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Sample records for neointimal formational pattern

  1. Vasohibin prevents arterial neointimal formation through angiogenesis inhibition

    SciTech Connect

    Yamashita, Hiroshi; Abe, Mayumi; Watanabe, Kazuhide; Shimizu, Kazue; Moriya, Takuya; Sato, Akira; Satomi, Susumu; Ohta, Hideki; Sonoda, Hikaru; Sato, Yasufumi . E-mail: y-sato@idac.tohoku.ac.jp

    2006-07-07

    Vasohibin is a VEGF-inducible angiogenesis inhibitor in vascular endothelium. Here we examined the presence of vasohibin in human arterial wall, and found it in endothelium of adventitial microvessels in atherosclerotic lesion. Adventitial angiogenesis is involved in the progression of neointimal formation. Even in the presence of endogenous angiogenesis inhibitors, pathological angiogenesis persists. However, the supplementation of exogenous angiogenesis inhibitors can prevent pathological angiogenesis. We evaluated the potential role of vasohibin in neointimal formation. Adenovirus-mediated human vasohibin gene transfer in mouse liver resulted in the release of vasohibin in plasma and exhibited anti-angiogenic effects at remote sites. This gene transfer inhibited adventitial angiogenesis, macrophage infiltration, and neointimal formation after cuff placement on mouse femoral artery. Vasohibin exhibited no direct effect on migration and proliferation of smooth muscle cells. Thus, vasohibin has an activity to prevent neointimal formation by inhibiting adventitial angiogenesis.

  2. Perivascular mast cells regulate vein graft neointimal formation and remodeling

    PubMed Central

    Grassia, Gianluca; Cambrook, Helen; Ialenti, Armando; MacRitchie, Neil; Carberry, Jaclyn; Lawrence, Catherine

    2015-01-01

    Objective. Emerging evidence suggests an important role for mast cells in vein graft failure. This study addressed the hypothesis that perivascular mast cells regulate in situ vascular inflammatory and proliferative responses and subsequent vein graft neointimal lesion formation, using an optimized local mast cell reconstitution method. Methods and Results. Neointimal hyperplasia was induced by insertion of a vein graft into the right carotid artery in wild type and mast cell deficient KitW−sh/W−sh mice. In some experiments, mast cells were reconstituted systemically (tail vein injection of bone marrow-derived mast cells) or locally (directly into the right neck area) prior to vein grafting. Vein graft neointimal lesion formation was significantly (P < 0.05) reduced in KitW−sh/W−sh mice. Mast cell deficiency reduced the number of proliferating cells, and inhibited L-selectin, CCL2, M-CSF and MIP-3α expression in the vein grafts. Local but not systemic mast cell reconstitution restored a perivascular mast cell population that subsequently promoted neointimal formation in mast cell deficient mice. Conclusion. Our data demonstrate that perivascular mast cells play a key role in promoting neointima formation by inducing local acute inflammatory and proliferative responses. These results suggest that ex vivo intraoperative targeting of mast cells may have therapeutic potential for the prevention of pathological vein graft remodeling. PMID:26312183

  3. Smooth Muscle Cell-targeted RNA Aptamer Inhibits Neointimal Formation.

    PubMed

    Thiel, William H; Esposito, Carla L; Dickey, David D; Dassie, Justin P; Long, Matthew E; Adam, Joshua; Streeter, Jennifer; Schickling, Brandon; Takapoo, Maysam; Flenker, Katie S; Klesney-Tait, Julia; Franciscis, Vittorio de; Miller, Francis J; Giangrande, Paloma H

    2016-04-01

    Inhibition of vascular smooth muscle cell (VSMC) proliferation by drug eluting stents has markedly reduced intimal hyperplasia and subsequent in-stent restenosis. However, the effects of antiproliferative drugs on endothelial cells (EC) contribute to delayed re-endothelialization and late stent thrombosis. Cell-targeted therapies to inhibit VSMC remodeling while maintaining EC health are necessary to allow vascular healing while preventing restenosis. We describe an RNA aptamer (Apt 14) that functions as a smart drug by preferentially targeting VSMCs as compared to ECs and other myocytes. Furthermore, Apt 14 inhibits phosphatidylinositol 3-kinase/protein kinase-B (PI3K/Akt) and VSMC migration in response to multiple agonists by a mechanism that involves inhibition of platelet-derived growth factor receptor (PDGFR)-β phosphorylation. In a murine model of carotid injury, treatment of vessels with Apt 14 reduces neointimal formation to levels similar to those observed with paclitaxel. Importantly, we confirm that Apt 14 cross-reacts with rodent and human VSMCs, exhibits a half-life of ~300 hours in human serum, and does not elicit immune activation of human peripheral blood mononuclear cells. We describe a VSMC-targeted RNA aptamer that blocks cell migration and inhibits intimal formation. These findings provide the foundation for the translation of cell-targeted RNA therapeutics to vascular disease. PMID:26732878

  4. Muscle-derived follistatin-like 1 functions to reduce neointimal formation after vascular injury

    PubMed Central

    Miyabe, Megumi; Ohashi, Koji; Shibata, Rei; Uemura, Yusuke; Ogura, Yasuhiro; Yuasa, Daisuke; Kambara, Takahiro; Kataoka, Yoshiyuki; Yamamoto, Takashi; Matsuo, Kazuhiro; Joki, Yusuke; Enomoto, Takashi; Hayakawa, Satoko; Hiramatsu-Ito, Mizuho; Ito, Masanori; Van Den Hoff, Maurice J.B.; Walsh, Kenneth; Murohara, Toyoaki; Ouchi, Noriyuki

    2014-01-01

    Aims It is well-established that exercise diminishes cardiovascular risk, but whether humoral factors secreted by muscle confer these benefits has not been conclusively shown. We have shown that the secreted protein follistatin-like 1 (Fstl1) has beneficial actions on cardiac and endothelial function. However, the role of muscle-derived Fstl1 in proliferative vascular disease remains largely unknown. Here, we investigated whether muscle-derived Fstl1 modulates vascular remodelling in response to injury. Methods and results The targeted ablation of Fstl1 in muscle led to an increase in neointimal formation following wire-induced arterial injury compared with control mice. Conversely, muscle-specific Fstl1 transgenic (TG) mice displayed a decrease in the neointimal thickening following arterial injury. Muscle-specific Fstl1 ablation and overexpression increased and decreased, respectively, the frequency of BrdU-positive proliferating cells in injured vessels. In cultured human aortic smooth muscle cells (HASMCs), treatment with human FSTL1 protein decreased proliferation and migration induced by stimulation with PDGF-BB. Treatment with FSTL1 enhanced AMPK phosphorylation, and inhibition of AMPK abrogated the inhibitory actions of FSTL1 on HASMC responses to PDGF-BB. The injured arteries of Fstl1-TG mice exhibited an increase in AMPK phosphorylation, and administration of AMPK inhibitor reversed the anti-proliferative actions of Fstl1 on the vessel wall. Conclusion Our findings indicate that muscle-derived Fstl1 attenuates neointimal formation in response to arterial injury by suppressing SMC proliferation through an AMPK-dependent mechanism. Thus, the release of protein factors from muscle, such as Fstl1, may partly explain why the maintenance of muscle function can have a therapeutic effect on the cardiovascular system. PMID:24743592

  5. Conditional expression of the type 2 angiotensin II receptor in mesenchymal stem cells inhibits neointimal formation after arterial injury.

    PubMed

    Feng, Jian; Liu, Jian-Ping; Miao, Li; He, Guo-Xiang; Li, De; Wang, Hai-Dong; Jing, Tao

    2014-10-01

    Percutaneous coronary interventions (PCIs) are an effective treatment for obstructive coronary artery diseases. However, the procedure's success is limited by remodeling and formation of neointima. In the present study, we engineered rat mesenchymal stem cells (MSCs) to express type 2 angiotensin II receptor (AT2R) using a tetracycline-regulated system that can strictly regulate AT2R expression. We tested the ability of the modified MSCs to reduce neointima formation following arterial injury. We subjected rats to balloon injury, and reverse transcriptase polymerase chain reaction (RT-PCR) indicated no significant AT2R expression in normal rat arteries. Low expression of AT2R was observed at 28 days after balloon-induced injury. Interestingly, MSCs alone were unable to reduce neointimal hyperplasia after balloon-induced injury; after transplantation of modified MSCs, doxycycline treatment significantly upregulated neointimal AT2R expression and inhibited osteopontin mRNA expression, as well as neointimal formation. Taken together, these results suggest that transplantation of MSCs conditionally expressing AT2R could effectively suppress neointimal hyperplasia following balloon-induced injury. Therefore, MSCs with a doxycycline-controlled gene induction system may be useful for the management of arterial injury after PCI. PMID:25119854

  6. Mebendazole Reduces Vascular Smooth Muscle Cell Proliferation and Neointimal Formation Following Vascular Injury in Mice

    PubMed Central

    Wang, Jintao; Wang, Hui; Guo, Chiao; Luo, Wei; Lawler, Alyssa; Reddy, Aswin; Wang, Julia; Sun, Eddy B.; Eitzman, Daniel T.

    2014-01-01

    Mebendazole is an antihelminthic drug that exerts its effects via interference with microtubule function in parasites. To determine the utility of mebendazole as a potential treatment for vascular diseases involving proliferation of vascular smooth muscle cells, the effects of mebendazole on vascular smooth muscle cell proliferation were tested in vitro and in a mouse model of arterial injury. In vitro, mebendazole inhibited proliferation and migration of murine vascular smooth muscle cells and this was associated with altered intracellular microtubule organization. To determine in vivo effects of mebendazole following vascular injury, femoral arterial wire injury was induced in wild-type mice treated with either mebendazole or placebo control. Compared with placebo-treated mice, mebendazole-treated mice formed less neointima at the site of injury. Mebendazole is effective at inhibiting vascular smooth muscle cell proliferation and migration, and neointimal formation following arterial injury in mice. PMID:24587248

  7. Nrf2/Keap1 system regulates vascular smooth muscle cell apoptosis for vascular homeostasis: role in neointimal formation after vascular injury

    PubMed Central

    Ashino, Takashi; Yamamoto, Masayuki; Numazawa, Satoshi

    2016-01-01

    Abnormal increases in vascular smooth muscle cells (VSMCs) in the intimal region after a vascular injury is a key event in developing neointimal hyperplasia. To maintain vascular function, proliferation and apoptosis of VSMCs is tightly controlled during vascular remodeling. NF-E2-related factor 2 (Nrf2)/Kelch-like ECH-associated protein 1 (Keap1) system, a key component of the oxidative stress response that acts in maintaining homeostasis, plays an important role in neointimal hyperplasia after a vascular injury; however, the role of Nrf2/Keap1 in VSMC apoptosis has not been clarified. Here we report that 14 days after arterial injury in mice, TUNEL-positive VSMCs are detected in both the neointimal and medial layers. These layers contain cells expressing high levels of Nrf2 but low Keap1 expression. In VSMCs, Keap1 depletion induces features of apoptosis, such as positive TUNEL staining and annexin V binding. These changes are associated with an increased expression of nuclear Nrf2. Simultaneous Nrf2 depletion inhibits Keap1 depletion-induced apoptosis. At 14 days after the vascular injury, Nrf2-deficient mice demonstrated fewer TUNEL-positive cells and increased neointimal formation in the neointimal and medial areas. The results suggest that the Nrf2/Keap1 system regulates VSMC apoptosis during neointimal formation, thereby inhibiting neointimal hyperplasia after a vascular injury. PMID:27198574

  8. Endothelial repair process and its relevance to longitudinal neointimal tissue patterns: comparing histology with in silico modelling

    PubMed Central

    Tahir, Hannan; Bona-Casas, Carles; Narracott, Andrew James; Iqbal, Javaid; Gunn, Julian; Lawford, Patricia; Hoekstra, Alfons G.

    2014-01-01

    Re-establishing a functional endothelium following endovascular treatment is an important factor in arresting neointimal proliferation. In this study, both histology (in vivo) and computational simulations (in silico) are used to evaluate neointimal growth patterns within coronary arteries along the axial direction of the stent. Comparison of the growth configurations in vivo and in silico was undertaken to identify candidate mechanisms for endothelial repair. Stent, lumen and neointimal areas were measured from histological sections obtained from eight right coronary stented porcine arteries. Two re-endothelialization scenarios (endothelial cell (EC) random seeding and EC growth from proximal and distal ends) were implemented in silico to evaluate their influence on the morphology of the simulated lesions. Subject to the assumptions made in the current simulations, comparison between in vivo and in silico results suggests that endothelial growth does not occur from the proximal and distal ends alone, but is more consistent with the assumption of a random seeding process. This may occur either from the patches of endothelium which survive following stent implantation or from attachment of circulating endothelial progenitor cells. PMID:24621816

  9. Decreased Neointimal Extracellular Matrix Formation in RAGE-Knockout Mice After Microvascular Denudation

    SciTech Connect

    Groezinger, Gerd Schmehl, Joerg Bantleon, Ruediger Kehlbach, Rainer; Mehra, Tarun; Claussen, Claus Wiesinger, Benjamin

    2012-12-15

    Purpose: To evaluate in vivo the role of RAGE (receptor for advanced glycated end products) in the development of restenosis and neointimal proliferation in RAGE-deficient knockout (KO) mice compared with wild-type (WT) mice in an animal model. Materials and Methods: Sixteen WT and 15 RAGE-deficient mice underwent microvascular denudation of the common femoral artery under general anaesthesia. Contralateral arteries underwent a sham operation and served as controls. Four weeks after the intervention, all animals were killed, and paraformaldehyde-fixed specimens of the femoral artery were analysed with different stains (hematoxylin and eosin and Elastica van Gieson) and several different types of immunostaining (proliferating cell nuclear antigen, {alpha}-actin, collagen, von Willebrand factor, RAGE). Luminal area, area of the neointima, and area of the media were measured in all specimens. In addition, colony-formation assays were performed, and collagen production by WT smooth muscle cells (SMCs) and RAGE-KO SMCs was determined. For statistical analysis, P < 0.05 was considered statistically significant. Results: Four weeks after denudation, WT mice showed a 49.6% loss of luminal area compared with 14.9% loss of luminal area in RAGE-deficient mice (sham = 0% loss) (P < 0.001). The neointima was 18.2 (*1000 {mu}m{sup 2} [n = 15) in the WT group compared with only 8.4 (*1000 {mu}m{sup 2} [n = 16]) in the RAGE-KO group. RAGE-KO SMCs showed significantly decreased proliferation activity and production of extracellular matrix protein. Conclusion: RAGE may be shown to play a considerable role in the formation of neointima leading to restenosis after vascular injury.

  10. Morelloflavone blocks injury-induced neointimal formation by inhibiting vascular smooth muscle cell migration

    PubMed Central

    Pinkaew, Decha; Cho, Sung Gook; Hui, David Y.; Wiktorowicz, John E.; Hutadilok-Towatana, Nongporn; Mahabusarakam, Wilawan; Tonganunt, Moltira; Stafford, Lewis J.; Phongdara, Amornrat; Liu, Mingyao; Fujise, Ken

    2014-01-01

    Background In-stent restenosis, or renarrowing within a coronary stent, is the most ominous complication of percutaneous coronary intervention, caused by vascular smooth muscle cell (VSMC) migration into and proliferation in the intima. Although drug-eluting stents reduce restenosis, they delay the tissue healing of the injured arteries. No promising alternative anti-restenosis treatments are currently on the horizon. Methods & Results In endothelium-denudated mouse carotid arteries, oral morelloflavone—an active ingredient of the Thai medicinal plant Garcinia dulcis—significantly decreased the degree of neointimal hyperplasia, without affecting neointimal cell cycle progression or apoptosis as evaluated by Ki-67 and TUNEL staining, respectively. At the cellular level, morelloflavone robustly inhibited VSMC migration as shown by both scratch wound and invasion assays. In addition, morelloflavone prevented VSMCs from forming lamellipodia, a VSMC migration apparatus. Mechanistically, the inhibition by morelloflavone of VSMC migration was through its negative regulatory effects on several migration-related kinases, including FAK, Src, ERK, and RhoA. Consistently with the animal data, morelloflavone did not affect VSMC cell cycle progression or induce apoptosis. Conclusion These data suggest that morelloflavone blocks injury-induced neointimal hyperplasia via the inhibition of VSMC migration, without inducing apoptosis or cell cycle arrest. General Significance We propose morelloflavone to be a viable oral agent for the prevention of restenosis, without compromising effects on the integrity and healing of the injured arteries. PMID:18930785

  11. Kir2.1 regulates rat smooth muscle cell proliferation, migration, and post-injury carotid neointimal formation.

    PubMed

    Qiao, Yong; Tang, Chengchun; Wang, Qingjie; Wang, Dong; Yan, Gaoliang; Zhu, Boqian

    2016-09-01

    Phenotype switching of vascular smooth muscle cells (VSMC) from the contractile type to the synthetic type is a hallmark of vascular disorders such as atherosclerosis and restenosis after angioplasty. Inward rectifier K(+) channel 2.1 (Kir2.1) has been identified in VSMC. However, whether it plays a functional role in regulating cellular transformation remains obscure. In this study, we evaluated the role of Kir2.1 on VSMC proliferation, migration, phenotype switching, and post-injury carotid neointimal formation. Kir2.1 knockdown significantly suppressed platelet-derived growth factor BB-stimulated rat vascular smooth muscle cells (rat-VSMC) proliferation and migration. Deficiency in Kir2.1 contributed to the restoration of smooth muscle α-actin, smooth muscle 22α, and calponin and to a reduction in osteopontin expression in rat-VSMC. Moreover, the in vivo study showed that rat-VSMC switched to proliferative phenotypes and that knockdown of Kir2.1 significantly inhibited neointimal formation after rat carotid injury. Kir2.1 may be a potential therapeutic target in the treatment of cardiovascular diseases, such as atherosclerosis and restenosis following percutaneous coronary intervention. PMID:27387235

  12. Pattern Formation

    NASA Astrophysics Data System (ADS)

    Hoyle, Rebecca

    2006-03-01

    From the stripes of a zebra and the spots on a leopard's back to the ripples on a sandy beach or desert dune, regular patterns arise everywhere in nature. The appearance and evolution of these phenomena has been a focus of recent research activity across several disciplines. This book provides an introduction to the range of mathematical theory and methods used to analyse and explain these often intricate and beautiful patterns. Bringing together several different approaches, from group theoretic methods to envelope equations and theory of patterns in large-aspect ratio-systems, the book also provides insight behind the selection of one pattern over another. Suitable as an upper-undergraduate textbook for mathematics students or as a fascinating, engaging, and fully illustrated resource for readers in physics and biology, Rebecca Hoyle's book, using a non-partisan approach, unifies a range of techniques used by active researchers in this growing field. Accessible description of the mathematical theory behind fascinating pattern formation in areas such as biology, physics and materials science Collects recent research for the first time in an upper level textbook Features a number of exercises - with solutions online - and worked examples

  13. Ceramide 1-phosphate induces neointimal formation via cell proliferation and cell cycle progression upstream of ERK1/2 in vascular smooth muscle cells

    SciTech Connect

    Kim, Tack-Joong; Kang, Yeo-Jin; Lim, Yong; Lee, Hyoung-Woo; Bae, Kiho; Lee, Youn-Sun; Yoo, Jae-Myung; Yoo, Hwan-Soo; Yun, Yeo-Pyo

    2011-08-15

    Ceramide 1-phosphate (C1P) is a novel bioactive sphingolipid formed by ceramide kinase (CERK)-catalyzed phosphorylation of ceramide. It has been implicated in the regulation of such vital pathophysiological functions as phagocytosis and inflammation, but there have been no reports ascribing a biological function to CERK in vascular disorders. Here the potential role of CERK/C1P in neointimal formation was investigated using rat aortic vascular smooth muscle cells (VSMCs) in primary culture and a rat carotid injury model. Exogenous C8-C1P stimulated cell proliferation, DNA synthesis, and cell cycle progression of rat aortic VSMCs in primary culture. In addition, wild-type CERK-transfected rat aortic VSMCs induced a marked increase in rat aortic VSMC proliferation and [{sup 3}H]-thymidine incorporation when compared to empty vector transfectant. C8-C1P markedly activated extracellular signal-regulated kinase 1 and 2 (ERK1/2) within 5 min, and the activation could be prevented by U0126, a MEK inhibitor. Also, K1, a CERK inhibitor, decreased the ERK1/2 phosphorylation and cell proliferation on platelet-derived growth factor (PDGF)-stimulated rat aortic VSMCs. CERK expression and C1P levels were found to be potently increased during neointimal formation using a rat carotid injury model. However, ceramide levels decreased during the neointimal formation process. These findings suggest that C1P can induce neointimal formation via cell proliferation through the regulation of the ERK1/2 protein in rat aortic VSMCs and that CERK/C1P may regulate VSMC proliferation as an important pathogenic marker in the development of cardiovascular disorders.

  14. BMSCs Interactions with Adventitial Fibroblasts Display Smooth Muscle Cell Lineage Potential in Differentiation and Migration That Contributes to Neointimal Formation.

    PubMed

    Wendan, Y; Changzhu, J; Xuhong, S; Hongjing, C; Hong, S; Dongxia, Y; Fang, X

    2016-01-01

    In this study a model of simulated vascular injury in vitro was used to study the characterization of bone-marrow-derived mesenchymal stem cells (BMSCs) morphology and to investigate the differentiation and migration of BMSCs in the presence of adventitial fibroblasts. BMSCs from rats were indirectly cocultured with adventitial fibroblasts in a transwell chamber apparatus for 7 days, and clonogenic assays demonstrated that BMSCs could be differentiated into smooth muscle-like cells with this process, including smooth muscle α-actin (α-SMA) expression by immunofluorescence staining. Cell morphology of BMSCs was assessed by inverted microscope, while cell proliferation was assessed by MTT assay. The expressions of TGF-β1, MMP-1, and NF-κB were detected by immunofluorescence staining and Smad3 mRNA was measured by reverse transcription PCR. Migration ability of BMSCs with DAPI-labeled nuclei was measured by laser confocal microscopy. Our results demonstrate that indirect interactions with adventitial fibroblasts can induce proliferation, differentiation, and migration of BMSCs that can actively participate in neointimal formation. Our results indicate that the pathogenesis of vascular remodeling might perform via TGF-β1/Smad3 signal transduction pathways. PMID:26880952

  15. BMSCs Interactions with Adventitial Fibroblasts Display Smooth Muscle Cell Lineage Potential in Differentiation and Migration That Contributes to Neointimal Formation

    PubMed Central

    Wendan, Y.; Changzhu, J.; Xuhong, S.; Hongjing, C.; Hong, S.; Dongxia, Y.; Fang, X.

    2016-01-01

    In this study a model of simulated vascular injury in vitro was used to study the characterization of bone-marrow-derived mesenchymal stem cells (BMSCs) morphology and to investigate the differentiation and migration of BMSCs in the presence of adventitial fibroblasts. BMSCs from rats were indirectly cocultured with adventitial fibroblasts in a transwell chamber apparatus for 7 days, and clonogenic assays demonstrated that BMSCs could be differentiated into smooth muscle-like cells with this process, including smooth muscle α-actin (α-SMA) expression by immunofluorescence staining. Cell morphology of BMSCs was assessed by inverted microscope, while cell proliferation was assessed by MTT assay. The expressions of TGF-β1, MMP-1, and NF-κB were detected by immunofluorescence staining and Smad3 mRNA was measured by reverse transcription PCR. Migration ability of BMSCs with DAPI-labeled nuclei was measured by laser confocal microscopy. Our results demonstrate that indirect interactions with adventitial fibroblasts can induce proliferation, differentiation, and migration of BMSCs that can actively participate in neointimal formation. Our results indicate that the pathogenesis of vascular remodeling might perform via TGF-β1/Smad3 signal transduction pathways. PMID:26880952

  16. Central role of endogenous Toll-like receptor-2 activation in regulating inflammation, reactive oxygen species production, and subsequent neointimal formation after vascular injury

    SciTech Connect

    Shishido, Tetsuro . E-mail: Tetsuro_Shishido@URMC.Rochester.edu; Nozaki, Naoki; Takahashi, Hiroki; Arimoto, Takanori; Niizeki, Takeshi; Koyama, Yo; Abe, Jun-ichi; Takeishi, Yasuchika; Kubota, Isao

    2006-07-14

    Background: It is now evident that inflammation after vascular injury has significant impact on the restenosis after revascularization procedures such as angioplasty, stenting, and bypass grafting. However, the mechanisms that regulate inflammation and repair after vascular injury are incompletely understood. Here, we report that vascular injury-mediated cytokine expression, reactive oxygen species (ROS) production, as well as subsequent neointimal formation requires Toll-like receptor-2 (TLR-2) mediated signaling pathway in vivo. Methods and results: Vascular injury was induced by cuff-placement around the femoral artery in non-transgenic littermates (NLC) and TLR-2 knockout (TLR-2KO) mice. After cuff-placement in NLC mice, expression of TLR-2 was significantly increased in both smooth muscle medial layer and adventitia. Interestingly, we found that inflammatory genes expression such as tumor necrosis factor-{alpha}, interleukin-1{beta} (IL-1{beta}), IL-6, and monocyte chemoattractant protein-1 were markedly decreased in TLR-2KO mice compared with NLC mice. In addition, ROS production after vascular injury was attenuated in TLR-2KO mice compared with NLC mice. Since we observed the significant role of endogenous TLR-2 activation in regulating inflammatory responses and ROS production after vascular injury, we determined whether inhibition of endogenous TLR-2 activation can inhibit neointimal proliferation after vascular injury. Neointimal hyperplasia was markedly suppressed in TLR-2KO mice compared with WT mice at both 2 and 4 weeks after vascular injury. Conclusions: These findings suggested that endogenous TLR-2 activation might play a central role in the regulation of vascular inflammation as well as subsequent neointimal formation in injured vessels.

  17. Detecting DNA synthesis of neointimal formation after catheter balloon injury in GK and in Wistar rats: using 5-ethynyl-2'-deoxyuridine

    PubMed Central

    2012-01-01

    Background Neointimal formation plays an important role in the pathogenesis of coronary restenosis after percutaneous coronary intervention (PCI), especially in patients with diabetes mellitus. Recently, some studies have shown that 5-ethynyl-2'-deoxyuridine (EdU) incorporation can serve as a novel alternative to the 5-bromo-2'-deoxyuridine (BrdU) antibody detection method for detection of DNA synthesis in regenerating avian cochlea, chick embryo and the adult nervous system. However, few studies have been performed to assess the suitability of EdU for detecting DNA synthesis in vascular neointima. Methods The carotid artery balloon injury model was established in Goto-Kakizaki (GK) and Wistar rats. A Cell-LightTM EdU Kit was used to detect EdU-labeled cell nuclei of common carotid arteries at day 7 after catheter balloon injury. Different methods of injecting EdU were tested. The protein levels of proliferating cell nuclear antigen (PCNA) and p-Akt (Ser473), as well as the mRNA levels of PCNA were evaluated by Western blotting and quantitative real-time PCR (qRT-PCR), respectively. Immunohistochemical staining was also employed to visualize PCNA-positive cells. Results At day 7 after catheter balloon injury, far more EdU-positive and PCNA-positive cells were observed in GK rats. When comparing groups that received different EdU doses, it was found that the percentage of EdU-positive cells at a dose of 100 mg/kg body weight was than at doses of 25 mg/kg and 50 mg/kg. The number of positive cells was significantly higher in the repeated injection group compared to the single injection group. Further, after balloon injury DNA synthesis in GK rats was more notable than in Wistar rats. Neointimal formation in GK rats was more obvious than in Wistar rats. The protein levels of PCNA and p-Akt (Ser473) and the mRNA levels of PCNA were increased in injured rats as compared to uninjured rats, and were significantly higher in GK rats than in Wistar rats. Conclusion By

  18. Progressive vascular remodeling and reduced neointimal formation after placement of a thermoelastic self-expanding nitinol stent in an experimental model.

    PubMed

    Carter, A J; Scott, D; Laird, J R; Bailey, L; Kovach, J A; Hoopes, T G; Pierce, K; Heath, K; Hess, K; Farb, A; Virmani, R

    1998-06-01

    Despite the improvements afforded by intracoronary stenting, restenosis remains a significant problem. The optimal physical properties of a stent have not been defined. We compared the vascular response to a thermoelastic self-expanding nitinol stent with a balloon-expandable tubular slotted stainless steel stent in normal porcine coronary arteries. Twenty-two stents (11 nitinol and 11 tubular slotted) were implanted in 11 miniature swine. The nitinol stents were deployed using the intrinsic thermal properties of the metal, without adjunctive balloon dilation. The tubular slotted stents were implanted using a noncompliant balloon with a mean inflation pressure of 12 atm. Intravascular ultrasound (IVUS) and histology were used to evaluate the vascular response to the stents. The mean cross-sectional area (CSA) of the nitinol stents (mm2) as measured by IVUS increased from 8.13 +/- 1.09 at implant to 9.10 +/- 0.99 after 28 days (P = 0.038), while the mean CSA of the tubular slotted stents was unchanged (7.84 +/- 1.39 mm2 vs. 7.10 +/- 1.07 mm2, P = 0.25). On histology at 3 days, the tubular slotted stents had more inflammatory cells adjacent to the stent wires (5.7 +/- 1.5 cells/0.1 mm2) than the nitinol (3.9 +/- 1.3 cells/0.1 mm2, P = 0.016). The tubular slotted also had increased thrombus thickness (83 +/- 85 microm) than the nitinol stents (43 +/- 25 microm, P = 0.0014). After 28 days, the vessel injury score was similar for the nitinol (0.6 +/- 0.3) and the tubular slotted (0.5 +/- 0.1, P = 0.73) designs. The mean neointimal area (0.97 +/- 0.46 mm2 vs. 1.96 +/- 0.34 mm2, P = 0.002) and percent area stenosis (15 +/- 7 vs. 33 +/- 7, P = 0.003) were significantly lower in the nitinol than in the tubular slotted stents, respectively. We conclude that a thermoelastic nitinol stent exerts a more favorable effect on vascular remodeling, with less neointimal formation, than a balloon-expandable design. Progressive intrinsic stent expansion after implant does not appear to

  19. Pattern Formation in Materials

    NASA Astrophysics Data System (ADS)

    Karma, Alain

    2011-04-01

    Pattern formation is ubiquitous in nature, from sand ripples formed by wind to the development of a complex biological organism with different organs and a central nervous system. In the realm of materials, patterns are formed invariably when matter is transformed between different solid, liquid or gaseous states far from thermodynamic equilibrium. Material failure is itself mediated by the propagation of cracks that form intricate patterns. Understanding how patterns form and evolve is key to design materials with desired properties and to optimize their performance and safety. This talk will discuss recent progress made to understand three distinct class of patterns including the highly branched snow-flake-like dendritic patterns formed during the solidification process, polycrystalline patterns shaped by grain boundaries, and crack patterns.

  20. Pattern formation today

    PubMed Central

    Chuong, Cheng-Ming; Richardson, Michael K.

    2010-01-01

    Patterns are orders embedded in randomness. They may appear as spatial arrangements or temporal series, and the elements may appear identical or with variations. Patterns exist in the physical world as well as in living systems. In the biological world, patterns can range from simple to complex, forming the basic building blocks of life. The process which generates this ordering in the biological world was termed pattern formation. Since Wolpert promoted this concept four decades ago, scientists from molecular biology, developmental biology, stem cell biology, tissue engineering, theoretical modeling and other disciplines have made remarkable progress towards understanding its mechanisms. It is time to review and re-integrate our understanding. Here, we explore the origin of pattern formation, how the genetic code is translated into biological form, and how complex phenotypes are selected over evolutionary time. We present four topics: Principles, Evolution, Development, and Stem Cells and Regeneration. We have interviewed several leaders in the field to gain insight into how their research and the field of pattern formation have shaped each other. We have learned that both molecular process and physico-chemical principles are important for biological pattern formation. New understanding will emerge through integration of the analytical approach of molecular-genetic manipulation and the systemic approach of model simulation. We regret that we could not include every major investigator in the field, but hope that this Special Issue of the Int. J. Dev. Biol. represents a sample of our knowledge of pattern formation today, which will help to stimulate more research on this fundamental process. PMID:19557673

  1. Pattern formation during vasculogenesis.

    PubMed

    Czirok, Andras; Little, Charles D

    2012-06-01

    Vasculogenesis, the assembly of the first vascular network, is an intriguing developmental process that yields the first functional organ system of the embryo. In addition to being a fundamental part of embryonic development, vasculogenic processes also have medical importance. To explain the organizational principles behind vascular patterning, we must understand how morphogenesis of tissue level structures can be controlled through cell behavior patterns that, in turn, are determined by biochemical signal transduction processes. Mathematical analyses and computer simulations can help conceptualize how to bridge organizational levels and thus help in evaluating hypotheses regarding the formation of vascular networks. Here, we discuss the ideas that have been proposed to explain the formation of the first vascular pattern: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and sprouting guided by cell-cell contacts. PMID:22692888

  2. Dynamics of interfacial pattern formation

    NASA Technical Reports Server (NTRS)

    Ben-Jacob, E.; Goldenfeld, N.; Langer, J. S.; Schon, G.

    1983-01-01

    A phenomenological model of dendritic solidification incorporating interfacial kinetics, crystalline anisotropy, and a local approximation for the dynamics of the thermal diffusion field is proposed. The preliminary results are in qualitative agreement with natural dendrite-like pattern formation.

  3. c-Kit signaling determines neointimal hyperplasia in arteriovenous fistulae

    PubMed Central

    Skartsis, Nikolaos; Martinez, Laisel; Duque, Juan Camilo; Tabbara, Marwan; Velazquez, Omaida C.; Asif, Arif; Andreopoulos, Fotios; Salman, Loay H.

    2014-01-01

    Stenosis of arteriovenous (A-V) fistulae secondary to neointimal hyperplasia (NIH) compromises dialysis delivery, which worsens patients' quality of life and increases medical costs associated with the maintenance of vascular accesses. In the present study, we evaluated the role of the receptor tyrosine kinase c-Kit in A-V fistula neointima formation. Initially, c-Kit was found in the neointima and adventitia of human brachiobasilic fistulae, whereas it was barely detectable in control veins harvested at the time of access creation. Using the rat A-V fistula model to study venous vascular remodeling, we analyzed the spatial and temporal pattern of c-Kit expression in the fistula wall. Interestingly, c-Kit immunoreactivity increased with time after anastomosis, which concurred with the accumulation of cells in the venous intima. In addition, c-Kit expression in A-V fistulae was positively altered by chronic kidney failure conditions. Both blockade of c-Kit with imatinib mesylate (Gleevec) and inhibition of stem cell factor production with a specific short hairpin RNA prevented NIH in the outflow vein of experimental fistulae. In agreement with these data, impaired c-Kit activity compromised the development of NIH in A-V fistulae created in c-KitW/Wv mutant mice. These results suggest that targeting of the c-Kit signaling pathway may be an effective approach to prevent postoperative NIH in A-V fistulae. PMID:25186298

  4. Pattern formation in multiplex networks

    PubMed Central

    Kouvaris, Nikos E.; Hata, Shigefumi; Guilera, Albert Díaz-

    2015-01-01

    The advances in understanding complex networks have generated increasing interest in dynamical processes occurring on them. Pattern formation in activator-inhibitor systems has been studied in networks, revealing differences from the classical continuous media. Here we study pattern formation in a new framework, namely multiplex networks. These are systems where activator and inhibitor species occupy separate nodes in different layers. Species react across layers but diffuse only within their own layer of distinct network topology. This multiplicity generates heterogeneous patterns with significant differences from those observed in single-layer networks. Remarkably, diffusion-induced instability can occur even if the two species have the same mobility rates; condition which can never destabilize single-layer networks. The instability condition is revealed using perturbation theory and expressed by a combination of degrees in the different layers. Our theory demonstrates that the existence of such topology-driven instabilities is generic in multiplex networks, providing a new mechanism of pattern formation. PMID:26042606

  5. Pattern Formation in Convective Instabilities

    NASA Astrophysics Data System (ADS)

    Friedrich, R.; Bestehorn, M.; Haken, H.

    The present article reviews recent progress in the study of pattern formation in convective instabilities. After a brief discussion of the relevant basic hydrodynamic equations as well as a short outline of the mathematical treatment of pattern formation in complex systems the self-organization of spatial and spatio-temporal structures due to convective instabilities is considered. The formation of various forms of convective patterns arising in the Bénard experiment, i.e. in a horizontal fluid layer heated from below, is discussed. Then the review considers pattern formation in the Bénard instability in spherical geometries. In that case it can be demonstrated how the interaction among several convective cells may lead to time dependent as well as chaotic evolution of the spatial structures. Finally, the convective instability in a binary fluid mixture is discussed. In contrast to the instability in a single component fluid the instability may be oscillatory. In that case convection sets in in the form of travelling wave patterns which in addition to a complicated and chaotic temporal behaviour exhibit more or less spatial irregularity already close to threshold.

  6. Pattern formation in the geosciences

    PubMed Central

    Goehring, Lucas

    2013-01-01

    Pattern formation is a natural property of nonlinear and non-equilibrium dynamical systems. Geophysical examples of such systems span practically all observable length scales, from rhythmic banding of chemical species within a single mineral crystal, to the morphology of cusps and spits along hundreds of kilometres of coastlines. This article briefly introduces the general principles of pattern formation and argues how they can be applied to open problems in the Earth sciences. Particular examples are then discussed, which summarize the contents of the rest of this Theme Issue. PMID:24191107

  7. Pattern formations and optimal packing.

    PubMed

    Mityushev, Vladimir

    2016-04-01

    Patterns of different symmetries may arise after solution to reaction-diffusion equations. Hexagonal arrays, layers and their perturbations are observed in different models after numerical solution to the corresponding initial-boundary value problems. We demonstrate an intimate connection between pattern formations and optimal random packing on the plane. The main study is based on the following two points. First, the diffusive flux in reaction-diffusion systems is approximated by piecewise linear functions in the framework of structural approximations. This leads to a discrete network approximation of the considered continuous problem. Second, the discrete energy minimization yields optimal random packing of the domains (disks) in the representative cell. Therefore, the general problem of pattern formations based on the reaction-diffusion equations is reduced to the geometric problem of random packing. It is demonstrated that all random packings can be divided onto classes associated with classes of isomorphic graphs obtained from the Delaunay triangulation. The unique optimal solution is constructed in each class of the random packings. If the number of disks per representative cell is finite, the number of classes of isomorphic graphs, hence, the number of optimal packings is also finite. PMID:26852668

  8. Zonal flow as pattern formation

    NASA Astrophysics Data System (ADS)

    Parker, Jeffrey B.; Krommes, John A.

    2013-10-01

    Zonal flows are well known to arise spontaneously out of turbulence. We show that for statistically averaged equations of the stochastically forced generalized Hasegawa-Mima model, steady-state zonal flows, and inhomogeneous turbulence fit into the framework of pattern formation. There are many implications. First, the wavelength of the zonal flows is not unique. Indeed, in an idealized, infinite system, any wavelength within a certain continuous band corresponds to a solution. Second, of these wavelengths, only those within a smaller subband are linearly stable. Unstable wavelengths must evolve to reach a stable wavelength; this process manifests as merging jets.

  9. Zonal flow as pattern formation

    SciTech Connect

    Parker, Jeffrey B.; Krommes, John A.

    2013-10-15

    Zonal flows are well known to arise spontaneously out of turbulence. We show that for statistically averaged equations of the stochastically forced generalized Hasegawa-Mima model, steady-state zonal flows, and inhomogeneous turbulence fit into the framework of pattern formation. There are many implications. First, the wavelength of the zonal flows is not unique. Indeed, in an idealized, infinite system, any wavelength within a certain continuous band corresponds to a solution. Second, of these wavelengths, only those within a smaller subband are linearly stable. Unstable wavelengths must evolve to reach a stable wavelength; this process manifests as merging jets.

  10. Epothilones Suppress Neointimal Thickening in the Rat Carotid Balloon-Injury Model by Inducing Vascular Smooth Muscle Cell Apoptosis through p53-Dependent Signaling Pathway

    PubMed Central

    Son, Dong Ju; Jung, Jae Chul; Hong, Jin Tae

    2016-01-01

    Microtubule stabilizing agents (MTSA) are known to inhibit vascular smooth muscle cell (VSMC) proliferation and migration, and effectively reduce neointimal hyperplasia and restenosis. Epothilones (EPOs), non-taxane MTSA, have been found to be effective in the inhibition of VSMC proliferation and neointimal formation by cell cycle arrest. However, effect of EPOs on apoptosis in hyper-proliferated VSMCs as a possible way to reduce neointimal formation and its action mechanism related to VSMC viability has not been suited yet. Thus, the purposes of the present study was to investigate whether EPOs are able to inhibit neointimal formation by inducing apoptosis within the region of neointimal hyperplasia in balloon-injured rat carotid artery, as well as underlying action mechanism. Treatment of EPO-B and EPO-D significantly induced apoptotic cell death and mitotic catastrophe in hyper-proliferated VSMCs, resulting in cell growth inhibition. Further, EPOs significantly suppressed VSMC proliferation and induced apoptosis by activation of p53-dependent apoptotic signaling pathway, Bax/cytochrome c/caspase-3. We further demonstrated that the local treatment of carotid arteries with EPOs potently inhibited neointimal lesion formation by induction of apoptosis in rat carotid injury model. Our findings demonstrate a potent anti-neointimal hyperplasia property of EPOs by inducing p53-depedent apoptosis in hyper-proliferated VSMCs. PMID:27218463

  11. Egr-1 Expression During Neointimal Development in Flow-Associated Pulmonary Hypertension

    PubMed Central

    Dickinson, Michael G.; Bartelds, Beatrijs; Molema, Grietje; Borgdorff, Marinus A.; Boersma, Bibiche; Takens, Janny; Weij, Michel; Wichers, Pieter; Sietsma, Hannie; Berger, Rolf M.F.

    2011-01-01

    In flow-associated pulmonary arterial hypertension (PAH), increased pulmonary blood flow is an essential trigger for neointimal formation. Using microarray analysis, we recently found that the early growth response protein 1 (Egr-1) transcription factor is increased in experimental flow-associated end-stage PAH. Its role in PAH development is unknown. Here, we assessed the spatiotemporal expression of Egr-1 during neointimal development in flow-associated PAH. Flow-associated PAH was produced in rats by combining monocrotaline administration with an aortocaval shunt. Animals were sacrificed 1 day before or 1 day, 1 week, or 4 to 5 weeks after flow addition. Egr-1 expression was spatiotemporally assessed using laser microdissection, quantitative real-time PCR and immunohistochemistry. In addition, Egr-1 expression was assessed in a non-neointimal pulmonary hypertension model and in human PAH associated with congenital shunt. In 4 to 5 weeks, rats subjected to increased flow developed PAH with neointimal lesions. Egr-1 mRNA was increased 1 day after flow addition and in end-stage PAH, whereas monocrotaline only did not result in increased Egr-1 mRNA. Directly after flow addition, Egr-1 was expressed in endothelial cells. During disease development, Egr-1 protein expression increased and migrated throughout the vessel wall. In PAH patients, Egr-1 was expressed in vessels with media hypertrophy and neointimal lesions, including plexiform lesions. Thus, Egr-1 may be an important regulator in the development of pulmonary neointimal lesions induced by increased pulmonary blood flow. PMID:21924231

  12. Egr-1 expression during neointimal development in flow-associated pulmonary hypertension.

    PubMed

    Dickinson, Michael G; Bartelds, Beatrijs; Molema, Grietje; Borgdorff, Marinus A; Boersma, Bibiche; Takens, Janny; Weij, Michel; Wichers, Pieter; Sietsma, Hannie; Berger, Rolf M F

    2011-11-01

    In flow-associated pulmonary arterial hypertension (PAH), increased pulmonary blood flow is an essential trigger for neointimal formation. Using microarray analysis, we recently found that the early growth response protein 1 (Egr-1) transcription factor is increased in experimental flow-associated end-stage PAH. Its role in PAH development is unknown. Here, we assessed the spatiotemporal expression of Egr-1 during neointimal development in flow-associated PAH. Flow-associated PAH was produced in rats by combining monocrotaline administration with an aortocaval shunt. Animals were sacrificed 1 day before or 1 day, 1 week, or 4 to 5 weeks after flow addition. Egr-1 expression was spatiotemporally assessed using laser microdissection, quantitative real-time PCR and immunohistochemistry. In addition, Egr-1 expression was assessed in a non-neointimal pulmonary hypertension model and in human PAH associated with congenital shunt. In 4 to 5 weeks, rats subjected to increased flow developed PAH with neointimal lesions. Egr-1 mRNA was increased 1 day after flow addition and in end-stage PAH, whereas monocrotaline only did not result in increased Egr-1 mRNA. Directly after flow addition, Egr-1 was expressed in endothelial cells. During disease development, Egr-1 protein expression increased and migrated throughout the vessel wall. In PAH patients, Egr-1 was expressed in vessels with media hypertrophy and neointimal lesions, including plexiform lesions. Thus, Egr-1 may be an important regulator in the development of pulmonary neointimal lesions induced by increased pulmonary blood flow. PMID:21924231

  13. Magnetic Assisted Colloidal Pattern Formation

    NASA Astrophysics Data System (ADS)

    Yang, Ye

    Pattern formation is a mysterious phenomenon occurring at all scales in nature. The beauty of the resulting structures and myriad of resulting properties occurring in naturally forming patterns have attracted great interest from scientists and engineers. One of the most convenient experimental models for studying pattern formation are colloidal particle suspensions, which can be used both to explore condensed matter phenomena and as a powerful fabrication technique for forming advanced materials. In my thesis, I have focused on the study of colloidal patterns, which can be conveniently tracked in an optical microscope yet can also be thermally equilibrated on experimentally relevant time scales, allowing for ground states and transitions between them to be studied with optical tracking algorithms. In particular, I have focused on systems that spontaneously organize due to particle-surface and particle-particle interactions, paying close attention to systems that can be dynamically adjusted with an externally applied magnetic or acoustic field. In the early stages of my doctoral studies, I developed a magnetic field manipulation technique to quantify the adhesion force between particles and surfaces. This manipulation technique is based on the magnetic dipolar interactions between colloidal particles and their "image dipoles" that appear within planar substrate. Since the particles interact with their own images, this system enables massively parallel surface force measurements (>100 measurements) in a single experiment, and allows statistical properties of particle-surface adhesion energies to be extracted as a function of loading rate. With this approach, I was able to probe sub-picoNewton surface interactions between colloidal particles and several substrates at the lowest force loading rates ever achieved. In the later stages of my doctoral studies, I focused on studying patterns formed from particle-particle interaction, which serve as an experimental model of

  14. Pattern formation in centrosome assembly.

    PubMed

    Mahen, Robert; Venkitaraman, Ashok R

    2012-02-01

    A striking but poorly explained feature of cell division is the ability to assemble and maintain organelles not bounded by membranes, from freely diffusing components in the cytosol. This process is driven by information transfer across biological scales such that interactions at the molecular scale allow pattern formation at the scale of the organelle. One important example of such an organelle is the centrosome, which is the main microtubule organising centre in the cell. Centrosomes consist of two centrioles surrounded by a cloud of proteins termed the pericentriolar material (PCM). Profound structural and proteomic transitions occur in the centrosome during specific cell cycle stages, underlying events such as centrosome maturation during mitosis, in which the PCM increases in size and microtubule nucleating capacity. Here we use recent insights into the spatio-temporal behaviour of key regulators of centrosomal maturation, including Polo-like kinase 1, CDK5RAP2 and Aurora-A, to propose a model for the assembly and maintenance of the PCM through the mobility and local interactions of its constituent proteins. We argue that PCM structure emerges as a pattern from decentralised self-organisation through a reaction-diffusion mechanism, with or without an underlying template, rather than being assembled from a central structural template alone. Self-organisation of this kind may have broad implications for the maintenance of mitotic structures, which, like the centrosome, exist stably as supramolecular assemblies on the micron scale, based on molecular interactions at the nanometer scale. PMID:22245706

  15. Selective endothelin A receptor antagonism with sitaxentan reduces neointimal lesion size in a mouse model of intraluminal injury

    PubMed Central

    Duthie, Karolina M; Hadoke, Patrick W F; Kirkby, Nicholas S; Miller, Eileen; Ivy, Jessica R; McShane, John F; Lim, Win Gel; Webb, David J

    2015-01-01

    Background and Purpose Endothelin (ET) receptor antagonism reduces neointimal lesion formation in animal models. This investigation addressed the hypothesis that the selective ETA receptor antagonist sitaxentan would be more effective than mixed ETA/B receptor antagonism at inhibiting neointimal proliferation in a mouse model of intraluminal injury. Experimental Approach Antagonism of ETA receptors by sitaxentan (1–100 nM) was assessed in femoral arteries isolated from adult, male C57Bl6 mice using isometric wire myography. Neointimal lesion development was induced by intraluminal injury in mice receiving sitaxentan (ETA antagonist; 15 mg·kg−1·day−1), A192621 (ETB antagonist; 30 mg·kg−1·day−1), the combination of both antagonists or vehicle. Treatment began 1 week before, and continued for 28 days after, surgery. Femoral arteries were then harvested for analysis of lesion size and composition. Key Results Sitaxentan produced a selective, concentration-dependent parallel rightward shift of ET-1-mediated contraction in isolated femoral arteries. Sitaxentan reduced neointimal lesion size, whereas ETB and combined ETA/B receptor antagonism did not. Macrophage and α-smooth muscle actin content were unaltered by ET receptor antagonism but sitaxentan reduced the amount of collagen in lesions. Conclusions and Implications These results suggest that ETA receptor antagonism would be more effective than combined ETA/ETB receptor antagonism at reducing neointimal lesion formation. PMID:25598351

  16. Pattern formation with proportionate growth

    NASA Astrophysics Data System (ADS)

    Dhar, Deepak

    It is a common observation that as baby animals grow, different body parts grow approximately at same rate. This property, called proportionate growth is remarkable in that it is not encountered easily outside biology. The models of growth that have been studied in Physics so far, e.g diffusion -limited aggregation, surface deposition, growth of crystals from melt etc. involve only growth at the surface, with the inner structure remaining frozen. Interestingly, patterns formed in growing sandpiles provide a very wide variety of patterns that show proportionate growth. One finds patterns with different features, with sharply defined boundaries. In particular, even with very simple rules, one can produce patterns that show striking resemblance to those seen in nature. We can characterize the asymptotic pattern exactly in some special cases. I will discuss in particular the patterns grown on noisy backgrounds. Supported by J. C. Bose fellowship from DST (India).

  17. Pattern formation in quantum networks

    NASA Astrophysics Data System (ADS)

    Kim, Ilki; Mahler, Günter

    1999-03-01

    We investigate the iteration of a sequence of local and pair unitary transformations (quantum gate approximation), which can be interpreted to result from a Turing-head (pseudo-spin S) rotating along a closed Turing-tape (M additional pseudo-spins). The dynamical evolution of the Bloch-vector of S, which can be decomposed into 2M primitive pure state Turing-head trajectories, gives rise to fascinating geometrical patterns reflecting the entanglement between head and tape. For specific initial states ("input"), these patterns ("output") can be easily calculated for any tape size. We thus show intuitive examples for quantum parallelism and, at the same time, means for local testing of quantum network dynamics.

  18. Blood drop patterns: Formation and applications.

    PubMed

    Chen, Ruoyang; Zhang, Liyuan; Zang, Duyang; Shen, Wei

    2016-05-01

    The drying of a drop of blood or plasma on a solid substrate leads to the formation of interesting and complex patterns. Inter- and intra-cellular and macromolecular interactions in the drying plasma or blood drop are responsible for the final morphologies of the dried patterns. Changes in these cellular and macromolecular components in blood caused by diseases have been suspected to cause changes in the dried drop patterns of plasma and whole blood, which could be used as simple diagnostic tools to identify the health of humans and livestock. However, complex physicochemical driving forces involved in the pattern formation are not fully understood. This review focuses on the scientific development in microscopic observations and pattern interpretation of dried plasma and whole blood samples, as well as the diagnostic applications of pattern analysis. Dried drop patterns of plasma consist of intricate visible cracks in the outer region and fine structures in the central region, which are mainly influenced by the presence and concentration of inorganic salts and proteins during drying. The shrinkage of macromolecular gel and its adhesion to the substrate surface have been thought to be responsible for the formation of the cracks. Dried drop patterns of whole blood have three characteristic zones; their formation as functions of drying time has been reported in the literature. Some research works have applied engineering treatment to the evaporation process of whole blood samples. The sensitivities of the resultant patterns to the relative humidity of the environment, the wettability of the substrates, and the size of the drop have been reported. These research works shed light on the mechanisms of spreading, evaporation, gelation, and crack formation of the blood drops on solid substrates, as well as on the potential applications of dried drop patterns of plasma and whole blood in diagnosis. PMID:26988066

  19. Pattern Formation in Driven Systems

    NASA Astrophysics Data System (ADS)

    Klymko, Katherine

    Model colloidal particles of two types, driven in opposite directions, will in two dimensions segregate into lanes, a phenomenon studied extensively by Lowen and co-workers [Dzubiella et al. Phys. Rev. E 65, 021402 (2002)]. We have simulated mixtures of oppositely-driven particles using three numerical protocols. We find that laning results from enhanced diffusion, in the direction perpendicular to the drive, of particles surrounded by particles of the opposite type, consistent with the observation of Vissers et al. [Soft Matter 7, 6, 2352 (2011)]. By comparing protocols we find that enhanced diffusion follows from a simple geometrical constraint: oppositely-driven particles must, in the time taken to encounter each other in the direction of the drive, diffuse in the perpendicular direction by about one particle diameter. This constraint implies that the effective lateral diffusion constant grows linearly with drive speed and as the square root of the packing fraction, a prediction supported by our numerics. By invoking an analogy between hard particles with environment-dependent mobilities and mutually attractive particles we argue that there exists an equilibrium system whose pattern-forming properties are similar to those of the driven system. Katherine Klymko acknowledges support from the NSF Graduate Research Fellowship.

  20. Pattern Formation in Excitable Media

    NASA Astrophysics Data System (ADS)

    Reynolds, William Nash

    1992-01-01

    The phenomenon of excitability is observed in a wide variety of physical and biological systems. In this work, spatially extended excitable systems are examined from several different perspectives. First, a pedagogical introduction is used to motivate the derivation of the dynamics of one dimensional excitable pulses. In the second part, coupled map techniques for numerical simulation of excitable media and other interfacial systems are described. Examples are given for both excitable media and crystal growth. The third chapter addresses the phenomenon of spiral formation in excitable media. Exact rotating solutions are found for a class of models of excitable media. The solutions consist of two regions: an outer region, consisting of the spiral proper, which exhibits a singularity at its tip, and the core region, obtained by rescaling space in the vicinity of the tip. The tip singularity is resolved in the core region, leading to a consistent solution in all of space. The stability of both the spiral and the core is investigated, with the result that the spiral is found to be stable, and the core unstable. Finally, the stability of excitable waves of the chemical cAMP traveling over aggregating colonies of the slime mold Dictyostelium discoideum is examined by coupling the excitable dynamics of the cAMP signalling system to a simple model of chemotaxis, with result that cellular motion is found to destabilize the waves, causing the initially uniform field of cells to break up into streams.

  1. New Developments in Our Understanding of Neointimal Hyperplasia.

    PubMed

    Lee, Timmy; Ul Haq, Naveed

    2015-11-01

    The vascular access remains the lifeline for the hemodialysis patient. The most common etiology of vascular access dysfunction is venous stenosis at the vein-artery anastomosis in arteriovenous fistula and at the vein-graft anastomosis in arteriovenous grafts (AVG). This stenotic lesion is typically characterized on histology as aggressive venous neointimal hyperplasia in both arteriovenous fistula and AVG. In recent years, we have advanced our knowledge and understanding of neointimal hyperplasia in vascular access and begun testing several novel therapies. This article will (1) review recent developments in our understanding of the pathophysiology of neointimal hyperplasia development in AVG and fistula failure, (2) discuss atypical factors leading to neointimal hyperplasia development, (3) highlight key novel therapies that have been evaluated in clinical trials, and (4) discuss future opportunities and challenges to improve our understanding of vascular access dysfunction and translate this knowledge into novel and innovative therapies. PMID:26524947

  2. Drumlins: A Classic Example of Pattern Formation.

    NASA Astrophysics Data System (ADS)

    Ely, Jeremy C.; Clark, Chris D.; Spagnolo, Matteo; Hahn, Ute; Hughes, Anna L. C.

    2014-05-01

    Drumlins are elongate streamlined hills, typically 250-1000 m long and 120-300 m wide, formed beneath ice sheets. They occur in fields or swarms, covering vast swathes of previously glaciated terrain, and are the most common variant of a continuum of subglacial bedforms. The processes of drumlin formation are currently elusive and contentious, hindering our understanding of the ice-bed interface. Yet, insight into drumlin formation can be gained through studying their spatial distribution and morphometric properties. When viewed from above, drumlins display striking regularity and self-similarity, suggesting that they form through a self-organising pattern forming process. However, the difficulty of observing drumlins forming in situ (i.e. beneath an ice sheet), and a focus upon individual drumlin forms, has hindered both the recognition and understanding of drumlin pattern formation. Hence, the nature of drumlin patterning is poorly understood, especially in comparison to bedforms generated by other geomorphic agents (e.g. dunes and ripples). To address these issues, here we analyse the morphometric properties of a large database of drumlins mapped from palaeo-ice sheet beds at a variety of geological and glaciological settings. Spatial statistical point pattern tests suggest that drumlins are regularly spaced across drumlin fields. However, defects to this regularity occur due to differences in preservation and initial formation conditions. Furthermore, drumlin morphometric parameters frequently conform to a log-normal distribution, common for phenomena which experience incremental growth or fragmentation. Hence, drumlin morphometrics can provide us with insight into how drumlin patterns have evolved. Between separate drumlin fields, variations in patterning and morphometrics vary, highlighting the response of drumlin patterning to local glaciological and geological factors. Hence, we suggest that many of the patterning principles which have been applied to other

  3. Theory of ocular dominance pattern formation

    NASA Astrophysics Data System (ADS)

    Scherf, O.; Pawelzik, K.; Wolf, F.; Geisel, T.

    1999-06-01

    We investigate a general and analytically tractable model for the activity-dependent formation of neuronal connectivity patterns. Previous models are contained as limiting cases. As an important example we analyze the formation of ocular dominance patterns in the visual cortex. A linear stability analysis reveals that the model undergoes a Turing-type instability as a function of interaction range and receptive field size. The phase transitions is of second order. After the linear instability the patterns may reorganize which we analyze in terms of a potential for the dynamics. Our analysis demonstrates that the experimentally observed dependency of ocular dominance patterns on interocular correlations of visual experience during development can emerge according to two generic scenarios: either the system is driven through the phase transition during development thereby selecting and stabilizing the first unstable mode or a primary pattern reorganizes towards larger wavelength according their lower energy. Experimentally observing the time course of ocular dominance pattern formation will decide which scenario is realized in the brain.

  4. Rear Polarization of the Microtubule-Organizing Center in Neointimal Smooth Muscle Cells Depends on PKCα, ARPC5, and RHAMM

    PubMed Central

    Silverman-Gavrila, Rosalind; Silverman-Gavrila, Lorelei; Hou, Guangpei; Zhang, Ming; Charlton, Milton; Bendeck, Michelle P.

    2011-01-01

    Directed migration of smooth muscle cells (SMCs) from the media to the intima in arteries occurs during atherosclerotic plaque formation and during restenosis after angioplasty or stent application. The polarized orientation of the microtubule-organizing center (MTOC) is a key determinant of this process, and we therefore investigated factors that regulate MTOC polarity in vascular SMCs. SMCs migrating in vivo from the medial to the intimal layer of the rat carotid artery following balloon catheter injury were rear polarized, with the MTOC located posterior of the nucleus. In tissue culture, migrating neointimal cells maintained rear polarization, whereas medial cells were front polarized. Using phosphoproteomic screening and mass spectrometry, we identified ARPC5 and RHAMM as protein kinase C (PKC)-phosphorylated proteins associated with rear polarization of the MTOC in neointimal SMCs. RNA silencing of ARPC5 and RHAMM, PKC inhibition, and transfection with a mutated nonphosphorylatable ARPC5 showed that these proteins regulate rear polarization by organizing the actin and microtubule cytoskeletons in neointimal SMCs. Both ARPC5 and RHAMM, in addition to PKC, were required for migration of neointimal SMCs. PMID:21281821

  5. Taming contact line instability for pattern formation.

    PubMed

    Deblais, A; Harich, R; Colin, A; Kellay, H

    2016-01-01

    Coating surfaces with different fluids is prone to instability producing inhomogeneous films and patterns. The contact line between the coating fluid and the surface to be coated is host to different instabilities, limiting the use of a variety of coating techniques. Here we take advantage of the instability of a receding contact line towards cusp and droplet formation to produce linear patterns of variable spacings. We stabilize the instability of the cusps towards droplet formation by using polymer solutions that inhibit this secondary instability and give rise to long slender cylindrical filaments. We vary the speed of deposition to change the spacing between these filaments. The combination of the two gives rise to linear patterns into which different colloidal particles can be embedded, long DNA molecules can be stretched and particles filtered by size. The technique is therefore suitable to prepare anisotropic structures with variable properties. PMID:27506626

  6. Taming contact line instability for pattern formation

    PubMed Central

    Deblais, A.; Harich, R.; Colin, A.; Kellay, H.

    2016-01-01

    Coating surfaces with different fluids is prone to instability producing inhomogeneous films and patterns. The contact line between the coating fluid and the surface to be coated is host to different instabilities, limiting the use of a variety of coating techniques. Here we take advantage of the instability of a receding contact line towards cusp and droplet formation to produce linear patterns of variable spacings. We stabilize the instability of the cusps towards droplet formation by using polymer solutions that inhibit this secondary instability and give rise to long slender cylindrical filaments. We vary the speed of deposition to change the spacing between these filaments. The combination of the two gives rise to linear patterns into which different colloidal particles can be embedded, long DNA molecules can be stretched and particles filtered by size. The technique is therefore suitable to prepare anisotropic structures with variable properties. PMID:27506626

  7. Taming contact line instability for pattern formation

    NASA Astrophysics Data System (ADS)

    Deblais, A.; Harich, R.; Colin, A.; Kellay, H.

    2016-08-01

    Coating surfaces with different fluids is prone to instability producing inhomogeneous films and patterns. The contact line between the coating fluid and the surface to be coated is host to different instabilities, limiting the use of a variety of coating techniques. Here we take advantage of the instability of a receding contact line towards cusp and droplet formation to produce linear patterns of variable spacings. We stabilize the instability of the cusps towards droplet formation by using polymer solutions that inhibit this secondary instability and give rise to long slender cylindrical filaments. We vary the speed of deposition to change the spacing between these filaments. The combination of the two gives rise to linear patterns into which different colloidal particles can be embedded, long DNA molecules can be stretched and particles filtered by size. The technique is therefore suitable to prepare anisotropic structures with variable properties.

  8. Mechanisms of scaling in pattern formation

    PubMed Central

    Umulis, David M.; Othmer, Hans G.

    2013-01-01

    Many organisms and their constituent tissues and organs vary substantially in size but differ little in morphology; they appear to be scaled versions of a common template or pattern. Such scaling involves adjusting the intrinsic scale of spatial patterns of gene expression that are set up during development to the size of the system. Identifying the mechanisms that regulate scaling of patterns at the tissue, organ and organism level during development is a longstanding challenge in biology, but recent molecular-level data and mathematical modeling have shed light on scaling mechanisms in several systems, including Drosophila and Xenopus. Here, we investigate the underlying principles needed for understanding the mechanisms that can produce scale invariance in spatial pattern formation and discuss examples of systems that scale during development. PMID:24301464

  9. Pattern Formation and Functionality in Swarm Models

    NASA Astrophysics Data System (ADS)

    Rauch, Erik; Millonas, Mark; Chialvo, Dante

    1996-03-01

    We explore a simplified class of models we call swarms, which are inspired by the collective behavior of social insects. We perform a mean-field type stability analysis and numerical simulations of the model. Several interesting types of functional behavior appear in the vicinity of a second order phase transition, including the formation of stable lines of traffic flow, memory consolidation, and bootstrapping. In addition to providing an understanding of certain classes of biological behavior, these models bear a generic resemblence to a number of pattern formation processes in the physical sciences.

  10. Pattern formation in Active Polar Fluids

    NASA Astrophysics Data System (ADS)

    Gopinath, Arvind; Hagan, Michael; Baskaran, Aparna

    2011-03-01

    Systems such as bacterial suspensions or cytoskeletal filaments and motility assays can be described within the paradigm of active polar fluids. These systems have been shown to exhibit pattern formation raging from asters and vortices to traveling stripes. A coarse-grained description of such a fluid is given by a scalar density field and a vector polarization field. We study such a macroscopic description of the system using weakly nonlinear analysis and numerical simulations to map out the emergent pattern formation as a function of the hydrodynamic parameters in the context of two specific microscopic models - a quasi-2D suspension of cytoskeletal filaments and motor proteins and a system of self propelled hard rods that interact through excluded volume interactions. The authors thank the Brandeis MRSEC center for financial support.

  11. Cellular pattern formation during Dictyostelium aggregation

    NASA Astrophysics Data System (ADS)

    Höfer, Thomas; Sherratt, Jonathan A.; Maini, Philip K.

    The development of multicellularity in the life cycle of Dictyostelium discoideum provides a paradigm model system for biological pattern formation. Previously, mathematical models have shown how a collective pattern of cell communication by waves of the messenger molecule cyclic adenosine 3‧5‧-monophosphate (cAMP) arises from excitable local cAMP kinetics and cAMP diffusion. Here we derive a model of the actual cell aggregation process by considering the chemotactic cell response to cAMP and its interplay with the cAMP dynamics. Cell density, which previously has been treated as a spatially homogeneous parameter, is a crucial variable of the aggregation model. We find that the coupled dynamics of cell chemotaxis and cAMP reaction-diffusion lead to the break-up of the initially uniform cell layer and to the formation of the striking cell stream morphology which characterizes the aggregation process in situ. By a combination of stability analysis and two-dimensional simulations of the model equations, we show cell streaming to be the consequence of the growth of a small-amplitude pattern in cell density forced by the large-amplitude cAMP waves, thus representing a novel scenario of spatial patterning in a cell chemotaxis system. The instability mechanism is further analysed by means of an analytic caricature of the model, and the condition for chemotaxis-driven instability is found to be very similar to the one obtained for the standard (non-oscillatory) Keller-Segel system. The growing cell stream pattern feeds back into the cAMP dynamics, which can explain in some detail experimental observations on the time evolution of the cAMP wave pattern, and suggests the characterization of the Dictyostelium aggregation field as a self-organized excitable medium.

  12. Pattern Formation on Networks: from Localised Activity to Turing Patterns

    PubMed Central

    McCullen, Nick; Wagenknecht, Thomas

    2016-01-01

    Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

  13. Pattern Formation on Networks: from Localised Activity to Turing Patterns

    NASA Astrophysics Data System (ADS)

    McCullen, Nick; Wagenknecht, Thomas

    2016-06-01

    Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system.

  14. Pattern Formation on Networks: from Localised Activity to Turing Patterns.

    PubMed

    McCullen, Nick; Wagenknecht, Thomas

    2016-01-01

    Networks of interactions between competing species are used to model many complex systems, such as in genetics, evolutionary biology or sociology and knowledge of the patterns of activity they can exhibit is important for understanding their behaviour. The emergence of patterns on complex networks with reaction-diffusion dynamics is studied here, where node dynamics interact via diffusion via the network edges. Through the application of a generalisation of dynamical systems analysis this work reveals a fundamental connection between small-scale modes of activity on networks and localised pattern formation seen throughout science, such as solitons, breathers and localised buckling. The connection between solutions with a single and small numbers of activated nodes and the fully developed system-scale patterns are investigated computationally using numerical continuation methods. These techniques are also used to help reveal a much larger portion of of the full number of solutions that exist in the system at different parameter values. The importance of network structure is also highlighted, with a key role being played by nodes with a certain so-called optimal degree, on which the interaction between the reaction kinetics and the network structure organise the behaviour of the system. PMID:27273339

  15. Geometry-induced protein pattern formation

    PubMed Central

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-01

    Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in Δ EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems. PMID:26739566

  16. Pattern formation in drying drops of blood

    NASA Astrophysics Data System (ADS)

    Brutin, D.; Sobac, B.; Loquet, B.; Sampol, J.

    2011-01-01

    The drying of a drop of human blood exhibits coupled physical mechanisms, such as Marangoni flow, evaporation and wettability. The final stage of a whole blood drop evaporation reveals regular patterns with a good reproducibility for a healthy person. Other experiments on anaemic and hyperlipidemic people were performed, and different patterns were revealed. The flow motion inside the blood drop is observed and analyzed with the use of a digital camera: the influence of the red blood cells (RBCs) motion is revealed at the drop periphery as well as its consequences on the final stage of drying. The mechanisms which lead to the final pattern of the dried blood drops are presented and explained on the basis of fluid mechanics in conjunction with the principles of haematology. The blood drop evaporation process is evidenced to be driven only by Marangoni flow. The same axisymetric pattern formation is observed, and can be forecast for different blood drop diameters. The evaporation mass flux can be predicted with a good agreement, assuming only the knowledge of the colloids mass concentration.

  17. Electrically induced structure formation and pattern transfer

    NASA Astrophysics Data System (ADS)

    Schäffer, Erik; Thurn-Albrecht, Thomas; Russell, Thomas P.; Steiner, Ullrich

    2000-02-01

    The wavelength of light represents a fundamental technological barrier to the production of increasingly smaller features on integrated circuits. New technologies that allow the replication of patterns on scales less than 100nm need to be developed if increases in computing power are to continue at the present rate. Here we report a simple electrostatic technique that creates and replicates lateral structures in polymer films on a submicrometre length scale. Our method is based on the fact that dielectric media experience a force in an electric field gradient. Strong field gradients can produce forces that overcome the surface tension in thin liquid films, inducing an instability that features a characteristic hexagonal order. In our experiments, pattern formation takes place in polymer films at elevated temperatures, and is fixed by cooling the sample to room temperature. The application of a laterally varying electric field causes the instability to be focused in the direction of the highest electric field. This results in the replication of a topographically structured electrode. We report patterns with lateral dimensions of 140nm, but the extension of the technique to pattern replication on scales smaller than 100nm seems feasible.

  18. Pattern formation during early floral development.

    PubMed

    Vaddepalli, Prasad; Scholz, Sebastian; Schneitz, Kay

    2015-06-01

    Flowers are central to sexual reproduction in plants. The study of floral development proved tremendously successful in obtaining key insight into processes, such as fate determination, pattern formation, and growth regulation. Recent advances relate to the complex mechanisms underlying the crosstalk between phytohormone signaling, cell and tissue mechanics, and regulatory gene networks that positions floral buds at the apex and directs floral specification, initiation and outgrowth. Furthermore, progress has been made in elucidating the intercellular communication and temporal coordination necessary to organize the behavior of the various functional subdomains within the young flower. PMID:25687790

  19. Optical Coherence Tomographic Observation of Morphological Features of Neointimal Tissue after Drug-Eluting Stent Implantation

    PubMed Central

    Lee, Seung-Yul; Shin, Dong-Ho; Kim, Jung-Sun; Kim, Byeong-Keuk; Ko, Young-Guk; Choi, Donghoon; Jang, Yangsoo

    2014-01-01

    Purpose The impacts of different time courses and the degree of neointimal growth on neointimal morphology have not yet been sufficiently investigated. Therefore, we evaluated the morphological features of neointimal tissue after drug-eluting stent (DES) implantation using optical coherence tomography (OCT). Materials and Methods The morphological features of neointimal tissue in stented segments with a maximal percentage of cross-sectional area (CSA) stenosis of neointima were evaluated in 507 DES-treated lesions with >100 µm mean neointimal thickness on follow-up OCT. Neointimal tissue was categorized as homogeneous, heterogeneous, layered, or neoatherosclerotic. Results In lesions with <50% of neointimal CSA stenosis, homogeneous neointima (68.2%) was predominant, followed by heterogeneous neointima (14.1%) and layered neointima (14.1%). In lesions with ≥50% of neointimal CSA stenosis, layered neointima was most frequently observed (68.3%), followed by neoatherosclerotic neointima (25.2%). In subgroup analysis of lesions with ≥50% of neointimal CSA stenosis, 89.5% of the lesions with a stent age <30 months were layered neointima, while 62.3% of the lesions with a stent age ≥30 months were neoatherosclerotic neointima. Conclusion This study suggests that the OCT-detected morphology of DES neointimal tissue was different according to the follow-up time course and degree of neointimal hyperplasia. PMID:24954322

  20. Pattern formation, logistics, and maximum path probability

    NASA Astrophysics Data System (ADS)

    Kirkaldy, J. S.

    1985-05-01

    The concept of pattern formation, which to current researchers is a synonym for self-organization, carries the connotation of deductive logic together with the process of spontaneous inference. Defining a pattern as an equivalence relation on a set of thermodynamic objects, we establish that a large class of irreversible pattern-forming systems, evolving along idealized quasisteady paths, approaches the stable steady state as a mapping upon the formal deductive imperatives of a propositional function calculus. In the preamble the classical reversible thermodynamics of composite systems is analyzed as an externally manipulated system of space partitioning and classification based on ideal enclosures and diaphragms. The diaphragms have discrete classification capabilities which are designated in relation to conserved quantities by descriptors such as impervious, diathermal, and adiabatic. Differentiability in the continuum thermodynamic calculus is invoked as equivalent to analyticity and consistency in the underlying class or sentential calculus. The seat of inference, however, rests with the thermodynamicist. In the transition to an irreversible pattern-forming system the defined nature of the composite reservoirs remains, but a given diaphragm is replaced by a pattern-forming system which by its nature is a spontaneously evolving volume partitioner and classifier of invariants. The seat of volition or inference for the classification system is thus transferred from the experimenter or theoretician to the diaphragm, and with it the full deductive facility. The equivalence relations or partitions associated with the emerging patterns may thus be associated with theorems of the natural pattern-forming calculus. The entropy function, together with its derivatives, is the vehicle which relates the logistics of reservoirs and diaphragms to the analog logistics of the continuum. Maximum path probability or second-order differentiability of the entropy in isolation are

  1. Local delivery of dexamethasone for prevention of neointimal proliferation in a rat model of balloon angioplasty.

    PubMed Central

    Villa, A E; Guzman, L A; Chen, W; Golomb, G; Levy, R J; Topol, E J

    1994-01-01

    A periadventitial polymer system is an alternative local drug delivery technique to obtain and maintain high tissue levels of the drug at the site of vascular injury. To determine if local periadventitial delivery of dexamethasone decreases neointimal proliferation after balloon vascular injury, in three groups of Sprague-Dawley rats, 5% dexamethasone, 0.5% dexamethasone, and placebo silicone polymers were implanted around the left common carotid artery after balloon injury. In a fourth group, placebo polymers were implanted without balloon injury. Dexamethasone serum and tissue levels after polymer implantation were significantly higher in the 5% dexamethasone group compared with the 0.5% dexamethasone group. There was no neointima formation in any of the arterial segments covered with placebo polymers for 3 wk, but without balloon injury. In the arterial segments covered by the 5 and 0.5% dexamethasone polymers, there was a 76 and 75% reduction in intima/media ratios, respectively, compared with the placebo group (5% dexamethasone, 0.26 +/- 0.04; 0.5% dexamethasone, 0.27 +/- 0.03; placebo, 1.09 +/- 0.16, respectively; P < 0.0001). These results suggest that: (a) silicone polymers wrapped around the common carotid arteries for 3 wk did not, without balloon injury, stimulate neointimal proliferation in the rat model; (b) the activity of the drug-eluting polymer for suppressing intimal proliferation was chiefly, but not exclusively, site specific; and (c) transadventitial local delivery of dexamethasone at two different doses markedly inhibits neointimal proliferation after balloon vascular injury. Images PMID:8132764

  2. Pattern formation in confined chemical gardens

    NASA Astrophysics Data System (ADS)

    De Wit, Anne; Haudin, Florence; Brau, Fabian; Cartwright, Julyan

    2014-05-01

    Chemical gardens are plant-like mineral structures first described in the seventeenth century and popularly known from chemistry sets for children. They are classically grown in three-dimensional containers by placing a solid metal-salt seed into a silicate solution. When the metal salt starts dissolving in the silicate solution, a semi-permeable membrane forms by precipitation across which water is pumped by osmosis from the silicate solution into the metal salt solution, further dissolving the salt. Above a given pressure, the membrane breaks. The dissolved metal salt solution being generally less dense than the reservoir silicate solution, it rises as a buoyant jet through the broken membrane and further precipitates in contact with the silicate solution, producing a collection of mineral forms that resemble a garden. Such gardens are the subject of increased interest as a model system to understand pattern formation in sea-ice brinicles and hydrothermal vents on the seafloor, among others. All these self-organized precipitation structures at the interface between chemistry, fluid dynamics and mechanics share indeed common chemical, mechanical and electrical properties. In this framework, we study experimentally spatial patterns resulting from the growth of chemical gardens in confined quasi-two-dimensional (2D) geometries upon radial injection of a metallic salt solution into a silicate solution in a horizontal Hele-Shaw cell. We find a large variety of patterns including spirals, fingers, worms, filiform tubes, and flower-like patterns. By exploring the phase space of reactant concentrations and injection flow rates, we observe transitions between these spatio-temporal structures resulting from a coupling between the precipitation reaction, mechanical effects and hydrodynamic instabilities.

  3. Patterning and Compartment Formation in the Diencephalon

    PubMed Central

    Chatterjee, Mallika; Li, James Y. H.

    2012-01-01

    The diencephalon gives rise to structures that play an important role in connecting the anterior forebrain with the rest of the central nervous system. The thalamus is the major diencephalic derivative that functions as a relay station between the cortex and other lower order sensory systems. Almost two decades ago, neuromeric/prosomeric models were proposed describing the subdivision and potential segmentation of the diencephalon. Unlike the laminar structure of the cortex, the diencephalon is progressively divided into distinct functional compartments consisting principally of thalamus, epithalamus, pretectum, and hypothalamus. Neurons generated within these domains further aggregate to form clusters called nuclei, which form specific structural and functional units. We review the recent advances in understanding the genetic mechanisms that are involved in the patterning and compartment formation of the diencephalon. PMID:22593732

  4. Effects of patterned topography on biofilm formation

    NASA Astrophysics Data System (ADS)

    Vasudevan, Ravikumar

    2011-12-01

    Bacterial biofilms are a population of bacteria attached to each other and irreversibly to a surface, enclosed in a matrix of self-secreted polymers, among others polysaccharides, proteins, DNA. Biofilms cause persisting infections associated with implanted medical devices and hospital acquired (nosocomial) infections. Catheter-associated urinary tract infections (CAUTIs) are the most common type of nosocomial infections accounting for up to 40% of all hospital acquired infections. Several different strategies, including use of antibacterial agents and genetic cues, quorum sensing, have been adopted for inhibiting biofilm formation relevant to CAUTI surfaces. Each of these methods pertains to certain types of bacteria, processes and has shortcomings. Based on eukaryotic cell topography interaction studies and Ulva linza spore studies, topographical surfaces were suggested as a benign control method for biofilm formation. However, topographies tested so far have not included a systematic variation of size across basic topography shapes. In this study patterned topography was systematically varied in size and shape according to two approaches 1) confinement and 2) wetting. For the confinement approach, using scanning electron microscopy and confocal microscopy, orienting effects of tested topography based on staphylococcus aureus (s. aureus) (SH1000) and enterobacter cloacae (e. cloacae) (ATCC 700258) bacterial models were identified on features of up to 10 times the size of the bacterium. Psuedomonas aeruginosa (p. aeruginosa) (PAO1) did not show any orientational effects, under the test conditions. Another important factor in medical biofilms is the identification and quantification of phenotypic state which has not been discussed in the literature concerning bacteria topography characterizations. This was done based on antibiotic susceptibility evaluation and also based on gene expression analysis. Although orientational effects occur, phenotypically no difference

  5. Instabilities and pattern formation in crystal growth

    NASA Astrophysics Data System (ADS)

    Langer, J. S.

    1980-01-01

    Several common modes of crystal growth provide particularly simple and elegant examples of spontaneous pattern formation in nature. Phenomena of interest here are those in which an advancing nonfaceted solidification front suffers an instability and subsequently reorganizes itself into a more complex mode of behavior. The purpose of this essay is to examine several such situations and, in doing this, to identify a few new theoretical ideas and a larger number of outstanding problems. The systems studied are those in which solidification is controlled entirely by a single diffusion process, either the flow of latent heat away from a moving interface or the analogous redistribution of chemical constituents. Convective effects are ignored, as are most effects of crystalline anisotropy. The linear theory of the Mullins-Sekerka instability is reviewed for simple planar and spherical cases and also for a special model of directional solidification. These techniques are then extended to the case of a freely growing dendrite, and it is shown how this analysis leads to an understanding of sidebranching and tip-splitting instabilities. A marginal-stability hypothesis is introduced; and it is argued that this intrinsically nonlinear theory, if valid, permits aone to use results of linear-stability analysis to predict dendritic growth rates. The review concludes with a discussion of nonlinear effects in directional solidication. The nonplanar, cellular interfaces which emerge in this situation have much in common with convection patterns in hydrodynamics. The cellular stability problem is discussed briefly, and some preliminary attempts to do calculations in the strongly nonlinear regime are summarized.

  6. Pattern formation in a sandpile of ternary granular mixtures.

    PubMed

    Shimokawa, Michiko; Suetsugu, Yuki; Hiroshige, Ryoma; Hirano, Takeru; Sakaguchi, Hidetsugu

    2015-06-01

    Pattern formation in a sandpile is investigated by pouring a ternary mixture of grains into a vertical narrow cell. Size segregation in avalanches causes the formation of patterns. Four kinds of patterns emerge: stratification, segregation, upper stratification-lower segregation, and upper segregation-lower stratification. A phase diagram is constructed in a parameter space of θ(11)/θ(33) and θ(22)/θ(33), where θ(11),θ(22), and θ(33) are the repose angles of small, intermediate, and large grains, respectively. To qualitatively understand pattern formation, a phenomenological model based on a roll-or-stay rule is proposed. A similar pattern formation is found in a numerical simulation of the phenomenological model. These results suggest that the ratios of the repose angles of three kinds of grains are important for pattern formation in a sandpile. PMID:26172703

  7. Pattern formation in a sandpile of ternary granular mixtures

    NASA Astrophysics Data System (ADS)

    Shimokawa, Michiko; Suetsugu, Yuki; Hiroshige, Ryoma; Hirano, Takeru; Sakaguchi, Hidetsugu

    2015-06-01

    Pattern formation in a sandpile is investigated by pouring a ternary mixture of grains into a vertical narrow cell. Size segregation in avalanches causes the formation of patterns. Four kinds of patterns emerge: stratification, segregation, upper stratification-lower segregation, and upper segregation-lower stratification. A phase diagram is constructed in a parameter space of θ11/θ33 and θ22/θ33 , where θ11,θ22 , and θ33 are the repose angles of small, intermediate, and large grains, respectively. To qualitatively understand pattern formation, a phenomenological model based on a roll-or-stay rule is proposed. A similar pattern formation is found in a numerical simulation of the phenomenological model. These results suggest that the ratios of the repose angles of three kinds of grains are important for pattern formation in a sandpile.

  8. Tongxinluo inhibits vascular inflammation and neointimal hyperplasia through blockade of the positive feedback loop between miR-155 and TNF-α.

    PubMed

    Zhang, Ruo-nan; Zheng, Bin; Li, Li-min; Zhang, Jing; Zhang, Xin-hua; Wen, Jin-kun

    2014-08-15

    Tongxinluo (TXL), a traditional Chinese medicine, has multiple vasoprotective effects, including anti-inflammation. MicroRNA-155 (miR-155) is involved in vascular inflammation and atherosclerosis. However, a direct relationship between TXL and miR-155 in the development of vascular inflammation and remodeling had not yet been shown. The objective of the present study was to investigate whether TXL exerts an inhibitory effect on the vascular inflammatory response and neointimal hyperplasia by regulating miR-155 expression. Using the carotid artery ligation model in mice, we have shown that TXL dose dependently inhibited neointimal formation and reduced the vascular inflammatory response by inhibiting inflammatory cytokine production and macrophage infiltration. miR-155 was induced by carotid artery ligation, and neointimal hyperplasia was strongly reduced in miR-155(−/−) mice. In contrast, miR-155 overexpression partly reversed the inhibitory effect of TXL on neointimal hyperplasia. In bone marrow-derived macrophages, miR-155 and TNF-α formed a positive feedback loop to promote the inflammatory response, which could be blocked by TXL. Furthermore, TXL increased Akt1 protein expression and phosphorylation in TNF-α-stimulated marrow-derived macrophages, and knockdown of Akt1 abrogated the TXL-induced suppression of miR-155. In conclusion, TXL inhibits the vascular inflammatory response and neointimal hyperplasia induced by carotid artery ligation in mice. Suppression of miR-155 expression mediated by Akt1 and blockade of the feedback loop between miR-155 and TNF-α are important pathways whereby TXL exerts its vasoprotective effects. PMID:24951754

  9. Pattern formation by a moving morphogen source

    NASA Astrophysics Data System (ADS)

    Zartman, Jeremiah J.; Cheung, Lily S.; Niepielko, Matthew G.; Bonini, Christine; Haley, Benjamin; Yakoby, Nir; Shvartsman, Stanislav Y.

    2011-08-01

    During Drosophila melanogaster oogenesis, the follicular epithelium that envelops the germline cyst gives rise to an elaborate eggshell, which houses the future embryo and mediates its interaction with the environment. A prominent feature of the eggshell is a pair of dorsal appendages, which are needed for embryo respiration. Morphogenesis of this structure depends on broad, a zinc-finger transcription factor, regulated by the EGFR pathway. While much has been learned about the mechanisms of broad regulation by EGFR, current understanding of processes that shape the spatial pattern of broad expression is incomplete. We propose that this pattern is defined by two different phases of EGFR activation: an early, posterior-to-anterior gradient of EGFR signaling sets the posterior boundary of broad expression, while the anterior boundary is set by a later phase of EGFR signaling, distributed in a dorsoventral gradient. This model can explain the wild-type pattern of broad in D. melanogaster, predicts how this pattern responds to genetic perturbations, and provides insight into the mechanisms driving diversification of eggshell patterning. The proposed model of the broad expression pattern can be used as a starting point for the quantitative analysis of a large number of gene expression patterns in Drosophila oogenesis.

  10. Pattern formation in flowing electrorheological fluids.

    PubMed

    von Pfeil, Karl; Graham, Michael D; Klingenberg, Daniel J; Morris, Jeffrey F

    2002-05-01

    A two-fluid continuum model is developed to describe mass transport in electro- and magnetorheological suspensions. The particle flux is related to the field-induced stresses. Solutions of the resulting mass balance show column formation in the absence of flow, and stripe formation when a suspension is subjected simultaneously to an applied electric field and shear flow. PMID:12005727

  11. Neointimal Hyperplasia in Low-Profile Nitinol Stents, Palmaz Stents, and Wallstents: A Comparative Experimental Study

    SciTech Connect

    Schuermann, Karl; Vorwerk, Dierk; Kulisch, Arthur; Stroehmer-Kulisch, Eva; Biesterfeld, Stefan; Stopinski, Tadeusz; Guenther, Rolf W.

    1996-04-15

    Purpose: To compare neointima formation following insertion of low-profile Nitinol stents, Palmaz stents, and Wallstents. Methods: Nitinol stents, Palmaz stents, and Wallstents similar in size were transfemorally inserted into the iliac arteries of 12 sheep. Four stents per sheep were deployed; the position of the stents was varied so that each type of stent was placed in each position (right or left, proximal or distal) with equal frequency. Stent patency was followed by angiography. Six sheep were euthanized after 1 month, and the remaining six after 6 months. Iliac arteries were removed en bloc and prepared for histological examination. Neointimal and medial thickness were measured by light microscopy, and measurements were analyzed statistically. Results: Mean neointimal thickness both over (NO) and between (NB) the stent struts was greater in Wallstents (NO = 0.341 mm, NB = 0.368 mm) than in the Nitinol (NO = 0.260 mm, NB = 0.220 mm) and Palmaz stents (NO = 0.199 mm, NB = 0.204 mm), but differences were not significant (p> 0.05). Medial atrophy in the area between the stent struts was greater in Wallstents compared with Nitinol and Palmaz stents (p < 0.007 and p < 0.02, respectively); in the area under the stent struts there was a significant difference only between Palmaz stents and Wallstents (p < 0.02). Conclusion: Under defined experimental conditions, none of the three types of stent appears to be preferable to the others regarding neointima formation in the short- to mid-term follow-up period.

  12. Pattern formation in oscillatory media without lateral inhibition.

    PubMed

    Ali, Rehman; Harris, Jeremy; Ermentrout, Bard

    2016-07-01

    Spontaneous symmetry breaking instabilities are the most common mechanism for how biological, chemical, and physical systems produce spatial patterns. Beginning with Turing's original paper, so-called lateral inhibition-in which negative feedback has greater spread than positive feedback-has been the underlying mechanism for pattern formation in biological models. Despite this, there are many biological systems that exhibit pattern formation but do not have lateral inhibition. In this paper, we present an example of such a system that is able to generate robust patterns emerging from a spatially homogeneous state. In fact, patterns can arise when there is only spatial spread of the activator. Unlike classic Turing pattern formation, these patterns arise from a spatially homogeneous oscillation rather than from a constant steady state. PMID:27575169

  13. Cellular pattern formation in circular domains.

    PubMed

    Palacios, Antonio; Gunaratne, Gemunu H.; Gorman, Michael; Robbins, Kay A.

    1997-09-01

    An analysis of stationary and nonstationary cellular patterns observed in premixed flames on a circular, porous plug burner is presented. A phenomenological model is introduced, that exhibits patterns similar to the experimental states. The primary modes of the model are combinations of Fourier-Bessel functions, whose radial parts have neighboring zeros. This observation explains several features of patterns, such as the existence of concentric rings of cells and the weak coupling between rings. Properties of rotating rings of cells, including the existence of modulated rotations and heteroclinic cycles can be deduced using mode coupling. For nonstationary patterns, the modal decomposition of experimental data can be carried out using the Karhunen-Loeve (KL) analysis. Experimental states are used to demonstrate the possibility of using KL analysis to differentiate between uniform and nonuniform rotations. The methodology can be extended to study more complicated nonstationary patterns. In particular, it is shown how the complexity of "hopping states" can be unraveled through the analysis. (c) 1997 American Institute of Physics. PMID:12779674

  14. Pattern Formation in Growing Polar Bacteria

    NASA Astrophysics Data System (ADS)

    Yang, Xingbo; Marchetti, M.; Marenduzzo, Davide

    2013-03-01

    We analyze a continuum model of a bacterial suspension that includes motility suppression from steric repulsion, polar alignment, and bacteria reproduction and death. Using a combination of linear stability analysis and numerical solution of the nonlinear equations, we demonstrate that the model exhibits a rich variety of emergent structures, corresponding to generic patterns seen in experiments. Motility suppression in a crowded environment gives rise to a density phase separation, regulated by the growth/death of the bacteria, as demonstrated earlier by Cates et al. [PNAS 107, 11715-11720(2010)], with spherically symmetric patterns similar to those observed in S. typhimurium. The addition of polar alignment yields new ring/band and swirl/spiral structures resembling those observed in E.coli colonies. The stationary/traveling nature of the patterns and their symmetry is classified and summarized in a phase diagram. This work was supported by the NSF through grant DMR-1004789.

  15. Pattern formation exhibited by biofilm formation within microfluidic chambers.

    PubMed

    Cogan, N G; Donahue, M R; Whidden, Mark; De La Fuente, Leonardo

    2013-05-01

    This article investigates the dynamics of an important bacterial pathogen, Xylella fastidiosa, within artificial plant xylem. The bacterium is the causative agent of a variety of diseases that strike fruit-bearing plants including Pierce's disease of grapevine. Biofilm colonization within microfluidic chambers was visualized in a laboratory setting, showing robust, regular spatial patterning. We also develop a mathematical model, based on a multiphase approach that is able to capture the spacing of the pattern and points to the role of the exopolymeric substance as the main source of control of the pattern dynamics. We concentrate on estimating the attachment/detachment processes within the chamber because these are two mechanisms that have the potential to be engineered by applying various chemicals to prevent or treat the disease. PMID:23663829

  16. Pattern Formation Exhibited by Biofilm Formation within Microfluidic Chambers

    PubMed Central

    Cogan, N.G.; Donahue, M.R.; Whidden, Mark; De La Fuente, Leonardo

    2013-01-01

    This article investigates the dynamics of an important bacterial pathogen, Xylella fastidiosa, within artificial plant xylem. The bacterium is the causative agent of a variety of diseases that strike fruit-bearing plants including Pierce’s disease of grapevine. Biofilm colonization within microfluidic chambers was visualized in a laboratory setting, showing robust, regular spatial patterning. We also develop a mathematical model, based on a multiphase approach that is able to capture the spacing of the pattern and points to the role of the exopolymeric substance as the main source of control of the pattern dynamics. We concentrate on estimating the attachment/detachment processes within the chamber because these are two mechanisms that have the potential to be engineered by applying various chemicals to prevent or treat the disease. PMID:23663829

  17. Leukotriene-C4 Synthase, a Critical Enzyme in the Activation of Store-independent Orai1/Orai3 Channels, Is Required for Neointimal Hyperplasia*

    PubMed Central

    Zhang, Wei; Zhang, Xuexin; González-Cobos, José C.; Stolwijk, Judith A.; Matrougui, Khalid; Trebak, Mohamed

    2015-01-01

    Leukotriene-C4 synthase (LTC4S) generates LTC4 from arachidonic acid metabolism. LTC4 is a proinflammatory factor that acts on plasma membrane cysteinyl leukotriene receptors. Recently, however, we showed that LTC4 was also a cytosolic second messenger that activated store-independent LTC4-regulated Ca2+ (LRC) channels encoded by Orai1/Orai3 heteromultimers in vascular smooth muscle cells (VSMCs). We showed that Orai3 and LRC currents were up-regulated in medial and neointimal VSMCs after vascular injury and that Orai3 knockdown inhibited LRC currents and neointimal hyperplasia. However, the role of LTC4S in neointima formation remains unknown. Here we show that LTC4S knockdown inhibited LRC currents in VSMCs. We performed in vivo experiments where rat left carotid arteries were injured using balloon angioplasty to cause neointimal hyperplasia. Neointima formation was associated with up-regulation of LTC4S protein expression in VSMCs. Inhibition of LTC4S expression in injured carotids by lentiviral particles encoding shRNA inhibited neointima formation and inward and outward vessel remodeling. LRC current activation did not cause nuclear factor for activated T cells (NFAT) nuclear translocation in VSMCs. Surprisingly, knockdown of either LTC4S or Orai3 yielded more robust and sustained Akt1 and Akt2 phosphorylation on Ser-473/Ser-474 upon serum stimulation. LTC4S and Orai3 knockdown inhibited VSMC migration in vitro with no effect on proliferation. Akt activity was suppressed in neointimal and medial VSMCs from injured vessels at 2 weeks postinjury but was restored when the up-regulation of either LTC4S or Orai3 was prevented by shRNA. We conclude that LTC4S and Orai3 altered Akt signaling to promote VSMC migration and neointima formation. PMID:25540197

  18. Dendrites, viscous fingers, and the theory of pattern formation

    NASA Technical Reports Server (NTRS)

    Langer, J. S.

    1989-01-01

    Recent developments in the theory of pattern formation in dendritic crystal growth and viscous fingering in fluids are reviewed. Consideration is given to the discovery that weak capillary forces act as singular perturbations which lead to selection mechanisms in dendritic crystal growth and fingering patterns. Other topics include the conventional thermodynamic model of the solidification of a pure substance from its melt, fingering instability, pattern selection, the solvability theory, dendritic growth rates, the bubble effect discovered by Couder et al. (1986), the dynamics of pattern-forming systems, and snowflake formation.

  19. Annular gel reactor for chemical pattern formation

    DOEpatents

    Nosticzius, Zoltan; Horsthemke, Werner; McCormick, William D.; Swinney, Harry L.; Tam, Wing Y.

    1990-01-01

    The present invention is directed to an annular gel reactor suitable for the production and observation of spatiotemporal patterns created during a chemical reaction. The apparatus comprises a vessel having at least a first and second chamber separated one from the other by an annular polymer gel layer (or other fine porous medium) which is inert to the materials to be reacted but capable of allowing diffusion of the chemicals into it.

  20. Hypoxic adipocytes pattern early heterotopic bone formation.

    PubMed

    Olmsted-Davis, Elizabeth; Gannon, Francis H; Ozen, Mustafa; Ittmann, Michael M; Gugala, Zbigniew; Hipp, John A; Moran, Kevin M; Fouletier-Dilling, Christine M; Schumara-Martin, Shannon; Lindsey, Ronald W; Heggeness, Michael H; Brenner, Malcolm K; Davis, Alan R

    2007-02-01

    The factors contributing to heterotopic ossification, the formation of bone in abnormal soft-tissue locations, are beginning to emerge, but little is known about microenvironmental conditions promoting this often devastating disease. Using a murine model in which endochondral bone formation is triggered in muscle by bone morphogenetic protein 2 (BMP2), we studied changes near the site of injection of BMP2-expressing cells. As early as 24 hours later, brown adipocytes began accumulating in the lesional area. These cells stained positively for pimonidazole and therefore generated hypoxic stress within the target tissue, a prerequisite for the differentiation of stem cells to chondrocytes and subsequent heterotopic bone formation. We propose that aberrant expression of BMPs in soft tissue stimulates production of brown adipocytes, which drive the early steps of heterotopic endochondral ossification by lowering oxygen tension in adjacent tissue, creating the correct environment for chondrogenesis. Results in misty gray lean mutant mice not producing brown fat suggest that white adipocytes convert into fat-oxidizing cells when brown adipocytes are unavailable, providing a compensatory mechanism for generation of a hypoxic microenvironment. Manipulation of the transcriptional control of adipocyte fate in local soft-tissue environments may offer a means to prevent or treat development of bone in extraskeletal sites. PMID:17255330

  1. Pattern formation in quantum Turing machines

    NASA Astrophysics Data System (ADS)

    Kim, Ilki; Mahler, Günter

    1999-07-01

    We investigate the iteration of a sequence of local and pair unitary transformations, which can be interpreted to result from a Turing-head (pseudospin S) rotating along a closed Turing tape (M additional pseudospins). The dynamical evolution of the Bloch vector of S, which can be decomposed into 2M primitive pure state Turing-head trajectories, gives rise to fascinating geometrical patterns reflecting the entanglement between head and tape. These machines thus provide intuitive examples for quantum parallelism and, at the same time, means for local testing of quantum network dynamics.

  2. Pattern formation and coarsening in crystalline membranes

    NASA Astrophysics Data System (ADS)

    Vega, Daniel A.; Pezzutti, Aldo D.

    2011-03-01

    We study through a Brazovskii-Helfrich Hamiltonian the process of defect formation, annealing and coarsening of two dimensional crystalline membranes. In good agreement with the cosmological model of Kibble and Zurek, proposed to determine the density of topological defects at the onset of a symmetry breaking phase transition, we found that the collision of orientationally uncorrelated domains produces a structure of grains with an average density of topological defects controlled by the temperature of the quench. The strain field of the dislocations and disclinations generated during the phase separation process can induce the buckling of the membrane, slowing down the Lifshitz-Safran mechanism of coarsening observed in flat systems.

  3. Turing pattern formation in the Brusselator system with nonlinear diffusion

    NASA Astrophysics Data System (ADS)

    Gambino, G.; Lombardo, M. C.; Sammartino, M.; Sciacca, V.

    2013-10-01

    In this work we investigate the effect of density-dependent nonlinear diffusion on pattern formation in the Brusselator system. Through linear stability analysis of the basic solution we determine the Turing and the oscillatory instability boundaries. A comparison with the classical linear diffusion shows how nonlinear diffusion favors the occurrence of Turing pattern formation. We study the process of pattern formation both in one-dimensional and two-dimensional spatial domains. Through a weakly nonlinear multiple scales analysis we derive the equations for the amplitude of the stationary patterns. The analysis of the amplitude equations shows the occurrence of a number of different phenomena, including stable supercritical and subcritical Turing patterns with multiple branches of stable solutions leading to hysteresis. Moreover, we consider traveling patterning waves: When the domain size is large, the pattern forms sequentially and traveling wave fronts are the precursors to patterning. We derive the Ginzburg-Landau equation and describe the traveling front enveloping a pattern which invades the domain. We show the emergence of radially symmetric target patterns, and, through a matching procedure, we construct the outer amplitude equation and the inner core solution.

  4. Spatial pattern formation in the lung

    PubMed Central

    Donovan, Graham M.; Kritter, Thibaut

    2014-01-01

    Clustered ventilation defects are a hallmark of asthma, typically seen via imaging studies during asthma attacks. The mechanisms underlying the formation of these clusters is of great interest in understanding asthma. Because the clusters vary from event to event, many researchers believe they occur due to dynamic, rather than structural, causes. To study the formation of these clusters, we formulate and analyze a lattice-based model of the lung, considering both the role of airway bistability and a mechanism for organizing the spatial structure. Within this model we show how and why the homogeneous ventilation solution becomes unstable, and under what circumstances the resulting heterogeneous solution is a clustered solution. The size of the resulting clusters is shown to arise from structure of the eigenvalues and eigenvectors of the system, admitting not only clustered solutions but also (aphysical) checkerboard solutions. We also consider the breathing efficiency of clustered solutions in severely constricted lungs, showing that stabilizing the homogeneous solution may be advantageous in some circumstances. Extensions to hexagonal and cubic lattices are also studied. PMID:24810407

  5. Effect of methanolic extract of Piper sarmentosum leaves on neointimal foam cell infiltration in rabbits fed with high cholesterol diet

    PubMed Central

    Amran, Adel A.; Zakaria, Zaiton; Othman, Faizah; Das, Srijit; Al-Mekhlafi, Hesham M.; Raj, Santhana; Nordin, Nor-Anita MM

    2012-01-01

    Previous research has shown the beneficial effects of aqueous extract of Piper sarmentosum (P.s) on atherosclerosis. The first stage in atherosclerosis is the formation of foam cell. The aim of this study was to investigate the effect of the methanol extract of P.s on fatty streaks by calculating neointimal foam cell infiltration in rabbits fed with high cholesterol diet. Thirty six male New Zealand white rabbits were divided equally into six groups: (i) C: control group fed normal rabbit chow; (ii) CH: cholesterol diet (1 % cholesterol); (iii) PM1: 1 % cholesterol with methanol extract of P.s (62.5 mg/kg); (iv) PM2: 1 % cholesterol with methanol extract of P.s (125 mg/kg); (v) PM3: 1 % cholesterol with methanol extract of P.s (250 mg/kg); (vi) SMV group fed 1 % cholesterol supplemented with Simvistatin drug (1.2 mg/kg). All animals were treated for 10 weeks. At the end of the treatment, the rabbits were fasted and sacrificed and the aortic tissues were collected for histological studies to measure the area of the neointimal foam cell infiltration using software. The thickening of intima ratio of atherosclerosis and morphological changes by scanning electron microscope were measured. The results showed that the atherosclerotic group had significantly bigger area of fatty streak compared to the control group. The area of fatty streak in the abdominal aorta was significantly reduced in the treatment groups which were similar with the SMV group. Similarly, there was a reduction in the number of foam cell in the treatment groups compared to the atherosclerotic group as seen under scanning microscope. In conclusion, histological study demonstrated that the methanol extract of the P.s could reduce the neointimal foam cell infiltration in the lumen of the aorta and the atherosclerotic lesion. PMID:27366140

  6. Instability-induced pattern formation of photoactivated functional polymers

    PubMed Central

    Ambrosio, Antonio; Maddalena, Pasqualino; Schenker, Iwan; Spolenak, Ralph; Capasso, Federico

    2014-01-01

    Since the pioneering work of Turing on the formation principles of animal coat patterns [Turing AM (1952) Phil Trans R Soc Lond B 237(641):37–72], such as the stripes of a tiger, great effort has been made to understand and explain various phenomena of self-assembly and pattern formation. Prominent examples are the spontaneous demixing in emulsions, such as mixtures of water and oil [Herzig EM, et al. (2007) Nat Mater 6:966–971]; the distribution of matter in the universe [Kibble TWB (1976) J Phys A: Math Gen 9(8):1387]; surface reconstruction in ionic crystals [Clark KW, et al. (2012) Nanotechnol 23(18):185306]; and the pattern formation caused by phase transitions in metal alloys, polymer mixtures and binary Bose–Einstein condensates [Sabbatini J, et al. (2011) Phys Rev Lett 107:230402]. Photoactivated pattern formation in functional polymers has attracted major interest due to its potential applications in molecular electronics and photoresponsive systems. Here we demonstrate that photoactivated pattern formation on azobenzene-containing polymer films can be entirely explained by the physical concept of phase separation. Using experiments and simulations, we show that phase separation is caused by an instability created by the photoactivated transitions between two immiscible states of the polymer. In addition, we have shown in accordance with theory, that polarized light has a striking effect on pattern formation indicated by enhanced phase separation. PMID:25404346

  7. Instability-induced pattern formation of photoactivated functional polymers.

    PubMed

    Galinski, Henning; Ambrosio, Antonio; Maddalena, Pasqualino; Schenker, Iwan; Spolenak, Ralph; Capasso, Federico

    2014-12-01

    Since the pioneering work of Turing on the formation principles of animal coat patterns [Turing AM (1952) Phil Trans R Soc Lond B 237(641):37-72], such as the stripes of a tiger, great effort has been made to understand and explain various phenomena of self-assembly and pattern formation. Prominent examples are the spontaneous demixing in emulsions, such as mixtures of water and oil [Herzig EM, et al. (2007) Nat Mater 6:966-971]; the distribution of matter in the universe [Kibble TWB (1976) J Phys A: Math Gen 9(8):1387]; surface reconstruction in ionic crystals [Clark KW, et al. (2012) Nanotechnol 23(18):185306]; and the pattern formation caused by phase transitions in metal alloys, polymer mixtures and binary Bose-Einstein condensates [Sabbatini J, et al. (2011) Phys Rev Lett 107:230402]. Photoactivated pattern formation in functional polymers has attracted major interest due to its potential applications in molecular electronics and photoresponsive systems. Here we demonstrate that photoactivated pattern formation on azobenzene-containing polymer films can be entirely explained by the physical concept of phase separation. Using experiments and simulations, we show that phase separation is caused by an instability created by the photoactivated transitions between two immiscible states of the polymer. In addition, we have shown in accordance with theory, that polarized light has a striking effect on pattern formation indicated by enhanced phase separation. PMID:25404346

  8. Comparison of neointimal coverage and extra-stent lumen between sirolimus and everolimus-eluting stent using optical coherence tomography.

    PubMed

    Oda, Takamasa; Okamura, Takayuki; Yamada, Jutaro; Miyagi, Naoto; Uehara, Hiroki; Nao, Tomoko; Tateishi, Hiroki; Maeda, Takao; Nakamura, Takeshi; Shiraishi, Kohzoh; Nakashima, Tadamitsu; Nishimura, Shigehiko; Miura, Toshiro; Matsuzaki, Masunori; Yano, Masafumi

    2016-04-01

    The external lumen of a stent [defined as extra-stent lumen (ESL)] assessed by optical coherence tomography (OCT) may be related to the risk of thrombus formation after sirolimus-eluting stent (SES) implantation. An everolimus-eluting stent (EES) might provide relatively minimal inflammatory reaction and appropriate neointimal coverage. The purpose of this study was to compare the neointimal thickness and ESL between SES and EES. Patients who underwent OCT examination more than 7 months after either SES or EES implantation were enrolled. Stent area (SA), lumen area (LA), neointimal area (NIA) and neointimal thickness (NIT) of each strut were measured at 1-mm intervals between stented segments. The area, angle (summation per cross-section) and depth (maximum distance from adjacent vessel surface to the outline of stent) of ESL were analyzed. A total of 49 lesions were included (SES n = 20, EES n = 29). Mean follow-up period was 11 months. A total of 998 cross-sections and 9874 struts were analyzed. There were no differences in stent area, lumen area and neointimal area (SA: 6.01 ± 1.60 vs. 6.02 ± 1.40 mm(2), p = 0.572, LA: 5.37 ± 1.52 vs. 5.29 ± 1.34 mm(2), p = 0.692, NIA: 0.64 ± 0.49 vs. 0.72 ± 0.37 mm(2), p = 0.493). Mean NIT of SES and EES were 0.11 ± 0.05 and 0.10 ± 0.05 mm, respectively (p = 0.367). Conversely, area, angle and depth of ESL in SES group were significantly greater than those in EES group (0.20 ± 0.39 vs. 0.03 ± 0.09 mm(2), p < 0.001, 56.2 ± 59.1° vs. 20.1 ± 41.9°, p < 0.001, 0.10 ± 0.09 vs. 0.03 ± 0.03 mm, p < 0.001). OCT showed that the efficacy of neointimal growth suppression is similar between SES and EES, whereas the adverse vascular response after EES implantation is smaller than that after SES implantation. PMID:25614415

  9. Geological pattern formation by growth and dissolution in aqueous systems

    SciTech Connect

    Paul Meakin

    2010-03-01

    Although many geological processes take place on time scales that are very long compared with the human experience, essentially all geological processes, fast or slow, are far from equilibrium processes. Surprisingly often, geological processes lead to the formation of quite simple and distinctive patterns, which hint at an underlying simplicity in many complex geological systems.. The ability to predict the seasons was critically important to early human society, and Halley’s prediction of the return of the comet that bears his name is still considered to be a scientific milestone. Spatial patterns have also attracted attention because of their aesthetic appeal, which depends in subtle ways on a combination of regularity and irregularity. In recent decades, rapid growth in the capabilities of digital computers has facilitated the simulation of pattern formation processes, and computer simulations have become an important tool for evaluating theoretical concepts and for scientific discovery. Computer technology in combination with other technologies such as high resolution digital cameras, scanning microprobes (atomic force microscopy AFM), confocal microscopy, and scanning tunneling microscopy (STM), for example) has facilitated the quantitative characterization of patterns over a wide range of scales and has enabled rapid advances in our ability to understand the links between large scale pattern formation and microscopic processes. The ability to quantitatively characterize patterns is important because it enables a more rigorous comparison between the predictions of computer models and real world patterns and their formation.In some cases, the idea that patterns with a high degree of regularity have simple origins appears to be justified, but in other cases, such as the formation of almost perfectly circular stone rings due to freeze-thaw cycles simple patterns appear to be the consequence of quite complex processes. In other cases, it has been shown that

  10. Chiral pattern formation in compact microbial colonies

    NASA Astrophysics Data System (ADS)

    Korolev, Kirill; Bino George, Ashish

    Chirality is ubiquitous in biology from single molecules to entire populations. Yet, we are still lacking a detailed understanding of how chiral patterns emerge from cell competition and growth, even in simple microbial colonies. Although many microbes grow as dense colonies with no apparent chirality, recent experiments with Escherichia coli have demonstrated that internal dynamics in such populations can be in fact chiral. We show that there is a unique way to extend the commonly-used reaction-diffusion models of colony growth to account for the emergent chirality. This new model connects microscopic and macroscopic chirality and explains the origin of logarithmic spirals separating different sub-populations in a colony. We also show that chirality is substantially enhanced by the cooperation among the cells at the expansion frontier. In heterogeneous populations composed of strains with different chiralities and growth rates, our model predicts a very rich set of possible dynamics. For example, different chiralities can result in either sharp boundaries between the strains or promote their intermixing depending on the preferred twisting directions of the strains.

  11. Optical pattern formation with a two-level nonlinearity

    NASA Astrophysics Data System (ADS)

    Camara, A.; Kaiser, R.; Labeyrie, G.; Firth, W. J.; Oppo, G.-L.; Robb, G. R. M.; Arnold, A. S.; Ackemann, T.

    2015-07-01

    We present an experimental and theoretical investigation of spontaneous pattern formation in the transverse section of a single retroreflected laser beam passing through a cloud of cold rubidium atoms. In contrast to previously investigated systems, the nonlinearity at work here is that of a two-level atom, which realizes the paradigmatic situation considered in many theoretical studies of optical pattern formation. In particular, we are able to observe the disappearance of the patterns at high intensity due to the intrinsic saturable character of two-level atomic transitions.

  12. Single cell pattern formation and transient cytoskeletal arrays

    PubMed Central

    Bement, William M.; von Dassow, George

    2015-01-01

    A major goal of developmental biology is to explain the emergence of pattern in cell layers, tissues and organs. Developmental biologists now accept that reaction diffusion-based mechanisms are broadly employed in developing organisms to direct pattern formation. Here we briefly consider these mechanisms and then apply some of the concepts derived from them to several processes that occur in single cells: wound repair, yeast budding, and cytokinesis. Two conclusions emerge from this analysis: first, there is considerable overlap at the level of general mechanisms between developmental and single cell pattern formation; second, dynamic structures based on the actin cytoskeleton may be far more ordered than is generally recognized. PMID:24529246

  13. Pattern formation in a minimal model of continuum dislocation plasticity

    NASA Astrophysics Data System (ADS)

    Sandfeld, Stefan; Zaiser, Michael

    2015-09-01

    The spontaneous emergence of heterogeneous dislocation patterns is a conspicuous feature of plastic deformation and strain hardening of crystalline solids. Despite long-standing efforts in the materials science and physics of defect communities, there is no general consensus regarding the physical mechanism which leads to the formation of dislocation patterns. In order to establish the fundamental mechanism, we formulate an extremely simplified, minimal model to investigate the formation of patterns based on the continuum theory of fluxes of curved dislocations. We demonstrate that strain hardening as embodied in a Taylor-type dislocation density dependence of the flow stress, in conjunction with the structure of the kinematic equations that govern dislocation motion under the action of external stresses, is already sufficient for the formation of dislocation patterns that are consistent with the principle of similitude.

  14. Neural pattern formation in networks with dendritic structure

    NASA Astrophysics Data System (ADS)

    Bressloff, P. C.; De Souza, B.

    1998-04-01

    We present a detailed analysis of a recently proposed model of neural pattern formation that is based on the combined effect of diffusion along a neuron's dendritic tree and recurrent interactions along axo-dendritic synaptic connections. For concreteness, we consider a one-dimensional array of analog neurons with the dendritic tree idealized as a one-dimensional cable. Linear stability analysis and bifurcation theory together with numerical simulations are used to establish conditions for the onset of a Turing instability leading to the formation of stable spatial patterns of network output activity. It is shown that the presence of dendritic structure can induce dynamic (time-periodic) spatial pattern formation. Moreover, correlations between the dendritic location of a synapse and the relative positions of neurons in the network are shown to result in spatially oscillating patterns of activity along the dendrites of each neuron.

  15. Pattern Formation in Drying Drops of Polystyrene/Water nanofluids

    NASA Astrophysics Data System (ADS)

    Brutin, David; Sobac, Benjamin

    2011-11-01

    We study the pattern formation and the evaporation dynamics of drying drops of polystyrene/water based nanofluids with concentrations ranging from 0.01% to 6%. Cracks formation is evidenced to depend on the nanoparticles concentration. The dynamics of evaporation is recorded using an electronic balance with an accuracy of 10 μg. A top view recording enables to analyze the pattern formation in relation with the mass evolution. We determine several key parameters such as the time of evaporation, the wetting diameter, the final solid deposition diameter, the number and the spacing of the cracks. We evidence a ring formation above a critical concentration. We evidenced by change of the surrounding humidity in the range of 10 to 90% that this pattern remains constant. The pattern formation is influenced by the liquid phase evaporation dynamics but only depends on the concentration in nanoparticles. These results are of great interest regarding the formation of droplets in several areas such as inkjet printing, pharmacology...

  16. Physical Mechanisms of Pattern Formation in the Early Chick Embryo

    NASA Astrophysics Data System (ADS)

    Balter, Ariel; Glazier, James; Zaitlen, Benji; Chaplain, Mark; Weijer, Cornelis

    2007-03-01

    Gastrulation marks a critical step in early embryogenesis when the first recognizable patterns are laid down. Although the genome maintains ultimate responsibility for this pattern formation, it cannot actually control the organization of individual cells. The robustness of embryogenic pattern formation suggests that a few simple, physical mechanisms are unleashed and that self-organization results. We perform numerical simulations of early chick gastrulation using an agent based method in which individual cells interact via a handful of behaviors including adhesivity, secretion and chemotaxis. Through these simulations we have identified certain behaviors as being important for various stages and morphological events. For instance, experimental results on primitive streak formation are best reproduced by a model in which the Kohler's Sickle secretes a chemo repellant for streak tip cells, and cell polarization appears to be important for initiating polonaise motion during streak elongation.

  17. Pattern formation via intermittence from microscopic deterministic dynamics

    NASA Astrophysics Data System (ADS)

    Hernández, Marco; Escaff, Daniel; Finger, Ricardo

    2012-05-01

    We propose a one-dimensional lattice model, inspired by population dynamics interaction. The model combines a variable coupling range with the Allee effect. The system is capable of exhibiting pattern formation that is similar to what occurs in similar continuous models for population dynamics. However, the formation features are quite different; in this case the pattern emerges from a disorder state via intermittence. We analytically estimated the selected wavelength of the formed pattern and numerically studied fluctuations around the mean wavelength. We also comment on the relationship between intermittence and the edge of chaos as well as sensitivity to initial conditions. Next, we present an analytical prediction of the influence of the world size on the intermittent regime which is in good agreement with the numerical observations. Moreover, the last calculation provided us an alternative way to compute the pattern wavelength. Finally, we discuss the continuous limit of our lattice model.

  18. On the mechanical theory for biological pattern formation

    NASA Astrophysics Data System (ADS)

    Bentil, D. E.; Murray, J. D.

    1993-02-01

    We investigate the pattern-forming potential of mechanical models in embryology proposed by Oster, Murray and their coworkers. We show that the presence of source terms in the tissue extracellular matrix and cell density equations give rise to spatio-temporal oscillations. An extension of one such model to include ‘biologically realistic long range effects induces the formation of stationary spatial patterns. Previous attempts to solve the full system were in one dimension only. We obtain solutions in one dimension and extend our simulations to two dimensions. We show that a single mechanical model alone is capable of generating complex but regular spatial patterns rather than the requirement of model interaction as suggested by Nagorcka et al. and Shaw and Murray. We discuss some biological applications of the models among which are would healing and formation of dermatoglyphic (fingerprint) patterns.

  19. Restenosis and the proportional neointimal response to coronary artery injury: results in a porcine model.

    PubMed

    Schwartz, R S; Huber, K C; Murphy, J G; Edwards, W D; Camrud, A R; Vlietstra, R E; Holmes, D R

    1992-02-01

    Restenosis is a reparative response to arterial injury occurring with percutaneous coronary revascularization. However, the quantitative characteristics of the relation between vessel injury and the magnitude of restenotic response remain unknown. This study was thus performed to determine the relation between severity of vessel wall injury and the thickness of resulting neointimal proliferation in a porcine model of coronary restenosis. Twenty-six porcine coronary artery segments in 24 pigs were subjected to deep arterial injury with use of overexpanded, percutaneously delivered tantalum wire coils. The vessels were studied microscopically 4 weeks after coil implantation to measure the relation between the extent of injury and the resulting neointimal thickness. For each wire site, a histopathologic score proportional to injury depth and the neointimal thicknesses at that site were determined. Mean injury scores were compared with both mean neointimal thickness and planimetry-derived area percent lumen stenosis. The severity of vessel injury strongly correlated with neointimal thickness and percent diameter stenosis (p less than 0.001). Neointimal proliferation resulting from a given wire was related to injury severity in adjacent wires, suggesting an interaction among effects at injured sites. If the results in this model apply to human coronary arteries, restenosis may depend on the degree of vessel injury sustained during angioplasty. PMID:1732351

  20. Pattern Formation in Nature: What Could Be Behind It

    NASA Astrophysics Data System (ADS)

    Kenkre, V. M.

    2012-10-01

    Pattern formation in nature is a ubiquitous and fascinating phenomenon. A simple description will be given of one possible mechanism among many: spatial nonlocality in competitive interactions [1-2]. A tutorial explanation will be presented of random walks or diffusion, then of the logistic equation, then of their combination to produce the Fisher equation, and finally of a generalization of the Fisher equation with spatial nonlocality which is capable of producing patterns. The role of diffusion in the pattern formation process will be discussed with possibilities of a remarkable shape shifting consequence of controlled motion that we have discovered recently [3].[4pt] [1] Nonlocal Interaction Effects on Pattern Formation in Population Dynamics, M. A. Fuentes, M. N. Kuperman, and V.M. Kenkre: Phys. Rev. Lett. 91, 158104-1 (2003).[2] Analytical Considerations in the Study of Spatial Patterns Arising from Nonlocal Interaction Effects, M. A. Fuentes, M. Kuperman, and V. M. Kenkre: J. Phys. Chem. B 108, 10505-10508(2004).[3] Shape Shifting in Patterns Produced by Control of Diffusion: Theoretical Considerations, M. Kuperman and V. M. Kenkre, Consortium Preprint, UNM (2012).

  1. Spongiosa Primary Development: A Biochemical Hypothesis by Turing Patterns Formations

    PubMed Central

    López-Vaca, Oscar Rodrigo; Garzón-Alvarado, Diego Alexander

    2012-01-01

    We propose a biochemical model describing the formation of primary spongiosa architecture through a bioregulatory model by metalloproteinase 13 (MMP13) and vascular endothelial growth factor (VEGF). It is assumed that MMP13 regulates cartilage degradation and the VEGF allows vascularization and advances in the ossification front through the presence of osteoblasts. The coupling of this set of molecules is represented by reaction-diffusion equations with parameters in the Turing space, creating a stable spatiotemporal pattern that leads to the formation of the trabeculae present in the spongy tissue. Experimental evidence has shown that the MMP13 regulates VEGF formation, and it is assumed that VEGF negatively regulates MMP13 formation. Thus, the patterns obtained by ossification may represent the primary spongiosa formation during endochondral ossification. Moreover, for the numerical solution, we used the finite element method with the Newton-Raphson method to approximate partial differential nonlinear equations. Ossification patterns obtained may represent the primary spongiosa formation during endochondral ossification. PMID:23193429

  2. Turing pattern formation in fractional activator-inhibitor systems.

    PubMed

    Henry, B I; Langlands, T A M; Wearne, S L

    2005-08-01

    Activator-inhibitor systems of reaction-diffusion equations have been used to describe pattern formation in numerous applications in biology, chemistry, and physics. The rate of diffusion in these applications is manifest in the single parameter of the diffusion constant, and stationary Turing patterns occur above a critical value of d representing the ratio of the diffusion constants of the inhibitor to the activator. Here we consider activator-inhibitor systems in which the diffusion is anomalous subdiffusion; the diffusion rates are manifest in both a diffusion constant and a diffusion exponent. A consideration of this problem in terms of continuous-time random walks with sources and sinks leads to a reaction-diffusion system with fractional order temporal derivatives operating on the spatial Laplacian. We have carried out an algebraic stability analysis of the homogeneous steady-state solution in fractional activator-inhibitor systems, with Gierer-Meinhardt reaction kinetics and with Brusselator reaction kinetics. For each class of reaction kinetics we identify a Turing instability bifurcation curve in the two-dimensional diffusion parameter space. The critical value of d , for Turing instabilities, decreases monotonically with the anomalous diffusion exponent between unity (standard diffusion) and zero (extreme subdiffusion). We have also carried out numerical simulations of the governing fractional activator-inhibitor equations and we show that the Turing instability precipitates the formation of complex spatiotemporal patterns. If the diffusion of the activator and inhibitor have the same anomalous scaling properties, then the surface profiles of these patterns for values of d slightly above the critical value varies from smooth stationary patterns to increasingly rough and nonstationary patterns as the anomalous diffusion exponent varies from unity towards zero. If the diffusion of the activator is anomalous subdiffusion but the diffusion of the inhibitor

  3. How does tidal flow affect pattern formation in mussel beds?

    PubMed

    Sherratt, Jonathan A; Mackenzie, Julia J

    2016-10-01

    In the Wadden Sea, mussel beds self-organise into spatial patterns consisting of bands parallel to the shore. A leading explanation for this phenomenon is that mussel aggregation reduces losses from dislodgement and predation, because of the adherence of mussels to one another. Previous mathematical modelling has shown that this can lead to spatial patterning when it is coupled to the advection from the open sea of algae-the main food source for mussels in the Wadden Sea. A complicating factor in this process is that the advection of algae will actually oscillate with the tidal flow. This has been excluded from previous modelling studies, and the present paper concerns the implications of this oscillation for pattern formation. The authors initially consider piecewise constant ("square-tooth") oscillations in advection, which enables analytical investigation of the conditions for pattern formation. They then build on this to study the more realistic case of sinusoidal oscillations. Their analysis shows that future research on the details of pattern formation in mussel beds will require an in-depth understanding of how the tides affect long-range inhibition among mussels. PMID:27343625

  4. Pattern formation in miniature: the female gametophyte of flowering plants.

    PubMed

    Sundaresan, Venkatesan; Alandete-Saez, Monica

    2010-01-01

    Plant reproduction involves gamete production by a haploid generation, the gametophyte. For flowering plants, a defining characteristic in the evolution from the 'naked-seed' plants, or gymnosperms, is a reduced female gametophyte, comprising just seven cells of four different types--a microcosm of pattern formation and gamete specification about which only little is known. However, several genes involved in the differentiation, fertilization and post-fertilization functions of the female gametophyte have been identified and, recently, the morphogenic activity of the plant hormone auxin has been found to mediate patterning and egg cell specification. This article reviews recent progress in understanding the pattern formation, maternal effects and evolution of this essential unit of plant reproduction. PMID:20040485

  5. Vinpocetine Attenuates Neointimal Hyperplasia in Diabetic Rat Carotid Arteries after Balloon Injury

    PubMed Central

    Peng, Wenhui; Li, Hailing; Zhuang, Jianhui; Lu, Yuyan; Liu, Baoxin; Li, Xiankai; Li, Weiming; Xu, Yawei

    2014-01-01

    Background Diabetes exacerbates abnormal vascular smooth muscle cell (VSMC) accumulation in response to arterial wall injury. Vinpocetine has been shown to improve vascular remolding; however, little is known about the direct effects of vinpocetine on vascular complications mediated by diabetes. The objective of this study was to determine the effects of vinpocetine on hyperglycemia-facilitated neointimal hyperplasia and explore its possible mechanism. Materials and Methods Nondiabetic and diabetic rats were subjected to balloon injury of the carotid artery followed by 3-week treatment with either vinpocetine (10 mg/kg/day) or saline. Morphological analysis and proliferating cell nuclear antigen (PCNA) immunostaining were performed on day 21. Rat VSMCs proliferation was determined with 5-ethynyl-20-deoxyuridine cell proliferation assays. Chemokinesis was monitored with scratch assays, and production of reactive oxygen species (ROS) was assessed using a 2′,7′-dichlorodihydrofluorescein diacetate (H2DCFDA) flow cytometric assay. Apoptosis was detected by annexin V-FITC/PI flow cytometric assay. Cell signaling was assessed by immunblotting. Results Vinpocetine prevented intimal hyperplasia in carotid arteries in both normal (I/M ratio: 93.83 ± 26.45% versus 143.2 ± 38.18%, P<0.05) and diabetic animals (I/M ratio: 120.5 ± 42.55% versus 233.46 ± 33.98%, P<0.05) when compared to saline. The in vitro study demonstrated that vinpocetine significantly inhibited VSMCs proliferation and chemokinesis as well as ROS generation and apoptotic resistance, which was induced by high glucose (HG) treatment. Vinpocetine significantly abolished HG-induced phosphorylation of Akt and JNK1/2 without affecting their total levels. For downstream targets, HG-induced phosphorylation of IκBα was significantly inhibited by vinpocetine. Vinpocetine also attenuated HG-enhanced expression of PCNA, cyclin D1 and Bcl-2. Conclusions Vinpocetine attenuated neointimal formation in diabetic

  6. Pattern formation in wet granular matter under vertical vibrations.

    PubMed

    Butzhammer, Lorenz; Völkel, Simeon; Rehberg, Ingo; Huang, Kai

    2015-07-01

    Experiments on a thin layer of cohesive wet granular matter under vertical vibrations reveal kink-separated domains that collide with the container at different phases. Due to the strong cohesion arising from the formation of liquid bridges between adjacent particles, the domains move collectively upon vibrations. Depending on the periodicity of this collective motion, the kink fronts may propagate, couple with each other, and form rotating spiral patterns in the case of period tripling or stay as standing wave patterns in the case of period doubling. Moreover, both patterns may coexist with granular "gas bubbles"-phase separation into a liquidlike and a gaslike state. Stability diagrams for the instabilities measured with various granular layer mass m and container height H are presented. The onsets for both types of patterns and their dependency on m and H can be quantitatively captured with a model considering the granular layer as a single particle colliding completely inelastically with the container. PMID:26274155

  7. PDGF-D contributes to neointimal hyperplasia in rat model of vessel injury

    SciTech Connect

    Chen Jingzhou; Han Yu; Lin Chunxia; Zhen Yisong; Song Xiaodong; Teng Siyong; Chen Chen; Chen Yu; Zhang Yinhui; Hui Rutai . E-mail: huirutai@sglab.org

    2005-04-15

    In this study, we determined the role of PDGF-D, a new member of the PDGF family, in a rat model of balloon injured artery made with a 2F catheter in Sprague-Dawley male rats. PDGF-D expression was studied in the injured and control segments of abdominal aorta. The function of PDGF-D was evaluated in rat vascular smooth muscle cells stably transfected with PDGF-D gene. We found that in normal abdominal aorta, PDGF-D was highly expressed in adventia, moderate in endothelia, and unidentified in media. Stable transfection of PDGF-D gene into vascular smooth muscle cells increased the cell migration by 2.2-fold, and the proliferation by 2.3-fold, respectively, and MMP-2 production and activity as well. These results support the fact that PDGF-D is involved in the formation of neointimal hyperplasia induced by balloon catheter injury and may serve as a target in preventing vascular restenosis after coronary angioplasty.

  8. A new mechanism for dendritic pattern formation in dense systems

    PubMed Central

    Oikawa, Noriko; Kurita, Rei

    2016-01-01

    Patterns are often formed when particles cluster: Since patterns reflect the connectivity of different types of material, the emergence of patterns affects the physical and chemical properties of systems and shares a close relationship to their macroscopic functions. A radial dendritic pattern (RDP) is observed in many systems such as snow crystals, polymer crystals and biological systems. Although most of these systems are considered as dense particle suspensions, the mechanism of RDP formation in dense particle systems is not yet understood. It should be noted that the diffusion limited aggregation model is not applicable to RDP formation in dense systems, but in dilute particle systems. Here, we propose a simple model that exhibits RDP formation in a dense particle system. The model potential for the inter-particle interaction is composed of two parts, a repulsive and an attractive force. The repulsive force is applied to all the particles all the time and the attractive force is exerted only among particles inside a circular domain, which expands at a certain speed as a wave front propagating from a preselected centre. It is found that an RDP is formed if the velocity of the wave front that triggers the attractive interaction is of the same order of magnitude as the time scale defined by the aggregation speed. PMID:27353447

  9. A new mechanism for dendritic pattern formation in dense systems.

    PubMed

    Oikawa, Noriko; Kurita, Rei

    2016-01-01

    Patterns are often formed when particles cluster: Since patterns reflect the connectivity of different types of material, the emergence of patterns affects the physical and chemical properties of systems and shares a close relationship to their macroscopic functions. A radial dendritic pattern (RDP) is observed in many systems such as snow crystals, polymer crystals and biological systems. Although most of these systems are considered as dense particle suspensions, the mechanism of RDP formation in dense particle systems is not yet understood. It should be noted that the diffusion limited aggregation model is not applicable to RDP formation in dense systems, but in dilute particle systems. Here, we propose a simple model that exhibits RDP formation in a dense particle system. The model potential for the inter-particle interaction is composed of two parts, a repulsive and an attractive force. The repulsive force is applied to all the particles all the time and the attractive force is exerted only among particles inside a circular domain, which expands at a certain speed as a wave front propagating from a preselected centre. It is found that an RDP is formed if the velocity of the wave front that triggers the attractive interaction is of the same order of magnitude as the time scale defined by the aggregation speed. PMID:27353447

  10. A new mechanism for dendritic pattern formation in dense systems

    NASA Astrophysics Data System (ADS)

    Oikawa, Noriko; Kurita, Rei

    2016-06-01

    Patterns are often formed when particles cluster: Since patterns reflect the connectivity of different types of material, the emergence of patterns affects the physical and chemical properties of systems and shares a close relationship to their macroscopic functions. A radial dendritic pattern (RDP) is observed in many systems such as snow crystals, polymer crystals and biological systems. Although most of these systems are considered as dense particle suspensions, the mechanism of RDP formation in dense particle systems is not yet understood. It should be noted that the diffusion limited aggregation model is not applicable to RDP formation in dense systems, but in dilute particle systems. Here, we propose a simple model that exhibits RDP formation in a dense particle system. The model potential for the inter-particle interaction is composed of two parts, a repulsive and an attractive force. The repulsive force is applied to all the particles all the time and the attractive force is exerted only among particles inside a circular domain, which expands at a certain speed as a wave front propagating from a preselected centre. It is found that an RDP is formed if the velocity of the wave front that triggers the attractive interaction is of the same order of magnitude as the time scale defined by the aggregation speed.

  11. Wavenumber Locking And Pattern Formation In Spatially Forced Systems

    SciTech Connect

    Hagberg, Aric; Meron, Ehud; Manor, Rotem

    2008-01-01

    We study wavenumber locking and pattern formation resulting from weak spatially periodic one-dimensional forcing of two-dimensional systems. We consider systems that support stationary or traveling stripe patterns in the absence of the forcing, and assume that the one-dimensional forcing is aligned with the direction of the stripe patterns. When the forcing wavenumber is about twice as large as the wavenumber of the unforced system we find that the forcing can either select or stabilize a resonant stripe solution at half the forcing wavenumber, or create a new resonant solution. When the wavenumber mismatch is high we find that the wave-vector component of the pattern in the direction of the forcing can stilI lock at half the forcing wavenumber, but a wave-vector component in the orthogonal direction develops to compensate for the total wavenumber. As a result stationary two-dimensional rectangular and oblique patterns form. When the unforced system supports traveling waves resonant rectangular patterns remain stationary but the oblique patterns travel in a direction orthogonal to the traveling-waves.

  12. Perspective: network-guided pattern formation of neural dynamics.

    PubMed

    Hütt, Marc-Thorsten; Kaiser, Marcus; Hilgetag, Claus C

    2014-10-01

    The understanding of neural activity patterns is fundamentally linked to an understanding of how the brain's network architecture shapes dynamical processes. Established approaches rely mostly on deviations of a given network from certain classes of random graphs. Hypotheses about the supposed role of prominent topological features (for instance, the roles of modularity, network motifs or hierarchical network organization) are derived from these deviations. An alternative strategy could be to study deviations of network architectures from regular graphs (rings and lattices) and consider the implications of such deviations for self-organized dynamic patterns on the network. Following this strategy, we draw on the theory of spatio-temporal pattern formation and propose a novel perspective for analysing dynamics on networks, by evaluating how the self-organized dynamics are confined by network architecture to a small set of permissible collective states. In particular, we discuss the role of prominent topological features of brain connectivity, such as hubs, modules and hierarchy, in shaping activity patterns. We illustrate the notion of network-guided pattern formation with numerical simulations and outline how it can facilitate the understanding of neural dynamics. PMID:25180302

  13. Poly(ADP-ribose) polymerase inhibition combined with irradiation: A dual treatment concept to prevent neointimal hyperplasia after endarterectomy

    SciTech Connect

    Beller, Carsten J. . E-mail: Carsten.Beller@urz.uni-heidelberg.de; Kosse, Jens; Radovits, Tamas; Geroe, Domokos; Krempien, Robert; Gross, Marie-Luise; Berger, Irina; Hagl, Siegfried; Szabo, Csaba; Szabo, Gabor

    2006-11-01

    Purpose: In a rat model of endarterectomy we investigated the potential role of the peroxynitrite-poly(ADP-ribose) polymerase (PARP) pathway in neointima formation and the effects of irradiation, pharmacologic inhibition of PARP, or combined pharmacologic inhibition of PARP and irradiation on vascular remodeling. Methods and Materials: Carotid endarterectomy was performed by incision of the left carotid artery with removal of intima in Sprague-Dawley rats. Six groups were studied: sham-operated rats (n = 10), control endarterectomized rats (n = 10), or endarterectomized rats irradiated with 15 Gy (n = 10), or treated with PARP inhibitor, INO-1001 (5 mg/kg/day) (n = 10), or with combined treatment with INO-1001 and irradiation with 5 Gy (n = 10) or with 15 Gy (n = 10). After 21 days, neointima formation and vascular remodeling were assessed. Results: Neointima formation after endarterectomy was inhibited by postoperative irradiation with 15 Gy and was attenuated by PARP inhibition. However, in parallel to inhibition of neointimal hyperplasia, activation of the peroxynitrite-PARP pathway in the outer vessel wall layers was triggered by postoperative irradiation. Combined pharmacologic PARP inhibition and irradiation with 15 Gy significantly reduced both neointimal hyperplasia and activation of the peroxynitrite-PARP pathway in the outer vessel wall layers. Combination of PARP inhibition and irradiation with 5 Gy was less effective than both PARP inhibition or irradiation with 15 Gy alone. Conclusions: We conclude, that combined PARP inhibition and irradiation with 15 Gy may be a new dual strategy for prevention of restenosis after surgical vessel reconstruction: combining the strong antiproliferative effect of irradiation and ameliorating irradiation-induced side effects caused by excessive PARP activation.

  14. Dynamic phases, pinning, and pattern formation for driven dislocation assemblies

    SciTech Connect

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-23

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Lastly, our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems.

  15. Dynamic phases, pinning, and pattern formation for driven dislocation assemblies

    DOE PAGESBeta

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-23

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Lastly, our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation andmore » dynamics in these systems.« less

  16. Boundary-layer model of pattern formation in solidification

    NASA Technical Reports Server (NTRS)

    Ben-Jacob, E.; Goldenfeld, N.; Langer, J. S.; Schon, G.

    1984-01-01

    A model of pattern formation in crystal growth is proposed, and its analytic properties are investigated. The principal dynamical variables in this model are the curvature of the solidification front and the thickness (or heat content) of a thermal boundary layer, both taken to be functions of position along the interface. This model is mathematically much more tractable than the realistic, fully nonlocal version of the free-boundary problem, and still recaptures many of the features that seem essential for studying dendritic behavior, for example. Preliminary numerical solutions produce snowflakelike patterns similar to those seen in nature.

  17. Controlling Pattern Formation in Nanoparticle Assemblies via Directed Solvent Dewetting

    NASA Astrophysics Data System (ADS)

    Martin, Christopher P.; Blunt, Matthew O.; Pauliac-Vaujour, Emmanuelle; Stannard, Andrew; Moriarty, Philip; Vancea, Ioan; Thiele, Uwe

    2007-09-01

    We have achieved highly localized control of pattern formation in two-dimensional nanoparticle assemblies by direct modification of solvent dewetting dynamics. A striking dependence of nanoparticle organization on the size of atomic force microscope-generated surface heterogeneities is observed and reproduced in numerical simulations. Nanoscale features induce a rupture of the solvent-nanoparticle film, causing the local flow of solvent to carry nanoparticles into confinement. Microscale heterogeneities instead slow the evaporation of the solvent, producing a remarkably abrupt interface between different nanoparticle patterns.

  18. Controlling pattern formation in nanoparticle assemblies via directed solvent dewetting.

    PubMed

    Martin, Christopher P; Blunt, Matthew O; Pauliac-Vaujour, Emmanuelle; Stannard, Andrew; Moriarty, Philip; Vancea, Ioan; Thiele, Uwe

    2007-09-14

    We have achieved highly localized control of pattern formation in two-dimensional nanoparticle assemblies by direct modification of solvent dewetting dynamics. A striking dependence of nanoparticle organization on the size of atomic force microscope-generated surface heterogeneities is observed and reproduced in numerical simulations. Nanoscale features induce a rupture of the solvent-nanoparticle film, causing the local flow of solvent to carry nanoparticles into confinement. Microscale heterogeneities instead slow the evaporation of the solvent, producing a remarkably abrupt interface between different nanoparticle patterns. PMID:17930453

  19. Dynamic Phases, Pinning, and Pattern Formation for Driven Dislocation Assemblies

    PubMed Central

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-01

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems. PMID:25613839

  20. Dynamic Phases, Pinning, and Pattern Formation for Driven Dislocation Assemblies

    NASA Astrophysics Data System (ADS)

    Zhou, Caizhi; Reichhardt, Charles; Olson Reichhardt, Cynthia J.; Beyerlein, Irene J.

    2015-01-01

    We examine driven dislocation assemblies and show that they can exhibit a set of dynamical phases remarkably similar to those of driven systems with quenched disorder such as vortices in superconductors, magnetic domain walls, and charge density wave materials. These phases include pinned-jammed, fluctuating, and dynamically ordered states, and each produces distinct dislocation patterns as well as specific features in the noise fluctuations and transport properties. Our work suggests that many of the results established for systems with quenched disorder undergoing plastic depinning transitions can be applied to dislocation systems, providing a new approach for understanding pattern formation and dynamics in these systems.

  1. Nonequilibrium breakdown of a correlated insulator through pattern formation

    NASA Astrophysics Data System (ADS)

    Ribeiro, Pedro; Antipov, Andrey E.; Rubtsov, Alexey N.

    2016-04-01

    We study the breakdown of an interaction-induced insulator under an imposed bias voltage. A rich voltage-temperature phase diagram is found that contains phases with a spatially patterned charge gap. Nonequilibrium conditions are shown to be able to change the antiferromagnetic nature of the equilibrium correlations. Above a threshold voltage, smaller than the charge gap, the formation of patterns occurs together with the emergence of midgap states yielding a finite conductance. We discuss the experimental implications of this proposed scenario for the breakdown of the insulating state.

  2. Clustering and Pattern Formation in Chemorepulsive Active Colloids.

    PubMed

    Liebchen, Benno; Marenduzzo, Davide; Pagonabarraga, Ignacio; Cates, Michael E

    2015-12-18

    We demonstrate that migration away from self-produced chemicals (chemorepulsion) generates a generic route to clustering and pattern formation among self-propelled colloids. The clustering instability can be caused either by anisotropic chemical production, or by a delayed orientational response to changes of the chemical environment. In each case, chemorepulsion creates clusters of a self-limiting area which grows linearly with self-propulsion speed. This agrees with recent observations of dynamic clusters in Janus colloids (albeit not yet known to be chemorepulsive). More generally, our results could inform design principles for the self-assembly of chemorepulsive synthetic swimmers and/or bacteria into nonequilibrium patterns. PMID:26722949

  3. Clustering and Pattern Formation in Chemorepulsive Active Colloids

    NASA Astrophysics Data System (ADS)

    Liebchen, Benno; Marenduzzo, Davide; Pagonabarraga, Ignacio; Cates, Michael E.

    2015-12-01

    We demonstrate that migration away from self-produced chemicals (chemorepulsion) generates a generic route to clustering and pattern formation among self-propelled colloids. The clustering instability can be caused either by anisotropic chemical production, or by a delayed orientational response to changes of the chemical environment. In each case, chemorepulsion creates clusters of a self-limiting area which grows linearly with self-propulsion speed. This agrees with recent observations of dynamic clusters in Janus colloids (albeit not yet known to be chemorepulsive). More generally, our results could inform design principles for the self-assembly of chemorepulsive synthetic swimmers and/or bacteria into nonequilibrium patterns.

  4. Impact of Age on Stent Strut Coverage and Neointimal Remodeling as Assessed by Optical Coherence Tomography.

    PubMed

    Han, Zhigang; Feng, Linxing; Du, Hongwei; Sun, Zhao; Hu, Sining; Dai, Jiannan; Sun, Meng; Xing, Lei; Hou, Jingbo; Zhang, Shaosong; Yu, Bo

    2015-12-01

    While older age associates with adverse percutaneous coronary intervention (PCI) outcomes, detailed information relating age to stent strut coverage and neointimal characteristics is lacking. One hundred nineteen patients with 123 sirolimus-eluting stents (SESs) were divided into 3 groups: group A (≤55 years), group B (56-65 years), and group C (>65 years). At 6 and 12 months of follow-up, optical coherence tomography was performed to assess strut coverage and neointimal remodeling. At 6 months, the proportion of uncovered struts increased with age: 6.1% in group A versus 7.3% in group B versus 11.7% in group C (P < 0.001) while the proportion of embedded struts decreased: 72.1% versus 57.0% vs. 55.0%, respectively (P < 0.001). Mean neointimal thicknesses were 90  μm versus 60  μm versus 60  μm, respectively (P < 0.001), and neointimal areas were 0.82  mm2 versus 0.52  mm2 versus 0.57  mm2 (P < 0.001). At 12 months, the proportion of uncovered struts increased with age (3.9% vs. 3.3% vs. 4.9 %; P < 0.001), while mean neointimal thicknesses were 100 versus 70 versus 80  μm (P < 0.001) and neointimal areas were 0.87 versus 0.60 versus 0.67  mm2 (P < 0.001). Patients ≤55 years receiving SES showed highest strut coverage and neointimal repair rate compared with the other 2 groups. A "catch-up phenomenon" appeared to occur in the oldest patients, as in the first 6 months the neointima showed lowest endothelial cell coverage and lowest neointimal proliferation rate, whereas from 6 to 12 months, the highest neointimal proliferation rate was seen in the oldest patients. PMID:26683940

  5. Femtosecond Laser Patterning of the Biopolymer Chitosan for Biofilm Formation.

    PubMed

    Estevam-Alves, Regina; Ferreira, Paulo Henrique Dias; Coatrini, Andrey C; Oliveira, Osvaldo N; Fontana, Carla Raquel; Mendonca, Cleber Renato

    2016-01-01

    Controlling microbial growth is crucial for many biomedical, pharmaceutical and food industry applications. In this paper, we used a femtosecond laser to microstructure the surface of chitosan, a biocompatible polymer that has been explored for applications ranging from antimicrobial action to drug delivery. The influence of energy density on the features produced on chitosan was investigated by optical and atomic force microscopies. An increase in the hydrophilic character of the chitosan surface was attained upon laser micromachining. Patterned chitosan films were used to observe Staphylococcus aureus (ATCC 25923) biofilm formation, revealing an increase in the biofilm formation in the structured regions. Our results indicate that fs-laser micromachining is an attractive option to pattern biocompatible surfaces, and to investigate basic aspects of the relationship between surface topography and bacterial adhesion. PMID:27548153

  6. Evaporation-Induced Pattern Formation of Decanol Droplets.

    PubMed

    Čejková, Jitka; Štěpánek, František; Hanczyc, Martin M

    2016-05-17

    Pattern formation in far-from-equilibrium systems is observed in several disciplines including biology, geophysics, and reaction-diffusion chemistry, comprising both living and nonliving systems. We aim to study such nonequilibrium dynamics on the laboratory scale with materials of simple composition. We present a novel system based on a 1-decanol droplet placed in a solution of alkaline decanoate. Previously, we showed the short time scale behavior of this system, which included chemotaxis and maze solving. Here we explore long time scale dynamics of the system (several hours) when open to the environment. We observe dramatic morphological changes in the droplet including long tentacular structures, and we analyze the morphology of these structures at both the macroscopic and microscopic scales across a large range of initial conditions. Such reproducible morphological changes in simple droplets open a path to the exploration of shape-based effects in larger-scale pattern-formation studies. PMID:27116007

  7. Femtosecond Laser Patterning of the Biopolymer Chitosan for Biofilm Formation

    PubMed Central

    Estevam-Alves, Regina; Ferreira, Paulo Henrique Dias; Coatrini, Andrey C.; Oliveira, Osvaldo N.; Fontana, Carla Raquel; Mendonca, Cleber Renato

    2016-01-01

    Controlling microbial growth is crucial for many biomedical, pharmaceutical and food industry applications. In this paper, we used a femtosecond laser to microstructure the surface of chitosan, a biocompatible polymer that has been explored for applications ranging from antimicrobial action to drug delivery. The influence of energy density on the features produced on chitosan was investigated by optical and atomic force microscopies. An increase in the hydrophilic character of the chitosan surface was attained upon laser micromachining. Patterned chitosan films were used to observe Staphylococcus aureus (ATCC 25923) biofilm formation, revealing an increase in the biofilm formation in the structured regions. Our results indicate that fs-laser micromachining is an attractive option to pattern biocompatible surfaces, and to investigate basic aspects of the relationship between surface topography and bacterial adhesion. PMID:27548153

  8. Modeling in pattern formation with applications to electrochemical phenomena

    NASA Astrophysics Data System (ADS)

    Stanton, Liam G.

    In this work, we examine pattern formation as a generic phenomenon as well as its occurrence in electrochemical systems. First, a global feedback control of pattern formation in a wide class of systems described by the Swift-Hohenberg (SH) equation is investigated theoretically, by means of stability analysis and numerical simulations. Two cases are considered: (i) feedback control of the competition between hexagon and roll patterns described by a supercritical SH equation, and (ii) the use of feedback control to suppress the blow-up in a system described by a subcritical SH equation. In case (i), it is shown that feedback control can change the hexagon and roll stability regions in the parameter space as well as cause a transition from up- to down-hexagons and stabilize a skewed (mixed mode) hexagonal pattern. In case (ii), it is demonstrated that feedback control can suppress blow-up and lead to the formation of spatially-localized patterns in the weakly nonlinear regime. The effects of a delayed feedback are also investigated for both cases, and it is shown that delay can induce temporal oscillations as well as blow-up. Next, pattern formation resulting from the self-organization of porous nanostructures in anodic metal oxide is considered. Two possible mechanisms are proposed: (i) elastic stress caused by electrostrictive effects, and (ii) electrochemical transport of oxygen ions within the oxide layer. In each case, a mathematical model is developed which also incorporates the chemical reactions at the metal-oxide and oxide-electrolyte interfaces. It is then shown through linear stability analysis that a short-wave instability exists in certain parameter regimes for both cases which can lead to the formation of hexagonally ordered pores observed in anodized aluminum oxide. Numerical simulations of case (ii) validate these results. Finally, we consider the self-organization of intercalating particles within crystals induced by spinodal decomposition and the

  9. Pattern formation during the CO-oxidation involving subsurface oxygen

    NASA Astrophysics Data System (ADS)

    Rotermund, Harm Hinrich; Pollmann, Michael; Kevrekidis, Ioannis G.

    2002-03-01

    This paper focuses on subsurface oxygen and its influence on pattern formation during CO-oxidation on platinum surfaces. For the observation of spatiotemporal pattern formation during catalytic reactions the photoelectron emission microscope (PEEM) has proven to be an excellent real-time imaging instrument, capable of tracking local work function changes. The existence of subsurface oxygen on platinumlike surfaces has been extensively discussed and for palladium its presence has been clearly established during rate oscillations. Subsurface oxygen is defined at this point as an atomic O species located directly underneath the uppermost metal crystal layer; its dipole moment therefore considerably lowers the work function of the surface. Here we review some of the investigations involving subsurface oxygen, focusing on the role subsurface oxygen might play in pattern formation during CO-oxidation on platinum. We will also present some new results, where this species clearly interacts with chemisorbed oxygen under restrictions by boundary conditions on the Pt(110) single crystal. These previously (through microlithography) constructed domain boundaries on the surface are made out of Rh or Pd, and they are acting as an additional source of CO molecules for the Pt surface.

  10. Spontaneous Pattern Formation in an Antiferromagnetic Quantum Gas

    SciTech Connect

    Kronjaeger, Jochen; Bongs, Kai; Becker, Christoph; Soltan-Panahi, Parvis; Sengstock, Klaus

    2010-08-27

    In this Letter we report on the spontaneous formation of surprisingly regular periodic magnetic patterns in an antiferromagnetic Bose-Einstein condensate (BEC). The structures evolve within a quasi-one-dimensional BEC of {sup 87}Rb atoms on length scales of a millimeter with typical periodicities of 20...30 {mu}m, given by the spin healing length. We observe two sets of characteristic patterns which can be controlled by an external magnetic field. We identify these patterns as linearly unstable modes within a mean-field approach and calculate their mode structure as well as time and energy scales, which we find to be in good agreement with observations. These investigations open new prospects for controlled studies of symmetry breaking and complex quantum magnetism in bulk BEC.

  11. Dynamics and pattern formation in a cancer network with diffusion

    NASA Astrophysics Data System (ADS)

    Zheng, Qianqian; Shen, Jianwei

    2015-10-01

    Diffusion is ubiquitous inside cells, and it is capable of inducing spontaneous pattern formation in reaction-diffusion systems on a spatially homogeneous domain. In this paper, we investigate the dynamics of a diffusive cancer network regulated by microRNA and obtain the condition that the network undergoes a Hopf bifurcation and a Turing pattern bifurcation. In addition, we also develop the amplitude equation of the network model by using Taylor series expansion, multi-scaling and further expansion in powers of a small parameter. As a result of these analyses, we obtain the explicit condition on how the dynamics of the diffusive cancer network evolve. These results reveal that this system has rich dynamics, such as spotted stripe and hexagon patterns. The bifurcation diagram helps us understand the biological mechanism in the cancer network. Finally, numerical simulations confirm our analytical results.

  12. Capillary-mediated interface perturbations: Deterministic pattern formation

    NASA Astrophysics Data System (ADS)

    Glicksman, Martin E.

    2016-09-01

    Leibniz-Reynolds analysis identifies a 4th-order capillary-mediated energy field that is responsible for shape changes observed during melting, and for interface speed perturbations during crystal growth. Field-theoretic principles also show that capillary-mediated energy distributions cancel over large length scales, but modulate the interface shape on smaller mesoscopic scales. Speed perturbations reverse direction at specific locations where they initiate inflection and branching on unstable interfaces, thereby enhancing pattern complexity. Simulations of pattern formation by several independent groups of investigators using a variety of numerical techniques confirm that shape changes during both melting and growth initiate at locations predicted from interface field theory. Finally, limit cycles occur as an interface and its capillary energy field co-evolve, leading to synchronized branching. Synchronous perturbations produce classical dendritic structures, whereas asynchronous perturbations observed in isotropic and weakly anisotropic systems lead to chaotic-looking patterns that remain nevertheless deterministic.

  13. Pattern formation gains interest in the Earth sciences

    NASA Astrophysics Data System (ADS)

    Durant, Dolores G.

    A huge diversity of intricate patterns can be found in our environment, ranging from zoned crystals, sand ripples, and columnar basalts to multiringed meteorite impact craters.Fundamental concepts of pattern formation in the Earth sciences can be traced back through time from Jean Perrin to Mandelbrot, and their studies of the lengths of coastlines. Similar concepts of fractal dimensions, multifractals, and diffusion-limited aggregation models can be applied to the study of many phenomena including the random walk of molecules in gases and liquids, avalanche dynamics, three-dimensional basin modeling, salt tectonics, and the spontaneous self-organization of sand grains. The largest terrestrial pattern is that of the Earth itself, forming from an undifferentiated solar dust cloud into the well-organized Earth of today (P. Ortoleva).

  14. A Model of Filamentous Cyanobacteria Leading to Reticulate Pattern Formation

    PubMed Central

    Tamulonis, Carlos; Kaandorp, Jaap

    2014-01-01

    The filamentous cyanobacterium, Pseudanabaena, has been shown to produce reticulate patterns that are thought to be the result of its gliding motility. Similar fossilized structures found in the geological record constitute some of the earliest signs of life on Earth. It is difficult to tie these fossils, which are billions of years old, directly to the specific microorganisms that built them. Identifying the physicochemical conditions and microorganism properties that lead microbial mats to form macroscopic structures can lead to a better understanding of the conditions on Earth at the dawn of life. In this article, a cell-based model is used to simulate the formation of reticulate patterns in cultures of Pseudanabaena. A minimal system of long and flexible trichomes capable of gliding motility is shown to be sufficient to produce stable patterns consisting of a network of streams. Varying model parameters indicate that systems with little to no cohesion, high trichome density and persistent movement are conducive to reticulate pattern formation, in conformance with experimental observations. PMID:25370380

  15. Multiscale analysis of pattern formation via intercellular signalling.

    PubMed

    O'Dea, R D; King, J R

    2011-06-01

    Lateral inhibition, a juxtacrine signalling mechanism by which a cell adopting a particular fate inhibits neighbouring cells from doing likewise, has been shown to be a robust mechanism for the formation of fine-grained spatial patterns (in which adjacent cells in developing tissues diverge to achieve contrasting states of differentiation), provided that there is sufficiently strong feedback. The fine-grained nature of these patterns poses problems for analysis via traditional continuum methods since these require that significant variation takes place only over lengthscales much larger than an individual cell and such systems have therefore been investigated primarily using discrete methods. Here, however, we apply a multiscale method to derive systematically a continuum model from the discrete Delta-Notch signalling model of Collier et al. (J.R. Collier, N.A.M. Monk, P.K. Maini, J.H. Lewis, Pattern formation by lateral inhibition with feedback: a mathematical model of Delta-Notch intercellular signalling, J. Theor. Biol., 183, 1996, 429-446) under particular assumptions on the parameters, which we use to analyse the generation of fine-grained patterns. We show that, on the macroscale, the contact-dependent juxtacrine signalling interaction manifests itself as linear diffusion, motivating the use of reaction-diffusion-based models for such cell-signalling systems. We also analyse the travelling-wave behaviour of our system, obtaining good quantitative agreement with the discrete system. PMID:21385590

  16. Rimming flows and pattern formation inside rapidly rotating cylinder

    NASA Astrophysics Data System (ADS)

    Polezhaev, Denis; Dyakova, Veronika; Kozlov, Victor

    2014-11-01

    The dynamics of fluid and granular medium in a rotating horizontal cylinder is experimentally studied. In a rapidly rotating cylinder liquid and granular medium coat the cylindrical wall under centrifugal force. In the cavity frame gravity field performs rotation and produces oscillatory fluid flow which is responsible for the series of novel effects of pattern formation, namely, axial segregation of heavy particles and pattern formation in the form of sand regular hills extended along the axis of rotation. At least two types of axial segregation are found: a) patterns of spatial period of the same order of magnitude as fluid layer thickness which induced by steady flows generated by inertial waves; b) fine patterns which manifests Gortler - Taylor vortices developing as a consequence of centrifugal instability of viscous boundary layer near the cylindrical wall. Under gravity, intensive fluid shear flow induces partial fluidization of annular layer of granular medium. The oscillatory motion is followed by onset of regular ripples extended along the axis of rotation. The work is supported by Russian Scientific Foundation (project 14-11-00476).

  17. How to Build Transcriptional Network Models of Mammalian Pattern Formation

    PubMed Central

    Kioussi, Chrissa; Gross, Michael K.

    2008-01-01

    Background Genetic regulatory networks of sequence specific transcription factors underlie pattern formation in multicellular organisms. Deciphering and representing the mammalian networks is a central problem in development, neurobiology, and regenerative medicine. Transcriptional networks specify intermingled embryonic cell populations during pattern formation in the vertebrate neural tube. Each embryonic population gives rise to a distinct type of adult neuron. The homeodomain transcription factor Lbx1 is expressed in five such populations and loss of Lbx1 leads to distinct respecifications in each of the five populations. Methodology/Principal Findings We have purified normal and respecified pools of these five populations from embryos bearing one or two copies of the null Lbx1GFP allele, respectively. Microarrays were used to show that expression levels of 8% of all transcription factor genes were altered in the respecified pool. These transcription factor genes constitute 20–30% of the active nodes of the transcriptional network that governs neural tube patterning. Half of the 141 regulated nodes were located in the top 150 clusters of ultraconserved non-coding regions. Generally, Lbx1 repressed genes that have expression patterns outside of the Lbx1-expressing domain and activated genes that have expression patterns inside the Lbx1-expressing domain. Conclusions/Significance Constraining epistasis analysis of Lbx1 to only those cells that normally express Lbx1 allowed unprecedented sensitivity in identifying Lbx1 network interactions and allowed the interactions to be assigned to a specific set of cell populations. We call this method ANCEA, or active node constrained epistasis analysis, and think that it will be generally useful in discovering and assigning network interactions to specific populations. We discuss how ANCEA, coupled with population partitioning analysis, can greatly facilitate the systematic dissection of transcriptional networks that

  18. Heating hydrocarbon containing formations in a checkerboard pattern staged process

    SciTech Connect

    de Rouffignac, Eric Pierre; Pingo-Almada, Monica M; Miller, David Scott

    2009-06-02

    Method for treating a hydrocarbon containing formation are described herein. Methods may include providing heat to two or more first sections of the formation with one or more first heaters in two or more of the first sections. The provided heat may mobilize first hydrocarbons in two or more of the first sections. At least some of the mobilized first hydrocarbons are produced through production wells located in two or more second sections of the formation. The first sections and the second sections are arranged in a checkerboard pattern. A portion of at least one of the second sections proximate at least one production well is provided some heat from the mobilized first hydrocarbons, but is not conductively heated by heat from the first heaters. Heat may be provided to the second sections with one or more second heaters in the second sections to further heat the second sections.

  19. Multiple stable states and pattern formation in tidal environments

    NASA Astrophysics Data System (ADS)

    Marani, M.

    2012-12-01

    Tidal environments display typical and widely occurring patterns on several scales. At the large scale, characteristic tidal morphological structures can be identified: subtidal areas, which are permanently flooded, tidal flats, usually non-vegetated expanses located between mean low water level and mean sea level, and tidal marshes, vegetated landforms located between mean sea level and mean high water level. At a smaller scale, marshes display zonation patterns, patches of nearly homogeneous vegetation species characterized by very sharp transitions in species composition and in the associated soil elevation. This contribution describes modelling and observational results which identify a common mechanism for the emergence of bio-geomorphic patterns in tidal environments. Our analyses show that the coupled dynamics of inorganic sediment transport and local biogenic soil formation leads to multiple stable states. Such states correspond to distinct geomorphic structures at the large scale (subtidal platforms, tidal flats, and marshes) and to zonation patterns at the marsh scale. In both cases the interaction between biotic and biotic processes turns out to be crucial for the emergence of the observed patterns.

  20. Whorl morphogenesis in the dasycladalean algae: the pattern formation viewpoint.

    PubMed Central

    Dumais, J; Harrison, L G

    2000-01-01

    The dasycladalean algae produce diverse whorled structures, among which the best known are the vegetative and reproductive whorls of Acetabularia acetabulum. In this paper, we review the literature pertaining to the origin of these structures. The question is addressed in terms of the necessary pattern-forming events and the possible mechanisms involved, an outlook we call the pattern formation viewpoint. The pattern-forming events involved in the morphogenesis of the vegetative and reproductive whorls of Acetabularia have been used to define five and six morphogenetic stages, respectively. We discuss three published mechanisms which account, at least in part, for the pattern-forming events. The mechanisms are mechanical buckling of the cell wall, reaction-diffusion of morphogen molecules along the cell membrane, and mechanochemical interactions between Ca2+ ions and the cytoskeleton in the cytosol. The numerous differences between these mechanisms provide experimental grounds to test their validity. To date, the results of these experiments point towards reaction diffusion as the most likely patterning mechanism. Finally, we consider the evolutionary origin of the vegetative and reproductive whorls and provide mechanistic explanations for some of the major evolutionary advances. PMID:10724462

  1. Neuropilins 1 and 2 mediate neointimal hyperplasia and re-endothelialization following arterial injury

    PubMed Central

    Pellet-Many, Caroline; Mehta, Vedanta; Fields, Laura; Mahmoud, Marwa; Lowe, Vanessa; Evans, Ian; Ruivo, Jorge; Zachary, Ian

    2015-01-01

    Aims Neuropilins 1 and 2 (NRP1 and NRP2) play crucial roles in endothelial cell migration contributing to angiogenesis and vascular development. Both NRPs are also expressed by cultured vascular smooth muscle cells (VSMCs) and are implicated in VSMC migration stimulated by PDGF-BB, but it is unknown whether NRPs are relevant for VSMC function in vivo. We investigated the role of NRPs in the rat carotid balloon injury model, in which endothelial denudation and arterial stretch induce neointimal hyperplasia involving VSMC migration and proliferation. Methods and results NRP1 and NRP2 mRNAs and proteins increased significantly following arterial injury, and immunofluorescent staining revealed neointimal NRP expression. Down-regulation of NRP1 and NRP2 using shRNA significantly reduced neointimal hyperplasia following injury. Furthermore, inhibition of NRP1 by adenovirally overexpressing a loss-of-function NRP1 mutant lacking the cytoplasmic domain (ΔC) reduced neointimal hyperplasia, whereas wild-type (WT) NRP1 had no effect. NRP-targeted shRNAs impaired, while overexpression of NRP1 WT and NRP1 ΔC enhanced, arterial re-endothelialization 14 days after injury. Knockdown of either NRP1 or NRP2 inhibited PDGF-BB-induced rat VSMC migration, whereas knockdown of NRP2, but not NRP1, reduced proliferation of cultured rat VSMC and neointimal VSMC in vivo. NRP knockdown also reduced the phosphorylation of PDGFα and PDGFβ receptors in rat VSMC, which mediate VSMC migration and proliferation. Conclusion NRP1 and NRP2 play important roles in the regulation of neointimal hyperplasia in vivo by modulating VSMC migration (via NRP1 and NRP2) and proliferation (via NRP2), independently of the role of NRPs in re-endothelialization. PMID:26410366

  2. Role of macrophage colony-stimulating factor in the development of neointimal thickening following arterial injury.

    PubMed

    Mishra, Vivek; Sinha, Satyesh K; Rajavashisth, Tripathi B

    2016-01-01

    Evidence suggests that macrophage colony-stimulating factor (M-CSF) participates critically in atherosclerosis; little is known about the role of M-CSF in the development of neointimal hyperplasia following mechanical vascular injury. We examined the expression of M-CSF and its receptor, c-fms, in rodent and rabbit models of arterial injury. Injured rat carotid arteries expressed 3- to 10-fold higher levels of M-CSF and c-fms mRNA and protein following balloon injury as compared to uninjured arteries. In the rabbit, M-CSF protein expression was greatest in neointimal smooth muscle cells (SMCs) postinjury, with some expression in medial SMCs. M-CSF-positive SMCs exhibited markers of proliferation. At 30days postinjury, neointimal SMCs in the adjacent healed area near the border between injured and uninjured zone lost both proliferative activity and overexpression of M-CSF. The presence of induced M-CSF and c-fms expression correlated with the initiation of SMCs proliferation. M-CSF stimulated incorporation of [(3)H] thymidine in human aortic smooth muscle cells in a concentration-dependent manner. Serum-free conditioned medium from aortic SMCs also promoted DNA synthesis, and this effect was blocked by M-CSF specific antibody. To test further the role of M-CSF in vivo, we induced arterial injury by placing a periadventitial collar around the carotid arteries in compound mutant mice lacking apolipoprotein apoE (apoE(-/-)) and M-CSF. Loss of M-CSF abolished the neointimal hyperplastic response to arterial injury in apoE(-/-) mice. Local delivery of M-CSF to the injured artery restored neointimal proliferation, suggesting a critical role of M-CSF for the development of neointimal thickening following arterial injury. PMID:27135205

  3. Dynamics of laser induced metal nanoparticle and pattern formation

    SciTech Connect

    Peláez, R. J. Kuhn, T.; Rodríguez, C. E.; Afonso, C. N.

    2015-02-09

    Discontinuous metal films are converted into either almost round, isolated, and randomly distributed nanoparticles (NPs) or fringed patterns of alternate non transformed film and NPs by exposure to single pulses (20 ns pulse duration and 193 nm wavelength) of homogeneous or modulated laser beam intensity. The dynamics of NPs and pattern formation is studied by measuring in real time the transmission and reflectivity of the sample upon homogeneous beam exposure and the intensity of the diffraction orders 0 and 1 in transmission configuration upon modulated beam exposure. The results show that laser irradiation induces melting of the metal either completely or at regions around intensity maxima sites for homogeneous and modulated beam exposure, respectively, within ≤10 ns. The aggregation and/or coalescence of the initially irregular metal nanostructures is triggered upon melting and continues after solidification (estimated to occur at ≤80 ns) for more than 1 μs. The present results demonstrate that real time transmission rather than reflectivity measurements is a valuable and easy-to-use tool for following the dynamics of NPs and pattern formation. They provide insights on the heat-driven processes occurring both in liquid and solid phases and allow controlling in-situ the process through the fluence. They also evidence that there is negligible lateral heat release in discontinuous films upon laser irradiation.

  4. Flow-driven instabilities during pattern formation of Dictyostelium discoideum

    NASA Astrophysics Data System (ADS)

    Gholami, A.; Steinbock, O.; Zykov, V.; Bodenschatz, E.

    2015-06-01

    The slime mold Dictyostelium discoideum is a well known model system for the study of biological pattern formation. In the natural environment, aggregating populations of starving Dictyostelium discoideum cells may experience fluid flows that can profoundly change the underlying wave generation process. Here we study the effect of advection on the pattern formation in a colony of homogeneously distributed Dictyostelium discoideum cells described by the standard Martiel-Goldbeter model. The external flow advects the signaling molecule cyclic adenosine monophosphate (cAMP) downstream, while the chemotactic cells attached to the solid substrate are not transported with the flow. The evolution of small perturbations in cAMP concentrations is studied analytically in the linear regime and by corresponding numerical simulations. We show that flow can significantly influence the dynamics of the system and lead to a flow-driven instability that initiate downstream traveling cAMP waves. We also show that boundary conditions have a significant effect on the observed patterns and can lead to a new kind of instability.

  5. Formation of Arbitrary Patterns in Ultraviolet Cured Polymer Film via Electrohydrodynamic Patterning

    PubMed Central

    2014-01-01

    Electrohydrodynamic patterning of arbitrary patterns is achieved by optimizing the critical parameters (applied voltage and spacer height). The applied voltage has a great influence on the fidelity of L-shaped line structures with different sizes. The L-shaped line structures with high fidelity are obtained by using the moderate applied voltage. The spacer height has a great influence on the fidelity of square structures with different sizes. The square structures with high fidelity are obtained by using the low height spacer. The multi-field coupling transient finite element simulation demonstrates that the lack of polymer owing to the high height spacer leads to the formation of defects. PMID:24723831

  6. The theory of pattern formation on directed networks

    NASA Astrophysics Data System (ADS)

    Asllani, Malbor; Challenger, Joseph D.; Pavone, Francesco Saverio; Sacconi, Leonardo; Fanelli, Duccio

    2014-07-01

    Dynamical processes on networks have generated widespread interest in recent years. The theory of pattern formation in reaction-diffusion systems defined on symmetric networks has often been investigated, due to its applications in a wide range of disciplines. Here we extend the theory to the case of directed networks, which are found in a number of different fields, such as neuroscience, computer networks and traffic systems. Owing to the structure of the network Laplacian, the dispersion relation has both real and imaginary parts, at variance with the case for a symmetric, undirected network. The homogeneous fixed point can become unstable due to the topology of the network, resulting in a new class of instabilities, which cannot be induced on undirected graphs. Results from a linear stability analysis allow the instability region to be analytically traced. Numerical simulations show travelling waves, or quasi-stationary patterns, depending on the characteristics of the underlying graph.

  7. Pattern formation in transparent media using ultrashort laser pulses

    NASA Astrophysics Data System (ADS)

    Thomas, J.; Bernard, R.; Alti, K.; Dharmadhikari, A. K.; Dharmadhikari, J. A.; Bhatnagar, A.; Santhosh, C.; Mathur, D.

    2013-09-01

    We report results of a systematic study of the morphology of laser-written structures within transparent media like fused silica, borosilicate glass (BK7), and polymethylmethylacrylate (PMMA) using a high-energy, 5.1 MHz repetition rate, femtosecond laser oscillator. Depending on experimental conditions, both smooth channels as well as dot patterns can be laser-written. The periodicity of the written dots is readily controlled by the energy dose, a single parameter that encompasses laser energy, translation speed at fixed repetition rate, and focusing conditions. We discover the importance of the direction in which laser-writing is carried out: the periodicity of the dot patterns written at fixed energy dose but with opposite writing directions is significantly different. In PMMA, extremely large rod-like structures (˜200 µm) are observed whose formation is also dependent on writing direction. We quantify guidance of 632 nm and 830 nm light in structures written in BK7.

  8. Localised pattern formation in a model for dryland vegetation.

    PubMed

    Dawes, J H P; Williams, J L M

    2016-07-01

    We analyse the model for vegetation growth in a semi-arid landscape proposed by von Hardenberg et al. (Phys. Rev. Lett. 87:198101, 2001), which consists of two parabolic partial differential equations that describe the evolution in space and time of the water content of the soil and the level of vegetation. This model is a generalisation of one proposed by Klausmeier but it contains additional terms that capture additional physical effects. By considering the limit in which the diffusion of water in the soil is much faster than the spread of vegetation, we reduce the system to an asymptotically simpler parabolic-elliptic system of equations that describes small amplitude instabilities of the uniform vegetated state. We carry out a thorough weakly nonlinear analysis to investigate bifurcations and pattern formation in the reduced model. We find that the pattern forming instabilities are subcritical except in a small region of parameter space. In the original model at large amplitude there are localised solutions, organised by homoclinic snaking curves. The resulting bifurcation structure is well known from other models for pattern forming systems. Taken together our results describe how the von Hardenberg model displays a sequence of (often hysteretic) transitions from a non-vegetated state, to localised patches of vegetation that exist with uniform low-level vegetation, to periodic patterns, to higher-level uniform vegetation as the precipitation parameter increases. PMID:26454759

  9. The physics of pattern formation at liquid interfaces

    SciTech Connect

    Maher, J.V.

    1992-06-01

    During the past year we have submitted six papers for publication, three related to the dynamics of macroscopic interfaces, and ultimately all related to solidification, and three related to the internal structure of disorderly materials, with possible applications to the processing of composite materials. In addition to completing all these projects during the past year, we have begun two new projects, one on pattern formation and one on aggregation within a composite system. A brief description is given of this research in this paper.

  10. Changing patterns of marriage and household formation in Peninsular Malaysia.

    PubMed

    Tan, P C; Jones, G W

    1990-01-01

    "Based on surveys conducted among different ethnic groups in rural and urban settings in Peninsular Malaysia in 1981-82, this paper analyses changes in patterns of marriage and household formation among Malays, Chinese, and Indians. Aspects covered include social mixing before marriage, choice of spouse, comparison of spouses' characteristics, and place of residence after marriage. There are important cultural differences between the main Malaysian ethnic groups in matters related to marriage, but in many important respects, attitudes and practice are tending to converge...." PMID:12283691

  11. Pattern formation in granular binary mixtures under shear flow

    NASA Astrophysics Data System (ADS)

    Gao, Xin; Narteau, Clement; Rozier, Olivier

    2013-04-01

    We study numerically the formation and evolution of bed forms using a binary granular mixture. The two types of particles may have different dynamic properties and angle of repose. We associate these changes to two different grain sizes, the so-called coarse and thin particles. Our computation are based on a real-space cellular automaton that combines a model of sediment transport with a lattice-gas cellular automaton. Thus, we implement the permanent feedbacks between fluid flow and topography. Keeping constant the strength of the flow, we explore a parameter-space by varying the size of the coarse particles and their proportion within the bed. As a result of avalanches and sediment transport, we systematically find regions of segregation and stratification. In a vast majority of cases, we also observe the formation of an armoring layer mainly composed of coarse particles. Its depth is mainly controlled by the proportion of coarse grains and not by the size of these larger particles. When there is a larger proportion of thin particles, transverse dunes develop on the top of the armoring layer. As this proportion decreases, we may observe barchans or even no clear bed forms. We conclude that the main control parameter for dune pattern formation is the thin sediment availability. Finally, we discuss the processes responsible for the formation of the armoring layer and show how it controls the overall sediment transport.

  12. Pattern-formation mechanisms in motility mutants of Myxococcus xanthus

    PubMed Central

    Starruß, Jörn; Peruani, Fernando; Jakovljevic, Vladimir; Søgaard-Andersen, Lotte; Deutsch, Andreas; Bär, Markus

    2012-01-01

    Formation of spatial patterns of cells is a recurring theme in biology and often depends on regulated cell motility. Motility of the rod-shaped cells of the bacterium Myxococcus xanthus depends on two motility machineries, type IV pili (giving rise to S-motility) and the gliding motility apparatus (giving rise to A-motility). Cell motility is regulated by occasional reversals. Moving M. xanthus cells can organize into spreading colonies or spore-filled fruiting bodies, depending on their nutritional status. To ultimately understand these two pattern-formation processes and the contributions by the two motility machineries, as well as the cell reversal machinery, we analyse spatial self-organization in three M. xanthus strains: (i) a mutant that moves unidirectionally without reversing by the A-motility system only, (ii) a unidirectional mutant that is also equipped with the S-motility system, and (iii) the wild-type that, in addition to the two motility systems, occasionally reverses its direction of movement. The mutant moving by means of the A-engine illustrates that collective motion in the form of large moving clusters can arise in gliding bacteria owing to steric interactions of the rod-shaped cells, without the need of invoking any biochemical signal regulation. The two-engine strain mutant reveals that the same phenomenon emerges when both motility systems are present, and as long as cells exhibit unidirectional motion only. From the study of these two strains, we conclude that unidirectional cell motion induces the formation of large moving clusters at low and intermediate densities, while it results in vortex formation at very high densities. These findings are consistent with what is known from self-propelled rod models, which strongly suggests that the combined effect of self-propulsion and volume exclusion interactions is the pattern-formation mechanism leading to the observed phenomena. On the other hand, we learn that when cells occasionally reverse

  13. Pattern formation in electrohydrodynamic convection of a nematic liquid crystal

    NASA Astrophysics Data System (ADS)

    Gheorghiu, Nadina

    2003-10-01

    The first part of this dissertation is a study of the selection mechanism for the dendritic growth pattern of electrohydrodynamic convection (EHC) in a nematic liquid crystal (NLC). The cell gap d, the magnetic field H, and the voltage V are systematically varied. The transition from the non-convective state to the convective state is first order-like, although in this case it occurs in a nonequilibrium one-phase system. In the layer plane, the two-fold dendritic pattern grows about the only anisotropy direction, perpendicular to the homogeneous director alignment. While for crystalline dendrites the tip radius of curvature rho and the growth speed v are sharply selected, these dendrites show partial selection. At fixed d, H, and V, rho or v for different dendrites varies each within a band. There is no systematic dependence of rho on V. Thus, these dendrites represent an entirely new selection problem for pattern formation. The non-convective state is anisotropic in the plane of the pattern within a (magnetic coherence) length xim of each substrate. The degree of anisotropy decays with xim/d and the selection becomes less sharp. In contrast to sharply interfaced solidification patterns, these dendrites are outlined by a diffuse boundary, which width w ˜ 2xim. While anisotropic surface tension stabilizes crystalline growth, the magnetic field stabilizes this dendritic growth. Finding where and what scale convection first starts is important for understanding pattern selection in EHC. In the second part of this dissertation, fluorescence confocal polarizing microscopy (FCPM) is employed to study normal dielectric rolls (NDRs) in a NLC. While polarizing microscopy gives a two-dimensional information of the integrated three-dimensional (3D) pattern of optical birefringence, FCPM can uniquely map 3D orientational patterns in LC. FCPM visualizes the intensity of polarized fluorescence light emitted by the dye molecules aligned by the LC molecules. The fluorescence

  14. G-jitter Effects on Transport and Pattern Formation

    NASA Technical Reports Server (NTRS)

    Schatz, Michael F.

    2003-01-01

    The research performed under this grant has led to an number of new insights into two general categories of fluid flows in the presence of time-dependent acceleration, as outlined briefly below. These results have been widely communicated in the scientific community through seven presentations at international conferences (4 invited, 3 contributed), five published papers (4 journal articles and 1 conference proceeding), and images from the research featured on the cover of all 2003 editions of the research journal, Nonlinearity. The work performed under this proposal also contained a substantial educational component by contributed significantly to the scientific training of one postdoctoral associate, one Ph.D. student and five undergraduate researchers. One main area of focus in this research was convective flow with time-dependent acceleration. Convection is one class of behavior that can arise from g-jitter effects. Our research focused on studies of Rayleigh-Benard system, which is an important model for understanding thermal convection; studies of this problem in the presence of acceleration modulations provided insight into the nature of g-jitter induced flow and of the effects of modulation and noise on non-equilibrium pattern formation. Our experiments on vertically vibrated Rayleigh-Benard convection demonstrated the existence of two classes of pure flow patterns (synchronous & subharmonic) patterns) that had long been predicted by theory but never before observed experimentally. Detailed studies of ranges of parameters where both classes of patterns exist simultaneously led to the discovery of a new type of patterns (called superlattices) in systems driven out of thermodynamic equilibrium.

  15. Pattern formation of Rho GTPases in single cell wound healing

    PubMed Central

    Simon, Cory M.; Vaughan, Emily M.; Bement, William M.; Edelstein-Keshet, Leah

    2013-01-01

    The Rho GTPases—Rho, Rac, and Cdc42—control an enormous variety of processes, many of which reflect activation of these GTPases in spatially confined and mutually exclusive zones. By using mathematical models and experimental results to establish model parameters, we analyze the formation and segregation of Rho and Cdc42 zones during Xenopus oocyte wound repair and the role played by Abr, a dual guanine nucleotide exchange factor–GTPase-activating protein, in this process. The Rho and Cdc42 zones are found to be best represented as manifestations of spatially modulated bistability, and local positive feedback between Abr and Rho can account for the maintenance and dynamic properties of the Rho zone. In contrast, the invocation of an Abr-independent positive feedback loop is required to account for Cdc42 spatial bistability. In addition, the model replicates the results of previous in vivo experiments in which Abr activity is manipulated. Further, simulating the model with two closely spaced wounds made nonintuitive predictions about the Rho and Cdc42 patterns; these predictions were confirmed by experiment. We conclude that the model is a useful tool for analysis of Rho GTPase signaling and that the Rho GTPases can be fruitfully considered as components of intracellular pattern formation systems. PMID:23264464

  16. Interfacial pattern formation in confined power-law fluids

    NASA Astrophysics Data System (ADS)

    Brandão, Rodolfo; Fontana, João V.; Miranda, José A.

    2014-07-01

    The interfacial pattern formation problem in an injection-driven radial Hele-Shaw flow is studied for the situation in which a Newtonian fluid of negligible viscosity displaces a viscous non-Newtonian power-law fluid. By utilizing a Darcy-law-like formulation, we tackle the fluid-fluid interface evolution problem perturbatively, and we derive second-order mode-coupling equations that describe the time evolution of the perturbation amplitudes. This allows us to investigate analytically how the non-Newtonian nature of the dislocated fluid determines the morphology of the emerging interfacial patterns. If the pushed fluid is shear-thinning, our results indicate the development of side-branching structures. On the other hand, if the displaced fluid is shear-thickening, one detects the formation of petal-like shapes, markedly characterized by strong tip-splitting events. Finally, a time-dependent injection protocol is presented that is able to restrain finger proliferation via side-branching and tip-splitting. This permits the emergence of symmetric n-fold interfacial shapes for which the number of fingers remains fixed as time progresses. This procedure generalizes existing controlling strategies for purely Newtonian flow circumstances to the case of a non-Newtonian, displaced power-law fluid.

  17. Chemical Pattern Formation in Far-From Systems.

    NASA Astrophysics Data System (ADS)

    Pearson, John Evan

    The diffusive instability was proposed as a mechanism for pattern formation in chemical systems, in the context of biological morphogenesis, by Alan Turing in 1952. The instability gives rise to a chemical pattern with an intrinsic "chemical wavelength" that is independent of the system size. Since 1952, the diffusive instability, or Turing bifurcation, has been invoked to explain pattern formation in a variety of fields. To date there has been no unambiguous observation of such an instability. Model studies of the instability are usually carried out on systems containing two variables. Such works do not address issues that are of fundamental importance in experimental studies. How does one go about finding Turing bifurcations in systems with many parameters and for which the chemical kinetics are only partially known? What is the chemical wavelength? Turing bifurcations cannot occur in systems with all diffusion coefficients exactly equal. How unequal must the diffusion coefficients be for a system to undergo a Turing bifurcation?. Reacting and diffusing systems obey a partial -differential equation which is a sum of a diffusion term and a reaction term. Dropping the diffusion term results in an ordinary differential equation describing the reaction kinetics in a well-mixed system. In this dissertation it is shown that, for systems with an arbitrary number of variables, Turing bifurcations can occur with diffusion coefficients arbitrarily close to equal, provided the corresponding well-mixed system is sufficiently close to a point of coalescence of Hopf and saddle-node bifurcations. Since the bifurcation set can be obtained directly from experiments, one does not need a detailed microscopic theory of the reaction kinetics. Similarly, the chemical wavelength can be estimated from experimental measurements without knowledge of the reaction kinetics.

  18. Pattern formation and mass transfer under stationary solutal Marangoni instability.

    PubMed

    Schwarzenberger, Karin; Köllner, Thomas; Linde, Hartmut; Boeck, Thomas; Odenbach, Stefan; Eckert, Kerstin

    2014-04-01

    According to the seminal theory by Sternling and Scriven, solutal Marangoni convection during mass transfer of surface-active solutes may occur as either oscillatory or stationary instability. With strong support of Manuel G. Velarde, a combined initiative of experimental works, in particular to mention those of Linde, Wierschem and coworkers, and theory has enabled a classification of dominant wave types of the oscillatory mode and their interactions. In this way a rather comprehensive understanding of the nonlinear evolution of the oscillatory instability could be achieved. A comparably advanced state-of-the-art with respect to the stationary counterpart seemed to be out of reach a short time ago. Recent developments on both the numerical and experimental side, in combination with assessing an extensive number of older experiments, now allow one to draw a more unified picture. By reviewing these works, we show that three main building blocks exist during the nonlinear evolution: roll cells, relaxation oscillations and relaxation oscillations waves. What is frequently called interfacial turbulence results from the interaction between these partly coexisting basic patterns which may additionally occur in different hierarchy levels. The second focus of this review lies on the practical importance of such convection patterns concerning their influence on mass transfer characteristics. Particular attention is paid here to the interaction between Marangoni and buoyancy effects which frequently complicates the pattern formation even more. To shed more light on these dependencies, new simulations regarding the limiting case of stabilizing density stratification and vanishing buoyancy are incorporated. PMID:24456800

  19. One-dimensional daisyworld: spatial interactions and pattern formation.

    PubMed

    Adams, B; Carr, J; Lenton, T M; White, A

    2003-08-21

    The zero-dimensional daisyworld model of Watson and Lovelock (1983) demonstrates that life can unconsciously regulate a global environment. Here that model is extended to one dimension, incorporating a distribution of incoming solar radiation and diffusion of heat consistent with a spherical planet. Global regulatory properties of the original model are retained. The daisy populations are initially restricted to hospitable regions of the surface but exert both global and local feedback to increase this habitable area, eventually colonizing the whole surface. The introduction of heat diffusion destabilizes the coexistence equilibrium of the two daisy types. In response, a striped pattern consisting of blocks of all black or all white daisies emerges. There are two mechanisms behind this pattern formation. Both are connected to the stability of the system and an overview of the mathematics involved is presented. Numerical experiments show that this pattern is globally determined. Perturbations in one region have an impact over the whole surface but the regulatory properties of the system are not compromised by transient perturbations. The relevance of these results to the Earth and the wider climate modelling field is discussed. PMID:12875827

  20. Endogenously Generated Omega‐3 Fatty Acids Attenuate Vascular Inflammation and Neointimal Hyperplasia by Interaction With Free Fatty Acid Receptor 4 in Mice

    PubMed Central

    Li, Xinzhi; Ballantyne, Laurel L.; Che, Xinghui; Mewburn, Jeffrey D.; Kang, Jing X.; Barkley, Robert M.; Murphy, Robert C.; Yu, Ying; Funk, Colin D.

    2015-01-01

    Background Omega‐3 polyunsaturated fatty acids (ω3 PUFAs) suppress inflammation through activation of free fatty acid receptor 4 (FFAR4), but this pathway has not been explored in the context of cardiovascular disease. We aimed to elucidate the involvement of FFAR4 activation by ω3 PUFAs in the process of vascular inflammation and neointimal hyperplasia in mice. Methods and Results We used mice with disruption of FFAR4 (Ffar4−/−), along with a strain that synthesizes high levels of ω3 PUFAs (fat‐1) and a group of crossed mice (Ffar4−/−/fat‐1), to elucidate the role of FFAR4 in vascular dysfunction using acute and chronic thrombosis/vascular remodeling models. The presence of FFAR4 in vascular‐associated cells including perivascular adipocytes and macrophages, but not platelets, was demonstrated. ω3 PUFAs endogenously generated in fat‐1 mice (n=9), but not in compound Ffar4−/−/fat‐1 mice (n=9), attenuated femoral arterial thrombosis induced by FeCl3. Neointimal hyperplasia and vascular inflammation in the common carotid artery were significantly curtailed 4 weeks after FeCl3 injury in fat‐1 mice (n=6). This included greater luminal diameter and enhanced blood flow, reduced intima:media ratio, and diminished macrophage infiltration in the vasculature and perivascular adipose tissue compared with control mice. These effects were attenuated in the Ffar4−/−/fat‐1 mice. Conclusions These results indicate that ω3 PUFAs mitigate vascular inflammation, arterial thrombus formation, and neointimal hyperplasia by interaction with FFAR4 in mice. Moreover, the ω3 PUFA–FFAR4 pathway decreases inflammatory responses with dampened macrophage transmigration and infiltration. PMID:25845931

  1. Non-Linear Pattern Formation in Bone Growth and Architecture

    PubMed Central

    Salmon, Phil

    2014-01-01

    The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here – chaotic non-linear pattern formation (NPF) – which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of “group intelligence” exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called “particle swarm optimization” (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating “socially” in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or “feedback” between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the

  2. Non-linear pattern formation in bone growth and architecture.

    PubMed

    Salmon, Phil

    2014-01-01

    The three-dimensional morphology of bone arises through adaptation to its required engineering performance. Genetically and adaptively bone travels along a complex spatiotemporal trajectory to acquire optimal architecture. On a cellular, micro-anatomical scale, what mechanisms coordinate the activity of osteoblasts and osteoclasts to produce complex and efficient bone architectures? One mechanism is examined here - chaotic non-linear pattern formation (NPF) - which underlies in a unifying way natural structures as disparate as trabecular bone, swarms of birds flying, island formation, fluid turbulence, and others. At the heart of NPF is the fact that simple rules operating between interacting elements, and Turing-like interaction between global and local signals, lead to complex and structured patterns. The study of "group intelligence" exhibited by swarming birds or shoaling fish has led to an embodiment of NPF called "particle swarm optimization" (PSO). This theoretical model could be applicable to the behavior of osteoblasts, osteoclasts, and osteocytes, seeing them operating "socially" in response simultaneously to both global and local signals (endocrine, cytokine, mechanical), resulting in their clustered activity at formation and resorption sites. This represents problem-solving by social intelligence, and could potentially add further realism to in silico computer simulation of bone modeling. What insights has NPF provided to bone biology? One example concerns the genetic disorder juvenile Pagets disease or idiopathic hyperphosphatasia, where the anomalous parallel trabecular architecture characteristic of this pathology is consistent with an NPF paradigm by analogy with known experimental NPF systems. Here, coupling or "feedback" between osteoblasts and osteoclasts is the critical element. This NPF paradigm implies a profound link between bone regulation and its architecture: in bone the architecture is the regulation. The former is the emergent

  3. Pattern formation in granular binary mixtures under shear flow

    NASA Astrophysics Data System (ADS)

    Gao, X.; Narteau, C.; Rozier, O.

    2012-12-01

    Polydisperse granular materials are ubiquitous in the field of geomorphology. Nevertheless, it remains a challenge to address the impact of segregation, stratification and mixing on landscape dynamics and sediment transport. Here, we study numerically the formation and evolution of bed forms using a binary granular mixture. The two types of particles may have different dynamic properties and angle of repose. We associate these changes to two different grain sizes, the so-called coarse and thin particles. Our computation are based on a real-space cellular automaton that combines a model of sediment transport with a lattice-gas cellular automaton. Thus, we implement the permanent feedbacks between fluid flow and topography. Keeping constant the strength of the flow, we explore a parameter-space by varying the size of the coarse particles and their proportion within the bed. As a result of avalanches and sediment transport, we systematically find regions of segregation and stratification. In a vast majority of cases, we also observe the formation of an armoring layer mainly composed of coarse particles. Its depth is mainly controlled by the proportion of coarse grains and not by the size of these larger particles. When there is a larger proportion of thin particles, transverse dunes develop on the top of the armoring layer. As this proportion decreases, we may observe barchans or even no clear bed forms. Not surprisingly, we conclude that the main control parameter for dune pattern formation is the thin sediment availability. Finally, we discuss the processes responsible for the formation of the armoring layer and show how it controls the overall sediment transport.

  4. Topology-generating interfacial pattern formation during liquid metal dealloying

    PubMed Central

    Geslin, Pierre-Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

    2015-01-01

    Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growth of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Moreover, we deduce scaling laws governing microstructural length scales and dealloying kinetics. PMID:26582248

  5. Topology-generating interfacial pattern formation during liquid metal dealloying.

    PubMed

    Geslin, Pierre-Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

    2015-01-01

    Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growth of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Moreover, we deduce scaling laws governing microstructural length scales and dealloying kinetics. PMID:26582248

  6. Topology-generating interfacial pattern formation during liquid metal dealloying

    NASA Astrophysics Data System (ADS)

    Geslin, Pierre-Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

    2015-11-01

    Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growth of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Moreover, we deduce scaling laws governing microstructural length scales and dealloying kinetics.

  7. Pattern formation and three-dimensional instability in rotating flows

    NASA Astrophysics Data System (ADS)

    Christensen, Erik A.; Aubry, Nadine; Sorensen, Jens N.

    1997-03-01

    A fluid flow enclosed in a cylindrical container where fluid motion is created by the rotation of one end wall as a centrifugal fan is studied. Direct numerical simulations and spatio-temporal analysis have been performed in the early transition scenario, which includes a steady-unsteady transition and a breakdown of axisymmetric to three-dimensional flow behavior. In the early unsteady regime of the flow, the central vortex undergoes a vertical beating motion, accompanied by axisymmetric spikes formation on the edge of the breakdown bubble. As traveling waves, the spikes move along the central vortex core toward the rotating end-wall. As the Reynolds number is increased further, the flow undergoes a three-dimensional instability. The influence of the latter on the previous patterns is studied.

  8. Topology-generating interfacial pattern formation during liquid metal dealloying

    DOE PAGESBeta

    Geslin, Pierre -Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

    2015-11-19

    Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growthmore » of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Furthermore, we deduce scaling laws governing microstructural length scales and dealloying kinetics.« less

  9. Topology-generating interfacial pattern formation during liquid metal dealloying

    SciTech Connect

    Geslin, Pierre -Antoine; McCue, Ian; Gaskey, Bernard; Erlebacher, Jonah; Karma, Alain

    2015-11-19

    Liquid metal dealloying has emerged as a novel technique to produce topologically complex nanoporous and nanocomposite structures with ultra-high interfacial area and other unique properties relevant for diverse material applications. This process is empirically known to require the selective dissolution of one element of a multicomponent solid alloy into a liquid metal to obtain desirable structures. However, how structures form is not known. Here we demonstrate, using mesoscale phase-field modelling and experiments, that nano/microstructural pattern formation during dealloying results from the interplay of (i) interfacial spinodal decomposition, forming compositional domain structures enriched in the immiscible element, and (ii) diffusion-coupled growth of the enriched solid phase and the liquid phase into the alloy. We highlight how those two basic mechanisms interact to yield a rich variety of topologically disconnected and connected structures. Furthermore, we deduce scaling laws governing microstructural length scales and dealloying kinetics.

  10. Time-Dependence and Pattern Formation in Flowing Granular Media.

    NASA Astrophysics Data System (ADS)

    Baxter, George William, III

    1990-01-01

    We study the time dependence and pattern formation of gravity driven flows of granular media in three experiments. In three dimensional flows of sand, the normal stress on the wall of a conical hopper is measured. There is no evidence of characteristic time scales predicted by a linear stability analysis of a current continuum theory of granular media. Instead, the signal is characterized by a power law power spectrum, and the time variation of the normal stress obeys a scaling law consistent with fractional Brownian motion with H ~ 0.2. As one of the best examples to date of fractional Brownian motion in a physical experiment, this provides a unique opportunity for a study of the theory's application. In digital subtraction radiography studies of sand flow through a thin (nearly two dimensional) wedge, density waves are found. The formation and motion of these depends on the geometry of the wedge and the roughness of the sand grains. The waves form in rough sand but not in smooth sand of the same approximate size, demonstrating that grain structure has a dramatic effect on the flow. Also, the position of stagnant regions along the sides of the wedge is found to scale as a power law of the wedge angle. Neither the density waves nor the position of the stagnant regions are predicted by current theories. Finally, a cellular automata model is proposed to model the two dimensional flow of ellipsoidal grains (such as grass seed) through a wedge. By including particle shape and orientation as degrees of freedom, this model is able to capture many features of real physical flows. In sum, these experiments demonstrate that flows of even simple materials like sand or grass seed contain time dependent patterns that are not predicted by current theoretical models. This demonstrates the need to include particle structure and orientation. Finally, the cellular automata model shows that even relatively simple models which include these added degrees of freedom can reproduce the

  11. Quantifying Contributions of Climate Feedbacks to Global Warming Pattern Formation

    NASA Astrophysics Data System (ADS)

    Song, X.; Zhang, G. J.; Cai, M.

    2013-12-01

    The ';';climate feedback-response analysis method'' (CFRAM) was applied to the NCAR CCSM3.0 simulation to analyze the strength and spatial distribution of climate feedbacks and to quantify their contributions to global and regional surface temperature changes in response to a doubling of CO2. Instead of analyzing the climate sensitivity, the CFRAM directly attributes the temperature change to individual radiative and non-radiative feedbacks. The radiative feedback decomposition is based on hourly model output rather than monthly mean data that are commonly used in climate feedback analysis. This gives a more accurate quantification of the cloud and albedo feedbacks. The process-based decomposition of non-radiative feedback enables us to understand the roles of GCM physical and dynamic processes in climate change. The pattern correlation, the centered root-mean-square (RMS) difference and the ratio of variations (represented by standard deviations) between the partial surface temperature change due to each feedback process and the total surface temperature change in CCSM3.0 simulation are examined to quantify the roles of each feedback process in the global warming pattern formation. The contributions of climate feedbacks to the regional warming are also discussed.

  12. Ternary eutectic dendrites: Pattern formation and scaling properties.

    PubMed

    Rátkai, László; Szállás, Attila; Pusztai, Tamás; Mohri, Tetsuo; Gránásy, László

    2015-04-21

    Extending previous work [Pusztai et al., Phys. Rev. E 87, 032401 (2013)], we have studied the formation of eutectic dendrites in a model ternary system within the framework of the phase-field theory. We have mapped out the domain in which two-phase dendritic structures grow. With increasing pulling velocity, the following sequence of growth morphologies is observed: flat front lamellae → eutectic colonies → eutectic dendrites → dendrites with target pattern → partitionless dendrites → partitionless flat front. We confirm that the two-phase and one-phase dendrites have similar forms and display a similar scaling of the dendrite tip radius with the interface free energy. It is also found that the possible eutectic patterns include the target pattern, and single- and multiarm spirals, of which the thermal fluctuations choose. The most probable number of spiral arms increases with increasing tip radius and with decreasing kinetic anisotropy. Our numerical simulations confirm that in agreement with the assumptions of a recent analysis of two-phase dendrites [Akamatsu et al., Phys. Rev. Lett. 112, 105502 (2014)], the Jackson-Hunt scaling of the eutectic wavelength with pulling velocity is obeyed in the parameter domain explored, and that the natural eutectic wavelength is proportional to the tip radius of the two-phase dendrites. Finally, we find that it is very difficult/virtually impossible to form spiraling two-phase dendrites without anisotropy, an observation that seems to contradict the expectations of Akamatsu et al. Yet, it cannot be excluded that in isotropic systems, two-phase dendrites are rare events difficult to observe in simulations. PMID:25903891

  13. Ternary eutectic dendrites: Pattern formation and scaling properties

    SciTech Connect

    Rátkai, László; Szállás, Attila; Pusztai, Tamás; Mohri, Tetsuo; Gránásy, László

    2015-04-21

    Extending previous work [Pusztai et al., Phys. Rev. E 87, 032401 (2013)], we have studied the formation of eutectic dendrites in a model ternary system within the framework of the phase-field theory. We have mapped out the domain in which two-phase dendritic structures grow. With increasing pulling velocity, the following sequence of growth morphologies is observed: flat front lamellae → eutectic colonies → eutectic dendrites → dendrites with target pattern → partitionless dendrites → partitionless flat front. We confirm that the two-phase and one-phase dendrites have similar forms and display a similar scaling of the dendrite tip radius with the interface free energy. It is also found that the possible eutectic patterns include the target pattern, and single- and multiarm spirals, of which the thermal fluctuations choose. The most probable number of spiral arms increases with increasing tip radius and with decreasing kinetic anisotropy. Our numerical simulations confirm that in agreement with the assumptions of a recent analysis of two-phase dendrites [Akamatsu et al., Phys. Rev. Lett. 112, 105502 (2014)], the Jackson-Hunt scaling of the eutectic wavelength with pulling velocity is obeyed in the parameter domain explored, and that the natural eutectic wavelength is proportional to the tip radius of the two-phase dendrites. Finally, we find that it is very difficult/virtually impossible to form spiraling two-phase dendrites without anisotropy, an observation that seems to contradict the expectations of Akamatsu et al. Yet, it cannot be excluded that in isotropic systems, two-phase dendrites are rare events difficult to observe in simulations.

  14. Territorial pattern formation in the absence of an attractive potential.

    PubMed

    Potts, Jonathan R; Lewis, Mark A

    2016-01-01

    Territoriality is a phenomenon exhibited throughout nature. On the individual level, it is the processes by which organisms exclude others of the same species from certain parts of space. On the population level, it is the segregation of space into separate areas, each used by subsections of the population. Proving mathematically that such individual-level processes can cause observed population-level patterns to form is necessary for linking these two levels of description in a non-speculative way. Previous mathematical analysis has relied upon assuming animals are attracted to a central area. This can either be a fixed geographical point, such as a den- or nest-site, or a region where they have previously visited. However, recent simulation-based studies suggest that this attractive potential is not necessary for territorial pattern formation. Here, we construct a partial differential equation (PDE) model of territorial interactions based on the individual-based model (IBM) from those simulation studies. The resulting PDE does not rely on attraction to spatial locations, but purely on conspecific avoidance, mediated via scent-marking. We show analytically that steady-state patterns can form, as long as (i) the scent does not decay faster than it takes the animal to traverse the terrain, and (ii) the spatial scale over which animals detect scent is incorporated into the PDE. As part of the analysis, we develop a general method for taking the PDE limit of an IBM that avoids destroying any intrinsic spatial scale in the underlying behavioral decisions. PMID:25822451

  15. Segment formation in Annelids: patterns, processes and evolution.

    PubMed

    Balavoine, Guillaume

    2014-01-01

    The debate on the origin of segmentation is a central question in the study of body plan evolution in metazoans. Annelids are the most conspicuously metameric animals as most of the trunk is formed of identical anatomical units. In this paper, I summarize the various patterns of evolution of the metameric body plan in annelids, showing the remarkable evolvability of this trait, similar to what is also found in arthropods. I then review the different modes of segment formation in the annelid tree, taking into account the various processes taking place in the life histories of these animals, including embryogenesis, post-embryonic development, regeneration and asexual reproduction. As an example of the variations that occur at the cellular and genetic level in annelid segment formation, I discuss the processes of teloblastic growth or posterior addition in key groups in the annelid tree. I propose a comprehensive definition for the teloblasts, stem cells that are responsible for sequential segment addition. There are a diversity of different mechanisms used in annelids to produce segments depending on the species, the developmental time and also the life history processes of the worm. A major goal for the future will be to reconstitute an ancestral process (or several ancestral processes) in the ancestor of the whole clade. This in turn will provide key insights in the current debate on ancestral bilaterian segmentation. PMID:25690963

  16. Tree island pattern formation in the Florida Everglades

    USGS Publications Warehouse

    Carr, Joel; D'Odorico, P.; Engel, Victor C.; Redwine, Jed

    2016-01-01

    The Florida Everglades freshwater landscape exhibits a distribution of islands covered by woody vegetation and bordered by marshes and wet prairies. Known as “tree islands”, these ecogeomorphic features can be found in few other low gradient, nutrient limited freshwater wetlands. In the last few decades, however, a large percentage of tree islands have either shrank or disappeared in apparent response to altered water depths and other stressors associated with human impacts on the Everglades. Because the processes determining the formation and spatial organization of tree islands remain poorly understood, it is still unclear what controls the sensitivity of these landscapes to altered conditions. We hypothesize that positive feedbacks between woody plants and soil accretion are crucial to emergence and decline of tree islands. Likewise, positive feedbacks between phosphorus (P) accumulation and trees explain the P enrichment commonly observed in tree island soils. Here, we develop a spatially-explicit model of tree island formation and evolution, which accounts for these positive feedbacks (facilitation) as well as for long range competition and fire dynamics. It is found that tree island patterns form within a range of parameter values consistent with field data. Simulated impacts of reduced water levels, increased intensity of drought, and increased frequency of dry season/soil consuming fires on these feedback mechanisms result in the decline and disappearance of tree islands on the landscape.

  17. Pattern formation and morphology transitions in bacterial systems

    NASA Astrophysics Data System (ADS)

    Arouh, Scott

    Bacteria grown on a semi-solid agar surface have been observed to form branching, chiral, and ring patterns as the colony envelope propagates outward. We model transitions between the branching and chiral patterns, analyze the effect of directed bacterial motion (chemotaxis) on the branching instability, and analyze a model for ring generation. Our model for transitions between branching and chiral patterns is a variant of Ben-Jacob's Communicating Walkers Models. We demonstrate that arbitrarily small nucleation regions of the new phase may be sufficient for the transformation to proceed. We also illustrate the phase transformations with plots of the colony envelope velocities as a function of environmental parameters. Based on the appearance of simulated colony patterns, we propose that experimentally observed global morphology transitions may be the result of single genetic mutations, and we predict biological values for the corresponding mutation rate. Our analysis of the effect of chemotaxis on a branching instability starts with an existing model for a branching instability. This instability is fundamentally caused by the need for limited nutrient to diffuse towards the colony. We add to this model the effect of bacteria moving chemotactically in response to the nutrient gradient. Our results show that this additional effect has a tendency to suppress the instability. Although we perform our calculations within the context of a simple "cutoff" model of colony dynamics, we expect our results to apply for more complex and hence more realistic approaches. We also analyze a model proposed by Medvedev, Kaper, and Kopell for ring formation. We perform a linear stability calculation for the model equations and find critical spatial decay rates to stability, but we later find that these are not relevant to the ring generation mechanism. By observing numerical bacterial density profiles near the colony edge, we identify a consolidation front distinct from the colony

  18. Complete vascular healing and sustained suppression of neointimal thickening after local delivery of advanced c-myc antisense at six months follow-up in a rabbit balloon injury model

    SciTech Connect

    Kipshidze, Nicholas; Iversen, Patrick; Keane, Eamon; Stein, David; Chawla, Paramjith; Skrinska, Victor; Shankar, Latha Raja; Mehran, Roxana; Chekanov, Valerie; Dangas, George; Komorowski, Richard; Haudenschild, Christian; Khanna, Ashwani; Leon, Martin; Keelan, Michael H.; Moses, Jeffrey

    2002-03-01

    Background: Neointimal hyperplasia following percutaneous transluminal coronary angioplasty (PTCA) is one of the major components of the process of restenosis. We evaluated the long-term impact of local delivery of c-myc neutrally charged antisense oligonucleotides (Resten-NG) upon neointimal formation following PTCA in a rabbit model.Methods:PTCA was performed in the iliac arteries of 10 New Zealand white rabbits at 8 atm for 30 s, three times. An infusion of 500 {mu}g Resten-NG (n=6) or saline (n=4) was delivered to the site at 2 atm via the outer balloon pores of the transport{sup TM} catheter over 2 min. The diet was supplemented with 0.25% cholesterol for 10 days before and 6 months following PTCA.Results:After 6 months, animals were sacrificed and vessels were fixed in formalin, processed and stained with hematoxylin, eosin, and movat. Histological analysis revealed complete vascular healing in both groups of animals. Planimetry showed that intimal areas were 1.71{+-}0.25 and 0.65{+-}0.36 mm{sup 2} in the control and antisense delivery groups, respectively (P<.05).Conclusion:We conclude that local delivery of Resten-NG significantly inhibited neointimal thickening following PTCA in a rabbit for up to 6 months.

  19. Family formation patterns among migrant women in Sydney.

    PubMed

    Yusuf, F; Siedlecky, S

    1996-01-01

    A demographic survey among a probability sample of 980 married migrant women was carried out in Sydney in 1988. The sample included 507 Lebanese, 250 Turkish and 223 Vietnamese women. The study revealed differences in family formation patterns within and between the three groups and between them and the general population. Family size had declined among all three groups compared with their family of origin, and it was clear that the younger women would not achieve the same family sizes as the older women. Migrant women tended to marry earlier than the general population and to start their families earlier. While they showed a strong preference for their children to marry within their own ethnic and religious group, nearly one-third said it was up to the choice of the individual. Overall, the future family size of younger migrant women is expected to converge towards the Australian norm. Migrant families are in a state of transition between two cultures which needs to be recognised by health and family planning service providers. PMID:8690746

  20. Pathological pattern formation and cortical propagation of epileptic seizures

    PubMed Central

    Kramer, Mark A; Kirsch, Heidi E; Szeri, Andrew J

    2005-01-01

    The stochastic partial differential equations (SPDEs) stated by Steyn-Ross and co-workers constitute a model of mesoscopic electrical activity of the human cortex. A simplification in which spatial variation and stochastic input are neglected yields ordinary differential equations (ODEs), which are amenable to analysis by techniques of dynamical systems theory. Bifurcation diagrams are developed for the ODEs with increased subcortical excitation, showing that the model predicts oscillatory electrical activity in a large range of parameters. The full SPDEs with increased subcortical excitation produce travelling waves of electrical activity. These model results are compared with electrocortical data recorded at two subdural electrodes from a human subject undergoing a seizure. The model and observational results agree in two important respects during seizure: (i) the average frequency of maximum power, and (ii) the speed of spatial propagation of voltage peaks. This suggests that seizing activity on the human cortex may be understood as an example of pathological pattern formation. Included is a discussion of the applications and limitations of these results. PMID:16849171

  1. Spatial pattern formation facilitates eradication of infectious diseases.

    PubMed

    Eisinger, Dirk; Thulke, Hans-Hermann

    2008-04-01

    Control of animal-born diseases is a major challenge faced by applied ecologists and public health managers. To improve cost-effectiveness, the effort required to control such pathogens needs to be predicted as accurately as possible. In this context, we reviewed the anti-rabies vaccination schemes applied around the world during the past 25 years.We contrasted predictions from classic approaches based on theoretical population ecology (which governs rabies control to date) with a newly developed individual-based model. Our spatially explicit approach allowed for the reproduction of pattern formation emerging from a pathogen's spread through its host population.We suggest that a much lower management effort could eliminate the disease than that currently in operation. This is supported by empirical evidence from historic field data. Adapting control measures to the new prediction would save one-third of resources in future control programmes.The reason for the lower prediction is the spatial structure formed by spreading infections in spatially arranged host populations. It is not the result of technical differences between models.Synthesis and applications. For diseases predominantly transmitted by neighbourhood interaction, our findings suggest that the emergence of spatial structures facilitates eradication. This may have substantial implications for the cost-effectiveness of existing disease management schemes, and suggests that when planning management strategies consideration must be given to methods that reflect the spatial nature of the pathogen-host system. PMID:18784795

  2. Transcriptional Switches Direct Plant Organ Formation and Patterning

    PubMed Central

    Moreno-Risueno, Miguel A.; Van Norman, Jaimie M.; Benfey, Philip N.

    2013-01-01

    Development of multicellular organisms requires specification of diverse cell types. In plants, development is continuous and because plant cells are surrounded by rigid cell walls, cell division and specification of daughter cell fate must be carefully orchestrated. During embryonic and postembryonic plant development, the specification of cell types is determined both by positional cues and cell lineage. The establishment of distinct transcriptional domains is a fundamental mechanism for determining different cell fates. In this review, we focus on four examples from recent literature of switches operating in cell fate decisions that are regulated by transcriptional mechanisms. First, we highlight a transcriptional mechanism involving a mobile transcription factor in formation of the two ground tissue cell types in roots. Specification of vascular cell types is then discussed, including new details about xylem cell-type specification via a mobile microRNA. Next, transcriptional regulation of two key embryonic developmental events is considered: establishment of apical–basal polarity in the single-celled zygote and specification of distinct root and shoot stem cell populations in the plant embryo. Finally, a dynamic transcriptional mechanism for lateral organ positioning that integrates spatial and temporal information into a repeating pattern is summarized. PMID:22305165

  3. Neutrophil, not macrophage, infiltration precedes neointimal thickening in balloon-injured arteries.

    PubMed

    Welt, F G; Edelman, E R; Simon, D I; Rogers, C

    2000-12-01

    Macrophages are abundant after stent-induced arterial injury. Inhibition of macrophage recruitment blocks neointimal growth in this model. In contrast, after superficial injury from balloon endothelial denudation, macrophages are sparse. However, many anti-inflammatory therapies remain effective against neointimal growth after balloon injury. To investigate further the role of leukocytes after injury, 41 New Zealand White rabbits underwent iliac artery balloon denudation. In 18, subcutaneous pumps were placed to deliver intravenous heparin (0.3 mg/kg per hour). Arteries were harvested at 6 hours and at 3, 7, and 14 days. In 8 animals, either M1/70 (a monoclonal antibody [mAb] against adhesion molecule Mac-1) or a nonspecific IgG was given (5 mg/kg IV bolus and then 1 mg/kg SC QOD), and arteries were harvested at 6 hours and 3 days. Computer-aided morphometry was performed as was immunohistochemistry to assess smooth muscle cell (SMC) proliferation (bromodeoxyuridine-positive cells), neutrophil content (RPN357, mAb against rabbit neutrophil/thymocyte), and macrophage content (RAM-11, mAb against rabbit macrophage). Heparin inhibited neointimal growth at 7 and 14 days (64% and 32.5% reduction, respectively; P:<0.05). Neutrophils were observed in the media early after balloon injury, and heparin and M1/70 inhibited this infiltration (82% and 83% reduction, respectively; P:<0.05 each) with a coincident inhibition of medial SMC proliferation at 3 days (49% and 84% reduction, respectively; P:<0.05 each). Macrophages were absent at all time points. Neutrophil, but not macrophage, infiltration occurs early after endothelial denudation. Inhibition of this process is associated with a reduction in medial SMC proliferation. These data suggest a central role for neutrophils in restenosis and help to explain prior reports of an inhibitory effect of anti-inflammatory therapies on neointimal growth after balloon injury. PMID:11116052

  4. Auxin distribution and transport during embryonic pattern formation in wheat.

    PubMed

    Fischer-Iglesias, C; Sundberg, B; Neuhaus, G; Jones, A M

    2001-04-01

    Inhibitors of auxin polar transport disrupt normal embryogenesis and thus specific spatial auxin distribution due to auxin movement may be important in establishing embryonic pattern formation in plants. In the present study, the distribution of the photoaffinity labeling agent tritiated 5-azidoindole-3-acetic acid ([3H],5-N3IAA), an analog of indole-3-acetic acid (IAA), was visualized in zygotic wheat (Triticum aestivum L.) embryos grown in vitro and in planta, and used to deduce auxin transport pathways in these embryos. This study provides the first direct evidence that the distribution of auxin, here [3H],5-N3IAA, is heterogeneous and changes during embryo development. In particular, the shift from radial to bilateral symmetry was correlated with a redistribution of [3H],5-N3IAA in the embryo. Furthermore, in bilaterally symmetrical embryos, that is, embryos in the late transition stage or older, the localization of [3H],5-N3IAA was altered by N-1-naphthylphthalamic acid, a specific inhibitor of auxin polar transport. No significant effect was observed in radially symmetrical embryos, that is, globular embryos, or very early transition embryos. Thus, the shift from radial to bilateral symmetry is associated with the onset of active, directed auxin transport involved in auxin redistribution. A change in the distribution of [3H],5-N3IAA was also observed in morphologically abnormal embryos induced on media supplemented with auxin or auxin polar transport inhibitors. By means of a microscale technique, free IAA concentration was measured in in vitro- and in planta-grown embryos and was found to increase during development. Therefore, IAA may be synthesized or released from conjugates in bilaterally symmetrical embryos, although import from surrounding tissues cannot be excluded. PMID:11389754

  5. Instabilities and pattern formation on the pore scale

    NASA Astrophysics Data System (ADS)

    Juel, Anne

    What links a baby's first breath to adhesive debonding, enhanced oil recovery, or even drop-on-demand devices? All these processes involve moving or expanding bubbles displacing fluid in a confined space, bounded by either rigid or elastic walls. In this talk, we show how spatial confinement may either induce or suppress interfacial instabilities and pattern formation in such flows. We demonstrate that a simple change in the bounding geometry can radically alter the behaviour of a fluid-displacing air finger both in rigid and elastic vessels. A rich array of propagation modes, including steady and oscillatory fingers, is uncovered when air displaces oil from axially uniform tubes that have local variations in flow resistance within their cross-sections. Moreover, we show that the experimentally observed states can all be captured by a two-dimensional depth-averaged model for bubble propagation through wide channels. Viscous fingering in Hele-Shaw cells is a classical and widely studied fluid-mechanical instability: when air is injected into the narrow, liquid-filled gap between parallel rigid plates, the axisymmetrically expanding air-liquid interface tends to be unstable to non-axisymmetric disturbances. We show how the introduction of wall elasticity (via the replacement of the upper bounding plate by an elastic membrane) can weaken or even suppress the fingering instability by allowing changes in cell confinement through the flow-induced deflection of the boundary. The presence of a deformable boundary also makes the system prone to additional solid-mechanical instabilities, and these wrinkling instabilities can in turn enhance viscous fingering. The financial support of EPSRC and the Leverhulme Trust is gratefully acknowledged.

  6. MicroRNA-24 Attenuates Neointimal Hyperplasia in the Diabetic Rat Carotid Artery Injury Model by Inhibiting Wnt4 Signaling Pathway

    PubMed Central

    Yang, Jian; Fan, Zhixing; Yang, Jun; Ding, Jiawang; Yang, Chaojun; Chen, Lihua

    2016-01-01

    The long-term stimulation of hyperglycemia greatly increases the incidence of vascular restenosis (RS) after angioplasty. Neointimal hyperplasia after vascular injury is the pathological cause of RS, but its mechanism has not been elucidated. MicroRNA-24 (miR-24) has low expression in the injured carotid arteries of diabetic rats. However, the role of miR-24 in the vascular system is unknown. In this study, we explore whether over-expression of miR-24 could attenuate neointimal formation in streptozotocin (STZ)-induced diabetic rats. Adenovirus (Ad-miR-24-GFP) was used to deliver the miR-24 gene to injured carotid arteries in diabetic rats. The level of neointimal hyperplasia was examined by hematoxylin-eosin (HE) staining. Vascular smooth muscle cell (VSMC) proliferation in the neointima was evaluated by immunostaining for proliferating cell nuclear antigen (PCNA). The mRNA levels of miR-24, PCNA, wingless-type MMTV integration site family member 4 (Wnt4), disheveled-1 (Dvl-1), β-catenin and cell cycle-associated molecules (Cyclin D1, p21) were determined by Quantitative Real-Time PCR (qRT-PCR). PCNA, Wnt4, Dvl-1, β-catenin, Cyclin D1 and p21 protein levels were measured by Western blotting analysis. STZ administration decreased plasma insulin and increased fasting blood glucose in Sprague-Dawley (SD) rats. The expression of miR-24 was decreased in the carotid artery after a balloon injury in diabetic rats, and adenoviral transfection (Ad-miR-24-GFP) increased the expression of miR-24. Over-expression of miR-24 suppressed VSMC proliferation and neointimal hyperplasia in diabetic rats at 14 days. Furthermore, compared with Sham group, the mRNA and protein levels of PCNA, Wnt4, Dvl-1, β-catenin, and Cyclin D1 were strikingly up-regulated in the carotid arteries of diabetic rats after a balloon injury. Interestingly, up-regulation of miR-24 significantly reduced the mRNA and protein levels of these above molecules. In contrast, the change trend in p21 mRNA and

  7. Pattern formation in polymer via electrohydrodynamic instabilities and glassy fracture

    NASA Astrophysics Data System (ADS)

    Pease, Leonard Franklin, III

    Fabrication of micro and nano structures from polymeric materials has attracted significant attention due to their promise of inexpensive, fast throughput and ease of integration into existing fabrication processes. This dissertation describes our contributions to two such processes. In the first process, electrohydrodynamic flow drives a thin polymer film sandwiched between electrodes with an intervening gap into multidomained, hexagonally packed pillars or concentric rings. We model the initial stages of formation by performing a linear stability analysis under the lubrication approximation. We find the presence of free charge at the free interface both decreases the pillar-to-pillars spacing and increases the growth rate. We examined the possible sources of electrostatic field in the absence of an applied voltage to find static charge to be the most likely candidate. In practice, however, the lubrication approximation may not strictly apply in the situations of greatest interest. Accordingly, we contrasted results of the linear stability analysis with and without the lubrication approximation to show that the approximation fails where surface tension is small and electric fields are large, typical of experiments with a polymer/organic liquid instead of air in the gap---precisely the conditions that predict the smallest pillar arrays. Motivated by the discovery of concentric rings, we adapted the form of the perturbation from sinusoids to Bessel functions to predict constant ring-to-ring spacings, constant annular widths and growth rates in agreement with experiment. In the second patterning technique, a thin film sandwiched between two substrates fractures into periodic ridges upon insertion of a razor blade. We investigated the conditions that selected for the presence or absence of the gratings, their fractional coverage, their period, and their alignment. Our key findings indicated that the gratings form from all glassy materials tested with periods of

  8. Pattern formation in plastic liquid films on elastomers by ratcheting.

    PubMed

    Huang, Jiangshui; Yang, Jiawei; Jin, Lihua; Clarke, David R; Suo, Zhigang

    2016-04-20

    Plastic liquids, also known as Bingham liquids, retain their shape when loads are small, but flow when loads exceed a threshold. We discovered that plastic liquid films coated on elastomers develop wavy patterns under cyclic loads. As the number of cycles increases, the wavelength of the patterns remains unchanged, but the amplitude of the patterns increases and then saturates. Because the patterns develop progressively under cyclic loads, we call this phenomenon as "patterning by ratcheting". We observe the phenomenon in plastic liquids of several kinds, and studied the effects of thickness, the cyclic frequency of the stretch, and the range of the stretch. Finite element simulations show that the ratcheting phenomenon can occur in materials described by a commonly used model of elastic-plastic deformation. PMID:27008927

  9. Optical Pattern Formation in Cold Atoms: Explaining the Red-Blue Asymmetry

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie; Gauthier, Daniel

    2013-05-01

    The study of pattern formation in atomic systems has provided new insight into fundamental many-body physics and low-light-level nonlinear optics. Pattern formation in cold atoms in particular is of great interest in condensed matter physics and quantum information science because atoms undergo self-organization at ultralow input powers. We recently reported the first observation of pattern formation in cold atoms but found that our results were not accurately described by any existing theoretical model of pattern formation. Previous models describing pattern formation in cold atoms predict that pattern formation should occur using both red and blue-detuned pump beams, favoring a lower threshold for blue detunings. This disagrees with our recent work, in which we only observed pattern formation with red-detuned pump beams. Previous models also assume a two-level atom, which cannot account for the cooling processes that arise when beams counterpropagate through a cold atomic vapor. We describe a new model for pattern formation that accounts for Sisyphus cooling in multi-level atoms, which gives rise to a new nonlinearity via spatial organization of the atoms. This spatial organization causes a sharp red-blue detuning asymmetry, which agrees well with our experimental observations. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

  10. Dynamics of skeletal pattern formation in developing chick limb.

    PubMed

    Newman, S A; Frisch, H L

    1979-08-17

    During development of the embryonic chick limb the skeletal pattern is laid out as cartilaginous primordia, which emerge in a proximodistal sequence over a period of 4 days. The differentiation of cartilage is preceded by changes in cellular contacts at specific locations in the precartilage mesenchyme. Under realistic assumptions, the biosynthesis and diffusion through the extracellular matrix of a cell surface protein, such as fibronectin, will lead to spatial patterns of this molecule that could be the basis of the emergent primordia. As cellular differentiation proceeds, the size of the mesenchymal diffusion chamber is reduced in descrete steps, leading to sequential reorganizations of the morphogen pattern. The successive patterns correspond to observed rows of skeletal elements, whose emergence, in theory and in practice, depends on the maintenance of a unique boundary condition at the limb bud apex. PMID:462174

  11. Endothelial cell motility, coordination and pattern formation during vasculogenesis.

    PubMed

    Czirok, Andras

    2013-01-01

    How vascular networks assemble is a fundamental problem of developmental biology that also has medical importance. To explain the organizational principles behind vascular patterning, we must understand how can tissue level structures be controlled through cell behavior patterns like motility and adhesion that, in turn, are determined by biochemical signal transduction processes? We discuss the various ideas that have been proposed as mechanisms for vascular network assembly: cell motility guided by extracellular matrix alignment (contact guidance), chemotaxis guided by paracrine and autocrine morphogens, and multicellular sprouting guided by cell-cell contacts. All of these processes yield emergent patterns, thus endothelial cells can form an interconnected structure autonomously, without guidance from an external pre-pattern. PMID:23857825

  12. Module Based Complexity Formation: Periodic Patterning in Feathers and Hairs

    PubMed Central

    Chuong, Cheng-Ming; Yeh, Chao-Yuan; Jiang, Ting-Xin; Widelitz, Randall

    2012-01-01

    Patterns describe order which emerges from homogeneity. Complex patterns on the integument are striking because of their visibility throughout an organism's lifespan. Periodic patterning is an effective design because the ensemble of hair or feather follicles (modules) allows the generation of complexity, including regional variations and cyclic regeneration, giving the skin appendages a new lease on life. Spatial patterns include the arrangements of feathers and hairs in specified number, size, and spacing. We explore how a field of equivalent progenitor cells can generate periodically arranged modules based on genetic information, physical-chemical rules and developmental timing. Reconstitution experiments suggest a competitive equilibrium regulated by activators / inhibitors involving Turing reaction-diffusion. Temporal patterns result from oscillating stem cell activities within each module (micro-environment regulation), reflected as growth (anagen) and resting (telogen) phases during the cycling of feather and hair follicles. Stimulating modules with activators initiates the spread of regenerative hair waves, while global inhibitors outside each module (macro-environment) prevent this. Different wave patterns can be simulated by Cellular Automata principles. Hormonal status and seasonal changes can modulate appendage phenotypes, leading to “organ metamorphosis”, with multiple ectodermal organ phenotypes generated from the same precursors. We discuss potential evolutionary novel steps using this module based complexity in several amniote integument organs, exemplified by the spectacular peacock feather pattern. We thus explore the application of the acquired knowledge of patterning in tissue engineering. New hair follicles can be generated after wounding. Hairs and feathers can be reconstituted through self-organization of dissociated progenitor cells. PMID:23539312

  13. Pattern Formation in Mississippi Valley-Type Deposits

    NASA Astrophysics Data System (ADS)

    Kelka, Ulrich; Koehn, Daniel

    2015-04-01

    Alternating, monomineralic dark and white bands are common features of ore hosting dolostones which are generally termed Zebra textures. These structures consist of coarse grained light and fine grained dark layers and accompany ore bodies of the Mississippi Valley-Type (MVT) worldwide. These deposits frequently develop in large hydrothermal systems, located in the flanks of foreland basins or in fold and thrust belts. The microstructural- and microchemical analysis in this study were performed on samples which were collected in the San Vicente mine. This large MVT deposit is hosted in Triassic/Jurassic Platform Carbonates located in an east-vergent fold and thrust belt of the Peruvian Andes. The thin sections were analyzed with petrographic- and scanning electron microscope. It is observed that one common striking feature is the high density of second-phase particles in the dark bands, whereas the coarser grained layers are virtually particle free. Furthermore, the particle distribution is found to be non-random. The highest particle densities in the samples occur on grain boundaries in the dark bands implying that grain boundaries can capture particles. Based on recent theories and the additional analytical findings, we developed a numerical simulation to study the pattern formation. The modelling is performed in 2D at the scale of a thin section, using a boundary-model coupled with a lattice-particle-code. During the simulation two processes are active, first a reaction takes place that replaces calcite with dolomite driven by a fluid that infiltrates the model, followed by a grain growth processes with an average grain size increase as a function of surface energy reduction. Fluid infiltration in the rock is modelled assuming Darcy Flow and an advection-diffusion equation coupled with a reaction which is a function of concentration. The reaction increases permeability of the solid and thus enhances infiltration. The reaction front in the model shifts particles

  14. Biological pattern formation: from basic mechanisms to complex structures

    SciTech Connect

    Koch, A.J.; Meinhardt, H. )

    1994-10-01

    The reliable development of highly complex organisms is an intriguing and fascinating problem. The genetic material is, as a rule, the same in each cell of an organism. How then do cells, under the influence of their common genes, produce spatial patterns Simple models are discussed that describe the generation of patterns out of an initially nearly homogeneous state. They are based on nonlinear interactions of at least two chemicals and on their diffusion. The concepts of local autocatalysis and of long-range inhibition play a fundamental role. Numerical simulations show that the models account for many basic biological observations such as the regeneration of a pattern after excision of tissue or the production of regular (or nearly regular) arrays of organs during (or after) completion of growth. Very complex patterns can be generated in a reproducible way by hierarchical coupling of several such elementary reactions. Applications to animal coats and to the generation of polygonally shaped patterns are provided. It is further shown how to generate a strictly periodic pattern of units that themselves exhibit a complex and polar fine structure. This is illustrated by two examples: the assembly of photoreceptor cells in the eye of [ital Drosophila] and the positioning of leaves and axillary buds in a growing shoot. In both cases, the substructures have to achieve an internal polarity under the influence of some primary pattern-forming system existing in the fly's eye or in the plant. The fact that similar models can describe essential steps in organisms as distantly related as animals and plants suggests that they reveal some universal mechanisms.

  15. Pattern formation of underwater sand ripples with a skewed drive.

    PubMed

    Bundgaard, F; Ellegaard, C; Scheibye-Knudsen, K; Bohr, T; Sams, T

    2004-12-01

    In this paper we present an experimental study of the dynamics of underwater sand ripples when a regular pattern of ripples is subjected to a skewed oscillatory flow, i.e., one not perpendicular to the direction of the ripple crests. Striking patterns with new, superposed ripples on top of the original ones occur very quickly with a characteristic angle, which is, in general, not perpendicular to the flow. A slower, more complex transition then follows, leading to the final state where the ripples are again perpendicular to the flow. We investigate the variation of the superposed pattern as a function of the direction, amplitude, and frequency of the drive, and as a function of the viscosity (by changing the temperature). We quantify the dynamics of the entire transition process and finally study the grain motion around idealized (solid) skewed ripples. This leads to a characteristic mean path of a single particle. The path has a shape close to a parallelogram, with no apparent connection to the pattern of real, superposed ripples. On the other hand, a thin layer of sand sprinkled on the solid ripples leads to qualitatively similar patterns. PMID:15697484

  16. Characteristics of pattern formation and evolution in approximations of Physarum transport networks.

    PubMed

    Jones, Jeff

    2010-01-01

    Most studies of pattern formation place particular emphasis on its role in the development of complex multicellular body plans. In simpler organisms, however, pattern formation is intrinsic to growth and behavior. Inspired by one such organism, the true slime mold Physarum polycephalum, we present examples of complex emergent pattern formation and evolution formed by a population of simple particle-like agents. Using simple local behaviors based on chemotaxis, the mobile agent population spontaneously forms complex and dynamic transport networks. By adjusting simple model parameters, maps of characteristic patterning are obtained. Certain areas of the parameter mapping yield particularly complex long term behaviors, including the circular contraction of network lacunae and bifurcation of network paths to maintain network connectivity. We demonstrate the formation of irregular spots and labyrinthine and reticulated patterns by chemoattraction. Other Turing-like patterning schemes were obtained by using chemorepulsion behaviors, including the self-organization of regular periodic arrays of spots, and striped patterns. We show that complex pattern types can be produced without resorting to the hierarchical coupling of reaction-diffusion mechanisms. We also present network behaviors arising from simple pre-patterning cues, giving simple examples of how the emergent pattern formation processes evolve into networks with functional and quasi-physical properties including tensionlike effects, network minimization behavior, and repair to network damage. The results are interpreted in relation to classical theories of biological pattern formation in natural systems, and we suggest mechanisms by which emergent pattern formation processes may be used as a method for spatially represented unconventional computation. PMID:20067403

  17. Mathematical study on robust tissue pattern formation in growing epididymal tubule.

    PubMed

    Hirashima, Tsuyoshi

    2016-10-21

    Tissue pattern formation during development is a reproducible morphogenetic process organized by a series of kinetic cellular activities, leading to the building of functional and stable organs. Recent studies focusing on mechanical aspects have revealed physical mechanisms on how the cellular activities contribute to the formation of reproducible tissue patterns; however, the understanding for what factors achieve the reproducibility of such patterning and how it occurs is far from complete. Here, I focus on a tube pattern formation during murine epididymal development, and show that two factors influencing physical design for the patterning, the proliferative zone within the tubule and the viscosity of tissues surrounding to the tubule, control the reproducibility of epididymal tubule pattern, using a mathematical model based on experimental data. Extensive numerical simulation of the simple mathematical model revealed that a spatially localized proliferative zone within the tubule, observed in experiments, results in more reproducible tubule pattern. Moreover, I found that the viscosity of tissues surrounding to the tubule imposes a trade-off regarding pattern reproducibility and spatial accuracy relating to the region where the tubule pattern is formed. This indicates an existence of optimality in material properties of tissues for the robust patterning of epididymal tubule. The results obtained by numerical analysis based on experimental observations provide a general insight on how physical design realizes robust tissue pattern formation. PMID:27396360

  18. Effect of gel network on pattern formation in the ferrocyanide-iodate-sulfite reaction.

    PubMed

    Ueno, Tomonaga; Yoshida, Ryo

    2011-06-01

    Stationary patterns have been researched experimentally since the discovery of the Turing pattern in the chlorite-iodide-malonic acid (CIMA) reaction and the self-replicating spot pattern in the ferrocyanide-iodate-sulfite (FIS) reaction. In this study, we reproduced the pattern formation in the FIS reaction by using poly(acrylamide) gels. Gels with different swelling ratios were prepared to use as a medium. The effect of the swelling ratio was compared with the effect of thickness. It was found that the swelling ratio greatly influenced pattern formation. Oscillating spot patterns appeared at high swelling ratios, and lamellar patterns appeared at a low swelling ratio. Self-replicating spot patterns appeared in between the two areas. The front velocities, which were observed in the initial stage of pattern formation, depended on the swelling ratio. Furthermore, this dependence obeys the free volume theory of diffusion. These results provide evidence that the change in front velocities is caused by a change in diffusion. Pattern formation can be controlled not only by thickness but also by swelling ratio, which may be useful for creating novel pattern templates. PMID:21557556

  19. Delayed inhaled carbon monoxide mediates the regression of established neointimal lesions

    PubMed Central

    Madigan, Michael; Entabi, Fateh; Zuckerbraun, Brian; Loughran, Patricia; Tzeng, Edith

    2014-01-01

    Objective Intimal hyperplasia (IH) contributes to the failure of vascular interventions. While many investigational therapies inhibit the development of IH in animal models, few of these potential therapies can reverse established lesions. Inhaled carbon monoxide (CO) dramatically inhibits IH in both rats and pigs when given peri-operatively. It also prevented the development of pulmonary arterial hypertension in rodents. Interestingly, CO could reverse pulmonary artery structural changes and right heart hemodynamic changes when administered after the establishment of pulmonary hypertension. Thus, we hypothesize that inhaled CO may mediate the regression of established neointimal lesions. Methods Rats underwent carotid artery balloon angioplasty injury. Carotid arteries were collected at 2 and 4 weeks after injury for morphometric analysis of the neointima. Another group was treated with inhaled CO (250 PPM) for 1 hour daily from week 2 until week 4. Additional rats were sacrificed 3 days after initiating CO treatment and the carotid arteries were examined for apoptosis by TUNEL, proliferation by Ki67 staining, and autophagy by LC3 I/II staining. Results At 2 weeks following injury, sizable neointimal lesions had developed (intimal/media = 0.92 ± 0.22). By 4 weeks, lesion size remained stable (0.80 ± 0.09). Delayed inhaled CO treatment greatly reduced neointimal lesion size versus the 2 and 4 week control mice (0.38 ± 0.05, p <0.05). Arteries from the CO treated rats exhibited significantly reduced apoptosis compared to control vessels (3.18 ± 1.94% vs 16.26 ± 5.91%; p = 0.036). Proliferation was also dramatically reduced in the CO treated animals (2.98 ± 1.55 vs 10.37 ± 2.80; p = 0.036). No difference in autophagy between control and CO treated rats was detected. Conclusion Delayed administration of inhaled CO reduced established neointimal lesion size. This effect was mediated by the antiproliferative effect of CO on medial and intimal smooth muscle cells

  20. Neointimal hyperplasia persists at six months after sirolimus-eluting stent implantation in diabetic porcine

    PubMed Central

    Zhang, Qi; Lu, Lin; Pu, LiJin; Zhang, RuiYan; Shen, Jie; Zhu, ZhengBing; Hu, Jian; Yang, ZhenKun; Chen, QiuJin; Shen, WeiFeng

    2007-01-01

    Background Observational clinical studies have shown that patients with diabetes have less favorable results after percutaneous coronary intervention compared with the non-diabetic counterparts, but its mechanism remains unclear. The aim of this study was to examine the changes of neointimal hyperplasia after sirolimus-eluting stent (SES) implantation in a diabetic porcine model, and to evaluate the impact of aortic inflammation on this proliferative process. Methods Diabetic porcine model was created with an intravenous administration of a single dose of streptozotocin in 15 Chinese Guizhou minipigs (diabetic group); each of them received 2 SES (Firebird, Microport Co, China) implanted into 2 separated major epicardial coronary arteries. Fifteen non-diabetic minipigs with SES implantation served as controls (control group). At 6 months, the degree of neointimal hyperplasia was determined by repeat coronary angiography, intravascular ultrasound (IVUS) and histological examination. Tumor necrosis factor (TNF)-α protein level in the aortic intima was evaluated by Western blotting, and TNF-α, interleukin (IL)-1β and IL-6 mRNA levels were assayed by reverse transcription and polymerase chain reaction. Results The distribution of stented vessels, diameter of reference vessels, and post-procedural minimal lumen diameter were comparable between the two groups. At 6-month follow-up, the degree of in-stent restenosis (40.4 ± 24.0% vs. 20.2 ± 17.7%, p < 0.05), late lumen loss (0.33 ± 0.19 mm vs. 0.10 ± 0.09 mm, p < 0.001) by quantitative angiography, percentage of intimal hyperplasia in the stented area (26.7 ± 19.2% vs. 7.3 ± 6.1%, p < 0.001) by IVUS, and neointimal area (1.59 ± 0.76 mm2 vs. 0.41 ± 0.18 mm2, p < 0.05) by histological examination were significantly exacerbated in the diabetic group than those in the controls. Significant increases in TNF-α protein and TNF-α, IL-1β and IL-6 mRNA levels were observed in aortic intima in the diabetic group

  1. Pattern formation in solutal convection: vermiculated rolls and isolated cells

    NASA Astrophysics Data System (ADS)

    Cartwright, Julyan H. E.; Piro, Oreste; Villacampa, Ana I.

    2002-11-01

    Observations of the peculiar behaviour of a drink of liqueur topped with cream led us to perform experiments showing that the instability is a convection phenomenon that arises through destabilizing surface-tension forces. The convection is solutal: driven by gradients of concentration of a solute, rather than by heat gradients as in the more commonly studied thermal convection. The convective patterns, vermiculated rolls and isolated cells, are quite unlike the usual planforms. They are associated with an elastic surface film, and the Marangoni number is high, characteristic of solutal convection. We have conducted further experiments that reproduce these patterns in simpler working fluids.

  2. LETTER: Self-organized pattern formation and noise-induced control based on particle computations

    NASA Astrophysics Data System (ADS)

    Rohlf, Thimo; Bornholdt, Stefan

    2005-12-01

    We propose a new non-equilibrium model for spatial pattern formation based on local information transfer. Unlike most standard models of pattern formation it is not based on the Turing instability or initially laid down morphogen gradients. Information is transmitted through the system via particle-like excitations whose collective dynamics results in pattern formation and control. Here, a simple problem of domain formation is addressed by means of this model in an implementation as stochastic cellular automata, and then generalized to a system of coupled dynamical networks. One observes stable pattern formation, even in the presence of noise and cell flow. Noise contributes through the production of quasi-particles to de novo pattern formation as well as to robust control of the domain boundary position. Pattern proportions are scale independent as regards system size. The dynamics of pattern formation is stable over large parameter ranges, with a discontinuity at vanishing noise and a second-order phase transition at increased cell flow.

  3. Neutrophil-derived cathelicidin protects from neointimal hyperplasia

    PubMed Central

    Soehnlein, Oliver; Wantha, Sarawuth; Simsekyilmaz, Sakine; Döring, Yvonne; Megens, Remco T. A.; Mause, Sebastian F.; Drechsler, Maik; Smeets, Ralf; Weinandy, Stefan; Schreiber, Fabian; Gries, Thomas; Jockenhoevel, Stefan; Möller, Martin; Vijayan, Santosh; van Zandvoort, Marc A. M. J.; Agerberth, Birgitta; Pham, Christine T.; Gallo, Richard L.; Hackeng, Tilman M.; Liehn, Elisa A.; Zernecke, Alma; Klee, Doris; Weber, Christian

    2011-01-01

    Percutaneous transluminal angioplasty with stent implantation is used to dilate of arteries narrowed by atherosclerotic plaques and to revascularize coronary arteries occluded by atherothrombosis in myocardial infarction. Commonly applied drug-eluting stents release anti-proliferative or anti-inflammatory agents to reduce the incidence of in-stent stenosis. However, these stents may lead to in-stent stenosis and increase the rate late stent thrombosis, an obstacle to optimal revascularization possibly related to endothelial recovery. Here we examined the contribution of neutrophils and neutrophilic granule proteins to arterial healing after injury. We found that neutrophil-born cathelicidin (mouse CRAMP, human LL-37) promoted re-endothelization and thereby limited neointima formation after stent implantation. We then translated these findings, generating a neutrophil-instructing biofunctionalized miniaturized Nitinol stent coated with LL-37. This stent reduced in-stent stenosis in a mouse model of atherosclerosis, suggesting that LL-37 may promote vascular healing after interventional therapy. PMID:21974936

  4. Pattern formation in the wake of triggered pushed fronts

    NASA Astrophysics Data System (ADS)

    Goh, Ryan; Scheel, Arnd

    2016-08-01

    Pattern-forming fronts are often controlled by an external stimulus which progresses through a stable medium at a fixed speed, rendering it unstable in its wake. By controlling the speed of excitation, such stimuli, or ‘triggers’, can mediate pattern forming fronts which freely invade an unstable equilibrium and control which pattern is selected. In this work, we analytically and numerically study when the trigger perturbs an oscillatory pushed free front. In such a situation, the resulting patterned front, which we call a pushed trigger front, exhibits a variety of phenomenon, including snaking, non-monotonic wave-number selection, and hysteresis. Assuming the existence of a generic oscillatory pushed free front, we use heteroclinic bifurcation techniques to prove the existence of trigger fronts in an abstract setting motivated by the spatial dynamics approach. We then derive a leading order expansion for the selected wave-number in terms of the trigger speed. Furthermore, we show that such a bifurcation curve is governed by the difference of certain strong-stable and weakly-stable spatial eigenvalues associated with the decay of the free pushed front. We also study prototypical examples of these phenomena in the cubic-quintic complex Ginzburg Landau equation and a modified Cahn–Hilliard equation.

  5. Pattern Formations in Polymer-Molecular Motor Networks

    NASA Astrophysics Data System (ADS)

    Smith, David; Humphrey, David; Duggan, Cynthia; Käs, Josef

    2001-03-01

    In previous studies with the microtubule-kinesin system, organized patterns such as asters and rotating vortices have been seen (Nedelec et al, Nature 1997), which were of a dynamic nature and dependent on active motors. A similar system was constructed using actin and myosin, which displays similar patterns, however, with drastically different dynamics. These patterns arise independent of the initial amount of immediate use energy (in the form of ATP), assembling only upon the near exhaustion of available ATP. Further studies have clearly shown that in fact these patterns are not dependent upon the motor activity of the myosin but its propensity to serve as a cross-linking element in an actin network, with the motor activity serving to prevent the arising of order in the system. We believe the dynamic differences inherent between the two polymer-motor systems studied lies primarily in the structural nature of the motor complexes, with the kinesin complex ordering the system by pushing multiple filaments in a parallel direction, and the myosin complexes disordering the system by pushing filaments in an antiparallel manner.

  6. Temporal control of self-organized pattern formation without morphogen gradients in bacteria

    PubMed Central

    Payne, Stephen; Li, Bochong; Cao, Yangxiaolu; Schaeffer, David; Ryser, Marc D; You, Lingchong

    2013-01-01

    Diverse mechanisms have been proposed to explain biological pattern formation. Regardless of their specific molecular interactions, the majority of these mechanisms require morphogen gradients as the spatial cue, which are either predefined or generated as a part of the patterning process. However, using Escherichia coli programmed by a synthetic gene circuit, we demonstrate here the generation of robust, self-organized ring patterns of gene expression in the absence of an apparent morphogen gradient. Instead of being a spatial cue, the morphogen serves as a timing cue to trigger the formation and maintenance of the ring patterns. The timing mechanism enables the system to sense the domain size of the environment and generate patterns that scale accordingly. Our work defines a novel mechanism of pattern formation that has implications for understanding natural developmental processes. PMID:24104480

  7. Waves and patterning in developmental biology: vertebrate segmentation and feather bud formation as case studies

    PubMed Central

    Baker, Ruth E.; Schnell, Santiago; Maini, Philip K.

    2014-01-01

    In this article we will discuss the integration of developmental patterning mechanisms with waves of competency that control the ability of a homogeneous field of cells to react to pattern forming cues and generate spatially heterogeneous patterns. We base our discussion around two well known patterning events that take place in the early embryo: somitogenesis and feather bud formation. We outline mathematical models to describe each patterning mechanism, present the results of numerical simulations and discuss the validity of each model in relation to our example patterning processes. PMID:19557684

  8. Effect of Salt Concentration on the Pattern Formation of Colloidal Suspension

    NASA Astrophysics Data System (ADS)

    Ma, Wenjie; Wang, Yuren

    We study the effect of salt concentration on the drying process and pattern of thin liquid layer colloidal suspension. Panasonic camera is used to capture the drying process and macroscopic pattern. Microscopic patterns are analyzed by optical microscopy. It is shown that broad-ring pattern is avoided by adding little amount of sodium chloide into colloidal suspension. with the increase of salt concentraion, convection strength and interface instability are weakened, thus the edge of film becomes smooth and more homogeneous film forms. Beautiful microscopic patterns demonstrate that the cooperative interaction between sodium chloide and silica spheres has important influence on the pattern formation.

  9. MicroRNA-30 inhibits neointimal hyperplasia by targeting Ca2+/calmodulin-dependent protein kinase IIδ (CaMKIIδ)

    PubMed Central

    Liu, Yong Feng; Spinelli, Amy; Sun, Li-Yan; Jiang, Miao; Singer, Diane V.; Ginnan, Roman; Saddouk, Fatima Z.; Van Riper, Dee; Singer, Harold A.

    2016-01-01

    The multifunctional Ca2+/calmodulin-dependent protein kinase II δ-isoform (CaMKIIδ) promotes vascular smooth muscle (VSM) proliferation, migration, and injury-induced vascular wall neointima formation. The objective of this study was to test if microRNA-30 (miR-30) family members are endogenous regulators of CaMKIIδ expression following vascular injury and whether ectopic expression of miR-30 can inhibit CaMKIIδ-dependent VSM cell function and neointimal VSM hyperplasia induced by vascular injury. The CaMKIIδ 3′UTR contains a consensus miR-30 binding sequence that is highly conserved across species. A significant decrease in miR-30 family members and increase in CaMKIIδ2 protein expression, with no change in CaMKIIδ mRNA expression, was observed in medial layers of VSM 7 days post-injury. In vitro, overexpression of miR-30c or miR-30e inhibited CaMKIIδ2 protein expression by ~50% in cultured rat aortic VSM cells, and inhibited VSM cell proliferation and migration. In vivo, lenti-viral delivery of miR-30c into injured rat carotid arteries prevented the injury-induced increase in CaMKIIδ2. Furthermore, neointima formation was dramatically inhibited by lenti-viral delivery of miR-30c in the injured medial smooth muscle. These studies define a novel mechanism for regulating CaMKIIδ expression in VSM and provide a new potential therapeutic strategy to reduce progression of vascular proliferative diseases, including atherosclerosis and restenosis. PMID:27199283

  10. Pattern formation induced by a differential Poiseuille flow

    NASA Astrophysics Data System (ADS)

    Stucchi, L.; Vasquez, D. A.

    2014-12-01

    Differential advection, where a reactant is advected while another one is immobilized, leads to instabilities in reaction-advection-diffusion systems. In particular, a homogeneous steady state looses stability for strong enough flows, leading to chemical patterns moving in the direction of the flow. In this paper we study the effects of differential advection due to a two-dimensional Poiseuille flow. We carry out a linear stability analysis on a homogeneous state using an activator-inhibitor reaction. We find that shear dispersion induced by the Poiseuille flow may lead to instabilities at slower flow rates. We find that contrary to the one-dimensional system, the instability depends on which substance is advected. We find a critical average flow speed for instability depending on tube size. Numerical solutions of the nonlinear reaction-advection-diffusion result in patterns of constant shape propagating along the tube.

  11. Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly

    PubMed Central

    Moore, Tyler G.; Garzon, Max H.; Deaton, Russell J.

    2015-01-01

    Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are “strong” assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self

  12. Probabilistic Analysis of Pattern Formation in Monotonic Self-Assembly.

    PubMed

    Moore, Tyler G; Garzon, Max H; Deaton, Russell J

    2015-01-01

    Inspired by biological systems, self-assembly aims to construct complex structures. It functions through piece-wise, local interactions among component parts and has the potential to produce novel materials and devices at the nanoscale. Algorithmic self-assembly models the product of self-assembly as the output of some computational process, and attempts to control the process of assembly algorithmically. Though providing fundamental insights, these computational models have yet to fully account for the randomness that is inherent in experimental realizations, which tend to be based on trial and error methods. In order to develop a method of analysis that addresses experimental parameters, such as error and yield, this work focuses on the capability of assembly systems to produce a pre-determined set of target patterns, either accurately or perhaps only approximately. Self-assembly systems that assemble patterns that are similar to the targets in a significant percentage are "strong" assemblers. In addition, assemblers should predominantly produce target patterns, with a small percentage of errors or junk. These definitions approximate notions of yield and purity in chemistry and manufacturing. By combining these definitions, a criterion for efficient assembly is developed that can be used to compare the ability of different assembly systems to produce a given target set. Efficiency is a composite measure of the accuracy and purity of an assembler. Typical examples in algorithmic assembly are assessed in the context of these metrics. In addition to validating the method, they also provide some insight that might be used to guide experimentation. Finally, some general results are established that, for efficient assembly, imply that every target pattern is guaranteed to be assembled with a minimum common positive probability, regardless of its size, and that a trichotomy exists to characterize the global behavior of typical efficient, monotonic self-assembly systems

  13. Relation of Internal Elastic Lamellar Layer Disruption to Neointimal Cellular Proliferation and Type III Collagen Deposition in Human Peripheral Artery Restenosis.

    PubMed

    Krishnan, Prakash; Purushothaman, K-Raman; Purushothaman, Meerarani; Baber, Usman; Tarricone, Arthur; Vasquez, Miguel; Wiley, Jose; Kini, Annapoorna; Sharma, Samin K; O'Connor, William N; Moreno, Pedro R

    2016-04-01

    Smooth muscle cell proliferation and extracellular matrix formation are responsible for disease progression in de novo and restenotic atherosclerosis. Internal elastic lamella (IEL) layer maintains the structural integrity of intima, and disruption of IEL may be associated with alterations in neointima, type III collagen deposition, and lesion progression in restenosis. Nineteen restenotic plaques (12 patients) procured during peripheral interventions were compared with 13 control plaques (12 patients) without restenosis. Hematoxylin & Eosin and elastic trichrome stains were used to measure length and percentage of IEL disruption, cellularity, and inflammation score. Type I and III collagens, smooth muscle cell (smc), fibroblast density, and nuclear proliferation (Ki67) percentage were evaluated by immunohistochemistry. IEL disruption percentage (28 ± 3.6 vs 6.1 ± 2.4; p = 0.0006), type III collagen content (0.33 ± 0.06 vs 0.17 ± 0.07; p = 0.0001), smc density (2014 ± 120 vs 923 ± 150; p = 0.0001), fibroblast density (2,282 ± 297 vs 906 ± 138; p = 0.0001), and Ki67 percentage (21.6 ± 2 vs 8.2 ± 0.65; p = 0.0001) were significantly increased in restenotic plaques compared to de novo plaques. Logistic regression analysis identified significant correlation between IEL disruption and neointimal smc density (r = 0.45; p = 0.01) and with type III collagen deposition (r = 0.61; p = 0.02) in restenosis. Increased IEL disruption may trigger cellular proliferation, altering collagen production, and enhancing restenotic neointima. In conclusion, understanding the pathologic and molecular basis of restenosis and meticulous-guided interventions oriented to minimize IEL damage may aid to reduce neointimal proliferation and the occurrence of restenosis. PMID:26857165

  14. Self-organized pattern formation in motor-microtubule mixtures

    NASA Astrophysics Data System (ADS)

    Sankararaman, Sumithra; Menon, Gautam I.; Sunil Kumar, P. B.

    2004-09-01

    We model the stable self-organized patterns obtained in the nonequilibrium steady states of mixtures of molecular motors and microtubules. In experiments [Nédélec , Nature (London) 389, 305 (1997); Surrey , Science 292, 1167 (2001)] performed in a quasi-two-dimensional geometry, microtubules are oriented by complexes of motor proteins. This interaction yields a variety of patterns, including arrangements of asters, vortices, and disordered configurations. We model this system via a two-dimensional vector field describing the local coarse-grained microtubule orientation and two scalar density fields associated to molecular motors. These scalar fields describe motors which either attach to and move along microtubules or diffuse freely within the solvent. Transitions between single aster, spiral, and vortex states are obtained as a consequence of confinement, as parameters in our model are varied. For systems in which the effects of confinement can be neglected, we present a map of nonequilibrium steady states, which includes arrangements of asters and vortices separately as well as aster-vortex mixtures and fully disordered states. We calculate the steady state distribution of bound and free motors in aster and vortex configurations of microtubules and compare these to our simulation results, providing qualitative arguments for the stability of different patterns in various regimes of parameter space. We study the role of crowding or “saturation” effects on the density profiles of motors in asters, discussing the role of such effects in stabilizing single asters. We also comment on the implications of our results for experiments.

  15. Pattern formation in Dictyostelium discoideum aggregates in confined microenvironments

    NASA Astrophysics Data System (ADS)

    Hallou, Adrien; Hersen, Pascal; di Meglio, Jean-Marc; Kabla, Alexandre

    Dictyostelium Discoideum (Dd) is often viewed as a model system to study the complex collective cell behaviours which shape an embryo. Under starvation, Dd cells form multicellular aggregates which soon elongate, starting to display an anterior-posterior axis by differentiating into two distinct cell populations; prestalk (front) and prespore (rear) cells zones. Different models, either based on positional information or on differentiation followed up by cell sorting, have been proposed to explain the origin and the regulation of this spatial pattern.To decipher between the proposed hypotheses, we have developed am experimental platform where aggregates, made of genetically engineered Dd cells to express fluorescent reporters of cell differentiation in either prestalk or prespore cells, are allowed to develop in 20 to 400 μm wide hydrogel channels. Such a setup allows us to both mimic Dd confined natural soil environment and to follow the patterning dynamics using time-lapse microscopy. Tracking cell lineage commitments and positions in space and time, we demonstrate that Dd cells differentiate first into prestalk and prespore cells prior to sorting into an organized spatial pattern on the basis of collective motions based on differential motility and adhesion mechanisms. A. Hallou would like to thank the University of Cambridge for the Award of an ``Oliver Gatty Studentship in Biophysical and Colloid Science''.

  16. Miniaturized pattern formation in elastic films cast on sinusoidally patterned substrates.

    PubMed

    Annepu, Hemalatha; Sarkar, Jayati

    2014-10-21

    The various morphologies that are formed when van der Waals forces or electric field is induced between film cast on a sinusoidal substrate and in contact proximity with a contactor or electrode are studied. Remarkably smaller length scales are achieved (λc < 2.96h) than those obtained with films cast on flat substrates. With van der Waals interactions, the patterns are uniformly formed throughout the film but are not regularly ordered. When electric field is used at critical voltage, more ordered, localized patterns are formed at the zones of large local interaction strengths. When these patterns are evolved by increasing the applied voltage, coexistence of all three phases-cavities, stripes, and columns-is observed throughout the film. The localized patterns that are initially formed vary with the voltage applied and strongly dictate the phases of evolution. A patterned substrate/patterned contactor assembly can be made to operate like its unpatterned counterpart by making the interaction strength same everywhere and yet yield uniform, regularly ordered, highly miniaturized patterns. Such patterns are very useful in various applications like microfluidics; they are formed with great ease and can be morphologically tuned by tuning the externally applied electric field. PMID:25238212

  17. The Dynamics of Visual Experience, an EEG Study of Subjective Pattern Formation

    PubMed Central

    Elliott, Mark A.; Twomey, Deirdre; Glennon, Mark

    2012-01-01

    Background Since the origin of psychological science a number of studies have reported visual pattern formation in the absence of either physiological stimulation or direct visual-spatial references. Subjective patterns range from simple phosphenes to complex patterns but are highly specific and reported reliably across studies. Methodology/Principal Findings Using independent-component analysis (ICA) we report a reduction in amplitude variance consistent with subjective-pattern formation in ventral posterior areas of the electroencephalogram (EEG). The EEG exhibits significantly increased power at delta/theta and gamma-frequencies (point and circle patterns) or a series of high-frequency harmonics of a delta oscillation (spiral patterns). Conclusions/Significance Subjective-pattern formation may be described in a way entirely consistent with identical pattern formation in fluids or granular flows. In this manner, we propose subjective-pattern structure to be represented within a spatio-temporal lattice of harmonic oscillations which bind topographically organized visual-neuronal assemblies by virtue of low frequency modulation. PMID:22292053

  18. Pattern Formation and Growth Kinetics in Eutectic Systems

    SciTech Connect

    Teng, Jing

    2007-01-01

    Growth patterns during liquid/solid phase transformation are governed by simultaneous effects of heat and mass transfer mechanisms, creation of new interfaces, jump of the crystallization units from liquid to solid and their rearrangement in the solid matrix. To examine how the above processes influence the scale of microstructure, two eutectic systems are chosen for the study: a polymeric system polyethylene glycol-p-dibromobenzene (PEG-DBBZ) and a simple molecular system succinonitrile (SCN)-camphor. The scaling law for SCN-camphor system is found to follow the classical Jackson-Hunt model of circular rod eutectic, where the diffusion in the liquid and the interface energy are the main physics governing the two-phase pattern. In contrast, a significantly different scaling law is observed for the polymer system. The interface kinetics of PEG phase and its solute concentration dependence thus have been critically investigated for the first time by directional solidification technique. A model is then proposed that shows that the two-phase pattern in polymers is governed by the interface diffusion and the interface kinetics. In SCN-camphor system, a new branch of eutectic, elliptical shape rodl, is found in thin samples where only one layer of camphor rods is present. It is found that the orientation of the ellipse can change from the major axis in the direction of the thickness to the direction of the width as the velocity and/or the sample thickness is decreased. A theoretical model is developed that predicts the spacing and orientation of the elliptical rods in a thin sample. The single phase growth patterns of SCN-camphor system were also examined with emphasis on the three-dimensional single cell and cell/dendrite transition. For the 3D single cell in a capillary tube, the entire cell shape ahead of the eutectic front can be described by the Saffmann-Taylor finger only at extremely low growth rate. A 3D directional solidification model is developed to

  19. Jamming and pattern formation in models of segregation

    NASA Astrophysics Data System (ADS)

    Rogers, Tim; McKane, Alan J.

    2012-04-01

    We investigate the Schelling model of social segregation, formulated as an intrinsically nonequilibrium system, in which the agents occupy districts (or patches) rather than sites on a grid. We show that this allows the equations governing the dynamical behavior of the model to be derived. Analysis of these equations reveals a jamming transition in the regime of low-vacancy density, and inclusion of a spatial dimension in the model leads to a pattern forming instability. Both of these phenomena exhibit unusual characteristics which may be studied through our approach.

  20. [The physics of pattern formation of liquid interfaces

    SciTech Connect

    Not Available

    1993-01-01

    Energy consumption in fabrication of materials for all applications is process dependent. Improvements in the ability to process materials are of great importance to the DOE mission. This project addresses basic science questions related to the processing of materials and is aimed at understanding growth of interfaces and evolution of patterns on interfaces, both macroscopic and microscopic. Three laboratory experiments are proposed: A study of the changes in patterns available to the growth of a macroscopic interface when that interface is grown over one of a variety of microscopic'' lattices; a study of reversible aggregation of colloidal particles in a mixed solvent, and of the interactions and relaxations of both solvent and suspended particles when thermodynamic conditions are changed for a liquid matrix with suspended particles or fibres; and, an investigation of the sedimentation of particles in a quasi-two-dimensional viscous fluid, with attention both to the dynamics of the flow and to the roughness of the resulting surface of settled particles.

  1. [The physics of pattern formation of liquid interfaces

    SciTech Connect

    Not Available

    1993-05-01

    Energy consumption in fabrication of materials for all applications is process dependent. Improvements in the ability to process materials are of great importance to the DOE mission. This project addresses basic science questions related to the processing of materials and is aimed at understanding growth of interfaces and evolution of patterns on interfaces, both macroscopic and microscopic. Three laboratory experiments are proposed: A study of the changes in patterns available to the growth of a macroscopic interface when that interface is grown over one of a variety of ``microscopic`` lattices; a study of reversible aggregation of colloidal particles in a mixed solvent, and of the interactions and relaxations of both solvent and suspended particles when thermodynamic conditions are changed for a liquid matrix with suspended particles or fibres; and, an investigation of the sedimentation of particles in a quasi-two-dimensional viscous fluid, with attention both to the dynamics of the flow and to the roughness of the resulting surface of settled particles.

  2. Pattern Formation of Bacterial Colonies by Escherichia coli

    NASA Astrophysics Data System (ADS)

    Tokita, Rie; Katoh, Takaki; Maeda, Yusuke; Wakita, Jun-ichi; Sano, Masaki; Matsuyama, Tohey; Matsushita, Mitsugu

    2009-07-01

    We have studied the morphological diversity and change in bacterial colonies, using the bacterial species Escherichia coli, as a function of both agar concentration Ca and nutrient concentration Cn. We observed various colony patterns, classified them into four types by pattern characteristics and established a morphological diagram by dividing it into four regions. They are regions A [diffusion-limited aggregation (DLA)-like], B (Eden-like), C (concentric-ring), and D (fluid-spreading). In particular, we have observed a concentric-ring colony growth for E. coli. We focused on the periodic growth in region C and obtained the following results: (i) A colony grows cyclically with the growing front repeating an advance (migration phase) and a momentary rest (consolidation phase) alternately. (ii) The growth width L and the bulge width W in one cycle decrease asymptotically to certain values, when Ca is increased. (iii) L does not depend on Cn, while W is an increasing function of Cn. Plausible mechanisms are proposed to explain the experimental results, by comparing them with those obtained for other bacterial species such as Proteus mirabilis and Bacillus subtilis.

  3. Pattern formation in the thiourea-iodate-sulfite system: Spatial bistability, waves, and stationary patterns

    NASA Astrophysics Data System (ADS)

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

    2010-06-01

    We present a detailed study of the reaction-diffusion patterns observed in the thiourea-iodate-sulfite (TuIS) reaction, operated in open one-side-fed reactors. Besides spatial bistability and spatio-temporal oscillatory dynamics, this proton autoactivated reaction shows stationary patterns, as a result of two back-to-back Turing bifurcations, in the presence of a low-mobility proton binding agent (sodium polyacrylate). This is the third aqueous solution system to produce stationary patterns and the second to do this through a Turing bifurcation. The stationary pattern forming capacities of the reaction are explored through a systematic design method, which is applicable to other bistable and oscillatory reactions. The spatio-temporal dynamics of this reaction is compared with that of the previous ferrocyanide-iodate-sulfite mixed Landolt system.

  4. Pattern formation in a gene network model with boundary shape dependence

    NASA Astrophysics Data System (ADS)

    Diambra, Luis; da Fontoura Costa, Luciano

    2006-03-01

    A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. Traditionally pattern formation have been modeled mainly using Turing-type mechanisms, where complex patterns arise by symmetry breaking. However, there is a growing experimental evidence that the influence of signals derived from surrounding tissues can contribute to the patterning processes. In this paper, we show that the interplay between the shape of surrounding tissues and a hierarchically organized gene regulatory network can be able to induce stable complex patterns. The rise of these patterns depends strongly on the shape of the surrounding tissues.

  5. Pattern formation in a gene network model with boundary shape dependence.

    PubMed

    Diambra, Luis; Costa, Luciano da Fontoura

    2006-03-01

    A fundamental task in developmental biology is to identify the mechanisms which drive morphogenesis. Traditionally pattern formation have been modeled mainly using Turing-type mechanisms, where complex patterns arise by symmetry breaking. However, there is a growing experimental evidence that the influence of signals derived from surrounding tissues can contribute to the patterning processes. In this paper, we show that the interplay between the shape of surrounding tissues and a hierarchically organized gene regulatory network can be able to induce stable complex patterns. The rise of these patterns depends strongly on the shape of the surrounding tissues. PMID:16605568

  6. Patterns of Family Formation in Response to Sex Ratio Variation.

    PubMed

    Schacht, Ryan; Kramer, Karen L

    2016-01-01

    The impact that unbalanced sex ratios have on health and societal outcomes is of mounting contemporary concern. However, it is increasingly unclear whether it is male- or female-biased sex ratios that are associated with family and social instability. From a socio-demographic perspective, male-biased sex ratios leave many men unable to find a mate, elevating competition among males, disrupting family formation and negatively affecting social stability. In contrast, from a mating-market perspective, males are expected to be less willing to marry and commit to a family when the sex ratio is female-biased and males are rare. Here we use U.S. data to evaluate predictions from these competing frameworks by testing the relationship between the adult sex ratio and measures of family formation. We find that when women are rare men are more likely to marry, be part of a family and be sexually committed to a single partner. Our results do not support claims that male-biased sex ratios lead to negative family outcomes due to a surplus of unmarried men. Rather, our results highlight the need to pay increased attention to female-biased sex ratios. PMID:27556401

  7. Patterns of Family Formation in Response to Sex Ratio Variation

    PubMed Central

    Schacht, Ryan; Kramer, Karen L.

    2016-01-01

    The impact that unbalanced sex ratios have on health and societal outcomes is of mounting contemporary concern. However, it is increasingly unclear whether it is male- or female-biased sex ratios that are associated with family and social instability. From a socio-demographic perspective, male-biased sex ratios leave many men unable to find a mate, elevating competition among males, disrupting family formation and negatively affecting social stability. In contrast, from a mating-market perspective, males are expected to be less willing to marry and commit to a family when the sex ratio is female-biased and males are rare. Here we use U.S. data to evaluate predictions from these competing frameworks by testing the relationship between the adult sex ratio and measures of family formation. We find that when women are rare men are more likely to marry, be part of a family and be sexually committed to a single partner. Our results do not support claims that male-biased sex ratios lead to negative family outcomes due to a surplus of unmarried men. Rather, our results highlight the need to pay increased attention to female-biased sex ratios. PMID:27556401

  8. STELLAR ELEMENTAL ABUNDANCE PATTERNS: IMPLICATIONS FOR PLANET FORMATION

    SciTech Connect

    Chambers, J. E.

    2010-11-20

    The solar photosphere is depleted in refractory elements compared to most solar twins, with the degree of depletion increasing with an element's condensation temperature. Here, I show that adding 4 Earth masses of Earth-like and carbonaceous-chondrite-like material to the solar convection zone brings the Sun's composition into line with the mean value for the solar twins. The observed solar composition could have arisen if the Sun's convection zone accreted material from the solar nebula that was depleted in refractory elements due to the formation of the terrestrial planets and ejection of rocky protoplanets from the asteroid belt. Most solar analogs are missing 0-10 Earth masses of rocky material compared to the most refractory-rich stars, providing an upper limit to the mass of rocky terrestrial planets that they possess. The missing mass is correlated with stellar metallicity. This suggests that the efficiency of planetesimal formation increases with stellar metallicity. Stars with and without known giant planets show a similar distribution of abundance trends. If refractory depletion is a signature of the presence of terrestrial planets, this suggests that there is not a strong correlation between the presence of terrestrial and giant planets in the same system.

  9. Lateral inhibition-induced pattern formation controlled by the size and geometry of the cell.

    PubMed

    Seirin Lee, Sungrim

    2016-09-01

    Pattern formation in development biology is one of the fundamental processes by which cells change their functions. It is based on the communication of cells via intra- and intercellular dynamics of biochemicals. Thus, the cell is directly involved in biochemical interactions. However, many theoretical approaches describing biochemical pattern formation have usually neglected the cell's role or have simplified the subcellular process without considering cellular aspects despite the cell being the environment where biochemicals interact. On the other hand, recent experimental observations suggest that a change in the physical conditions of cell-to-cell contact can result in a change in cell fate and tissue patterning in a lateral inhibition system. Here we develop a mathematical model by which biochemical dynamics can be directly observed with explicitly expressed cell structure and geometry in higher dimensions, and reconsider pattern formation by lateral inhibition of the Notch-Delta signaling pathway. We explore how the physical characteristic of cell, such as cell geometry or size, influences the biochemical pattern formation in a multi-cellular system. Our results suggest that a property based on cell geometry can be a novel mechanism for symmetry breaking inducing cell asymmetry. We show that cell volume can critically influence cell fate determination and pattern formation at the tissue level, and the surface area of the cell-to-cell contact can directly affect the spatial range of patterning. PMID:27229622

  10. Morphology-Induced Collective Behaviors: Dynamic Pattern Formation in Water-Floating Elements

    PubMed Central

    Nakajima, Kohei; Ngouabeu, Aubery Marchel Tientcheu; Miyashita, Shuhei; Göldi, Maurice; Füchslin, Rudolf Marcel; Pfeifer, Rolf

    2012-01-01

    Complex systems involving many interacting elements often organize into patterns. Two types of pattern formation can be distinguished, static and dynamic. Static pattern formation means that the resulting structure constitutes a thermodynamic equilibrium whose pattern formation can be understood in terms of the minimization of free energy, while dynamic pattern formation indicates that the system is permanently dissipating energy and not in equilibrium. In this paper, we report experimental results showing that the morphology of elements plays a significant role in dynamic pattern formation. We prepared three different shapes of elements (circles, squares, and triangles) floating in a water-filled container, in which each of the shapes has two types: active elements that were capable of self-agitation with vibration motors, and passive elements that were mere floating tiles. The system was purely decentralized: that is, elements interacted locally, and subsequently elicited global patterns in a process called self-organized segregation. We showed that, according to the morphology of the selected elements, a different type of segregation occurs. Also, we quantitatively characterized both the local interaction regime and the resulting global behavior for each type of segregation by means of information theoretic quantities, and showed the difference for each case in detail, while offering speculation on the mechanism causing this phenomenon. PMID:22715370

  11. Noise-induced pattern formation in a semiconductor nanostructure.

    PubMed

    Stegemann, G; Balanov, A G; Schöll, E

    2005-01-01

    We investigate the influence of noise upon the dynamics of the current density distribution in a model of a semiconductor nanostructure, namely, a double barrier resonant tunneling diode. We fix the parameters of the device below the Hopf bifurcation, where the only stable state of the system is a spatially inhomogeneous "filamentary" steady state. We show that the addition of weak Gaussian white noise to the system gives rise to spatially inhomogeneous oscillations that can be quite coherent. As the noise intensity grows, the oscillations tend to become more and more spatially homogeneous, while simultaneously the temporal correlation of the oscillations decreases. Thus, while on one hand noise destroys temporal coherence, on the other hand it enhances the spatial coherence of the current density pattern. PMID:15697712

  12. Pattern formation in crystal growth under parabolic shear flow.

    PubMed

    Ueno, K

    2003-08-01

    Morphological instability of the solid-liquid interface occurring in a crystal growing from an undercooled thin liquid bounded on one side by a free surface and flowing down inclined plane, is investigated by a linear stability analysis under shear flow. It is found that restoring forces due to gravity and surface tension is an important factor for stabilization of the solid-liquid interface on long length scales. This is a stabilizing effect different from the Gibbs-Thomson effect. A particular long wavelength mode of about 1 cm of wavy pattern, observed on the surface of icicles covered with a thin layer of flowing water is obtained from the dispersion relation, including the effect of flow and restoring forces. PMID:14524982

  13. Experimental study of pattern formation during carbon dioxide mineralization

    NASA Astrophysics Data System (ADS)

    Schuszter, Gabor; Brau, Fabian; de Wit, Anne

    2015-11-01

    Injection of supercritical carbon dioxide in deep porous aquifers, where mineral carbonation takes place via chemical reactions, is one of the possible long-term storage of this greenhouse gas. This mineralization process is investigated experimentally under controlled conditions in a confined horizontal Hele-Shaw geometry where an aqueous solution of sodium carbonate is injected radially into a solution of calcium chloride. Precipitation of calcium carbonate in various finger, flower or tube-like patterns is observed in the mixing zone between the two solutions. These precipitation structures and their growth dynamics are studied quantitatively as a function of the parameters of the problem, which are the injection rate and the reactant concentrations. In particular, we show the existence of critical concentrations of reactants above which the amount of the calcium carbonate precipitate produced drops significantly.

  14. Prevention of neointimal hyperplasia in balloon-injured rat carotid artery via small interference RNA mediated downregulation of osteopontin gene.

    PubMed

    Xu, Jian; Sun, Yingxian; Wang, Tairan; Liu, Guinan

    2013-05-01

    The aim of the present study was to take osteopontin (OPN) as molecular target to study its effects on injured intima model of carotid artery in rat using perivascular transfer of OPN-small interference RNA (siRNA). OPN mRNA in cultured VSMCs was quantified by real-time RT-PCR, and OPN-siRNA-002 was determined as the most sensitive sequence and used as transfected siRNA in the subsequent animal experiments. We established rat carotid arterial intima-injured model with balloon-injured method, and then perivascularly transfected OPN-siRNA-002 to study the role of OPN-siRNA in regulating several related genes including proliferating cell nuclear antigen (PCNA), transforming growth factor β1(TGF-β1), matrix metalloproteinase-2 (MMP-2), and matrix metalloproteinase-14 (MMP-14), as well as its role in neointimal formation. OPN mRNA and protein decreased about 50 % with corresponding decrease in intima thickness after transfecting with specific OPN-siRNA-002 compared with Pluronic control group and OPN-SCR-siRNA group on each time point (n = 6, p < 0.001), and this inhibiting effects persisted up to 14 days after balloon injury. PCNA, TGF-β1, MMP-2, and MMP-14 mRNA and protein correlated directly with the respective levels of OPN, suggesting its functions via regulating these downstream factors (n = 6, p < 0.001). OPN may be a potential target gene in reducing the risk for arterial restenosis after vascular intervention. PMID:23467880

  15. Formation and control of Turing patterns in a coherent quantum fluid

    PubMed Central

    Ardizzone, Vincenzo; Lewandowski, Przemyslaw; Luk, M. H.; Tse, Y. C.; Kwong, N. H.; Lücke, Andreas; Abbarchi, Marco; Baudin, Emmanuel; Galopin, Elisabeth; Bloch, Jacqueline; Lemaitre, Aristide; Leung, P. T.; Roussignol, Philippe; Binder, Rolf; Tignon, Jerome; Schumacher, Stefan

    2013-01-01

    Nonequilibrium patterns in open systems are ubiquitous in nature, with examples as diverse as desert sand dunes, animal coat patterns such as zebra stripes, or geographic patterns in parasitic insect populations. A theoretical foundation that explains the basic features of a large class of patterns was given by Turing in the context of chemical reactions and the biological process of morphogenesis. Analogs of Turing patterns have also been studied in optical systems where diffusion of matter is replaced by diffraction of light. The unique features of polaritons in semiconductor microcavities allow us to go one step further and to study Turing patterns in an interacting coherent quantum fluid. We demonstrate formation and control of these patterns. We also demonstrate the promise of these quantum Turing patterns for applications, such as low-intensity ultra-fast all-optical switches. PMID:24145394

  16. Formation and control of Turing patterns in a coherent quantum fluid

    NASA Astrophysics Data System (ADS)

    Ardizzone, Vincenzo; Lewandowski, Przemyslaw; Luk, M. H.; Tse, Y. C.; Kwong, N. H.; Lücke, Andreas; Abbarchi, Marco; Baudin, Emmanuel; Galopin, Elisabeth; Bloch, Jacqueline; Lemaitre, Aristide; Leung, P. T.; Roussignol, Philippe; Binder, Rolf; Tignon, Jerome; Schumacher, Stefan

    2013-10-01

    Nonequilibrium patterns in open systems are ubiquitous in nature, with examples as diverse as desert sand dunes, animal coat patterns such as zebra stripes, or geographic patterns in parasitic insect populations. A theoretical foundation that explains the basic features of a large class of patterns was given by Turing in the context of chemical reactions and the biological process of morphogenesis. Analogs of Turing patterns have also been studied in optical systems where diffusion of matter is replaced by diffraction of light. The unique features of polaritons in semiconductor microcavities allow us to go one step further and to study Turing patterns in an interacting coherent quantum fluid. We demonstrate formation and control of these patterns. We also demonstrate the promise of these quantum Turing patterns for applications, such as low-intensity ultra-fast all-optical switches.

  17. The formation of labyrinths, spots and stripe patterns in a biochemical approach to cardiovascular calcification

    NASA Astrophysics Data System (ADS)

    Yochelis, A.; Tintut, Y.; Demer, L. L.; Garfinkel, A.

    2008-05-01

    Calcification and mineralization are fundamental physiological processes, yet the mechanisms of calcification, in trabecular bone and in calcified lesions in atherosclerotic calcification, are unclear. Recently, it was shown in in vitro experiments that vascular-derived mesenchymal stem cells can display self-organized calcified patterns. These patterns were attributed to activator/inhibitor dynamics in the style of Turing, with bone morphogenetic protein 2 acting as an activator, and matrix GLA protein acting as an inhibitor. Motivated by this qualitative activator-inhibitor dynamics, we employ a prototype Gierer-Meinhardt model used in the context of activator-inhibitor-based biological pattern formation. Through a detailed analysis in one and two spatial dimensions, we explore the pattern formation mechanisms of steady state patterns, including their dependence on initial conditions. These patterns range from localized holes to labyrinths and localized peaks, or in other words, from dense to sparse activator distributions (respectively). We believe that an understanding of the wide spectrum of activator-inhibitor patterns discussed here is prerequisite to their biochemical control. The mechanisms of pattern formation suggest therapeutic strategies applicable to bone formation in atherosclerotic lesions in arteries (where it is pathological) and to the regeneration of trabecular bone (recapitulating normal physiological development).

  18. The formation of labyrinths, spots and stripe patterns in a biochemical approach to cardiovascular calcification

    NASA Astrophysics Data System (ADS)

    Yochelis, A.; Tintut, Y.; Demer, L. L.; Garfinkel, A.

    2008-05-01

    Calcification and mineralization are fundamental physiological processes, yet the mechanisms of calcification, in trabecular bone and in calcified lesions in atherosclerotic calcification, are unclear. Recently, it was shown in in vitro experiments that vascular-derived mesenchymal stem cells can display self-organized calcified patterns. These patterns were attributed to activator/inhibitor dynamics in the style of Turing, with bone morphogenetic protein 2 acting as an activator, and matrix GLA protein acting as an inhibitor. Motivated by this qualitative activator inhibitor dynamics, we employ a prototype Gierer Meinhardt model used in the context of activator inhibitor-based biological pattern formation. Through a detailed analysis in one and two spatial dimensions, we explore the pattern formation mechanisms of steady state patterns, including their dependence on initial conditions. These patterns range from localized holes to labyrinths and localized peaks, or in other words, from dense to sparse activator distributions (respectively). We believe that an understanding of the wide spectrum of activator inhibitor patterns discussed here is prerequisite to their biochemical control. The mechanisms of pattern formation suggest therapeutic strategies applicable to bone formation in atherosclerotic lesions in arteries (where it is pathological) and to the regeneration of trabecular bone (recapitulating normal physiological development).

  19. Pattern formation in stromatolites: insights from mathematical modelling

    PubMed Central

    Cuerno, R.; Escudero, C.; García-Ruiz, J. M.; Herrero, M. A.

    2012-01-01

    To this day, computer models for stromatolite formation have made substantial use of the Kardar–Parisi–Zhang (KPZ) equation. Oddly enough, these studies yielded mutually exclusive conclusions about the biotic or abiotic origin of such structures. We show in this paper that, at our current state of knowledge, a purely biotic origin for stromatolites can neither be proved nor disproved by means of a KPZ-based model. What can be shown, however, is that whatever their (biotic or abiotic) origin might be, some morphologies found in actual stromatolite structures (e.g. overhangs) cannot be formed as a consequence of a process modelled exclusively in terms of the KPZ equation and acting over sufficiently large times. This suggests the need to search for alternative mathematical approaches to model these structures, some of which are discussed in this paper. PMID:21993008

  20. Two-dimensional colloidal fluids exhibiting pattern formation

    NASA Astrophysics Data System (ADS)

    Chacko, Blesson; Chalmers, Christopher; Archer, Andrew J.

    2015-12-01

    Fluids with competing short range attraction and long range repulsive interactions between the particles can exhibit a variety of microphase separated structures. We develop a lattice-gas (generalised Ising) model and analyse the phase diagram using Monte Carlo computer simulations and also with density functional theory (DFT). The DFT predictions for the structures formed are in good agreement with the results from the simulations, which occur in the portion of the phase diagram where the theory predicts the uniform fluid to be linearly unstable. However, the mean-field DFT does not correctly describe the transitions between the different morphologies, which the simulations show to be analogous to micelle formation. We determine how the heat capacity varies as the model parameters are changed. There are peaks in the heat capacity at state points where the morphology changes occur. We also map the lattice model onto a continuum DFT that facilitates a simplification of the stability analysis of the uniform fluid.

  1. Genetic oscillations. A Doppler effect in embryonic pattern formation.

    PubMed

    Soroldoni, Daniele; Jörg, David J; Morelli, Luis G; Richmond, David L; Schindelin, Johannes; Jülicher, Frank; Oates, Andrew C

    2014-07-11

    During embryonic development, temporal and spatial cues are coordinated to generate a segmented body axis. In sequentially segmenting animals, the rhythm of segmentation is reported to be controlled by the time scale of genetic oscillations that periodically trigger new segment formation. However, we present real-time measurements of genetic oscillations in zebrafish embryos showing that their time scale is not sufficient to explain the temporal period of segmentation. A second time scale, the rate of tissue shortening, contributes to the period of segmentation through a Doppler effect. This contribution is modulated by a gradual change in the oscillation profile across the tissue. We conclude that the rhythm of segmentation is an emergent property controlled by the time scale of genetic oscillations, the change of oscillation profile, and tissue shortening. PMID:25013078

  2. Formation of periodic and localized patterns in an oscillating granular layer.

    SciTech Connect

    Aranson, I.; Tsimring, L. S.; Materials Science Division; Bar Ilan Univ.; Univ. of California at San Diego

    1998-02-01

    A simple phenomenological model for pattern formation in a vertically vibrated layer of granular particles is proposed. This model exhibits a variety of stable cellular patterns including standing rolls and squares as well as localized excitations (oscillons and worms), similar to recent experimental observations (Umbanhowar et al., 1996). The model is an order parameter equation for the parametrically excited waves coupled to the mass conservation law. The structure and dynamics of the solutions resemble closely the properties of patterns observed in the experiments.

  3. Exploring Formative E-Assessment: Using Case Stories and Design Patterns

    ERIC Educational Resources Information Center

    Daly, Caroline; Pachler, Norbert; Mor, Yishay; Mellar, Harvey

    2010-01-01

    This article presents key findings from a Joint Information Systems Committee-funded project, which aimed to identify existing practices where technologies contribute to formative assessment and identify processes that take place around formative assessment where technologies play a significant role. Using a design pattern methodology, the project…

  4. Structure Formation of Ultrathin PEO Films at Solid Interfaces—Complex Pattern Formation by Dewetting and Crystallization

    PubMed Central

    Braun, Hans-Georg; Meyer, Evelyn

    2013-01-01

    The direct contact of ultrathin polymer films with a solid substrate may result in thin film rupture caused by dewetting. With crystallisable polymers such as polyethyleneoxide (PEO), molecular self-assembly into partial ordered lamella structures is studied as an additional source of pattern formation. Morphological features in ultrathin PEO films (thickness < 10 nm) result from an interplay between dewetting patterns and diffusion limited growth pattern of ordered lamella growing within the dewetting areas. Besides structure formation of hydrophilic PEO molecules, n-alkylterminated (hydrophobic) PEO oligomers are investigated with respect to self-organization in ultrathin films. Morphological features characteristic for pure PEO are not changed by the presence of the n-alkylgroups. PMID:23385233

  5. Instability and pattern formation in electrifield liquid layers

    NASA Astrophysics Data System (ADS)

    Wang, Qiming; Papageorgiou, Demetrios

    2015-11-01

    The stability and axisymmetric deformation of two immiscible, viscous, perfect or leaky dielectric fluids confined in the annulus between two concentric cylinders are studied in the presence of radial electric fields. The fields are set up by imposing a constant voltage potential difference between the inner and outer cylinders. We derive a set of equations for the interface in the long-wavelength approximation which retains the essential physics of the system and allows for interfacial deformations to be as large as the annular gap hence accounting for possible touchdown at the inner or outer electrode. As the layer thickness is asymptotically small, the system recovers the standard (modified) Hammond equation in the absence (presence) of electric fields. For both perfect and leaky dielectric liquids, the full nonlinear system is investigated numerically. It is shown that a two-side touching solution is possible for both the non-electrified and perfect dielectric cases, while only one-side touching is found in the case of leaky dielectric liquids, where the flattened interface shape resembles the pattern solutions found in literature. Meanwhile the finite-time singular solution agrees qualitatively with the experiments.

  6. Things fall apart: Topics in biophysics and pattern formation

    NASA Astrophysics Data System (ADS)

    Betterton, Meredith Diane

    2000-11-01

    This thesis is made up of three distinct projects. Chapter 2 considers the effect of electrostatics on the stability of a charged membrane. We show that at low ionic strength and high surface charge density, repulsion between membrane charges renders it unstable to the formation of holes. An edge is unstable to modulations with wavelength longer than the Debye screening length. Hence at low ionic strength, membranes will disintegrate into vesicles. We use these results-to interpret experiments on stable holes in red blood cell ghosts. Chapter 3 discusses cylindrical chemotactic collapse. Under special conditions bacteria excrete an attractant and aggregate. The high density regions initially collapse into cylindrical structures, which subsequently destabilize into spherical aggregates. We present a theoretical description of this process. We show that cylindrical collapse involves a balance in which bacterial attraction and diffusion nearly cancel, leading to corrections to the collapse laws expected from dimensional analysis. The cylinder instability is composed of two stages: Initially, slow modulations to the cylinder develop, which correspond to a variation of the collapse time along the cylinder axis. Ultimately, one point on the cylinder pinches off. At this final stage, a front propagates from the pinch into the remainder of the cylinder. The spacing of the resulting spherical aggregates is determined by the front propagation. Chapter 4 describes penitentes, columns of snow several meters tall which form on glaciers at high altitudes. They form by reflection of sunlight: depressions in the snow receive more reflected sunlight than the top edges, and therefore melt more quickly. Although this explanation is accepted in the literature, no one has previously formulated a mathematical model of penitente formation. This work models the process, aiming to quantify the ideas in the literature. We describe what size and shape penitentes appear, and how this depends

  7. Spontaneous pattern formation in a thin film of bacteriorhodopsin with mixed absorptive-dispersive nonlinearity

    NASA Astrophysics Data System (ADS)

    Glückstad, J.; Saffman, M.

    1995-03-01

    We have observed the spontaneous formation of transverse spatial patterns in a thin film of bacteriorhodopsin with a feedback mirror. Bacteriorhodopsin has a mixed absorptive-dispersive nonlinearity at the wavelength used in the experiments (633 nm). Threshold values of the incident intensity for observation of pattern formation are found from a linear stability analysis of a model that describes bacteriorhodopsin as a sluggish saturable nonlinear medium with a complex Kerr coefficient. The calculated threshold intensity is in good agreement with the experimental observations, and the patterns are predicted to be frequency offset from the pump radiation.

  8. Towards understanding speckle pattern formation in optical coherence tomography (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Demidov, Valentin; Meglinski, Igor; Doronin, Alexander; Vitkin, I. Alex

    2016-03-01

    We consider the mechanism of speckle patterns formation in time-domain and swept source optical coherence tomography (OCT), and introduce a Monte Carlo based model for simulating OCT signals and images. The model takes into account polarization and coherent properties of light, mutual interference of the back-scattering light, and its interference with the reference beam. The developed model is employed to generate OCT images, and to analyze the resultant OCT speckle pattern properties. The model simulation results are compared with experimental measurements, and an interpretation of the speckle patterns formation in terms of its underlying physics is provided.

  9. One-dimensional pattern of Au nanodots by ion-beam sputtering: formation and mechanism.

    PubMed

    Kim, J-H; Ha, N-B; Kim, J-S; Joe, M; Lee, K-R; Cuerno, R

    2011-07-15

    Highly ordered one-dimensional arrays of nanodots, or nanobeads, are fabricated by forming nanoripples and nanodots in sequence, entirely by ion-beam sputtering (IBS) of Au(001). This demonstrates the capability of IBS for the fabrication of sophisticated nanostructures via hierarchical self-assembly. The intricate nanobead pattern ideally serves to identify the governing mechanisms for the pattern formation: nonlinear effects, especially local redeposition and surface-confined transport, are essential both for the formation and the preservation of the one-dimensional order of the nanobead pattern. PMID:21625038

  10. Formation of spatially patterned colloidal photonic crystals through the control of capillary forces and template recognition.

    PubMed

    Brozell, Adrian M; Muha, Michelle A; Parikh, Atul N

    2005-12-01

    We report the formation of microscopic patterns of substrate-supported, 3D planar colloidal crystals using physical confinement in conjunction with surfaces displaying predetermined binary patterns of hydropholicity. The formation process involves a primary self-assembly wherein nano- and microscale colloids order into a photonic fcc lattice via capillary interactions followed by a secondary template-induced crystal cleavage step. Following this method, arbitrary arrays of pattern elements, which preserve structural and orientational properties of the parent crystal, can be easily obtained. PMID:16316085

  11. Role of metabolic environment on nitric oxide mediated inhibition of neointimal hyperplasia in type 1 and type 2 diabetes.

    PubMed

    Rodriguez, Monica P; Emond, Zachary M; Wang, Zheng; Martinez, Janet; Jiang, Qun; Kibbe, Melina R

    2014-01-30

    Nitric oxide (NO) is well known to inhibit neointimal hyperplasia following arterial injury. Previously, we reported that NO was more effective at inhibiting neointimal hyperplasia in a type 2 diabetic environment than control. We also found that NO was ineffective in an uncontrolled type 1 diabetic environment; however, insulin restored the efficacy of NO. Thus, the goal of this study was to more closely evaluate the effect of insulin and glucose on the efficacy of NO at inhibiting neointimal hyperplasia in both type 1 and type 2 diabetic environments using different doses of insulin as well as pioglitazone. Type 1 diabetes was induced in male lean Zucker (LZ) rats with streptozotocin (60 mg/kg IP). Groups included control, moderate glucose control, and tight glucose control. Zucker diabetic fatty (ZDF) rats fed Purina 5008 chow were used as a type 2 diabetic model. Groups included no therapy, insulin therapy, or pioglitazone therapy. After 4 weeks of maintaining group assignments, the carotid artery injury model was performed. Treatment groups included: control, injury and injury plus NO. 2 weeks following arterial injury, in the type 1 diabetic rats, NO most effectively reduced the neointimal area in the moderate and tightly controlled groups (81% and 88% vs. 33%, respectively, p=0.01). In type 2 diabetic rats, the metabolic environment had no impact on the efficacy of NO (81-82% reduction for all groups). Thus, in this study, we show NO is effective at inhibiting neointimal hyperplasia in both type 1 and type 2 diabetic environments. A greater understanding of how the metabolic environment may impact the efficacy of NO may lead to the development of more effective NO-based therapies for patients with diabetes. PMID:24333562

  12. Pattern Formation and Reaction Textures during Dunite Carbonation

    NASA Astrophysics Data System (ADS)

    Lisabeth, H. P.; Zhu, W.

    2015-12-01

    Alteration of olivine-bearing rocks by fluids is one of the most pervasive geochemical processes on the surface of the Earth. Serpentinized and/or carbonated ultramafic rocks often exhibit characteristic textures on many scales, from polygonal mesh textures on the grain-scale to onion-skin or kernel patterns on the outcrop scale. Strong disequilibrium between pristine ultramafic rocks and common geological fluids such as water and carbon dioxide leads to rapid reactions and coupled mechanical and chemical feedbacks that manifest as characteristic textures. Textural evolution during metasomatic reactions can control effective reaction rates by modulating dynamic porosity and therefore reactant supply and reactive surface area. We run hydrostatic experiments on thermally cracked dunites saturated with carbon dioxide bearing brine at 15 MPa confining pressure and 150°C to explore the evolution of physical properties and reaction textures as carbon mineralization takes place in the sample. Compaction and permeability reduction are observed throughout experiments. Rates of porosity and permeability changes are sensitive to pore fluid chemistry. After reaction, samples are imaged in 3-dimension (3D) using a dual-beam FIB-SEM. Analysis of the high resolution 3D microstructure shows that permeable, highly porous domains are created by olivine dissolution at a characteristic distance from pre-existing crack surfaces while precipitation of secondary minerals such as serpentine and magnesite is limited largely to the primary void space. The porous dissolution channels provide an avenue for fluid ingress, allow reactions to continue and could lead to progressive hierarchical fracturing. Initial modeling of the system indicates that this texture is the result of coupling between dissolution-precipitation reactions and the local stress state of the sample.

  13. Dependence of Initial Value on Pattern Formation for a Logistic Coupled Map Lattice

    PubMed Central

    Xu, Li; Zhang, Guang; Cui, Haoyue

    2016-01-01

    The logistic coupled map lattices (LCML) have been widely investigated as well as their pattern dynamics. The patterns formation may depend on not only fluctuations of system parameters, but variation of the initial conditions. However, the mathematical discussion is quite few for the effect of initial values so far. The present paper is concerned with the pattern formation for a two-dimensional Logistic coupled map lattice, where any initial value can be linear expressed by corresponding eigenvectors, and patterns formation can be determined by selecting the corresponding eigenvectors. A set of simulations are conducted whose results demonstrate the fact. The method utilized in the present paper could be applied to other discrete systems as well. PMID:27382964

  14. Pattern formation in vibrated beds of dry and wet granular materials

    NASA Astrophysics Data System (ADS)

    Chuan Lim, Eldin Wee

    2014-01-01

    The Discrete Element Method was coupled with a capillary liquid bridge force model for computational studies of pattern formation in vibrated granular beds containing dry or wet granular materials. Depending on the vibration conditions applied, hexagonal, stripes, or cellular pattern was observed in the dry vibrated granular bed. In each of these cases, the same hexagonal, stripes, or cellular pattern was also observed in the spatial distribution of the magnitudes of particle-particle collision forces prior to the formation of the corresponding actual pattern in physical distributions of the particles. This seemed to suggest that the pattern formation phenomenon of vibrated granular bed systems might be the result of a two-dimensional Newton's cradle effect. In the presence of a small amount of wetness, these patterns were no longer formed in the vibrated granular beds under the same corresponding set of vibration conditions. Despite the relatively much weaker capillary forces arising from the simulated liquid bridges between particles compared with particle-particle collision forces, the spatial distributions of these collision forces, physical distributions of particles, as well as time profiles of average collision forces were altered significantly in comparison with the corresponding distributions and profiles observed for the dry vibrated granular beds. This seemed to suggest the presence of a two-dimensional Stokes' cradle effect in these wet vibrated granular bed systems which disrupted the formation of patterns in the wet granular materials that would have been observed in their dry counterparts.

  15. Pattern formation during gastrulation in the sea urchin embryo.

    PubMed

    McClay, D R; Armstrong, N A; Hardin, J

    1992-01-01

    The sea urchin embryo follows a relatively simple cell behavioral sequence in its gastrulation movements. To form the mesoderm, primary mesenchyme cells ingress from the vegetal plate and then migrate along the basal lamina lining the blastocoel. The presumptive secondary mesenchyme and endoderm then invaginate from the vegetal pole of the embryo. The archenteron elongates and extends across the blastocoel until the tip of the archenteron touches and attaches to the opposite side of the blastocoel. Secondary mesenchyme cells, originally at the tip of the archenteron, differentiate to form a variety of structures including coelomic pouches, esophageal muscles, pigment cells and other cell types. After migration of the secondary mesenchyme cells from their original position at the tip of the archenteron, the endoderm fuses with an invagination of the ventral ectoderm (the stomodaem), to form the mouth and complete the process of gastrulation. A larval skeleton is made by primary mesenchyme cells during the time of archenteron and mouth formation. A number of experiments have established that these morphogenetic movements involve a number of cell autonomous behaviors plus a series of cell interactions that provide spatial, temporal and scalar information to cells of the mesoderm and endoderm. The cell autonomous behaviors can be demonstrated by the ability of micromeres or endoderm to perform their morphogenetic functions if either is isolated and grown in culture. The requirement for cell interactions has been demonstrated by manipulative experiments where it has been shown that axial information, temporal information, spatial information and scalar information is obtained by mesoderm and endoderm from other embryonic cells.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1299366

  16. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes.

    PubMed

    Hannezo, Edouard; Dong, Bo; Recho, Pierre; Joanny, Jean-François; Hayashi, Shigeo

    2015-07-14

    An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. PMID:26077909

  17. Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes

    PubMed Central

    Hannezo, Edouard; Dong, Bo; Recho, Pierre; Joanny, Jean-François; Hayashi, Shigeo

    2015-01-01

    An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. PMID:26077909

  18. Pattern formation through spatial interactions in a modified Daisyworld model

    NASA Astrophysics Data System (ADS)

    Alberti, Tommaso; Primavera, Leonardo; Lepreti, Fabio; Vecchio, Antonio; Carbone, Vincenzo

    2015-04-01

    The Daisyworld model is based on a hypothetical planet, like the Earth, which receives the radiant energy coming from a Sun-like star, and populated by two kinds of identical plants differing by their colour: white daisies reflecting light and black daisies absorbing light. The interactions and feedbacks between the collective biota of the planet and the incoming radiation form a self-regulating system where the conditions for life are maintained. We investigate a modified version of the Daisyworld model where a spatial dependency on latitude is introduced, and both a variable heat diffusivity along latitude and a simple greenhouse model are included. We show that the spatial interactions between the variables of the system can generate some equilibrium patterns which can locally stabilize the coexistence of the two vegetation types. The feedback on albedo is able to generate new equilibrium solutions which can efficiently self-regulate the planet climate, even for values of the solar luminosity relatively far from the current Earth conditions. The extension to spatial Daisyworld gives room to the possibility of inhomogeneous solar forcing in a curved planet, with explicit differences between poles and equator and the direct use of the heat diffusion equation. As a first approach, to describe a spherical planet, we consider the temperature T(θ,t) and the surface coverage as depending only on time and on latitude θ (-90° ≤ θ ≤ 90°). A second step is the introduction of the greenhouse effect in the model, the process by which outgoing infrared radiation is partly screened by greenhouse gases. This effect can be described by relaxing the black-body radiation hypothesis and by introducing a grayness function g(T) in the heat equation. As a third step, we consider a latitude dependence of the Earth's conductivity, χ = χ(θ). Considering these terms, using spherical coordinates and symmetry with respect to θ, the modified Daisyworld equations reduce to the

  19. Automatic detection of stent struts with thick neointimal growth in intravascular optical coherence tomography image sequences

    NASA Astrophysics Data System (ADS)

    Xu, Chenyang; Schmitt, Joseph M.; Akasaka, Takashi; Kubo, Takashi; Huang, Kun

    2011-10-01

    To assist cardiologists investigating neointimal tissue growth on stents during follow-up with optical coherence tomography (OCT), we developed an automatic algorithm to locate deeply buried stent struts and to quantify the restenosis burden. The technique is based on an improved steerable filter for computing the local ridge strength and orientation. It also uses an ellipsoid fitting algorithm and continuity criteria to obtain globally optimal stent localization. The restenosis burden calculations were compared to manual assessment of OCT coronary artery image data obtained from in vivo human clinical studies. Compared to manual assessment by expert readers, the algorithm operated with > 97% accuracy in the measurement of mean and maximum restenosis burden. The results indicated that the technique yielded comparable accuracy in measuring restenosis burden, and significantly reduced user interaction time.

  20. Age-related changes in monocytes exacerbate neointimal hyperplasia after vascular injury

    PubMed Central

    Martinez, Laisel; Gomez, Camilo; Vazquez-Padron, Roberto I.

    2015-01-01

    Neointimal hyperplasia is the leading cause of restenosis after endovascular interventions. It is characterized by the accumulation of myofibroblast-like cells and extracellular matrix in the innermost layer of the wall and is exacerbated by inflammation. Monocytes from either young or aged rats were applied perivascularly to injured vascular walls of young recipient animals. Monocytes from aged rats, but not young donors, increased neointima thickness. Accordingly, the gene expression profiles of CD11b+ monocytes from aged rats showed significant up-regulation of genes involved in cellular adhesion, lipid degradation, cytotoxicity, differentiation, and inflammation. These included cadherin 13 (Cdh13), colony stimulating factor 1 (Csf1), chemokine C-X-C motif ligand 1 (Cxcl1), endothelial cell-selective adhesion molecule (Esam), and interferon gamma (Ifng). In conclusion, our results suggest that the increased inflammatory and adhesive profile of monocytes contributes to pathological wall remodeling in aged-related vascular diseases. PMID:25965835

  1. Impact of Neointimal Calcifications on Acute Stent Performance during the Treatment of In-Stent Restenosis

    PubMed Central

    Mehanna, Emile; Attizzani, Guilherme Ferragut; Nakamura, Daisuke; Nishino, Setsu; Fares, Anas; Aoun, Reem; Costa, Marco Aurelio; Bezerra, Hiram Grando

    2016-01-01

    Optical coherence tomography (OCT) has become the invasive imaging modality of choice for coronary stent assessment due to its unmatched spatial resolution. Neointimal calcification (NC) is a rare finding, observed in 5-10% of in-stent restenosis (ISR) neointima. The impact of NC on percutaneous coronary intervention of ISR is unknown. We therefore present the outcome of six unique cases of ISR and NC in which OCT was used to evaluate the impact of NC on the quality of stent-in-stent deployment for the treatment of ISR. This series demonstrates for the first time the impact of NC on stent expansion, a finding which might help guiding percutaneous coronary intervention for ISR with NC. PMID:27305286

  2. Age-related changes in monocytes exacerbate neointimal hyperplasia after vascular injury.

    PubMed

    Martinez, Laisel; Gomez, Camilo; Vazquez-Padron, Roberto I

    2015-07-10

    Neointimal hyperplasia is the leading cause of restenosis after endovascular interventions. It is characterized by the accumulation of myofibroblast-like cells and extracellular matrix in the innermost layer of the wall and is exacerbated by inflammation. Monocytes from either young or aged rats were applied perivascularly to injured vascular walls of young recipient animals. Monocytes from aged rats, but not young donors, increased neointima thickness. Accordingly, the gene expression profiles of CD11b+ monocytes from aged rats showed significant up-regulation of genes involved in cellular adhesion, lipid degradation, cytotoxicity, differentiation, and inflammation. These included cadherin 13 (Cdh13), colony stimulating factor 1 (Csf1), chemokine C-X-C motif ligand 1 (Cxcl1), endothelial cell-selective adhesion molecule (Esam), and interferon gamma (Ifng). In conclusion, our results suggest that the increased inflammatory and adhesive profile of monocytes contributes to pathological wall remodeling in aged-related vascular diseases. PMID:25965835

  3. A New Arteriovenous Fistula Model to Study the Development of Neointimal Hyperplasia

    PubMed Central

    Manning, Eddie; Skartsis, Nikolaos; Orta, Armando M.; Velazquez, Omaida C.; Liu, Zhao-Jun; Asif, Arif; Salman, Loay H.; Vazquez-Padron, Roberto I.

    2012-01-01

    This study describes an alternative arteriovenous fistula (AVF) model in the rat in which the animals develop significant neointimal hyperplasia (NIH) not only at the distal anastomotic site, but also throughout the fistula body. This aortocaval fistula was established by anastomosing the distal end of the renal vein to the abdominal aorta after unilateral nephrectomy. The increased hemodynamic stress resulting from exposing the renal vein to the arterial circulation induced venous NIH as early as 7 days after surgery. This experimental AVF was characterized by the early lack of endothelium, the accumulation of proliferating vascular smooth muscle cells and the neovascularization of the fistula adventitia. In summary, we have described an informative animal model to study the pathobiology of NIH in native AVF. PMID:22249138

  4. Retinoic acid, local cell-cell interactions, and pattern formation in vertebrate limbs.

    PubMed

    Bryant, S V; Gardiner, D M

    1992-07-01

    Retinoic acid (RA), a derivative of vitamin A, has remarkable effects on developing and regenerating limbs. These effects include teratogenesis, arising from RA's ability to inhibit growth and pattern formation. They also include pattern duplication, arising as a result of the stimulation of additional growth and pattern formation. In this review we present evidence that the diverse effects of RA are consistent with a singular, underlying explanation. We propose that in all cases exogenously applied RA causes the positional information of pattern formation-competent cells to be reset to a value that is posterior-ventral-proximal with respect to the limb. The diversity of outcomes can be seen as a product of the mode of application of exogenous RA (global versus local) coupled with the unifying concept that growth and pattern formation in both limb development and limb regeneration are controlled by local cell-cell interactions, as formulated in the polar coordinate model. We explore the possibility that the major role of endogenous RA in limb development is in the establishment of the limb field rather than as a diffusible morphogen that specifies graded positional information across the limb as previously proposed. Finally, we interpret the results of the recent finding that RA can turn tail regenerates into limbs, as evidence that intercalary interactions may also be involved in the formation of the primary body axis. PMID:1628749

  5. Effect of substrate temperature on pattern formation of nanoparticles from volatile drops.

    PubMed

    Parsa, Maryam; Harmand, Souad; Sefiane, Khellil; Bigerelle, Maxence; Deltombe, Raphaël

    2015-03-24

    This study investigates pattern formation during evaporation of water-based nanofluid sessile droplets placed on a smooth silicon surface at various temperatures. An infrared thermography technique was employed to observe the temperature distribution along the air-liquid interface of evaporating droplets. In addition, an optical interferometry technique is used to quantify and characterize the deposited patterns. Depending on the substrate temperature, three distinctive deposition patterns are observed: a nearly uniform coverage pattern, a "dual-ring" pattern, and multiple rings corresponding to "stick-slip" pattern. At all substrate temperatures, the internal flow within the drop builds a ringlike cluster of the solute on the top region of drying droplets, which is found essential for the formation of the secondary ring deposition onto the substrate for the deposits with the "dual-ring" pattern. The size of the secondary ring is found to be dependent on the substrate temperature. For the deposits with the rather uniform coverage pattern, the ringlike cluster of the solute does not deposit as a distinct secondary ring; instead, it is deformed by the contact line depinning. In the case of the "stick-slip" pattern, the internal flow behavior is complex and found to be vigorous with rapid circulating flow which appears near the edge of the drop. PMID:25742508

  6. Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

    PubMed

    Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

    2012-01-01

    Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system. PMID:22068976

  7. Integument pattern formation involves genetic and epigenetic controls: feather arrays simulated by digital hormone models.

    PubMed

    Jiang, Ting-Xin; Widelitz, Randall B; Shen, Wei-Min; Will, Peter; Wu, Da-Yu; Lin, Chih-Min; Jung, Han-Sung; Chuong, Cheng-Ming

    2004-01-01

    Pattern formation is a fundamental morphogenetic process. Models based on genetic and epigenetic control have been proposed but remain controversial. Here we use feather morphogenesis for further evaluation. Adhesion molecules and/or signaling molecules were first expressed homogenously in feather tracts (restrictive mode, appear earlier) or directly in bud or inter-bud regions ( de novo mode, appear later). They either activate or inhibit bud formation, but paradoxically colocalize in the bud. Using feather bud reconstitution, we showed that completely dissociated cells can reform periodic patterns without reference to previous positional codes. The patterning process has the characteristics of being self-organizing, dynamic and plastic. The final pattern is an equilibrium state reached by competition, and the number and size of buds can be altered based on cell number and activator/inhibitor ratio, respectively. We developed a Digital Hormone Model which consists of (1) competent cells without identity that move randomly in a space, (2) extracellular signaling hormones which diffuse by a reaction-diffusion mechanism and activate or inhibit cell adhesion, and (3) cells which respond with topological stochastic actions manifested as changes in cell adhesion. Based on probability, the results are cell clusters arranged in dots or stripes. Thus genetic control provides combinational molecular information which defines the properties of the cells but not the final pattern. Epigenetic control governs interactions among cells and their environment based on physical-chemical rules (such as those described in the Digital Hormone Model). Complex integument patterning is the sum of these two components of control and that is why integument patterns are usually similar but non-identical. These principles may be shared by other pattern formation processes such as barb ridge formation, fingerprints, pigmentation patterning, etc. The Digital Hormone Model can also be applied to

  8. On the dynamics of Liesegang-type pattern formation in a gaseous system

    NASA Astrophysics Data System (ADS)

    Ramírez-Álvarez, Elizeth; Montoya, Fernando; Buhse, Thomas; Rios-Herrera, Wady; Torres-Guzmán, José; Rivera, Marco; Martínez-Mekler, Gustavo; Müller, Markus F.

    2016-03-01

    Liesegang pattern formations are widely spread in nature. In spite of a comparably simple experimental setup under laboratory conditions, a variety of spatio-temporal structures may arise. Presumably because of easier control of the experimental conditions, Liesegang pattern formation was mainly studied in gel systems during more than a century. Here we consider pattern formation in a gas phase, where beautiful but highly complex reaction-diffusion-convection dynamics are uncovered by means of a specific laser technique. A quantitative analysis reveals that two different, apparently independent processes, both highly correlated and synchronized across the extension of the reaction cloud, act on different time scales. Each of them imprints a different structure of salt precipitation at the tube walls.

  9. A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells

    PubMed Central

    Higaki, Takumi; Kutsuna, Natsumaro; Akita, Kae; Takigawa-Imamura, Hisako; Yoshimura, Kenji; Miura, Takashi

    2016-01-01

    Plant leaf epidermal cells exhibit a jigsaw puzzle–like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo. PMID:27054467

  10. Mechanisms of pattern formation in grazing-incidence ion bombardment of Pt(111)

    SciTech Connect

    Hansen, Henri; Redinger, Alex; Messlinger, Sebastian; Stoian, Georgiana; Michely, Thomas; Rosandi, Yudi; Urbassek, Herbert M.; Linke, Udo

    2006-06-15

    Ripple patterns forming on Pt(111) due to 5 keV Ar{sup +} grazing-incidence ion bombardment were investigated by scanning tunneling microscopy in a broad temperature range from 100 to 720 K and for ion fluences up to 3x10{sup 20} ions/m{sup 2}. A detailed morphological analysis together with molecular dynamics simulations of single ion impacts allow us to develop atomic scale models for the formation of these patterns. The large difference in step edge versus terrace damage is shown to be crucial for ripple formation under grazing incidence. The importance of distinct diffusion processes--step adatom generation at kinks and adatom lattice gas formation--for temperature dependent transitions in the surface morphology is highlighted. Surprisingly, ion bombardment effects like thermal spike induced adatom production and planar subsurface channeling are important for pattern ordering.

  11. A Theoretical Model of Jigsaw-Puzzle Pattern Formation by Plant Leaf Epidermal Cells.

    PubMed

    Higaki, Takumi; Kutsuna, Natsumaro; Akita, Kae; Takigawa-Imamura, Hisako; Yoshimura, Kenji; Miura, Takashi

    2016-04-01

    Plant leaf epidermal cells exhibit a jigsaw puzzle-like pattern that is generated by interdigitation of the cell wall during leaf development. The contribution of two ROP GTPases, ROP2 and ROP6, to the cytoskeletal dynamics that regulate epidermal cell wall interdigitation has already been examined; however, how interactions between these molecules result in pattern formation remains to be elucidated. Here, we propose a simple interface equation model that incorporates both the cell wall remodeling activity of ROP GTPases and the diffusible signaling molecules by which they are regulated. This model successfully reproduces pattern formation observed in vivo, and explains the counterintuitive experimental results of decreased cellulose production and increased thickness. Our model also reproduces the dynamics of three-way cell wall junctions. Therefore, this model provides a possible mechanism for cell wall interdigitation formation in vivo. PMID:27054467

  12. On the dynamics of Liesegang-type pattern formation in a gaseous system.

    PubMed

    Ramírez-Álvarez, Elizeth; Montoya, Fernando; Buhse, Thomas; Rios-Herrera, Wady; Torres-Guzmán, José; Rivera, Marco; Martínez-Mekler, Gustavo; Müller, Markus F

    2016-01-01

    Liesegang pattern formations are widely spread in nature. In spite of a comparably simple experimental setup under laboratory conditions, a variety of spatio-temporal structures may arise. Presumably because of easier control of the experimental conditions, Liesegang pattern formation was mainly studied in gel systems during more than a century. Here we consider pattern formation in a gas phase, where beautiful but highly complex reaction-diffusion-convection dynamics are uncovered by means of a specific laser technique. A quantitative analysis reveals that two different, apparently independent processes, both highly correlated and synchronized across the extension of the reaction cloud, act on different time scales. Each of them imprints a different structure of salt precipitation at the tube walls. PMID:27025405

  13. On the dynamics of Liesegang-type pattern formation in a gaseous system

    PubMed Central

    Ramírez-Álvarez, Elizeth; Montoya, Fernando; Buhse, Thomas; Rios-Herrera, Wady; Torres-Guzmán, José; Rivera, Marco; Martínez-Mekler, Gustavo; Müller, Markus F.

    2016-01-01

    Liesegang pattern formations are widely spread in nature. In spite of a comparably simple experimental setup under laboratory conditions, a variety of spatio-temporal structures may arise. Presumably because of easier control of the experimental conditions, Liesegang pattern formation was mainly studied in gel systems during more than a century. Here we consider pattern formation in a gas phase, where beautiful but highly complex reaction-diffusion-convection dynamics are uncovered by means of a specific laser technique. A quantitative analysis reveals that two different, apparently independent processes, both highly correlated and synchronized across the extension of the reaction cloud, act on different time scales. Each of them imprints a different structure of salt precipitation at the tube walls. PMID:27025405

  14. Interfacial force-driven pattern formation during drying of Aβ (25-35) fibrils.

    PubMed

    Sett, Ayantika; Bag, Sudipta; Dasgupta, Swagata; DasGupta, Sunando

    2015-08-01

    Pattern formation during evaporation of biofluids finds significant applications in the biomedical field for disease identification. Aβ (25-35) is the smallest peptide in the amyloid peptide family that retains the toxicity of a full length peptide responsible for Alzheimer's disease and is chosen here as the model solute. Drying experiments on substrates of varying wettability exhibit unique drying patterns of Aβ (25-35) fibrils visualized through fluorescence microscopy and transmission electron microscopy. The unique pattern formations can be interpreted as manifestations of the changes in the self-pinning mechanism with changes in wettability, which in some cases resembles the well-known coffee ring effect. Additionally, the delicate balance between the drag and capillary forces has been perturbed by initiating controlled rates of evaporation and probing their effects on the fibril patterning. PMID:25964177

  15. Hormone-Mediated Pattern Formation in Seedling of Plants: a Competitive Growth Dynamics Model

    NASA Astrophysics Data System (ADS)

    Kawaguchi, Satoshi; Mimura, Masayasu; Ohya, Tomoyuki; Oikawa, Noriko; Okabe, Hirotaka; Kai, Shoichi

    2001-10-01

    An ecologically relevant pattern formation process mediated by hormonal interactions among growing seedlings is modeled based on the experimental observations on the effects of indole acetic acid, which can act as an inhibitor and activator of root growth depending on its concentration. In the absence of any lateral root with constant hormone-sensitivity, the edge effect phenomenon is obtained depending on the secretion rate of hormone from the main root. Introduction of growth-stage-dependent hormone-sensitivity drastically amplifies the initial randomness, resulting in spatially irregular macroscopic patterns. When the lateral root growth is introduced, periodic patterns are obtained whose periodicity depends on the length of lateral roots. The growth-stage-dependent hormone-sensitivity and the lateral root growth are crucial for macroscopic periodic-pattern formation.

  16. Pattern Formation in Self-Propelled Particles with Density-Dependent Motility

    NASA Astrophysics Data System (ADS)

    Farrell, F. D. C.; Marchetti, M. C.; Marenduzzo, D.; Tailleur, J.

    2012-06-01

    We study the behavior of interacting self-propelled particles, whose self-propulsion speed decreases with their local density. By combining direct simulations of the microscopic model with an analysis of the hydrodynamic equations obtained by explicitly coarse graining the model, we show that interactions lead generically to the formation of a host of patterns, including moving clumps, active lanes, and asters. This general mechanism could explain many of the patterns seen in recent experiments and simulations.

  17. Inhibited pattern formation by asymmetrical high-voltage excitation in nematic fluids.

    PubMed

    Salamon, Péter; Éber, Nándor; Fekete, Balázs; Buka, Ágnes

    2014-08-01

    In contrast to the predictions of the standard theory of electroconvection (EC), our experiments showed that the action of superposed ac and dc voltages rather inhibits pattern formation than favors the emergence of instabilities; the patternless region may extend to much higher voltages than the individual ac or dc thresholds. The pattern formation induced by such asymmetrical voltage was explored in a nematic liquid crystal in a wide frequency range. The findings could be qualitatively explained for the conductive EC, but represent a challenging problem for the dielectric EC. PMID:25215747

  18. Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems

    NASA Astrophysics Data System (ADS)

    Golovin, Alexander A.; Nepomnyashchy, Alexander A.

    Nano-science and nano-technology are rapidly developing scientific and technological areas that deal with physical, chemical and biological processes that occur on nano-meter scale -- one millionth of a millimeter. Self-organization and pattern formation play crucial role on nano-scales and promise new, effective routes to control various nano-scales processes. This book contains lecture notes written by the lecturers of the NATO Advanced Study Institute "Self-Assembly, Pattern Formation and Growth Phenomena in Nano-Systems" that took place in St Etienne de Tinee, France, in the fall 2004.

  19. Trickle-down boundary conditions in aeolian dune-field pattern formation

    NASA Astrophysics Data System (ADS)

    Ewing, R. C.; Kocurek, G.

    2015-12-01

    One the one hand, wind-blown dune-field patterns emerge within the overarching boundary conditions of climate, tectonics and eustasy implying the presence of these signals in the aeolian geomorphic and stratigraphic record. On the other hand, dune-field patterns are a poster-child of self-organization, in which autogenic processes give rise to patterned landscapes despite remarkable differences in the geologic setting (i.e., Earth, Mars and Titan). How important are climate, tectonics and eustasy in aeolian dune field pattern formation? Here we develop the hypothesis that, in terms of pattern development, dune fields evolve largely independent of the direct influence of 'system-scale' boundary conditions, such as climate, tectonics and eustasy. Rather, these boundary conditions set the stage for smaller-scale, faster-evolving 'event-scale' boundary conditions. This 'trickle-down' effect, in which system-scale boundary conditions indirectly influence the event scale boundary conditions provides the uniqueness and richness of dune-field patterned landscapes. The trickle-down effect means that the architecture of the stratigraphic record of dune-field pattern formation archives boundary conditions, which are spatially and temporally removed from the overarching geologic setting. In contrast, the presence of an aeolian stratigraphic record itself, reflects changes in system-scale boundary conditions that drive accumulation and preservation of aeolian strata.

  20. Evaluating the formation mechanisms of the equatorial Pacific SST warming pattern in CMIP5 models

    NASA Astrophysics Data System (ADS)

    Ying, Jun; Huang, Ping; Huang, Ronghui

    2016-04-01

    Based on the historical and RCP8.5 runs of the multi-model ensemble of 32 models participating in CMIP5, the present study evaluates the formation mechanisms for the patterns of changes in equatorial Pacific SST under global warming. Two features with complex formation processes, the zonal El Ni˜no-like pattern and the meridional equatorial peak warming (EPW), are investigated. The climatological evaporation is the main contributor to the El Ni˜no-like pattern, while the ocean dynamical thermostat effect plays a comparable negative role. The cloud-shortwave-radiation-SST feedback and the weakened Walker circulation play a small positive role in the El Ni˜no-like pattern. The processes associated with ocean dynamics are confined to the equator. The climatological evaporation is also the dominant contributor to the EPW pattern, as suggested in previous studies. However, the effects of some processes are inconsistent with previous studies. For example, changes in the zonal heat advection due to the weakened Walker circulation have a remarkable positive contribution to the EPW pattern, and changes in the shortwave radiation play a negative role in the EPW pattern.

  1. Preparation of highly water-repellent surface by spontaneous formation of double scale roughness pattern.

    PubMed

    Joly, Pascal; Kuroda, Akihiro; Asakura, Kouichi

    2010-01-01

    Hydrophobic organic-inorganic hybrid composite suspensions were prepared by mixing hydrophobic octylsilyl titanium dioxide particles having average diameter of 35 nm with drying oil or moisture cure room temperature vulcanization silicone gum in volatile silicone. They were spread on a glass plate by using a linear motor coater and an applicator. Spatially periodic stripe patterns parallel to the direction of dragging the applicator were usually generated. The phenomenon is called directional viscous fingering, i.e. spontaneous pattern formation by the growth of fluctuation in morphology of mobile interface during the dragging coat. The pattern spontaneously formed on the surface became double scale when stored samples were coated. In this case, the large scale spatially periodic pattern was formed by the directional viscous fingering and the small ragged random pattern may be due to the giant molecules formed by cross-linking of silicone gum. Double scale roughness patterns were also generated by double dragging coat. The large and small scale pattern was formed by the first and second dragging coat, respectively. The formation of double scale roughness enhanced the water-repellent property of the hydrophobic surface. In some cases, water contact angle increased by 20 degrees to realize super water-repellent surface with a value exceeding 150 degrees. PMID:20103981

  2. Drying bacterial biosaline patterns capable of vital reanimation upon rehydration: novel hibernating biomineralogical life formations.

    PubMed

    Gómez Gómez, José María; Medina, Jesús; Hochberg, David; Mateo-Martí, Eva; Martínez-Frías, Jesús; Rull, Fernando

    2014-07-01

    Water is the fundamental molecule for life on Earth. Thus, the search for hibernating life-forms in waterless environments is an important research topic for astrobiology. To date, however, the organizational patterns containing microbial life in extremely dry places, such as the deserts of Earth, the Dry Valleys of Antarctica, or Mars analog regolith, have been poorly characterized. Here, we report on the formation of bacterial biosaline self-organized drying patterns formed over plastic surfaces. These emerge during the evaporation of sessile droplets of aqueous NaCl salt 0.15 M solutions containing Escherichia coli cells. In the present study, scanning electron microscopy (SEM) and energy dispersive X-ray spectrometry (EDS) analyses indicated that the bacterial cells and the NaCl in these biosaline formations are organized in a two-layered characteristic 3-D architectural morphology. A thin filmlike top layer formed by NaCl conjugated to, and intermingled with, "mineralized" bacterial cells covers a bottom layer constructed by the bulk of the nonmineralized bacterial cells; both layers have the same morphological pattern. In addition, optical microscopic time-lapsed movies show that the formation of these patterns is a kinetically fast process that requires the coupled interaction between the salt and the bacterial cells. Apparently, this mutual interaction drives the generative process of self-assembly that underlies the drying pattern formation. Most notably, the bacterial cells inside these drying self-assembled patterns enter into a quiescent suspended anhydrobiotic state resistant to complete desiccation and capable of vital reanimation upon rehydration. We propose that these E. coli biosaline drying patterns represent an excellent experimental model for understanding different aspects of anhydrobiosis phenomena in bacteria as well as for revealing the mechanisms of bacterially induced biomineralization, both highly relevant topics for the search of life in

  3. A Formative Evaluation of Biological Science: Patterns and Processes, Final Report.

    ERIC Educational Resources Information Center

    Mayer, William V.; And Others

    Reported is a formative evaluation of the Biological Science Curriculum Study "Biological Science: Patterns and Processes", designed for academically unsuccessful students. "Criterion referenced" tests were developed, with items selected to indicate the extent of students' learning rather than to discriminate between students. An alternate form,…

  4. Transverse Mode Structure and Pattern Formation in Oxide Confined Vertical Cavity Semiconductor Lasers

    SciTech Connect

    Choquette, K.D.; Geib, K.M.; Hegarty, S.P.; Hou, H.Q.; Huyet, G.; McInerney, J.G.; Porta, P.

    1999-07-06

    We analyze the transverse profiles of oxide-confined vertical cavity laser diodes as a function of aperture size. For small apertures we demonstrate that thermal lensing can be the dominant effect in determining the transverse resonator properties. We also analyze pattern formation in lasers with large apertures where we observe the appearance of tilted waves.

  5. Pattern formation on networks with reactions: A continuous-time random-walk approach

    NASA Astrophysics Data System (ADS)

    Angstmann, C. N.; Donnelly, I. C.; Henry, B. I.

    2013-03-01

    We derive the generalized master equation for reaction-diffusion on networks from an underlying stochastic process, the continuous time random walk (CTRW). The nontrivial incorporation of the reaction process into the CTRW is achieved by splitting the derivation into two stages. The reactions are treated as birth-death processes and the first stage of the derivation is at the single particle level, taking into account the death process, while the second stage considers an ensemble of these particles including the birth process. Using this model we have investigated different types of pattern formation across the vertices on a range of networks. Importantly, the CTRW defines the Laplacian operator on the network in a non-ad hoc manner and the pattern formation depends on the structure of this Laplacian. Here we focus attention on CTRWs with exponential waiting times for two cases: one in which the rate parameter is constant for all vertices and the other where the rate parameter is proportional to the vertex degree. This results in nonsymmetric and symmetric CTRW Laplacians, respectively. In the case of symmetric Laplacians, pattern formation follows from the Turing instability. However in nonsymmetric Laplacians, pattern formation may be possible with or without a Turing instability.

  6. Three-dimensional pattern formation of magnetically labeled microgel beads for biological tissue engineering

    NASA Astrophysics Data System (ADS)

    Kawamoto, H.; Inoue, H.; Nakamura, M.

    2009-03-01

    We commenced basic research on the three-dimensional (3D) pattern formation of microgel beads for applications in biological tissue engineering. In this new technique, microgel beads are premagnetized by doping them with magnetic nanoparticles. Living cells will be included in the beads for actual use. If a nonuniform magnetic field is applied to a solution containing these magnetized beads, the beads will align, contact, and form a 3D structure. The structure is controlled by the seed pattern of the magnetic particles plugged in a substrate and the profile of the magnetic field distribution. We constructed tubes, which imitate blood vessels, for demonstration using gel beads whose diameters are of the order of several tens of micrometers. The diameter of the demonstrated tube was less than 0.5 mm and its length was 6.6 mm, although living cells were not included in the beads. Numerical calculations by using the discrete element method were conducted to confirm the formation of the tube and to predict the effect of centrifugal force, which will be applied to fill cells in the space between magnetically patterned beads. Although this unique technology is in the nascent stage, this 3D pattern formation technique by the control of the magnetic field has potential to be one of the effective engineering technologies for manufacturing 3D patterned biological tissues in the future.

  7. Spatial Heterogeneity and Imperfect Mixing in Chemical Reactions: Visualization of Density-Driven Pattern Formation

    DOE PAGESBeta

    Sobel, Sabrina G.; Hastings, Harold M.; Testa, Matthew

    2009-01-01

    Imore » mperfect mixing is a concern in industrial processes, everyday processes (mixing paint, bread machines), and in understanding salt water-fresh water mixing in ecosystems. The effects of imperfect mixing become evident in the unstirred ferroin-catalyzed Belousov-Zhabotinsky reaction, the prototype for chemical pattern formation. Over time, waves of oxidation (high ferriin concentration, blue) propagate into a background of low ferriin concentration (red); their structure reflects in part the history of mixing in the reaction vessel. However, it may be difficult to separate mixing effects from reaction effects. We describe a simpler model system for visualizing density-driven pattern formation in an essentially unmixed chemical system: the reaction of pale yellow Fe 3 + with colorless SCN − to form the blood-red Fe ( SCN ) 2 + complex ion in aqueous solution. Careful addition of one drop of Fe ( NO 3 ) 3 to KSCN yields striped patterns after several minutes. The patterns appear reminiscent of Rayleigh-Taylor instabilities and convection rolls, arguing that pattern formation is caused by density-driven mixing.« less

  8. Collective Motion of Cells Mediates Segregation and Pattern Formation in Co-Cultures

    PubMed Central

    Méhes, Előd; Mones, Enys; Németh, Valéria; Vicsek, Tamás

    2012-01-01

    Pattern formation by segregation of cell types is an important process during embryonic development. We show that an experimentally yet unexplored mechanism based on collective motility of segregating cells enhances the effects of known pattern formation mechanisms such as differential adhesion, mechanochemical interactions or cell migration directed by morphogens. To study in vitro cell segregation we use time-lapse videomicroscopy and quantitative analysis of the main features of the motion of individual cells or groups. Our observations have been extensive, typically involving the investigation of the development of patterns containing up to 200,000 cells. By either comparing keratocyte types with different collective motility characteristics or increasing cells' directional persistence by the inhibition of Rac1 GTP-ase we demonstrate that enhanced collective cell motility results in faster cell segregation leading to the formation of more extensive patterns. The growth of the characteristic scale of patterns generally follows an algebraic scaling law with exponent values up to 0.74 in the presence of collective motion, compared to significantly smaller exponents in case of diffusive motion. PMID:22359617

  9. Influence of cell-to-cell variability on spatial pattern formation.

    PubMed

    Greese, B; Wester, K; Bensch, R; Ronneberger, O; Timmer, J; Huulskamp, M; Fleck, C

    2012-08-01

    Many spatial patterns in biology arise through differentiation of selected cells within a tissue, which is regulated by a genetic network. This is specified by its structure, parameterisation and the noise on its components and reactions. The latter, in particular, is not well examined because it is rather difficult to trace. The authors use suitable local mathematical measures based on the Voronoi diagram of experimentally determined positions of epidermal plant hairs (trichomes) to examine the variability or noise in pattern formation. Although trichome initiation is a highly regulated process, the authors show that the experimentally observed trichome pattern is substantially disturbed by cell-to-cell variations. Using computer simulations, they find that the rates concerning the availability of the protein complex that triggers trichome formation plays a significant role in noise-induced variations of the pattern. The focus on the effects of cell noise yields further insights into pattern formation of trichomes. The authors expect that similar strategies can contribute to the understanding of other differentiation processes by elucidating the role of naturally occurring fluctuations in the concentration of cellular components or their properties. PMID:23039695

  10. Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury.

    PubMed

    Ho, Karen J; Xiong, Liqun; Hubert, Nathaniel J; Nadimpalli, Anuradha; Wun, Kelly; Chang, Eugene B; Kibbe, Melina R

    2015-12-01

    Gut microbial metabolites are increasingly recognized as determinants of health and disease. However, whether host -: microbe crosstalk influences peripheral arteries is not understood. Neointimal hyperplasia, a proliferative and inflammatory response to arterial injury, frequently limits the long-term benefits of cardiovascular interventions such as angioplasty, stenting, and bypass surgery. Our goal is to assess the effect of butyrate, one of the principal short chain fatty acids produced by microbial fermentation of dietary fiber, on neointimal hyperplasia development after angioplasty. Treatment of male Lewis Inbred rats with oral vancomycin for 4 weeks changed the composition of gut microbes as assessed by 16S rRNA-based taxonomic profiling and decreased the concentration of circulating butyrate by 69%. In addition, rats treated with oral vancomycin had exacerbated neointimal hyperplasia development after carotid angioplasty. Oral supplementation of butyrate reversed these changes. Butyrate also inhibited vascular smooth muscle cell proliferation, migration, and cell cycle progression in a dose-dependent manner in vitro. Our results suggest for the first time that gut microbial composition is associated with the severity of arterial remodeling after injury, potentially through an inhibitory effect of butyrate on VSMC. PMID:26660548

  11. The effect of the signalling scheme on the robustness of pattern formation in development

    PubMed Central

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

    2012-01-01

    Pattern formation in development is a complex process which involves spatially distributed signals called morphogens that influence gene expression and thus the phenotypic identity of cells. Usually different cell types are spatially segregated, and the boundary between them may be determined by a threshold value of some state variable. The question arises as to how sensitive the location of such a boundary is to variations in properties, such as parameter values, that characterize the system. Here, we analyse both deterministic and stochastic reaction-diffusion models of pattern formation with a view towards understanding how the signalling scheme used for patterning affects the variability of boundary determination between cell types in a developing tissue. PMID:22649582

  12. Two-Dimensionality of Yeast Colony Expansion Accompanied by Pattern Formation

    PubMed Central

    Chen, Lin; Noorbakhsh, Javad; Adams, Rhys M.; Samaniego-Evans, Joseph; Agollah, Germaine; Nevozhay, Dmitry; Kuzdzal-Fick, Jennie; Mehta, Pankaj; Balázsi, Gábor

    2014-01-01

    Yeasts can form multicellular patterns as they expand on agar plates, a phenotype that requires a functional copy of the FLO11 gene. Although the biochemical and molecular requirements for such patterns have been examined, the mechanisms underlying their formation are not entirely clear. Here we develop quantitative methods to accurately characterize the size, shape, and surface patterns of yeast colonies for various combinations of agar and sugar concentrations. We combine these measurements with mathematical and physical models and find that FLO11 gene constrains cells to grow near the agar surface, causing the formation of larger and more irregular colonies that undergo hierarchical wrinkling. Head-to-head competition assays on agar plates indicate that two-dimensional constraint on the expansion of FLO11 wild type (FLO11) cells confers a fitness advantage over FLO11 knockout (flo11Δ) cells on the agar surface. PMID:25504059

  13. Nanostructured diffusion-limited-aggregation crystal pattern formation in a reactive microemulsion system

    NASA Astrophysics Data System (ADS)

    Srivastava, Rohit; Srivastava, P. K.

    2014-03-01

    Nanostructured diffusion-limited-aggregation (DLA) crystal pattern formation in microemulsion consisting of water, styrene, cetyltrimethylammonium chloride (CTACl), potassium persulphate and an oscillating Belousov-Zhabotinsky (BZ) reactant is reported. A variety of spatiotemporal patterns like concentric wave, spatial (stripe) and chaotic patterns appear. A colloidal phase composed of numerous nano-sized particles has been observed. The solid phase nucleation has been found to occur in the colloidal phase and has been found to grow in a symmetric crystal pattern with the progress of the reaction finally exhibiting DLA structures. We show that the formation of a nanostructured DLA crystal pattern is governed by spatial structures emerging in the BZ microemulsion system. Without any spatial structure in the microemulsion system only hydrogel of high viscosity is formed. A nano-sized branched crystal pattern was formed with a particle diameter in the range of 60-100 nm, as evident by transmission electron microscope, powder x-ray diffraction and particle size analyser studies.

  14. Techniques for analysing pattern formation in populations of stem cells and their progeny

    PubMed Central

    2011-01-01

    Background To investigate how patterns of cell differentiation are related to underlying intra- and inter-cellular signalling pathways, we use a stochastic individual-based model to simulate pattern formation when stem cells and their progeny are cultured as a monolayer. We assume that the fate of an individual cell is regulated by the signals it receives from neighbouring cells via either diffusive or juxtacrine signalling. We analyse simulated patterns using two different spatial statistical measures that are suited to planar multicellular systems: pair correlation functions (PCFs) and quadrat histograms (QHs). Results With a diffusive signalling mechanism, pattern size (revealed by PCFs) is determined by both morphogen decay rate and a sensitivity parameter that determines the degree to which morphogen biases differentiation; high sensitivity and slow decay give rise to large-scale patterns. In contrast, with juxtacrine signalling, high sensitivity produces well-defined patterns over shorter lengthscales. QHs are simpler to compute than PCFs and allow us to distinguish between random differentiation at low sensitivities and patterned states generated at higher sensitivities. Conclusions PCFs and QHs together provide an effective means of characterising emergent patterns of differentiation in planar multicellular aggregates. PMID:21991994

  15. The Developmental Genetics of Vertebrate Color Pattern Formation: Lessons from Zebrafish.

    PubMed

    Irion, Uwe; Singh, Ajeet Pratap; Nüsslein-Volhard, Christiane

    2016-01-01

    Color patterns are prominent features of many animals; they are highly variable and evolve rapidly leading to large diversities even within a single genus. As targets for natural as well as sexual selection, they are of high evolutionary significance. The zebrafish (Danio rerio) has become an important model organism for developmental biology and biomedical research in general, and it is the model organism to study color pattern formation in vertebrates. The fish display a conspicuous pattern of alternating blue and golden stripes on the body and on the anal and tail fins. This pattern is produced by three different types of pigment cells (chromatophores) arranged in precise layers in the hypodermis of the fish. In this essay, we will summarize the recent advances in understanding the developmental and genetic basis for stripe formation in the zebrafish. We will describe the cellular events leading to the formation of stripes during metamorphosis based on long-term lineage imaging. Mutant analysis has revealed that a number of signaling pathways are involved in the establishment and maintenance of the individual pigment cells. However, the striped pattern itself is generated by self-organizing mechanisms requiring interactions between all three pigment cell types. The involvement of integral membrane proteins, including connexins and potassium channels, suggests that direct physical contacts between chromatophores are involved, and that the directed transport of small molecules or bioelectrical coupling is important for these interactions. This mode of patterning by transmitting spatial information between adjacent tissues within three superimposed cell layers is unprecedented in other developmental systems. We propose that variations in the patterns among Danio species are caused by allelic differences in the genes responsible for these interactions. PMID:26969976

  16. Simultaneous formation of fine and large-area electrode patterns using screen-offset printing and its application to the patterning on adhesive materials

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Ushijima, Hirobumi; Nagase, Kazuro; Ikedo, Hiroaki; Mitsui, Ryosuke; Sato, Junya; Takahashi, Seiya; Nakajima, Shin-ichiro; Arai, Masahiro; Kurata, Yuji; Iwata, Shiro

    2016-03-01

    Additive-type printing techniques such as gravure-offset printing and screen printing are effective for low-cost and ecofriendly electrode pattern formation. Gravure-offset printing is effective for fine pattern formation with widths on the order of 10-20 µm, whereas screen printing is effective for the formation of large-area patterns. However, it is difficult to simultaneously form fine and large-area patterns using these printing techniques. In this study, we demonstrate that fine (minimum width of 15 µm) and medium- as well as large-area patterns can be formed simultaneously using our developed screen-offset printing technique, which is a combination of screen printing on a silicone blanket and transfer printing from the blanket to a substrate. Furthermore, we demonstrate the application of our method to printing on adhesive materials, which allows electrode formation without applying heat to the film substrate.

  17. A Turing-Hopf Bifurcation Scenario for Pattern Formation on Growing Domains.

    PubMed

    Castillo, Jorge A; Sánchez-Garduño, Faustino; Padilla, Pablo

    2016-07-01

    In this paper, we study the emergence of different patterns that are formed on both static and growing domains and their bifurcation structure. One of these is the so-called Turing-Hopf morphogenetic mechanism. The reactive part we consider is of FitzHugh-Nagumo type. The analysis was carried out on a flat square by considering both fixed and growing domain. In both scenarios, sufficient conditions on the parameter values are given for the formation of specific space-time structures or patterns. A series of numerical solutions of the corresponding initial and boundary value problems are obtained, and a comparison between the resulting patterns on the fixed domain and those arising when the domain grows is established. We emphasize the role of growth of the domain in the selection of patterns. The paper ends by listing some open problems in this area. PMID:27412157

  18. Pattern Formation in Diffusion Flames Embedded in von Karman Swirling Flows

    NASA Technical Reports Server (NTRS)

    Nayagam, Vedha

    2006-01-01

    Pattern formation is observed in nature in many so-called excitable systems that can support wave propagation. It is well-known in the field of combustion that premixed flames can exhibit patterns through differential diffusion mechanism between heat and mass. However, in the case of diffusion flames where fuel and oxidizer are separated initially there have been only a few observations of pattern formation. It is generally perceived that since diffusion flames do not possess an inherent propagation speed they are static and do not form patterns. But in diffusion flames close to their extinction local quenching can occur and produce flame edges which can propagate along stoichiometric surfaces. Recently, we reported experimental observations of rotating spiral flame edges during near-limit combustion of a downward-facing polymethylmethacrylate disk spinning in quiescent air. These spiral flames, though short-lived, exhibited many similarities to patterns commonly found in quiescent excitable media including compound tip meandering motion. Flame disks that grow or shrink with time depending on the rotational speed and in-depth heat loss history of the fuel disk have also been reported. One of the limitations of studying flame patterns with solid fuels is that steady-state conditions cannot be achieved in air at normal atmospheric pressure for experimentally reasonable fuel thickness. As a means to reproduce the flame patterns observed earlier with solid fuels, but under steady-state conditions, we have designed and built a rotating, porous-disk burner through which gaseous fuels can be injected and burned as diffusion flames. The rotating porous disk generates a flow of air toward the disk by a viscous pumping action, generating what is called the von K rm n boundary layer which is of constant thickness over the entire burner disk. In this note we present a map of the various dynamic flame patterns observed during the combustion of methane in air as a function of

  19. Shifting Arctic Sea-ice Formation and Melt Patterns in a Warming World

    NASA Astrophysics Data System (ADS)

    Newton, R.; Fowler, C.; Tremblay, B.; Pfirman, S. L.

    2011-12-01

    As the Arctic warms, sea-ice formation and melt regions are shifting. Ice retreats earlier, open water extends farther north, and fall freeze-up comes later. The changes are already having an impact on important features of the aquatic Arctic system such as surface productivity, water-column stratification, sea-ice velocities, and the export of freshwater (and buoyancy) to the Nordic Seas. These changes are likely to amplify as the trend toward warmer conditions continues. In this contribution we present ice formation and melt patterns over the duration of the polar satellite observation period, from 1979 to the current. The changes are complex, reflecting latitudinal and temporal shifts with warming of the Northern Hemisphere as well as dynamical trends, such as changes in the prevailing surface wind stress patterns and reduction of internal ice stress. We analyze the satellite-derived sea-ice formation and melt dataset with an eye on: the potential impacts on melt/deposition regions (nutrient delivery, water column stratification, contaminant release); the timing of ice formation anddeposition; changes in bathymetric regimes of the formatino and deposition (which imply changes in sea-ice rafted material transport); shifting freshwater transport patterns; and the underlying dynamical mechanisms driving the observed changes.

  20. Formation of spacing pattern and morphogenesis of chick feather buds is regulated by cytoskeletal structures.

    PubMed

    Kim, Jae-Young; Cho, Sung-Won; Song, Wu-Chul; Lee, Min-Jung; Cai, Jinglei; Ohk, Seung-Ho; Song, Hee-Kyung; Degan, Alexander; Jung, Han-Sung

    2005-06-01

    Chick feather buds develop sequentially in a hexagonal array. Each feather bud develops with anterior posterior polarity, which is thought to develop in response to signals derived from specialized regions of mesenchymal condensation and epithelial thickening. These developmental processes are performed by cellular mechanisms, such as cell proliferation and migration, which occur during chick feather bud development. In order to understand the mechanisms regulating the formation of mesenchymal condensation and their role in feather bud development, we explanted chick dorsal skin at stage HH29+ with cytochalasin D, which inhibits cytoskeletal formation. We show that the aggregation of mesenchymal cells can be prevented by cytochalasin D treatment in a concentration-dependent manner. Subsequently, cytochalasin D disrupts the spacing pattern and inhibits feather bud axis formation as well. In addition, expression patterns of Bmp-4 and Msx-2, key molecules for early feather bud development, were disturbed by cytochalasin D treatment. Our results fully indicate that both the cytoskeletal structure and cell activity via gene regulation are of fundamental importance in mesenchymal condensation leading to proper morphogenesis of feather bud and spacing pattern formation. PMID:16026546

  1. Spatiotemporal pattern formation in two-dimensional neural circuits: roles of refractoriness and noise.

    PubMed

    Gong, Pulin; Loi, S T C; Robinson, P A; Yang, C Y J

    2013-02-01

    Refractoriness is one of the most fundamental states of neural firing activity, in which neurons that have just fired are unable to produce another spike, regardless of the strength of afferent stimuli. Another essential and unavoidable feature of neural systems is the existence of noise. To study the role of these essential factors in spatiotemporal pattern formation in neural systems, a spatially expended neural network model is constructed, with the dynamics of its individual neurons capturing the three most essential states of the neural firing behavior: firing, refractory and resting, and the network topology consistent with the widely observed center-surround coupling manner in the real brain. By changing the refractory period with and without noise in a systematic way in the network, it is shown numerically and analytically that without refractoriness, or when the refractory period is smaller than a certain value, the collective activity pattern of the system consists of localized, oscillating patterns. However, when the refractory period is greater than a certain value, crescent-shaped, localized propagating patterns emerge in the presence of noise. It is further illustrated that the formation of the dynamical spiking patterns is due to a symmetry breaking mechanism, refractoriness-induced symmetry breaking; that is generated by the interplay of noise and refractoriness in the network model. This refractoriness-induced symmetry breaking provides a novel perspective on the emergence of localized, spiking wave patterns or spike timing sequences as ubiquitously observed in real neural systems; it therefore suggests that refractoriness may benefit neural systems in their temporal information processing, rather than limiting the performance of neurons, as has been conventionally thought. Our results also highlight the importance of considering noise in studying spatially extended neural systems, where it may facilitate the formation of spatiotemporal order. PMID

  2. Adequately-Sized Nanocarriers Allow Sustained Targeted Drug Delivery to Neointimal Lesions in Rat Arteries.

    PubMed

    Taniguchi, Ryosuke; Miura, Yutaka; Koyama, Hiroyuki; Chida, Tsukasa; Anraku, Yasutaka; Kishimura, Akihiro; Shigematsu, Kunihiro; Kataoka, Kazunori; Watanabe, Toshiaki

    2016-06-01

    In atherosclerotic lesions, the endothelial barrier against the bloodstream can become compromised, resulting in the exposure of the extracellular matrix (ECM) and intimal cells beneath. In theory, this allows adequately sized nanocarriers in circulation to infiltrate into the intimal lesion intravascularly. We sought to evaluate this possibility using rat carotid arteries with induced neointima. Cy5-labeled polyethylene glycol-conjugated polyion complex (PIC) micelles and vesicles, with diameters of 40, 100, or 200 nm (PICs-40, PICs-100, and PICs-200, respectively) were intravenously administered to rats after injury to the carotid artery using a balloon catheter. High accumulation and long retention of PICs-40 in the induced neointima was confirmed by in vivo imaging, while the accumulation of PICs-100 and PICs-200 was limited, indicating that the size of nanocarriers is a crucial factor for efficient delivery. Furthermore, epirubicin-incorporated polymeric micelles with a diameter similar to that of PICs-40 showed significant curative effects in rats with induced neointima, in terms of lesion size and cell number. Specific and effective drug delivery to pre-existing neointimal lesions was demonstrated with adequate size control of the nanocarriers. We consider that this nanocarrier-based drug delivery system could be utilized for the treatment of atherosclerosis. PMID:27183493

  3. Formation and all-optical control of optical patterns in semiconductor microcavities

    NASA Astrophysics Data System (ADS)

    Binder, R.; Tsang, C. Y.; Tse, Y. C.; Luk, M. H.; Kwong, N. H.; Chan, Chris K. P.; Leung, P. T.; Lewandowski, P.; Schumacher, Stefan; Lafont, O.; Baudin, E.; Tignon, J.

    2016-05-01

    Semiconductor microcavities offer a unique way to combine transient all-optical manipulation of GaAs quantum wells with the benefits of structural advantages of microcavities. In these systems, exciton-polaritons have dispersion relations with very small effective masses. This has enabled prominent effects, for example polaritonic Bose condensation, but it can also be exploited for the design of all-optical communication devices. The latter involves non-equilibrium phase transitions in the spatial arrangement of exciton-polaritons. We consider the case of optical pumping with normal incidence, yielding a spatially homogeneous distribution of exciton-polaritons in optical cavities containing the quantum wells. Exciton-exciton interactions can trigger instabilities if certain threshold behavior requirements are met. Such instabilities can lead, for example, to the spontaneous formation of hexagonal polariton lattices (corresponding to six-spot patterns in the far field), or to rolls (corresponding to two-spot far field patterns). The competition among these patterns can be controlled to a certain degree by applying control beams. In this paper, we summarize the theory of pattern formation and election in microcavities and illustrate the switching between patterns via simulation results.

  4. Flow-driven pattern formation in the calcium-oxalate system.

    PubMed

    Bohner, Bíborka; Endrődi, Balázs; Horváth, Dezső; Tóth, Ágota

    2016-04-28

    The precipitation reaction of calcium oxalate is studied experimentally in the presence of spatial gradients by controlled flow of calcium into oxalate solution. The density difference between the reactants leads to strong convection in the form of a gravity current that drives the spatiotemporal pattern formation. The phase diagram of the system is constructed, the evolving precipitate patterns are analyzed and quantitatively characterized by their diameters and the average height of the gravity flow. The compact structures of calcium oxalate monohydrate produced at low flow rates are replaced by the thermodynamically unstable calcium oxalate dihydrate favored in the presence of a strong gravity current. PMID:27131554

  5. Flow-driven pattern formation in the calcium-oxalate system

    NASA Astrophysics Data System (ADS)

    Bohner, Bíborka; Endrődi, Balázs; Horváth, Dezső; Tóth, Ágota

    2016-04-01

    The precipitation reaction of calcium oxalate is studied experimentally in the presence of spatial gradients by controlled flow of calcium into oxalate solution. The density difference between the reactants leads to strong convection in the form of a gravity current that drives the spatiotemporal pattern formation. The phase diagram of the system is constructed, the evolving precipitate patterns are analyzed and quantitatively characterized by their diameters and the average height of the gravity flow. The compact structures of calcium oxalate monohydrate produced at low flow rates are replaced by the thermodynamically unstable calcium oxalate dihydrate favored in the presence of a strong gravity current.

  6. Spike Train Dynamics Underlying Pattern Formation in Integrate-and-Fire Oscillator Networks

    NASA Astrophysics Data System (ADS)

    Bressloff, P. C.; Coombes, S.

    1998-09-01

    A dynamical mechanism underlying pattern formation in a spatially extended network of integrate-and-fire oscillators with synaptic interactions is identified. It is shown how in the strong coupling regime the network undergoes a discrete Turing-Hopf bifurcation of the firing times from a synchronous state to a state with periodic or quasiperiodic variations of the interspike intervals on closed orbits. The separation of these orbits in phase space results in a spatially periodic pattern of mean firing rate across the network that is modulated by deterministic fluctuations of the instantaneous firing rate.

  7. Multiplicative Noise-Induced Electrohydrodynamic Pattern Formations by Controlling Electric Conductivity

    NASA Astrophysics Data System (ADS)

    Huh, Jong-Hoon

    2016-02-01

    We report multiplicative noise impacts on electroconvections (ECs) in a nematic liquid crystal. By controlling the intensity and cutoff frequency of a superposed electric noise (on a sinusoidal field for ECs), we investigate the variation in the characteristics of ECs such as thresholds and pattern diagrams in high-conductivity cells (σ ˜ 10-6 Ω-1 m-1), in comparison with that in usual conventional cells (σ ˜ 10-8 - 10-7 Ω-1 m-1). Unpredictable threshold behaviors, unknown pattern formations such as isotropic liquid bubbles and EC-sustained phases, and undesirable dielectric breakdown induced by thermal focusing are found in high-conductivity cells.

  8. Formation of Somitogenesis-like Pattern in a Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Sakamoto, Fumitaka; Miyakawa, Kenji

    2008-08-01

    The Belousov-Zhabotinsky reaction system showing stationary patterns is realized on the basis of water-in-oil microemulsions with the surfactant sodium bis(2-ethylhexyl)sulfosuccinate. We experimentally demonstrate the formation of somitogenesis-like pattern in which chemical waves arising from spontaneous bulk oscillations are successively arrested and then stacked. The experimental results are qualitatively reproduced by numerical simulations using the two-variable oregonator model. These show that a somitogenesis can be accounted for by the genuine reaction-diffusion model.

  9. Patterned Formation of Highly Coherent Nitrogen-Vacancy Centers Using a Focused Electron Irradiation Technique.

    PubMed

    McLellan, Claire A; Myers, Bryan A; Kraemer, Stephan; Ohno, Kenichi; Awschalom, David D; Bleszynski Jayich, Ania C

    2016-04-13

    We demonstrate fully three-dimensional and patterned localization of nitrogen-vacancy (NV) centers in diamond with coherence times in excess of 1 ms. Nitrogen δ-doping during chemical vapor deposition diamond growth vertically confines nitrogen to 4 nm while electron irradiation with a transmission electron microscope laterally confines vacancies to less than 450 nm. We characterize the effects of electron energy and dose on NV formation. Importantly, our technique enables the formation of reliably high-quality NV centers inside diamond nanostructures with applications in quantum information and sensing. PMID:27010642

  10. Patterned Formation of Highly Coherent Nitrogen-Vacancy Centers Using a Focused Electron Irradiation Technique

    NASA Astrophysics Data System (ADS)

    McLellan, Claire A.; Myers, Bryan A.; Kraemer, Stephan; Ohno, Kenichi; Awschalom, David D.; Bleszynski Jayich, Ania C.

    2016-04-01

    We demonstrate fully three-dimensional and patterned localization of nitrogen-vacancy (NV) centers in diamond with coherence times in excess of 1 ms. Nitrogen {\\delta}-doping during CVD diamond growth vertically confines nitrogen to 4 nm while electron irradiation with a transmission electron microscope (TEM) laterally confines vacancies to less than 1 {\\mu}m. We characterize the effects of electron energy and dose on NV formation. Importantly, our technique enables the formation of reliably high-quality NV centers inside diamond nanostructures, with applications in quantum information and sensing.

  11. On the mechanism of pattern formation in glow dielectric barrier discharge

    NASA Astrophysics Data System (ADS)

    Qiao, Yajun; Li, Ben; Ouyang, Jiting

    2016-01-01

    The formation mechanism of pattern in glow dielectric barrier discharge is investigated by two-dimensional fluid modeling. Experimental results are shown for comparison. The simulation results show that the non-uniform distribution of space charges makes the discharge be enhanced in the high-density region but weakened in its neighborhood, which is considered as an activation-inhibition effect. This effect shows through during a current pulse (one discharge event) but also in a certain period of time after discharge that determines a driving frequency range for the non-uniformity of space charges to be enhanced. The effects of applied voltage, surface charge, electrode boundary, and external field are also discussed. All these factors affect the formation of dielectric-barrier-discharge pattern by changing the distribution or the dynamics of space charges and hence the activation-inhibition effect of non-uniform space charges.

  12. Topology regulates pattern formation capacity of binary cellular automata on graphs

    NASA Astrophysics Data System (ADS)

    Marr, Carsten; Hütt, Marc-Thorsten

    2005-08-01

    We study the effect of topology variation on the dynamic behavior of a system with local update rules. We implement one-dimensional binary cellular automata on graphs with various topologies by formulating two sets of degree-dependent rules, each containing a single parameter. We observe that changes in graph topology induce transitions between different dynamic domains (Wolfram classes) without a formal change in the update rule. Along with topological variations, we study the pattern formation capacities of regular, random, small-world and scale-free graphs. Pattern formation capacity is quantified in terms of two entropy measures, which for standard cellular automata allow a qualitative distinction between the four Wolfram classes. A mean-field model explains the dynamic behavior of random graphs. Implications for our understanding of information transport through complex, network-based systems are discussed.

  13. A Mechanochemical Model for Embryonic Pattern Formation: Coupling Tissue Mechanics and Morphogen Expression

    PubMed Central

    Mercker, Moritz; Hartmann, Dirk; Marciniak-Czochra, Anna

    2013-01-01

    Motivated by recent experimental findings, we propose a novel mechanism of embryonic pattern formation based on coupling of tissue curvature with diffusive signaling by a chemical factor. We derive a new mathematical model using energy minimization approach and show that the model generates a variety of morphogen and curvature patterns agreeing with experimentally observed structures. The mechanism proposed transcends the classical Turing concept which requires interactions between two morphogens with a significantly different diffusivity. Our studies show how biomechanical forces may replace the elusive long-range inhibitor and lead to formation of stable spatially heterogeneous structures without existence of chemical prepatterns. We propose new experimental approaches to decisively test our central hypothesis that tissue curvature and morphogen expression are coupled in a positive feedback loop. PMID:24376555

  14. Pattern Formation in Keller-Segel Chemotaxis Models with Logistic Growth

    NASA Astrophysics Data System (ADS)

    Jin, Ling; Wang, Qi; Zhang, Zengyan

    In this paper, we investigate pattern formation in Keller-Segel chemotaxis models over a multidimensional bounded domain subject to homogeneous Neumann boundary conditions. It is shown that the positive homogeneous steady state loses its stability as chemoattraction rate χ increases. Then using Crandall-Rabinowitz local theory with χ being the bifurcation parameter, we obtain the existence of nonhomogeneous steady states of the system which bifurcate from this homogeneous steady state. Stability of the bifurcating solutions is also established through rigorous and detailed calculations. Our results provide a selection mechanism of stable wavemode which states that the only stable bifurcation branch must have a wavemode number that minimizes the bifurcation value. Finally, we perform extensive numerical simulations on the formation of stable steady states with striking structures such as boundary spikes, interior spikes, stripes, etc. These nontrivial patterns can model cellular aggregation that develop through chemotactic movements in biological systems.

  15. Lung adenocarcinoma with giant cyst formation showing a variety of histologic patterns: a case report

    PubMed Central

    2010-01-01

    Introduction Lung cancer with large cyst formation is relatively rare. This is a case report of a patient with lung cystic adenocarcinoma with multiple histologic patterns. This type of lung adenocarcinoma is believed to be the first reported case in English language medical literature. Case presentation A 60-year-old Japanese woman was admitted to hospital complaining of dyspnea and died of respiratory failure. She had been suffering from lung cancer with pleural effusion for five years. Autopsy analysis revealed lung adenocarcinoma with large cyst formation showing a variety of histologic patterns. Conclusions Autopsy analysis of this atypical case of lung cancer may provide insight and lead to a better understanding of the heterogeneity and clonal expansion of lung adenocarcinoma. PMID:21108775

  16. Pattern formation and dynamics of plasma filaments in dielectric barrier discharges

    NASA Astrophysics Data System (ADS)

    Callegari, T.; Bernecker, B.; Boeuf, J. P.

    2014-10-01

    Dielectric barrier discharges (DBDs) operating in a transient glow discharge regime offer a large variety of self-organized filamentary static or dynamical structures and constitute an excellent physical system for the study of nonlinear dynamics and pattern formation. The plasma filaments of DBDs can exhibit particle-like behavior, with motion, generation, annihilation, and scattering as well as collective effects leading to self-organized structures (hexagons, stripes, concentric rings, spirals, etc) that are typical of reaction-diffusion systems. The purpose of this paper is to analyze the detailed physics of pattern formation in DBDs on the basis of numerical fluid simulations and experiments in order to provide a deeper understanding of the nonlinear mechanisms responsible for the self-organization and dynamics of filaments.

  17. Phase Separation and Pattern Formation in a Binary Bose-Einstein Condensate

    NASA Astrophysics Data System (ADS)

    Sabbatini, Jacopo; Zurek, Wojciech H.; Davis, Matthew J.

    2011-12-01

    The miscibility-immiscibility phase transition in binary Bose-Einstein condensates (BECs) can be controlled by a coupling between the two components. Here we propose a new scheme that uses coupling-induced pattern formation to test the Kibble-Zurek mechanism (KZM) of topological-defect formation in a quantum phase transition. For a binary BEC in a ring trap we find that the number of domains forming the pattern scales as a function of the coupling quench rate with an exponent as predicted by the KZM. For a binary BEC in an elongated harmonic trap we find a different scaling law due to the transition being spatially inhomogeneous. We perform a “quantum simulation” of the harmonically trapped system in a ring trap to verify the scaling exponent.

  18. Phase Separation and Pattern Formation in a Binary Bose-Einstein Condensate

    SciTech Connect

    Sabbatini, Jacopo; Davis, Matthew J.; Zurek, Wojciech H.

    2011-12-02

    The miscibility-immiscibility phase transition in binary Bose-Einstein condensates (BECs) can be controlled by a coupling between the two components. Here we propose a new scheme that uses coupling-induced pattern formation to test the Kibble-Zurek mechanism (KZM) of topological-defect formation in a quantum phase transition. For a binary BEC in a ring trap we find that the number of domains forming the pattern scales as a function of the coupling quench rate with an exponent as predicted by the KZM. For a binary BEC in an elongated harmonic trap we find a different scaling law due to the transition being spatially inhomogeneous. We perform a ''quantum simulation'' of the harmonically trapped system in a ring trap to verify the scaling exponent.

  19. Patterned electrospun nanofiber matrices via localized dissolution: potential for guided tissue formation.

    PubMed

    Jia, Chao; Yu, Dou; Lamarre, Marven; Leopold, Philip L; Teng, Yang D; Wang, Hongjun

    2014-12-23

    With the assistance of an ink-jet printer, solvent (the "ink") can be controllably and reproducibly printed onto electrospun nanofiber meshes (the "paper") to generate various micropatterns and subsequently guide distinct cellular organization and phenotype expression. In combination with the nanofiber-assisted layer-by-layer cell assembly, the patterned electrospun meshes will define an instructive microenvironment for guided tissue formation. PMID:25352221

  20. Mosaic-pattern vegetation formation and dynamics driven by the water-wind crisscross erosion

    NASA Astrophysics Data System (ADS)

    Wu, Gao-Lin; Wang, Dong; Liu, Yu; Hao, Hong-Min; Fang, Nu-Fang; Shi, Zhi-Hua

    2016-07-01

    Theoretical explanations for vegetation pattern dynamic emphasized on banded pattern-forming systems on the dynamics of the spot pattern. In this context, we explore the patch pattern forming and development in the desertification land. We hypothesized that spatial heterogeneity of microtopography and soil properties with different patch sizes would determine vegetation pattern dynamics theory. The spatial heterogeneity of microtopography and soil properties with different patch sizes were studied. Differences between the inside and outside of the canopy of soil carbon content and soil total nitrogen content were significantly increasing with patches sizes. Sampling location across vegetation patch was the main factor controlling soil properties. Soil nutrient content and saturated hydraulic conductivity were the largest, while bulk density and the coarse sand content were the lowest at the sampling location of half-way between taproot and downslope edge of the canopy. The height of the mound relative to the adjacent soil interspace between shrubs increased as patches diameter increased at the upslope of the taproot. Hydrological and aeolian processes resulted in spatial distributions of soil moisture, nutrition properties, which lead to patch migrated to downslope rather than upslope. A conceptual model was integrated hydrological and nutrient facilitation and competition effects among the plant-soil in mosaic-pattern patch formation and succession process.

  1. Stability of synchronized dynamics and pattern formation in coupled systems: Review of some recent results

    NASA Astrophysics Data System (ADS)

    Chen, Yonghong; Rangarajan, Govindan; Ding, Mingzhou

    2006-12-01

    In arbitrarily coupled dynamical systems (maps or ordinary differential equations), the stability of synchronized states (including equilibrium point, periodic orbit or chaotic attractor) and the formation of patterns from loss of stability of the synchronized states are two problems of current research interest. These two problems are often treated separately in the literature. Here, we present a unified framework in which we show that the eigenvalues of the coupling matrix determine the stability of the synchronized state, while the eigenvectors correspond to patterns emerging from desynchronization. Based on this simple framework three results are derived: First, general approaches are developed that yield constraints directly on the coupling strengths which ensure the stability of synchronized dynamics. Second, when the synchronized state becomes unstable spatial patterns can be selectively realized by varying the coupling strengths. Distinct temporal evolution of the spatial pattern can be obtained depending on the bifurcating synchronized state. Third, given a desired spatiotemporal pattern, one is able to design coupling schemes which give rise to that pattern as the coupled system evolves. Systems with specific coupling schemes are used as examples to illustrate the general methods.

  2. How memory of direct animal interactions can lead to territorial pattern formation.

    PubMed

    Potts, Jonathan R; Lewis, Mark A

    2016-05-01

    Mechanistic home range analysis (MHRA) is a highly effective tool for understanding spacing patterns of animal populations. It has hitherto focused on populations where animals defend their territories by communicating indirectly, e.g. via scent marks. However, many animal populations defend their territories using direct interactions, such as ritualized aggression. To enable application of MHRA to such populations, we construct a model of direct territorial interactions, using linear stability analysis and energy methods to understand when territorial patterns may form. We show that spatial memory of past interactions is vital for pattern formation, as is memory of 'safe' places, where the animal has visited but not suffered recent territorial encounters. Additionally, the spatial range over which animals make decisions to move is key to understanding the size and shape of their resulting territories. Analysis using energy methods, on a simplified version of our system, shows that stability in the nonlinear system corresponds well to predictions of linear analysis. We also uncover a hysteresis in the process of territory formation, so that formation may depend crucially on initial space-use. Our analysis, in one dimension and two dimensions, provides mathematical groundwork required for extending MHRA to situations where territories are defended by direct encounters. PMID:27146687

  3. Formation of ordered polymer patterns from benzene vapors in a barrier discharge

    NASA Astrophysics Data System (ADS)

    Kudryashov, S.; Ryabov, A.; Shchyogoleva, G.; Tsyro, L.

    2014-10-01

    The experimental conditions are found under which the impact of the barrier discharge (BD) on a gas-vapor mixture of benzene, argon and helium results in a spontaneous formation of ordered polymer structures similar to the luminous BD patterns on the electrodes of the reactor. It is shown that the impact of a BD on a Ar-C6H6 mixture leads to the formation of two types of materials: black color column-structure materials (CSMs), measuring ˜100 µm in diameter and 2 mm in height and ˜4-6 mm honeycomb polymer patterns with a well-defined bead-like interface ˜50-100 µm in height. In a He-C6H6 mixture, the CSMs form dendrite-like structures on the dielectric barrier surface of the high-voltage electrode. The patterns formed on the grounded electrode have no clear boundaries. In this paper, the properties of the materials are investigated and the mechanism of their formation is discussed.

  4. Formation mechanism of dot-line square superlattice pattern in dielectric barrier discharge

    SciTech Connect

    Liu, Weibo; Dong, Lifang E-mail: pyy1616@163.com; Wang, Yongjie; Zhang, Xinpu; Pan, Yuyang E-mail: pyy1616@163.com

    2014-11-15

    We investigate the formation mechanism of the dot-line square superlattice pattern (DLSSP) in dielectric barrier discharge. The spatio-temporal structure studied by using the intensified-charge coupled device camera shows that the DLSSP is an interleaving of three different subpatterns in one half voltage cycle. The dot square lattice discharges first and, then, the two kinds of line square lattices, which form square grid structures discharge twice. When the gas pressure is varied, DLSSP can transform from square superlattice pattern (SSP). The spectral line profile method is used to compare the electron densities, which represent the amounts of surface charges qualitatively. It is found that the amount of surface charges accumulated by the first discharge of DLSSP is less than that of SSP, leading to a bigger discharge area of the following discharge (lines of DLSSP instead of halos of SSP). The spatial distribution of the electric field of the surface charges is simulated to explain the formation of DLSSP. This paper may provide a deeper understanding for the formation mechanism of complex superlattice patterns in DBD.

  5. Optical Pattern Formation in Spatially Bunched Atoms: A Self-Consistent Model and Experiment

    NASA Astrophysics Data System (ADS)

    Schmittberger, Bonnie L.; Gauthier, Daniel J.

    2014-05-01

    The nonlinear optics and optomechanical physics communities use different theoretical models to describe how optical fields interact with a sample of atoms. There does not yet exist a model that is valid for finite atomic temperatures but that also produces the zero temperature results that are generally assumed in optomechanical systems. We present a self-consistent model that is valid for all atomic temperatures and accounts for the back-action of the atoms on the optical fields. Our model provides new insights into the competing effects of the bunching-induced nonlinearity and the saturable nonlinearity. We show that it is crucial to keep the fifth and seventh-order nonlinearities that arise when there exists atomic bunching, even at very low optical field intensities. We go on to apply this model to the results of our experimental system where we observe spontaneous, multimode, transverse optical pattern formation at ultra-low light levels. We show that our model accurately predicts our experimentally observed threshold for optical pattern formation, which is the lowest threshold ever reported for pattern formation. We gratefully acknowledge the financial support of the NSF through Grant #PHY-1206040.

  6. Formation mechanism of dot-line square superlattice pattern in dielectric barrier discharge

    NASA Astrophysics Data System (ADS)

    Liu, Weibo; Dong, Lifang; Wang, Yongjie; Zhang, Xinpu; Pan, Yuyang

    2014-11-01

    We investigate the formation mechanism of the dot-line square superlattice pattern (DLSSP) in dielectric barrier discharge. The spatio-temporal structure studied by using the intensified-charge coupled device camera shows that the DLSSP is an interleaving of three different subpatterns in one half voltage cycle. The dot square lattice discharges first and, then, the two kinds of line square lattices, which form square grid structures discharge twice. When the gas pressure is varied, DLSSP can transform from square superlattice pattern (SSP). The spectral line profile method is used to compare the electron densities, which represent the amounts of surface charges qualitatively. It is found that the amount of surface charges accumulated by the first discharge of DLSSP is less than that of SSP, leading to a bigger discharge area of the following discharge (lines of DLSSP instead of halos of SSP). The spatial distribution of the electric field of the surface charges is simulated to explain the formation of DLSSP. This paper may provide a deeper understanding for the formation mechanism of complex superlattice patterns in DBD.

  7. Plant development. Integration of growth and patterning during vascular tissue formation in Arabidopsis.

    PubMed

    De Rybel, Bert; Adibi, Milad; Breda, Alice S; Wendrich, Jos R; Smit, Margot E; Novák, Ondřej; Yamaguchi, Nobutoshi; Yoshida, Saiko; Van Isterdael, Gert; Palovaara, Joakim; Nijsse, Bart; Boekschoten, Mark V; Hooiveld, Guido; Beeckman, Tom; Wagner, Doris; Ljung, Karin; Fleck, Christian; Weijers, Dolf

    2014-08-01

    Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue. PMID:25104393

  8. Pattern formation in liquid-vapor systems under periodic potential and shear.

    PubMed

    Coclite, A; Gonnella, G; Lamura, A

    2014-06-01

    In this paper the phase behavior and pattern formation in a sheared nonideal fluid under a periodic potential is studied. An isothermal two-dimensional formulation of a lattice Boltzmann scheme for a liquid-vapor system with the van der Waals equation of state is presented and validated. Shear is applied by moving walls and the periodic potential varies along the flow direction. A region of the parameter space, where in the absence of flow a striped phase with oscillating density is stable, will be considered. At low shear rates the periodic patterns are preserved and slightly distorted by the flow. At high shear rates the striped phase loses its stability and traveling waves on the interface between the liquid and vapor regions are observed. These waves spread over the whole system with wavelength only depending on the length of the system. Velocity field patterns, characterized by a single vortex, will also be shown. PMID:25019908

  9. An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments

    PubMed Central

    Torres-Sánchez, Alejandro; Gómez-Gardeñes, Jesús; Falo, Fernando

    2015-01-01

    Heterocyst differentiation in cyanobacteria filaments is one of the simplest examples of cellular differentiation and pattern formation in multicellular organisms. Despite of the many experimental studies addressing the evolution and sustainment of heterocyst patterns and the knowledge of the genetic circuit underlying the behavior of single cyanobacterium under nitrogen deprivation, there is still a theoretical gap connecting these two macroscopic and microscopic processes. As an attempt to shed light on this issue, here we explore heterocyst differentiation under the paradigm of systems biology. This framework allows us to formulate the essential dynamical ingredients of the genetic circuit of a single cyanobacterium into a set of differential equations describing the time evolution of the concentrations of the relevant molecular products. As a result, we are able to study the behavior of a single cyanobacterium under different external conditions, emulating nitrogen deprivation, and simulate the dynamics of cyanobacteria filaments by coupling their respective genetic circuits via molecular diffusion. These two ingredients allow us to understand the principles by which heterocyst patterns can be generated and sustained. In particular, our results point out that, by including both diffusion and noisy external conditions in the computational model, it is possible to reproduce the main features of the formation and sustainment of heterocyst patterns in cyanobacteria filaments as observed experimentally. Finally, we discuss the validity and possible improvements of the model. PMID:25816286

  10. The Intersection of Theory and Application in Elucidating Pattern Formation in Developmental Biology

    PubMed Central

    Othmer, Hans G.; Painter, Kevin; Umulis, David; Xue, Chuan

    2009-01-01

    We discuss theoretical and experimental approaches to three distinct developmental systems that illustrate how theory can influence experimental work and vice-versa. The chosen systems – Drosophila melanogaster, bacterial pattern formation, and pigmentation patterns – illustrate the fundamental physical processes of signaling, growth and cell division, and cell movement involved in pattern formation and development. These systems exemplify the current state of theoretical and experimental understanding of how these processes produce the observed patterns, and illustrate how theoretical and experimental approaches can interact to lead to a better understanding of development. As John Bonner said long ago ‘We have arrived at the stage where models are useful to suggest experiments, and the facts of the experiments in turn lead to new and improved models that suggest new experiments. By this rocking back and forth between the reality of experimental facts and the dream world of hypotheses, we can move slowly toward a satisfactory solution of the major problems of developmental biology.’ PMID:19844610

  11. Formation and maintenance of nitrogen-fixing cell patterns in filamentous cyanobacteria.

    PubMed

    Muñoz-García, Javier; Ares, Saúl

    2016-05-31

    Cyanobacteria forming one-dimensional filaments are paradigmatic model organisms of the transition between unicellular and multicellular living forms. Under nitrogen-limiting conditions, in filaments of the genus Anabaena, some cells differentiate into heterocysts, which lose the possibility to divide but are able to fix environmental nitrogen for the colony. These heterocysts form a quasiregular pattern in the filament, representing a prototype of patterning and morphogenesis in prokaryotes. Recent years have seen advances in the identification of the molecular mechanism regulating this pattern. We use these data to build a theory on heterocyst pattern formation, for which both genetic regulation and the effects of cell division and filament growth are key components. The theory is based on the interplay of three generic mechanisms: local autoactivation, early long-range inhibition, and late long-range inhibition. These mechanisms can be identified with the dynamics of hetR, patS, and hetN expression. Our theory reproduces quantitatively the experimental dynamics of pattern formation and maintenance for wild type and mutants. We find that hetN alone is not enough to play the role as the late inhibitory mechanism: a second mechanism, hypothetically the products of nitrogen fixation supplied by heterocysts, must also play a role in late long-range inhibition. The preponderance of even intervals between heterocysts arises naturally as a result of the interplay between the timescales of genetic regulation and cell division. We also find that a purely stochastic initiation of the pattern, without a two-stage process, is enough to reproduce experimental observations. PMID:27162328

  12. The expansion of neighborhood and pattern formation on spatial prisoner's dilemma

    NASA Astrophysics Data System (ADS)

    Qian, Xiaolan; Xu, Fangqian; Yang, Junzhong; Kurths, Jürgen

    2015-04-01

    The prisoner's dilemma (PD), in which players can either cooperate or defect, is considered a paradigm for studying the evolution of cooperation in spatially structured populations. There the compact cooperator cluster is identified as a characteristic pattern and the probability of forming such pattern in turn depends on the features of the networks. In this paper, we investigate the influence of expansion of neighborhood on pattern formation by taking a weak PD game with one free parameter T, the temptation to defect. Two different expansion methods of neighborhood are considered. One is based on a square lattice and expanses along four directions generating networks with degree increasing with K = 4 m . The other is based on a lattice with Moore neighborhood and expanses along eight directions, generating networks with degree of K = 8 m . Individuals are placed on the nodes of the networks, interact with their neighbors and learn from the better one. We find that cooperator can survive for a broad degree 4 ≤ K ≤ 70 by taking a loose type of cooperator clusters. The former simple corresponding relationship between macroscopic patterns and the microscopic PD interactions is broken. Under a condition that is unfavorable for cooperators such as large T and K, systems prefer to evolve to a loose type of cooperator clusters to support cooperation. However, compared to the well-known compact pattern, it is a suboptimal strategy because it cannot help cooperators dominating the population and always corresponding to a low cooperation level.

  13. Is keV ion-induced pattern formation on Si(001) caused by metal impurities?

    PubMed

    Macko, Sven; Frost, Frank; Ziberi, Bashkim; Förster, Daniel F; Michely, Thomas

    2010-02-26

    We present ion beam erosion experiments performed in ultrahigh vacuum using a differentially pumped ion source and taking care that the ion beam hits the Si(001) sample only. Under these conditions no ion beam patterns form on Si for angles theta < or = 45 degrees with respect to the global surface normal using 2 keV Kr+ and fluences of approximately 2 x 10(22) ions m(-2). In fact, the ion beam induces a smoothening of preformed patterns. Simultaneous sputter deposition of stainless steel in this angular range creates a variety of patterns, similar to those previously ascribed to clean ion-beam-induced destabilization of the surface profile. Only for grazing incidence with 60 degrees < or = theta < or = 83 degrees do pronounced ion beam patterns form. It appears that the angular-dependent stability of Si(001) against pattern formation under clean ion beam erosion conditions is related to the angular dependence of the sputtering yield, and not primarily to a curvature-dependent yield as invoked frequently in continuum theory models. PMID:20097973

  14. Is keV ion-induced pattern formation on Si(001) caused by metal impurities?

    NASA Astrophysics Data System (ADS)

    Macko, Sven; Frost, Frank; Ziberi, Bashkim; Förster, Daniel F.; Michely, Thomas

    2010-02-01

    We present ion beam erosion experiments performed in ultrahigh vacuum using a differentially pumped ion source and taking care that the ion beam hits the Si(001) sample only. Under these conditions no ion beam patterns form on Si for angles thetav<=45° with respect to the global surface normal using 2 keV Kr+ and fluences of ≈ 2 × 1022 ions m-2. In fact, the ion beam induces a smoothening of preformed patterns. Simultaneous sputter deposition of stainless steel in this angular range creates a variety of patterns, similar to those previously ascribed to clean ion-beam-induced destabilization of the surface profile. Only for grazing incidence with 60°<=thetav<=83° do pronounced ion beam patterns form. It appears that the angular-dependent stability of Si(001) against pattern formation under clean ion beam erosion conditions is related to the angular dependence of the sputtering yield, and not primarily to a curvature-dependent yield as invoked frequently in continuum theory models.

  15. Pattern formation--A missing link in the study of ecosystem response to environmental changes.

    PubMed

    Meron, Ehud

    2016-01-01

    Environmental changes can affect the functioning of an ecosystem directly, through the response of individual life forms, or indirectly, through interspecific interactions and community dynamics. The feasibility of a community-level response has motivated numerous studies aimed at understanding the mutual relationships between three elements of ecosystem dynamics: the abiotic environment, biodiversity and ecosystem function. Since ecosystems are inherently nonlinear and spatially extended, environmental changes can also induce pattern-forming instabilities that result in spatial self-organization of life forms and resources. This, in turn, can affect the relationships between these three elements, and make the response of ecosystems to environmental changes far more complex. Responses of this kind can be expected in dryland ecosystems, which show a variety of self-organizing vegetation patterns along the rainfall gradient. This paper describes the progress that has been made in understanding vegetation patterning in dryland ecosystems, and the roles it plays in ecosystem response to environmental variability. The progress has been achieved by modeling pattern-forming feedbacks at small spatial scales and up-scaling their effects to large scales through model studies. This approach sets the basis for integrating pattern formation theory into the study of ecosystem dynamics and addressing ecologically significant questions such as the dynamics of desertification, restoration of degraded landscapes, biodiversity changes along environmental gradients, and shrubland-grassland transitions. PMID:26529391

  16. Concerning mechanisms for the zebra pattern formation in the solar radio emission

    SciTech Connect

    Laptukhov, A. I.; Chernov, G. P.

    2009-02-15

    The nature of the zebra patterns in continuous type-IV solar radio bursts is discussed. The most comprehensively developed models of such patterns involve mechanisms based on the double plasma resonance and plasma wave-whistler interaction. Over the last five years, there have appeared a dozen papers concerning the refinement of the mechanism based on the double plasma resonance, because, in its initial formulation, this mechanism failed to describe many features of the zebra pattern. It is shown that the improved model of this mechanism with a power-law distribution function of hot electrons within the loss cone is inapplicable to the coronal plasma. In recent papers, the formation of the zebra pattern in the course of electromagnetic wave propagation through the solar corona was considered. In the present paper, all these models are estimated comparatively. An analysis of recent theories shows that any types of zebra patterns can form in the course of radio wave propagation in the corona, provided that there are plasma inhomogeneities of different scales on the wave path. The superfine structure of zebra stripes in the form of millisecond spikes with a strict period of {approx}30 ms can be attributed to the generation of continuous radio emission in the radio source itself, assuming that plasma inhomogeneities are formed by a finite-amplitude wave with the same period.

  17. Dynamics of fast pattern formation in porous silicon by laser interference

    SciTech Connect

    Peláez, Ramón J.; Kuhn, Timo; Afonso, Carmen N.; Vega, Fidel

    2014-10-20

    Patterns are fabricated on 290 nm thick nanostructured porous silicon layers by phase-mask laser interference using single pulses of an excimer laser (193 nm, 20 ns pulse duration). The dynamics of pattern formation is studied by measuring in real time the intensity of the diffraction orders 0 and 1 at 633 nm. The results show that a transient pattern is formed upon melting at intensity maxima sites within a time <30 ns leading to a permanent pattern in a time <100 ns upon solidification at these sites. This fast process is compared to the longer one (>1 μs) upon melting induced by homogeneous beam exposure and related to the different scenario for releasing the heat from hot regions. The diffraction efficiency of the pattern is finally controlled by a combination of laser fluence and initial thickness of the nanostructured porous silicon layer and the present results open perspectives on heat release management upon laser exposure as well as have potential for alternative routes for switching applications.

  18. Controlled Formation of Surface Patterns in Metal Films Deposited on Elasticity-Gradient PDMS Substrates.

    PubMed

    Yu, Senjiang; Sun, Yadong; Ni, Yong; Zhang, Xiaofei; Zhou, Hong

    2016-03-01

    Controlled surface patterns are useful in a wide range of applications including flexible electronics, elastomeric optics, fluidic channels, surface engineering, measurement technique, biological templates, stamps, and sensors. In this work, we report on the controlled formation of surface patterns in metal films deposited on elasticity-gradient polydimethylsiloxane (PDMS) substrates. Because of the temperature gradient during the curing process, the PDMS substrate in each sample successively changes from a purely liquid state at one side to a purely elastic state at the opposite side. It is found that surface folds appear in the liquid or viscous PDMS region while wrinkles form in the elastic region. In the transition region from the liquid to elastic PDMS, a nested pattern (i.e., the coexisting of folds and wrinkles) can be observed. The folding wave is triggered by the intrinsic stress during the film deposition and its wavelength is independent of the film thickness. The wrinkling wave is induced by the thermal compression after deposition and its wavelength is proportional to the film thickness. The report in this work could promote better understanding of the effect of substrate elasticity on the surface patterns and fabrication of such patterns (folds and wrinkles) by tuning the substrate property. PMID:26859513

  19. Late Stent Expansion and Neointimal Proliferation of Oversized Nitinol Stents in Peripheral Arteries

    SciTech Connect

    Zhao, Hugh Q. Nikanorov, Alexander; Virmani, Renu; Jones, Russell; Pacheco, Erica; Schwartz, Lewis B.

    2009-07-15

    For peripheral endovascular intervention, self-expanding (SE) stents are commonly oversized in relation to target arteries to assure optimal wall apposition and prevent migration. However, the consequences of oversizing have not been well studied. The purpose of this study was to examine the effects of SE stent oversizing (OS) with respect to the kinetics of late stent expansion and the long-term histological effects of OS. Pairs of overlapped 8 x 28-mm Nitinol SE stents were implanted into the iliofemoral arteries of 14 Yucatan swine. Due to variations in target artery size, the stent-to-artery ratio ranged from 1.2:1 to 1.9:1. Lumen and stent diameters were assessed by quantitative angiography at the time of implantation. Following angiographic assessment at 6 months, stented arteries were perfusion-fixed, sectioned, and stained for histological analysis. Immediately following implantation, the stents were found to be expanded to a range of 4.7-7.1 mm, largely conforming to the diameter of the recipient target artery. The stents continued to expand over time, however, and all stents had enlarged to nearly their 8-mm nominal diameter by 6 months. The histological effects of OS were profound, with marked increases in injury and luminal area stenosis, including a statistically significant linear correlation between stent-to-artery ratio and area stenosis. In this experimental model of peripheral endovascular intervention, oversized Nitinol SE stents are constrained by their target artery diameter upon implantation but expand to their nominal diameter within 6 months. Severe OS (stent-to-artery ratio >1.4:1) results in a profound long-term histological response including exuberant neointimal proliferation and luminal stenosis.

  20. Temporal patterns and behavioral characteristics of aggregation formation and spawning in the Bermuda chub ( Kyphosus sectatrix)

    NASA Astrophysics Data System (ADS)

    Nemeth, Richard S.; Kadison, Elizabeth

    2013-12-01

    Reef fish spawning aggregations are important life history events that occur at specific times and locations and represent the primary mode of reproduction for many species. This paper provides detailed descriptions of aggregation formation and mass spawning of the Bermuda chub ( Kyphosus sectatrix). Spawning coloration and gamete release of K. sectatrix were observed and filmed at the Grammanik Bank, a deep spawning aggregation site used by many different species located on the southern edge of the Puerto Rican shelf 10 km south of St. Thomas, US Virgin Islands. Underwater visual surveys using technical Nitrox and closed circuit re-breathers were conducted from December 2002 to March 2013 and documented spatial and temporal patterns of movement and aggregation formation along 1.5 km of mesophotic reef. The largest aggregations of K. sectatrix (>200 fish) were observed on the Grammanik Bank January to March from 0 to 11 d after the full moon with peak abundance from 60 to 80 d after the winter solstice across all survey years. Aggregation formation of K. sectatrix coincided with the spawning season of Nassau ( Epinephelus striatus) and yellowfin ( Mycteroperca venenosa) groupers. These spatial and temporal patterns of aggregation formation and spawning suggest that K. sectatrix, an herbivore, may also be a transient aggregating species. On several occasions, chubs were observed both pair spawning and mass spawning. Color patterns and behaviors associated with aggregation and spawning are described and compared to spawning characteristics observed in other species, many of which are similar but others that appear unique to K. sectatrix. This represents the first report of a kyphosid species aggregating to spawn and illuminates a portion of the poorly understood life history of the Bermuda chub.

  1. Quasi-iso-focal hole pattern formation by Checker-Board PSM (CB-PSM)

    NASA Astrophysics Data System (ADS)

    Nakao, S.; Maejima, S.; Minamide, A.; Saitoh, H.; Hanawa, T.; Suko, K.

    2008-03-01

    A novel RET, which enables on-grid sub-50 nm hole pattern formation with ArF immersion lithography, has been developed. One of the authors has found quasi-iso-focal point image generation at the center of square area of high transmission embedded attenuating phase shift mask (EA-PSM), where four small openings are laid out at the corners of the area, utilizing an optimized quadrupole illumination. As an extension of continuous configuration, checker-board like mask pattern arrangement is created. In the mask, small openings and opaque pads are arranged like as checkerboard, whose base pitch is around resolution limit of targeted optical system. The mask pattern arrangement is named as "Checker-Board PSM (CB-PSM)". By eliminating any one opening from "checker-board", very fine point image is generated at the place. Because four openings around the eliminated one are necessary for the fine imaging characteristic, minimum distance between the point images is about the double of that for resolution limit. After simulation study of imaging, experiments are carried out to prove the fine imaging performance utilizing ArF immersion optics with NA=1.07 and a tri-level resist system. As a result, sub-50nm isolated hole is successfully formed with DOF larger than 200 nm. Simultaneously, ~ 60 nm semi-dense hole with pitch of 240 nm is printed with over 200 nm DOF. Moreover, application of conventional mask pattern arrangement, ultimately dense hole of 140nm pitch is well formed. As a conclusion, we believe that CB-PSM is a promising candidate for hole pattern formation at 32 nm node and beyond.

  2. Pattern formation by a cell surface-associated morphogen in Myxococcus xanthus

    PubMed Central

    Jelsbak, Lars; Søgaard-Andersen, Lotte

    2002-01-01

    In response to starvation, an unstructured population of identical Myxococcus xanthus cells rearranges into an asymmetric, stable pattern of multicellular fruiting bodies. Central to this pattern formation process are changes in organized cell movements from swarming to aggregation. Aggregation is induced by the cell surface-associated C-signal. To understand how aggregation is accomplished, we have analyzed how C-signal modulates cell behavior. We show that C-signal induces a motility response that includes increases in transient gliding speeds and in the duration of gliding intervals and decreases in stop and reversal frequencies. This response results in a switch in cell behavior from an oscillatory to a unidirectional type of behavior in which the net-distance traveled by a cell per minute is increased. We propose that the C-signal-dependent regulation of the reversal frequency is essential for aggregation and that the remaining C-signal-dependent changes in motility parameters contribute to aggregation by increasing the net-distance traveled by starving cells per minute. In our model for symmetry-breaking and aggregation, C-signal transmission is a local event involving direct contacts between cells that results in a global organization of cells. This pattern formation mechanism does not require a diffusible substance or other actions at a distance. Rather it depends on contact-induced changes in motility behavior to direct cells appropriately PMID:11842199

  3. Structure and formation of the twisted plywood pattern of collagen fibrils in rat lamellar bone.

    PubMed

    Yamamoto, Tsuneyuki; Hasegawa, Tomoka; Sasaki, Muneteru; Hongo, Hiromi; Tabata, Chihiro; Liu, Zhusheng; Li, Minqi; Amizuka, Norio

    2012-04-01

    This study was designed to elucidate details of the structure and formation process of the alternate lamellar pattern known to exist in lamellar bone. For this purpose, we examined basic internal lamellae in femurs of young rats by transmission and scanning electron microscopy, the latter employing two different macerations with NaOH at concentrations of 10 and 24%. Observations after the maceration with 10% NaOH showed that the regular and periodic rotation of collagen fibrils caused an alternation between two types of lamellae: one consisting of transversely and nearly transversely cut fibrils, and the other consisting of longitudinally and nearly longitudinally cut fibrils. This finding confirms the consistency of the twisted plywood model. The maceration method with 24% NaOH removed bone components other than cells, thus allowing for three-dimensional observations of osteoblast morphology. Osteoblasts extended finger-like processes paralleling the inner bone surface, and grouped in such a way that, within a group, the processes arranged in a similar direction. Transmission electron microscopy showed that newly deposited fibrils were arranged alongside these processes. For the formation of the alternating pattern, our findings suggest that: (1) osteoblasts control the collagen fibril arrangement through their finger-like process position; (2) osteoblasts behave similarly within a group; (3) osteoblasts move their processes synchronously and periodically to promote alternating different fibril orientation; and (4) this dynamic sequential deposition of fibrils results in the alternate lamellar (or twisted plywood) pattern. PMID:22362877

  4. Pattern Formation in the Arabidopsis Embryo Revealed by Position-Specific Lipid Transfer Protein Gene Expression.

    PubMed Central

    Vroemen, C. W.; Langeveld, S.; Mayer, U.; Ripper, G.; Jurgens, G.; Van Kammen, A.; De Vries, S. C.

    1996-01-01

    During Arabidopsis embryogenesis, the zygote divides asymmetrically in the future apical-basal axis; however, a radial axis is initiated only within the eight-celled embryo. Mutations in the GNOM, KNOLLE, and KEULE genes affect these processes: gnom zygotes tend to divide symmetrically; knolle embryos lack oriented cell divisions that initiate protoderm formation; and in keule embryos, an outer cell layer is present that consists of abnormally enlarged cells from early development. Pattern formation along the two axes is reflected by the position-specific expression of the Arabidopsis lipid transfer protein (AtLTP1) gene. In wild-type embryos, the AtLTP1 gene is expressed in the protoderm and initially in all protodermal cells; later, AtLTP1 expression is confined to the cotyledons and the upper end of the hypocotyl. Analysis of AtLTP1 expression in gnom, knolle, and keule embryos showed that gnom embryos also can have no or reversed apical-basal polarity, whereas radial polarity is unaffected. knolle embryos initially lack but eventually form a radial pattern, and keule embryos are affected in protoderm cell morphology rather than in the establishment of the radial pattern. PMID:12239400

  5. Molecular dynamics of single-particle impacts predicts phase diagrams for large scale pattern formation.

    PubMed

    Norris, Scott A; Samela, Juha; Bukonte, Laura; Backman, Marie; Djurabekova, Flyura; Nordlund, Kai; Madi, Charbel S; Brenner, Michael P; Aziz, Michael J

    2011-01-01

    Energetic particle irradiation can cause surface ultra-smoothening, self-organized nanoscale pattern formation or degradation of the structural integrity of nuclear reactor components. A fundamental understanding of the mechanisms governing the selection among these outcomes has been elusive. Here we predict the mechanism governing the transition from pattern formation to flatness using only parameter-free molecular dynamics simulations of single-ion impacts as input into a multiscale analysis, obtaining good agreement with experiment. Our results overturn the paradigm attributing these phenomena to the removal of target atoms via sputter erosion: the mechanism dominating both stability and instability is the impact-induced redistribution of target atoms that are not sputtered away, with erosive effects being essentially irrelevant. We discuss the potential implications for the formation of a mysterious nanoscale topography, leading to surface degradation, of tungsten plasma-facing fusion reactor walls. Consideration of impact-induced redistribution processes may lead to a new design criterion for stability under irradiation. PMID:21505432

  6. NFI-C2 temporal-spatial expression and cellular localization pattern during tooth formation.

    PubMed

    Lamani, Ejvis; Gluhak-Heinrich, Jelica; MacDougall, Mary

    2015-12-01

    Currently, little is known regarding critical signaling pathways during later stages of tooth development, especially those associated with root formation. Nfi-c null mice, lacking molar roots, have implicated the transcription factor NFI-C as having an essential role in root development. Previously, we identified three NFI-C isoforms expressed in dental tissues with NFI-C2 being the major transcript. However, the expression pattern of the NFI-C2 protein is not characterized. In this study we performed in situ hybridization and immunohistochemistry using isoform specific probes. We show the production of a NFI-C2 peptide antibody, its characterization, the temporal-spatial expression pattern of the NFI-C2 protein during odontogenesis and sub-cellular localization in dental cells. Moderate NFI-C2 staining, as early as bud stage, was detected mostly in the condensing dental ectomesenchyme. This staining intensified within the dental pulp at later stages culminating in high expression in the dentin producing odontoblasts. The dental epithelium showed slight staining until cytodifferentiation of enamel organ into ameloblasts and stratum intermedium. During root formation NFI-C2 expression was high in the Hertwig's epithelial root sheath and later was found in the fully developed root and its supporting tissues. NFI-C2 cellular staining was cytosolic, associated with the Golgi, and nuclear. These data suggest a broader role for NFI-C during tooth formation than limited to root and periodontal ligament development. PMID:26687982

  7. Pattern formation and control in polymeric systems: From Minkowski measures to in situ AFM imaging

    NASA Astrophysics Data System (ADS)

    Jacobs, Karin

    2014-03-01

    Thin liquid polymer films are not only of great technical importance, they also exhibit a variety of dynamical instabilities. Some of them may be desired, some rather not. To analyze and finally control pattern formation, modern thin film theories are as vital as techniques to characterize the morphologies and structures in and on the films. Examples for the latter are atomic force microscopy (AFM) as well as scattering techniques. The talk will introduce into the practical applications of Minkowski measures to characterize patterns and explain what thin film properties (e.g. capillary number, solid/liquid boundary condition, glass transition temperature, chain mobility) can further be extracted including new technical possibilities by AFM and scattering techniques.

  8. Pattern formation in multiphase flow through porous media: continuum models and phase diagrams

    NASA Astrophysics Data System (ADS)

    Cueto-Felgueroso, L.; Juanes, R.

    2009-12-01

    Carbon capture and geologic storage, dissociation of methane hydrates in permafrost, infiltration of water in soil, and enhanced oil recovery, are some relevant examples of multiphase flow in porous media. While flow instabilities and pattern formation play a central role in these processes, our ability to describe them using mathematical models has been hampered by the lack of a macroscopic theory that explains the patterns observed in experimental and field conditions. We propose a new approach —phase-field modeling— to advance our fundamental understanding of multiphase porous media flow. The basic tenet, with origins in the mathematical description of solidification processes, is that the energy of the system is a function of the inhomogeneous distribution of fluid phases in the pore space, and should account for the presence of macroscopic interfaces. We present numerical simulations and compare our predictions with experimental observations. Numerical simulation of viscous fingering in a Hele-Shaw cell using the proposed phase-field modeling approach

  9. Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales.

    PubMed

    Martínez-García, Ricardo; Murgui, Clara; Hernández-García, Emilio; López, Cristóbal

    2015-01-01

    We study the spatial patterns formed by a system of interacting particles where the mobility of any individual is determined by the population crowding at two different spatial scales. In this way we model the behavior of some biological organisms (like mussels) that tend to cluster at short ranges as a defensive strategy, and strongly disperse if there is a high population pressure at large ranges for optimizing foraging. We perform stochastic simulations of a particle-level model of the system, and derive and analyze a continuous density description (a nonlinear diffusion equation). In both cases we show that this interplay of scale-dependent-behaviors gives rise to a rich formation of spatial patterns ranging from labyrinths to periodic cluster arrangements. In most cases these clusters have the very peculiar appearance of ring-like structures, i.e., organisms arranging in the perimeter of the clusters, which we discuss in detail. PMID:26147351

  10. Pattern formation from consistent dynamical closures of uniaxial nematic liquid crystals.

    PubMed

    Híjar, Humberto; de Hoyos, Diego Marquina; Santamaría-Holek, Iván

    2012-03-21

    Pattern formation in uniaxial polymeric liquid crystals is studied for different dynamic closure approximations. Using the principles of mesoscopic non-equilibrium thermodynamics in a mean-field approach, we derive a Fokker-Planck equation for the single-particle non-homogeneous distribution function of particle orientations and the evolution equations for the second and fourth order orientational tensor parameters. Afterwards, two dynamic closure approximations are discussed, one of them considering the relaxation of the fourth order orientational parameter and leading to a novel expression for the free-energy like function in terms of the scalar order parameter. Considering the evolution equation of the density of the system and values of the interaction parameter for which isotropic and nematic phases coexist, our analysis predicts that patterns and traveling waves can be produced in lyotropic uniaxial nematics even in the absence of external driving. PMID:22443750

  11. Continuous fine pattern formation by screen-offset printing using a silicone blanket

    NASA Astrophysics Data System (ADS)

    Nomura, Ken-ichi; Kusaka, Yasuyuki; Ushijima, Hirobumi; Nagase, Kazuro; Ikedo, Hiroaki; Mitsui, Ryosuke; Takahashi, Seiya; Nakajima, Shin-ichiro; Iwata, Shiro

    2014-09-01

    Screen-offset printing combines screen-printing on a silicone blanket with transference of the print from the blanket to a substrate. The blanket absorbs organic solvents in the ink, and therefore, the ink does not disperse through the material. This prevents blurring and allows fine patterns with widths of a few tens of micrometres to be produced. However, continuous printing deteriorates the pattern’s shape, which may be a result of decay in the absorption abilities of the blanket. Thus, we have developed a new technique for refreshing the blanket by substituting high-boiling-point solvents present on the blanket surface with low-boiling-point solvents. We analyse the efficacy of this technique, and demonstrate continuous fine pattern formation for 100 screen-offset printing processes.

  12. Spatiotemporal Pattern Formation and Chaos in the Belousov-Zhabotinsky Reaction in a Reverse Microemulsion

    NASA Astrophysics Data System (ADS)

    Epstein, Irving R.; Vanag, Vladimir K.

    2003-08-01

    We study the spatiotemporal behavior of the oscillatory Belousov-Zhabotinsky (BZ) reaction in a reverse microemulsion consisting of water, octane and the surfactant sodium bis(2-ethylhexyl)sulfosuccinate (AOT). By varying the microemulsion composition, we can "tune" its structure, specifically the size and spacing between the nanometer-sized water droplets in which the polar BZ reactants reside. We find a remarkable array of pattern formation as the microemulsion structure and BZ chemistry are varied. Behaviors observed include stationary Turing patterns, traveling and standing waves, spirals, targets, antispirals and antitargets (which travel into rather than out from their center), and spatiotemporal chaos. A simple reaction-diffusion model, which accounts for the BZ chemistry and the differential diffusion of species within water droplets and in the bulk oil phase, is able to reproduce nearly all of the observed behavior.

  13. Three dimensional simulations of pattern formation during high-pressure, freely localized microwave breakdown in air

    SciTech Connect

    Kourtzanidis, K. Boeuf, J. P.; Rogier, F.

    2014-12-15

    Recent experiments have demonstrated that a freely localized 100 GHz microwave discharge can propagate towards the microwave source with high speed, forming a complex pattern of self-organized filaments. We present three-dimensional simulations of the formation and propagation of such patterns that reveal more information on their nature and interaction with the electromagnetic waves. The developed three-dimensional Maxwell-plasma solver permits the study of different forms of incident field polarization. Results for linear and circular polarization of the wave are presented and comparisons with recent experiments show a good overall agreement. The three dimensional simulations provide a quantitative analysis of the parameters controlling the time and length scales of the strongly non-linear plasma dynamics and could be useful for potential microwave plasma applications such as aerodynamic flow and combustion control.

  14. Primary mesenchyme cell-ring pattern formation in 2D-embryos of the sea urchin.

    PubMed

    Katow, H; Nakajima, Y; Uemura, I

    2000-02-01

    Primary mesenchyme cell (PMC) migration during PMC-ring pattern formation was analyzed using computer-assisted time-lapse video microscopy in spread embryos (2D-embryo) of the sea urchin, Mespilia globulus, and a computer simulation. The PMC formed a near normal ring pattern in the 2D-embryos, which were shown to be an excellent model for the examination of cell behavior in vivo by time-lapse computer analysis. The average migration distance of the ventro-lateral PMC aggregate-forming cells (AFC) and that of the dorso-ventral PMC cable-forming cells (CFC) showed no significant difference. All PMC took a rather straightforward migration path to their destinations with little lag time after ingression. This in vivo cell behavior fitted well to a computer simulation with a non-diffusable chemotaxis factor in the cyber-cell migration field. This simulation suggests that PMC recognize their destination from a very early moment of cell migration from the vegetal plate, and implicates that a chemoattractive region is necessary for making the PMC migration pattern. The left- and right-lateral AFC and dorso and ventral CFC were each derived from an unequally divided one-quarter segment of the vegetal plate. This suggests that AFC and CFC have a distinctive ancestor in the vegetal plate, and the PMC are a heterogeneous population at least in terms of their destination in the PMC-ring pattern. PMID:10831039

  15. Disappearing scales in carps: re-visiting Kirpichnikov's model on the genetics of scale pattern formation.

    PubMed

    Casas, Laura; Szűcs, Réka; Vij, Shubha; Goh, Chin Heng; Kathiresan, Purushothaman; Németh, Sándor; Jeney, Zsigmond; Bercsényi, Miklós; Orbán, László

    2013-01-01

    The body of most fishes is fully covered by scales that typically form tight, partially overlapping rows. While some of the genes controlling the formation and growth of fish scales have been studied, very little is known about the genetic mechanisms regulating scale pattern formation. Although the existence of two genes with two pairs of alleles (S&s and N&n) regulating scale coverage in cyprinids has been predicted by Kirpichnikov and colleagues nearly eighty years ago, their identity was unknown until recently. In 2009, the 'S' gene was found to be a paralog of fibroblast growth factor receptor 1, fgfr1a1, while the second gene called 'N' has not yet been identified. We re-visited the original model of Kirpichnikov that proposed four major scale pattern types and observed a high degree of variation within the so-called scattered phenotype due to which this group was divided into two sub-types: classical mirror and irregular. We also analyzed the survival rates of offspring groups and found a distinct difference between Asian and European crosses. Whereas nude × nude crosses involving at least one parent of Asian origin or hybrid with Asian parent(s) showed the 25% early lethality predicted by Kirpichnikov (due to the lethality of the NN genotype), those with two Hungarian nude parents did not. We further extended Kirpichnikov's work by correlating changes in phenotype (scale-pattern) to the deformations of fins and losses of pharyngeal teeth. We observed phenotypic changes which were not restricted to nudes, as described by Kirpichnikov, but were also present in mirrors (and presumably in linears as well; not analyzed in detail here). We propose that the gradation of phenotypes observed within the scattered group is caused by a gradually decreasing level of signaling (a dose-dependent effect) probably due to a concerted action of multiple pathways involved in scale formation. PMID:24386179

  16. Disappearing Scales in Carps: Re-Visiting Kirpichnikov's Model on the Genetics of Scale Pattern Formation

    PubMed Central

    Goh, Chin Heng; Kathiresan, Purushothaman; Németh, Sándor; Jeney, Zsigmond; Bercsényi, Miklós; Orbán, László

    2013-01-01

    The body of most fishes is fully covered by scales that typically form tight, partially overlapping rows. While some of the genes controlling the formation and growth of fish scales have been studied, very little is known about the genetic mechanisms regulating scale pattern formation. Although the existence of two genes with two pairs of alleles (S&s and N&n) regulating scale coverage in cyprinids has been predicted by Kirpichnikov and colleagues nearly eighty years ago, their identity was unknown until recently. In 2009, the ‘S’ gene was found to be a paralog of fibroblast growth factor receptor 1, fgfr1a1, while the second gene called ‘N’ has not yet been identified. We re-visited the original model of Kirpichnikov that proposed four major scale pattern types and observed a high degree of variation within the so-called scattered phenotype due to which this group was divided into two sub-types: classical mirror and irregular. We also analyzed the survival rates of offspring groups and found a distinct difference between Asian and European crosses. Whereas nude × nude crosses involving at least one parent of Asian origin or hybrid with Asian parent(s) showed the 25% early lethality predicted by Kirpichnikov (due to the lethality of the NN genotype), those with two Hungarian nude parents did not. We further extended Kirpichnikov's work by correlating changes in phenotype (scale-pattern) to the deformations of fins and losses of pharyngeal teeth. We observed phenotypic changes which were not restricted to nudes, as described by Kirpichnikov, but were also present in mirrors (and presumably in linears as well; not analyzed in detail here). We propose that the gradation of phenotypes observed within the scattered group is caused by a gradually decreasing level of signaling (a dose-dependent effect) probably due to a concerted action of multiple pathways involved in scale formation. PMID:24386179

  17. The formation and distribution of hippocampal synapses on patterned neuronal networks

    NASA Astrophysics Data System (ADS)

    Dowell-Mesfin, Natalie M.

    Communication within the central nervous system is highly orchestrated with neurons forming trillions of specialized junctions called synapses. In vivo, biochemical and topographical cues can regulate neuronal growth. Biochemical cues also influence synaptogenesis and synaptic plasticity. The effects of topography on the development of synapses have been less studied. In vitro, neuronal growth is unorganized and complex making it difficult to study the development of networks. Patterned topographical cues guide and control the growth of neuronal processes (axons and dendrites) into organized networks. The aim of this dissertation was to determine if patterned topographical cues can influence synapse formation and distribution. Standard fabrication and compression molding procedures were used to produce silicon masters and polystyrene replicas with topographical cues presented as 1 mum high pillars with diameters of 0.5 and 2.0 mum and gaps of 1.0 to 5.0 mum. Embryonic rat hippocampal neurons grown unto patterned surfaces. A developmental analysis with immunocytochemistry was used to assess the distribution of pre- and post-synaptic proteins. Activity-dependent pre-synaptic vesicle uptake using functional imaging dyes was also performed. Adaptive filtering computer algorithms identified synapses by segmenting juxtaposed pairs of pre- and post-synaptic labels. Synapse number and area were automatically extracted from each deconvolved data set. In addition, neuronal processes were traced automatically to assess changes in synapse distribution. The results of these experiments demonstrated that patterned topographic cues can induce organized and functional neuronal networks that can serve as models for the study of synapse formation and plasticity as well as for the development of neuroprosthetic devices.

  18. Zonal Flow as Pattern Formation: Merging Jets and the Ultimate Jet Length Scale

    SciTech Connect

    Jeffrey B. Parker and John A. Krommes

    2013-01-30

    Zonal flows are well known to arise spontaneously out of turbulence. It is shown that for statisti- cally averaged equations of quasigeostrophic turbulence on a beta plane, zonal flows and inhomoge- neous turbulence fit into the framework of pattern formation. There are many implications. First, the zonal flow wavelength is not unique. Indeed, in an idealized, infinite system, any wavelength within a certain continuous band corresponds to a solution. Second, of these wavelengths, only those within a smaller subband are linearly stable. Unstable wavelengths must evolve to reach a stable wavelength; this process manifests as merging jets.

  19. The pattern of secondary root formation in curving roots of Arabidopsis thaliana (L.) Heynh

    NASA Technical Reports Server (NTRS)

    Fortin, M. C.; Pierce, F. J.; Poff, K. L.

    1989-01-01

    A gravitational stimulus was used to induce the curvature of the main root of Arabidopsis thaliana. The number of secondary roots increased on the convex side and decreased on the concave side of any curved main root axes in comparison with straight roots used as the control. The same phenomenon was observed with the curved main roots of plants grown on a clinostat and of mutant plants exhibiting random root orientation. The data suggest that the pattern of lateral root formation is associated with curvature but is independent of the environmental stimuli used to induce curvature.

  20. The physics of pattern formation at liquid interfaces. Progress report, June 1, 1991--May 31, 1992

    SciTech Connect

    Maher, J.V.

    1992-06-01

    During the past year we have submitted six papers for publication, three related to the dynamics of macroscopic interfaces, and ultimately all related to solidification, and three related to the internal structure of disorderly materials, with possible applications to the processing of composite materials. In addition to completing all these projects during the past year, we have begun two new projects, one on pattern formation and one on aggregation within a composite system. A brief description is given of this research in this paper.

  1. DSA patterning options for FinFET formation at 7nm node

    NASA Astrophysics Data System (ADS)

    Liu, Chi-Chun C.; Franke, Elliott; Lie, Fee Li; Sieg, Stuart; Tsai, Hsinyu; Lai, Kafai; Truong, Hoa; Farrell, Richard; Somervell, Mark; Sanders, Daniel; Felix, Nelson; Guillorn, Michael; Burns, Sean; Hetzer, David; Ko, Akiteru; Arnold, John; Colburn, Matthew

    2016-03-01

    Several 27nm-pitch directed self-assembly (DSA) processes targeting fin formation for FinFET device fabrication are studied in a 300mm pilot line environment, including chemoepitaxy for a conventional Fin arrays, graphoepitaxy for a customization approach and a hybrid approach for self-aligned Fin cut. The trade-off between each DSA flow is discussed in terms of placement error, Fin CD/profile uniformity, and restricted design. Challenges in pattern transfer are observed and process optimization are discussed. Finally, silicon Fins with 100nm depth and on-target CD using different DSA options with either lithographic or self-aligned customization approach are demonstrated.

  2. Laser Patterning of Diamond. Part II. Surface Nondiamond Carbon Formation and its Removal

    SciTech Connect

    Smedley, J.; Jaye, C; Bohon, J; Rao, T; Fischer, D

    2009-01-01

    As diamond becomes more prevalent for electronic and research applications, methods of patterning diamond will be required. One such method, laser ablation, has been investigated in a related work. We report on the formation of surface nondiamond carbon during laser ablation of both polycrystalline and single-crystal synthetic diamonds. Near edge x-ray absorption fine structure spectroscopy was used to confirm that the nondiamond carbon layer formed during the ablation was amorphous, and Fourier transform infrared absorption spectroscopy (FTIR) was used to estimate the thickness of this layer to be {approx} 60 nm. Ozone cleaning was used to remove the nondiamond carbon layer.

  3. E × B shear pattern formation by radial propagation of heat flux waves

    SciTech Connect

    Kosuga, Y.; Diamond, P. H.; Dif-Pradalier, G.; Gürcan, Ö. D.

    2014-05-15

    A novel theory to describe the formation of E×B flow patterns by radially propagating heat flux waves is presented. A model for heat avalanche dynamics is extended to include a finite delay time between the instantaneous heat flux and the mean flux, based on an analogy between heat avalanche dynamics and traffic flow dynamics. The response time introduced here is an analogue of the drivers' response time in traffic dynamics. The microscopic foundation for the time delay is the time for mixing of the phase space density. The inclusion of the finite response time changes the model equation for avalanche dynamics from Burgers equation to a nonlinear telegraph equation. Based on the telegraph equation, the formation of heat flux jams is predicted. The growth rate and typical interval of jams are calculated. The connection of the jam interval to the typical step size of the E×B staircase is discussed.

  4. Pattern formation in chemically interacting active rotors with self-propulsion.

    PubMed

    Liebchen, Benno; Cates, Michael E; Marenduzzo, Davide

    2016-09-21

    We demonstrate that active rotations in chemically signalling particles, such as autochemotactic E. coli close to walls, create a route for pattern formation based on a nonlinear yet deterministic instability mechanism. For slow rotations, we find a transient persistence of the uniform state, followed by a sudden formation of clusters contingent on locking of the average propulsion direction by chemotaxis. These clusters coarsen, which results in phase separation into a dense and a dilute region. Faster rotations arrest phase separation leading to a global travelling wave of rotors with synchronized roto-translational motion. Our results elucidate the physics resulting from the competition of two generic paradigms in active matter, chemotaxis and active rotations, and show that the latter provides a tool to design programmable self-assembly of active matter, for example to control coarsening. PMID:27526180

  5. Hydrologic Connectivity as a Window into Pattern Conditions and Formation Processes in Aquatic Ecosystems

    NASA Astrophysics Data System (ADS)

    Larsen, L. G.; Choi, J.; Nungesser, M. K.; Harvey, J. W.

    2011-12-01

    Patterned aquatic ecosystems exhibit different types and degrees of hydrologic connectivity, from isolated open-water patches in some inland marshes, to cross-slope strings and flarks of striped fens, to along-slope ridges and sloughs of low-gradient subtropical wetlands, to dendritic channels of coastal marshes. The nature and degree of this connectivity are closely linked to landscape function. For example, hydrologic connectivity perpendicular to river channel thalwegs relates to the exchange of sediment and nutrients between channels and floodplains, whereas connectivity parallel to a dominant flow direction affects fish migration or the likelihood of contaminant transport. Characteristics of hydrologic connectivity reflect not only the results of landscape pattern but also the mechanisms responsible for pattern creation. Quantifying those connectivity characteristics provides a robust means to identify landscapes likely formed under a consistent set of processes or to compare the output of landscape simulation models to actual landscapes in order to determine whether the models capture the most relevant landscape formation processes. However, established methods for quantifying isotropic patch connectivity are often ill suited for strongly patterned landscapes or hydroscapes in which directional flow is important. Using graph theory principles, we developed two alternative indices of directional hydrologic connectivity: the maximum flow index (MFI) and directional connectivity index (DCI), which quantify the connectivity of flow paths along a particular axis of interest. The MFI is sensitive to the existence of any hydrologic connection along the direction of interest, whereas the DCI is sensitive to the linearity of connections along that direction. Curves of directional connectivity over a range of angular bearings provide a quantitative, information-dense representation of landscape structure that can be related to subtle differences in the physical

  6. Bone morphogenetic proteins, eye patterning, and retinocollicular map formation in the mouse

    PubMed Central

    Plas, Daniel T.; Dhande, Onkar; Lopez, Joshua E.; Murali, Deepa; Thaller, Christina; Henkemeyer, Mark; Furuta, Yasuhide; Overbeek, Paul; Crair, Michael C.

    2009-01-01

    Patterning events during early eye formation determine retinal cell fate and can dictate the behavior of retinal ganglion cell (RGC) axons as they navigate toward central brain targets. The temporally and spatially regulated expression of bone morphogenetic proteins (BMPs) and their receptors in the retina are thought to play a key role in this process, initiating gene expression cascades that distinguish different regions of the retina, particularly along the dorsoventral axis. Here, we examine the role of BMP and a potential downstream effector, EphB, in retinotopic map formation in the lateral geniculate nucleus (LGN) and superior colliculus (SC). RGC axon behaviors during retinotopic map formation in wild type mice are compared with those in several strains of mice with engineered defects of BMP and EphB signaling. Normal RGC axon sorting produces axon order in the optic tract that reflects the dorsoventral position of the parent RGCs in the eye. A dramatic consequence of disrupting BMP signaling is a missorting of RGC axons as they exit the optic chiasm. This sorting is not dependent on EphB. When BMP signaling in the developing eye is genetically modified, RGC order in the optic tract and targeting in the LGN and SC are correspondingly disrupted. These experiments show that BMP signaling regulates dorsoventral RGC cell fate, RGC axon behavior in the ascending optic tract and retinotopic map formation in the LGN and SC through mechanisms that are in part distinct from EphB signaling in the LGN and SC. PMID:18614674

  7. GM-CSF deficiency delays neointima formation in a normolipidemic mouse model of endoluminal endothelial damage.

    PubMed

    Harris, Angie K; Shen, Jie; Radford, Jane; Bao, Shisan; Hambly, Brett D

    2009-02-01

    Granulocyte-macrophage colony-stimulating factor (GM-CSF) has been implicated in atherogenesis and has been shown to have both pro- and antiatherogenic properties. Neointimal thickening is a prominent feature of early atherogenesis. This study aimed to examine the role of GM-CSF in neointimal formation induced by endothelial injury using a GM-CSF(-/-) mouse model. Neointimal thickening was induced by endothelial damage in the common iliac arteries of normolipidemic C57Bl/6 (wild-type) and GM-CSF(-/-) mice. Arteries were collected weekly for 3-7 weeks following surgery. A significant delay in neointimal formation in the GM-CSF(-/-) compared with wild-type mice was detected by morphometric analysis of the intimal area. Neointimal size was approximately 10% smaller in GM-CSF(-/-) mice at 4-6 weeks post-surgery, compared with wild-type mice. The neointima was composed predominantly of smooth muscle cells and there was no difference in the extent of endothelial cell coverage between the wild-type and GM-CSF(-/-) mice. Using immunohistochemistry, reduced macrophages (F4/80(+) cells), proliferating cells (proliferating cell nuclear antigen (PCNA)(+) cells) and platelet-derived growth factor-B were detected within the arteries of GM-CSF(-/-) mice compared with wild types at 4 weeks post-surgery. GM-CSF(-/-) mice had reduced connective tissue within the neointima compared with wild types at 5 weeks post-surgery, determined by trichrome staining. We conclude that GM-CSF deficiency reduces neointimal formation in a normolipidemic model, primarily due to reduced macrophage recruitment. PMID:18839015

  8. Mechanical Regulation of Three-Dimensional Epithelial Fold Pattern Formation in the Mouse Oviduct.

    PubMed

    Koyama, Hiroshi; Shi, Dongbo; Suzuki, Makoto; Ueno, Naoto; Uemura, Tadashi; Fujimori, Toshihiko

    2016-08-01

    Epithelia exhibit various three-dimensional morphologies linked to organ function in animals. However, the mechanisms of three-dimensional morphogenesis remain elusive. The luminal epithelium of the mouse oviduct forms well-aligned straight folds along the longitudinal direction of the tubes. Disruption of the Celsr1 gene, a planar cell polarity-related gene, causes ectopically branched folds. Here, we evaluated the mechanical contributions of the epithelium to the fold pattern formation. In the mutant oviduct, the epithelium was more intricate along the longitudinal direction than in the wild-type, suggesting a higher ratio of the longitudinal length of the epithelial layer to that of the surrounding smooth muscle (SM) layer (L-Epi/SM ratio). Our mathematical modeling and computational simulations suggested that the L-Epi/SM ratio could explain the differences in fold branching between the two genotypes. Longitudinal epithelial tensions were increased in well-aligned folds compared with those in disorganized folds both in the simulations and in experimental estimations. Artificially increasing the epithelial tensions suppressed the branching in simulations, suggesting that the epithelial tensions can regulate fold patterning. The epithelial tensions could be explained by the combination of line tensions along the epithelial cell-cell boundaries with the polarized cell arrays observed in vivo. These results suggest that the fold pattern is associated with the polarized cell array through the longitudinal epithelial tension. Further simulations indicated that the L-Epi/SM ratio could contribute to fold pattern diversity, suggesting that the L-Epi/SM ratio is a critical parameter in the fold patterning in tubular organs. PMID:27508448

  9. Turing instability and pattern formation in a two-population neuronal network model

    NASA Astrophysics Data System (ADS)

    Wyller, John; Blomquist, Patrick; Einevoll, Gaute T.

    2007-01-01

    A two-population firing-rate model describing the dynamics of excitatory and inhibitory neural activity in one spatial dimension is investigated with respect to formation of patterns, in particular stationary periodic patterns and spatiotemporal oscillations. Conditions for existence of spatially homogeneous equilibrium states are first determined, and the stability properties of these equilibria are investigated. It is shown that the nonlocal synaptic interactions may promote a finite bandwidth instability in a way analogous to diffusion effects in the classical Turing instability for reaction-diffusion equations and modulational instability in the theory of nonlinear waves in nonlocal defocusing Kerr media. Our analysis relies on the wave-number dependent invariants of the 2×2-matrix representing the spatially Fourier-transformed linearized evolution equations. The generic picture which emerges is an instability consisting of a finite set of well-separated unstable bands in wave-number space (gain bands). The case with symmetrical, exponentially decaying connectivity functions is investigated in detail, allowing for a more comprehensive analysis of the gain-band structure, and, in particular, conditions for the excitation of a single gain band through a Turing-Hopf bifurcation with the relative inhibition time constant as control parameter. Two typical situations emerge depending on the thresholds and inclinations of the sigmoidal firing-rate functions: (i) A single gain-band is excited through a Turing-Hopf bifurcation, and the resulting state is a spatiotemporally oscillating pattern, or (ii) the instability develops into a stationary periodic pattern, i.e. a set of equidistant bumps. The dependence of instability-type on the inclinations of the firing-rate function and the time constant are comprehensively investigated, demonstrating, for example, that only stationary patterns can be generated for sufficiently small inhibitory time constants. The nonlinear

  10. Dynamic Pattern Formation for Wings of Pterygota in an Eclosion ---Pattern Analysis for Wings with the Imago---

    NASA Astrophysics Data System (ADS)

    Seino, M.; Kakazu, Y.

    The vein and cell patterns for the fore and hind wing of Lepidoptera, Hemiptera, Orthoptera and Odonata are analyzed and discussed. For vein patterns of them, the fractal properties are shown and the inequality between four orders is obtained. The nature of wings observed by mass distributions for fractal dimensions of the vein pattern is presented.

  11. Pickering emulsions stabilized by oppositely charged colloids: Stability and pattern formation

    NASA Astrophysics Data System (ADS)

    Christdoss Pushpam, Sam David; Basavaraj, Madivala G.; Mani, Ethayaraja

    2015-11-01

    A binary mixture of oppositely charged colloids can be used to stabilize water-in-oil or oil-in-water emulsions. A Monte Carlo simulation study to address the effect of charge ratio of colloids on the stability of Pickering emulsions is presented. The colloidal particles at the interface are modeled as aligned dipolar hard spheres, with attractive interaction between unlike-charged and repulsive interaction between like-charged particles. The optimum composition (fraction of positively charged particles) required for the stabilization corresponds to a minimum in the interaction energy per particle. In addition, for each charge ratio, there is a range of compositions where emulsions can be stabilized. The structural arrangement of particles or the pattern formation at the emulsion interface is strongly influenced by the charge ratio. We find well-mixed isotropic, square, and hexagonal arrangements of particles on the emulsion surface for different compositions at a given charge ratio. The distribution of coordination numbers is calculated to characterize structural features. The simulation study is useful for the rational design of Pickering emulsifications wherein oppositely charged colloids are used, and for the control of pattern formation that can be useful for the synthesis of colloidosomes and porous shells derived thereof.

  12. Energy approach to rivalry dynamics, soliton stability, and pattern formation in neuronal networks

    NASA Astrophysics Data System (ADS)

    Loxley, P. N.; Robinson, P. A.

    2007-10-01

    Hopfield’s Lyapunov function is used to view the stability and topology of equilibria in neuronal networks for visual rivalry and pattern formation. For two neural populations with reciprocal inhibition and slow adaptation, the dynamics of neural activity is found to include a pair of limit cycles: one for oscillations between states where one population has high activity and the other has low activity, as in rivalry, and one for oscillations between states where both populations have the same activity. Hopfield’s Lyapunov function is used to find the dynamical mechanism for oscillations and the basin of attraction of each limit cycle. For a spatially continuous population with lateral inhibition, stable equilibria are found for local regions of high activity (solitons) and for bound states of two or more solitons. Bound states become stable when moving two solitons together minimizes the Lyapunov function, a result of decreasing activity in regions between peaks of high activity when the firing rate is described by a sigmoid function. Lowering the barrier to soliton formation leads to a pattern-forming instability, and a nonlinear solution to the dynamical equations is found to be given by a soliton lattice, which is completely characterized by the soliton width and the spacing between neighboring solitons. Fluctuations due to noise create lattice vacancies analogous to point defects in crystals, leading to activity which is spatially inhomogeneous.

  13. The dependence of contrail formation on the weather pattern and altitude in the North Atlantic

    NASA Astrophysics Data System (ADS)

    Irvine, E. A.; Hoskins, B. J.; Shine, K. P.

    2012-06-01

    Aircraft flying through cold ice-supersaturated air produce persistent contrails which contribute to the climate impact of aviation. Here, we demonstrate the importance of the weather situation, together with the route and altitude of the aircraft through this, on estimating contrail coverage. The results have implications for determining the climate impact of contrails as well as potential mitigation strategies. Twenty-one years of re-analysis data are used to produce a climatological assessment of conditions favorable for persistent contrail formation between 200 and 300 hPa over the north Atlantic in winter. The seasonal-mean frequency of cold ice-supersaturated regions is highest near 300 hPa, and decreases with altitude. The frequency of occurrence of ice-supersaturated regions varies with large-scale weather pattern; the most common locations are over Greenland, on the southern side of the jet stream and around the northern edge of high pressure ridges. Assuming aircraft take a great circle route, as opposed to a more realistic time-optimal route, is likely to lead to an error in the estimated contrail coverage, which can exceed 50% for westbound north Atlantic flights. The probability of contrail formation can increase or decrease with height, depending on the weather pattern, indicating that the generic suggestion that flying higher leads to fewer contrails is not robust.

  14. Surface induced phase separation and pattern formation at the isotropic interface in chiral nematic liquid crystals.

    PubMed

    Zola, R S; Evangelista, L R; Yang, Y-C; Yang, D-K

    2013-02-01

    We study the pattern formation of a chiral nematic liquid crystal under a wetting transition. In the isotropic-liquid crystal transition, a surface-enhanced effect happens and a thin liquid crystal layer forms at the substrates of the cell. In this confined system, chirality, elastic anisotropy, surface anchoring, and wetting strength interplay. A striped pattern is formed due to the chiral nature of the material and the tilted anchoring at the isotropic boundary. As the wetting layer grows from cooling the sample, first the stripes rotate through a process where dislocation defects are formed. As the wetting layer grows further, the periodicity of the stripe structure changes, and finally a splitting of the stripes occurs. Because of the unique properties of this system, new insights about pitch-thickness ratio, interface anchoring, and elastic anisotropy effect are found. Since the anchoring at the isotropic boundary is weak, the critical ratio between the thickness of the wetting layer and the helical pitch is different from that reported in the literature. We also discover that the elastic anisotropy and elastic constant ratios play a critical role in stripe formation. Because of the similarity with biological fibrous composites (twisted plywood), our system may be used as a synthetic version to mimic the naturally occurring one. We carry out a simulation study to explain the experimental results. PMID:23414046

  15. Surface Induced Phase Separation and Pattern Formation at the Isotropic Interface in Chiral Nematic Liquid Crystals

    NASA Astrophysics Data System (ADS)

    Zola, R. S.; Evangelista, L. R.; Yang, Y.-C.; Yang, D.-K.

    2013-02-01

    We study the pattern formation of a chiral nematic liquid crystal under a wetting transition. In the isotropic-liquid crystal transition, a surface-enhanced effect happens and a thin liquid crystal layer forms at the substrates of the cell. In this confined system, chirality, elastic anisotropy, surface anchoring, and wetting strength interplay. A striped pattern is formed due to the chiral nature of the material and the tilted anchoring at the isotropic boundary. As the wetting layer grows from cooling the sample, first the stripes rotate through a process where dislocation defects are formed. As the wetting layer grows further, the periodicity of the stripe structure changes, and finally a splitting of the stripes occurs. Because of the unique properties of this system, new insights about pitch-thickness ratio, interface anchoring, and elastic anisotropy effect are found. Since the anchoring at the isotropic boundary is weak, the critical ratio between the thickness of the wetting layer and the helical pitch is different from that reported in the literature. We also discover that the elastic anisotropy and elastic constant ratios play a critical role in stripe formation. Because of the similarity with biological fibrous composites (twisted plywood), our system may be used as a synthetic version to mimic the naturally occurring one. We carry out a simulation study to explain the experimental results.

  16. Regulatory logic and pattern formation in the early sea urchin embryo.

    PubMed

    Sun, Mengyang; Cheng, Xianrui; Socolar, Joshua E S

    2014-12-21

    We model the endomesoderm tissue specification process in the vegetal half of the early sea urchin embryo using Boolean models with continuous-time updating to represent the regulatory network that controls gene expression. Our models assume that the network interaction rules remain constant over time and the dynamics plays out on a predetermined program of cell divisions. An exhaustive search of two-node models, in which each node may represent a module of several genes in the real regulatory network, yields a unique network architecture that can accomplish the pattern formation task at hand--the formation of three latitudinal tissue bands from an initial state with only two distinct cell types. Analysis of an eight-gene model constructed from available experimental data reveals that it has a modular structure equivalent to the successful two-node case. Our results support the hypothesis that the gene regulatory network provides sufficient instructions for producing the correct pattern of tissue specification at this stage of development (between the fourth and tenth cleavages in the urchin embryo). PMID:25093827

  17. An in vitro-in silico interface platform for spatiotemporal analysis of pattern formation in collective epithelial cells.

    PubMed

    Hagiwara, M

    2016-08-01

    A multicellular organization is a complex resulting from the coordinated migration of cells to form a specific pattern. The directionality of migration is governed by the mechanical and molecular dynamics of factors secreted from the cells. The mechanism underlying pattern formation is too complex to unveil by culture experiments alone. A mathematical model could provide a powerful tool for elucidating the mechanism of pattern formation by computing the molecular dynamics, which are difficult to visualize by culture experiments. However, there tends to be a gap between mathematical models and experimental research due to incongruity between the idealized conditions of the model and the experimental results. This paper presents an in vitro-in silico interface platform for elucidating the logic of multicellular pattern formation. Two-dimensional collective cell pattern formation was developed using normal human bronchial epithelial cells. Then, geometrical control of collective cells followed by feedback iteration was used to bridge the gap between the mathematical model and in vitro experiments. The mechanisms underlying the pattern formation of bronchial epithelial cells were evaluated using a reaction-diffusion model. The results indicated that differences in the diffusion rates of the activator and inhibitor determine the direction of collective cell migration to form a specific pattern. PMID:27452205

  18. Dynamic coupling of pattern formation and morphogenesis in the developing vertebrate retina.

    PubMed

    Picker, Alexander; Cavodeassi, Florencia; Machate, Anja; Bernauer, Sabine; Hans, Stefan; Abe, Gembu; Kawakami, Koichi; Wilson, Stephen W; Brand, Michael

    2009-10-01

    During embryonic development, pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of the spatial identities of cells with their movements. In the vertebrate retina, patterning along the dorsal-ventral and nasal-temporal (anterior-posterior) axes is required for correct spatial representation in the retinotectal map. However, it is unknown how specification of axial cell positions in the retina occurs during the complex process of early eye morphogenesis. Studying zebrafish embryos, we show that morphogenetic tissue rearrangements during eye evagination result in progenitor cells in the nasal half of the retina primordium being brought into proximity to the sources of three fibroblast growth factors, Fgf8/3/24, outside the eye. Triple-mutant analysis shows that this combined Fgf signal fully controls nasal retina identity by regulating the nasal transcription factor Foxg1. Surprisingly, nasal-temporal axis specification occurs very early along the dorsal-ventral axis of the evaginating eye. By in vivo imaging GFP-tagged retinal progenitor cells, we find that subsequent eye morphogenesis requires gradual tissue compaction in the nasal half and directed cell movements into the temporal half of the retina. Balancing these processes drives the progressive alignment of the nasal-temporal retina axis with the anterior-posterior body axis and is controlled by a feed-forward effect of Fgf signaling on Foxg1-mediated cell cohesion. Thus, the mechanistic coupling and dynamic synchronization of tissue patterning with morphogenetic cell behavior through Fgf signaling leads to the graded allocation of cell positional identity in the eye, underlying retinotectal map formation. PMID:19823566

  19. Dynamic Coupling of Pattern Formation and Morphogenesis in the Developing Vertebrate Retina

    PubMed Central

    Picker, Alexander; Cavodeassi, Florencia; Machate, Anja; Bernauer, Sabine; Hans, Stefan; Abe, Gembu; Kawakami, Koichi; Wilson, Stephen W.; Brand, Michael

    2009-01-01

    During embryonic development, pattern formation must be tightly synchronized with tissue morphogenesis to coordinate the establishment of the spatial identities of cells with their movements. In the vertebrate retina, patterning along the dorsal-ventral and nasal-temporal (anterior-posterior) axes is required for correct spatial representation in the retinotectal map. However, it is unknown how specification of axial cell positions in the retina occurs during the complex process of early eye morphogenesis. Studying zebrafish embryos, we show that morphogenetic tissue rearrangements during eye evagination result in progenitor cells in the nasal half of the retina primordium being brought into proximity to the sources of three fibroblast growth factors, Fgf8/3/24, outside the eye. Triple-mutant analysis shows that this combined Fgf signal fully controls nasal retina identity by regulating the nasal transcription factor Foxg1. Surprisingly, nasal-temporal axis specification occurs very early along the dorsal-ventral axis of the evaginating eye. By in vivo imaging GFP-tagged retinal progenitor cells, we find that subsequent eye morphogenesis requires gradual tissue compaction in the nasal half and directed cell movements into the temporal half of the retina. Balancing these processes drives the progressive alignment of the nasal-temporal retina axis with the anterior-posterior body axis and is controlled by a feed-forward effect of Fgf signaling on Foxg1-mediated cell cohesion. Thus, the mechanistic coupling and dynamic synchronization of tissue patterning with morphogenetic cell behavior through Fgf signaling leads to the graded allocation of cell positional identity in the eye, underlying retinotectal map formation. PMID:19823566

  20. A possible formation mechanism of rampart-like ejecta pattern in a laboratory

    NASA Astrophysics Data System (ADS)

    Suzuki, A.; Kadono, T.; Nakamura, A. M.; Arakawa, M.; Wada, K.; Yamamoto, S.

    2011-12-01

    The ejecta morphologies around impact craters represent highly diverse appearance on the surface of solid bodies in our Solar System. It is considered that the varied ejecta morphologies result from the environments such as the atmospheric pressure, the volatile content in the subsurface, because they affect the emplacement process of the ejecta. Clarifying the relationships between the ejecta morphologies and the formation processes and environments could constrain the ancient surface environment and the evolution of the planets. We have investigated the ejecta patterns around the impact craters which formed on a glass beads layer in a laboratory, and found that the patterns depend on impact velocity, atmospheric pressure, and initial state of packing of the target [Suzuki et al., 2010, JpGU abstract]. Now, we focus on one of the ejecta patterns which has a petal-like (or sometimes concentric) ridges on the distal edge of the continuous ejecta. This ejecta pattern looks very similar to the rampart ejecta morphology observed around Martian impact craters [e.g. Barlow et al., 2000]. The experiments are conducted with the small light gas gun placed in Kobe University, Japan. The projectile is a cylinder with a diameter of 10 mm and a height of 10 mm, and is made of aluminum, nylon, or stainless. The target is a layer of glass beads (nearly uniform diameter) in a tub with ~28 cm in diameter. The bulk density is about 1.7 g/cm^3. The following three parameters are varied: 1) the diameter of the target glass beads (50, 100, 420 microns), 2) the ambient atmospheric pressure in the chamber (from ~500 Pa to atmospheric pressure), 3) the impact velocity of the projectile (from a few to ~120 m/s). In our experiments, the rampart-like ridged patterns are observed within the following conditions: 1) the diameter of the target glass beads is 50 and 100 microns, 2) the ambient pressure in the chamber is higher than ~10^4 Pa, and 3) the impact velocity is higher than 16 m

  1. Dynamic model based on voltage transfer curve for pattern formation in dielectric barrier glow discharge

    SciTech Connect

    Li, Ben; He, Feng; Ouyang, Jiting; Duan, Xiaoxi

    2015-12-15

    Simulation work is very important for understanding the formation of self-organized discharge patterns. Previous works have witnessed different models derived from other systems for simulation of discharge pattern, but most of these models are complicated and time-consuming. In this paper, we introduce a convenient phenomenological dynamic model based on the basic dynamic process of glow discharge and the voltage transfer curve (VTC) to study the dielectric barrier glow discharge (DBGD) pattern. VTC is an important characteristic of DBGD, which plots the change of wall voltage after a discharge as a function of the initial total gap voltage. In the modeling, the combined effect of the discharge conditions is included in VTC, and the activation-inhibition effect is expressed by a spatial interaction term. Besides, the model reduces the dimensionality of the system by just considering the integration effect of current flow. All these greatly facilitate the construction of this model. Numerical simulations turn out to be in good accordance with our previous fluid modeling and experimental result.

  2. Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish.

    PubMed

    Frohnhöfer, Hans Georg; Geiger-Rudolph, Silke; Pattky, Martin; Meixner, Martin; Huhn, Carolin; Maischein, Hans-Martin; Geisler, Robert; Gehring, Ines; Maderspacher, Florian; Nüsslein-Volhard, Christiane; Irion, Uwe

    2016-01-01

    Polyamines are small poly-cations essential for all cellular life. The main polyamines present in metazoans are putrescine, spermidine and spermine. Their exact functions are still largely unclear; however, they are involved in a wide variety of processes affecting cell growth, proliferation, apoptosis and aging. Here we identify idefix, a mutation in the zebrafish gene encoding the enzyme spermidine synthase, leading to a severe reduction in spermidine levels as shown by capillary electrophoresis-mass spectrometry. We show that spermidine, but not spermine, is essential for early development, organogenesis and colour pattern formation. Whereas in other vertebrates spermidine deficiency leads to very early embryonic lethality, maternally provided spermidine synthase in zebrafish is sufficient to rescue the early developmental defects. This allows us to uncouple them from events occurring later during colour patterning. Factors involved in the cellular interactions essential for colour patterning, likely targets for spermidine, are the gap junction components Cx41.8, Cx39.4, and Kir7.1, an inwardly rectifying potassium channel, all known to be regulated by polyamines. Thus, zebrafish provide a vertebrate model to study the in vivo effects of polyamines. PMID:27215328

  3. Mechanism Underlying the Spatial Pattern Formation of Dominant Tree Species in a Natural Secondary Forest

    PubMed Central

    Jia, Guodong; Yu, Xinxiao; Fan, Dengxing; Jia, Jianbo

    2016-01-01

    Studying the spatial pattern of plant species may provide significant insights into processes and mechanisms that maintain stand stability. To better understand the dynamics of naturally regenerated secondary forests, univariate and bivariate Ripley’s L(r) functions were employed to evaluate intra-/interspecific relationships of four dominant tree species (Populus davidiana, Betula platyphylla, Larix gmelinii and Acer mono) and to distinguish the underlying mechanism of spatial distribution. The results showed that the distribution of soil, water and nutrients was not fragmented but presented clear gradients. An overall aggregated distribution existed at most distances. No correlation was found between the spatial pattern of soil conditions and that of trees. Both positive and negative intra- and interspecific relationships were found between different DBH classes at various distances. Large trees did not show systematic inhibition of the saplings. By contrast, the inhibition intensified as the height differences increased between the compared pairs. Except for Larix, universal inhibition of saplings by upper layer trees occurred among other species, and this reflected the vertical competition for light. Therefore, we believe that competition for light rather than soil nutrients underlies the mechanism driving the formation of stand spatial pattern in the rocky mountainous areas examined. PMID:27028757

  4. Dynamic model based on voltage transfer curve for pattern formation in dielectric barrier glow discharge

    NASA Astrophysics Data System (ADS)

    Li, Ben; He, Feng; Duan, Xiaoxi; Ouyang, Jiting

    2015-12-01

    Simulation work is very important for understanding the formation of self-organized discharge patterns. Previous works have witnessed different models derived from other systems for simulation of discharge pattern, but most of these models are complicated and time-consuming. In this paper, we introduce a convenient phenomenological dynamic model based on the basic dynamic process of glow discharge and the voltage transfer curve (VTC) to study the dielectric barrier glow discharge (DBGD) pattern. VTC is an important characteristic of DBGD, which plots the change of wall voltage after a discharge as a function of the initial total gap voltage. In the modeling, the combined effect of the discharge conditions is included in VTC, and the activation-inhibition effect is expressed by a spatial interaction term. Besides, the model reduces the dimensionality of the system by just considering the integration effect of current flow. All these greatly facilitate the construction of this model. Numerical simulations turn out to be in good accordance with our previous fluid modeling and experimental result.

  5. Spermidine, but not spermine, is essential for pigment pattern formation in zebrafish

    PubMed Central

    Frohnhöfer, Hans Georg; Geiger-Rudolph, Silke; Pattky, Martin; Meixner, Martin; Huhn, Carolin; Maischein, Hans-Martin; Geisler, Robert; Gehring, Ines; Maderspacher, Florian; Nüsslein-Volhard, Christiane

    2016-01-01

    ABSTRACT Polyamines are small poly-cations essential for all cellular life. The main polyamines present in metazoans are putrescine, spermidine and spermine. Their exact functions are still largely unclear; however, they are involved in a wide variety of processes affecting cell growth, proliferation, apoptosis and aging. Here we identify idefix, a mutation in the zebrafish gene encoding the enzyme spermidine synthase, leading to a severe reduction in spermidine levels as shown by capillary electrophoresis-mass spectrometry. We show that spermidine, but not spermine, is essential for early development, organogenesis and colour pattern formation. Whereas in other vertebrates spermidine deficiency leads to very early embryonic lethality, maternally provided spermidine synthase in zebrafish is sufficient to rescue the early developmental defects. This allows us to uncouple them from events occurring later during colour patterning. Factors involved in the cellular interactions essential for colour patterning, likely targets for spermidine, are the gap junction components Cx41.8, Cx39.4, and Kir7.1, an inwardly rectifying potassium channel, all known to be regulated by polyamines. Thus, zebrafish provide a vertebrate model to study the in vivo effects of polyamines. PMID:27215328

  6. Mechanism Underlying the Spatial Pattern Formation of Dominant Tree Species in a Natural Secondary Forest.

    PubMed

    Jia, Guodong; Yu, Xinxiao; Fan, Dengxing; Jia, Jianbo

    2016-01-01

    Studying the spatial pattern of plant species may provide significant insights into processes and mechanisms that maintain stand stability. To better understand the dynamics of naturally regenerated secondary forests, univariate and bivariate Ripley's L(r) functions were employed to evaluate intra-/interspecific relationships of four dominant tree species (Populus davidiana, Betula platyphylla, Larix gmelinii and Acer mono) and to distinguish the underlying mechanism of spatial distribution. The results showed that the distribution of soil, water and nutrients was not fragmented but presented clear gradients. An overall aggregated distribution existed at most distances. No correlation was found between the spatial pattern of soil conditions and that of trees. Both positive and negative intra- and interspecific relationships were found between different DBH classes at various distances. Large trees did not show systematic inhibition of the saplings. By contrast, the inhibition intensified as the height differences increased between the compared pairs. Except for Larix, universal inhibition of saplings by upper layer trees occurred among other species, and this reflected the vertical competition for light. Therefore, we believe that competition for light rather than soil nutrients underlies the mechanism driving the formation of stand spatial pattern in the rocky mountainous areas examined. PMID:27028757

  7. Nanoscale topographic pattern formation on Kr{sup +}-bombarded germanium surfaces

    SciTech Connect

    Perkinson, Joy C.; Madi, Charbel S.; Aziz, Michael J.

    2013-03-15

    The nanoscale pattern formation of Ge surfaces uniformly irradiated by Kr{sup +} ions was studied in a low-contamination environment at ion energies of 250 and 500 eV and at angles of 0 Degree-Sign through 80 Degree-Sign . The authors present a phase diagram of domains of pattern formation occurring as these two control parameters are varied. The results are insensitive to ion energy over the range covered by the experiments. Flat surfaces are stable from normal incidence up to an incidence angle of {theta} = 55 Degree-Sign from normal. At higher angles, the surface is linearly unstable to the formation of parallel-mode ripples, in which the wave vector is parallel to the projection of the ion beam on the surface. For {theta} {>=} 75 Degree-Sign the authors observe perpendicular-mode ripples, in which the wave vector is perpendicular to the ion beam. This behavior is qualitatively similar to those of Madi et al. for Ar{sup +}-irradiated Si but is inconsistent with those of Ziberi et al. for Kr{sup +}-irradiated Ge. The existence of a window of stability is qualitatively inconsistent with a theory based on sputter erosion [R. M. Bradley and J. M. Harper, J. Vac. Sci. Technol. A 6, 2390 (1988)] and qualitatively consistent with a model of ion impact-induced mass redistribution [G. Carter and V. Vishnyakov, Phys. Rev. B 54, 17647 (1996)] as well as a crater function theory incorporating both effects [S. A. Norris et al., Nat. Commun. 2, 276 (2011)]. The critical transition angle between stable and rippled surfaces occurs 10 Degree-Sign -15 Degree-Sign above the value of 45 Degree-Sign predicted by the mass redistribution model.

  8. The effect of phosphorus on the formation of the Widmanstaetten pattern in iron meteorites.

    NASA Technical Reports Server (NTRS)

    Goldstein, J. I.; Doan, A. S., Jr.

    1972-01-01

    Use of a combination of a revised Fe-Ni-P phase diagram and laboratory cooling experiments on Fe-Ni-P alloys to determine the effect of P on the formation of the Widmanstaetten pattern. From the phase diagram results, two reaction paths were found for the formation of kamacite (1) gamma (taenite) yields alpha (kamacite) + gamma (taenite) and (2) gamma yields gamma + Ph /phosphide, (FeNi)3P/ yields alpha + gamma + Ph. The reaction path gamma yields alpha + gamma is preferred at low P contents, while at higher P contents and at Ni contents greater than 7.0 wt.%, the reaction path gamma yields gamma + Ph yields alpha + gamma + Ph controls the formation of kamacite. Above 7 wt.% Ni, the effect of P on the equilibrium nucleation temperature of kamacite is quite small, less than about plus or minus 30 C with respect to the Fe-Ni binary diagram. The addition of P (greater than 0.1 wt.%) to meteorites promotes nucleation of kamacite at higher temperatures and effectively lowers the amount of undercooling necessary to nucleate kamacite homogeneously. Ni has just the opposite effect, decreasing the temperature of nucleation and increasing the amount of undercooling. It is concluded that significant amounts of undercooling, 50 to 100 C, are necessary for the nucleation of the Widmanstaetten structure in meteorites, and that chemical equilibrium is maintained in the various phases of slowly cooled iron meteorites to 650 C and probably to 600 C.

  9. Pattern formation of down-built salt structures: insights from 3D numerical models

    NASA Astrophysics Data System (ADS)

    Fernandez, Naiara; Kaus, Boris

    2015-04-01

    Many salt diapirs are thought to have formed as a result of down-building, which implies that the top of the diapir remained close to the surface during sediment deposition. This process is largely three-dimensional and in order to better understand what controls the patterns that form as a result of this down-building process, we here perform three-dimensional numerical models and compare the results with analytical models. In our models, we vary several parameters such as initial salt thickness, sedimentation rate, salt viscosity, salt-sediment viscosity contrast as well as the density of sediments. Down-building of three-dimensional diapirs only occurs for a certain range of parameters and is favored by lower sediment/salt viscosity contrasts and sedimentation rates in agreement with analytical predictions and findings from previous 2D models. However, the models show that the sedimentation rate has an additional effect on the formation and evolution of three-dimensional diapir patterns. At low sedimentation rates, salt ridges that form during early model stages remain preserved at later stages as well. For higher sedimentation rates, the initial salt ridges break up and form finger-like diapirs at the junction of salt ridges, which results in different salt exposure patterns at the surface. Once the initial pattern of diapirs is formed, higher sedimentation rate can also result in covered diapirs if the diapir extrusion velocity is insufficiently large. We quantify the effect of sedimentation rate on the number of diapirs exposed at the surface as well as on their spacing. In some cases, this final pattern is distinctly different from the initial polygonal pattern. We also study the extrusion of salt through time in the simulations, and show that it can be related to the geometries of the sedimentary layers surrounding the diapirs. Acknowledgements. Funding was provided by the European Research Council under the European Community's Seventh Framework Program

  10. New patterns of family formation in Italy. Which tools for which interpretations?

    PubMed

    Micheli, G A

    1996-01-01

    This paper presents a detailed discussion of the impact of World War II on subsequent fertility behavior a generation later in Italy. The changes in fertility were delayed and induced by a transgenerational process precipitated by war. War anomie and anomie in the rules of family formation are "symptoms" and not effects of the broad structural changes and historical upheavals during the 30 years of war. Fertility behavior is not construed to be an inevitable outcome of causal processes, but as alternative responses to life situations. The author bases this explanatory model of macrodemographic processes on a variant of Brown and Harris' etiological model that explains the occurrence of depression. It is argued that demographic models of European fertility are needed that acknowledge "a radical form of war that acts on reciprocity systems susceptible to change" and "intervenes to modify the subsequent transgenerational (family) relations." A research design is not now available that relies on the tools of history and anthropology. Thus, the demography of fertility may be reduced to a "mere bookkeeping of vital statistical data or simple economics of resources." The author's new pattern of family formation in Italy considers the "regional family culture and structure to be symptom-formation factors relating to the war and transformations in systems of family relations and exchange." These family changes are linked to war anomie and "changes in the logic of transition strategies from suppression to disconfirmation." War anomie is linked with a generational impact that intervenes in the relationship between changes in the logic of transition strategies and the decline in births. The decline in births is the response to background factors, precipitating events, and symptom-formation or structural factors. The author states that the second demographic transition does not represent a break with prior urban lifestyles and does not modify general trends continuing from the

  11. In vitro studies of heparin-coated magnetic nanoparticles for potential use in the treatment of neointimal hyperplasia

    NASA Astrophysics Data System (ADS)

    Hargett, Andrew

    Purpose: Though recent decades have developed a myriad of treatments in response to atherosclerosis, prevalence remains high and complications, especially restenosis, may occur. Restenosis following stents is often caused by excessive vascular smooth muscle cell (VSMCS) migration and proliferation into the intima, known as neointimal hyperplasia. The shear number of angioplasty and stent procedures throughout the world makes this a major concern of all endovascular surgery. Our lab has proposed the pairing of heparin and magnetic nanoparticles for targeted drug delivery to the stent location. Utilizing the high surface area of nanoparticles, we hope to deliver higher heparin dosing to inhibit VSMC proliferation without systemic effects. This study evaluates synthesis of these particles as well as preliminary in vitro controls on relevant cell lines found within the vasculature system. Materials and Methods: Heparin-coated iron oxide nanoparticles were synthesized and characterized according to size (TEM), hydrodynamic diameter (DLS), zeta potential, iron concentration, and heparin loading (DMMB assay). Assays were then performed using these particles as experimental conditions on VSMCs, Endothelial Cells (PECs), and Fibroblasts (3T3s) for determination of cell uptake (Prussian Blue, TEM), effects on proliferation (MTS assay), cytotoxicity (Live/Dead assay), and phenotype changes (immunofluorescent staining). Experimental conditions were assessed against control nanoparticles without heparin and raw heparin in solution for dosage effects. Results: Particles were successfully synthesized, loaded with heparin, and characterized to validate each step of synthesis. Proliferation and cytotoxicity cell assays determined heparin-coated nanoparticles to be more potent in effects at lower concentrations of heparin when compared to raw heparin in solution. Immunostaining of VSMCs demonstrated a relatively higher tendency towards nonproliferative phenotypes following

  12. Chemical pattern formation driven by a neutralization reaction. I. Mechanism and basic features

    NASA Astrophysics Data System (ADS)

    Eckert, Kerstin; Acker, Margret; Shi, Ying

    2004-02-01

    We study the chemohydrodynamic pattern formation during interfacial mass transfer accompanied by a neutralization reaction. The system, which is placed in a Hele-Shaw cell, is a configuration of two immiscible liquid phases in contact along a plane interface. In the upper, organic layer a carboxylic acid is dissolved, the concentration of which is far beyond the equilibrium partition ratio. Interfacial acid transfer initiates the neutralization with an organic base dissolved in the lower, aqueous layer. Focus is on the exploration of a novel instability consisting of a regular cellular structure penetrating into the aqueous bulk solution. By several complementary experimental methods, including shadowgraph visualization with different magnifications, particle image velocimetry, differential interferometry, and detailed measurements of relevant material properties, the driving mechanism of the instability is identified. Synthesis of the experimental results suggests that lateral differences in buoyancy are responsible for the convection.

  13. Dichotomous-noise-induced pattern formation in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Das, Debojyoti; Ray, Deb Shankar

    2013-06-01

    We consider a generic reaction-diffusion system in which one of the parameters is subjected to dichotomous noise by controlling the flow of one of the reacting species in a continuous-flow-stirred-tank reactor (CSTR) -membrane reactor. The linear stability analysis in an extended phase space is carried out by invoking Furutzu-Novikov procedure for exponentially correlated multiplicative noise to derive the instability condition in the plane of the noise parameters (correlation time and strength of the noise). We demonstrate that depending on the correlation time an optimal strength of noise governs the self-organization. Our theoretical analysis is corroborated by numerical simulations on pattern formation in a chlorine-dioxide-iodine-malonic acid reaction-diffusion system.

  14. Pattern Formation and Force Generation by Cell Ensembles in a Filamentous Matrix

    NASA Astrophysics Data System (ADS)

    Paul, R.; Schwarz, U. S.

    Adhesion-dependent soft tissue cells both create and sense tension in the extracellular matrix. Therefore cells can actively interact through the mechanics of the surrounding matrix. An intracellular positive feedback loop upregulates cellular contractility in stiff or tensed environments. Here we theoretically address the resulting pattern formation and force generation for the case of a filamentous matrix, which we model as a two-dimensional cable network. Cells are modeled as anisotropic contraction dipoles which move in favor of tensed directions in the matrix. Our Monte Carlo simulations suggest that at small densities, cells align in strings, while at high densities, they form interconnected meshworks. Cellular activation both by biochemical factors and by tension leads to a hyperbolic increase in tissue tension. We also discuss the effect of cell density on tissue tension and shape.

  15. The non-equilibrium charge screening effects in diffusion-driven systems with pattern formation

    NASA Astrophysics Data System (ADS)

    Kuzovkov, V. N.; Kotomin, E. A.; de la Cruz, M. Olvera

    2011-07-01

    The effects of non-equilibrium charge screening in mixtures of oppositely charged interacting molecules on surfaces are analyzed in a closed system. The dynamics of charge screening and the strong deviation from the standard Debye-Hückel theory are demonstrated via a new formalism based on computing radial distribution functions suited for analyzing both short-range and long-range spacial ordering effects. At long distances the inhomogeneous molecular distribution is limited by diffusion, whereas at short distances (of the order of several coordination spheres) by a balance of short-range (Lennard-Jones) and long-range (Coulomb) interactions. The non-equilibrium charge screening effects in transient pattern formation are further quantified. It is demonstrated that the use of screened potentials, in the spirit of the Debye-Hückel theory, leads to qualitatively incorrect results.

  16. The Fokker-Planck law of diffusion and pattern formation in heterogeneous environments.

    PubMed

    Bengfort, Michael; Malchow, Horst; Hilker, Frank M

    2016-09-01

    We analyze the influence of spatially inhomogeneous diffusion on several common ecological problems. Diffusion is modeled with Fick's law and the Fokker-Planck law of diffusion. We discuss the differences between the two formalisms and when to use either the one or the other. In doing so, we start with a pure diffusion equation, then turn to a reaction-diffusion system with one logistically growing component which invades the spatial domain. We also look at systems of two reacting components, namely a trimolecular oscillating chemical model system and an excitable predator-prey model. Contrary to Fickian diffusion, spatial inhomogeneities promote spatial and spatiotemporal pattern formation in case of Fokker-Planck diffusion. PMID:26803768

  17. Direct observation of electric field induced pattern formation and particle aggregation in ferrofluids

    SciTech Connect

    Rajnak, Michal; Kopcansky, Peter; Timko, Milan; Petrenko, Viktor I.; Avdeev, Mikhail V.; Ivankov, Olexandr I.; Feoktystov, Artem; Dolnik, Bystrik; Kurimsky, Juraj

    2015-08-17

    Ferrofluids typically respond to magnetic fields and can be manipulated by external magnetic fields. Here, we report on formation of visually observable patterns in a diluted low-polarity ferrofluid exposed to external electric fields. This presents a specific type of ferrofluid structure driven by a combined effect of electrohydrodynamics and electrical body forces. The free charge and permittivity variation are considered to play a key role in the observed phenomenon. The corresponding changes in the ferrofluid structure have been found at nanoscale as well. By small-angle neutron scattering (SANS), we show that the magnetic nanoparticles aggregate in direct current (dc) electric field with a strong dependence on the field intensity. The anisotropic aggregates preferably orient in the direction of the applied electric field. Conducting SANS experiments with alternating current (ac) electric fields of various frequencies, we found a critical frequency triggering the aggregation process. Our experimental study could open future applications of ferrofluids based on insulating liquids.

  18. Developmental transcriptomics in Atlantic haddock: Illuminating pattern formation and organogenesis in non-model vertebrates.

    PubMed

    Sørhus, Elin; Incardona, John P; Furmanek, Tomasz; Jentoft, Sissel; Meier, Sonnich; Edvardsen, Rolf B

    2016-03-15

    Gadiforms such as Atlantic haddock comprise some of the world's most economically important fisheries. Understanding the early life history of these fish is a prerequisite for predicting effects of a changing environment and increased human activities. Robust assessment of the effects of environmental impacts on the embryos of non-model vertebrates is hampered by a lack of molecular resources and detailed knowledge regarding the regulation of genes and pathways in early development. Here we used mRNA sequencing to link transcriptional changes to developmental processes in haddock, specifically, pattern formation and organogenesis. Temporal expression of key developmental genes was tightly anchored to either the appearance of visible structures or cellular processes characterised in model organisms. These findings demonstrate the high potential of developmental transcriptomics as an analytical tool for improved understanding of pathophysiological mechanisms leading to abnormal development in any vertebrate. PMID:26875497

  19. Identification of genes from pattern formation, tyrosine kinase, and potassium channel families by DNA amplification

    SciTech Connect

    Kamb, A.; Weir, M.; Rudy, B.; Varmus, H.; Kenyon, C. )

    1989-06-01

    The study of gene family members has been aided by the isolation of related genes on the basis of DNA homology. The authors have adapted the polymerase chain reaction to screen animal genomes very rapidly and reliably for likely gene family members. Using conserved amino acid sequences to design degenerate oligonucleotide primers, they have shown that the genome of the nematode Caenorhabditis elegans contains sequences homologous to many Drosophila genes involved in pattern formation, including the segment polarity gene wingless (vertebrate int-1), and homeobox sequences characteristic of the Antennapedia, engrailed, and paired families. In addition, they have used this method to show that C. elegans contains at least five different sequences homologous to genes in the tyrosine kinase family. Lastly, they have isolated six potassium channel sequences from humans, a result that validates the utility of the method with large genomes and suggests that human potassium channel gene diversity may be extensive.

  20. Direct observation of electric field induced pattern formation and particle aggregation in ferrofluids

    NASA Astrophysics Data System (ADS)

    Rajnak, Michal; Petrenko, Viktor I.; Avdeev, Mikhail V.; Ivankov, Olexandr I.; Feoktystov, Artem; Dolnik, Bystrik; Kurimsky, Juraj; Kopcansky, Peter; Timko, Milan

    2015-08-01

    Ferrofluids typically respond to magnetic fields and can be manipulated by external magnetic fields. Here, we report on formation of visually observable patterns in a diluted low-polarity ferrofluid exposed to external electric fields. This presents a specific type of ferrofluid structure driven by a combined effect of electrohydrodynamics and electrical body forces. The free charge and permittivity variation are considered to play a key role in the observed phenomenon. The corresponding changes in the ferrofluid structure have been found at nanoscale as well. By small-angle neutron scattering (SANS), we show that the magnetic nanoparticles aggregate in direct current (dc) electric field with a strong dependence on the field intensity. The anisotropic aggregates preferably orient in the direction of the applied electric field. Conducting SANS experiments with alternating current (ac) electric fields of various frequencies, we found a critical frequency triggering the aggregation process. Our experimental study could open future applications of ferrofluids based on insulating liquids.

  1. Trends in ice formation at Lake Neusiedl since 1931 and large-scale oscillation patterns

    NASA Astrophysics Data System (ADS)

    Soja, Anna-Maria; Maracek, Karl; Soja, Gerhard

    2013-04-01

    Ice formation at Lake Neusiedl (Neusiedler See, Fertitó), a shallow steppe lake (area 320 km2, mean depth 1.2 m) at the border of Austria/Hungary, is of ecological and economic importance. Ice sailing and skating help to keep a touristic off-season alive. Reed harvest to maintain the ecological function of the reed belt (178 km2) is facilitated when lake surface is frozen. Changes in ice formation were analysed in the frame of the EULAKES-project (European Lakes under Environmental Stressors, www.eulakes.eu), financed by the Central Europe Programme of the EU. Data records of ice-on, ice duration and ice-off at Lake Neusiedl starting with the year 1931, and air temperature (nearby monitoring station Eisenstadt - Sopron (HISTALP database and ZAMG)) were used to investigate nearly 80 winters. Additionally, influences of 8 teleconnection patterns, i.e. the Atlantic Multidecadal Oscillation (AMO), the East Atlantic pattern (EAP), the East Atlantic/West Russia pattern (EA/WR), the Eastern Mediterranean Pattern (EMP), the Mediterranean Oscillation (MO) for Algiers and Cairo, and for Israel and Gibraltar, resp., the North Atlantic Oscillation (NAO) and the Scandinavia pattern (SCA) were assessed. Ice cover of Lake Neusiedl showed a high variability between the years (mean duration 71±27 days). Significant trends for later ice-on (p=0.02), shorter ice duration (p=0.07) and earlier ice-off (p=0.02) for the period 1931-2011 were found by regression analysis and trend analysis tests. On an average, freezing of Lake Neusiedl started 2 days later per decade and ice melting began 2 days earlier per decade. Close relationships between mean air temperature and ice formation could be found: ice-on showed a dependency on summer (R=+0.28) and autumn air temperatures (R=+0.51), ice duration and ice off was related to autumn (R=-0.36 and -0.24), winter (R=-0.73 and -0.61) and concurrent spring air temperatures (R=-0.44). Increases of air temperature by 1° C caused an 8.4 days later

  2. Delay-driven pattern formation in a reaction-diffusion predator-prey model incorporating a prey refuge

    NASA Astrophysics Data System (ADS)

    Lian, Xinze; Wang, Hailing; Wang, Weiming

    2013-04-01

    In this paper, we consider a diffusive predation model with a delay effect, which is based on a modified version of the Leslie-Gower scheme incorporating a prey refuge. We mainly investigate the effects of time delay on the stability of the homogeneous state point and the formation of spatial patterns. We give the conditions for diffusion-driven and delay-diffusion-driven instability in detail. Furthermore, we illustrate the spatial patterns via numerical simulations, which show that the model dynamics exhibits a delay and diffusion controlled formation growth not only of spots, stripes and holes, but also of self-replicating spiral patterns. The results indicate that the delay plays an important role in the pattern selection. This may enrich the pattern dynamics for a delay diffusive model.

  3. Statistical analysis of granular gases, pattern formation, and crumpling through real space imaging

    NASA Astrophysics Data System (ADS)

    Blair, Daniel L.

    The statistical properties of driven dissipative systems is investigated experimentally with the use of high speed, and high resolution imaging. A variety of experiments that range from idealized granular gases to systems with anisotropic interactions and pattern formation is explored. These experiments can be divided into three classes: granular gases, granular fluids with anisotropic interactions, and pattern formation. The statistical properties of spherical particles that are excited into a dilute gas state are investigated. The particles are constrained to roll on an inclined plane, which reduces the effects of gravity, allowing real space particle tracking with high precision. Energy is given to the particles through a single vibrating boundary. If the driving is at a high frequency and amplitude, the particles resemble molecules of equilibrium liquids or gases. I will demonstrate that a number of fundamental statistical measures of equilibrium fluids, such as distribution of velocities and path lengths are not consistent with those of inelastic gases. However, the particle motion remains diffusive and the velocity autocorrelation functions decays exponentially. Recent theoretical approaches to granular hydrodynamics also are discussed. In the case where the driving frequency and amplitude are sufficiently low, the particles undergo a spontaneous transition from a quiescent to patterned state. The patterns formed are similar to those found in three-dimensional granular fluids. By introducing a temporally dependent measure of the spatial correlation of the velocities, an accurate determination of the wavelength and onset of patterns is determined. The phase averaged temperature is measured to show that patterns arise when the temperature of the layer is at minimum. These results could be used to develop a linear stability analysis of granular fluids. A quasi-two-dimensional granular system of particles with embedded dipole moments is investigated, and it is

  4. Northern-Hemisphere snow cover patterns and formation conditions in winter 2007 and 2012

    NASA Astrophysics Data System (ADS)

    Cui, Hongyan; Qiao, Fangli; Shu, Qi; Yu, Long

    2016-06-01

    The Arctic sea ice minimum records appeared in the Septembers of 2007 and 2012, followed by high snow cover areas in the Northern Hemisphere winters. The snow cover distributions show different spatial patterns in these two years: increased snow cover in Central Asia and Central North America in 2007, while increased snow cover in East Asia and northwestern Europe in 2012. The high snow cover anomaly shifted to higher latitudes in winter of 2012 compared to 2007. It is noticed that the snow cover had positive anomaly in 2007 and 2012 with the following conditions: the negative geopotential height and the related cyclonic wind anomaly were favorable for upwelling, and, with the above conditions, the low troposphere and surface air temperature anomaly and water vapor anomaly were favorable for the formation and maintenance of snowfalls. The negative geopotential height, cyclonic wind and low air temperature conditions were satisfied in different locations in 2007 and 2012, resulting in different spatial snow cover patterns. The cross section of lower air temperature move to higher latitudes in winter of 2012 compared to 2007.

  5. Multi-scale modeling of complex neuronal networks: a view towards striatal cholinergic pattern formations.

    PubMed

    Noori, Hamid Reza

    2012-09-01

    The phenomena related to brain function occur as the interplay of various modules at different spatial and temporal scales. Particularly, the integration of the dynamical behavior of cells within the complex brain topology reveals a heterogeneous multi-scale problem, which has, to date, mainly been addressed by methods of statistical physics such as mean-field approximations. In contrast, the present study introduces an abstract mathematical model of a deterministic nature that provides a robust integral transformation of the microscopic activities into macroscopic spatiotemporal patterns. The existence of the transformation operator is guaranteed by the convergence of a repetitive patching of the network domain with its fundamental domains that express the local topologies of the tissue. Depending on the choice of the local connectivity function, this framework represents a computationally efficient generalization of the classical Kirchhoff's, Hebbian, and Hopfield's approaches. The capabilities of this multi-scale method have been evaluated within the structure of the dorsal striatum of rats, a brain region with major involvement in motor and cognitive information processing. Numerical simulations suggest the formation of characteristic spatiotemporal patterns due to the activation of cholinergic interneurons. PMID:24615222

  6. Pattern formation and molecular transport of histidine-tagged GFPs using supported lipid bilayers.

    PubMed

    Nakashima, Hiroshi; Furukawa, Kazuaki; Kashimura, Yoshiaki; Sumitomo, Koji; Shinozaki, Youichi; Torimitsu, Keiichi

    2010-08-01

    We fabricated a heterogeneous supported lipid bilayer (SLB) by employing binary lipid mixtures comprising a saturated acyl chain DSPC and an unsaturated acyl chain nickel-chelating lipid. By using the specific adsorption properties of histidine-tagged proteins (His-tagged GFPs) in relation to nickel-chelating lipids, we demonstrated protein pattern formation on the SLB corresponding to the phase separation pattern of the SLB. In addition, by using a lipid mixture consisting of an unsaturated acyl chain DOPC and a nickel-chelating lipid, and His-tagged GFPs, we succeeded in transporting the proteins along a hydrophilic micropattern on a SiO(2) substrate. The protein transport is induced by the self-spreading behavior of a fluid SLB with a kinetic spreading coefficient beta = 10.4 microm(2) s(-1). This method provides a guide for strategically carrying various biomolecules to specific positions by using a soft biointerface on a solid surface. In addition, the results demonstrate the importance of using techniques that allow the controlled manipulation of biomolecules based on the static or dynamic properties of the SLB platform. PMID:20666418

  7. Nanoscale pattern formation at surfaces under ion-beam sputtering: A perspective from continuum models

    NASA Astrophysics Data System (ADS)

    Cuerno, Rodolfo; Castro, Mario; Muñoz-García, Javier; Gago, Raúl; Vázquez, Luis

    2011-05-01

    Although reports on surface nanostructuring of solid targets by low to medium energy ion irradiation date back to the 1960s, only with the advent of high resolution tools for surface/interface characterization has the high potential of this procedure been recognized as a method for efficient production of surface patterns. Such morphologies are made up of periodic arrangements of nanometric sized features, like ripples and dots, with interest for technological applications due to their electronic, magnetic, and optical properties. Thus, roughly for the last ten years large efforts have been directed towards harnessing this nanofabrication technique. However, and particularly in view of recent experimental developments, we can say that the basic mechanisms controlling these pattern formation processes remain poorly understood. The lack of nanostructuring at low angles of incidence on some pure monoelemental targets, the role of impurities in the surface dynamics and other recent observations are challenging the classic view on the phenomenon as the mere interplay between the curvature dependence of the sputtering yield and surface diffusion. We review the main attempts at a theoretical (continuum) description of these systems, with emphasis on recent developments. Strong hints already exist that the nature of the morphological instability has to be rethought as originating in the material flow that is induced by the ion beam.

  8. Pattern Formation by Staphylococcus epidermidis via Droplet Evaporation on Micropillars Arrays at a Surface.

    PubMed

    Susarrey-Arce, A; Marin, A; Massey, A; Oknianska, A; Díaz-Fernandez, Y; Hernández-Sánchez, J F; Griffiths, E; Gardeniers, J G E; Snoeijer, J H; Lohse, Detlef; Raval, R

    2016-07-19

    We evaluate the effect of epoxy surface structuring on the evaporation of water droplets containing Staphylococcus epidermidis (S. epidermidis). During evaporation, droplets with S. epidermidis cells yield to complex wetting patterns such as the zipping-wetting1-3 and the coffee-stain effects. Depending on the height of the microstructure, the wetting fronts propagate circularly or in a stepwise manner, leading to the formation of octagonal or square-shaped deposition patterns.4,5 We observed that the shape of the dried droplets has considerable influence on the local spatial distribution of S. epidermidis deposited between micropillars. These changes are attributed to an unexplored interplay between the zipping-wetting1 and the coffee-stain6 effects in polygonally shaped droplets containing S. epidermidis. Induced capillary flows during evaporation of S. epidermidis are modeled with polystyrene particles. Bacterial viability measurements for S. epidermidis show high viability of planktonic cells, but low biomass deposition on the microstructured surfaces. Our findings provide insights into design criteria for the development of microstructured surfaces on which bacterial propagation could be controlled, limiting the use of biocides. PMID:27341165

  9. Pattern formation, synchronization, and outbreak of biodiversity in cyclically competing games

    NASA Astrophysics Data System (ADS)

    Wang, Wen-Xu; Ni, Xuan; Lai, Ying-Cheng; Grebogi, Celso

    2011-01-01

    Species in nature are typically mobile over diverse distance scales, examples of which range from bacteria run to long-distance animal migrations. These behaviors can have a significant impact on biodiversity. Addressing the role of migration in biodiversity microscopically is fundamental but remains a challenging problem in interdisciplinary science. We incorporate both intra- and inter-patch migrations in stochastic games of cyclic competitions and find that the interplay between the migrations at the local and global scales can lead to robust species coexistence characterized dynamically by the occurrence of remarkable target-wave patterns in the absence of any external control. The waves can emerge from either mixed populations or isolated species in different patches, regardless of the size and the location of the migration target. We also find that, even in a single-species system, target waves can arise from rare mutations, leading to an outbreak of biodiversity. A surprising phenomenon is that target waves in different patches can exhibit synchronization and time-delayed synchronization, where the latter potentially enables the prediction of future evolutionary dynamics. We provide a physical theory based on the spatiotemporal organization of the target waves to explain the synchronization phenomena. We also investigate the basins of coexistence and extinction to establish the robustness of biodiversity through migrations. Our results are relevant to issues of general and broader interest such as pattern formation, control in excitable systems, and the origin of order arising from self-organization in social and natural systems.

  10. Instantaneous Formation of Block Copolymer Patterns via Solvo-Thermal Casting Process

    NASA Astrophysics Data System (ADS)

    Jung, Hyun Jung; Woo, Sanghoon; Huh, June; Bang, Joona

    2015-03-01

    A self-assembly of block copolymers (BCPs) exhibits one of the most promising alternative methods for the next-generation lithography. Many semiconductor companies have explored the possibility of implementing this process in actual chip process, whereas the critical challenges such as feature size control, defect density, and long processing time need to be overcome. Regarding the BCP process, the formation of BCP patterns usually requires long processing time via thermal or solvent annealing. Herein we developed a simple processing method to promote a microphase separation of BCPs using solvo-thermal spin casting process. Spin casting has a very similar mechanism to solvent vapor annealing but its short process time prevents BCP chains from reaching equilibrium morphology. To maximize the chain mobility, we employed a high boiling point solvent and also applied the heat during spin casting. As a result, a well ordered BCP patterns were obtained within less than 5 min via solvo-thermal casting process without further additional annealing step.

  11. Seasonal and temporal patterns of NDMA formation potentials in surface waters.

    PubMed

    Uzun, Habibullah; Kim, Daekyun; Karanfil, Tanju

    2015-02-01

    The seasonal and temporal patterns of N-nitrosodimethylamine (NDMA) formation potentials (FPs) were examined with water samples collected monthly for 21 month period in 12 surface waters. This long term study allowed monitoring the patterns of NDMA FPs under dynamic weather conditions (e.g., rainy and dry periods) covering several seasons. Anthropogenically impacted waters which were determined by high sucralose levels (>100 ng/L) had higher NDMA FPs than limited impacted sources (<100 ng/L). In most sources, NDMA FP showed more variability in spring months, while seasonal mean values remained relatively consistent. The study also showed that watershed characteristics played an important role in the seasonal and temporal patterns. In the two dam-controlled river systems (SW A and G), the NDMA FP levels at the downstream sampling locations were controlled by the NDMA levels in the dams independent of either the increases in discharge rates due to water releases from the dams prior to or during the heavy rain events or intermittent high NDMA FP levels observed at the upstream of dams. The large reservoirs and impoundments on rivers examined in this study appeared serving as an equalization basin for NDMA precursors. On the other hand, in a river without an upstream reservoir (SW E), the NDMA levels were influenced by the ratio of an upstream wastewater treatment plant (WWTP) effluent discharge to the river discharge rate. The impact of WWTP effluent decreased during the high river flow periods due to rain events. Linear regression with independent variables DOC, DON, and sucralose yielded poor correlations with NDMA FP (R(2) < 0.27). Multiple linear regression analysis using DOC and log [sucralose] yielded a better correlation with NDMA FP (R(2) = 0.53). PMID:25481075

  12. Intracellular Trafficking in Drosophila Visual System Development: A Basis for Pattern Formation Through Simple Mechanisms

    PubMed Central

    Chan, Chih-Chiang; Epstein, Daniel; Hiesinger, P. Robin

    2012-01-01

    Intracellular trafficking underlies cellular functions ranging from membrane remodeling to receptor activation. During multicellular organ development, these basic cell biological functions are required as both passive machinery and active signaling regulators. Exocytosis, endocytosis, and recycling of several key signaling receptors have long been known to actively regulate morphogenesis and pattern formation during Drosophila eye development. Hence, intracellular membrane trafficking not only sets the cell biological stage for receptor-mediated signaling but also actively controls signaling through spatiotemporally regulated receptor localization. In contrast to eye development, the role of intracellular trafficking for the establishment of the eye-to-brain connectivity map has only recently received more attention. It is still poorly understood how guidance receptors are spatiotemporally regulated to serve as meaningful synapse formation signals. Yet, the Drosophila visual system provides some of the most striking examples for the regulatory role of intracellular trafficking during multicellular organ development. In this review we will first highlight the experimental and conceptual advances that motivate the study of intracellular trafficking during Drosophila visual system development. We will then illuminate the development of the eye, the eye-to-brain connectivity map and the optic lobe from the perspective of cell biological dynamics. Finally, we provide a conceptual framework that seeks to explain how the interplay of simple genetically encoded intracellular trafficking events governs the seemingly complex cellular behaviors, which in turn determine the developmental product. PMID:21714102

  13. Modeling the PbI2 formation in perovskite solar cells using XRD/XPS patterns

    NASA Astrophysics Data System (ADS)

    Sohrabpoor, Hamed; Elyasi, Majid; Aldosari, Marouf; Gorji, Nima E.

    2016-09-01

    The impact of prolonged irradiation and air humidity on the stability of perovskite solar cells is modeled using X-ray diffraction and X-ray photoelectron spectroscopy patterns reported in the literature. Light or air-moisture causes the formation of a thin PbI2 or oxide defective layers (in nanoscale) at the interface of perovskite/hole-transport-layer or at the junction with metallic back contact. This thin layer blocks the carrier transport/passivation at the interfaces and cause degradation of device parameters. Variation in thickness of defective layers, changes the XRD and XPS peaks. This allows detection and estimation of the type, crystallinity and thickness of the defective layer. A simple model is developed here to extract the thickness of such thin defective layers formed in nanometer scale at the back region of several perovskite devices. Based on this information, corrected energy band diagram of every device before and after degradation/aging is drawn and discussed in order to obtain insight into the carrier transport and charge collection at the barrier region. In addition, graphene contacted perovskite devices are investigated showing that honey-comb network of graphene contact reduces the effect of aging leading to formation of a thinner defective layer at the perovskite surface compared to perovskite devices with conventional inorganic contacts i.e. Au, Al.

  14. Large-scale pattern formation in active particles suspensions: from interacting microtubules to swimming bacteria

    NASA Astrophysics Data System (ADS)

    Aranson, Igor

    2006-03-01

    We consider two biological systems of active particles exhibiting large-scale collective behavior: microtubules interacting with molecular motors and hydrodynamically entrained swimming bacteria. Starting from a generic stochastic microscopic model of inelastically colliding polar rods with an anisotropic interaction kernel, we derive set of equations for the local rods concentration and orientation. Above certain critical density of rods the model exhibits orientational instability and onset of large-scale coherence. For the microtubules and molecular motors system we demonstrate that the orientational instability leads to the formation of vortices and asters seen in recent experiments. Similar approach is applied to colonies of swimming bacteria Bacillus subtilis confined in thin fluid film. The model is formulated in term of two-dimensional equations for local density and orientation of bacteria coupled to the low Reynolds number Navier-Stokes equation for the fluid flow velocity. The collective swimming of bacteria is represented by additional source term in the Navier-Stokes equation. We demonstrate that this system exhibits formation of dynamic large-scale patterns with the typical scale determined by the density of bacteria.

  15. Frequency of Teriparatide Administration Affects the Histological Pattern of Bone Formation in Young Adult Male Mice.

    PubMed

    Yamamoto, Tomomaya; Hasegawa, Tomoka; Sasaki, Muneteru; Hongo, Hiromi; Tsuboi, Kanako; Shimizu, Tomohiro; Ota, Masahiro; Haraguchi, Mai; Takahata, Masahiko; Oda, Kimimitsu; Luiz de Freitas, Paulo Henrique; Takakura, Aya; Takao-Kawabata, Ryoko; Isogai, Yukihiro; Amizuka, Norio

    2016-07-01

    Evidence supports that daily and once-weekly administration of teriparatide, human (h)PTH(1-34), enhance bone mass in osteoporotic patients. However, it is uncertain whether different frequencies of hPTH(1-34) administration would induce bone formation similarly in terms of quantity and quality. To investigate that issue, mice were subjected to different frequencies of PTH administration, and their bones were histologically examined. Frequencies of administration were 1 time/2 days, 1 time a day, and 2 and 4 times a day. Mice were allocated to either to control or to 3 different dosing regimens: 80 μg/kg of hPTH(1-34) per injection (80 μg/kg per dose), 80 μg/kg of hPTH(1-34) per day (80 μg/kg · d), or 20 μg/kg of hPTH(1-34) per day (20 μg/kg · d). With the regimens of 80 μg/kg per dose and 80 μg/kg · d, high-frequency hPTH(1-34) administration increased metaphyseal trabecular number. However, 4 doses per day induced the formation of thin trabeculae, whereas the daily PTH regimen resulted in thicker trabeculae. A similar pattern was observed with the lower daily hPTH(1-34) dose (20 μg/kg · d): more frequent PTH administration led to the formation of thin trabeculae, showing a thick preosteoblastic cell layer, several osteoclasts, and scalloped cement lines that indicated accelerated bone remodeling. On the other hand, low-frequency PTH administration induced new bone with mature osteoblasts lying on mildly convex surfaces representative of arrest lines, which suggests minimodeling-based bone formation. Thus, high-frequency PTH administration seems to increase bone mass rapidly by forming thin trabeculae through accelerated bone remodeling. Alternatively, low-frequency PTH administration leads to the formation of thicker trabeculae through bone remodeling and minimodeling. PMID:27227535

  16. X-ray photoemission spectromicroscopy of titanium silicide formation in patterned microstructures

    SciTech Connect

    Singh, S.; Solak, H.; Cerrina, F.

    1997-04-01

    Titanium silicide has the lowest resistivity of all the refractory metal silicides and has good thermal stability as well as excellent compatibility with Al metallization. It is used as an intermediate buffer layer between W vias and the Si substrate to provide good electrical contact in ULSI technology, whose submicron patterned features form the basis of the integrated circuits of today and tomorrow, in the self aligned silicide (salicide) formation process. TiSi{sub 2} exists in two phases: a metastable C49 base-centered orthorhombic phase with specific resistivity of 60-90 {mu}{Omega}-cm that is formed at a lower temperature (formation anneal) and the stable 12-15 {mu}{Omega}-cm resistivity face-centered orthorhombic C54 phase into which C49 is transformed with a higher temperature (conversion anneal) step. C54 is clearly the target for low resistivity VLSI interconnects. However, it has been observed that when dimensions shrink below 1/mic (or when the Ti thickness drops below several hundred angstroms), the transformation of C49 into C54 is inhibited and agglomeration often occurs in fine lines at high temperatures. This results in a rise in resistivity due to incomplete transformation to C54 and because of discontinuities in the interconnect line resulting from agglomeration. Spectromicroscopy is an appropriate tool to study the evolution of the TiSi2 formation process because of its high resolution chemical imaging ability which can detect bonding changes even in the absence of changes in the relative amounts of species and because of the capability of studying thick {open_quotes}as is{close_quotes} industrial samples.

  17. Geologically Controlled Isotope-Time Patterns Reveal Early Differentiation and Crust Formation Processes

    NASA Astrophysics Data System (ADS)

    Bennett, V. C.; Nutman, A. P.

    2014-12-01

    The mechanisms of continental crust production and evolution in the early Earth remain controversial, as are questions of the relative roles of early differentiation versus subsequent tectonic procssing in creating Earth's chemical signatures. Here we present geologic observations integrated with whole rock major, trace element and Sm-Nd isotopic signatures and combined with U-Pb and Lu-Hf isotopic compositions of zircon populations from the same rocks, from the most extensive early rock record comprising the 3.9 Ga to 3.6 Ga terranes of southwest Greenland. These data reveal repeated patterns of formation of juvenile TTG crust and associated mafic and ultramafic rocks in convergent margin settings followed by formation of more evolved granites [1]. Our new zircon Lu-Hf data from rare 3.6-3.7 Ga tonalites within the Itsaq Gneiss Complex, obtained from single component, non-migmatitic gneisses with simple zircon populations, limited within sample Hf isotopic variability and accurate U-Pb ages, now document extraction of juvenile tonalites from a near chondritic mantle source between 3.9 Ga and 3.6 Ga. The more evolved, granitic rocks in each area show slightly negative initial ɛHf in accord with crustal reworking of the older (3.8-3.9 Ga) gniesses. There is no evidence for Hadean material in the sources of the granitoids. The Hf isotope-time patterns are consistent with juvenile crust production from a mantle source that experienced only modest amounts of prior crustal extraction. They are distinct from those predicted by reprocessing of an enriched Hadean mafic crust, as has been proposed for this region [2] and for the source of the Hadean Jack Hills zircons [3]. The well-documented, time decreasing, positive 142Nd anomalies [e.g., 4] from these rocks are further evidence of crustal derivation from a convecting mantle source, rather than reworking of an enriched mafic lithosphere. The 143Nd isotopic -time patterns are more complex, reflecting the interplay

  18. Switch and template pattern formation in a discrete reaction-diffusion system inspired by the Drosophila eye

    PubMed Central

    Pennington, Matthew W.; Lubensky, David K.

    2011-01-01

    We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is known to be capable of generating a regular hexagonal pattern of gene expression behind a moving front, as observed in the fly system. In order to better understand the novel “switch and template” mechanism behind this pattern formation, we present here a detailed study of the model's behavior in one dimension, using a combination of analytic methods and numerical searches of parameter space. We find that patterns are created robustly provided that there is an appropriate separation of timescales and that self-activation is sufficiently strong, and we derive expressions in this limit for the front speed and the pattern wavelength. Moving fronts in pattern-forming systems near an initial linear instability generically select a unique pattern, but our model operates in a strongly nonlinear regime where the final pattern depends on the initial conditions as well as on parameter values. Our work highlights the important role that cellularization and cell-autonomous feedback can play in biological pattern formation. PMID:20862598

  19. A generic model of pattern formation in Mississippi Valley-Type deposits based on analytical findings

    NASA Astrophysics Data System (ADS)

    Kelka, Ulrich; Veveakis, Manolis; Beaudoin, Nicolas; Poulet, Thomas; Koehn, Daniel; Regenauer-Lieb, Klaus; Chung, Peter; Berndt, Jasper

    2016-04-01

    Rhythmically banded dolomites (zebra dolomite) are found worldwide, and are frequently associated with mineralization of the Mississippi Valley-Type (MVT). These rocks consist of dark fine grained and impurity-rich layers alternating with light coarse grained and virtually impurity-free layers. The texture of the light layers is similar to the one of tectonic syntaxial veins where crystals grow towards a median line. We present petrographic and chemical analysis of zebra dolomite samples from the San Vicente mine, Central Peru. The applied methods are petrographic microscopy, SEM, EBSD, EMP and LA-ICP-MS. The findings influence the development of a generic model of pattern formation. We found the density and the distribution of second-phase material to be one striking feature. The impurities are accumulated in the dark layers, which show an even higher density of second-phase material than the surrounding impurity-rich dolomite. With CL, it was possible to detect a luminescent structure in the center of the light bands which seems to be present independent of the thickness and spacing of the respective layers. This structure was analysed in more detail with EMP. We further found that the dolomite crystals in the dark and light layers are chemically similar but show a variation in some trace elements. Based on the analytical findings, we put forward a mathematical model of zebra dolomite formation based on Cnoidal waves. We believe that the light coarse grained layers represent hydromechanical instabilities arising during the diagenetic compaction of a fluid saturated, impurity-rich dolomite. Our approach is based on the extension of the classical compaction bands theory to a viscose, non-linear rheology. In the model, the spacing between two light coarse grained layers is linked to the compaction length during the pattern formation. With the formulation of a 1D steady-state solution we can relate the genesis of the structure to physical parameter, such as

  20. Effect of pattern formation on C and N turnover heterogeneity in initial soils

    NASA Astrophysics Data System (ADS)

    Schaaf, Wolfgang; Zimmermann, Claudia

    2013-04-01

    The formation of vegetation patterns and hydrological processes, among others, result in soil heterogeneity in newly exposed land surfaces. We studied the effect of these developling structures on carbon and nitrogen trunover in soils of the artificial catchment Chicken Creek (Schaaf et al. 2011, 2012). Substrates with different physical and geochemical properties in combination with different labelled plant litter materials were studied in a microcosm experiment over a period of 80 weeks. Main objectives of the microcosm experiment were to determine the transformation processes of C and N from litter decomposition within the gaseous, liquid and solid phase, the interaction with mineral surfaces and its role for the establishment of biogeochemical cycles. The microcosm experiments were established in a climate chamber at constant 10 °C. In total, 48 soil columns (diameter: 14.4 cm; height: 30 cm) were filled with two different quaternary substrates (sand and loamy sand) representing the textural variation within the catchment at a bulk density of 1.4-1.5 g cm-3. The columns were automatically irrigated with artificial rainwater four times a day with 6.6 ml each (corresponding to 600 mm yr-1). The gaseous phase in the headspace of the microcosms was analyzed continuously for CO2 and N2O concentrations. C and N transformation processes were studied using 13C and 15N labelled litter of two different plant species occurring at the catchment (Lotus corniculatus, Calamagrostis epigejos) that was incorporated into the microcosm surface. By including litter from species with wide distribution within the catchment and soil substrates representing the main variation types of the sediments used for catchment construction we were able to characterize the general function of these sub-patches within the catchment with respect to litter decomposition, soil solution composition, DOC and nutrient leaching, and impact on the mineral soil phase. The results suggest that initial

  1. Fluorine-containing composition for forming anti-reflection film on resist surface and pattern formation method

    DOEpatents

    Nishi, Mineo; Makishima, Hideo

    1996-01-01

    A composition for forming anti-reflection film on resist surface which comprises an aqueous solution of a water soluble fluorine compound, and a pattern formation method which comprises the steps of coating a photoresist composition on a substrate; coating the above-mentioned composition for forming anti-reflection film; exposing the coated film to form a specific pattern; and developing the photoresist, are provided. Since the composition for forming anti-reflection film can be coated on the photoresist in the form of an aqueous solution, not only the anti-reflection film can be formed easily, but also, the film can be removed easily by rinsing with water or alkali development. Therefore, by the pattern formation method according to the present invention, it is possible to form a pattern easily with a high dimensional accuracy.

  2. Rayleigh-Taylor instability and mushroom-pattern formation in a two-component Bose-Einstein condensate

    SciTech Connect

    Sasaki, Kazuki; Suzuki, Naoya; Saito, Hiroki; Akamatsu, Daisuke

    2009-12-15

    The Rayleigh-Taylor instability at the interface in an immiscible two-component Bose-Einstein condensate is investigated using the mean field and Bogoliubov theories. Rayleigh-Taylor fingers are found to grow from the interface and mushroom patterns are formed. Quantized vortex rings and vortex lines are then generated around the mushrooms. The Rayleigh-Taylor instability and mushroom-pattern formation can be observed in a trapped system.

  3. Increase of island density via formation of secondary ordered islands on pit-patterned Si (001) substrates

    SciTech Connect

    Zhong, Z.; Schmidt, O.G.; Bauer, G.

    2005-09-26

    Site-controlled groups of Ge islands are grown on pit-patterned Si (001) substrates. By varying the deposited amount of Ge, we find that the growth starts with the formation of a single island at the pit bottom and then proceeds to the formation of a highly symmetric Ge island group around the pit top. A bimodal size distribution of dome-shaped islands at the bottom and at the top corners of the pits is observed. A growth mechanism is proposed to qualitatively explain these phenomena. Our experiments help to promote a further understanding of Ge island growth on patterned substrates.

  4. Metolachlor and alachlor breakdown product formation patterns in aquatic field mesocosms

    USGS Publications Warehouse

    Graham, W.H.; Graham, D.W.; DeNoyelles, F., Jr.; Smith, V.H.; Larive, C.K.; Thurman, E.M.

    1999-01-01

    The transformation of metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)- N-(2-methoxy-1-methyl)ethyl)acetamide] and alachlor [2-chloro-N-(2,6- diethylphenyl)-N-methoxymethyl)acetamide] in aquatic systems was investigated using outdoor tank mesocosms. Metolachlor and alachlor levels and their ethane sulfonic acid (ESA) and oxanillic acid breakdown products were monitored over time under five experimental treatments (each in quadruplicate). Background water conditions were identical in all treatments with each treatment differing based on the level and type(s) of herbicide present. Treatments included a noherbicide control, 10 ??g/L metolachlor, 25 ??g/L metolachlor, 25 ??g/L alachlor, and 25 ??g/L alachlor plus 25 ??g/L metolachlor in combination. The experiment was initiated by adding herbicide(s) to the units to the target concentrations; herbicide and breakdown product levels and other chemical parameters were then monitored for 85 days. In general, metolachlor half-lives were longer than alachlor half-lives under all treatments, although the differences were not statistically significant. Metolachlor half-lives (??95% confidence limits) ranged from 33.0 d (??14.1 d) to 46.2 d (??40.0 d), whereas alachlor half- lives ranged from 18.7 d (??3.5 d) to 21.0 d (??6.5 d) for different treatments. Formation patterns of ESA were similar in all treatments, whereas oxanillic acid formation differed for the two herbicides. Alachlor oxanillic acid was produced in larger quantities than metolachlor oxanillic acid and either ESA under equivalent conditions. Our results suggest that the transformation pathways for alachlor and metolachlor in aquatic systems are similar and resemble the acetochlor pathway in soils proposed by Feng (Pestic. Biochem. Physiol. 1991, 34, 136); however, the oxanillic acid branch of the pathway is favored for alachlor as compared with metolachlor.The transformation of metolachlor [2-chloro-N-(2-ethyl-6-methylphenyl)-N- (2-methoxy-1-methylethy

  5. Individual rules for trail pattern formation in Argentine ants (Linepithema humile).

    PubMed

    Perna, Andrea; Granovskiy, Boris; Garnier, Simon; Nicolis, Stamatios C; Labédan, Marjorie; Theraulaz, Guy; Fourcassié, Vincent; Sumpter, David J T

    2012-01-01

    We studied the formation of trail patterns by Argentine ants exploring an empty arena. Using a novel imaging and analysis technique we estimated pheromone concentrations at all spatial positions in the experimental arena and at different times. Then we derived the response function of individual ants to pheromone concentrations by looking at correlations between concentrations and changes in speed or direction of the ants. Ants were found to turn in response to local pheromone concentrations, while their speed was largely unaffected by these concentrations. Ants did not integrate pheromone concentrations over time, with the concentration of pheromone in a 1 cm radius in front of the ant determining the turning angle. The response to pheromone was found to follow a Weber's Law, such that the difference between quantities of pheromone on the two sides of the ant divided by their sum determines the magnitude of the turning angle. This proportional response is in apparent contradiction with the well-established non-linear choice function used in the literature to model the results of binary bridge experiments in ant colonies (Deneubourg et al. 1990). However, agent based simulations implementing the Weber's Law response function led to the formation of trails and reproduced results reported in the literature. We show analytically that a sigmoidal response, analogous to that in the classical Deneubourg model for collective decision making, can be derived from the individual Weber-type response to pheromone concentrations that we have established in our experiments when directional noise around the preferred direction of movement of the ants is assumed. PMID:22829756

  6. Electrostatic entrapment of chloroaurate ions in patterned lipid films and the in situ formation of gold nanoparticles

    NASA Astrophysics Data System (ADS)

    Mandal, Saikat; Sainkar, S. R.; Sastry, Murali

    2001-09-01

    The formation of gold nanoparticle assemblies in a patterned manner on suitable substrates is described. The protocol for realizing such structures comprises the following steps. In the first step, patterned films of a fatty amine are thermally evaporated onto solid supports using suitable masks (e.g. a TEM grid). Thereafter, the fatty amine film is immersed in chloroauric acid solution and chloroaurate (AuCl4-) ions entrapped in the lipid matrix by electrostatic complexation with the ammonium ions of the fatty amine molecules. The final step involves the reduction of the AuCl4- ions in situ thus leading to the formation of gold nanoparticles within the patterned lipid matrix. The process of metal ion incorporation and reduction may be repeated a number of times to increase the nanoparticle density in the lipid matrix. AuCl4- ion entrapment and formation of gold nanoparticles within the patterned lipid matrix has been followed by quartz crystal microgravimetry, UV-vis spectroscopy, Fourier transform infrared spectroscopy, scanning electron microscopy and energy dispersive analysis of x-ray measurements. The protocol described shows immense potential for extension to assemblies of nanoparticles in more intricate patterns as well as to the growth of semiconductor quantum dots in such patterns.

  7. On the role of vegetation in the formation of river anabranching patterns

    NASA Astrophysics Data System (ADS)

    Crouzy, B.; D'Odorico, P.; Wütrich, D.; Perona, P.

    2012-04-01

    Part of studies on the couplings between the evolution of riparian vegetation and the river morphodynamics, we investigate the effect of spatial interactions between vegetation located at different positions within the channel. This work generalizes the experimental and theoretical results by Perona et al. and by Crouzy and Perona (both Advances in Water Resources, in Press) on colonization of riverbars by seedlings or large woody debris by relaxing the hypothesis made in those two works of the biomass growth and uprooting being independent on the presence of neighboring plants. While the hypothesis of independent vegetation growth and uprooting is justified for sparse vegetation cover or young seedlings, it fails as soon as the canopy significantly disturbs the flow or changes the sediment stability. Then, flow-mediated interactions between riparian vegetation located at different positions within the channel can be observed. Those interactions are either constructive or destructive. For example, a region favorable to the development of biomass appears on the lee side of a vegetated obstacle (with bleed flow) due to increased deposition of seeds and sediment (Schnauder and Moggridge, 2008) while conversely scouring can be increased laterally due to obstacle-induced flow diversion (Roulund et al., 2005; Melville and Sutherland, 1988; Zong and Nepf, 2008). We focus on the role of vegetation in the formation of the regular vegetated ridge patterns found in ephemeral rivers (see for example the work by Tooth and Nanson, 2004 on anabranching patterns) or as a succession of swales and ridges on the inside of meander bends (scroll bars). From the analysis of aerial images, we obtain the characteristic length scale of the patterns. We show how in the limit where the hydrological (interarrival time of floods) and the biological (germination and growth rates) timescales are comparable the combination between both positive and negative feedbacks between vegetation located at

  8. Polar pattern formation in driven filament systems requires non-binary particle collisions

    NASA Astrophysics Data System (ADS)

    Suzuki, Ryo; Weber, Christoph A.; Frey, Erwin; Bausch, Andreas R.

    2015-10-01

    From the self-organization of the cytoskeleton to the synchronous motion of bird flocks, living matter has the extraordinary ability to behave in a concerted manner. The Boltzmann equation for self-propelled particles is frequently used in silico to link a system’s meso- or macroscopic behaviour to the microscopic dynamics of its constituents. But so far such studies have relied on an assumption of simplified binary collisions owing to a lack of experimental data suggesting otherwise. We report here experimentally determined binary-collision statistics by studying a recently introduced molecular system, the high-density actomyosin motility assay. We demonstrate that the alignment induced by binary collisions is too weak to account for the observed ordering transition. The transition density for polar pattern formation decreases quadratically with filament length, indicating that multi-filament collisions drive the observed ordering phenomenon and that a gas-like picture cannot explain the transition of the system to polar order. Our findings demonstrate that the unique properties of biological active-matter systems require a description that goes well beyond that developed in the framework of kinetic theories.

  9. Dynamical pattern formation in a low-concentration magnetorheological fluid under two orthogonal sinusoidal fields

    NASA Astrophysics Data System (ADS)

    Yépez, L. D.; Carrillo, J. L.; Donado, F.; Sausedo-Solorio, J. M.; Miranda-Romagnoli, P.

    2016-06-01

    The dynamical pattern formation of clusters of magnetic particles in a low-concentration magnetorheological fluid, under the influence of a superposition of two perpendicular sinusoidal fields, is studied experimentally. By varying the frequency and phase shift of the perpendicular fields, this configuration enables us to experimentally analyze a wide range of field configurations, including the case of a pure rotating field and the case of an oscillating unidirectional field. The fields are applied parallel to the horizontal plane where the fluid lies or in the vertical plane. For fields applied in the horizontal plane, we observed that, when the ratio of the frequencies increases, the average cluster size exhibits a kind of periodic resonances. When the phase shift between the fields is varied, the average chain length reaches maximal values for the cases of the rotating field and the unidirectional case. We analyze and discuss these results in terms of a weighted average of the time-dependent Mason number. In the case of a rotating field on the vertical plane, we also observe that the competition between the magnetic and the viscous forces determines the average cluster size. We show that this configuration generates a series of physically meaningful self-organization of clusters and transport phenomena.

  10. Peptide induced crystallization of calcium carbonate on wrinkle patterned substrate: implications for chitin formation in molluscs.

    PubMed

    Ghatak, Anindita Sengupta; Koch, Marcus; Guth, Christina; Weiss, Ingrid M

    2013-01-01

    We here present the nucleation and growth of calcium carbonate under the influence of synthetic peptides on topographically patterned poly(dimethylsiloxane) (PDMS) substrates, which have a controlled density of defects between the wrinkles. Experiments with two lysine-rich peptides derived from the extracellular conserved domain E22 of the mollusc chitin synthase Ar-CS1, AKKKKKAS (AS8) and EEKKKKKES (ES9) on these substrates showed their influence on the calcium carbonate morphology. A transition from polycrystalline composites to single crystalline phases was achieved with the peptide AS8 by changing the pH of the buffer solution. We analyzed three different pH values as previous experiments showed that E22 interacts with aragonite biominerals more strongly at pH 7.75 than at pH 9.0. At any given pH, crystals appeared in characteristic morphologies only on wrinkled substrates, and did not occur on the flat, wrinkle-free PDMS substrate. These results suggest that these wrinkled substrates could be useful for controlling the morphologies of other mineral/peptide and mineral/protein composites. In nature, these templates are formed enzymatically by glycosyltransferases containing pH-sensitive epitopes, similar to the peptides investigated here. Our in vitro test systems may be useful to gain understanding of the formation of distinct 3D morphologies in mollusc shells in response to local pH shifts during the mineralization of organic templates. PMID:23736692

  11. [Pattern formation in microcosm: the role of self-assembly in complex biological envelopes development].

    PubMed

    Gabaraeva, N I; Hemsley, A R

    2010-01-01

    The data on the development of pollen/spore walls (of sporoderm) were reconsidered in the light of our hypothesis regarding a considerable role of self-assembling processes in the formation of this complex pattern. The premises that (1) glycocalyx (cell surface coating) is a self-assembling colloidal solution, and that (2) exine, formed on a glycocalyx framework, appears as a result of the self-assembly of the biopolymer (sporopollenin microemulsion), were independently suggested by the authors of this paper (Gabarayeva, 1990, 1993; Hemsley et al., 1992). Afterwards a joint hypothesis has been worked out which interpreted the processes of sporoderm development through regularities of colloidal chemistry. It was shown that all of the successive developmental stages, seen in transmission electron microscope (TEM) in the course of pollen wall development, correspond to successive micelle mesophases of a colloidal solution of surface-active substances which self-assemble when their concentration increases. Such an interpretation implies that all of the microstructures, observed in mature pollen walls (granules; rods-columellae; hexagonally packed layers of rods; bilayers, separated with a gap) are somewhat like "stiff history" of their appearance as a micellar sequence, immortalized by chemically resistant sporopollenin. Since self-assembling processes have nonlinear, spasmodic character, and microstructures of pollen wall, mentioned above, are arranged, as a rule, in successive layers, it has been suggested that these layers of heterogeneous microstructures occur as a result of the abrupt phase transitions typical for self-assembling micellar systems. PMID:20865932

  12. Biofilm formation over surface patterned with pico-liter oil micro-drop array

    NASA Astrophysics Data System (ADS)

    Jalali, Maryam; Sheng, Jian

    2015-11-01

    It has been suggested that biodegradation by microbes is an effective process in the cleansing of oil polluted marine environments. It has also been speculated that dispersants could further enhance processes amid no direct evidence. The studies in the relevant scales are severely hampered by lack of techniques to generate uniform micro-scale drops allowing in-situ monitoring of these processes. In this paper, we present a microfabrication technique allowing patterning microfluidic surfaces with arrays of micro oil drops. The array of oil drops was printed by micro transfer molding/printing with negative PDMS stamps. The printed micro-drops have dimensions ranging from 5 μm to 50 μm. Non-circular shapes, such as square and triangle, can also be printed and maintained for weeks. Atomic force microscopy is used to characterize the topology and interfacial structures of droplets. The results reveal that although the drop with different base shapes assumes dome like profile asymptotically, donut and top-hat shapes are also observed. Time evolution measurement elucidates that in the absences of inviscid mechanisms in comparison to a micro-liter drop, subtle interplays between interfacial forces and viscosity play crucial role in the shape of pico-liter drop. With the developed surfaces, the effects of oil drop sizes and interfacial structures on biofilm formation are studied and reported.

  13. The shock-induced star formation sequence resulting from a constant spiral pattern speed

    SciTech Connect

    Martínez-García, Eric E.; Puerari, Ivânio E-mail: puerari@inaoep.mx

    2014-08-01

    We utilize a suite of multiwavelength data of nine nearby spirals to analyze the shock-induced star formation sequence that may result from a constant spiral pattern speed. The sequence involves tracers as the H I, CO 24 μm, and FUV, where the spiral arms were analyzed with Fourier techniques in order to obtain their azimuthal phases as a function of radius. It was found that only two of the objects, NGC 628 and NGC 5194, present coherent phases resembling the theoretical expectations, as indicated by the phase shifts of CO- 24 μm. The evidence is more clear for NGC 5194 and moderate for NGC 628. It was also found that the phase shifts are different for the two spiral arms. With the exception on NGC 3627, a two-dimensional Fourier analysis showed that the rest of the objects do not exhibit bi-symmetric spiral structures of stellar mass, i.e., grand-design spirals. A phase order inversion indicates a corotation radius of ∼89'' for NGC 628 and ∼202'' for NGC 5194. For these two objects, the CO-Hα phase shifts corroborate the CO-24 μm azimuthal offsets. Also for NGC 5194, the CO-70 μm, CO-140 μm, and CO-250 μm phase shifts indicate a corotation region.

  14. Hierarchical pattern formation through photo-induced disorder in block copolymer/additive composite films

    NASA Astrophysics Data System (ADS)

    Yao, Li; Watkins, James

    2013-03-01

    Segregation strength in hybrid materials can be increased through selective hydrogen bonding between organic or nanoparticle additives and one block of weakly segregated block copolymers to generate well ordered hybrid materials. Here, we report the use of enantiopure tartaric acid as the additive to dramatically improve ordering in poly(ethylene oxide-block-tert-butyl acrylate) (PEO-b-PtBA) copolymers. Phase behavior and morphologies within both bulk and thin films were studied by TEM, AFM and X-ray scattering. Suppression of PEO crystallization by the interaction between tartaric acid and the PEO block enables the formation of well ordered smooth thin films. With the addition of a photo acid generator, photo-induced disorder in PEO-b-PtBA/tartaric acid composite system can be achieved upon UV exposure to deprotect PtBA block to yield poly(acrylic acid) (PAA), which is phase-miscible with PEO. Due to the strong interaction of tartaric acid with both blocks, the system undergoes a disordering transition within seconds during a post-exposure baking. With the assistance of trace-amounts of base quencher, high resolution, hierarchical patterns of sub-micron regions of ordered and disordered domains were achieved in thin films through area-selective UV exposure using a photo-mask. Funding from Center for Hierarchical Manufacturing (CHM); Facility support from Materials Research Science and Engineering Center at UMass Amherst and Cornell High Energy Synchrotron Source

  15. PS-b-PDMS Block Copolymer Thin Film: Pattern Formation and Phase Behavior

    NASA Astrophysics Data System (ADS)

    Hsieh, I.-Fan; Cheng, Stephen Z. D.; Department of Polymer Science, The University of Akron Team

    2011-03-01

    Recently, block copolymer thin films attract great attention due to their potential applications in surface nano-lithography. In our work, PS- b -PDMS with cylinder morphology is chosen due to extremely large χ value between two blocks. Besides, PS- b -PDMS can be transformed into silicon oxide under UV/O3 exposure and a layer of silicon oxide with the self-assembled block copolymer patterns can be made. By utilizing the PGMEA as solvent, we can easily obtain sphere morphology in cylindrical composition block copolymer by preserved block copolymer solution morphology during film formation. Furthermore, in thermal annealing process, the phase behavior of the PS- b -PDMS thin film is strongly affects by molecular weight, film thickness and annealing temperature. In larger-molecular-weight PS- b -PDMS, we only observed spherical domains rearrangement and without morphology transition between sphere and cylinder due to high energy barrier, whereas, in the case of smaller-molecular-weight polymer, depending on the film thickness and annealing temperature, its thin film morphology transits between sphere and cylinder alternatively, which is similar to what we found in solvent annealing.

  16. Formation of Ga droplets on patterned GaAs (100) by molecular beam epitaxy

    PubMed Central

    2012-01-01

    In this paper, the formation of Ga droplets on photo-lithographically patterned GaAs (100) and the control of the size and density of Ga droplets by droplet epitaxy using molecular beam epitaxy are demonstrated. In extension of our previous result from the journal Physical Status Solidi A, volume 209 in 2012, the sharp contrast of the size and density of Ga droplets is clearly observed by high-resolution scanning electron microscope, atomic force microscope, and energy dispersive X-ray spectrometry. Also, additional monolayer (ML) coverage is added to strength the result. The density of droplets is an order of magnitude higher on the trench area (etched area), while the size of droplets is much larger on the strip top area (un-etched area). A systematic variation of ML coverage results in an establishment of the control of size and density of Ga droplets. The cross-sectional line profile analysis and root mean square roughness analysis show that the trench area (etched area) is approximately six times rougher. The atomic surface roughness is suggested to be the main cause of the sharp contrast of the size and density of Ga droplets and is discussed in terms of surface diffusion. PMID:23033893

  17. Bubble and pattern formation in liquid induced by an electron beam.

    PubMed

    Grogan, Joseph M; Schneider, Nicholas M; Ross, Frances M; Bau, Haim H

    2014-01-01

    Liquid cell electron microscopy has emerged as a powerful technique for in situ studies of nanoscale processes in liquids. An accurate understanding of the interactions between the electron beam and the liquid medium is essential to account for, suppress, and exploit beam effects. We quantify the interactions of high energy electrons with water, finding that radiolysis plays an important role, while heating is typically insignificant. For typical imaging conditions, we find that radiolysis products such as hydrogen and hydrated electrons achieve equilibrium concentrations within seconds. At sufficiently high dose-rate, the gaseous products form bubbles. We image bubble nucleation, growth, and migration. We develop a simplified reaction-diffusion model for the temporally and spatially varying concentrations of radiolysis species and predict the conditions for bubble formation by H2. We discuss the conditions under which hydrated electrons cause precipitation of cations from solution and show that the electron beam can be used to "write" structures directly, such as nanowires and other complex patterns, without the need for a mask. PMID:24299122

  18. Simple and non-toxic fabrication of poly(vinyl alcohol)-patterned polymer surface for the formation of cell patterns

    NASA Astrophysics Data System (ADS)

    Hwang, In-Tae; Jin, Yu-Ran; Oh, Min-Suk; Jung, Chan-Hee; Choi, Jae-Hak

    2014-10-01

    In this study, a facile and non-toxic method for the formation of cell-adhesive poly(vinyl alcohol) (PVA) patterns on the surface of a non-biological polystyrene substrate (NPS) is developed to control cellular micro-organization. PVA thin films spin-coated onto the NPS are selectively irradiated with 150 keV H+ ions through a pattern mask and developed with deionized water to form negative-type PVA patterns. Well-defined stripe patterns of PVA with a width of 100 μm are created on the NPS at a higher fluence than 5 × 1015 ions/cm2, and their surface chemical compositions are changed by ion irradiation without any significant morphological change. Based on the results of the protein adsorption test and in vitro cell culture, cancer cells are preferentially adhered and proliferated onto the more hydrophilic PVA regions of the PVA-patterned NPS, resulting in well-defined cell patterns.

  19. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity.

    PubMed

    Bennett, James E M; Bair, Wyeth

    2015-08-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  20. Refinement and Pattern Formation in Neural Circuits by the Interaction of Traveling Waves with Spike-Timing Dependent Plasticity

    PubMed Central

    Bennett, James E. M.; Bair, Wyeth

    2015-01-01

    Traveling waves in the developing brain are a prominent source of highly correlated spiking activity that may instruct the refinement of neural circuits. A candidate mechanism for mediating such refinement is spike-timing dependent plasticity (STDP), which translates correlated activity patterns into changes in synaptic strength. To assess the potential of these phenomena to build useful structure in developing neural circuits, we examined the interaction of wave activity with STDP rules in simple, biologically plausible models of spiking neurons. We derive an expression for the synaptic strength dynamics showing that, by mapping the time dependence of STDP into spatial interactions, traveling waves can build periodic synaptic connectivity patterns into feedforward circuits with a broad class of experimentally observed STDP rules. The spatial scale of the connectivity patterns increases with wave speed and STDP time constants. We verify these results with simulations and demonstrate their robustness to likely sources of noise. We show how this pattern formation ability, which is analogous to solutions of reaction-diffusion systems that have been widely applied to biological pattern formation, can be harnessed to instruct the refinement of postsynaptic receptive fields. Our results hold for rich, complex wave patterns in two dimensions and over several orders of magnitude in wave speeds and STDP time constants, and they provide predictions that can be tested under existing experimental paradigms. Our model generalizes across brain areas and STDP rules, allowing broad application to the ubiquitous occurrence of traveling waves and to wave-like activity patterns induced by moving stimuli. PMID:26308406

  1. Feedback-free single-beam pattern formation by nanosecond pulses in dye-doped liquid crystals

    NASA Astrophysics Data System (ADS)

    Lepeshkin, Nick N.; Lukishova, Svetlana G.; Boyd, Robert W.; Marshall, Kenneth L.

    2006-08-01

    Generally, optical feedback and/or two counter-propagating beams are necessary to form high-definition patterns in the cross section of a laser beam after passing through a nonlinear medium. In this paper we present an observation of pattern formation in liquid crystal media in a single laser beam without any external feedback. We found that after irradiation of a dye-doped liquid crystal cell with repetitive nanosecond pulses, the beam coming out of the liquid crystal cell exhibits a spectacular kaleidoscopic change of beam patterns in the far field. The patterns vary from pulse to pulse in an ordered manner cycling through a variety of complicated forms. We speculate that localized phase separation of the dye from the liquid crystal host occurs in the focal region of the beam in our experiments, and that the observed far-field patterns result from the laser-beam diffraction on these absorptive and refractive inhomogeneities.

  2. The influence of tetrad shape and intersporal callose wall formation on pollen aperture pattern ontogeny in two eudicot species

    PubMed Central

    Albert, Béatrice; Nadot, Sophie; Dreyer, Leanne; Ressayre, Adrienne

    2010-01-01

    Background and Aims In flowering plants, microsporogenesis is accompanied by various types of cytoplasmic partitioning (cytokinesis). Patterns of male cytokinesis are suspected to play a role in the diversity of aperture patterns found in pollen grains of angiosperms. The relationships between intersporal wall formation, tetrad shape and pollen aperture pattern ontogeny are studied. Methods A comparative analysis of meiosis and aperture distribution was performed within tetrads in two triporate eudicot species with contrasting aperture arrangements within their tetrads [Epilobium roseum (Onagraceae) and Paranomus reflexus (Proteaceae)]. Key Results and Conclusions Intersporal wall formation is a two-step process in both species. Cytokinesis is first achieved by the formation of naked centripetal cell plates. These naked cell plates are then covered by additional thick, localized callose deposits that differ in location between the two species. Apertures are finally formed in areas in which additional callose is deposited on the cell plates. The recorded variation in tetrad shape is correlated with variations in aperture pattern, demonstrating the role of cell partitioning in aperture pattern ontogeny. PMID:20685726

  3. The Effect of Short-term Intra-arterial Delivery of Paclitaxel on Neointimal Hyperplasia and the Local Thrombotic Environment after Angioplasty

    SciTech Connect

    Yajun, E; He Nengshu Fan Hailun

    2013-08-01

    PurposeTo evaluate the effects of short-term intra-arterial delivery of paclitaxel on neointimal hyperplasia and the local thrombotic environment after angioplasty.MethodsAn experimental common carotid artery injury model was established in 60 rats, which were divided into experimental groups (40 rats) and controls (20 rats). Local intra-arterial administration of paclitaxel was applied at 2 doses (90 and 180 {mu}g/30 {mu}l), and the effects of short-term delivery of paclitaxel on neointimal hyperplasia and the expression of tissue factor (TF), plasminogen activator inhibitor-1 (PAI-1) and tissue-type plasminogen activator (t-PA) were evaluated at days 15 and 30 by hematoxylin and eosin staining and immunohistochemistry.ResultsAt 15 and 30 days after injury, neointimal thickness and area, the ratio of intimal area to medial area and the stenotic rate were all significantly decreased in the group provided the high concentrations (180 {mu}g/30 {mu}l) of paclitaxel for 2 min or 10 min and in the group provided the low concentration (90 {mu}g/30 {mu}l) of paclitaxel for 10 min (p < 0.05). At 30 days after injury, there were no significant changes in TF expression among all experimental groups. PAI-1 expression increased in the neointima of the high concentration 10 min group (p < 0.05), while t-PA expression decreased in the neointima of the high concentration 2 min group (p < 0.05).ConclusionIn the rat common carotid artery injury model, the short-term delivery of paclitaxel could effectively inhibit neointimal hyperplasia in the long term, with very little influence on the local expression of TF and PAI-1.

  4. Pigment Pattern Formation in the Guppy, Poecilia reticulata, Involves the Kita and Csf1ra Receptor Tyrosine Kinases

    PubMed Central

    Kottler, Verena A.; Fadeev, Andrey; Weigel, Detlef; Dreyer, Christine

    2013-01-01

    Males of the guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of guppy males, which in the case of csf1ra might be mediated by xanthophore–melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics. PMID:23666934

  5. Kinetic trapping through coalescence and the formation of patterned Ag-Cu nanoparticles

    NASA Astrophysics Data System (ADS)

    Grammatikopoulos, Panagiotis; Kioseoglou, Joseph; Galea, Antony; Vernieres, Jerome; Benelmekki, Maria; Diaz, Rosa E.; Sowwan, Mukhles

    2016-05-01

    In recent years, due to its inherent flexibility, magnetron-sputtering has been widely used to synthesise bi-metallic nanoparticles (NPs) via subsequent inert-gas cooling and gas-phase condensation of the sputtered atomic vapour. Utilising two separate sputter targets allows for good control over composition. Simultaneously, it involves fast kinetics and non-equilibrium processes, which can trap the nascent NPs into metastable configurations. In this study, we observed such configurations in immiscible, bi-metallic Ag-Cu NPs by scanning transmission electron microscopy (S/TEM) and electron energy-loss spectroscopy (EELS), and noticed a marked difference in the shape of NPs belonging to Ag- and Cu-rich samples. We explained the formation of Janus or Ag@Cu core/shell metastable structures on the grounds of in-flight mixed NP coalescence. We utilised molecular dynamics (MD) and Monte Carlo (MC) computer simulations to demonstrate that such configurations cannot occur as a result of nanoalloy segregation. Instead, sintering at relatively low temperatures can give rise to metastable structures, which eventually can be stabilised by subsequent quenching. Furthermore, we compared the heteroepitaxial diffusivities along various surfaces of both Ag and Cu NPs, and emphasised the differences between the sintering mechanisms of Ag- and Cu-rich NP compositions: small Cu NPs deform as coherent objects on large Ag NPs, whereas small Ag NPs dissolve into large Cu NPs, with their atoms diffusing along specific directions. Taking advantage of this observation, we propose controlled NP coalescence as a method to engineer mixed NPs of a unique, patterned core@partial-shell structure, which we refer to as a ``glass-float'' (ukidama) structure.In recent years, due to its inherent flexibility, magnetron-sputtering has been widely used to synthesise bi-metallic nanoparticles (NPs) via subsequent inert-gas cooling and gas-phase condensation of the sputtered atomic vapour. Utilising two

  6. Effect of a Dipeptidyl Peptidase-IV Inhibitor, Des-Fluoro-Sitagliptin, on Neointimal Formation after Balloon Injury in Rats

    PubMed Central

    Lim, Soo; Choi, Sung Hee; Shin, Hayley; Cho, Bong Jun; Park, Ho Seon; Ahn, Byung Yong; Kang, Seon Mee; Yoon, Ji Won; Jang, Hak Chul; Kim, Young-Bum; Park, Kyong Soo

    2012-01-01

    Background Recently, it has been suggested that enhancement of incretin effect improves cardiac function. We investigated the effect of a DPP-IV inhibitor, des-fluoro-sitagliptin, in reducing occurrence of restenosis in carotid artery in response to balloon injury and the related mechanisms. Methods and Findings Otsuka Long-Evans Tokushima Fatty rats were grouped into four: control (normal saline) and sitagliptin 100, 250 and 500 mg/kg per day (n = 10 per group). Sitagliptin or normal saline were given orally from 1 week before to 2 weeks after carotid injury. After 3 weeks of treatment, sitagliptin treatment caused a significant and dose-dependent reduction in intima-media ratio (IMR) in obese diabetic rats. This effect was accompanied by improved glucose homeostasis, decreased circulating levels of high-sensitivity C-reactive protein (hsCRP) and increased adiponectin level. Moreover, decreased IMR was correlated significantly with reduced hsCRP, tumor necrosis factor-α and monocyte chemoattractant protein-1 levels and plasminogen activator inhibitor-1 activity. In vitro evidence with vascular smooth muscle cells (VSMCs) demonstrated that proliferation and migration were decreased significantly after sitagliptin treatment. In addition, sitagliptin increased caspase-3 activity and decreased monocyte adhesion and NFκB activation in VSMCs. Conclusions Sitagliptin has protective properties against restenosis after carotid injury and therapeutic implications for treating macrovascular complications of diabetes. PMID:22493727

  7. Kinetic trapping through coalescence and the formation of patterned Ag-Cu nanoparticles.

    PubMed

    Grammatikopoulos, Panagiotis; Kioseoglou, Joseph; Galea, Antony; Vernieres, Jerome; Benelmekki, Maria; Diaz, Rosa E; Sowwan, Mukhles

    2016-05-14

    In recent years, due to its inherent flexibility, magnetron-sputtering has been widely used to synthesise bi-metallic nanoparticles (NPs) via subsequent inert-gas cooling and gas-phase condensation of the sputtered atomic vapour. Utilising two separate sputter targets allows for good control over composition. Simultaneously, it involves fast kinetics and non-equilibrium processes, which can trap the nascent NPs into metastable configurations. In this study, we observed such configurations in immiscible, bi-metallic Ag-Cu NPs by scanning transmission electron microscopy (S/TEM) and electron energy-loss spectroscopy (EELS), and noticed a marked difference in the shape of NPs belonging to Ag- and Cu-rich samples. We explained the formation of Janus or Ag@Cu core/shell metastable structures on the grounds of in-flight mixed NP coalescence. We utilised molecular dynamics (MD) and Monte Carlo (MC) computer simulations to demonstrate that such configurations cannot occur as a result of nanoalloy segregation. Instead, sintering at relatively low temperatures can give rise to metastable structures, which eventually can be stabilised by subsequent quenching. Furthermore, we compared the heteroepitaxial diffusivities along various surfaces of both Ag and Cu NPs, and emphasised the differences between the sintering mechanisms of Ag- and Cu-rich NP compositions: small Cu NPs deform as coherent objects on large Ag NPs, whereas small Ag NPs dissolve into large Cu NPs, with their atoms diffusing along specific directions. Taking advantage of this observation, we propose controlled NP coalescence as a method to engineer mixed NPs of a unique, patterned core@partial-shell structure, which we refer to as a "glass-float" (ukidama) structure. PMID:27119383

  8. Induction of secondary axis in hydra revisited: New insights into pattern formation

    PubMed Central

    Kadu, Vishal; S. Ghaskadbi, Saroj; Ghaskadbi, Surendra

    2012-01-01

    In 1909, several years before the famous `Organizer’ experiments of Spemann and Mangold, Ethel Browne demonstrated induction of a secondary axis in hydra by grafting a hypostome. Based on this and subsequent work, in the late sixties, Lewis Wolpert proposed the theory of morphogen gradients and positional information. We have studied secondary axis induction by hypostome and foot tissue using three species of hydra as well as transgenic, GFP-expressing lines of hydra. We have found that pieces of hypostome and complete foot of a donor hydra can induce a secondary axis all along (in upper, middle or lower parts of) the body column of a host hydra, both within and across species with comparable rates. Thus, contrary to the available literature, our results show that the host hypostome does not completely inhibit the induction of a secondary axis. The length of the induced axis though is determined by the position of the graft. By using GFP-expressing lines of hydra we have demonstrated that host ectodermal and endodermal cells actively contribute to the secondary axis. On comparison, the hypostome was found to be a stronger and dominant Organizer than the foot. Foot grafting experiments show a transient increase in the host length as well as the distance between the two Organizers. The length becomes normal once the grafted foot reaches the budding zone. Our work brings out several new aspects of the role of positional cues in pattern formation in hydra that can be now be explored at cellular and molecular levels. PMID:24551754

  9. Ancestral Patterning of Tergite Formation in a Centipede Suggests Derived Mode of Trunk Segmentation in Trilobites

    PubMed Central

    Ortega-Hernández, Javier; Brena, Carlo

    2012-01-01

    Trilobites have a rich and abundant fossil record, but little is known about the intrinsic mechanisms that orchestrate their body organization. To date, there is disagreement regarding the correspondence, or lack thereof, of the segmental units that constitute the trilobite trunk and their associated exoskeletal elements. The phylogenetic position of trilobites within total-group Euarthropoda, however, allows inferences about the underlying organization in these extinct taxa to be made, as some of the fundamental genetic processes for constructing the trunk segments are remarkably conserved among living arthropods. One example is the expression of the segment polarity gene engrailed, which at embryonic and early postembryonic stages is expressed in extant panarthropods (i.e. tardigrades, onychophorans, euarthropods) as transverse stripes that define the posteriormost region of each trunk segment. Due to its conservative morphology and allegedly primitive trunk tagmosis, we have utilized the centipede Strigamia maritima to study the correspondence between the expression of engrailed during late embryonic to postembryonic stages, and the development of the dorsal exoskeletal plates (i.e. tergites). The results corroborate the close correlation between the formation of the tergite borders and the dorsal expression of engrailed, and suggest that this association represents a symplesiomorphy within Euarthropoda. This correspondence between the genetic and phenetic levels enables making accurate inferences about the dorsoventral expression domains of engrailed in the trunk of exceptionally preserved trilobites and their close relatives, and is suggestive of the widespread occurrence of a distinct type of genetic segmental mismatch in these extinct arthropods. The metameric organization of the digestive tract in trilobites provides further support to this new interpretation. The wider evolutionary implications of these findings suggest the presence of a derived

  10. The Arabidopsis Exine Formation Defect (EFD) gene is required for primexine patterning and is critical for pollen fertility.

    PubMed

    Hu, Jun; Wang, Zhaodan; Zhang, Liyao; Sun, Meng-xiang

    2014-07-01

    Exine, the outermost layer of a pollen grain, has important roles in protecting microspore cytoplasm and determining species-specific interactions between pollen and stigma. The molecular mechanism underlying pollen exine formation, however, remains largely unknown. Here, we report the characterization of an Arabidopsis male-sterile mutant, efd, which exhibits male sterility in first-forming flowers. The Exine Formation Defect (EFD) gene is strongly expressed in microsporocytes, tetrads and the tapetum, and encodes a nuclear-localized de novo DNA methyltransferase. Detailed observations revealed that EFD is involved in both callose wall and primexine formation during microsporogenesis. Microspores in tetrads are not well separated in efd due to an abnormal callose wall. Its plasma membrane undulation appears normal, but primexine patterning is impaired. Primexine matrix establishment and sporopollenin accumulation at specific positions are disturbed, and thus exine formation is totally blocked in efd. We confirmed that EFD is required for pollen exine formation and male fertility via the regulation of callose wall and primexine formation. We also found that positional sporopollenin accumulation is not involved in regulating membrane undulation, but is related to the complete separation of tetrad microspores during primary exine patterning. PMID:24697753

  11. A Study on Optimal Pattern and Leader Shift of Formation Flight

    NASA Astrophysics Data System (ADS)

    Kawabe, Hiroyasu

    The aerodynamics of formation flight are studied by modeling wings using a horseshoe vortex. During flight in formation, wings receive upwash created by other wings, and the required power consequently decreases. The leading wing in a V formation receives less benefit, while in a U formation, the power reduction rate remains identical over all wings. In long-distance flights, the U formation is optimal. However, when the process of shifting the leader position in a V formation is considered, as is often observed in actual bird flocks in long-distance flights, the power reduction rates of all wings converge into the same value after several shifts. This value is identical to that of the U formation.

  12. Turing Pattern Formation in a Semiarid Vegetation Model with Fractional-in-Space Diffusion.

    PubMed

    Tian, Canrong

    2015-11-01

    A fractional power of the Laplacian is introduced to a reaction-diffusion system to describe water's anomalous diffusion in a semiarid vegetation model. Our linear stability analysis shows that the wavenumber of Turing pattern increases with the superdiffusive exponent. A weakly nonlinear analysis yields a system of amplitude equations, and the analysis of these amplitude equations shows that the spatial patterns are asymptotic stable due to the supercritical Turing bifurcation. Numerical simulations exhibit a bistable regime composed of hexagons and stripes, which confirm our analytical results. Moreover, the characteristic length of the emergent spatial pattern is consistent with the scale of vegetation patterns observed in field studies. PMID:26511752

  13. Poly (methyl methacrylate) Formation and Patterning Initiated by Synchrotron X-ray Illumination

    SciTech Connect

    Xiao, J.; Je, J. H.; Wang, C. H.; Yang, T. Y.; Hwu, Y.

    2007-01-19

    A facile radiation method was developed to obtain micro-sized poly (methyl methacrylate) (PMMA) particles and create patterned coating on different substrates by a synchrotron x-ray induced dispersion polymerization. The polymerization of MMA monomer and well defined patterning was successfully realized. The produced PMMA particles and patterning were characterized by Fourier transformation infrared (FTIR), 1H-Nuclear Magnetic Resonance (NMR), and Scanning Electron Microscope (SEM). The observed patterning contrast essentially derived from a variation of size, density and morphology of particles and the type of substrate materials used.

  14. Electrohydrodynamic Pattern Formation in Nematic Liquid Crystals by External Pure Noise

    NASA Astrophysics Data System (ADS)

    Huh, Jong-Hoon

    2010-12-01

    Pure noise-induced electrohydrodynamic convections (EHCs) in nematic liquid crystals are presented in comparison with ac field-induced ones. There exists a characteristic cutoff frequency fc* of noise dividing EHC patterns qualitatively. Sufficiently colored noise with fc < fc* can induce a variety of well-ordered patterns such as Williams domains, fluctuating Williams domains, and grid patterns. The amplitude of the primary pattern (Williams domains) and its wavelength are investigated with varying intensity VN and/or cutoff frequency fc of noise. The present noise-induced EHCs are discussed on the basis of the conventional (ac-based) Carr-Helfrich mechanism.

  15. Alterations in wall shear stress predict sites of neointimal hyperplasia after stent implantation in rabbit iliac arteries.

    PubMed

    LaDisa, John F; Olson, Lars E; Molthen, Robert C; Hettrick, Douglas A; Pratt, Phillip F; Hardel, Michael D; Kersten, Judy R; Warltier, David C; Pagel, Paul S

    2005-05-01

    Restenosis resulting from neointimal hyperplasia (NH) limits the effectiveness of intravascular stents. Rates of restenosis vary with stent geometry, but whether stents affect spatial and temporal distributions of wall shear stress (WSS) in vivo is unknown. We tested the hypothesis that alterations in spatial WSS after stent implantation predict sites of NH in rabbit iliac arteries. Antegrade iliac artery stent implantation was performed under angiography, and blood flow was measured before casting 14 or 21 days after implantation. Iliac artery blood flow domains were obtained from three-dimensional microfocal X-ray computed tomography imaging and reconstruction of the arterial casts. Indexes of WSS were determined using three-dimensional computational fluid dynamics. Vascular histology was unchanged proximal and distal to the stent. Time-dependent NH was localized within the stented region and was greatest in regions exposed to low WSS and acute elevations in spatial WSS gradients. The lowest values of WSS spatially localized to the stented area of a theoretical artery progressively increased after 14 and 21 days as NH occurred within these regions. This NH abolished spatial disparity in distributions of WSS. The results suggest that stents may introduce spatial alterations in WSS that modulate NH in vivo. PMID:15653759

  16. Patterns of biofilm formation in intermittent and permanent streams: analysis of biofilm structure and metabolism

    NASA Astrophysics Data System (ADS)

    Artigas, J.; Schwartz, T.; Kirchen, S.; Romaní, A. M.; Fund, K.; Obst, U.; Sabater, S.

    2009-04-01

    The development and functioning of benthic microbial communities in streams is largely dependent on the hydrological conditions. Climate change projections predict that the hydrological characteristics will probably be affected because of the rainfall regime. Hence, rivers from the Mediterranean region will become more similar to those draining arid or desert regions, while temperate streams will suffer of higher water flow fluctuations. In this study, we compared the process of biofilm formation between an intermittent (the Fuirosos, Mediterranean) and a permanent (the Walzbach, Central European) stream. Specifically, we analyzed the succession of bacterial and algal populations in the biofilm through bacterial rDNA sequences analysis (16S rDNA and 16S-23S intergenic sequence) and diatom taxa identification over a 60-days colonization experiment. Moreover, changes in biofilm structural (microbial biomass and extracellular polysaccharide content) and metabolic (extracellular enzyme activities) parameters were also analyzed. The successional patterns of microbial populations in the Fuirosos showed clear discontinutities coinciding with flood episodes while at the Walzbach the time sequence was more gradual. Although both study sites were forested, greater microbial biomass standing stock (algal and bacterial) and greater species biodiversity was detected during biofilm development at the Mediterranean site. The higher bacterial biodiversity may be related to the potential effect of flooding episodes in reducing biological interactions in complex microbial communities, such as the competitive exclusion of species. Moreover, the presence of rapid colonizing diatom species might be an adaptation to hydrological changes. In contrast, species competition could define the more stable environments, such as that observed in the Central European stream. Overall, the hystorical evolutionary pressure from the different bioclimatic regions could be also affecting the microbial

  17. Thrombus formation patterns in the HeartMate II ventricular assist device: clinical observations can be predicted by numerical simulations.

    PubMed

    Chiu, Wei-Che; Slepian, Marvin J; Bluestein, Danny

    2014-01-01

    Postimplant device thrombosis remains a life-threatening complication and limitation of continuous-flow ventricular assist devices (VADs). Using advanced computational fluid dynamic (CFD) simulations, we successfully depicted various flow patterns, recirculation zones, and stagnant platelet trajectories which promote thrombus formation and observed that they matched actual thrombus formation patterns observed in Thoratec HeartMate II VADs explanted from patients with pump thrombosis. Previously, these small eddies could not be captured by either digital particle image velocimetry or CFD due to insufficient resolution. Our study successfully demonstrated the potential capability of advanced CFD to be adopted for device optimization, leading to enhanced safety and efficacy of VADs for long-term destination therapy. PMID:24399065

  18. Physical mechanisms of self-organization and formation of current patterns in gas discharges of the Townsend and glow types

    SciTech Connect

    Raizer, Yu. P.; Mokrov, M. S.

    2013-10-15

    The paper discusses current filamentation and formation of current structures (in particular, hexagonal current patterns) in discharges of the Townsend and glow types. The aim of the paper, which is in part a review, is to reveal basic reasons for formation of current patterns in different cases, namely, in dielectric barrier discharge, discharge with semiconductor cathode, and micro-discharge between metallic electrodes. Pursuing this goal, we give a very brief review of observations and discuss only those theoretical, computational, and experimental papers that shed light on the physical mechanisms involved. The mechanisms are under weak currents—the thermal expansion of the gas as a result of Joule heating; under enhanced currents—the electric field and ionization rate redistribution induced by space charge. Both mechanisms lead to instability of the homogeneous discharges. In addition, we present new results of numerical simulations of observed short-living current filaments which are chaotic in space and time.

  19. Dynamics and pattern formation in a diffusive predator-prey system with strong Allee effect in prey

    NASA Astrophysics Data System (ADS)

    Wang, Jinfeng; Shi, Junping; Wei, Junjie

    The dynamics of a reaction-diffusion predator-prey system with strong Allee effect in the prey population is considered. Nonexistence of nonconstant positive steady state solutions are shown to identify the ranges of parameters of spatial pattern formation. Bifurcations of spatially homogeneous and nonhomogeneous periodic solutions as well as nonconstant steady state solutions are studied. These results show that the impact of the Allee effect essentially increases the system spatiotemporal complexity.

  20. Formation and coarsening of the concertina magnetization pattern in elongated thin-film elements

    NASA Astrophysics Data System (ADS)

    Steiner, Jutta; Schäfer, Rudolf; Wieczoreck, Holm; McCord, Jeffrey; Otto, Felix

    2012-03-01

    The concertina is a magnetization pattern in elongated thin-film elements of a soft ferromagnetic material. It is a ubiquitous domain pattern that occurs in the process of magnetization reversal in the direction of the long axis of the small element. Van den Berg and Vatvani [IEEE Trans. Magn.IEMGAQ0018-946410.1109/TMAG.1982.1061919 18, 880 (1982)] argued that this pattern grows out of the flux-closure domains at the sample's tips as the external field is reduced. Based on experimental observations and theory, we argue that in sufficiently elongated thin-film elements the concertina pattern rather bifurcates from an oscillatory buckling mode. Typical sample widths and thicknesses are of the order of 10-100 μm and of the order of 10-150 nm, respectively. Using a reduced model that is derived by asymptotic analysis from the micromagnetic energy and that is also investigated by means of numerical simulation, we quantitatively predict the average period of the concertina pattern and qualitatively predict its hysteresis. In particular, we argue that the experimentally observed coarsening of the concertina pattern is due to secondary bifurcations related to an Eckhaus instability. We also link the concertina pattern to the magnetization ripple and discuss the effect of a weak (crystalline or induced) anisotropy.

  1. Target morphology and cell memory: a model of regenerative pattern formation

    PubMed Central

    Bessonov, Nikolai; Levin, Michael; Morozova, Nadya; Reinberg, Natalia; Tosenberger, Alen; Volpert, Vitaly

    2015-01-01

    Despite the growing body of work on molecular components required for regenerative repair, we still lack a deep understanding of the ability of some animal species to regenerate their appropriate complex anatomical structure following damage. A key question is how regenerating systems know when to stop growth and remodeling – what mechanisms implement recognition of correct morphology that signals a stop condition? In this work, we review two conceptual models of pattern regeneration that implement a kind of pattern memory. In the first one, all cells communicate with each other and keep the value of the total signal received from the other cells. If a part of the pattern is amputated, the signal distribution changes. The difference fromthe original signal distribution stimulates cell proliferation and leads to pattern regeneration, in effect implementing an error minimization process that uses signaling memory to achieve pattern correction. In the second model, we consider a more complex pattern organization with different cell types. Each tissue contains a central (coordinator) cell that controls the tissue and communicates with the other central cells. Each of them keeps memory about the signals received from other central cells. The values of these signals depend on the mutual cell location, and the memory allows regeneration of the structure when it is modified. The purpose of these models is to suggest possible mechanisms of pattern regeneration operating on the basis of cell memory which are compatible with diverse molecular implementation mechanisms within specific organisms. PMID:26889161

  2. Target morphology and cell memory: a model of regenerative pattern formation.

    PubMed

    Bessonov, Nikolai; Levin, Michael; Morozova, Nadya; Reinberg, Natalia; Tosenberger, Alen; Volpert, Vitaly

    2015-12-01

    Despite the growing body of work on molecular components required for regenerative repair, we still lack a deep understanding of the ability of some animal species to regenerate their appropriate complex anatomical structure following damage. A key question is how regenerating systems know when to stop growth and remodeling - what mechanisms implement recognition of correct morphology that signals a stop condition? In this work, we review two conceptual models of pattern regeneration that implement a kind of pattern memory. In the first one, all cells communicate with each other and keep the value of the total signal received from the other cells. If a part of the pattern is amputated, the signal distribution changes. The difference fromthe original signal distribution stimulates cell proliferation and leads to pattern regeneration, in effect implementing an error minimization process that uses signaling memory to achieve pattern correction. In the second model, we consider a more complex pattern organization with different cell types. Each tissue contains a central (coordinator) cell that controls the tissue and communicates with the other central cells. Each of them keeps memory about the signals received from other central cells. The values of these signals depend on the mutual cell location, and the memory allows regeneration of the structure when it is modified. The purpose of these models is to suggest possible mechanisms of pattern regeneration operating on the basis of cell memory which are compatible with diverse molecular implementation mechanisms within specific organisms. PMID:26889161

  3. A Gain-of-Function Screen Identifying Genes Required for Growth and Pattern Formation of the Drosophila melanogaster Wing

    PubMed Central

    Cruz, Cristina; Glavic, Alvaro; Casado, Mar; de Celis, Jose F.

    2009-01-01

    The Drosophila melanogaster wing is a model system for analyzing the genetic control of organ size, shape, and pattern formation. The formation of the wing involves a variety of processes, such as cell growth, proliferation, pattern formation, and differentiation. These developmental processes are under genetic control, and many genes participating in specific aspects of wing development have already being characterized. In this work, we aim to identify novel genes regulating wing growth and patterning. To this end, we have carried out a gain-of-function screen generating novel P-UAS (upstream activating sequences) insertions allowing forced gene expression. We produced 3340 novel P-UAS insertions and isolated 300 that cause a variety of wing phenotypes in combination with a Gal4 driver expressed exclusively in the central domain of the presumptive wing blade. The mapping of these P-UAS insertion sites allowed us to identify the gene that causes the gain-of-function phenotypes. We show that a fraction of these phenotypes are related to the induction of cell death in the domain of ectopic gene expression. Finally, we present a preliminary characterization of a gene identified in the screen, the function of which is required for the development of the L5 longitudinal vein. PMID:19737745

  4. AUXIN RESPONSE FACTOR17 Is Essential for Pollen Wall Pattern Formation in Arabidopsis1[C][W][OA

    PubMed Central

    Yang, Jun; Tian, Lei; Sun, Ming-Xi; Huang, Xue-Yong; Zhu, Jun; Guan, Yue-Feng; Jia, Qi-Shi; Yang, Zhong-Nan

    2013-01-01

    In angiosperms, pollen wall pattern formation is determined by primexine deposition on the microspores. Here, we show that AUXIN RESPONSE FACTOR17 (ARF17) is essential for primexine formation and pollen development in Arabidopsis (Arabidopsis thaliana). The arf17 mutant exhibited a male-sterile phenotype with normal vegetative growth. ARF17 was expressed in microsporocytes and microgametophytes from meiosis to the bicellular microspore stage. Transmission electron microscopy analysis showed that primexine was absent in the arf17 mutant, which leads to pollen wall-patterning defects and pollen degradation. Callose deposition was also significantly reduced in the arf17 mutant, and the expression of CALLOSE SYNTHASE5 (CalS5), the major gene for callose biosynthesis, was approximately 10% that of the wild type. Chromatin immunoprecipitation and electrophoretic mobility shift assays showed that ARF17 can directly bind to the CalS5 promoter. As indicated by the expression of DR5-driven green fluorescent protein, which is an synthetic auxin response reporter, auxin signaling appeared to be specifically impaired in arf17 anthers. Taken together, our results suggest that ARF17 is essential for pollen wall patterning in Arabidopsis by modulating primexine formation at least partially through direct regulation of CalS5 gene expression. PMID:23580594

  5. [Formation of a "crow's foot pattern" in the smoke residue in homicide by forehead gunshot injury].

    PubMed

    Hochmeister, M; Dirnhofer, R

    1989-01-01

    We report a "crowsfoot-like" pattern in the smoke marks around the entrance of a close-range bullet wound in the center of the forehead; the weapon in this homicide was a revolver. This pattern only occurs if the facial muscles that form expression are completely contracted at the moment the shooting occurs and if the victim expects the event. The wrinkles gather around the entrance of the bullet, and this wound pattern may indicate that the shot was expected by the victim and represent a piece of the mosaic that might help clarify the circumstances in a case. PMID:2800733

  6. Pattern formation in Dictyostelium via the dynamics of cooperative biological entities

    NASA Astrophysics Data System (ADS)

    Kessler, David A.; Levine, Herbert

    1993-12-01

    The cellular slime mold Dictyostelium discoideum exhibits a variety of spatial patterns as it aggregates to form a multicellular slug. These patterns arise via the interaction of the aggregating amoebae, either via contact or as mediated by chemical signals involving cyclic adenosine monophosphate (AMP). We model this system as a set of reaction-diffusion equations coupled to dynamical biological entities (bions), each of which is endowed with signal receptors and response rules. Simulations of our model reveal a close correspondence with the observed structures. Also, the general framework we propose should be suitable for modeling other biological pattern-forming processes.

  7. Spontaneous Symmetry Breaking Turing-Type Pattern Formation in a Confined Dictyostelium Cell Mass

    NASA Astrophysics Data System (ADS)

    Sawai, Satoshi; Maeda, Yasuo; Sawada, Yasuji

    2000-09-01

    We have discovered a new type of patterning which occurs in a two-dimensionally confined cell mass of the cellular slime mold Dictyostelium discoideum. Besides the longitudinal structure reported earlier, we observed a spontaneous symmetry breaking spot pattern whose wavelength shows similar strain dependency to that of the longitudinal pattern. We propose that these structures are due to a reaction-diffusion Turing instability similar to the one which has been exemplified by CIMA (chlorite-iodide-malonic acid) reaction. The present finding may exhibit the first biochemical Turing structure in a developmental system with a controllable boundary condition.

  8. Autonomous Pattern Formation of Micro-organic Cell Density with Optical Interlink between Two Isolated Culture Dishes.

    PubMed

    Ozasa, Kazunari; Lee, Jeesoo; Song, Simon; Hara, Masahiko; Maeda, Mizuo

    2015-01-01

    Artificial linking of two isolated culture dishes is a fascinating means of investigating interactions among multiple groups of microbes or fungi. We examined artificial interaction between two isolated dishes containing Euglena cells, which are photophobic to strong blue light. The spatial distribution of swimming Euglena cells in two micro-aquariums in the dishes was evaluated as a set of new measures: the trace momentums (TMs). The blue light patterns next irradiated onto each dish were deduced from the set of TMs using digital or analogue feedback algorithms. In the digital feedback experiment, one of two different pattern-formation rules was imposed on each feedback system. The resultant cell distribution patterns satisfied the two rules with an and operation, showing that cooperative interaction was realized in the interlink feedback. In the analogue experiment, two dishes A and B were interlinked by a feedback algorithm that illuminated dish A (B) with blue light of intensity proportional to the cell distribution in dish B (A). In this case, a distribution pattern and its reverse were autonomously formed in the two dishes. The autonomous formation of a pair of reversal patterns reflects a type of habitat separation realized by competitive interaction through the interlink feedback. According to this study, interlink feedback between two or more separate culture dishes enables artificial interactions between isolated microbial groups, and autonomous cellular distribution patterns will be achieved by correlating various microbial species, despite environmental and spatial scale incompatibilities. The optical interlink feedback is also useful for enhancing the performance of Euglena-based soft biocomputing. PMID:25622016

  9. Module-based complexity formation: periodic patterning in feathers and hairs.

    PubMed

    Chuong, Cheng-Ming; Yeh, Chao-Yuan; Jiang, Ting-Xin; Widelitz, Randall

    2013-01-01

    Patterns describe order which emerges from homogeneity. Complex patterns on the integument are striking because of their visibility throughout an organism’s lifespan. Periodic patterning is an effective design because the ensemble of hair or feather follicles (modules) allows the generation of complexity, including regional variations and cyclic regeneration, giving the skin appendages a new lease on life. Spatial patterns include the arrangements of feathers and hairs in specific number, size, and spacing.We explorehowa field of equivalent progenitor cells can generate periodically arranged modules based on genetic information, physical–chemical rules and developmental timing. Reconstitution experiments suggest a competitive equilibrium regulated by activators/inhibitors involving Turing reaction-diffusion. Temporal patterns result from oscillating stem cell activities within each module (microenvironment regulation), reflected as growth (anagen) and resting (telogen) phases during the cycling of feather and hair follicles. Stimulating modules with activators initiates the spread of regenerative hair waves, while global inhibitors outside each module (macroenvironment) prevent this. Different wave patterns can be simulated by cellular automata principles. Hormonal status and seasonal changes can modulate appendage phenotypes, leading to ‘organ metamorphosis’, with multiple ectodermal organ phenotypes generated from the same precursors. We discuss potential novel evolutionary steps using this module-based complexity in several amniote integument organs, exemplified by the spectacular peacock feather pattern. We thus explore the application of the acquired knowledge of patterning in tissue engineering. New hair follicles can be generated after wounding. Hairs and feathers can be reconstituted through self-organization of dissociated progenitor cells. PMID:23539312

  10. Fractures Patterns of Tight Carbonates of Upper Jurassic Arab-D Member and Upper Jubaila Formation Outcrops, Central Saudi Arabia

    NASA Astrophysics Data System (ADS)

    Abdullatif, Osman; Abdlmutalib, Ammar

    2015-04-01

    This study investigates the fracture patterns of the upper Jurassic Arab-D member and upper Jubaila Formation outcropping in central Saudi Arabia. These strata represent the outcrop equivalent for Arab-D reservoir. The upper Jubaila Formation was deposited in the lower to upper slope to ramp crest leading to deposition Stromatoporoid lithofacies association, while Arab-D member deposited under deep to shallow lagoonal settings including skeletal bank and tidal flat lithofacies associations. This study utilized high resolution outcrop scale integrated fracture analysis, sedimentological and stratigraphical approach and methods.The field data included lithofacies, stratigraphic hierarchy, cyclicity and fracture measurements of orientation, length, spacing, intensity, and aperture. The Arab-D member is affected by five fracture patterns: (a) regular large scale fractures NW striking, several meters widely spaced, vertically dipping and cutting through several beds; (b) regular medium scale fractures striking NE and vertically dipping, moderately spaced and extending from two to three meters in length and cut through two or three beds; (c) regular small scale fractures that are arrested near the bed boundary vertically dipping and having less than one meter length and spacing; (d) irregular fractures filled with chemically weathered materials; (e) large scale fractures oriented perpendicular to the first fracture pattern in (a) along the outcrop strike and also cut on the top of the resistive sandy grainstone lithofacies of Arab D member. In contrast, the Upper Jubaila Formation is characterized mostly by medium scale NW and NE striking fractures that near vertically dipping and extended within one or two beds. Irregular small scale fractures also occur within parts of the beds of this group.Fracture formation and development in the Arab D and Jubaila Formation are partially attributed to regional tectonics affected the study area and locally to stratigraphic and

  11. The dynamics of spatio-temporal Rho GTPase signaling: formation of signaling patterns

    PubMed Central

    Fritz, Rafael Dominik; Pertz, Olivier

    2016-01-01

    Rho GTPases are crucial signaling molecules that regulate a plethora of biological functions. Traditional biochemical, cell biological, and genetic approaches have founded the basis of Rho GTPase biology. The development of biosensors then allowed measuring Rho GTPase activity with unprecedented spatio-temporal resolution. This revealed that Rho GTPase activity fluctuates on time and length scales of tens of seconds and micrometers, respectively. In this review, we describe Rho GTPase activity patterns observed in different cell systems. We then discuss the growing body of evidence that upstream regulators such as guanine nucleotide exchange factors and GTPase-activating proteins shape these patterns by precisely controlling the spatio-temporal flux of Rho GTPase activity. Finally, we comment on additional mechanisms that might feed into the regulation of these signaling patterns and on novel technologies required to dissect this spatio-temporal complexity. PMID:27158467

  12. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    NASA Astrophysics Data System (ADS)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  13. Information capacity and pattern formation in a tent map network featuring statistical periodicity

    NASA Astrophysics Data System (ADS)

    Hauptmann, C.; Touchette, H.; Mackey, M. C.

    2003-02-01

    We provide quantitative support to the observation that lattices of coupled maps are “efficient” information coding devices. It has been suggested recently that lattices of coupled maps may provide a model of information coding in the nervous system because of their ability to create structured and stimulus-dependent activity patterns which have the potential to be used for storing information. In this paper, we give an upper bound to the effective number of patterns that can be used to store information in the lattice by evaluating numerically its information capacity or information rate as a function of the coupling strength between the maps. We also estimate the time taken by the lattice to establish a limiting activity pattern.

  14. Linking Pattern Formation and Alternative Stable States: Ecohydrologic Thresholds and Critical Transitions in the Everglades Peatlands

    NASA Astrophysics Data System (ADS)

    Heffernan, J. B.; Ross, M. S.; Sah, J. P.; Isherwood, E.; Cohen, M. J.

    2015-12-01

    Spatial patterning occurs in a variety of ecosystems, and is important for the functional properties of landscapes; for testing spatial models of ecological processes; and as an indicator of landscape condition and resilience. Theory suggests that regular patterns arise from coupled local- and landscape-scale feedbacks that can also create multiple stable landscape states. In the Florida Everglades, hydrologic modification has degraded much of the historically-extensive ridge-slough landscape, a patterned peatland mosaic with distinct, flow-parallel patches. However, in the Everglades and in general, the hypothesis that patterned landscapes have homogeneous alternative states has little direct empirical support. Here we use microtopographic and vegetative heterogeneity, and their relation to hydrologic conditions, to infer the existence of multiple landscape equilibria and identify the hydrologic thresholds for critical transitions between these states. Dual relationships between elevation variance and water depth, and bi-modal distributions of both elevation variance and plant community distinctness, are consistent with generic predictions of multiple states, and covariation between these measures suggests that microtopography is the leading indicator of landscape degradation. Furthermore, a simple ecohydrologic multiple-state model correctly predicts the hydrologic thresholds for persistence of distinct ridges and sloughs. Predicted ridge-slough elevation differences and their relation to water depth are much greater than observed in the contemporary Everglades, but correspond closely with historical observations of pre-drainage conditions. These multiple lines of evidence represent the broadest and most direct support for the link between regular spatial pattern and landscape-scale alternative states in any ecosystem, and suggest that other patterned landscapes could undergo sudden collapse in response to changing environmental conditions. Hydrologic thresholds

  15. Transduction of interleukin-10 through renal artery attenuates vascular neointimal proliferation and infiltration of immune cells in rat renal allograft.

    PubMed

    Xie, Jingxin; Li, Xueyi; Meng, Dan; Liang, Qiujuan; Wang, Xinhong; Wang, Li; Wang, Rui; Xiang, Meng; Chen, Sifeng

    2016-08-01

    Renal transplantation is the treatment of choice for end-stage renal failure. Although acute rejection is not a major issue anymore, chronic rejection, especially vascular rejection, is still a major factor that might lead to allograft dysfunction on the long term. The role of the local immune-regulating cytokine interleukin-10 (IL-10) in chronic renal allograft is unclear. Many clinical observations showed that local IL-10 level was negatively related to kidney allograft function. It is unknown this negative relationship was the result of immunostimulatory property or insufficient immunosuppression property of local IL-10. We performed ex vivo transduction before transplantation through artery of the renal allograft using adeno-associated viral vectors carrying IL-10 gene. Twelve weeks after transplantation, we found intrarenal IL-10 gene transduction significantly inhibited arterial neointimal proliferation, the number of occluded intrarenal artery, interstitial fibrosis, peritubular capillary congestion and glomerular inflammation in renal allografts compared to control allografts receiving PBS or vectors carrying YFP. IL-10 transduction increased serum IL-10 level at 4 weeks but not at 8 and 12 weeks. Renal IL-10 level increased while serum creatinine decreased significantly in IL-10 group at 12 weeks compared to PBS or YFP controls. Immunohistochemical staining showed unchanged total T cells (CD3) and B cells (CD45R/B220), decreased cytotoxic T cells (CD8), macrophages (CD68) and increased CD4+ and FoxP3+ cells in IL-10 group. In summary, intrarenal IL-10 inhibited the allograft rejection while modulated immune response. PMID:27317647

  16. Impact of Insulin Resistance on Neointimal Tissue Proliferation after 2nd-Generation Drug-Eluting Stent Implantation

    PubMed Central

    Yaguchi, Isao; Komatsu, Sachiko; Nakahara, Shiro; Kobayashi, Sayuki; Sakai, Yoshihiko; Taguchi, Isao

    2015-01-01

    Percutaneous coronary intervention is established as an effective treatment for patients with ischemic heart disease; in particular, drug-eluting stent implantation is known to suppress in-stent restenosis. Diabetes mellitus is an independent risk factor for restenosis, so reducing insulin resistance is being studied as a new treatment approach. In this prospective study, we sought to clarify the factors associated with in-stent restenosis after percutaneous coronary intervention, and we evaluated the homeostasis model assessment of insulin resistance (HOMA-IR) index as a predictor of restenosis. We enrolled 136 consecutive patients who underwent elective percutaneous coronary intervention at our hospital from February 2010 through April 2013. All were implanted with a 2nd-generation drug-eluting stent. We distributed the patients in accordance with their HOMA-IR index values into insulin-resistant Group P (HOMA-IR, ≥2.5; n=77) and noninsulin-resistant Group N (HOMA-IR, <2.5; n=59). Before and immediately after stenting, we measured reference diameter, minimal lumen diameter, and percentage of stenosis, and after 8 months we measured the last 2 factors and late lumen loss, all by means of quantitative coronary angiography. After 8 months, the mean minimal lumen diameter was smaller in Group P than that in Group N (1.85 ± 1.02 vs 2.37 ± 0.66 mm; P=0.037), and the mean late lumen loss was larger (0.4 ± 0.48 vs 0.16 ± 0.21 mm; P=0.025). These results suggest that insulin resistance affects neointimal tissue proliferation after 2nd-generation drug-eluting stent implantation. PMID:26413014

  17. Pattern formation in icosahedral virus capsids: the papova viruses and Nudaurelia capensis beta virus.

    PubMed Central

    Marzec, C J; Day, L A

    1993-01-01

    The capsids of the spherical viruses all show underlying icosahedral symmetry, yet they differ markedly in capsomere shape and in capsomere position and orientation. The capsid patterns presented by the capsomere shapes, positions, and orientations of three viruses (papilloma, SV40, and N beta V) have been generated dynamically through a bottom-up procedure which provides a basis for understanding the patterns. A capsomere shape is represented in two-dimensional cross-section by a mass or charge density on the surface of a sphere, given by an expansion in spherical harmonics, and referred to herein as a morphological unit (MU). A capsid pattern is represented by an icosahedrally symmetrical superposition of such densities, determined by the positions and orientations of its MUs on the spherical surface. The fitness of an arrangement of MUs is measured by an interaction integral through which all capsid elements interact with each other via an arbitrary function of distance. A capsid pattern is generated by allowing the correct number of approximately shaped MUs to move dynamically on the sphere, positioning themselves until an extremum of the fitness function is attained. The resulting patterns are largely independent of the details of both the capsomere representation and the interaction function; thus the patterns produced are generic. The simplest useful fitness function is sigma 2, the average square of the mass (or charge) density, a minimum of which corresponds to a "uniformly spaced" MU distribution; to good approximation, the electrostatic free energy of charged capsomeres, calculated from the linearized Poisson-Boltzmann equation, is proportional to sigma 2. With disks as MUs, the model generates the coordinated lattices familiar from the quasi-equivalence theory, indexed by triangulation numbers. Using fivefold MUs, the model generates the patterns observed at different radii within the T = 7 capsid of papilloma and at the surface of SV40; threefold MUs

  18. Comparison of defect cluster accumulation and pattern formation in irradiated copper and nickel

    SciTech Connect

    Zinkle, S.J.; Snead, L.L.; Edwards, D.J.

    1995-04-01

    The objective of this study is to compare the contrasting behavior of defect cluster formation in neutron-irradiated copper and nickel specimens. Transmission electron microscopy was used to examine the density and spatial distribution of defect clusters produced in copper and nickel as the result of fission neutron irradiation to damage levels of 0.01 to 0.25 displacements per atom (dpa) at irradiation temperature between 50 and 230{degrees}C. A comparison with published results in the literature indicates that defect cluster wall formation occurs in nickel irradiated at 0.2 to 0.4 T{sub M} in a wide variety of irradiation spectra. Defect cluster wall formation apparently only occurs in copper during low temperature irradiation with electrons and light ions. These results are discussed in terms of the thermal spike model for energetic displacement cascades.

  19. Dynamic pattern formation of liquid crystals using binary self-assembled monolayers on an ITO surface under DC voltage.

    PubMed

    Ishida, Takao; Oyama, Makiko; Terada, Kei-ichi; Haga, Masa-aki

    2014-12-01

    There have been numerous studies of liquid crystal (LC) convection using sandwich-type LC cells under AC voltage. In contrast to previous LC convection studies under AC voltage, we propose the use of a binary self-assembled monolayer (SAM) with a redox-active Ru complex and insulating octadecyl phosphonic acid (C18) molecules on an indium tin oxide (ITO) surface as the electrode of sandwich-type LC cells under DC bias voltage. This is because the functionalized molecules immobilized on the ITO surface are expected to control the LC orientation and electrical conduction of LC cells, under an exact DC bias voltage. We successfully achieved LC pattern formation using ITO electrodes with binary SAMs in LC cells. Moreover, we confirmed that the LC pattern size was increased by increasing the coverage of the Ru complex in binary SAMs. We consider that a combination of three factors, electrical conduction change, controlling of LC orientation in the initial stage and redox-activity of the Ru-complex, is the reason for LC convection although we cannot fully explain the distribution of these three factors. We believe that our LC pattern formation is promising for new type devices e.g., artificial compound eyes using the LC device technology. PMID:25327940

  20. Sub-Minute Formation of Supported Nanoporous Mesoscale Patterns Programmed by Surface Energy

    PubMed Central

    Korampally, Venumadhav; Mamidi, Vamshi Krishna; Harris, Bryant; Gangopadhyay, Keshab; Baker, Gary A.; Gangopadhyay, Shubhra

    2011-01-01

    We demonstrate an original and powerful concept for elaborating spontaneous, high fidelity patterns of nanoporosity from nanoscale building blocks using patterned surface chemistry (i.e., “surface energy gating”) to corral the growth of colloidal structures at a solid surface. Composite films consisting of polymethylsilsesquioxane nanoparticles uniformly dispersed in polypropylene glycol polymer were examined at temperatures beyond the decomposition of the polymer as a function of the substrate surface energy to clarify nanoparticulate ensemble behavior. The principle behind this colloidal assembly can be understood by taking into consideration the entropy and enthalpy dictating the mutual interactions between substrate surface, polymeric solvent, and dispersed colloids in the decomposition regime. The relevance of this research is shown by demonstrating how the principle of surface energy gating can be utilized to achieve spontaneous and controllable spatial patterns of nanoporous, high surface area thin films in a cost-effective and energy-efficient manner via brief thermal exposure. The simplicity and general nature of this methodology are further exemplified by showing the facility with which high-contrast fluorescent bioconjugate arrays can be prepared from nanoporous organosilicate patterns. PMID:21945672

  1. Tree island pattern formation and alternative equilibria in the Florida Everglades

    NASA Astrophysics Data System (ADS)

    Carr, J. A.; D'Odorico, P.; Engel, V.

    2012-12-01

    The tree islands of the Florida Everglades are patterned ecogeomorphic features where elevated woody vegetation patches are surrounded by wet marsh filled with herbaceous vegetation. This wet savanna landscape exhibits an uneven distribution of soil resources with enhanced soil phosphorus concentrations underlying elevated tree islands. In contrast, the surrounding low lying marsh has low phosphorous availability. This patchy patterned landscape sustains high levels of biodiversity, but the processes determining the stability and resilience of the patterned tree island landscape remains poorly understood. In particular, it is unclear what controls the relation between individual form and processes within a tree island and the spatial organization of tree islands on the landscape. To this end, a process-based model that relates vegetation dynamics to nutrients and soil accretion/loss through ecogeomorphic feedbacks and interactions with hydrologic drivers was developed. The model reveals that the stable coexistence of tree islands and marshes emerges as an effect of their both being (meta-) stable states of the system. Self organization of patterns on the landscape occurs within a subset of the parameter space. As such, tree islands are found to have only a limited resilience. Change in hydroperiod and or vegetation cover can result in an rapid shift to a stable marsh state. Under certain hydrologic conditions this state can become destabilized and promote once again ontogenesis of tree islands. As such, the tree island susceptibility to a rapid (slow) transition between alternative equilibria needs to be accounted for while developing a plan for their management, conservation and restoration.

  2. Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se–Te films

    PubMed Central

    Sadtler, Bryce; Burgos, Stanley P.; Batara, Nicolas A.; Beardslee, Joseph A.; Atwater, Harry A.; Lewis, Nathan S.

    2013-01-01

    Photoresponsive materials that adapt their morphologies, growth directions, and growth rates dynamically in response to the local incident electromagnetic field would provide a remarkable route to the synthesis of complex 3D mesostructures via feedback between illumination and the structure that develops under optical excitation. We report the spontaneous development of ordered, nanoscale lamellar patterns in electrodeposited selenium–tellurium (Se–Te) alloy films grown under noncoherent, uniform illumination on unpatterned substrates in an isotropic electrolyte solution. These inorganic nanostructures exhibited phototropic growth in which lamellar stripes grew toward the incident light source, adopted an orientation parallel to the light polarization direction with a period controlled by the illumination wavelength, and showed an increased growth rate with increasing light intensity. Furthermore, the patterns responded dynamically to changes during growth in the polarization, wavelength, and angle of the incident light, enabling the template-free and pattern-free synthesis, on a variety of substrates, of woodpile, spiral, branched, or zigzag structures, along with dynamically directed growth toward a noncoherent, uniform intensity light source. Full-wave electromagnetic simulations in combination with Monte Carlo growth simulations were used to model light–matter interactions in the Se–Te films and produced a model for the morphological evolution of the lamellar structures under phototropic growth conditions. The experiments and simulations are consistent with a phototropic growth mechanism in which the optical near-field intensity profile selects and reinforces the dominant morphological mode in the emergent nanoscale patterns. PMID:24218617

  3. The splicing factor SRSF1 modulates pattern formation by inhibiting transcription of tissue specific genes during embryogenesis.

    PubMed

    Lee, Soo-Ho; Lee, Hyun-Kyung; Kim, Chowon; Kim, Yoo-Kyung; Ismail, Tayaba; Jeong, Youngeun; Park, Kyeongyeon; Park, Jeen-Woo; Kwon, Oh-Shin; Kang, Beom Sik; Lee, Dong-Seok; Park, Mae-Ja; Park, Do-Sim; Lee, Hyun-Shik

    2016-09-01

    Alternative splicing is a major mechanism regulating pattern of gene expression through the production of multiple mRNAs from a single gene transcript. Any misregulation can cause various human diseases and also have severe effects on embryogenesis. SRSF1 is one of the critical factors regulating alternative splicing at many stages of vertebrate development and any disturbance in SRSF1 leads to serious consequences. In current study, we investigated the effects of loss of the SRSF1 gene using antisense morpholino oligonucleotides (MO) in Xenopus embryogenesis. It is evident from the results of RT-PCR and whole-mount in situ hybridization that SRSF1 is a maternal gene having strong expression in head, eyes and central nervous system. Moreover, SRSF1 morphants exhibited malformed phenotypes, including miscoiled guts, heart and cartilage formation, edema in the head and heart, and small eyes. Especially, in SRSF1 morphants, bone cartilage formation was reduced in the brain and Nkx-2.5 expression was dramatically reduced in the heart of SRSF1 morphants. In addition, a dramatic reduction in functional chordin RNA in SRSF1 morphants was observed suggesting that chordin is one of the targets of SRSF1. Thus, we concluded that SRSF1 is an essential factor for pattern formation including heart, cartilage and germ layers through the regulation of specific genes. PMID:27396620

  4. The influence of projectile ion induced chemistry on surface pattern formation

    NASA Astrophysics Data System (ADS)

    Karmakar, Prasanta; Satpati, Biswarup

    2016-07-01

    We report the critical role of projectile induced chemical inhomogeneity on surface nanostructure formation. Experimental inconsistency is common for low energy ion beam induced nanostructure formation in the presence of uncontrolled and complex contamination. To explore the precise role of contamination on such structure formation during low energy ion bombardment, a simple and clean experimental study is performed by selecting mono-element semiconductors as the target and chemically inert or reactive ion beams as the projectile as well as the source of controlled contamination. It is shown by Atomic Force Microscopy, Cross-sectional Transmission Electron Microscopy, and Electron Energy Loss Spectroscopy measurements that bombardment of nitrogen-like reactive ions on Silicon and Germanium surfaces forms a chemical compound at impact zones. Continuous bombardment of the same ions generates surface instability due to unequal sputtering and non-uniform re-arrangement of the elemental atom and compound. This instability leads to ripple formation during ion bombardment. For Argon-like chemically inert ion bombardment, the chemical inhomogeneity induced boost is absent; as a result, no ripples are observed in the same ion energy and fluence.

  5. Regulation of Pattern Formation and Gene Amplification During Drosophila Oogenesis by the miR-318 microRNA

    PubMed Central

    Ge, Wanzhong; Deng, Qiannan; Guo, Ting; Hong, Xin; Kugler, Jan-Michael; Yang, Xiaohang; Cohen, Stephen M.

    2015-01-01

    Pattern formation during epithelial development requires the coordination of multiple signaling pathways. Here, we investigate the functions of an ovary-enriched miRNA, miR-318, in epithelial development during Drosophila oogenesis. mir-318 maternal loss-of-function mutants were female-sterile and laid eggs with abnormal morphology. Removal of mir-318 disrupted the dorsal–anterior follicle cell patterning, resulting in abnormal dorsal appendages. mir-318 mutant females also produced thin and fragile eggshells due to impaired chorion gene amplification. We provide evidence that the ecdysone signaling pathway activates expression of miR-318 and that miR-318 cooperates with Tramtrack69 to control the switch from endocycling to chorion gene amplification during differentiation of the follicular epithelium. The multiple functions of miR-318 in oogenesis illustrate the importance of miRNAs in maintaining cell fate and in promoting the developmental transition in the female follicular epithelium. PMID:25786856

  6. Studying the optical second-order interference pattern formation process with classical light in the photon counting regime.

    PubMed

    He, Yuchen; Liu, Jianbin; Zhang, Songlin; Wang, Wentao; Bai, Bin; Le, Mingnan; Xu, Zhuo

    2015-12-01

    The formation process of the second-order interference pattern is studied experimentally in the photon counting regime by superposing two independent single-mode continuous-wave lasers. Two-photon interference based on the superposition principle in Feynman's path integral theory is employed to interpret the experimental results. The second-order interference pattern of classical light can be formulated when, with high probability, there are only two photons in the interferometer at one time. The studies are helpful in understanding the second-order interference of classical light in the language of photons. The method and conclusions can be generalized to the third- and higher-order interference of light and interference of massive particles. PMID:26831397

  7. Predicting the Distribution of Spiral Waves from Cell Properties in a Developmental-Path Model of Dictyostelium Pattern Formation

    PubMed Central

    Geberth, Daniel; Hütt, Marc-Thorsten

    2009-01-01

    The slime mold Dictyostelium discoideum is one of the model systems of biological pattern formation. One of the most successful answers to the challenge of establishing a spiral wave pattern in a colony of homogeneously distributed D. discoideum cells has been the suggestion of a developmental path the cells follow (Lauzeral and coworkers). This is a well-defined change in properties each cell undergoes on a longer time scale than the typical dynamics of the cell. Here we show that this concept leads to an inhomogeneous and systematic spatial distribution of spiral waves, which can be predicted from the distribution of cells on the developmental path. We propose specific experiments for checking whether such systematics are also found in data and thus, indirectly, provide evidence of a developmental path. PMID:19593362

  8. Gap junctions composed of connexins 41.8 and 39.4 are essential for colour pattern formation in zebrafish

    PubMed Central

    Irion, Uwe; Frohnhöfer, Hans Georg; Krauss, Jana; Çolak Champollion, Tuǧba; Maischein, Hans-Martin; Geiger-Rudolph, Silke; Weiler, Christian; Nüsslein-Volhard, Christiane

    2014-01-01

    Interactions between all three pigment cell types are required to form the stripe pattern of adult zebrafish (Danio rerio), but their molecular nature is poorly understood. Mutations in leopard (leo), encoding Connexin 41.8 (Cx41.8), a gap junction subunit, cause a phenotypic series of spotted patterns. A new dominant allele, leotK3, leads to a complete loss of the pattern, suggesting a dominant negative impact on another component of gap junctions. In a genetic screen, we identified this component as Cx39.4 (luchs). Loss-of-function alleles demonstrate that luchs is required for stripe formation in zebrafish; however, the fins are almost not affected. Double mutants and chimeras, which show that leo and luchs are only required in xanthophores and melanophores, but not in iridophores, suggest that both connexins form heteromeric gap junctions. The phenotypes indicate that these promote homotypic interactions between melanophores and xanthophores, respectively, and those cells instruct the patterning of the iridophores. DOI: http://dx.doi.org/10.7554/eLife.05125.001 PMID:25535837

  9. Antagonistic Gene Activities Determine the Formation of Pattern Elements along the Mediolateral Axis of the Arabidopsis Fruit

    PubMed Central

    González-Reig, Santiago; Ripoll, Juan José; Vera, Antonio; Yanofsky, Martin F.; Martínez-Laborda, Antonio

    2012-01-01

    The Arabidopsis fruit mainly consists of a mature ovary that shows three well defined territories that are pattern elements along the mediolateral axis: the replum, located at the medial plane of the flower, and the valve and the valve margin, both of lateral nature. JAG/FIL activity, which includes the combined functions of JAGGED (JAG), FILAMENTOUS FLOWER (FIL), and YABBY3 (YAB3), contributes to the formation of the two lateral pattern elements, whereas the cooperating genes BREVIPEDICELLUS (BP) and REPLUMLESS (RPL) promote replum development. A recent model to explain pattern formation along the mediolateral axis hypothesizes that JAG/FIL activity and BP/RPL function as antagonistic lateral and medial factors, respectively, which tend to repress each other. In this work, we demonstrate the existence of mutual exclusion mechanisms between both kinds of factors, and how this determines the formation and size of the three territories. Medial factors autonomously constrain lateral factors so that they only express outside the replum, and lateral factors negatively regulate the medially expressed BP gene in a non-autonomous fashion to ensure correct replum development. We also have found that ASYMMETRIC LEAVES1 (AS1), previously shown to repress BP both in leaves and ovaries, collaborates with JAG/FIL activity, preventing its repression by BP and showing synergistic interactions with JAG/FIL activity genes. Therefore AS gene function (the function of the interacting genes AS1 and AS2) has been incorporated in the model as a new lateral factor. Our model of antagonistic factors provides explanation for mutant fruit phenotypes in Arabidopsis and also may help to understand natural variation of fruit shape in Brassicaceae and other species, since subtle changes in gene expression may cause conspicuous changes in the size of the different tissue types. PMID:23133401

  10. Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study

    PubMed Central

    Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K. W.; Zhang, Yong-Wei

    2016-01-01

    We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures. PMID:27580943

  11. Nanostructure Formation by controlled dewetting on patterned substrates: A combined theoretical, modeling and experimental study.

    PubMed

    Lu, Liang-Xing; Wang, Ying-Min; Srinivasan, Bharathi Madurai; Asbahi, Mohamed; Yang, Joel K W; Zhang, Yong-Wei

    2016-01-01

    We perform systematic two-dimensional energetic analysis to study the stability of various nanostructures formed by dewetting solid films deposited on patterned substrates. Our analytical results show that by controlling system parameters such as the substrate surface pattern, film thickness and wetting angle, a variety of equilibrium nanostructures can be obtained. Phase diagrams are presented to show the complex relations between these system parameters and various nanostructure morphologies. We further carry out both phase field simulations and dewetting experiments to validate the analytically derived phase diagrams. Good agreements between the results from our energetic analyses and those from our phase field simulations and experiments verify our analysis. Hence, the phase diagrams presented here provide guidelines for using solid-state dewetting as a tool to achieve various nanostructures. PMID:27580943

  12. Intramolecular vibrations and noise effects on pattern formation in a molecular helix.

    PubMed

    Fouda, H P Ekobena; Tabi, C B; Mohamadou, A; Kofané, T C

    2011-09-21

    Modulational instability in a biexciton molecular chain is addressed. We show that the model can be reduced to a set of three coupled equations: two nonlinear Schrödinger equations and a Boussinesq equation. The linear stability analysis of continuous wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. Simulations of the full discrete systems reveal some behaviors of modulational instability, since wave patterns are observed for the excitons and the phonon spectrum. We also take the effect of thermal fluctuations into account and we numerically study both the stability and the instability of the plane waves under 300 K. The plane wave is found to be stable under modulation, but displays a gradual increase of the wave amplitudes. Under modulation, the same behaviors are observed and wave patterns are found to resist thermal fluctuations, which is in agreement with earlier research on localized structure stability under thermal noise. PMID:21878712

  13. Immunological synapse arrays: Patterned protein surfaces that modulate immunological synapse structure formation in T cells

    PubMed Central

    Doh, Junsang; Irvine, Darrell J.

    2006-01-01

    T cells are activated by recognition of foreign peptides displayed on the surface of antigen presenting cells (APCs), an event that triggers assembly of a complex microscale structure at the T cell–APC interface known as the immunological synapse (IS). It remains unresolved whether the unique physical structure of the synapse itself impacts the functional response of T cells, independent of the quantity and quality of ligands encountered by the T cell. As a first step toward addressing this question, we created multicomponent protein surfaces presenting lithographically defined patterns of tethered T cell receptor (TCR) ligands (anti-CD3 “activation sites”) surrounded by a field of tethered intercellular adhesion molecule-1 (ICAM-1), as a model substrate on which T cells could be seeded to mimic T cell–APC interactions. CD4+ T cells seeded on these surfaces polarized and migrated; on contact with activation sites, T cells assembled an IS with a structure modulated by the physical pattern of ligand encountered. On surfaces patterned with focal spots of TCR ligand, T cells stably interacted with activation sites, proliferated, and secreted cytokines. In contrast, T cells interacting with activation sites patterned to preclude centralized clustering of TCR ligand failed to form stable contacts with activation sites, exhibited aberrant PKC-θ clustering in a fraction of cells, and had significantly reduced production of IFN-γ. These results suggest that focal clustering of TCR ligand characteristic of the “mature” IS may be required under some conditions for full T cell activation. PMID:16585528

  14. Dorsoventral patterning by the Chordin-BMP pathway: a unified model from a pattern-formation perspective for Drosophila, vertebrates, sea urchins and Nematostella.

    PubMed

    Meinhardt, Hans

    2015-09-01

    Conserved from Cnidarians to vertebrates, the dorsoventral (DV) axis is patterned by the Chordin-BMP pathway. However, the functions of the pathway's components are very different in different phyla. By modeling it is shown that many observations can be integrated by the assumption that BMP, acting as an inhibitory component in more ancestral systems, became a necessary and activating component for the generation of a secondary and antipodal-located signaling center. The different realizations seen in v