concentration on a particle is outside the range of the adjacent nodal values, it will automatically be adjusted in the direction of the acceptable range of values. The new method is inherently mass conservative. ?? US Government 2010.

  7. Measurements of Bed Load Particle Diffusion at Low Transport Rates

    NASA Astrophysics Data System (ADS)

    Ball, A. E.; Furbish, D. J.; Schmeeckle, M. W.

    2012-12-01

    High-speed imaging of coarse sand particles transported as bed load reveals how particle motions possess intrinsic periodicities associated with their start-and-stop behavior. The dominant harmonics in these motions have a primary influence on the rate at which the mean squared particle displacement R(τ) increases with the time interval τ. The mean squared displacement R(τ) is conventionally used to assess the possibility of anomalous diffusion, and over a timescale corresponding to the typical travel time of particles, calculations of R(τ) may ostensibly indicate non-Fickian behavior while actually reflecting the effects of periodicities in particle motions, not anomalous diffusion. We provide the theoretical basis for this observed behavior, and we illustrate how the effective (Fickian) particle diffusivity obtains from G. I. Taylor's classic definition involving the particle velocity autocovariance, including its relation to the ensemble-averaged particle velocity as articulated by O. M. Phillips. Cross-stream diffusivities are an order of magnitude smaller than streamwise diffusivities.

  8. Modeling reactive transport with particle tracking and kernel estimators

    NASA Astrophysics Data System (ADS)

    Rahbaralam, Maryam; Fernandez-Garcia, Daniel; Sanchez-Vila, Xavier

    2015-04-01

    Groundwater reactive transport models are useful to assess and quantify the fate and transport of contaminants in subsurface media and are an essential tool for the analysis of coupled physical, chemical, and biological processes in Earth Systems. Particle Tracking Method (PTM) provides a computationally efficient and adaptable approach to solve the solute transport partial differential equation. On a molecular level, chemical reactions are the result of collisions, combinations, and/or decay of different species. For a well-mixed system, the chem- ical reactions are controlled by the classical thermodynamic rate coefficient. Each of these actions occurs with some probability that is a function of solute concentrations. PTM is based on considering that each particle actually represents a group of molecules. To properly simulate this system, an infinite number of particles is required, which is computationally unfeasible. On the other hand, a finite number of particles lead to a poor-mixed system which is limited by diffusion. Recent works have used this effect to actually model incomplete mix- ing in naturally occurring porous media. In this work, we demonstrate that this effect in most cases should be attributed to a defficient estimation of the concentrations and not to the occurrence of true incomplete mixing processes in porous media. To illustrate this, we show that a Kernel Density Estimation (KDE) of the concentrations can approach the well-mixed solution with a limited number of particles. KDEs provide weighting functions of each particle mass that expands its region of influence, hence providing a wider region for chemical reactions with time. Simulation results show that KDEs are powerful tools to improve state-of-the-art simulations of chemical reactions and indicates that incomplete mixing in diluted systems should be modeled based on alternative conceptual models and not on a limited number of particles.

  9. Transport of particle-laden viscoelastic suspensions: tuning particle behavior with elasticity and geometry

    NASA Astrophysics Data System (ADS)

    Barbati, Alexander; Robisson, Agathe; Dussan, Elizabeth; McKinley, Gareth

    2015-11-01

    The transport of particle-laden viscoelastic suspensions is routine in several industrial and natural systems. Many applications, such as hydraulic fracturing in the oilfield, require the successive (and occasionally simultaneous) flow and placement or rigid particles, commonly known as proppant. Hydraulically-generated fractures are routinely less than 6 particle diameters in width. We investigate the flow of viscoelastic particle-laden suspensions in microfabricated geometries mimicking hydraulically-generated fractures under a variety of dynamic conditions to illustrate the interaction between inertia, elasticity, and geometry on particle behavior during flow. We characterize the flow in these model geometries with a combination of streakline imaging, particle image velocimetry, and direct imaging of model proppant particles embedded in the flow. We accompany these small-scale measurements with macro-scale interrogation of fluid rheology by measuring material functions of the working fluid in under shear and extension. These material functions are used in concert with imposed flow conditions and imaging results to identify dominant transport mechanisms on the channel and particle scale, which indicate overall system behavior.

  10. Transport of sputtered particles in capacitive sputter sources

    NASA Astrophysics Data System (ADS)

    Trieschmann, Jan; Mussenbrock, Thomas

    2015-07-01

    The transport of sputtered aluminum inside a multi frequency capacitively coupled plasma chamber is simulated by means of a kinetic test multi-particle approach. A novel consistent set of scattering parameters obtained for a modified variable hard sphere collision model is presented for both argon and aluminum. An angular dependent Thompson energy distribution is fitted to results from Monte Carlo simulations and used for the kinetic simulation of the transport of sputtered aluminum. For the proposed configuration, the transport of sputtered particles is characterized under typical process conditions at a gas pressure of p = 0.5 Pa. It is found that—due to the peculiar geometric conditions—the transport can be understood in a one dimensional picture, governed by the interaction of the imposed and backscattered particle fluxes. It is shown that the precise geometric features play an important role only in proximity to the electrode edges, where the effect of backscattering from the outside chamber volume becomes the governing mechanism.

  11. Full f gyrokinetic method for particle simulation of tokamak transport

    SciTech Connect

    Heikkinen, J.A. Janhunen, S.J.; Kiviniemi, T.P.; Ogando, F.

    2008-05-10

    A gyrokinetic particle-in-cell approach with direct implicit construction of the coefficient matrix of the Poisson equation from ion polarization and electron parallel nonlinearity is described and applied in global electrostatic toroidal plasma transport simulations. The method is applicable for calculation of the evolution of particle distribution function f including as special cases strong plasma pressure profile evolution by transport and formation of neoclassical flows. This is made feasible by full f formulation and by recording the charge density changes due to the ion polarization drift and electron acceleration along the local magnetic field while particles are advanced. The code has been validated against the linear predictions of the unstable ion temperature gradient mode growth rates and frequencies. Convergence and saturation in both turbulent and neoclassical limit of the ion heat conductivity is obtained with numerical noise well suppressed by a sufficiently large number of simulation particles. A first global full f validation of the neoclassical radial electric field in the presence of turbulence for a heated collisional tokamak plasma is obtained. At high Mach number (M{sub p}{approx}1) of the poloidal flow, the radial electric field is significantly enhanced over the standard neoclassical prediction. The neoclassical radial electric field together with the related GAM oscillations is found to regulate the turbulent heat and particle diffusion levels particularly strongly in a large aspect ratio tokamak at low plasma current.

  12. Quantum interference effects in particle transport through square lattices.

    PubMed

    Cuansing, E; Nakanishi, H

    2004-12-01

    We study the transport of a quantum particle through square lattices of various sizes by employing the tight-binding Hamiltonian from quantum percolation. Input and output semi-infinite chains are attached to the lattice either by diagonal point-to-point contacts or by a busbar connection. We find resonant transmission and reflection occurring whenever the incident particle's energy is near an eigenvalue of the lattice alone (i.e., the lattice without the chains attached). We also find the transmission to be strongly dependent on the way the chains are attached to the lattice. PMID:15697469

  13. Particle acceleration, transport and turbulence in cosmic and heliospheric physics

    NASA Technical Reports Server (NTRS)

    Matthaeus, W.

    1992-01-01

    In this progress report, the long term goals, recent scientific progress, and organizational activities are described. The scientific focus of this annual report is in three areas: first, the physics of particle acceleration and transport, including heliospheric modulation and transport, shock acceleration and galactic propagation and reacceleration of cosmic rays; second, the development of theories of the interaction of turbulence and large scale plasma and magnetic field structures, as in winds and shocks; third, the elucidation of the nature of magnetohydrodynamic turbulence processes and the role such turbulence processes might play in heliospheric, galactic, cosmic ray physics, and other space physics applications.

  14. Dust particle diffusion in ion beam transport region.

    PubMed

    Miyamoto, N; Okajima, Y; Romero, C F; Kuwata, Y; Kasuya, T; Wada, M

    2016-02-01

    Dust particles of μm size produced by a monoplasmatron ion source are observed by a laser light scattering. The scattered light signal from an incident laser at 532 nm wavelength indicates when and where a particle passes through the ion beam transport region. As the result, dusts with the size more than 10 μm are found to be distributed in the center of the ion beam, while dusts with the size less than 10 μm size are distributed along the edge of the ion beam. Floating potential and electron temperature at beam transport region are measured by an electrostatic probe. This observation can be explained by a charge up model of the dust in the plasma boundary region. PMID:26932116

  15. Dust particle diffusion in ion beam transport region

    NASA Astrophysics Data System (ADS)

    Miyamoto, N.; Okajima, Y.; Romero, C. F.; Kuwata, Y.; Kasuya, T.; Wada, M.

    2016-02-01

    Dust particles of μm size produced by a monoplasmatron ion source are observed by a laser light scattering. The scattered light signal from an incident laser at 532 nm wavelength indicates when and where a particle passes through the ion beam transport region. As the result, dusts with the size more than 10 μm are found to be distributed in the center of the ion beam, while dusts with the size less than 10 μm size are distributed along the edge of the ion beam. Floating potential and electron temperature at beam transport region are measured by an electrostatic probe. This observation can be explained by a charge up model of the dust in the plasma boundary region.

  16. Code System to Calculate Particle Penetration Through Aerosol Transport Lines.

    Energy Science and Technology Software Center (ESTSC)

    1999-07-14

    Version 00 Distribution is restricted to US Government Agencies and Their Contractors Only. DEPOSITION1.03 is an interactive software program which was developed for the design and analysis of aerosol transport lines. Models are presented for calculating aerosol particle penetration through straight tubes of arbitrary orientation, inlets, and elbows. An expression to calculate effective depositional velocities of particles on tube walls is derived. The concept of maximum penetration is introduced, which is the maximum possible penetrationmore » through a sampling line connecting any two points in a three-dimensional space. A procedure to predict optimum tube diameter for an existing transport line is developed. Note that there is a discrepancy in this package which includes the DEPOSITION 1.03 executable and the DEPOSITION 2.0 report. RSICC was unable to obtain other executables or reports.« less

  17. Gyrokinetics Simulation of Energetic Particle Turbulence and Transport

    SciTech Connect

    Diamond, Patrick H.

    2011-09-21

    Progress in research during this year elucidated the physics of precession resonance and its interaction with radial scattering to form phase space density granulations. Momentum theorems for drift wave-zonal flow systems involving precession resonance were derived. These are directly generalizable to energetic particle modes. A novel nonlinear, subcritical growth mechanism was identified, which has now been verified by simulation. These results strengthen the foundation of our understanding of transport in burning plasmas

  18. Chemically generated convective transport of micron sized particles

    NASA Astrophysics Data System (ADS)

    Shklyaev, Oleg; Das, Sambeeta; Altemose, Alicia; Shum, Henry; Balazs, Anna; Sen, Ayusman

    2015-11-01

    A variety of chemical and biological applications require manipulation of micron sized objects like cells, viruses, and large molecules. Increasing the size of particles up to a micron reduces performance of techniques based on diffusive transport. Directional transport of cargo toward detecting elements reduces the delivery time and improves performance of sensing devices. We demonstrate how chemical reactions can be used to organize fluid flows carrying particles toward the assigned destinations. Convection is driven by density variations caused by a chemical reaction occurring at a catalyst or enzyme-covered target site. If the reaction causes a reduction in fluid density, as in the case of catalytic decomposition of hydrogen peroxide, then fluid and suspended cargo is drawn toward the target along the bottom surface. The intensity of the fluid flow and the time of cargo delivery are controlled by the amount of reagent in the system. After the reagent has been consumed, the fluid pump stops and particles are found aggregated on and around the enzyme-coated patch. The pumps are reusable, being reactivated upon injection of additional reagent. The developed technique can be implemented in lab-on-a-chip devices for transportation of micro-scale object immersed in solution.

  19. Particle Tracking Model and Abstraction of Transport Processes

    SciTech Connect

    B. Robinson

    2004-10-21

    The purpose of this report is to document the abstraction model being used in total system performance assessment (TSPA) model calculations for radionuclide transport in the unsaturated zone (UZ). The UZ transport abstraction model uses the particle-tracking method that is incorporated into the finite element heat and mass model (FEHM) computer code (Zyvoloski et al. 1997 [DIRS 100615]) to simulate radionuclide transport in the UZ. This report outlines the assumptions, design, and testing of a model for calculating radionuclide transport in the UZ at Yucca Mountain. In addition, methods for determining and inputting transport parameters are outlined for use in the TSPA for license application (LA) analyses. Process-level transport model calculations are documented in another report for the UZ (BSC 2004 [DIRS 164500]). Three-dimensional, dual-permeability flow fields generated to characterize UZ flow (documented by BSC 2004 [DIRS 169861]; DTN: LB03023DSSCP9I.001 [DIRS 163044]) are converted to make them compatible with the FEHM code for use in this abstraction model. This report establishes the numerical method and demonstrates the use of the model that is intended to represent UZ transport in the TSPA-LA. Capability of the UZ barrier for retarding the transport is demonstrated in this report, and by the underlying process model (BSC 2004 [DIRS 164500]). The technical scope, content, and management of this report are described in the planning document ''Technical Work Plan for: Unsaturated Zone Transport Model Report Integration'' (BSC 2004 [DIRS 171282]). Deviations from the technical work plan (TWP) are noted within the text of this report, as appropriate. The latest version of this document is being prepared principally to correct parameter values found to be in error due to transcription errors, changes in source data that were not captured in the report, calculation errors, and errors in interpretation of source data.

  20. Quasilinear Line Broadened Model for Energetic Particle Transport

    NASA Astrophysics Data System (ADS)

    Ghantous, Katy; Gorelenkov, Nikolai; Berk, Herbert

    2011-10-01

    We present a self-consistent quasi-linear model that describes wave-particle interaction in toroidal geometry and computes fast ion transport during TAE mode evolution. The model bridges the gap between single mode resonances, where it predicts the analytically expected saturation levels, and the case of multiple modes overlapping, where particles diffuse across phase space. Results are presented in the large aspect ratio limit where analytic expressions are used for Fourier harmonics of the power exchange between waves and particles, . Implemention of a more realistic mode structure calculated by NOVAK code are also presented. This work is funded by DOE contract DE-AC02-09CH11466.

  1. Simulation of Cell Adhesion using a Particle Transport Model

    NASA Astrophysics Data System (ADS)

    Chesnutt, Jennifer

    2005-11-01

    An efficient computational method for simulation of cell adhesion through protein binding forces is discussed. In this method, the cells are represented by deformable elastic particles, and the protein binding is represented by a rate equation. The method is first developed for collision and adhesion of two similar cells impacting on each other from opposite directions. The computational method is then applied in a particle-transport model for a cloud of interacting and colliding cells, each of which are represented by particles of finite size. One application might include red blood cells adhering together to form rouleaux, which are chains of red blood cells that are found in different parts of the circulatory system. Other potential applications include adhesion of platelets to a blood vessel wall or mechanical heart valve, which is a precursor of thrombosis formation, or adhesion of cancer cells to organ walls in the lymphatic, circulatory, digestive or pulmonary systems.

  2. Transient Characterization of Type B Particles in a Transport Riser

    SciTech Connect

    Shadle, L.J.; Monazam, E.R.; Mei, J.S.

    2007-01-01

    Simple and rapid dynamic tests were used to evaluate fluid dynamic behavior of granular materials in the transport regime. Particles with densities ranging from 189 to 2,500 kg/m3 and Sauter mean size from 61 to 812 μm were tested in a 0.305 m diameter, 15.5 m height circulating fluidized bed (CFB) riser. The transient tests involved the abrupt stoppage of solids flow for each granular material over a wide range gas flow rates. The riser emptying time was linearly related to the Froude number in each of three different operating regimes. The flow structure along the height of the riser followed a distinct pattern as tracked through incremental pressures. These results are discussed to better understand the transformations that take place when operating over various regimes. During the transients the particle size distribution was measured. The effects of pressure, particle size, and density on test performance are also presented.

  3. Particle Simulations of DARHT-II Transport System

    SciTech Connect

    Poole, B; Chen, Y J

    2001-06-11

    The DARHT-II beam line utilizes a fast stripline kicker to temporally chop a high current electron beam from a single induction LINAC and deliver multiple temporal electron beam pulses to an x-ray converter target. High beam quality needs to be maintained throughout the transport line from the end of the accelerator through the final focus lens to the x-ray converter target to produce a high quality radiographic image. Issues that will affect beam quality such as spot size and emittance at the converter target include dynamic effects associated with the stripline kicker as well as emittance growth due to the nonlinear forces associated with the kicker and various focusing elements in the transport line. In addition, dynamic effects associated with transverse resistive wall instability as well as gas focusing will affect the beam transport. A particle-in-cell code is utilized to evaluate beam transport in the downstream transport line in DARHT-II. External focusing forces are included utilizing either analytic expressions or field maps. Models for wakefields from the beam kicker, transverse resistive wall instability, and gas focusing are included in the simulation to provide a more complete picture of beam transport in DARHT-II. From these simulations, for various initial beam loads based on expected accelerator performance the temporally integrated target spot size and emittance can be estimated.

  4. Transport of Particle Swarms Through Variable Aperture Fractures

    NASA Astrophysics Data System (ADS)

    Boomsma, E.; Pyrak-Nolte, L. J.

    2012-12-01

    Particle transport through fractured rock is a key concern with the increased use of micro- and nano-size particles in consumer products as well as from other activities in the sub- and near surface (e.g. mining, industrial waste, hydraulic fracturing, etc.). While particle transport is often studied as the transport of emulsions or dispersions, particles may also enter the subsurface from leaks or seepage that lead to particle swarms. Swarms are drop-like collections of millions of colloidal-sized particles that exhibit a number of unique characteristics when compared to dispersions and emulsions. Any contaminant or engineered particle that forms a swarm can be transported farther, faster, and more cohesively in fractures than would be expected from a traditional dispersion model. In this study, the effects of several variable aperture fractures on colloidal swarm cohesiveness and evolution were studied as a swarm fell under gravity and interacted with the fracture walls. Transparent acrylic was used to fabricate synthetic fracture samples with (1) a uniform aperture, (2) a converging region followed by a uniform region (funnel shaped), (3) a uniform region followed by a diverging region (inverted funnel), and (4) a cast of a an induced fracture from a carbonate rock. All of the samples consisted of two blocks that measured 100 x 100 x 50 mm. The minimum separation between these blocks determined the nominal aperture (0.5 mm to 20 mm). During experiments a fracture was fully submerged in water and swarms were released into it. The swarms consisted of a dilute suspension of 3 micron polystyrene fluorescent beads (1% by mass) with an initial volume of 5μL. The swarms were illuminated with a green (525 nm) LED array and imaged optically with a CCD camera. The variation in fracture aperture controlled swarm behavior. Diverging apertures caused a sudden loss of confinement that resulted in a rapid change in the swarm's shape as well as a sharp increase in its velocity

  5. Measurement of particle transport coefficients on Alcator C-Mod

    SciTech Connect

    Luke, T.C.T.

    1994-10-01

    The goal of this thesis was to study the behavior of the plasma transport during the divertor detachment in order to explain the central electron density rise. The measurement of particle transport coefficients requires sophisticated diagnostic tools. A two color interferometer system was developed and installed on Alcator C-Mod to measure the electron density with high spatial ({approx} 2 cm) and high temporal ({le} 1.0 ms) resolution. The system consists of 10 CO{sub 2} (10.6 {mu}m) and 4 HeNe (.6328 {mu}m) chords that are used to measure the line integrated density to within 0.08 CO{sub 2} degrees or 2.3 {times} 10{sup 16}m{sup {minus}2} theoretically. Using the two color interferometer, a series of gas puffing experiments were conducted. The density was varied above and below the threshold density for detachment at a constant magnetic field and plasma current. Using a gas modulation technique, the particle diffusion, D, and the convective velocity, V, were determined. Profiles were inverted using a SVD inversion and the transport coefficients were extracted with a time regression analysis and a transport simulation analysis. Results from each analysis were in good agreement. Measured profiles of the coefficients increased with the radius and the values were consistent with measurements from other experiments. The values exceeded neoclassical predictions by a factor of 10. The profiles also exhibited an inverse dependence with plasma density. The scaling of both attached and detached plasmas agreed well with this inverse scaling. This result and the lack of change in the energy and impurity transport indicate that there was no change in the underlying transport processes after detachment.

  6. PAHs loadings of particles as tracer for origin and transport dynamics of particles in river networks

    NASA Astrophysics Data System (ADS)

    Schwientek, Marc; Hermann, Rügner; Bennett, Jeremy-Paul; Grathwohl, Peter

    2015-04-01

    Transport of many urban pollutants in rivers is coupled to transport of suspended particles, potentially dominated by storm water overflows and mobilization of legacy contamination of sediments. Concentration of these pollutants depends on the mixture of "polluted" urban and "clean" background particles. In the current study, the total concentration of polycyclic aromatic hydrocarbons (PAHs) and the amount of total suspended solids (TSS) were meaured in the course of pronounced flood events in 3 catchments with contrast¬ing land use in Southwest Germany. Average PAHs loadings were calculated based on linear regressions of total PAHs concentrations versus TSS. For single samples PAHs loadings were estimated based on PAHs/TSS quotients. Average loadings are characteristic for each catchment and represent the number of inhabitants within the catchment per load of suspended sediment. The absence of significant long-term trends or pronounced changes of the catchment-specific loadings indicate that either input and output of PAHs into the stream networks are largely at steady state or that storage of PAHs in the sediments within the stream network are sufficient to smooth out larger fluctuations. Sampling at high temporal resolution during flood events revealed that loadings do show some short-term fluctuations and, additionally, that loadings show generally slightly decreasing trends during flood events. This is attributed to temporally and spatially varying contributions of particle inputs from sewer overflows and subcatchments which causes a changing proportion of urban and background particles. The decreasing trend is interpreted as the existence of a PAHs storage within the stream network and a slowly depletion therof in PAHs by the inputs of fresh particles in the course of the events. To better understand origin, transport and storage of contaminated particles, also metals, total organic carbon and carbonate content were measured for suspended particles

  7. Charged Particle Energization and Transport in the Magnetotail during Substorms

    NASA Astrophysics Data System (ADS)

    Pan, Qingjiang

    This dissertation addresses the problem of energization of particles (both electrons and ions) to tens and hundreds of keV and the associated transport process in the magnetotail during substorms. Particles energized in the magnetotail are further accelerated to even higher energies (hundreds of keV to MeV) in the radiation belts, causing space weather hazards to human activities in space and on ground. We develop an analytical model to quantitatively estimate flux changes caused by betatron and Fermi acceleration when particles are transported along narrow high-speed flow channels from the magnetotail to the inner magnetosphere. The model shows that energetic particle flux can be significantly enhanced by a modest compression of the magnetic field and/or shrinking of the distance between the magnetic mirror points. We use coordinated spacecraft measurements, global magnetohydrodynamic (MHD) simulations driven by measured upstream solar wind conditions, and large-scale kinetic (LSK) simulations to quantify electron local acceleration in the near-Earth reconnection region and nonlocal acceleration during plasma earthward transport. Compared to the analytical model, application of the LSK simulations is much less restrictive because trajectories of millions of test particles are calculated in the realistically determined global MHD fields and the results are statistical. The simulation results validated by the observations show that electrons following a power law distribution at high energies are generated earthward of the reconnection site, and that the majority of the energetic electrons observed in the inner magnetosphere are caused by adiabatic acceleration in association with magnetic dipolarizations and fast flows during earthward transport. We extend the global MHD+LSK simulations to examine ion energization and compare it with electron energization. The simulations demonstrate that ions in the magnetotail are first nonadiabatically accelerated in the weak

  8. Interplanetary particle transport simulation for warning system for aviation exposure to solar energetic particles

    NASA Astrophysics Data System (ADS)

    Kubo, Yûki; Kataoka, Ryuho; Sato, Tatsuhiko

    2015-07-01

    Solar energetic particles (SEPs) are one of the extreme space weather phenomena. A huge SEP event increases the radiation dose received by aircrews, who should be warned of such events as early as possible. We developed a warning system for aviation exposure to SEPs. This article describes one component of the system, which calculates the temporal evolution of the SEP intensity and the spectrum immediately outside the terrestrial magnetosphere. To achieve this, we performed numerical simulations of SEP transport in interplanetary space, in which interplanetary SEP transport is described by the focused transport equation. We developed a new simulation code to solve the equation using a set of stochastic differential equations. In the code, the focused transport equation is expressed in a magnetic field line coordinate system, which is a non-orthogonal curvilinear coordinate system. An inverse Gaussian distribution is employed as the injection profile of SEPs at an inner boundary located near the Sun. We applied the simulation to observed SEP events as a validation test. The results show that our simulation can closely reproduce observational data for the temporal evolution of particle intensity. By employing the code, we developed the WArning System for AVIation Exposure to Solar energetic particles (WASAVIES).

  9. Particle Communication and Domain Neighbor Coupling: Scalable Domain Decomposed Algorithms for Monte Carlo Particle Transport

    SciTech Connect

    O'Brien, M. J.; Brantley, P. S.

    2015-01-20

    In order to run Monte Carlo particle transport calculations on new supercomputers with hundreds of thousands or millions of processors, care must be taken to implement scalable algorithms. This means that the algorithms must continue to perform well as the processor count increases. In this paper, we examine the scalability of:(1) globally resolving the particle locations on the correct processor, (2) deciding that particle streaming communication has finished, and (3) efficiently coupling neighbor domains together with different replication levels. We have run domain decomposed Monte Carlo particle transport on up to 221 = 2,097,152 MPI processes on the IBM BG/Q Sequoia supercomputer and observed scalable results that agree with our theoretical predictions. These calculations were carefully constructed to have the same amount of work on every processor, i.e. the calculation is already load balanced. We also examine load imbalanced calculations where each domain’s replication level is proportional to its particle workload. In this case we show how to efficiently couple together adjacent domains to maintain within workgroup load balance and minimize memory usage.

  10. A concurrent vector-based steering framework for particle transport

    NASA Astrophysics Data System (ADS)

    Apostolakis, John; Brun, René; Carminati, Federico; Gheata, Andrei; Wenzel, Sandro

    2014-06-01

    High Energy Physics has traditionally been a technology-limited science that has pushed the boundaries of both the detectors collecting the information about the particles and the computing infrastructure processing this information. However, since a few years the increase in computing power comes in the form of increased parallelism at all levels, and High Energy Physics has now to optimise its code to take advantage of the new architectures, including GPUs and hybrid systems. One of the primary targets for optimisation is the particle transport code used to simulate the detector response, as it is largely experiment independent and one of the most demanding applications in terms of CPU resources. The Geant Vector Prototype project aims to explore innovative designs in particle transport aimed at obtaining maximal performance on the new architectures. This paper describes the current status of the project and its future perspectives. In particular we describe how the present design tries to expose the parallelism of the problem at all possible levels, in a design that is aimed at minimising contentions and maximising concurrency, both at the coarse granularity level (threads) and at the micro granularity one (vectorisation, instruction pipelining, multiple instructions per cycle). The future plans and perspectives will also be mentioned.

  11. Parallelization of a Monte Carlo particle transport simulation code

    NASA Astrophysics Data System (ADS)

    Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.

    2010-05-01

    We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.

  12. Production and global transport of Titan's sand particles

    NASA Astrophysics Data System (ADS)

    Barnes, Jason W.; Lorenz, Ralph D.; Radebaugh, Jani; Hayes, Alexander G.; Arnold, Karl; Chandler, Clayton

    2015-06-01

    Previous authors have suggested that Titan's individual sand particles form by either sintering or by lithification and erosion. We suggest two new mechanisms for the production of Titan's organic sand particles that would occur within bodies of liquid: flocculation and evaporitic precipitation. Such production mechanisms would suggest discrete sand sources in dry lakebeds. We search for such sources, but find no convincing candidates with the present Cassini Visual and Infrared Mapping Spectrometer coverage. As a result we propose that Titan's equatorial dunes may represent a single, global sand sea with west-to-east transport providing sources and sinks for sand in each interconnected basin. The sand might then be transported around Xanadu by fast-moving Barchan dune chains and/or fluvial transport in transient riverbeds. A river at the Xanadu/Shangri-La border could explain the sharp edge of the sand sea there, much like the Kuiseb River stops the Namib Sand Sea in southwest Africa on Earth. Future missions could use the composition of Titan's sands to constrain the global hydrocarbon cycle.

  13. Dust-Particle Transport in Tokamak Edge Plasmas

    SciTech Connect

    Pigarov, A Y; Krasheninnikov, S I; Soboleva, T K; Rognlien, T D

    2005-09-12

    Dust particulates in the size range of 10nm-100{micro}m are found in all fusion devices. Such dust can be generated during tokamak operation due to strong plasma/material-surface interactions. Some recent experiments and theoretical estimates indicate that dust particles can provide an important source of impurities in the tokamak plasma. Moreover, dust can be a serious threat to the safety of next-step fusion devices. In this paper, recent experimental observations on dust in fusion devices are reviewed. A physical model for dust transport simulation, and a newly developed code DUSTT, are discussed. The DUSTT code incorporates both dust dynamics due to comprehensive dust-plasma interactions as well as the effects of dust heating, charging, and evaporation. The code tracks test dust particles in realistic plasma backgrounds as provided by edge-plasma transport codes. Results are presented for dust transport in current and next-step tokamaks. The effect of dust on divertor plasma profiles and core plasma contamination is examined.

  14. Overview of Particle and Heavy Ion Transport Code System PHITS

    NASA Astrophysics Data System (ADS)

    Sato, Tatsuhiko; Niita, Koji; Matsuda, Norihiro; Hashimoto, Shintaro; Iwamoto, Yosuke; Furuta, Takuya; Noda, Shusaku; Ogawa, Tatsuhiko; Iwase, Hiroshi; Nakashima, Hiroshi; Fukahori, Tokio; Okumura, Keisuke; Kai, Tetsuya; Chiba, Satoshi; Sihver, Lembit

    2014-06-01

    A general purpose Monte Carlo Particle and Heavy Ion Transport code System, PHITS, is being developed through the collaboration of several institutes in Japan and Europe. The Japan Atomic Energy Agency is responsible for managing the entire project. PHITS can deal with the transport of nearly all particles, including neutrons, protons, heavy ions, photons, and electrons, over wide energy ranges using various nuclear reaction models and data libraries. It is written in Fortran language and can be executed on almost all computers. All components of PHITS such as its source, executable and data-library files are assembled in one package and then distributed to many countries via the Research organization for Information Science and Technology, the Data Bank of the Organization for Economic Co-operation and Development's Nuclear Energy Agency, and the Radiation Safety Information Computational Center. More than 1,000 researchers have been registered as PHITS users, and they apply the code to various research and development fields such as nuclear technology, accelerator design, medical physics, and cosmic-ray research. This paper briefly summarizes the physics models implemented in PHITS, and introduces some important functions useful for specific applications, such as an event generator mode and beam transport functions.

  15. Simulations of reactive transport and precipitation with smoothed particle hydrodynamics

    NASA Astrophysics Data System (ADS)

    Tartakovsky, Alexandre M.; Meakin, Paul; Scheibe, Timothy D.; Eichler West, Rogene M.

    2007-03-01

    A numerical model based on smoothed particle hydrodynamics (SPH) was developed for reactive transport and mineral precipitation in fractured and porous materials. Because of its Lagrangian particle nature, SPH has several advantages for modeling Navier-Stokes flow and reactive transport including: (1) in a Lagrangian framework there is no non-linear term in the momentum conservation equation, so that accurate solutions can be obtained for momentum dominated flows and; (2) complicated physical and chemical processes such as surface growth due to precipitation/dissolution and chemical reactions are easy to implement. In addition, SPH simulations explicitly conserve mass and linear momentum. The SPH solution of the diffusion equation with fixed and moving reactive solid-fluid boundaries was compared with analytical solutions, Lattice Boltzmann [Q. Kang, D. Zhang, P. Lichtner, I. Tsimpanogiannis, Lattice Boltzmann model for crystal growth from supersaturated solution, Geophysical Research Letters, 31 (2004) L21604] simulations and diffusion limited aggregation (DLA) [P. Meakin, Fractals, scaling and far from equilibrium. Cambridge University Press, Cambridge, UK, 1998] model simulations. To illustrate the capabilities of the model, coupled three-dimensional flow, reactive transport and precipitation in a fracture aperture with a complex geometry were simulated.

  16. Evaluation of Baltic Sea transport properties using particle tracking

    NASA Astrophysics Data System (ADS)

    Dargahi, Bijan; Cvetkovic, Vladimir

    2014-05-01

    Particle tracking model (PTM) is an effective tool for quantifying transport properties of large water bodies such as the Baltic Sea. We have applied PTM to our fully calibrated and validated Baltic Sea 3D hydrodynamic model for a 10-years period (2000-9). One hundred particles were released at a constant rate during an initial 10-days period from all the Baltic Sea sub-basins, the major rivers, and the open boundary in the Arkona Basin. In each basin, the particles were released at two different depths corresponding to the deep water and middle water layers. The objectives of the PTM simulations were to analyse the intra-exchange processes between the Baltic Sea basins and to estimate the arrival times and the paths of particles released from the rivers. The novel contribution of this study is determining the paths and arrival times of deeper water masses rather than the surface masses. Advective and diffusive transport processes in the Bornholm and Arkona basins are both driven by the interacting flows of the northern basins of the Baltic Sea and the North Sea. Particles released from Arkona basin flows northwards along the Stople Channel. The Gotland basins are the major contributors to the exchange process in the Baltic Sea. We find high values of the advection ratio, indicative of a forced advective transport process. The Bay of Gdansk is probably the most vulnerable region in the Baltic Sea. This is despite the fact that the main exchanging basins are the Bornholm Sea and the Easter Gotland Basin. The main reason is the intensive supply of the particles from the northern basins that normally take about 3000 days to reach the Bay of Gdansk. The process maintains a high level of particle concentration (90%) along its coastlines even after the 10-years period. Comparing the particle paths in the Western and Eastern Gotland basins two interesting features were found. Particles travelled in all four directions in the former basin and the middle layer particles

  17. Size segregation in bedload sediment transport at the particle scale

    NASA Astrophysics Data System (ADS)

    Frey, P.; Martin, T.

    2011-12-01

    Bedload, the larger material that is transported in stream channels, has major consequences, for the management of water resources, for environmental sustainability, and for flooding alleviation. Most particularly, in mountains, steep slopes drive intense transport of a wide range of grain sizes. Our ability to compute local and even bulk quantities such as the sediment flux in rivers is poor. One important reason is that grain-grain interactions in stream channels may have been neglected. An arguably most important difficulty pertains to the very wide range of grain size leading to grain size sorting or segregation. This phenomenon largely modifies fluxes and results in patterns that can be seen ubiquitously in nature such as armoring or downstream fining. Most studies have concerned the spontaneous percolation of fine grains into immobile gravels, because of implications for salmonid spawning beds, or stratigraphical interpretation. However when the substrate is moving, the segregation process is different as statistically void openings permit downward percolation of larger particles. This process also named "kinetic sieving" has been studied in industrial contexts where segregation of granular or powder materials is often non-desirable. We present an experimental study of two-size mixtures of coarse spherical glass beads entrained by a shallow turbulent and supercritical water flow down a steep channel with a mobile bed. The particle diameters were 4 and 6mm, the channel width 6.5mm and the channel inclination ranged from 7.5 to 12.5%. The water flow rate and the particle rate were kept constant at the upstream entrance. First only the coarser particle rate was input and adjusted to obtain bed load equilibrium, that is, neither bed degradation nor aggradation over sufficiently long time intervals. Then a low rate of smaller particles (about 1% of the total sediment rate) was introduced to study the spatial and temporal evolution of segregating smaller particles

  18. Transport coefficients of solid particles immersed in a viscous gas

    NASA Astrophysics Data System (ADS)

    Garzó, Vicente; Fullmer, William D.; Hrenya, Christine M.; Yin, Xiaolong

    2016-01-01

    Transport properties of a suspension of solid particles in a viscous gas are studied. The dissipation in such systems arises from two sources: inelasticity in particle collisions and viscous dissipation due to the effect of the gas phase on the particles. Here we consider a simplified case in which the mean relative velocity between the gas and solid phases is taken to be zero, such that "thermal drag" is the only remaining gas-solid interaction. Unlike the previous, more general, treatment of the drag force [Garzó et al., J. Fluid Mech. 712, 129 (2012)], 10.1017/jfm.2012.404, here we take into account contributions to the (scaled) transport coefficients η* (shear viscosity), κ* (thermal conductivity), and μ* (Dufour-like coefficient) coming from the temperature dependence of the (dimensionless) friction coefficient γ* characterizing the amplitude of the drag force. At moderate densities, the thermal drag model (which is based on the Enskog kinetic equation) is solved by means of the Chapman-Enskog method and the Navier-Stokes transport coefficients are determined in terms of the coefficient of restitution, the solid volume fraction, and the friction coefficient. The results indicate that the effect of the gas phase on η* and μ* is non-negligible (especially in the case of relatively dilute systems) while the form of κ* is the same as the one obtained in the dry granular limit. Finally, as an application of these results, a linear stability analysis of the hydrodynamic equations is carried out to analyze the conditions for stability of the homogeneous cooling state. A comparison with direct numerical simulations shows a good agreement for conditions of practical interest.

  19. Transport coefficients of solid particles immersed in a viscous gas.

    PubMed

    Garzó, Vicente; Fullmer, William D; Hrenya, Christine M; Yin, Xiaolong

    2016-01-01

    Transport properties of a suspension of solid particles in a viscous gas are studied. The dissipation in such systems arises from two sources: inelasticity in particle collisions and viscous dissipation due to the effect of the gas phase on the particles. Here we consider a simplified case in which the mean relative velocity between the gas and solid phases is taken to be zero, such that "thermal drag" is the only remaining gas-solid interaction. Unlike the previous, more general, treatment of the drag force [Garzó et al., J. Fluid Mech. 712, 129 (2012)]JFLSA70022-112010.1017/jfm.2012.404, here we take into account contributions to the (scaled) transport coefficients η^{*} (shear viscosity), κ^{*} (thermal conductivity), and μ^{*} (Dufour-like coefficient) coming from the temperature dependence of the (dimensionless) friction coefficient γ^{*} characterizing the amplitude of the drag force. At moderate densities, the thermal drag model (which is based on the Enskog kinetic equation) is solved by means of the Chapman-Enskog method and the Navier-Stokes transport coefficients are determined in terms of the coefficient of restitution, the solid volume fraction, and the friction coefficient. The results indicate that the effect of the gas phase on η^{*} and μ^{*} is non-negligible (especially in the case of relatively dilute systems) while the form of κ^{*} is the same as the one obtained in the dry granular limit. Finally, as an application of these results, a linear stability analysis of the hydrodynamic equations is carried out to analyze the conditions for stability of the homogeneous cooling state. A comparison with direct numerical simulations shows a good agreement for conditions of practical interest. PMID:26871141

  20. Probabilistic description of particle transport. III. Inelastic scattering

    SciTech Connect

    Goulet, T.; Keszei, E.; Jay-Gerin, J. Departement de Medecine Nucleaire et de Radiobiologie, Faculte de Medecine, Universite de Sherbrooke, Sherbrooke, PQ )

    1990-06-01

    We extend our probabilistic model of quasielastic particle transport to include possible inelastic scatterings of the particles in the bulk of the studied media. We show that this extended model can be used to describe different types of experiments involving electrons that go through or are reflected by a plane-parallel layer deposited on a substrate. In particular, we reanalyze the experimental results of low-energy ({approx lt}10 eV) electron transmission through solid xenon and solid molecular nitrogen. This analysis shows that the extended model is consistent with the quasielastic one, but is more powerful since we can now determine both the elastic and inelastic electron mean free paths. The analysis allows one to study the threshold creation of excitons that can be observed at about 8.5 and 9.5 eV in solid xenon, and around 7.5 eV in solid molecular nitrogen.

  1. Field-aligned Transport and Acceleration of Solar Energetic Particles

    NASA Astrophysics Data System (ADS)

    Borovikov, D.; Sokolov, I.; Tenishev, V.; Gombosi, T. I.

    2015-12-01

    Solar Energetic Particle (SEP) phenomena represent one of the major components of space weather. Often, but not exclusively associated with Coronal Mass Ejections (CMEs), they pose a significant scientific as well as practical interest. As these particles originate at such explosive events, they have energies up to several GeV. SEP may cause disruptions in operations of space instruments and spacecrafts and are dangerous to astronauts. For this reason, studies of SEP events and predictions of their impact are of great importance. The motion and acceleration of SEP, though kinetic in nature, is governed by Interplanetary Magnetic Field (IMF) and its disturbances. Therefore, a consistent and accurate simulation and predictive tool must include a realistic MHD model of IMF. At the same time, transport of SEP is essentially one-dimensional as at high energies particles are tied to magnetic field lines. This allows building a model that can effectively map active regions on the solar surface onto various regions of the Solar System thus predicting the affected regions of the at any distance from the Sun. We present the first attempt to construct a model that employs coupling of MHD and kinetic models. The former describes the evolution of IMF disturbed by CME, while the latter simulates particles moving along the field lines extracted from MHD model. The first results are provided.

  2. Transport and discrete particle noise in gyrokinetic simulations

    NASA Astrophysics Data System (ADS)

    Jenkins, Thomas; Lee, W. W.

    2006-10-01

    We present results from our recent investigations regarding the effects of discrete particle noise on the long-time behavior and transport properties of gyrokinetic particle-in-cell simulations. It is found that the amplitude of nonlinearly saturated drift waves is unaffected by discreteness-induced noise in plasmas whose behavior is dominated by a single mode in the saturated state. We further show that the scaling of this noise amplitude with particle count is correctly predicted by the fluctuation-dissipation theorem, even though the drift waves have driven the plasma from thermal equilibrium. As well, we find that the long-term behavior of the saturated system is unaffected by discreteness-induced noise even when multiple modes are included. Additional work utilizing a code with both total-f and δf capabilities is also presented, as part of our efforts to better understand the long- time balance between entropy production, collisional dissipation, and particle/heat flux in gyrokinetic plasmas.

  3. Quantum interference effects in particle transport through square lattices

    NASA Astrophysics Data System (ADS)

    Cuansing, E.; Nakanishi, H.

    2004-12-01

    We study the transport of a quantum particle through square lattices of various sizes by employing the tight-binding Hamiltonian from quantum percolation. Input and output semi-infinite chains are attached to the lattice either by diagonal point-to-point contacts or by a busbar connection. We find resonant transmission and reflection occurring whenever the incident particle’s energy is near an eigenvalue of the lattice alone (i.e., the lattice without the chains attached). We also find the transmission to be strongly dependent on the way the chains are attached to the lattice.

  4. Hollow-core waveguide characterization by optically induced particle transport.

    PubMed

    Measor, Philip; Kühn, Sergei; Lunt, Evan J; Phillips, Brian S; Hawkins, Aaron R; Schmidt, Holger

    2008-04-01

    We introduce a method for optical characterization of hollow-core optical waveguides. Radiation pressure exerted by the waveguide modes on dielectric microspheres is used to analyze salient properties such as propagation loss and waveguide mode profiles. These quantities were measured for quasi-single-mode and multimode propagation in on-chip liquid-filled hollow-core antiresonant reflecting optical waveguides. Excellent agreement with analytical and numerical models is found, demonstrating that optically induced particle transport provides a simple, inexpensive, and nondestructive alternative to other characterization methods. PMID:18382513

  5. Fluid flow and particle transport in mechanically ventilated airways. Part II: particle transport.

    PubMed

    Alzahrany, Mohammed; Van Rhein, Timothy; Banerjee, Arindam; Salzman, Gary

    2016-07-01

    The flow mechanisms that play a role on aerosol deposition were identified and presented in a companion paper (Timothy et al. in Med Biol Eng Comput. doi: 10.1007/s11517-015-1407-3 , 2015). In the current paper, the effects of invasive conventional mechanical ventilation waveforms and endotracheal tube (ETT) on the aerosol transport were investigated. In addition to the enhanced deposition seen at the carinas of the airway bifurcations, enhanced deposition was also seen in the right main bronchus due to impaction and turbulent dispersion resulting from the fluid structures created by jet caused by the ETT. The orientation of the ETT toward right bronchus resulted in a substantial deposition inside right lung compared to left lung. The deposition inside right lung was ~12-fold higher than left lung for all considered cases, except for the case of using pressure-controlled sinusoidal waveform where a reduction of this ratio by ~50 % was found. The total deposition during pressure constant, volume ramp, and ascending ramp waveforms was similar and ~1.44 times higher than deposition fraction when using pressure sinusoidal waveform. Varying respiratory waveform demonstrated a significant role on the deposition enhancement factors and give evidence of drug aerosol concentrations in key deposition sites, which may be significant for drugs with negative side effects in high concentrations. These observations are thought to be important for ventilation treatment strategy. PMID:26541600

  6. From flow and particle transport modeling to vibration isolation

    NASA Astrophysics Data System (ADS)

    Ellison, Joseph Fabian

    2001-08-01

    This thesis is composed of two parts. Part I is devoted to the analysis of particle transport and deposition. In this part, flow and particle transport and deposition in a furnace and under microgravity conditions are analyzed. In the first study of Part I, fluid flow, combustion, heat and mass transfer involved in a methane/air furnace were studied. The purpose of this study was to investigate variations in the flow field and thermal conditions in the furnace and to develop methods for improving its efficiency. The analysis of the combustor model was performed using an unstructured grid model developed with the Gambit grid generator of FLUENT version 5. In the second study of Part I, particle dispersion in a liquid filled box under orbital g-jitter excitation is analyzed. The study investigated particle motion experiments that were performed aboard the orbiting shuttle. The experiments have provided confusing data as to the nature of particle dispersion in the orbital environment. To obtain a better understanding of the dynamics involved, a series of numerical simulations are performed to study the dispersion of suspended particles subject to g-jitter excitations. Part II of the thesis is devoted to the analysis of vibration and vibration isolation problems. Following along the lines of vibration effecting system performance, a study of vibration isolation used to protect avionics equipment from adverse aircraft vibration environments was conducted. Passive isolation is the simplest means to achieve this goal. The system used here consisted of a circular steel ring with a lump mass on top and exposed to base excitation. Sinusoidal and filtered zero-mean Gaussian white noise were used to excite the structure and the acceleration response spectra at the top of the ring were computed. An experiment was performed to identify the natural frequencies and modal damping of the circular ring. The polished homogeneity measurement of large optics mounted in a vertical ring

  7. Particle transport and flow modulation in particle-laden mixing layers

    NASA Astrophysics Data System (ADS)

    Tong, Xiao-Ling

    Shear flows provide a means to rapidly mix and disperse discrete solid particles and droplets in natural and industrial processes. Moderate mass loadings of particles in a gas mixing layer may also alter the gas shear flow. While the modeling of single-phase shear flows has undergone several decades of development and validation, the consideration of the corresponding problem in two- phase shear flows has just began. This dissertation represents a systematic effort to use a tool known as direct numerical simulations (DNS) to advance our understanding of particle transport and flow modulation in a gas mixing layer laden with solid particles. In DNS, almost all dynamically important flow scales are directly resolved. Previously, DNS of three-dimensional (3D) particle-laden shear flows have not been possible due to their high computational cost. Therefore, we first set out to develop and validate a computationally efficient and numerically accurate DNS methodology for particle-laden mixing layer. The method relies on a Fourier vorticity-based formulation together with a divergence-free decomposition. While almost all previous numerical studies adopted the trajectory approach for the dispersed phase in the context of DNS, a continuum approach has been developed and shown to reduce the computational time by a factor of 15 for the simulations of 3D particle-laden mixing layers. The validity and interpretation of the continuum approach were illustrated analytically with a stagnation point flow model. Detailed comparisons showed that the continuum approach and the trajectory approach yielded very similar results. Since the particulate field is compressible, numerical diffusion must be applied to remove local singularities. A dynamic-diffusion model has been developed as an optimum numerical diffusion model to ensure spectral resolution of particulate continuum fields. The numerical method was then used to study the interactions of finite-inertia particles with 3D flow

  8. Exposure visualisation of ultrafine particle counts in a transport microenvironment

    NASA Astrophysics Data System (ADS)

    Kaur, S.; Clark, R. D. R.; Walsh, P. T.; Arnold, S. J.; Colvile, R. N.; Nieuwenhuijsen, M. J.

    An increasing number of studies indicate that short-term peak exposures, such as those seen in the transport microenvironment, pose particular health threats. Short-term exposure can only be sufficiently characterised using portable, fast-response monitoring instrumentation with detailed summaries of individual activity. In this paper, we present an exposure visualisation system that addresses this issue—it allows the simultaneous presentation of mobile video imagery synchronised with measured real-time ultrafine particle count exposure of an individual. The combined data can be examined in detail for the contribution of the surrounding environment and the individual's activities to their peak and overall exposure. The exposure visualisation system is demonstrated and evaluated around the DAPPLE study site in Central London using different modes of transport (walking, cycling, bus, car and taxi). The video images, synchronised with the exposure profile, highlight the extent to which ultrafine particle exposure is associated with traffic density and proximity to pollutant source. The extremely rapid decline in concentration with increasing distance away from the pollutant source, such as from the main street to the backstreets, is clearly evident. The visualisation technique allows these data to be presented to both technical audiences and laypersons thus making it an effective environmental risk communication tool. Some exposure peaks however are not obviously associated with any event recorded on video—in these cases it will be necessary to use advanced dispersion modelling techniques to investigate meteorological conditions and other variables influencing in-street conditions to identify their possible causes.

  9. High energy electromagnetic particle transportation on the GPU

    SciTech Connect

    Canal, P.; Elvira, D.; Jun, S. Y.; Kowalkowski, J.; Paterno, M.; Apostolakis, J.

    2014-01-01

    We present massively parallel high energy electromagnetic particle transportation through a finely segmented detector on a Graphics Processing Unit (GPU). Simulating events of energetic particle decay in a general-purpose high energy physics (HEP) detector requires intensive computing resources, due to the complexity of the geometry as well as physics processes applied to particles copiously produced by primary collisions and secondary interactions. The recent advent of hardware architectures of many-core or accelerated processors provides the variety of concurrent programming models applicable not only for the high performance parallel computing, but also for the conventional computing intensive application such as the HEP detector simulation. The components of our prototype are a transportation process under a non-uniform magnetic field, geometry navigation with a set of solid shapes and materials, electromagnetic physics processes for electrons and photons, and an interface to a framework that dispatches bundles of tracks in a highly vectorized manner optimizing for spatial locality and throughput. Core algorithms and methods are excerpted from the Geant4 toolkit, and are modified and optimized for the GPU application. Program kernels written in C/C++ are designed to be compatible with CUDA and OpenCL and with the aim to be generic enough for easy porting to future programming models and hardware architectures. To improve throughput by overlapping data transfers with kernel execution, multiple CUDA streams are used. Issues with floating point accuracy, random numbers generation, data structure, kernel divergences and register spills are also considered. Performance evaluation for the relative speedup compared to the corresponding sequential execution on CPU is presented as well.

  10. Simulating the transport of heavy charged particles through trabecular spongiosa

    NASA Astrophysics Data System (ADS)

    Gersh, Jacob A.

    As planning continues for manned missions far beyond Low Earth Orbit, a paramount concern remains the flight crew's exposure to galactic cosmic radiation. When humans exit the protective magnetic field of Earth, they become subject to bombardment by highly-reactive heavy charged (HZE) particles. A possible consequence of this two- to three-year-long mission is the onset of radiation-induced leukemia, a disorder with a latency period as short as two to three years. Because data on risk to humans from exposure to HZE particles is non-existent, studies of leukemia in animals are now underway to investigate the relative effectiveness of HZE exposures. Leukemogenesis can result from energy depositions occurring within marrow contained in the trabecular spongiosa. Trabecular spongiosa is found in flat bones and within the ends of long bones, and is characterized by an intricate matrix of interconnected bone tissue forming cavities that house marrow. The microscopic internal dimensions of spongiosa vary between species. As radiation traverses this region, interface-induced dose perturbations that occur at the interfaces between bone and marrow affect the patterns of energy deposition within the region. An aim of this project is to determine the extent by which tissue heterogeneity and microscopic dimensions have on patterns of energy deposition within the trabecular spongiosa. This leads to the development of PATHFIT, a computer code capable of generating simple quadric-based geometric models of trabecular spongiosa for both humans and mice based on actual experimentally-determined internal dimensions of trabecular spongiosa. Following the creation of spongiosa models, focus is placed on the development of HITSPAP, a hybrid Monte Carlo (MC) radiation transport code system that combines capabilities of the MC code PENELOPE and MC code PARTRAC. This code is capable of simulating the transport of HZE particles through accurate models of trabecular spongiosa. The final and

  11. Evidence for particle transport between alveolar macrophages in vivo

    SciTech Connect

    Benson, J.M.; Nikula, K.J.; Guilmette, R.A.

    1995-12-01

    Recent studies at this Institute have focused on determining the role of alveolar macrophages (AMs) in the transport of particles within and form the lung. For those studies, AMs previously labeled using the nuclear stain Hoechst 33342 and polychromatic Fluoresbrite microspheres (1 {mu}m diameter, Polysciences, Inc., Warrington, PA) were instilled into lungs of recipient F344 rats. The fate of the donor particles and the doubly labeled AMs within recipient lungs was followed for 32 d. Within 2-4 d after instillation, the polychromatic microspheres were found in both donor and resident AMs, suggesting that particle transfer occurred between the donor and resident AMs. However, this may also have been an artifact resulting from phagocytosis of the microspheres form dead donor cells or from the fading or degradation of Hoechst 33342 within the donor cells leading to their misidentification as resident AMs. The results support the earlier findings that microspheres in donor AMs can be transferred to resident AMs within 2 d after instillation.

  12. Transport of large particles in flow through porous media

    NASA Astrophysics Data System (ADS)

    Imdakm, A. O.; Sahimi, Muhammad

    1987-12-01

    There is considerable evidence indicating that significant reduction in the efficiency of many processes in porous media, such as enhancing oil recovery, heterogeneous chemical reactions, deep-bed filtration, gel permeation, and liquid chromatography, is due to the reduction in the permeability of the pore space. This reduction is due to the transport of particles, whose sizes are comparable with those of the pores, and the subsequent blocking of the pores by various mechanisms. In this paper we develop a novel Monte Carlo method for theoretical modeling of this phenomenon. Particles of various sizes are injected into the medium, and their migration in the flow field is modeled by a random walk whose transition porbability is proportional to the local pore fluxes. Pores are blocked and their flow capacity is reduced (or vanished) when large particles pass through them (and reduce their flow) or totally block them. The permeability of the medium can ultimately vanish and, therefore, this phenomenon is a percolation process. Various quantities of interest such as the variations of the permeability with process time and the distribution of pore-plugging times are computed. The critical exponent characterizing the vanishing of the permeability near the percolation threshold appears to be different from that of percolation conductivity. The agreement between our results and the available experimental data is excellent.

  13. Particle Swarm Transport through Immiscible Fluid Layers in a Fracture

    NASA Astrophysics Data System (ADS)

    Teasdale, N. D.; Boomsma, E.; Pyrak-Nolte, L. J.

    2011-12-01

    Immiscible fluids occur either naturally (e.g. oil & water) or from anthropogenic processes (e.g. liquid CO2 & water) in the subsurface and complicate the transport of natural or engineered micro- or nano-scale particles. In this study, we examined the effect of immiscible fluids on the formation and evolution of particle swarms in a fracture. A particle swarm is a collection of colloidal-size particles in a dilute suspension that exhibits cohesive behavior. Swarms fall under gravity with a velocity that is greater than the settling velocity of a single particle. Thus a particle swarm of colloidal contaminants can potentially travel farther and faster in a fracture than expected for a dispersion or emulsion of colloidal particles. We investigated the formation, evolution, and break-up of colloidal swarms under gravity in a uniform aperture fracture as hydrophobic/hydrophyllic particle swarms move across an oil-water interface. A uniform aperture fracture was fabricated from two transparent acrylic rectangular prisms (100 mm x 50 mm x 100 mm) that are separated by 1, 2.5, 5, 10 or 50 mm. The fracture was placed, vertically, inside a glass tank containing a layer of pure silicone oil (polydimethylsiloxane) on distilled water. Along the length of the fracture, 30 mm was filled with oil and 70 mm with water. Experiments were conducted using silicone oils with viscosities of 5, 10, 100, or 1000 cSt. Particle swarms (5 μl) were comprised of a 1% concentration (by mass) of 25 micron glass beads (hydrophilic) suspended in a water drop, or a 1% concentration (by mass) of 3 micron polystyrene fluorescent beads (hydrophobic) suspended in a water drop. The swarm behavior was imaged using an optical fluorescent imaging system composed of a CCD camera and by green (525 nm) LED arrays for illumination. Swarms were spherical and remained coherent as they fell through the oil because of the immiscibility of oil and water. However, as a swarm approached the oil-water interface, it

  14. Charged Particle Energization and Transport in Reservoirs throughout the Heliosphere: 1. Solar Energetic Particles

    NASA Astrophysics Data System (ADS)

    Roelof, E. C.

    2015-09-01

    “Reservoirs” of energetic charged particles are regions where the particle population is quasi-trapped in large-scale (relative to the gyroradii) magnetic field structures. Reservoirs are found throughout the heliosphere: the huge heliosheath (90particles within these reservoirs is produced by the interaction when the particle magnetic drifts have a component along the large-scale electric fields produced by plasma convection. The appropriate description of this transport is “weak scattering”, in which the particle's first adiabatic invariant (magnetic moment) is approximately conserved while the particle itself moves rather freely along magnetic field lines. Considerable insight into the observed properties of energization processes can be gained from a remarkably simple equation that describes the particle's fractional time-rate-of-change of momentum (dlnp/dt) which depends only upon its pitch angle, the divergence of the plasma velocity (V⊥) transverse to the magnetic field), and the inner product of (V⊥) with the curvature vector of the field lines. The possibilities encompassed in this simple (but general) equation are quite rich, so we restrict our application of it in this paper to the compressive acceleration of SEPs within CMEs.

  15. Particle-bound polycyclic aromatic hydrocarbon concentrations in transportation microenvironments

    NASA Astrophysics Data System (ADS)

    Houston, Douglas; Wu, Jun; Yang, Dongwoo; Jaimes, Guillermo

    2013-06-01

    This study is one of the first case studies to characterize the exposure of urban residents to traffic-related air pollution across locations and transportation microenvironments during everyday activities. Twenty-four adult residents of Boyle Heights, a neighborhood near downtown Los Angeles, carried a portable air pollution monitor and a Global Positioning Systems (GPS) tracking device for a total of 96 days. We found significant spatial and temporal variation in the particle-bound polycyclic aromatic hydrocarbon (pPAH) concentrations in transportation microenvironments. Average pPAH concentrations were higher while walking outdoors (190 ng m-3) compared to traveling in private passenger vehicles (138-155 ng m-3) or traveling in public transportation (61-124 ng m-3). Although travel comprised 5% of participant days, it was associated with 27% of overall daily pPAH exposure. Regression models explained 40-55% of the variation in daily average pPAH concentrations, and 40-44% of the variation in 1-min interval concentrations. Important factors included time spent traveling, travel speed, meteorological and nearby land use factors, time of day, and proximity to roadways. Although future research is needed to develop stronger predictive models, our study demonstrates portable tracking devices can provide a more complete, diurnal characterization of air pollution exposures for urban populations.

  16. Helium, Iron and Electron Particle Transport and Energy Transport Studies on the TFTR Tokamak

    DOE R&D Accomplishments Database

    Synakowski, E. J.; Efthimion, P. C.; Rewoldt, G.; Stratton, B. C.; Tang, W. M.; Grek, B.; Hill, K. W.; Hulse, R. A.; Johnson, D .W.; Mansfield, D. K.; McCune, D.; Mikkelsen, D. R.; Park, H. K.; Ramsey, A. T.; Redi, M. H.; Scott, S. D.; Taylor, G.; Timberlake, J.; Zarnstorff, M. C. (Princeton Univ., NJ (United States). Plasma Physics Lab.); Kissick, M. W. (Wisconsin Univ., Madison, WI (United States))

    1993-03-01

    Results from helium, iron, and electron transport on TFTR in L-mode and Supershot deuterium plasmas with the same toroidal field, plasma current, and neutral beam heating power are presented. They are compared to results from thermal transport analysis based on power balance. Particle diffusivities and thermal conductivities are radially hollow and larger than neoclassical values, except possibly near the magnetic axis. The ion channel dominates over the electron channel in both particle and thermal diffusion. A peaked helium profile, supported by inward convection that is stronger than predicted by neoclassical theory, is measured in the Supershot The helium profile shape is consistent with predictions from quasilinear electrostatic drift-wave theory. While the perturbative particle diffusion coefficients of all three species are similar in the Supershot, differences are found in the L-Mode. Quasilinear theory calculations of the ratios of impurity diffusivities are in good accord with measurements. Theory estimates indicate that the ion heat flux should be larger than the electron heat flux, consistent with power balance analysis. However, theoretical values of the ratio of the ion to electron heat flux can be more than a factor of three larger than experimental values. A correlation between helium diffusion and ion thermal transport is observed and has favorable implications for sustained ignition of a tokamak fusion reactor.

  17. Helium, iron and electron particle transport and energy transport studies on the TFTR tokamak

    SciTech Connect

    Synakowski, E.J.; Efthimion, P.C.; Rewoldt, G.; Stratton, B.C.; Tang, W.M.; Grek, B.; Hill, K.W.; Hulse, R.A.; Johnson, D.W.; Mansfield, D.K.; McCune, D.; Mikkelsen, D.R.; Park, H.K.; Ramsey, A.T.; Redi, M.H.; Scott, S.D.; Taylor, G.; Timberlake, J.; Zarnstorff, M.C.; Kissick, M.W.

    1993-03-01

    Results from helium, iron, and electron transport on TFTR in L-mode and Supershot deuterium plasmas with the same toroidal field, plasma current, and neutral beam heating power are presented. They are compared to results from thermal transport analysis based on power balance. Particle diffusivities and thermal conductivities are radially hollow and larger than neoclassical values, except possibly near the magnetic axis. The ion channel dominates over the electron channel in both particle and thermal diffusion. A peaked helium profile, supported by inward convection that is stronger than predicted by neoclassical theory, is measured in the Supershot The helium profile shape is consistent with predictions from quasilinear electrostatic drift-wave theory. While the perturbative particle diffusion coefficients of all three species are similar in the Supershot, differences are found in the L-Mode. Quasilinear theory calculations of the ratios of impurity diffusivities are in good accord with measurements. Theory estimates indicate that the ion heat flux should be larger than the electron heat flux, consistent with power balance analysis. However, theoretical values of the ratio of the ion to electron heat flux can be more than a factor of three larger than experimental values. A correlation between helium diffusion and ion thermal transport is observed and has favorable implications for sustained ignition of a tokamak fusion reactor.

  18. The importance of gradients in particle activity during sediment transport: Insights from a probabilistic description of particle motions

    NASA Astrophysics Data System (ADS)

    Furbish, D. J.

    2009-04-01

    Sediment particles transported by rainsplash, by bioturbation, and as bedload in turbulent flows, undergo motions that are quasi-random in magnitude and direction. Moreover, these motions characteristically are intermittent, in that particles are mostly at rest most of the time, and heterogeneous, in that the volumetric or areal concentration of particles in motion at any instant is spatially patchy. These particle motions can be formulated as a stochastic processes involving both advective and dispersive parts. By taking into account the intermittent activity of particles, and separating this activity from the physics of motion in the parametric description of transport, the formulation indicates that gradients in particle activity can have a key role in transport. The formulation illustrates, for example, how the growth of soil mounds beneath desert shrubs involves differential rainsplash that initially causes more grains to be splashed inward beneath protective shrub canopies than outward. This ‘harvesting' of nearby soil material, including nutrients, means that shrubs locally participate in regulating the rate sediment transport down a hillslope. With soil bioturbation, spatial variations in the disturbance frequency strongly influence the mixing of soil constituents, including distinct particle fractions (such as specific size or mineral fractions, seeds, or debitage), or elements and compounds adsorbed to particles. The formulation also provides a probabilistic version of the Exner equation. During bedload transport, gradients in particle activity, through both advective and dispersive effects, may contribute importantly to the local divergence of the particle flux, thereby influencing initial bedform growth.

  19. Transport of inertial particles by viscous streaming in arrays of oscillating probes

    NASA Astrophysics Data System (ADS)

    Chong, Kwitae; Kelly, Scott D.; Smith, Stuart T.; Eldredge, Jeff D.

    2016-01-01

    A mechanism for the transport of microscale particles in viscous fluids is demonstrated. The mechanism exploits the trapping of such particles by rotational streaming cells established in the vicinity of an oscillating cylinder, recently analyzed in previous work. The present work explores a strategy of transporting particles between the trapping points established by multiple cylinders undergoing oscillations in sequential intervals. It is demonstrated that, by controlling the sequence of oscillation intervals, an inertial particle is effectively and predictably transported between the stable trapping points. Arrays of cylinders in various arrangements are investigated, revealing a technique for constructing arbitrary particle trajectories. It is found that the domain from which particles can be transported and trapped by an oscillator is extended, even to regions in which particles are shielded, by the presence of other stationary cylinders. The timescales for transport are examined, as are the mechanisms by which particles are drawn away from an obstacle toward the trapping point of an oscillator.

  20. Transport coefficients from the two particle irreducible effective action

    NASA Astrophysics Data System (ADS)

    Aarts, Gert; Martínez Resco, Jose M.

    2003-10-01

    We show that the lowest nontrivial truncation of the two-particle irreducible (2PI) effective action correctly determines transport coefficients in a weak coupling or 1/N expansion at leading (logarithmic) order in several relativistic field theories. In particular, we consider a single real scalar field with cubic and quartic interactions in the loop expansion, the O(N) model in the 2PI-1/N expansion, and QED with single and many fermion fields. Therefore, these truncations will provide a correct description, to leading (logarithmic) order, of the long time behavior of these systems, i.e. the approach to equilibrium. This supports the promising results obtained for the dynamics of quantum fields out of equilibrium using 2PI effective action techniques.

  1. Directed transport of active particles over asymmetric energy barriers.

    PubMed

    Koumakis, N; Maggi, C; Di Leonardo, R

    2014-08-21

    We theoretically and numerically investigate the transport of active colloids to target regions, delimited by asymmetric energy barriers. We show that it is possible to introduce a generalized effective temperature that is related to the local variance of particle velocities. The stationary probability distributions can be derived from a simple diffusion equation in the presence of an inhomogeneous effective temperature resulting from the action of external force fields. In particular, transition rates over asymmetric energy barriers can be unbalanced by having different effective temperatures over the two slopes of the barrier. By varying the type of active noise, we find that equal values of diffusivity and persistence time may produce strongly varied effective temperatures and thus stationary distributions. PMID:24978345

  2. Magnetic-Fluctuation-Induced Particle Transport and Density Relaxation in a High-Temperature Plasma

    SciTech Connect

    Ding, W. X.; Brower, D. L.; Fiksel, G.; Den Hartog, D. J.; Prager, S. C.; Sarff, J. S.

    2009-07-10

    The first direct measurement of magnetic-fluctuation-induced particle flux in the core of a high-temperature plasma is reported. Transport occurs due to magnetic field fluctuations associated with global tearing instabilities. The electron particle flux, resulting from the correlated product of electron density and radial magnetic fluctuations, accounts for density profile relaxation during a magnetic reconnection event. The measured particle transport is much larger than that expected for ambipolar particle diffusion in a stochastic magnetic field.

  3. A unified transport equation for both cosmic rays and thermal particles

    NASA Technical Reports Server (NTRS)

    Williams, L. L.; Schwadron, N.; Jokipii, J. R.; Gombosi, T. I.

    1993-01-01

    We present a unified transport equation that is valid for particles of all energies if the particle mean free paths are much smaller than macroscopic fluid length scales. If restricted to particles with random speeds much greater than fluid flow speeds, this equation reduces to the previously discussed extended cosmic-ray transport equation. It is significant that this allows one to describe the acceleration of particles from thermal energies to cosmic-ray energies using one transport equation. This is in contrast to previous transport equations (the Parker equation and the extended cosmic-ray transport equation), which were restricted to fast particles. The close connection to the extended cosmic-ray transport equation is demonstrated.

  4. An approach to improving transporting velocity in the long-range ultrasonic transportation of micro-particles

    SciTech Connect

    Meng, Jianxin; Mei, Deqing Yang, Keji; Fan, Zongwei

    2014-08-14

    In existing ultrasonic transportation methods, the long-range transportation of micro-particles is always realized in step-by-step way. Due to the substantial decrease of the driving force in each step, the transportation is lower-speed and stair-stepping. To improve the transporting velocity, a non-stepping ultrasonic transportation approach is proposed. By quantitatively analyzing the acoustic potential well, an optimal region is defined as the position, where the largest driving force is provided under the condition that the driving force is simultaneously the major component of an acoustic radiation force. To keep the micro-particle trapped in the optimal region during the whole transportation process, an approach of optimizing the phase-shifting velocity and phase-shifting step is adopted. Due to the stable and large driving force, the displacement of the micro-particle is an approximately linear function of time, instead of a stair-stepping function of time as in the existing step-by-step methods. An experimental setup is also developed to validate this approach. Long-range ultrasonic transportations of zirconium beads with high transporting velocity were realized. The experimental results demonstrated that this approach is an effective way to improve transporting velocity in the long-range ultrasonic transportation of micro-particles.

  5. DANTSYS: a system for deterministic, neutral particle transport calculations

    SciTech Connect

    Alcouffe, R.E.; Baker, R.S.

    1996-12-31

    The THREEDANT code is the latest addition to our system of codes, DANTSYS, which perform neutral particle transport computations on a given system of interest. The system of codes is distinguished by geometrical or symmetry considerations. For example, ONEDANT and TWODANT are designed for one and two dimensional geometries respectively. We have TWOHEX for hexagonal geometries, TWODANT/GQ for arbitrary quadrilaterals in XY and RZ geometry, and THREEDANT for three-dimensional geometries. The design of this system of codes is such that they share the same input and edit module and hence the input and output is uniform for all the codes (with the obvious additions needed to specify each type of geometry). The codes in this system are also designed to be general purpose solving both eigenvalue and source driven problems. In this paper we concentrate on the THREEDANT module since there are special considerations that need to be taken into account when designing such a module. The main issues that need to be addressed in a three-dimensional transport solver are those of the computational time needed to solve a problem and the amount of storage needed to accomplish that solution. Of course both these issues are directly related to the number of spatial mesh cells required to obtain a solution to a specified accuracy, but is also related to the spatial discretization method chosen and the requirements of the iteration acceleration scheme employed as will be noted below. Another related consideration is the robustness of the resulting algorithms as implemented; because insistence on complete robustness has a significant impact upon the computation time. We address each of these issues in the following through which we give reasons for the choices we have made in our approach to this code. And this is useful in outlining how the code is evolving to better address the shortcomings that presently exist.

  6. M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas

    NASA Astrophysics Data System (ADS)

    Shen, Wei; Fu, G. Y.; Sheng, Zheng-Mao; Breslau, J. A.; Wang, Feng

    2014-09-01

    Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.

  7. M3D-K Simulations of Sawteeth and Energetic Particle Transport in Tokamak Plasmas

    NASA Astrophysics Data System (ADS)

    Shen, Wei; Fu, Guoyong; Sheng, Zhengmao; Breslau, Joshua; Wang, Feng

    2013-10-01

    Nonlinear simulations of Sawteeth and energetic particle transport are carried out using the kinetic/MHD hybrid code M3D-K. MHD simulations show repeated sawtooth cycles due to a resistive (1,1) internal kink mode for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in plasma core depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with previous theory. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases as particle energy becomes large.

  8. M3D-K simulations of sawteeth and energetic particle transport in tokamak plasmas

    SciTech Connect

    Shen, Wei; Sheng, Zheng-Mao; Fu, G. Y.; Breslau, J. A.; Wang, Feng

    2014-09-15

    Nonlinear simulations of sawteeth and related energetic particle transport are carried out using the kinetic/magnetohydrodynamic (MHD) hybrid code M3D-K. MHD simulations show repeated sawtooth cycles for a model tokamak equilibrium. Furthermore, test particle simulations are carried out to study the energetic particle transport due to a sawtooth crash. The results show that energetic particles are redistributed radially in the plasma core, depending on pitch angle and energy. For trapped particles, the redistribution occurs for particle energy below a critical value in agreement with existing theories. For co-passing particles, the redistribution is strong with little dependence on particle energy. In contrast, the redistribution level of counter-passing particles decreases with increasing particle energy.

  9. Coherent pulses in the diffusive transport of charged particles`

    NASA Technical Reports Server (NTRS)

    Kota, J.

    1994-01-01

    We present exact solutions to the diffusive transport of charged particles following impulsive injection for a simple model of scattering. A modified, two-parameter relaxation-time model is considered that simulates the low rate of scattering through perpendicular pitch-angle. Scattering is taken to be isotropic within each of the foward- and backward-pointing hemispheres, respectively, but, at the same time, a reduced rate of sccattering is assumed from one hemisphere to the other one. By applying a technique of Fourier- and Laplace-transform, the inverse transformation can be performed and exact solutions can be reached. By contrast with the first, and so far only exact solutions of Federov and Shakov, this wider class of solutions gives rise to coherent pulses to appear. The present work addresses omnidirectional densities for isotropic injection from an instantaneous and localized source. The dispersion relations are briefly discussed. We find, for this particular model, two diffusive models to exist up to a certain limiting wavenumber. The corresponding eigenvalues are real at the lowest wavenumbers. Complex eigenvalues, which are responsible for coherent pulses, appear at higher wavenumbers.

  10. Forced transport of self-propelled particles in a two-dimensional separate channel

    NASA Astrophysics Data System (ADS)

    Wu, Jian-Chun; Ai, Bao-Quan

    2016-04-01

    Transport of self-propelled particles in a two-dimensional (2D) separate channel is investigated in the presence of the combined forces. By applying an ac force, the particles will be trapped by the separate walls. A dc force produces the asymmetry of the system and induces the longitudinal directed transport. Due to the competition between self-propulsion and the combined external forces, the transport is sensitive to the self-propelled speed and the particle radius, thus one can separate the particles based on these properties.

  11. Forced transport of self-propelled particles in a two-dimensional separate channel

    PubMed Central

    Wu, Jian-chun; Ai, Bao-quan

    2016-01-01

    Transport of self-propelled particles in a two-dimensional (2D) separate channel is investigated in the presence of the combined forces. By applying an ac force, the particles will be trapped by the separate walls. A dc force produces the asymmetry of the system and induces the longitudinal directed transport. Due to the competition between self-propulsion and the combined external forces, the transport is sensitive to the self-propelled speed and the particle radius, thus one can separate the particles based on these properties. PMID:27035860

  12. Particle and energy transport studies on TFTR and implications for helium ash in future fusion devices

    SciTech Connect

    Synakowski, E.J.; Efthimion, P.C.; Rewoldt, G.; Stratton, B.C.; Tang, W.M.; Bell, R.E.; Grek, B.; Hulse, R.A.; Johnson, D.W.; Hill, K.W.; Mansfield, D.K.; McCune, D.; Mikkelsen, D.R.; Park, H.K.; Ramsey, A.T.; Scott, S.D.; Taylor, G.; Timberlake, J.; Zarnstorff, M.C.

    1992-12-31

    Particle and energy transport in tokamak plasmas have long been subjects of vigorous investigation. Present-day measurement techniques permit radially resolved studies of the transport of electron perturbations, low- and high-Z impurities, and energy. In addition, developments in transport theory provide tools that can be brought to bear on transport issues. Here, we examine local particle transport measurements of electrons, fully-stripped thermal helium, and helium-like iron in balanced-injection L-mode and enhanced confinement deuterium plasmas on TFTR of the same plasma current, toroidal field, and auxiliary heating power. He{sup 2{plus}} and Fe{sup 24{plus}} transport has been studied with charge exchange recombination spectroscopy, while electron transport has been studied by analyzing the perturbed electron flux following the same helium puff used for the He{sup 2{plus}} studies. By examining the electron and He{sup 2{plus}} responses following the same gas puff in the same plasmas, an unambiguous comparison of the transport of the two species has been made. The local energy transport has been examined with power balance analysis, allowing for comparisons to the local thermal fluxes. Some particle and energy transport results from the Supershot have been compared to a transport model based on a quasilinear picture of electrostatic toroidal drift-type microinstabilities. Finally, implications for future fusion reactors of the observed correlation between thermal transport and helium particle transport is discussed.

  13. Flow and particle dispersion in a pulmonary alveolus--part II: effect of gravity on particle transport.

    PubMed

    Chhabra, Sudhaker; Prasad, Ajay K

    2010-05-01

    The acinar region of the human lung comprises about 300x10(6) alveoli, which are responsible for gas exchange between the lung and the blood. As discussed in Part I (Chhabra and Prasad, "Flow and Particle Dispersion in a Pulmonary Alveolus-Part I: Velocity Measurements and Convective Particle Transport," ASME J. Biomech. Eng., 132, p. 051009), the deposition of aerosols in the acinar region can either be detrimental to gas exchange (as in the case of harmful particulate matter) or beneficial (as in the case of inhalable pharmaceuticals). We measured the flow field inside an in-vitro model of a single alveolus mounted on a bronchiole and calculated the transport and deposition of massless particles in Part I. This paper focuses on the transport and deposition of finite-sized particles ranging from 0.25 microm to 4 microm under the combined influence of flow-induced advection (computed from velocity maps obtained by particle image velocimetry) and gravitational settling. Particles were introduced during the first inhalation cycle and their trajectories and deposition statistics were calculated for subsequent cycles for three different particle sizes (0.25 microm, 1 microm, and 4 microm) and three alveolar orientations. The key outcome of the study is that particles particles (d(p)=1 microm) deviate to some extent from streamlines and exhibit complex trajectories. The motion of large particles >or=4 microm is dominated by gravitational settling and shows little effect of fluid advection. Additionally, small and midsize particles deposit at about two-thirds height in the alveolus irrespective of the gravitational orientation whereas the deposition of large particles is governed primarily by the orientation of the gravity vector. PMID:20459211

  14. The persistence, transport and health effects of regional ultrafine particles

    NASA Astrophysics Data System (ADS)

    Spada, Nicholas James

    Due to the multitude of health studies that have shown the ability of ultrafine particles (UFPs, DP < 100 nm) to penetrate deep into lung tissue, diffuse into the bloodstream, and eventually cause heart and lung disease, my thesis will focus on these effectively unmonitored airborne pollutants. UFPs are commonly detected near busy roadways and other high-temperature combustion sources in the form of heavy metals (copper, lead, zinc, iron) and toxic organics (benzo{a}pyrene, coronene). Studies of UFPs during the 1970s expressed a nucleic propensity for coagulation and growth. Because many of the UFPs studied were generated from heavy-duty diesel engines operating with ≥0.3 wt % sulfur, the resulting sulfur-containing UFPs were hydrophilic and water vapor readily condensed on the generated nuclei. Due to their increased size, UFPs tend to settle out of air streams quickly; thus, limiting their impact regime to near-roadway influence and labeling them as local pollutants. By using highly size- and time-resolved impactors with TeflonRTM ultrafine after-filters (targeting DP < 90 nm), new evidence suggests the persistence of UFPs for greater periods of time and transport than previously predicted. Techniques developed during the Roseville rail yard study, refined during the Watt Ave/Arden Way study and applied across California's central valley have shown low levels of UFPs in a regional background. For cities in constrictive topography and meteorology (such as Bakersfield, Fresno and Los Angeles), winter inversions and stagnant weather can saturate the region with ultrafine heavy metals and carcinogenic organics, similar to the disasters during the middle of the last century.

  15. Particle and energy transport studies on TFTR and implications for helium ash in future fusion devices

    SciTech Connect

    Synakowski, E.J.; Efthimion, P.C.; Rewoldt, G.; Stratton, B.C.; Tang, W.M.; Bell, R.E.; Grek, B.; Hulse, R.A.; Johnson, D.W.; Hill, K.W.; Mansfield, D.K.; McCune, D.; Mikkelsen, D.R.; Park, H.K.; Ramsey, A.T.; Scott, S.D.; Taylor, G.; Timberlake, J.; Zarnstorff, M.C.

    1992-01-01

    Particle and energy transport in tokamak plasmas have long been subjects of vigorous investigation. Present-day measurement techniques permit radially resolved studies of the transport of electron perturbations, low- and high-Z impurities, and energy. In addition, developments in transport theory provide tools that can be brought to bear on transport issues. Here, we examine local particle transport measurements of electrons, fully-stripped thermal helium, and helium-like iron in balanced-injection L-mode and enhanced confinement deuterium plasmas on TFTR of the same plasma current, toroidal field, and auxiliary heating power. He[sup 2[plus

  16. Ciliary intraflagellar transport protein 80 balances canonical versus non-canonical hedgehog signaling for osteoblast differentiation

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mutation of different IFT proteins cause numerous different clinical bone disorders accompanied with or without the disruption of cilia formation. Currently, there is no any effective treatment for these disorders due to lack of understanding in the function and mechanism of these proteins. IFT80 is...

  17. WDR19: An ancient, retrograde, intraflagellar ciliary protein is mutated in autosomal recessive retinitis pigmentosa and in Senior-Loken syndrome

    PubMed Central

    Coussa, RG; Otto, EA; Gee, H-Y; Arthurs, P; Ren, H; Lopez, I; Keser, V; Fu, Q; Faingold, R; Khan, A; Schwartzentruber, J; Majewski, J; Hildebrandtand, F; Koenekoop, RK

    2014-01-01

    Autosomal recessive retinitis pigmentosa (arRP) is a clinically and genetically heterogeneous retinal disease that causes blindness. Our purpose was to identify the causal gene, describe the phenotype and delineate the mutation spectrum in a consanguineous Quebec arRP family. We performed Arrayed Primer Extension (APEX) technology to exclude ~500 arRP mutations in ~20 genes. Homozygosity mapping [single nucleotide polymorphism (SNP) genotyping] identified 10 novel significant homozygous regions. We performed next generation sequencing and whole exome capture. Sanger sequencing provided cosegregation. We screened another 150 retinitis pigmentosa (RP) and 200 patients with Senior-Løken Syndrome (SLS). We identified a novel missense mutation in WDR19, c.2129T>C which lead to a p.Leu710Ser. We found the same mutation in a second Quebec arRP family. Interestingly, two of seven affected members of the original family developed ‘sub-clinical’ renal cysts. We hypothesized that more severe WDR19 mutations may lead to severe ciliopathies and found seven WDR19 mutations in five SLS families. We identified a new gene for both arRP and SLS. WDR19 is a ciliary protein associated with the intraflagellar transport machinery. We are currently investigating the full extent of the mutation spectrum. Our findings are crucial in expanding the understanding of childhood blindness and identifying new genes. PMID:23683095

  18. Suspended load and bed-load transport of particle-laden gravity currents: the role of particle-bed interaction

    NASA Astrophysics Data System (ADS)

    Dufek, J.; Bergantz, G. W.

    2007-03-01

    The development of particle-enriched regions (bed-load) at the base of particle-laden gravity currents has been widely observed, yet the controls and relative partitioning of material into the bed-load is poorly understood. We examine particle-laden gravity currents whose initial mixture (particle and fluid) density is greater than the ambient fluid, but whose interstitial fluid density is less than the ambient fluid (such as occurs in pyroclastic flows produced during volcanic eruptions or when sediment-enriched river discharge enters the ocean, generating hyperpycnal turbidity currents). A multifluid numerical approach is employed to assess suspended load and bed-load transport in particle-laden gravity currents under varying boundary conditions. Particle-laden flows that traverse denser fluid (such as pyroclastic flows crossing water) have leaky boundaries that provide the conceptual framework to study suspended load in isolation from bed-load transport. We develop leaky and saltation boundary conditions to study the influence of flow substrate on the development of bed-load. Flows with saltating boundaries develop particle-enriched basal layers (bed-load) where momentum transfer is primarily a result of particle-particle collisions. The grain size distribution is more homogeneous in the bed-load and the saltation boundaries increase the run-out distance and residence time of particles in the flow by as much as 25% over leaky boundary conditions. Transport over a leaky substrate removes particles that reach the bottom boundary and only the suspended load remains. Particle transport to the boundary is proportional to the settling velocity of particles, and flow dilution results in shear and buoyancy instabilities at the upper interface of these flows. These instabilities entrain ambient fluid, and the continued dilution ultimately results in these currents becoming less dense than the ambient fluid. A unifying concept is energy dissipation due to particle

  19. Turbulent transport of alpha particles in reactor plasmas

    SciTech Connect

    Estrada-Mila, C.; Candy, J.; Waltz, R. E.

    2006-11-15

    A systematic study of the behavior of energetic ions in reactor plasmas is presented. Using self-consistent gyrokinetic simulations, in concert with an analytic asymptotic theory, it is found that alpha particles can interact significantly with core ion-temperature-gradient turbulence. Specifically, the per-particle flux of energetic alphas is comparable to the per-particle flux of thermal species (deuterium or helium ash). This finding opposes the conventional wisdom that energetic ions, because of their large gyroradii, do not interact with the turbulence. For the parameters studied, a turbulent modification of the alpha-particle density profile appears to be stronger than turbulent modification of the alpha-particle pressure profile. Crude estimates indicate that the alpha density modification, which is directly proportional to the core turbulence intensity, could be in the range of 15% at midradius in a reactor. The corresponding modification of the alpha-particle pressure profile is predicted to be smaller (in the 1% range)

  20. Transport and Retention of Engineered Nanoporous Particles in Porous Media: Effects of Concentration and Flow Dynamics

    SciTech Connect

    Shang, Jianying; Liu, Chongxuan; Wang, Zheming

    2013-01-20

    Engineered nanoporous particles are an important class of nano-structured materials that can be functionalized in their internal surfaces for various applications including groundwater contaminant sequestration. This paper reported a study of transport and retention of engineered nanoporous silicate particles (ENSPs) that are designed for treatment and remediation of contaminants such as uranium in groundwater and sediments. The transport and retention of ENSPs were investigated under variable particle concentrations and dynamic flow conditions in a synthetic groundwater that mimics field groundwater chemical composition. The dynamic flow condition was achieved using a flow-interruption (stop-flow) approach with variable stop-flow durations to explore particle retention and release kinetics. The results showed that the ENSPs transport was strongly affected by the particle concentrations and dynamic flow conditions. A lower injected ENSPs concentration and longer stop-flow duration led to a more particle retention. The experimental data were used to evaluate the applicability of various kinetic models that were developed for colloidal particle retention and release in describing ENSPs transport. Model fits suggested that the transport and retention of ENSPs were subjected to a complex coupling of reversible attachment/detachment and straining/liberation processes. Both experimental and modeling results indicated that dynamic groundwater flow condition is an important parameter to be considered in exploring and modeling engineered particle transport in subsurface porous media.

  1. Particle Transport and Energization Associated with Disturbed Magnetospheric Events

    SciTech Connect

    C.Z. Cheng; J.R. Johnson; S. Zaharia

    1999-11-01

    Energetic particle flux enhancement events observed by satellites during strongly disturbed events in the magnetosphere (e.g., substorms, storm sudden commencements, etc.) are studied by considering interaction of particles with Earthward propagating electromagnetic pulses of westward electric field and consistent magnetic field of localized radial and azimuthal extent in a background magnetic field. The energetic particle flux enhancement is mainly due to the betatron acceleration process: particles are swept by the Earthward propagating electric field pulses via the EXB drift toward the Earth to higher magnetic field locations and are energized because of magnetic moment conservation. The most energized particles are those which stay in the pulse for the longest time and are swept the longest radial distance toward the Earth. Assuming a constant propagating velocity of the pulse we obtain analytical solutions of particle orbits. We examine substorm energetic particle injection by computing the particle flux and comparing with geosynchronous satellite observations. Our results show that for pulse parameters leading to consistency with observed flux values, the bulk of the injected particles arrive from distances less than 9 R(subscript E), which is closer to the Earth than the values obtained by the previous model and is also closer to the distances obtained by the injection boundary model.

  2. Molecular approach to intracellular cargo transport

    NASA Astrophysics Data System (ADS)

    Yildiz, Ahmet

    2010-03-01

    Landmark discoveries in the study of cytoplasmic motors have been made through advances in single molecule biophysics and detailed mechanistic models exist for kinesin and dynein. However, the function of motors in physiological conditions has not been carefully tested. In cells, more than few dyneins can attach to the same cargo and interact with the opposite polarity motors of kinesin. To study the molecular crosstalk between the motors, we have used intraflagellar transport (IFT) in Chlamydomonas reinhardtii as a model system. Ultrahigh spatio-temporal tracking of single cargo movement showed that IFT particles move for long distances unidirectionally with 8 nm increments, agreeing with measured step sizes of kinesin and dynein. To measure how many motors transport each cargo, we have linked large polystyrene beads to internal IFT particles through a transmembrane protein. Force measurements indicated that, on average, 3-4 motors transport cargoes in each direction. The results showed that IFT motors are tightly coordinated and might be involved in recycling each other to the appropriate end of the flagellum.

  3. Airflow, transport and regional deposition of aerosol particles during chronic bronchitis of human central airways.

    PubMed

    Farkhadnia, Fouad; Gorji, Tahereh B; Gorji-Bandpy, Mofid

    2016-03-01

    In the present study, the effects of airway blockage in chronic bronchitis disease on the flow patterns and transport/deposition of micro-particles in a human symmetric triple bifurcation lung airway model, i.e., Weibel's generations G3-G6 was investigated. A computational fluid and particle dynamics model was implemented, validated and applied in order to evaluate the airflow and particle transport/deposition in central airways. Three breathing patterns, i.e., resting, light activity and moderate exercise, were considered. Using Lagrangian approach for particle tracking and random particle injection, an unsteady particle tracking method was performed to simulate the transport and deposition of micron-sized aerosol particles in human central airways. Assuming laminar, quasi-steady, three-dimensional air flow and spherical non-interacting particles in sequentially bifurcating rigid airways, airflow patterns and particle transport/deposition in healthy and chronic bronchitis (CB) affected airways were evaluated and compared. Comparison of deposition efficiency (DE) of aerosols in healthy and occluded airways showed that at the same flow rates DE values are typically larger in occluded airways. While in healthy airways, particles deposit mainly around the carinal ridges and flow dividers-due to direct inertial impaction, in CB affected airways they deposit mainly on the tubular surfaces of blocked airways because of gravitational sedimentation. PMID:26541595

  4. Transport of airborne particles in straight and curved microchannels

    NASA Astrophysics Data System (ADS)

    Schaap, Allison; Chu, Winnie C.; Stoeber, Boris

    2012-08-01

    The measurement of airborne particles is important for environmental and exposure monitoring. Microfluidic technologies present potential advantages for aerosol monitoring but have been applied very little to the handling of airborne particles. In this paper, we examine the flow focusing and cross-streamline diffusion of aerosols in straight microchannels, and the size-based lateral displacement of aerosols caused by centrifugal forces in a curved channel. We present calculations, simulations, and experimental results verifying the models: measurements of the focusing and diffusion of 0.2 μm and 0.75 μm particles in straight channels and of the size-dependent lateral displacement of particles between 0.2 μm and 2 μm in curved channels are demonstrated and shown to match well with the simulations. We observe lateral dispersion of the particles: particles closer to the top and bottom wall of the channel experience less lateral displacement than particles near the center due to the flow velocity distribution across the channel cross section. These results confirm that the microchannel techniques presented are a viable method for the size-based manipulation of airborne particles.

  5. Transport of inertial particles in a turbulent premixed jet flame

    NASA Astrophysics Data System (ADS)

    Battista, F.; Picano, F.; Troiani, G.; Casciola, C. M.

    2011-12-01

    The heat release, occurring in reacting flows, induces a sudden fluid acceleration which particles follow with a certain lag, due to their finite inertia. Actually, the coupling between particle inertia and the flame front expansion strongly biases the spatial distribution of the particles, by inducing the formation of localized clouds with different dimensions downstream the thin flame front. A possible indicator of this preferential localization is the so-called Clustering Index, quantifying the departure of the actual particle distribution from the Poissonian, which would correspond to a purely random spatial arrangement. Most of the clustering is found in the flame brush region, which is spanned by the fluctuating instantaneous flame front. The effect is significant also for very light particles. In this case a simple model based on the Bray-Moss-Libby formalism is able to account for most of the deviation from the Poissonian. When the particle inertia increases, the effect is found to increases and persist well within the region of burned gases. The effect is maximum when the particle relaxation time is of the order of the flame front time scale. The evidence of this peculiar source of clustering is here provided by data from a direct numerical simulation of a turbulent premixed jet flame and confirmed by experimental data.

  6. Co-transport of Pseudomonas putida and kaolinite colloid particles through water saturated porous media

    NASA Astrophysics Data System (ADS)

    Vasiliadou, I. A.; Chrysikopoulos, C. V.

    2009-04-01

    Groundwater contamination is often associated with the presence of dissolved contaminants and/or suspended particles, which are either harmful biocolloids or toxic substances sorbed onto colloid particles. The present study focuses on the transport of bacteria in porous media in the presence of suspended kaolinite colloid particles. The bacteria used are the species Pseudomonas putida. Batch sorption experiments were conducted to investigate the adsorption of Pseudomonas putida onto the surfaces of kaolinite particles. The results from the batch experiments indicate that Pseudomonas putida significantly adsorbed onto kaolinite colloid particles. The adsorption process is adequately described by a Langmuir type isotherm. Transport experiments were conducted under various flow conditions in water saturated columns packed with glass beads. Initial flowthrough experiments were performed with bacteria and kaolinite alone in order to better understand their individual transport characteristics. Finally, Pseudomonas putida and kaolinite colloid particles were injected simultaneously into the packed column in order to investigate their co-transport behavior. The flowthrough experimental data suggest that the presence of the clay particles significantly inhibit the transport of bacteria in water saturated porous media. The observed reduction of Pseudomonas putida recovery at the packed column exit is mainly attributed to the attachment of bacteria onto kaolinite particles, which are adsorbed onto the solid matrix of the column.

  7. Transport and Attenuation of Particles of Different Density and Surface Charge: A Karst Aquifer Field Study.

    PubMed

    Schiperski, Ferry; Zirlewagen, Johannes; Scheytt, Traugott

    2016-08-01

    Although karst aquifers are far more susceptible to contamination than porous aquifers, with the transport of particulate matter being an important factor, little is known about the attenuation of solutes within karst aquifers and even less about the attenuation of particulate matter. These in situ investigations have therefore aimed to systematically identify the processes that influence the transport and attenuation of particles within a karst aquifer through multitracer testing, using four different types of 1 μm fluorescent particles and the fluorescent dye uranine. Each of the types of particles used were detected at the observed spring, which drains the investigated aquifer. However, the transport behavior varied significantly between the various particles and the uranine dye, with the breakthrough of particles occurring slightly earlier than that of uranine. Attenuation was determined from the tracer recovery and attributed to filtration processes. These processes were affected by the hydrophobicity and surface charge of the particles. Carboxylated polystyrene particles with a density and surface charge comparable to pathogenic microorganisms were found to be mobile in groundwater over a distance of about 3 km. No attenuation was observed for plain silica particles. Particles with these characteristics thus pose a major threat to karst spring water as they might occur as contaminants themselves or facilitate the transport of other contaminants. PMID:27348254

  8. Small particle transport across turbulent nonisothermal boundary layers

    NASA Technical Reports Server (NTRS)

    Rosner, D. E.; Fernandez De La Mora, J.

    1982-01-01

    The interaction between turbulent diffusion, Brownian diffusion, and particle thermophoresis in the limit of vanishing particle inertial effects is quantitatively modeled for applications in gas turbines. The model is initiated with consideration of the particle phase mass conservation equation for a two-dimensional boundary layer, including the thermophoretic flux term directed toward the cold wall. A formalism of a turbulent flow near a flat plate in a heat transfer problem is adopted, and variable property effects are neglected. Attention is given to the limit of very large Schmidt numbers and the particle concentration depletion outside of the Brownian sublayer. It is concluded that, in the parameter range of interest, thermophoresis augments the high Schmidt number mass-transfer coefficient by a factor equal to the product of the outer sink and the thermophoretic suction.

  9. The role of particle collisions in pneumatic transport

    NASA Technical Reports Server (NTRS)

    Mastorakos, E.; Louge, M.; Jenkins, J. T.

    1989-01-01

    A model of dilute gas-solid flow in vertical risers is developed in which the particle phase is treated as a granular material, the balance equations for rapid granular flow are modified to incorporate the drag force from the gas, and boundary conditions, based on collisional exchanges of momentum and energy at the wall, are employed. In this model, it is assumed that the particle fluctuations are determined by inter-particle collisions only and that the turbulence of the gas is unaffected by the presence of the particles. The model is developed in the context of, but not limited to, steady, fully developed flow. A numerical solution of the resulting governing equations provides concentration profiles generally observed in dilute pneumatic flow, velocity profiles in good agreement with the measurements of Tsuji, et al. (1984), and an explanation for the enhancement of turbulence that they observed.

  10. Investigating the role of particle shape on colloid transport and retention in saturated porous media (Invited)

    NASA Astrophysics Data System (ADS)

    Li, Y.; Seymour, M.; Chen, G.; Su, C.

    2011-12-01

    Mechanistic understanding of the transport and retention of nanoparticles in porous media is essential both for environmental applications of nanotechnology and assessing the potential environmental impacts of engineered nanomaterials. Engineered and naturally occurring nanoparticles can be found in various shapes including rod-shape carbon nanotubes that have high aspect ratios. Although it is expected that nonspherical shape could play an important role on their transport and retention behaviors, current theoretical models for particle transport in porous media, however, are mostly based on spherical particle shape. In this work, the effect of particle shape on its transport and retention in porous media was evaluated by stretching carboxylate-modified fluorescent polystyrene spheres into rod shapes with aspect ratios of 2:1 and 4:1. Quartz crystal microbalance with dissipation experiments (QCM-D) were conducted to measure the deposition rates of spherical and rod-shaped nanoparticles to the collector (poly-L-lysine coated silica sensor) surface under favorable conditions. Under unfavorable conditions, the retention of nanoparticles in a microfluidic flow cell packed with glass beads was studied with the use of laser scanning cytometry (LSC). Under favorable conditions, the spherical particles displayed a significantly higher deposition rate compared with that of the rod-shaped particles. Theoretical analysis based on Smoluchowski-Levich approximation indicated that the rod-shaped particles largely counterbalance the attractive energies due to higher hydrodynamic forces and torques experienced during their transport and rotation. Under unfavorable conditions, significantly more attachment was observed for rod-shaped particles than spherical particles, and the attachment rate of the rod-shaped particles showed an increasing trend with the increase in injection volume. Rod-shaped particles were found to be less sensitive to the surface charge heterogeneity change

  11. Investigating the role of particle shape on colloid transport and retention in saturated porous media (Invited)

    NASA Astrophysics Data System (ADS)

    Li, Y.; Seymour, M.; Chen, G.; Su, C.

    2013-12-01

    Mechanistic understanding of the transport and retention of nanoparticles in porous media is essential both for environmental applications of nanotechnology and assessing the potential environmental impacts of engineered nanomaterials. Engineered and naturally occurring nanoparticles can be found in various shapes including rod-shape carbon nanotubes that have high aspect ratios. Although it is expected that nonspherical shape could play an important role on their transport and retention behaviors, current theoretical models for particle transport in porous media, however, are mostly based on spherical particle shape. In this work, the effect of particle shape on its transport and retention in porous media was evaluated by stretching carboxylate-modified fluorescent polystyrene spheres into rod shapes with aspect ratios of 2:1 and 4:1. Quartz crystal microbalance with dissipation experiments (QCM-D) were conducted to measure the deposition rates of spherical and rod-shaped nanoparticles to the collector (poly-L-lysine coated silica sensor) surface under favorable conditions. Under unfavorable conditions, the retention of nanoparticles in a microfluidic flow cell packed with glass beads was studied with the use of laser scanning cytometry (LSC). Under favorable conditions, the spherical particles displayed a significantly higher deposition rate compared with that of the rod-shaped particles. Theoretical analysis based on Smoluchowski-Levich approximation indicated that the rod-shaped particles largely counterbalance the attractive energies due to higher hydrodynamic forces and torques experienced during their transport and rotation. Under unfavorable conditions, significantly more attachment was observed for rod-shaped particles than spherical particles, and the attachment rate of the rod-shaped particles showed an increasing trend with the increase in injection volume. Rod-shaped particles were found to be less sensitive to the surface charge heterogeneity change

  12. Smoothed Particle Hydrodynamics Model for Reactive Transport and Mineral Precipitation

    SciTech Connect

    Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Redden, George; Meakin, Paul; Fang, Yilin

    2006-06-30

    A new Lagrangian particle model based on smoothed particle hydrodynamics was used to simulate pore scale precipitation reactions. The side-by-side injection of reacting solutions into two halves of a two-dimensional granular porous medium was simulated. Precipitation on grain surfaces occurred along a narrow zone in the middle of the domain, where the reacting solutes mixed to generate a supersaturated reaction product. The numerical simulations qualitatively reproduced the behavior observed in related laboratory experiments.

  13. Single Particle Tracking Reveals Biphasic Transport During Nanorod Magnetophoresis Through Extracellular Matrix

    PubMed Central

    Mair, L.O.; Superfine, R.

    2014-01-01

    Magnetic drug targeting has been proposed as a means of efficiently targeting drugs to tumors. However, the extracellular matrix (ECM) remains a significant barrier to long-range magnetophoretic transport through the tumor volume. While ensemble measurements of nanoparticle magnetophoresis have been reported, a single particle level understanding of magnetophoretic transport remains at large. We quantify nanorod magnetophoresis through ECM based on single particle observations. We find that smaller diameter particles achieve larger velocities through ECM despite experiencing smaller magnetic forces. Additionally, two interesting dynamics are elucidated. First, 18 nm diameter nanorods experience bimodal stick-slip motion through ECM during static field magnetophoresis, while similar bimodal transport is not observed for 55 nm nor 200 nm diameter nanorods. Second, smaller particles experience larger deviations in their orientation angle with respect to the magnetic field. This work elucidates important dynamics of nanoparticle transport through complex, porous biomaterials that may go unnoticed during ensemble measurements. PMID:24744160

  14. Changes in particle transport as a result of resonant magnetic perturbations in DIII-D

    SciTech Connect

    Mordijck, S.; Doyle, E. J.; McKee, G. R.; Moyer, R.A.; Rhodes, T. L.; Zeng, L.; Commaux, Nicolas JC; Fenstermacher, M. E.; Gentle, T. K.; Reimerdes, H.; Schmitz, O.; Solomon, W. M.; Staebler, G. M.; Wang, G. Y.

    2012-01-01

    In this paper, we introduce the first direct perturbed particle transport measurements in resonant magnetic perturbation (RMP) H-mode plasmas. The perturbed particle transport increases as a result of application of RMP deep into the core. In the core, a large reduction in E x B shear to a value below the linear growth rate, in conjunction with increasing density fluctuations, is consistent with an increase in turbulent particle transport. In the edge, the changes in turbulent particle transport are less obvious. There is a clear correlation between the linear growth rates and the density fluctuations measured at different scales, but it is uncertain which is the cause and which is the consequence.

  15. Changes in particle transport as a result of resonant magnetic perturbations in DIII-D

    SciTech Connect

    Mordijck, S.; Doyle, E. J.; Rhodes, T. L.; Zeng, L.; Wang, G.; McKee, G. R.; Moyer, R. A.; Commaux, N.; Fenstermacher, M. E.; Gentle, K. W.; Reimerdes, H.; Schmitz, O.; Solomon, W. M.; Staebler, G. M.

    2012-05-15

    In this paper, we introduce the first direct perturbed particle transport measurements in resonant magnetic perturbation (RMP) H-mode plasmas. The perturbed particle transport increases as a result of application of RMP deep into the core. In the core, a large reduction in E Multiplication-Sign B shear to a value below the linear growth rate, in conjunction with increasing density fluctuations, is consistent with an increase in turbulent particle transport. In the edge, the changes in turbulent particle transport are less obvious. There is a clear correlation between the linear growth rates and the density fluctuations measured at different scales, but it is uncertain which is the cause and which is the consequence.

  16. Review of the facile (F/sub N/) method in particle transport theory

    SciTech Connect

    Garcia, R.D.M.

    1985-10-01

    The facile (F/sub N/) method for solving particle transport problems is reviewed. The fundamentals of the method are summarized, recent developments are discussed and several applications of the method are described in detail.

  17. Modeling particle transport by bubbles for performance guidelines in airlift fermentors.

    PubMed

    Snape, J B; Thomas, N H

    1992-07-01

    A calculation method has been developed to model the statistical transport of biological particles in bubble-driven flows, with special reference to the biokinetics of environmental excursions experienced by individual cells, aggregated cells, or immobilization beads in airlift bioreactors. Interim developments on modeling the transport of such particles in concentric tube devices are reported. The calculation is driven by user-prescribed global parameters for the bioreactor geometry, bulk air flow rate, and particle parameters (size and slip speed). The algorithm calls on empirical data correlations for void fraction, bulk liquid flow rate, and bubble sizes and slip speeds, optimally selected from a large bibliographic database. The Monte Carlo algorithm concentrates on simulating particle transport in the bubbly riser flows.The packaged family of correlations and calculations represents, in effect, an expert system augmented by a transport simulation suited to characterizing the biokinetic response of cells cultured in airlift bioreactors. PMID:18601123

  18. DANTSYS: A diffusion accelerated neutral particle transport code system

    SciTech Connect

    Alcouffe, R.E.; Baker, R.S.; Brinkley, F.W.; Marr, D.R.; O`Dell, R.D.; Walters, W.F.

    1995-06-01

    The DANTSYS code package includes the following transport codes: ONEDANT, TWODANT, TWODANT/GQ, TWOHEX, and THREEDANT. The DANTSYS code package is a modular computer program package designed to solve the time-independent, multigroup discrete ordinates form of the boltzmann transport equation in several different geometries. The modular construction of the package separates the input processing, the transport equation solving, and the post processing (or edit) functions into distinct code modules: the Input Module, one or more Solver Modules, and the Edit Module, respectively. The Input and Edit Modules are very general in nature and are common to all the Solver Modules. The ONEDANT Solver Module contains a one-dimensional (slab, cylinder, and sphere), time-independent transport equation solver using the standard diamond-differencing method for space/angle discretization. Also included in the package are solver Modules named TWODANT, TWODANT/GQ, THREEDANT, and TWOHEX. The TWODANT Solver Module solves the time-independent two-dimensional transport equation using the diamond-differencing method for space/angle discretization. The authors have also introduced an adaptive weighted diamond differencing (AWDD) method for the spatial and angular discretization into TWODANT as an option. The TWOHEX Solver Module solves the time-independent two-dimensional transport equation on an equilateral triangle spatial mesh. The THREEDANT Solver Module solves the time independent, three-dimensional transport equation for XYZ and RZ{Theta} symmetries using both diamond differencing with set-to-zero fixup and the AWDD method. The TWODANT/GQ Solver Module solves the 2-D transport equation in XY and RZ symmetries using a spatial mesh of arbitrary quadrilaterals. The spatial differencing method is based upon the diamond differencing method with set-to-zero fixup with changes to accommodate the generalized spatial meshing.

  19. Directed Magnetic Particle Transport above Artificial Magnetic Domains Due to Dynamic Magnetic Potential Energy Landscape Transformation.

    PubMed

    Holzinger, Dennis; Koch, Iris; Burgard, Stefan; Ehresmann, Arno

    2015-07-28

    An approach for a remotely controllable transport of magnetic micro- and/or nanoparticles above a topographically flat exchange-bias (EB) thin film system, magnetically patterned into parallel stripe domains, is presented where the particle manipulation is achieved by sub-mT external magnetic field pulses. Superparamagnetic core-shell particles are moved stepwise by the dynamic transformation of the particles' magnetic potential energy landscape due to the external magnetic field pulses without affecting the magnetic state of the thin film system. The magnetic particle velocity is adjustable in the range of 1-100 μm/s by the design of the substrate's magnetic field landscape (MFL), the particle-substrate distance, and the magnitude of the applied external magnetic field pulses. The agglomeration of magnetic particles is avoided by the intrinsic magnetostatic repulsion of particles due to the parallel alignment of the particles' magnetic moments perpendicular to the transport direction and parallel to the surface normal of the substrate during the particle motion. The transport mechanism is modeled by a quantitative theory based on the precise knowledge of the sample's MFL and the particle-substrate distance. PMID:26134922

  20. Third-order TRANSPORT: A computer program for designing charged particle beam transport systems

    SciTech Connect

    Carey, D.C.; Brown, K.L.; Rothacker, F.

    1995-05-01

    TRANSPORT has been in existence in various evolutionary versions since 1963. The present version of TRANSPORT is a first-, second-, and third-order matrix multiplication computer program intended for the design of static-magnetic beam transport systems. This report discusses the following topics on TRANSPORT: Mathematical formulation of TRANSPORT; input format for TRANSPORT; summaries of TRANSPORT elements; preliminary specifications; description of the beam; physical elements; other transformations; assembling beam lines; operations; variation of parameters for fitting; and available constraints -- the FIT command.

  1. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    SciTech Connect

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates mass balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.

  2. Particle tracking approach for transport in three-dimensional discrete fracture networks: Particle tracking in 3-D DFNs

    DOE PAGESBeta

    Makedonska, Nataliia; Painter, Scott L.; Bui, Quan M.; Gable, Carl W.; Karra, Satish

    2015-09-16

    The discrete fracture network (DFN) model is a method to mimic discrete pathways for fluid flow through a fractured low-permeable rock mass, and may be combined with particle tracking simulations to address solute transport. However, experience has shown that it is challenging to obtain accurate transport results in three-dimensional DFNs because of the high computational burden and difficulty in constructing a high-quality unstructured computational mesh on simulated fractures. We present a new particle tracking capability, which is adapted to control volume (Voronoi polygons) flow solutions on unstructured grids (Delaunay triangulations) on three-dimensional DFNs. The locally mass-conserving finite-volume approach eliminates massmore » balance-related problems during particle tracking. The scalar fluxes calculated for each control volume face by the flow solver are used to reconstruct a Darcy velocity at each control volume centroid. The groundwater velocities can then be continuously interpolated to any point in the domain of interest. The control volumes at fracture intersections are split into four pieces, and the velocity is reconstructed independently on each piece, which results in multiple groundwater velocities at the intersection, one for each fracture on each side of the intersection line. This technique enables detailed particle transport representation through a complex DFN structure. Verified for small DFNs, the new simulation capability enables numerical experiments on advective transport in large DFNs to be performed. As a result, we demonstrate this particle transport approach on a DFN model using parameters similar to those of crystalline rock at a proposed geologic repository for spent nuclear fuel in Forsmark, Sweden.« less

  3. FACTORS IN GEOTROPOSPHERIC PARTICLE-GAS TRANSPORT OF SEMIVOLATILE ORGANIC COMPOUNDS

    EPA Science Inventory

    Semivolatile organic compounds (SVOCs) can exist in solid, liquid, or gas phases under ambient environmental conditions. The geotropospheric transport of SVOCs varies according to the particle type. Two classes of SVOCs and two types of particles were analyzed to determine possib...

  4. NANO-PARTICLE TRANSPORT AND DEPOSITION IN BIFURCATING TUBES WITH DIFFERENT INLET CONDITIONS

    EPA Science Inventory

    Transport and deposition of ultrafine particles in straight, bend and bifurcating tubes are considered for different inlet Reynolds numbers, velocity profiles, and particle sizes i.e., 1 nm= =150 nm. A commercial finite-volume code with user-supplied programs was validated with a...

  5. Collisional interactions of ring particles - The ballistic transport process

    NASA Astrophysics Data System (ADS)

    Ip, W.-H.

    1983-05-01

    The role of variations in the size distribution, optical depth, and surface composition of Saturnian ring material in the dynamics of production and recycling of dust particles in the whole ring system is examined. A simple Monte Carlo model incorporating the ballistic motion of small dust particles ejected by meteoroid impact as well as the inelastic collision of the ejected particles with the ring plane is presented. It is found that the redistribution of the ejected matter depends on the optical depth variation across the ring system and the initial ejection speed, and hence the scale length of random walk on the ring plane. For small values of the scale length, the ejecta would accumulate at positions of sharp change in optical depth. On the basis of this result, it is conjectured that the double-peaked feature observed for a number of narrow ringlets may be generated in this manner also.

  6. Transport of transient solar wind particles in Earth's cusps

    SciTech Connect

    Parks, G. K.; Lee, E.; Teste, A.; Wilber, M.; Lin, N.; Canu, P.; Dandouras, I.; Reme, H.; Fu, S. Y.; Goldstein, M. L.

    2008-08-15

    An important problem in space physics still not understood well is how the solar wind enters the Earth's magnetosphere. Evidence is presented that transient solar wind particles produced by solar disturbances can appear in the Earth's mid-altitude ({approx}5 R{sub E} geocentric) cusps with densities nearly equal to those in the magnetosheath. That these are magnetosheath particles is established by showing they have the same ''flattop'' electron distributions as magnetosheath electrons behind the bow shock. The transient ions are moving parallel to the magnetic field (B) toward Earth and often coexist with ionospheric particles that are flowing out. The accompanying waves include electromagnetic and broadband electrostatic noise emissions and Bernstein mode waves. Phase-space distributions show a mixture of hot and cold electrons and multiple ion species including field-aligned ionospheric O{sup +} beams.

  7. Using ACE and Ulysses to investigate the heliographic transport of energetic particles

    NASA Astrophysics Data System (ADS)

    Robinson, Ian M.

    2002-03-01

    The Advanced Composition Explorer (ACE) and the Ulysses spacecraft follow radically different trajectories, allowing the Sun to be simultaneously studied from 2 different perspectives. Data from the low energy particle instruments carried by these spacecraft reveals energetic particles accelerated at the Sun can access large angular extents of the interplanetary medium. We look at a rare case when the heliographic transport of energetic electrons was apparently prevented and speculate upon the ability of the corona to inhibit the propagation of these particles.

  8. Probabilistic description of particle transport. I. General theory of quasielastic scattering in plane-parallel media

    SciTech Connect

    Goulet, T.; Keszei, E.; Jay-Gerin, J.

    1988-03-15

    We present a three-dimensional probabilistic model of particle transport in a medium where the particles suffer quasielastic collisions. The model accounts for bulk and surface scattering, as well as partial reflections at the boundaries of the medium. We give analytical and numerical methods for the evaluation of the particle transmission probability in the case of a medium with a plane-parallel geometry. The influence of the various parameters of the model on this probability is also discussed.

  9. Sandia Computational Engine for Particle Transport for Radiation Effects v 1.4

    Energy Science and Technology Software Center (ESTSC)

    2014-01-24

    The SCEPTRE code solves the linear Boltzmann transport equation for general two- and three-dimensional geometries. SCEPTRE is capable of handling any particle type for which multigroup-Legendre cross sections are available. However, the code is designed primarily to model the transport of photons, electrons, and positrons through matter.

  10. Onset Times of Solar Particle Events Observed by MSL/RAD - Constraints on Particle Transport

    NASA Astrophysics Data System (ADS)

    Wimmer-Schweingruber, R. F.; Hassler, D. M.; Boettcher, S.; Martin, C.; Zeitlin, C.; Brinza, D.; Koehler, J.; Guo, J.; Posner, A.; Appel, J.

    2012-12-01

    En route to Mars, Mars Science Laboratory's (MSL's) Radiation Assessment Detector (RAD) was already operational and observed a number of solar particle events. These were also seen by an array of spacecraft in the heliosphere. This constellation provides an unique opportunity to investigate particle propagation in the ecliptic plane and thus constrain particle propagation models. RAD measures energetic ions up to approximately 100 MeV/nuc, but was buried deep inside the Mars Science Laboratory (MSL). Due to the significant shielding provided by the MSL cruise stage, back-shell, heat shield, and skycrane, RAD was sensitive to particles in a significantly higher and somewhat uncertain energy range. Even behind the aforementioned shielding, onset times of particle events can be clearly identified. In this work, we will provide them for the particle events observed by RAD in 2012. We will also relate them to other data and solar/interplanetary acceleration sites.