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Sample records for neointimal formational pattern

  1. 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

  2. Pioglitazone Ameliorates Smooth Muscle Cell Proliferation in Cuff-Induced Neointimal Formation by Both Adiponectin-Dependent and -Independent Pathways

    PubMed Central

    Kubota, Tetsuya; Kubota, Naoto; Sato, Hiroyuki; Inoue, Mariko; Kumagai, Hiroki; Iwamura, Tomokatsu; Takamoto, Iseki; Kobayashi, Tsuneo; Moroi, Masao; Terauchi, Yasuo; Tobe, Kazuyuki; Ueki, Kohjiro; Kadowaki, Takashi

    2016-01-01

    The aim of this study is to elucidate to what degree adiponectin is involved in TZD-mediated amelioration of neointimal formation. We investigated the effect of 3- or 8-weeks’ pioglitazone on cuff-induced neointimal formation in adiponectin-deficient (APN-KO) and wild-type (WT) mice. Pioglitazone for 3 weeks reduced neointimal formation in the WT mice with upregulation of the plasma adiponectin levels, but failed to reduce neointimal formation in the APN-KO mice, suggesting that pioglitazone suppressed neointimal formation by adiponectin-dependent mechanisms. Pioglitazone for 3 weeks suppressed vascular smooth muscle cell (VSMC) proliferation and increased AdipoR2 expression in the WT mice. In vitro, globular adiponectin activated AMPK through both AdipoR1 and AdipoR2, resulting in the inhibition of VSMC proliferation. Interestingly, 8-weeks’ pioglitazone was reduced neointimal formation in APN-KO mice to degree similar to that seen in the WT mice, suggesting that pioglitazone can also suppress neointimal formation via a mechanism independent of adiponectin. Pioglitazone for 8 weeks completely abrogated the increased VSMC proliferation, along with a reduction of cyclin B1 and cyclin D1 expressions and cardiovascular risk profile in the APN-KO mice. In vitro, pioglitazone suppressed these expressions, leading to inhibition of VSMC proliferation. Pioglitazone suppresses neointimal formation via both adiponectin-dependent and adiponectin-independent mechanisms. PMID:27703271

  3. Use of rosiglitazone before and after vascular injury in hypercholesterolemic rabbits: Assessment of neointimal formation

    PubMed Central

    Alessi, Alexandre; França Neto, Olímpio Ribeiro; Brofman, Paulo Roberto Slud; Prim, Camila; Noronha, Lucia; Silva, Ruy Fernando Kuenzer Caetano; Baroncini, Liz Andréa Villela; Précoma, Dalton Bertolim

    2008-01-01

    Objectives To analyse the effects of rosiglitazone administered at different times on neointimal formation in hypercholesterolemic rabbits following vascular injury. Methods Thirty-nine rabbits on a hypercholesterolemic diet were included. The animals underwent balloon catheter injury to the right iliac artery on day 14. They were divided into three groups as follows: control group, 13 rabbits without rosiglitazone; group I, 13 rabbits treated with rosiglitazone (3 mg/Kg body weight/day) for 28 days after the vascular injury; and group II, 13 rabbits treated with rosiglitazone (3 mg/Kg body weight/day) during all the experiment (42 days). Histological analysis was done by an experienced pathologist who was unaware of the rosiglitazone treatment. Histomorphometric parameters were performed by calculation of the luminal and intimal layer area, and intima/media layer area ratio (the area of the intimal layer divided by the area of the medial layer). Results Intimal area was significantly lower in group II vs. CG (p = 0.024) and group I (p = 0.006). Luminal layer area was higher in group II vs. CG (p < 0.0001) and group I (p < 0.0001). Intima/media layer area ratio was equal between CG and group I. Intima/media layer ratio area was significantly lower in group II vs. control group (p < 0.021) and group I (p < 0.003). There was a significant reduction of 65% and 71% in intima/media layer area ratio in group II vs. control group and group I, respectively. Conclusion Pretreatment with rosiglitazone in hypercholesterolemic rabbits submitted to vascular injury significantly reduces neointimal formation. PMID:18752684

  4. 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

  5. Acceleration of re-endothelialization and inhibition of neointimal formation using hybrid biodegradable nanofibrous rosuvastatin-loaded stents.

    PubMed

    Lee, Cheng-Hung; Chang, Shang-Hung; Lin, Yu-Huang; Liu, Shih-Jung; Wang, Chao-Jan; Hsu, Ming-Yi; Hung, Kuo-Chun; Yeh, Yung-Hsin; Chen, Wei-Jan; Hsieh, I-Chang; Wen, Ming-Shien

    2014-05-01

    Incomplete endothelialization and neointimal hyperplasia of injured arteries can cause acute and late stent thromboses. This work develops hybrid stent/biodegradable nanofibers for the local and sustained delivery of rosuvastatin to denuded artery walls. Biodegradable nanofibers were firstly prepared by dissolving poly(D,L)-lactide-co-glycolide and rosuvastatin in 1,1,1,3,3,3-hexafluoro-2-propanol. The solution was then electrospun into nanofibrous tubes, which were mounted onto commercially available bare-metal stents. The in vitro release rates of the pharmaceuticals from the nanofibers were determined using an elution method and a high-performance liquid chromatography assay. The experimental results thus obtained suggest that the biodegradable nanofibers released high concentrations of rosuvastatin for four weeks. The effectiveness of the local delivery of rosuvastatin in reducing platelets was studied. The tissue inflammatory reaction caused by the hybrid stents that were used to treat diseased arteries was also documented. The proposed hybrid stent/biodegradable rosuvastatin-loaded nanofibers contributed substantially to the local and sustainable delivery of a high concentration of drugs to promote re-endothelialization, improve endothelial function, reduce inflammatory reaction, and inhibit neointimal formation of the injured artery. The results of this work provide insight into how patients with a high risk of stent restenosis should be treated for accelerating re-endothelialization and inhibiting neointimal hyperplasia.

  6. 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.

  7. 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

  8. 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.

  9. Long term impact of balloon post-dilatation on neointimal formation: an experimental comparative study between second-generation self-expanding versus balloon-expandable stent technologies.

    PubMed

    Aboodi, Michael S; Milewski, Krzysztof; Tellez, Armando; Cheng, Yanping; Yi, Geng-Hua; Kaluza, Greg L; Granada, Juan F

    2014-02-15

    Background: Self-expanding stents (SES) are reemerging as therapeutic alternatives to treat coronary artery disease. It has been proposed that SES can improve clinical outcomes by inducing less injury at implantation and achieving better vessel wall apposition.To date, little data exists comparing the vascular response to both methods of deployment in a controlled experimental setting. Objective: To quantify differences in vascular injury and healing between second-generation SES and balloon-expandable stents (BES) and the effects of balloon post-dilatation in a porcine coronary model. Methods: Seventy-five bare SES (AXXESS or vProtect) and 42 BES (Vision) were implanted in porcine coronaries. A subset of these received balloon post-dilatation(SES 1 D 5 22, BES 1 D 5 20). Follow-up was scheduled at 30 (BES 5 10, BES 1 D 56, SES 5 19, SES 1 D 5 8), 90 (BES 5 6, BES 1 D 5 8, SES 5 19, SES 1 D 5 8), and 180 days (BES 5 6, BES 1 D 5 6, SES 5 15, SES 1 D 5 6). Results: In vivo imaging and histological analysis showed that neointimal formation peaks early (30 days) in BES. Conversely, for SES, the peak occurred later (90 days). However, the neointimal formation achieved in either group equalized at 180 days. For SES, post-dilatation shortened the peak of neointimal formation to 30 days. Conversely, for BES, post-dilatation delayed the peak of neointimal formation to 90 days. At 30 days, histology showed that SES had significantly less injury. However, at 90 days, injury scores tended to be higher for SES. By 180 days, injury scores were comparable between both groups. Conclusions: The mechanism of stent expansion influences the degree of vascular injury and healing. The synergistic use of balloon post dilatation changes the dynamics of healing and may impact the potential beneficial effects inherent to SES technologies.

  10. 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

  11. 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.

  12. Phloretin Inhibits Platelet-derived Growth Factor-BB-induced Rat Aortic Smooth Muscle Cell Proliferation, Migration, and Neointimal Formation After Carotid Injury.

    PubMed

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

    2015-05-01

    Abnormal vascular smooth muscle cell proliferation and migration are key factors in many cardiovascular diseases. Here, we investigated the effects of phloretin on platelet-derived growth factor homodimer (PDGF-BB)-induced rat aortic smooth muscle cell (RASMC) proliferation, migration, and neointimal formation after carotid injury. Phloretin significantly inhibited the PDGF-BB-stimulated RASMC proliferation in a concentration-dependent manner (10-100 μM). Also, PDGF-BB-stimulated RASMC migration was inhibited by phloretin at 50 μM. Pretreating RASMC with phloretin dose-dependently inhibited PDGF-BB-induced Akt and p38 mitogen-activated protein kinases activation. Furthermore, phloretin increased p27 and decreased cyclin-dependent kinase 2, CDK4 expression, and p-Rb activation in PDGF-BB-stimulated RASMC in a concentration-dependent manner (10-50 μM). PDGF-BB-induced cell adhesion molecules and matrix metalloproteinase-9 expression were blocked by phloretin at 50 μM. Preincubation with phloretin dose-dependently reduced the intracellular reactive oxygen species production. In vivo study showed that phloretin (20 mg/kg) significantly reduced neointimal formation 14 days after carotid injury in rats. Thus, phloretin may have potential as a treatment against atherosclerosis and restenosis after vascular injury. PMID:25945863

  13. Neointimal tissue healing patterns after paclitaxel-eluting balloon treatment of in-stent restenosis: optical coherence tomography and intravascular ultrasound insights.

    PubMed

    Sandoval, Jorge; Medina, Miguel; Alfonso, Fernando

    2012-10-01

    An 80-year-old patient presented with severe in-stent restenosis of an everolimus-eluting stent implanted in the left anterior descending coronary artery 3 years previously. We obtained good angiographic result after paclitaxel-eluting balloon dilation. However, on optical coherence tomography (OCT), multiple, angiographically silent, in-stent, and edge-related dissections were readily recognized. Intravascular ultrasound (IVUS) revealed residual neointima with minor disruptions. At 9-month follow-up, an excellent angiographic result was demonstrated with complete resolution of the stent-related dissections on OCT. IVUS and OCT confirmed complete neointimal healing with a larger lumen. This case illustrates the value of OCT and IVUS to provide unique insights on the pathophysiological mechanisms and healing patterns of paclitaxel-eluting balloon treatment of in-stent restenosis.

  14. 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

  15. Stimulation of activin A expression in rat aortic smooth muscle cells by thrombin and angiotensin II correlates with neointimal formation in vivo.

    PubMed Central

    Pawlowski, J E; Taylor, D S; Valentine, M; Hail, M E; Ferrer, P; Kowala, M C; Molloy, C J

    1997-01-01

    Vasoactive GTP-binding protein-coupled receptor agonists (e.g., angiotensin II [AII] and alpha-thrombin) stimulate the production of mitogenic factors from vascular smooth muscle cells. In experiments to identify mitogens secreted from AII- or alpha-thrombin-stimulated rat aortic smooth muscle (RASM) cells, neutralizing antibodies directed against several growth factors (e.g., PDGF and basic fibroblast growth factor [basic FGF]) failed to inhibit the mitogenic activity of conditioned media samples derived from the cells. In this report, we found that polyclonal neutralizing antibodies directed against purified human placental basic FGF reduced the mitogenic activity of AII-stimulated RASM cell-conditioned media and in immunoblot experiments identified a 26-kD protein (14 kD under reducing conditions) that was distinct from basic FGF. After purification from RASM cell-conditioned medium, amino acid sequence analysis identified the protein as activin A, a member of the TGF-beta superfamily. Increased activin A expression was observed after treatment of the RASM cells with AII, alpha-thrombin, and the protein kinase C agonist PMA. In contrast, PDGF-BB or serum caused only a minor induction of this protein. Although activin A alone only weakly stimulated RASM cell DNA synthesis, it demonstrated a potent comitogenic effect in combination with either EGF or heparin-binding EGF-like growth factor in the RASM cells, increasing DNA synthesis by up to fourfold. Furthermore, in a rat carotid injury model, activin A mRNA was upregulated within 6 h after injury followed by increases in immunoreactive protein detected in the expanding neointima 7 and 14 d later. Taken together, these results indicate that activin A is a vascular smooth muscle cell-derived factor induced by vasoactive agonists that may, either alone or in combination with other vascular derived growth factors, have a role in neointimal formation after arterial injury. PMID:9239411

  16. 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

  17. Frequency of Vascular Inflammation and Impact on Neointimal Proliferation of Drug Eluting Stents in Porcine Coronary Arteries

    PubMed Central

    Yeh, Jong Shiuan; Oh, Seung Jin; Hsueh, Chun Mei

    2016-01-01

    Background We aimed to describe the frequency of vascular inflammatory reactions with second generation drug eluting stents (DES) compared to first generation DES, and analyze the impact on inflammation and neointimal proliferation in a porcine coronary model. Methods A total of 26 stents (7 multi-link VISION, 6 CYPHER, 6 TAXUS and 7 XIENCE V) were deployed in the coronary arteries of 10 domestic swine for 28 days, after which each stent was harvested and processed (divided into 8 or 9 segments) for histomorphometric analysis. Results A total of 202 histological segments [146 DES and 56 bare metal stents (BMS)] were included in this study. The mean neointimal thickness was significantly reduced in the DES group compared to the BMS group. The DES group had higher injury scores (DES = 0.99 ± 0.79 versus BMS = 0.67 ± 0.44, p < 0.004), inflammatory scores (DES = 2.09 ± 1.54 versus BMS = 0.64 ± 0.98, p < 0.001) and presence of para-strut granulomas (DES = 35% versus BMS = 2%, p < 0.001). In logistic regression analysis, the presence of para-strut granulomas correlated with an area of stenosis > 50% (RR: 6.11, 95% CI: 2.97 to 12.59, p = 0.001). In the DES group, the second generation stents had a lower neointimal area (XIENCE V: 1.64 ± 0.90 mm2) compared to the first generation stents (TAXUS: 2.36 ± 1.56 mm2, p = 0.005; CYPHER 2.78 ± 1.82 mm2, p = 0.001). The XIENCE V stents had lower inflammatory scores and lower frequency of para-strut granulomas compared to the first generation stents. Conclusions Second generation DES had a lower incidence of vascular inflammatory reactions compared to first generation DES. This biological phenomenon appears to influence the patterns of neointimal formation. PMID:27713606

  18. Pattern Formation without Patterning Proteins in Cyanobacteria

    NASA Astrophysics Data System (ADS)

    Allard, Jun; Rutenberg, Andrew

    2006-03-01

    Filaments of cyanobacteria respond to nitrogen starvation by differentiating one cell in ten into a heterocyst, which is devoted to fixing atmospheric nitrogen. This is an example of self-organized pattern formation. We present a dynamical model explaining the initial selection of heterocysts in mutated cyanobacteria that are effectively without normal patterning proteins. Our simulations of this model produce distributions of heterocyst spacings that are consistent with experimental data, and lead to new qualitative predictions on the mechanisms of pattern formation in filamentous cyanobacteria. We discuss possible experimental tests of our results.

  19. Aliskiren Inhibits Neointimal Matrix Metalloproteinases in Experimental Atherosclerosis

    PubMed Central

    Wu, Tao-Cheng; Lee, Chiu-Yang; Lin, Shing-Jong; Chen, Jaw-Wen

    2016-01-01

    Background The renin-angiotensin system (RAS) plays an important role in atherosclerosis. Acting via the angiotensin II receptor, type 1, oxidative stress increases and contributes to endothelial dysfunction and vascular inflammation. Renin exerts effects through a renin receptor causing an increase in the efficiency of angiotensinogen cleavage and facilitates angiotensin II (Ang II) generation and action on cell surfaces. Ang II enhances proliferation and migration of vascular smooth muscle cells, indicating a direct involvement of the RAS in smooth muscle cell proliferation during neointimal formation. Aliskiren, a direct renin inhibitor, is a new oral antihypertensive drug. However, the role of the direct renin inhibitor in neointimal formation and vascular matrix metalloproteinases remains unclear. Methods To investigate the effects of aliskiren on the expression of vascular matrix metalloproteinases, we evaluated the aortic neointimal formation of high-cholesterol-fed animals after vascular injury in vivo and the cellular function of the tumor necrosis factor-α stimulated human aortic smooth muscle cells in vitro. Thereafter, we evaluated vascular expression (by western blot), activity (by gelatin zymography) and molecular pathway. Results In this study we demonstrated that aliskiren reduced neointimal hyperplasia in hypercholesterolemic rabbits after vascular injury and the expression of matrix metalloproteinases in the neointima. Aliskiren also inhibited the expression and activities of matrix metalloproteinases on tumor necrosis factor-α (TNF-α)-stimulated human aortic smooth muscle cells via the mitogen-activated protein kinase pathway. Conclusions The present study showed that aliskiren inhibited the expression of vascular matrix metalloproteinases. With these results, we have better clarified the potential role of renin inhibitors in human atherosclerosis. PMID:27713608

  20. 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

  1. 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

  2. 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.

  3. Pattern formation in geochemical systems

    NASA Astrophysics Data System (ADS)

    Katsev, Sergei

    2002-08-01

    Compositional patterns are extremely common in natural minerals. While, in many cases, variations in the solid mineral composition reflect the external changes in the environment at the time of the mineral formation, the role of self-organization is increasingly acknowledged. For example, in reaction-transport systems, the patterns may form spontaneously from an unpatterned state at the time of crystal growth and then become preserved by being "frozen" in the solid mineral. In this work, the pattern formation by self-organization is investigated by means of model construction and computer simulations in several minerals from different geologic environments. The impact of environmental noise is investigated on a model of oscillatory zoning in plagioclase feldspar. It is shown that environmental noise can lead to pattern formation such as oscillatory zoning, even when no deterministic periodic solutions exist. Coherence resonance close to the Hopf bifurcation is observed. Oscillatory zoning in barite-celestite system is simulated to quantitatively describe the results of the previously reported nucleation and growth experiments. The zoning is thought to be formed by autocatalytic growth from an aqueous solution. In addition to the description of the reaction-diffusion system in terns of partial and ordinary differential equations, a cellular automata model is proposed for the first time for this oscillatory crystallization type of problems. A quantitative model of banding in Mississippi Valley-type sphalerite is presented. Banded ring-like patterns are shown to arise due to a self-propagating sequence of growth and dissolution (coarsening wave). A two-dimensional model is presented for the first time and the conditions for the pattern generation and preservation are discussed. A number of time series analysis techniques are applied to characterize the compositional patterns observed in natural minerals as well as in the colored rythmites found in the marine clay

  4. 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

  5. Vascular pattern formation in plants.

    PubMed

    Scarpella, Enrico; Helariutta, Ykä

    2010-01-01

    Reticulate tissue systems exist in most multicellular organisms, and the principles underlying the formation of cellular networks have fascinated philosophers, mathematicians, and biologists for centuries. In particular, the beautiful and varied arrangements of vascular tissues in plants have intrigued mankind since antiquity, yet the organizing signals have remained elusive. Plant vascular tissues form systems of interconnected cell files throughout the plant body. Vascular cells are aligned with one another along continuous lines, and vascular tissues differentiate at reproducible positions within organ environments. However, neither the precise path of vascular differentiation nor the exact geometry of vascular networks is fixed or immutable. Several recent advances converge to reconcile the seemingly conflicting predictability and plasticity of vascular tissue patterns. A control mechanism in which an apical-basal flow of signal establishes a basic coordinate system for body axis formation and vascular strand differentiation, and in which a superimposed level of radial organizing cues elaborates cell patterns, would generate a reproducible tissue configuration in the context of an underlying robust, self-organizing structure, and account for the simultaneous regularity and flexibility of vascular tissue patterns.

  6. 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.

  7. 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.

  8. 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

  9. Pattern Formation and Complexity Emergence

    NASA Astrophysics Data System (ADS)

    Berezin, Alexander A.

    2001-03-01

    Success of nonlinear modelling of pattern formation and self-organization encourages speculations on informational and number theoretical foundations of complexity emergence. Pythagorean "unreasonable effectiveness of integers" in natural processes is perhaps extrapolatable even to universal emergence "out-of-nothing" (Leibniz, Wheeler). Because rational numbers (R = M/N) are everywhere dense on real axis, any digital string (hence any "book" from "Library of Babel" of J.L.Borges) is "recorded" infinitely many times in arbitrary many rationals. Furthermore, within any arbitrary small interval there are infinitely many Rs for which (either or both) integers (Ms and Ns) "carry" any given string of any given length. Because any iterational process (such as generation of fractal features of Mandelbrot Set) is arbitrary closely approximatable with rational numbers, the infinite pattern of integers expresses itself in generation of complexity of the world, as well as in emergence of the world itself. This "tunnelling" from Platonic World ("Platonia" of J.Barbour) to a real (physical) world is modern recast of Leibniz's motto ("for deriving all from nothing there suffices a single principle").

  10. 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

  11. Separation vortices and pattern formation

    NASA Astrophysics Data System (ADS)

    Andersen, Anders; Bohr, Tomas; Schnipper, Teis

    2010-03-01

    In this paper examples are given of the importance of flow separation for fluid patterns at moderate Reynolds numbers—both in the stationary and in the time-dependent domain. In the case of circular hydraulic jumps, it has been shown recently that it is possible to generalise the Prandtl-Kármán-Pohlhausen approach to stationary boundary layers with free surfaces going through separation, and thus obtain a quantitative theory of the simplest type of hydraulic jump, where a single separation vortex is present outside the jump. A second type of jump, where an additional roller appears at the surface, cannot be captured by this approach and has not been given an adequate theoretical description. Such a model is needed to describe “polygonal” hydraulic jumps, which occur by spontaneous symmetry breaking of the latter state. Time-dependent separation is of importance in the formation of sand ripples under oscillatory flow, where the separation vortices become very strong. In this case no simple theory exists for the determination of the location and strengths of separation vortices over a wavy bottom of arbitrary profile. We have, however, recently suggested an amplitude equation describing the long-time evolution of the sand ripple pattern, which has the surprising features that it breaks the local sand conservation and has long-range interaction, features that can be underpinned by experiments. Very similar vortex dynamics takes place around oscillating structures such as wings and fins. Here, we present results for the vortex patterns behind a flapping foil in a flowing soap film, which shows the interaction and competition between the vortices shed from the round leading edge (like the von Kármán vortex street) and those created at the sharp trailing edge.

  12. Central role of RAGE-dependent neointimal expansion in arterial restenosis

    PubMed Central

    Sakaguchi, Taichi; Yan, Shi Fang; Yan, Shi Du; Belov, Dmitri; Rong, Ling Ling; Sousa, Monica; Andrassy, Martin; Marso, Steven P.; Duda, Stephan; Arnold, Bernd; Liliensiek, Birgit; Nawroth, Peter P.; Stern, David M.; Schmidt, Ann Marie; Naka, Yoshifumi

    2003-01-01

    Cellular proliferation, migration, and expression of extracellular matrix proteins and MMPs contribute to neointimal formation upon vascular injury. Wild-type mice undergoing arterial endothelial denudation displayed striking upregulation of receptor for advanced glycation end products (RAGE) in the injured vessel, particularly in activated smooth muscle cells of the expanding neointima. In parallel, two of RAGE’s signal transducing ligands, advanced glycation end products (AGEs) and S100/calgranulins, demonstrated increased deposition/expression in the injured vessel wall. Blockade of RAGE, employing soluble truncated receptor or antibodies, or in homozygous RAGE null mice, resulted in significantly decreased neointimal expansion after arterial injury and decreased smooth muscle cell proliferation, migration, and expression of extracellular matrix proteins. A critical role for smooth muscle cell RAGE signaling was demonstrated in mice bearing a transgene encoding a RAGE cytosolic tail-deletion mutant, specifically in smooth muscle cells, driven by the SM22α promoter. Upon arterial injury, neointimal expansion was strikingly suppressed compared with that observed in wild-type littermates. Taken together, these data highlight key roles for RAGE in modulating smooth muscle cell properties after injury and suggest that RAGE is a logical target for suppression of untoward neointimal expansion consequent to arterial injury. PMID:12671045

  13. Adenosine A(2A) receptor stimulation reduces inflammation and neointimal growth in a murine carotid ligation model.

    PubMed

    McPherson, J A; Barringhaus, K G; Bishop, G G; Sanders, J M; Rieger, J M; Hesselbacher, S E; Gimple, L W; Powers, E R; Macdonald, T; Sullivan, G; Linden, J; Sarembock, I J

    2001-05-01

    Endothelial activation and leukocyte recruitment are early events in atherosclerosis and the vascular response to injury. Adenosine has anti-inflammatory effects on leukocytes and endothelial cells mediated through its A(2A) receptor. We tested the hypothesis that A(2A) activation would reduce inflammation and neointimal formation in a murine carotid ligation model. Before injury, mice were randomized to a 7-day subcutaneous infusion of a specific A(2A) receptor agonist (ATL-146e, 0.004 microg/kg per minute), vehicle control, ATL-146e plus ZM241385 (a selective A(2A) antagonist), or ZM241385 alone. Leukocyte recruitment and adhesion molecule expression were assessed at early time points, and the neointimal area was measured at 14 and 28 days after injury. Compared with control mice, ATL-146e-treated mice had significantly less neutrophil and macrophage recruitment and vascular cell adhesion molecule-1, intercellular adhesion molecule-1, and P-selectin expression in the first 7 days after injury. Neointimal area was markedly and persistently reduced by 80% at 14 and 28 days, despite termination of ATL infusion at 7 days. ATL-146e+ZM241385-treated and ZM241385-treated animals had neointimal areas similar to those of control animals, confirming that the observed effects of ATL-146e were mediated specifically by the A(2A) receptor. These data demonstrate that novel stimulation of adenosine A(2A) receptors can inhibit early inflammatory processes that are important in neointimal formation after vascular injury.

  14. 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

  15. 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).

  16. 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.

  17. 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.

  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 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.

  20. 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

  1. Pattern formation in evaporating drops

    NASA Astrophysics Data System (ADS)

    Li, Fang-I.

    The redistribution of organic solutes during drop evaporation is a nanoscale self assembly process with relevance to technologies ranging from inkjet printing of organic displays to synthesis of bio-smart interfaces for sensing and screening. Atomic force microscopy studies comparing the behavior of different generation dendrimers with different surface chemistry in two solvent alcohols on mica substrates confirm that the detailed morphologies of condensed dendrimer ring structures resulting from micro-droplet evaporation sensitively depend on the surface chemistry, the solute evaporation rate and the dendrimer generation. For the dilute concentration studied here the presence of periodically 'scalloped' molecular rings is ubiquitous. The instability wavelength of the scalloped rings is found to be proportional to the width of the ring, similar to observations of the rim instability in dewetting holes. The effect of the surface chemistry of the dendrimer molecules is obvious in the detailed structure of the self assembled rings. Varying the chain length of solvent alcohol leads to modification of ring patterns. The influence of dendrimer generation on ring structure primarily reflects the increase in dendrimer density with generation number. The evolution of G2-50%C12 -pentanol rings as a function of dendrimer concentration is also described. High surface mobility and phase transformation phenomena in condensed, micro-scale dendrimer structures are documented, again using atomic force microscopy. Stratified dendrimer rings undergo dramatic temperature, time and dendrimer generation dependent morphological changes associated with large-scale molecular rearrangements and partial melting. These transformations produce ring structures consisting of a highly stable first monolayer of the scalloped structure in equilibrium with spherical cap shaped dendrimer islands that form at the center of each pre-existing scallop (creating a 'pearl necklace' structure). Analysis of

  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. 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

  4. Nonlinear pattern formation in Dielectric barrier discharge

    NASA Astrophysics Data System (ADS)

    Dong, Lifang; Fan, Weili; He, Yafeng; Pattern Formation in DBD Team

    2015-11-01

    Dielectric barrier discharge (DBD) has proven to be a fascinating system for the study of nonlinear pattern formation, which presents an extraordinary variety and richness of patterns with the prominent convenience and practicality of experimental setups. In recent years, by using the special designed DBD system with two water electrodes, we have obtained a rich variety of patterns through nonlinear self-organization of the filaments [Phys. Rev. E 87, 042914 (2013), Phys. Rev. E 85, 066403 (2012), Phys. Rev. E 86, 036211 (2012)]. The spatio-temporal dynamics of these patterns have been studied systematically, and furthermore, the detailed plasma diagnostics have been carried out. These results are of great significance to give deep insight into the nature of nonlinear pattern formation. Based on our previous studies, here we will present the first report on a new complex superlattice pattern, as so called concentric superlattice. It evolves from hexagon pattern and transits to homogenous glow discharge with an increasing of the applied voltage. The spatio-temporal dynamics of the patterns have been investigated by a high speed camera. Results show that the concentric superlattice is an interleaving of three different sub-lattices, which are concentric-ring, concentric-framework, and concentric-dot embedded in the concentric-framework. Based on the experimental measurements, the involved intrinsic physical mechanism will be demonstrated.

  5. 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.

  6. Lysozyme pattern formation in evaporating droplets

    NASA Astrophysics Data System (ADS)

    Gorr, Heather Meloy

    Liquid droplets containing suspended particles deposited on a solid, flat surface generally form ring-like structures due to the redistribution of solute during evaporation (the "coffee ring effect"). The forms of the deposited patterns depend on complex interactions between solute(s), solvent, and substrate in a rapidly changing, far from equilibrium system. Solute self-organization during evaporation of colloidal sessile droplets has attracted the attention of researchers over the past few decades due to a variety of technological applications. Recently, pattern formation during evaporation of various biofluids has been studied due to potential applications in medical screening and diagnosis. Due to the complexity of 'real' biological fluids and other multicomponent systems, a comprehensive understanding of pattern formation during droplet evaporation of these fluids is lacking. In this PhD dissertation, the morphology of the patterns remaining after evaporation of droplets of a simplified model biological fluid (aqueous lysozyme solutions + NaCl) are examined by atomic force microscopy (AFM) and optical microscopy. Lysozyme is a globular protein found in high concentration, for example, in human tears and saliva. The drop diameters, D, studied range from the micro- to the macro- scale (1 microm -- 2 mm). In this work, the effect of evaporation conditions, solution chemistry, and heat transfer within the droplet on pattern formation is examined. In micro-scale deposits of aqueous lysozyme solutions (1 microm < D < 50 microm), the protein motion and the resulting dried residue morphology are highly influenced by the decreased evaporation time of the drop. The effect of electrolytes on pattern formation is also investigated by adding varying concentrations NaCl to the lysozyme solutions. Finally, a novel pattern recognition program is described and implemented which classifies deposit images by their solution chemistries. The results presented in this Ph

  7. 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

  8. 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.

  9. Pattern formation in superdiffusion Oregonator model

    NASA Astrophysics Data System (ADS)

    Feng, Fan; Yan, Jia; Liu, Fu-Cheng; He, Ya-Feng

    2016-10-01

    Pattern formations in an Oregonator model with superdiffusion are studied in two-dimensional (2D) numerical simulations. Stability analyses are performed by applying Fourier and Laplace transforms to the space fractional reaction-diffusion systems. Antispiral, stable turing patterns, and travelling patterns are observed by changing the diffusion index of the activator. Analyses of Floquet multipliers show that the limit cycle solution loses stability at the wave number of the primitive vector of the travelling hexagonal pattern. We also observed a transition between antispiral and spiral by changing the diffusion index of the inhibitor. Project supported by the National Natural Science Foundation of China (Grant Nos. 11205044 and 11405042), the Research Foundation of Education Bureau of Hebei Province, China (Grant Nos. Y2012009 and ZD2015025), the Program for Young Principal Investigators of Hebei Province, China, and the Midwest Universities Comprehensive Strength Promotion Project.

  10. 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

  11. 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.

  12. Sarcomeric Pattern Formation by Actin Cluster Coalescence

    PubMed Central

    Friedrich, Benjamin M.; Fischer-Friedrich, Elisabeth; Gov, Nir S.; Safran, Samuel A.

    2012-01-01

    Contractile function of striated muscle cells depends crucially on the almost crystalline order of actin and myosin filaments in myofibrils, but the physical mechanisms that lead to myofibril assembly remains ill-defined. Passive diffusive sorting of actin filaments into sarcomeric order is kinetically impossible, suggesting a pivotal role of active processes in sarcomeric pattern formation. Using a one-dimensional computational model of an initially unstriated actin bundle, we show that actin filament treadmilling in the presence of processive plus-end crosslinking provides a simple and robust mechanism for the polarity sorting of actin filaments as well as for the correct localization of myosin filaments. We propose that the coalescence of crosslinked actin clusters could be key for sarcomeric pattern formation. In our simulations, sarcomere spacing is set by filament length prompting tight length control already at early stages of pattern formation. The proposed mechanism could be generic and apply both to premyofibrils and nascent myofibrils in developing muscle cells as well as possibly to striated stress-fibers in non-muscle cells. PMID:22685394

  13. 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

  14. 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.

  15. 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

  16. Geometry-induced protein pattern formation.

    PubMed

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-19

    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 [Formula: see text] 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.

  17. 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.

  18. Excitable Pattern Formation in Inhomogeneous Systems

    NASA Astrophysics Data System (ADS)

    Prabhakara, Kaumudi; Gholami, Azam; Zykov, Vladimir; Bodenschatz, Eberhard

    2015-03-01

    On starvation, the amoebae Dictyostelium discoideum signal via the chemo-attractant cyclic adenosine monophosphate (cAMP). The amoebae sense cAMP through membrane receptors and produce their own cAMP. Simultaneously they produce a basal level of Phosphodiesterase, an enzyme that degrades cAMP. Soon a pattern of rotating spiral waves or circular waves is formed at the multi-cellular level. The causal reasons for the selection of one or the other pattern are still unclear. Here we report experimental and theoretical investigations of the pattern-formation of mixtures of cells starved for different times. The excitability of the amoebae depends on the starvation time due to time dependent gene expressions. Cells starved for longer times are known to exhibit increased excitability. We report phase maps of the patterns for mixtures of different combinations of excitability. Numerical simulations of a modified Kessler-Levine model allow us to explain the experimental results and provide new insights into the dynamical behavior of the system. This work is supported by the Max Planck Society.

  19. Pattern formation in the Brusselator system

    NASA Astrophysics Data System (ADS)

    Peng, Rui; Wang, Mingxin

    2005-09-01

    In the paper, we deal with a reaction-diffusion system well known as the Brusselator model and some improved results for the steady states of this model are presented. We first give an a priori estimates (positive upper and lower bounds) of positive steady states. Then, we obtain the non-existence and existence of positive non-constant steady states as the parameters [lambda], [theta] and b are varied, which means some certain conditions under which the pattern formation occurs or not.

  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. 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.

  2. Chemerin Stimulates Vascular Smooth Muscle Cell Proliferation and Carotid Neointimal Hyperplasia by Activating Mitogen-Activated Protein Kinase Signaling

    PubMed Central

    Xiong, Wei; Luo, Yu; Wu, Lin; Liu, Feng; Liu, Huadong; Li, Jianghua; Liao, Bihong; Dong, Shaohong

    2016-01-01

    Vascular neointimal hyperplasia and remodeling arising from local inflammation are characteristic pathogeneses of proliferative cardiovascular diseases, such as atherosclerosis and post angioplasty restenosis. The molecular mechanisms behind these pathological processes have not been fully determined. The adipokine chemerin is associated with obesity, metabolism, and control of inflammation. Recently, chemerin has gained increased attention as it was found to play a critical role in the development of cardiovascular diseases. In this study, we investigated the effects of chemerin on the regulation of vascular smooth muscle cells and carotid neointimal formation after angioplasty. We found that circulating chemerin levels increased after carotid balloon injury, and that knockdown of chemerin significantly inhibited the proliferative aspects of vascular smooth muscle cells induced by platelet-derived growth factor-BB and pro-inflammatory chemokines in vitro as well as prohibited carotid neointimal hyperplasia and pro-inflammatory chemokines in vivo after angioplasty. Additionally, inhibition of chemerin down-regulated the expression of several proteins, including phosphorylated p38 mitogen-activated protein kinase, phosphorylated extracellular signal regulated kinase 1/2, nuclear factor-kappa B p65, and proliferation cell nuclear antigen. The novel finding of this study is that chemerin stimulated vascular smooth muscle cells proliferation and carotid intimal hyperplasia through activation of the mitogen-activated protein kinase signaling pathway, which may lead to vascular inflammation and remodeling, and is relevant to proliferative cardiovascular diseases. PMID:27792753

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. Pattern formation by a moving morphogen source

    PubMed Central

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

    2013-01-01

    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. PMID:21750363

  9. Pattern formation by vascular mesenchymal cells

    NASA Astrophysics Data System (ADS)

    Garfinkel, Alan; Tintut, Yin; Petrasek, Danny; Boström, Kristina; Demer, Linda L.

    2004-06-01

    In embryogenesis, immature mesenchymal cells aggregate and organize into patterned tissues. Later in life, a pathological recapitulation of this process takes place in atherosclerotic lesions, when vascular mesenchymal cells organize into trabecular bone tissue within the artery wall. Here we show that multipotential adult vascular mesenchymal cells self-organize in vitro into patterns that are predicted by a mathematical model based on molecular morphogens interacting in a reaction-diffusion process. We identify activator and inhibitor morphogens for stripe, spot, and labyrinthine patterns and confirm the model predictions in vitro. Thus, reaction-diffusion principles may play a significant role in morphogenetic processes in adult mesenchymal cells.

  10. Sequential pattern formation governed by signaling gradients

    NASA Astrophysics Data System (ADS)

    Jörg, David J.; Oates, Andrew C.; Jülicher, Frank

    2016-10-01

    Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the interplay of cell oscillations with tissue elongation and shortening and with signaling gradients, is still missing. Here we show that a set of coupled genetic oscillators in an elongating tissue that is regulated by diffusing and advected signaling molecules can account for segmentation as a self-organized patterning process. This system can form a finite number of segments and the dynamics of segmentation and the total number of segments formed depend strongly on kinetic parameters describing tissue elongation and signaling molecules. The model accounts for existing experimental perturbations to signaling gradients, and makes testable predictions about novel perturbations. The variety of different patterns formed in our model can account for the variability of segmentation between different animal species.

  11. Pattern formation in oscillatory media without lateral inhibition

    NASA Astrophysics Data System (ADS)

    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.

  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. Acetylbritannilactone Inhibits Neointimal Hyperplasia after Balloon Injury of Rat Artery by Suppressing Nuclear Factor-{kappa}B Activation.

    PubMed

    Liu, Bin; Han, Mei; Wen, Jin-Kun

    2008-01-01

    Based on our previous observations that 1-O-acetylbritannilactone (R)-4((3aS,4S,7aR)-4-hydroxy-6-methyl-3-methylene-2-oxo-2,3,3a,4,7,7a-hexahydrobenzofuran-5-yl)pentyl acetate (ABL) suppresses prostaglandin E(2) and nitric oxide synthesis in macrophages, the present study was designed to explore the effect of ABL on neointimal hyperplasia after balloon injury and its mechanism of action. In male Sprague-Dawley rats, 26 mg/kg ABL or polyglycol (control) was administered daily from 3 days before injury to 2 weeks after conventional balloon injury. ABL administration led to a significant reduction in neointimal formation (neointima to media ratio, 1.94 +/- 0.43 versus 0.84 +/- 0.29, P < 0.01) and proliferative activity of vascular smooth muscle cells after balloon injury in rats. Western blot analysis revealed that this is correlated to the inhibition of nuclear factor (NF)-kappaB activation and to the reduced expression of cyclooxygenase-2. Investigation of potential signaling pathways demonstrated that ABL inhibited NF-kappaB activation via the blockade of the inhibitor of NF-kappaB kinase-beta activation and the suppression of the degradation of the inhibitors of NF-kappaB-alpha. These findings suggest that ABL is a potential inhibitor of neointimal formation because it blocks injury-induced NF-kappaB activation and may have beneficial effects in reducing the risk of restenosis after angioplasty. PMID:17911374

  14. Spongiosa primary development: a biochemical hypothesis by Turing patterns formations.

    PubMed

    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.

  15. Dynamics of pattern formation in bacterial swarms

    NASA Astrophysics Data System (ADS)

    Steager, Edward B.; Kim, Chang-Beom; Kim, Min Jun

    2008-07-01

    To gain a more thorough understanding of the dynamics of swarming bacteria, a nonlabeled cell tracking algorithm was used to study the velocity field of flagellated bacteria, Serratia marcescens, swarming on a soft agar plate. The average velocities for local regions regularly arranged over the entire flow field were investigated. The velocity field of the bacteria typically featured the combination of curvilinear translation and vortex modes. They repeated these patterns for short periods of time, forming several groups and dissipating. To further investigate the flow patterns generated by the collective motion of the swarming bacteria, the velocity field on the swarm was spatially correlated. The highest velocities and correlation lengths have been found to occur in the region from 0.5to1mm from the swarm edge, followed by a steady decline as distance from the edge increases, and a sudden decrease in motion typically occurs between 2 and 4mm from the swarm edge.

  16. 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.

  17. 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

  18. 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

  19. 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.

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

    PubMed

    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. PMID:24229267

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. Pattern formation and eyespot determination in butterfly wings.

    PubMed

    Carroll, S B; Gates, J; Keys, D N; Paddock, S W; Panganiban, G E; Selegue, J E; Williams, J A

    1994-07-01

    Butterfly wings display pattern elements of many types and colors. To identify the molecular processes underlying the generation of these patterns, several butterfly cognates of Drosophila appendage patterning genes have been cloned and their expression patterns have been analyzed. Butterfly wing patterns are organized by two spatial coordinate systems. One system specifies positional information with respect to the entire wing field and is conserved between fruit flies and butterflies. A second system, superimposed on the general system and involving several of the same genes, operates within each wing subdivision to elaborate discrete pattern elements. Eyespots, which form from discrete developmental organizers, are marked by Distal-less gene expression. These circular pattern elements appear to be generated by a process similar to, and perhaps evolved from, proximodistal pattern formation in insect appendages. PMID:7912449

  6. Pattern formation and eyespot determination in butterfly wings.

    PubMed

    Carroll, S B; Gates, J; Keys, D N; Paddock, S W; Panganiban, G E; Selegue, J E; Williams, J A

    1994-07-01

    Butterfly wings display pattern elements of many types and colors. To identify the molecular processes underlying the generation of these patterns, several butterfly cognates of Drosophila appendage patterning genes have been cloned and their expression patterns have been analyzed. Butterfly wing patterns are organized by two spatial coordinate systems. One system specifies positional information with respect to the entire wing field and is conserved between fruit flies and butterflies. A second system, superimposed on the general system and involving several of the same genes, operates within each wing subdivision to elaborate discrete pattern elements. Eyespots, which form from discrete developmental organizers, are marked by Distal-less gene expression. These circular pattern elements appear to be generated by a process similar to, and perhaps evolved from, proximodistal pattern formation in insect appendages.

  7. (The physics of pattern formation at liquid interfaces)

    SciTech Connect

    Not Available

    1990-01-01

    This paper discusses pattern formation at liquid interfaces and interfaces within disordered materials. The particular topics discussed are: a racetrack for competing viscous fingers; an experimental realization of periodic boundary conditions; what sets the length scale for patterns between miscible liquids; the fractal dimension of radial Hele-Shaw patterns; detailed analyses of low-contrast Saffman-Taylor flows; and the wetting/absorption properties of polystyrene spheres in binary liquid mixtures. (LSP)

  8. Pattern Formation in Cathode Boundary Layer Microdischarges

    NASA Astrophysics Data System (ADS)

    Schoenbach, K. H.; Moselhy, M. M.

    2003-10-01

    Direct current glow discharges in xenon between a planar, 100 μm thick cathode and a ring shaped anode, separated by 250 μm, were found to be stable up to atmospheric pressure. Photographs in the visible and VUV (172 nm) range of the spectrum show the transition from a homogeneous to a structured plasma. The plasma patterns, regularly arranged filaments that are most pronounced at lower pressures (100 Torr), show discrete changes when the current is decreased by fractions of mA. This selforganization of the plasma requires the presence of a second stable branch in addition to the abnormal cathode fall in the voltage-current density characteristic of the "cathode boundary layer" (CBL) discharges. A model of the cathode fall by von Engel and Steenbeck [1], which was modified to take thermal conduction as a loss process into account, in addition to radiation, indicates the presence of stable plasma filaments at current densities in the range from 10 to 100 A/cm^2, before transition into an arc. [1] A. von Engel and M. Steenbeck, "Elektrische Gasentladungen, ihre Physik und Technik," Vol. 2, p. 121. Work supported by NSF (CTS-0078618 and INT-0001438).

  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. 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

  11. Soliton interactions and the formation of solitonic patterns

    NASA Astrophysics Data System (ADS)

    Sears, Suzanne M.

    From the stripes of a zebra, to the spirals of cream in a hot cup of coffee, we are surrounded by patterns in the natural world. But why are there patterns? Why drives their formation? In this thesis we study some of the diverse ways patterns can arise due to the interactions between solitary waves in nonlinear systems, sometimes starting from nothing more than random noise. What follows is a set of three studies. In the first, we show how a nonlinear system that supports solitons can be driven to generate exact (regular) Cantor set fractals. As an example, we use numerical simulations to demonstrate the formation of Cantor set fractals by temporal optical solitons. This fractal formation occurs in a cascade of nonlinear optical fibers through the dynamical evolution of a single input soliton. In the second study, we investigate pattern formation initiated by modulation instability in nonlinear partially coherent wave fronts and show that anisotropic noise and/or anisotropic correlation statistics can lead to ordered patterns such as grids and stripes. For the final study, we demonstrate the spontaneous clustering of solitons in partially coherent wavefronts during the final stages of pattern formation initiated by modulation instability and noise. Experimental observations are in agreement with theoretical predictions and are confirmed using numerical simulations.

  12. 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.

  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. Argon ion beam induced surface pattern formation on Si

    NASA Astrophysics Data System (ADS)

    Hofsäss, H.; Bobes, O.; Zhang, K.

    2016-01-01

    The development of self-organized surface patterns on Si due to noble gas ion irradiation has been studied extensively in the past. In particular, Ar ions are commonly used and the pattern formation was analyzed as function of ion incidence angle, ion fluence, and ion energies between 250 eV and 140 keV. Very few results exist for the energy regime between 1.5 keV and 10 keV and it appears that pattern formation is completely absent for these ion energies. In this work, we present experimental data on pattern formation for Ar ion irradiation between 1 keV and 10 keV and ion incidence angles between 50° and 75°. We confirm the absence of patterns at least for ion fluences up to 1018 ions/cm2. Using the crater function formalism and Monte Carlo simulations, we calculate curvature coefficients of linear continuum models of pattern formation, taking into account contribution due to ion erosion and recoil redistribution. The calculations consider the recently introduced curvature dependence of the erosion crater function as well as the dynamic behavior of the thickness of the ion irradiated layer. Only when taking into account these additional contributions to the linear theory, our simulations clearly show that that pattern formation is strongly suppressed between about 1.5 keV and 10 keV, most pronounced at 3 keV. Furthermore, our simulations are now able to predict whether or not parallel oriented ripple patterns are formed, and in case of ripple formation the corresponding critical angles for the whole experimentally studied energies range between 250 eV and 140 keV.

  15. Gene therapy inhibiting neointimal vascular lesion: in vivo transfer of endothelial cell nitric oxide synthase gene.

    PubMed Central

    von der Leyen, H E; Gibbons, G H; Morishita, R; Lewis, N P; Zhang, L; Nakajima, M; Kaneda, Y; Cooke, J P; Dzau, V J

    1995-01-01

    It is postulated that vascular disease involves a disturbance in the homeostatic balance of factors regulating vascular tone and structure. Recent developments in gene transfer techniques have emerged as an exciting therapeutic option to treat vascular disease. Several studies have established the feasibility of direct in vivo gene transfer into the vasculature by using reporter genes such as beta-galactosidase or luciferase. To date no study has documented therapeutic effects with in vivo gene transfer of a cDNA encoding a functional enzyme. This study tests the hypothesis that endothelium-derived nitric oxide is an endogenous inhibitor of vascular lesion formation. After denudation by balloon injury of the endothelium of rat carotid arteries, we restored endothelial cell nitric oxide synthase (ec-NOS) expression in the vessel wall by using the highly efficient Sendai virus/liposome in vivo gene transfer technique. ec-NOS gene transfection not only restored NO production to levels seen in normal untreated vessels but also increased vascular reactivity of the injured vessels. Neointima formation at day 14 after balloon injury was inhibited by 70%. These findings provide direct evidence that NO is an endogenous inhibitor of vascular lesion formation in vivo (by inhibiting smooth muscle cell proliferation and migration) and suggest the possibility of ec-NOS transfection as a potential therapeutic approach to treat neointimal hyperplasia. Images Fig. 1 Fig. 2 Fig. 5 PMID:7532305

  16. Gene Therapy Inhibiting Neointimal Vascular Lesion: In vivo Transfer of Endothelial Cell Nitric Oxide Synthase Gene

    NASA Astrophysics Data System (ADS)

    von der Leyen, Heiko E.; Gibbons, Gary H.; Morishita, Ryuichi; Lewis, Neil P.; Zhang, Lunan; Nakajima, Masatoshi; Kaneda, Yasufumi; Cooke, John P.; Dzau, Victor J.

    1995-02-01

    It is postulated that vascular disease involves a disturbance in the homeostatic balance of factors regulating vascular tone and structure. Recent developments in gene transfer techniques have emerged as an exciting therapeutic option to treat vascular disease. Several studies have established the feasibility of direct in vivo gene transfer into the vasculature by using reporter genes such as β-galactosidase or luciferase. To date no study has documented therapeutic effects with in vivo gene transfer of a cDNA encoding a functional enzyme. This study tests the hypothesis that endothelium-derived nitric oxide is an endogenous inhibitor of vascular lesion formation. After denudation by balloon injury of the endothelium of rat carotid arteries, we restored endothelial cell nitric oxide synthase (ec-NOS) expression in the vessel wall by using the highly efficient Sendai virus/liposome in vivo gene transfer technique. ec-NOS gene transfection not only restored NO production to levels seen in normal untreated vessels but also increased vascular reactivity of the injured vessel. Neointima formation at day 14 after balloon injury was inhibited by 70%. These findings provide direct evidence that NO is an endogenous inhibitor of vascular lesion formation in vivo (by inhibiting smooth muscle cell proliferation and migration) and suggest the possibility of ec-NOS transfection as a potential therapeutic approach to treat neointimal hyperplasia.

  17. Role of cAMP-Phosphodiesterase 1C Signaling in Regulating Growth Factor Receptor Stability, Vascular Smooth Muscle Cell Growth, Migration, and Neointimal Hyperplasia

    PubMed Central

    Cai, Yujun; Nagel, David J.; Zhou, Qian; Cygnar, Katherine D.; Zhao, Haiqing; Li, Faqian; Pi, Xinchun; Knight, Peter A.; Yan, Chen

    2015-01-01

    Objective Neointimal hyperplasia characterized by abnormal accumulation of vascular smooth muscle cells (SMCs) is a hallmark of occlusive disorders such as atherosclerosis, post-angioplasty restenosis, vein graft stenosis, and allograft vasculopathy. Cyclic nucleotides are vital in SMC proliferation and migration, which are regulated by cyclic nucleotide phosphodiesterases (PDEs). Our goal is to understand the regulation and function of PDEs in SMC pathogenesis of vascular diseases. Methods & Results We performed screening for genes differentially expressed in normal contractile versus proliferating synthetic SMCs. We observed that PDE1C expression was low in contractile SMCs but drastically elevated in synthetic SMCs in vitro and in various mouse vascular injury models in vivo. Additionally, PDE1C was highly induced in neointimal SMCs of human coronary arteries. More importantly, injury-induced neointimal formation was significantly attenuated by PDE1C deficiency or PDE1 inhibition in vivo. PDE1 inhibition suppressed vascular remodeling of human saphenous vein explants ex vivo. In cultured SMCs, PDE1C deficiency or PDE1 inhibition attenuated SMC proliferation and migration. Mechanistic studies revealed that PDE1C plays a critical role in regulating the stability of growth factor receptors, such as PDGF-receptor-beta (PDGFRβ) known to be important in pathological vascular remodeling. PDE1C interacts with LDL-receptor-related-protein-1 (LRP1) and PDGFRβ, thus regulating PDGFRβ endocytosis and lysosome-dependent degradation in an LRP1-dependent manner. A transmembrane-adenylyl-cyclase (tmAC)-cAMP-PKA cascade modulated by PDE1C is critical in regulating PDGFRβ degradation. Conclusion These findings demonstrated that PDE1C is an important regulator of SMC proliferation, migration, and neointimal hyperplasia, in part through modulating endosome/lysosome dependent PDGFRβ protein degradation via LRP1. PMID:25608528

  18. Comparison of neointimal morphology of in-stent restenosis with sirolimus-eluting stents versus bare metal stents: virtual histology-intravascular ultrasound analysis.

    PubMed

    Yamamoto, Yoshihiro; Otani, Hajime; Iwasaka, Junji; Park, Haengnam; Sakuma, Takao; Kamihata, Hiroshi; Iwasaka, Toshiji

    2011-09-01

    Sirolimus-eluting stents (SES) have reduced the incidence of restenosis and target lesion revascularization compared to bare metal stents (BMS). However, inhibition of endothelialization and neointimal formation after SES implantation may produce vulnerable plaques. The present study compared the neointimal morphology of in-stent restenosis (ISR) between SES and BMS using virtual histology-intravascular ultrasound (VH-IVUS). Thirty ISR lesions (SES n = 15, BMS n = 15) demonstrated by coronary angiography in 30 patients with stable angina pectoris were analyzed with VH-IVUS between 6 months to 3 years after stent implantation. Tissue maps were reconstructed from radiofrequency data using VH-IVUS software. ISR lesions after SES implantation consisted of a significantly increased necrotic core (NC) compared to BMS (12.9 vs. 5.6% of neointimal volume, p < 0.01). However, the NC in ISR lesions after SES implantation was covered with a thick fibrous cap. An increase in the size of NC covered with a thick fibrous cap is a characteristic morphological feature of ISR after SES implantation. Further studies are needed to clarify whether such a morphological change is related to the attenuation of stent thrombosis after SES implantation.

  19. 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...

  20. 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.

  1. Zebrafish stripes as a model for vertebrate colour pattern formation.

    PubMed

    Singh, Ajeet Pratap; Nüsslein-Volhard, Christiane

    2015-01-19

    Colour patterns are prominent features of many animals and have important functions in communication, such as camouflage, kin recognition and mate choice. As targets for natural as well as sexual selection, they are of high evolutionary significance. The molecular mechanisms underlying colour pattern formation in vertebrates are not well understood. Progress in transgenic tools, in vivo imaging and the availability of a large collection of mutants make the zebrafish (Danio rerio) an attractive model to study vertebrate colouration. Zebrafish display golden and blue horizontal stripes that form during metamorphosis as mosaics of yellow xanthophores, silvery or blue iridophores and black melanophores in the hypodermis. Lineage tracing revealed the origin of the adult pigment cells and their individual cellular behaviours during the formation of the striped pattern. Mutant analysis indicated that interactions between all three pigment cell types are required for the formation of the pattern, and a number of cell surface molecules and signalling systems have been identified as mediators of these interactions. The understanding of the mechanisms that underlie colour pattern formation is an important step towards deciphering the genetic basis of variation in evolution. PMID:25602311

  2. Dynamics of precipitation pattern formation at geothermal hot springs.

    PubMed

    Goldenfeld, Nigel; Chan, Pak Yuen; Veysey, John

    2006-06-30

    We formulate and model the dynamics of spatial patterns arising during the precipitation of calcium carbonate from a supersaturated shallow water flow. The model describes the formation of travertine deposits at geothermal hot springs and rimstone dams of calcite in caves. We find explicit solutions for travertine domes at low flow rates, identify the linear instabilities which generate dam and pond formation on sloped substrates, and present simulations of statistical landscape evolution. PMID:16907308

  3. Dynamics of precipitation pattern formation at geothermal hot springs.

    PubMed

    Goldenfeld, Nigel; Chan, Pak Yuen; Veysey, John

    2006-06-30

    We formulate and model the dynamics of spatial patterns arising during the precipitation of calcium carbonate from a supersaturated shallow water flow. The model describes the formation of travertine deposits at geothermal hot springs and rimstone dams of calcite in caves. We find explicit solutions for travertine domes at low flow rates, identify the linear instabilities which generate dam and pond formation on sloped substrates, and present simulations of statistical landscape evolution.

  4. Bioconvective pattern formation of Tetrahymena under altered gravity.

    PubMed

    Mogami, Yoshihiro; Yamane, Akiko; Gino, Atsuko; Baba, Shoji A

    2004-09-01

    Bioconvection is a result of the negative gravitactic behavior of microorganisms. When the top-heavy density gradient generated by gravitaxis grows sufficiently large, an overturning convection occurs leading to a formation of characteristic patterns, which involve highly concentrated aggregation of cells into extended two-dimensional structures. Although gravity is a crucial factor, few experiments have been done with reference to gravity as an experimental variable. In order to gain an insight into the hydrodynamic as well as biological dependence of the convective motion on gravity, we investigated changes in bioconvective patterns of Tetrahymena under altered gravity acceleration generated by a long-arm centrifuge. Bioconvective patterns recorded of three different cell strains (T. pyriformis, T. thermophila and its behavioral mutant, TNR) were analyzed quantitatively using space-time plot and Fourier analysis. For example, under subcritical conditions, when T. pyriformis (1.0 x 10(6) cells ml(-1)) was placed in a 2 mm-deep chamber, no spatial pattern was observed at 1 g. When the suspension was centrifuged, however, patterns began to appear as acceleration increased over a critical value (1.5 g), and then remained steady. The formation was reversible, i.e. the patterns disappeared again as acceleration decreased. Under supracritical conditions, i.e. when a suspension of the same density was placed in a 4 mm-deep chamber, a steady state pattern was formed at 1 g. The pattern spacing in the steady state was observed to decrease stepwise in response to step increases in acceleration. Fourier analysis demonstrated that for TNR the mean wave number changed almost simultaneously with step changes in acceleration, whereas the responses were less sharp in the wild-type strains. This may suggest that the locomotor phenotype of the cell, such as its avoiding response ability, has a crucial role in bioconvective pattern formation. These findings are discussed in relation

  5. 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

  6. Dynamic Pattern Formation in Electron-Beam-Induced Etching.

    PubMed

    Martin, Aiden A; Bahm, Alan; Bishop, James; Aharonovich, Igor; Toth, Milos

    2015-12-18

    We report highly ordered topographic patterns that form on the surface of diamond, span multiple length scales, and have a symmetry controlled by the precursor gas species used in electron-beam-induced etching (EBIE). The pattern formation dynamics reveals an etch rate anisotropy and an electron energy transfer pathway that is overlooked by existing EBIE models. We, therefore, modify established theory such that it explains our results and remains universally applicable to EBIE. The patterns can be exploited in controlled wetting, optical structuring, and other emerging applications that require nano- and microscale surface texturing of a wide band-gap material. PMID:26722926

  7. Vegetation pattern formation in a fog-dependent ecosystem.

    PubMed

    Borthagaray, Ana I; Fuentes, Miguel A; Marquet, Pablo A

    2010-07-01

    Vegetation pattern formation is a striking characteristic of several water-limited ecosystems around the world. Typically, they have been described on runoff-based ecosystems emphasizing local interactions between water, biomass interception, growth and dispersal. Here, we show that this situation is by no means general, as banded patterns in vegetation can emerge in areas without rainfall and in plants without functional root (the Bromeliad Tillandsia landbeckii) and where fog is the principal source of moisture. We show that a simple model based on the advection of fog-water by wind and its interception by the vegetation can reproduce banded patterns which agree with empirical patterns observed in the Coastal Atacama Desert. Our model predicts how the parameters may affect the conditions to form the banded pattern, showing a transition from a uniform vegetated state, at high water input or terrain slope to a desert state throughout intermediate banded states. Moreover, the model predicts that the pattern wavelength is a decreasing non-linear function of fog-water input and slope, and an increasing function of plant loss and fog-water flow speed. Finally, we show that the vegetation density is increased by the formation of the regular pattern compared to the density expected by the spatially homogeneous model emphasizing the importance of self-organization in arid ecosystems. PMID:20417646

  8. Vegetation pattern formation in a fog-dependent ecosystem.

    PubMed

    Borthagaray, Ana I; Fuentes, Miguel A; Marquet, Pablo A

    2010-07-01

    Vegetation pattern formation is a striking characteristic of several water-limited ecosystems around the world. Typically, they have been described on runoff-based ecosystems emphasizing local interactions between water, biomass interception, growth and dispersal. Here, we show that this situation is by no means general, as banded patterns in vegetation can emerge in areas without rainfall and in plants without functional root (the Bromeliad Tillandsia landbeckii) and where fog is the principal source of moisture. We show that a simple model based on the advection of fog-water by wind and its interception by the vegetation can reproduce banded patterns which agree with empirical patterns observed in the Coastal Atacama Desert. Our model predicts how the parameters may affect the conditions to form the banded pattern, showing a transition from a uniform vegetated state, at high water input or terrain slope to a desert state throughout intermediate banded states. Moreover, the model predicts that the pattern wavelength is a decreasing non-linear function of fog-water input and slope, and an increasing function of plant loss and fog-water flow speed. Finally, we show that the vegetation density is increased by the formation of the regular pattern compared to the density expected by the spatially homogeneous model emphasizing the importance of self-organization in arid ecosystems.

  9. A combinatorial code for pattern formation in Drosophila oogenesis

    PubMed Central

    Yakoby, N.; Bristow, C.A.; Gong, D.; Schafer, X.; Lembong, J.; Zartman, J.J.; Halfon, M.S.; Schüpbach, T.; Shvartsman, S.Y.

    2010-01-01

    Summary Two-dimensional patterning of the follicular epithelium in Drosophila oogenesis is required for the formation of three-dimensional eggshell structures. Our analysis of a large number of published gene expression patterns in the follicle cells suggested that they follow a simple combinatorial code, based on six spatial building blocks and the operations of union, difference, intersection, and addition. The building blocks are related to the distribution of the inductive signals, provided by the highly conserved EGFR and DPP pathways. We demonstrated the validity of the code by testing it against a set of newly identified expression patterns, obtained in a large-scale transcriptional profiling experiment. Using the proposed code, we distinguished 36 distinct patterns for 81 genes expressed in the follicular epithelium and characterized their joint dynamics over four stages of oogenesis. This work provides the first systematic analysis of the diversity and dynamics of two-dimensional gene expression patterns in a developing tissue. PMID:19000837

  10. COX-2-Derived PGE2 Promotes Injury-induced Vascular Neointimal Hyperplasia through the EP3 Receptor

    PubMed Central

    Zhang, Jian; Zou, Fangfang; Tang, Juan; Zhang, Qianqian; Gong, Yanjun; Wang, Qingsong; Shen, Yujun; Xiong, Lixia; Breyer, Richard; Lararus, Michael; Funk, Colin D.; Yu, Ying

    2014-01-01

    Rationale Vascular smooth muscle cell (VSMC) migration and proliferation are the hallmarks of restenosis pathogenesis after angioplasty. Cyclooxygenase (COX)-derived prostaglandin (PG)E2 is implicated in the vascular remodeling response to injury. However, its precise molecular role remains unknown. Objective This study investigates the impact of COX-2-derived PGE2 on neointima formation after injury. Methods and Results Vascular remodeling was induced by wire-injury in femoral arteries of mice. Both neointima formation and the restenosis ratio were diminished in COX-2 KO mice as compared to controls, whereas these parameters were enhanced in COX-1>COX-2 mice where COX-1 is governed by COX-2 regulatory elements. PG profile analysis revealed that the reduced PGE2 by COX-2 deficiency, but not PGI2, could be rescued by COX-1 replacement, indicating COX-2-derived PGE2 enhanced neointima formation. Through multiple approaches, the EP3 receptor was identified to mediate the VSMC migration response to various stimuli. Disruption of EP3 impaired VSMC polarity for directional migration by depressing small GTPase activity and retarded vascular neointimal hyperplasia while overexpression of EP3α and EP3β aggravated neointima formation. Inhibition or deletion of EP3α/β, a Gαs protein-coupled receptor, activated thecAMP/PKA pathway and depressed activation of RhoA in VSMCs. PGE2 could stimulate PI3K/Akt/GSK3β signaling in VSMCs through Gβγ subunits upon EP3α/β activation. Abolition of EP3 suppressed PI3K signaling and reduced GTPase activity in VSMCs, and altered cell polarity and directional migration. Conclusions COX-2-derived PGE2 facilitated the neointimal hyperplasia response to injury through EP3α/β-mediated cAMP/PKA and PI3K pathways, indicating EP3 inhibition maybe a promising therapeutic strategy for percutaneous transluminal coronary angioplasty. PMID:23595951

  11. 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

  12. Turing pattern formation in fractional activator-inhibitor systems

    NASA Astrophysics Data System (ADS)

    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

  13. 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

  14. Self-organized surface ripple pattern formation by ion implantation

    NASA Astrophysics Data System (ADS)

    Hofsäss, Hans; Zhang, Kun; Bobes, Omar

    2016-10-01

    Ion induced ripple pattern formation on solid surfaces has been extensively studied in the past and the theories describing curvature dependent ion erosion as well as redistribution of recoil atoms have been very successful in explaining many features of the pattern formation. Since most experimental studies use noble gas ion irradiation, the incorporation of the ions into the films is usually neglected. In this work we show that the incorporation or implantation of non-volatile ions also leads to a curvature dependent term in the equation of motion of a surface height profile. The implantation of ions can be interpreted as a negative sputter yield; and therefore, the effect of ion implantation is opposite to the one of ion erosion. For angles up to about 50°, implantation of ions stabilizes the surface, whereas above 50°, ion implantation contributes to the destabilization of the surface. We present simulations of the curvature coefficients using the crater function formalism and we compare the simulation results to the experimental data on the ion induced pattern formation using non-volatile ions. We present several model cases, where the incorporation of ions is a crucial requirement for the pattern formation.

  15. 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

  16. 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

  17. Pattern formation in oscillatory complex networks consisting of excitable nodes

    NASA Astrophysics Data System (ADS)

    Liao, Xuhong; Xia, Qinzhi; Qian, Yu; Zhang, Lisheng; Hu, Gang; Mi, Yuanyuan

    2011-05-01

    Oscillatory dynamics of complex networks has recently attracted great attention. In this paper we study pattern formation in oscillatory complex networks consisting of excitable nodes. We find that there exist a few center nodes and small skeletons for most oscillations. Complicated and seemingly random oscillatory patterns can be viewed as well-organized target waves propagating from center nodes along the shortest paths, and the shortest loops passing through both the center nodes and their driver nodes play the role of oscillation sources. Analyzing simple skeletons we are able to understand and predict various essential properties of the oscillations and effectively modulate the oscillations. These methods and results will give insights into pattern formation in complex networks and provide suggestive ideas for studying and controlling oscillations in neural networks.

  18. Simple, simpler, simplest: Spontaneous pattern formation in a commonplace system

    NASA Astrophysics Data System (ADS)

    Strombom, Evelyn H.; Caicedo-Carvajal, Carlos E.; Thyagu, N. Nirmal; Palumbo, Daniel; Shinbrot, Troy

    2012-07-01

    In 1855, Lord Kelvin's brother, James Thomson, wrote a paper describing "certain curious motions" on liquid surfaces. In the present paper, we describe several curious motions produced in the simplest possible manner: by introducing a droplet of food coloring into a shallow dish of water. These motions include the spontaneous formation of labyrinthine stripes, the periodic pulsation leading to chaotic stretching and folding, and the formation of migrating slugs of coloring. We use this simple experiment to demonstrate that the formation of ordered macroscopic patterns is consistent with the requirement of the second law of Thermodynamics that microscopic disorder must increase. This system is suitable for undergraduate experimentation and can be modeled by advanced students in a straightforward finite difference simulation that reproduces the labyrinths and other patterns.

  19. 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.

  20. Surface mechanics mediate pattern formation in the developing retina.

    PubMed

    Hayashi, Takashi; Carthew, Richard W

    2004-10-01

    Pattern formation of biological structures involves organizing different types of cells into a spatial configuration. In this study, we investigate the physical basis of biological patterning of the Drosophila retina in vivo. We demonstrate that E- and N-cadherins mediate apical adhesion between retina epithelial cells. Differential expression of N-cadherin within a sub-group of retinal cells (cone cells) causes them to form an overall shape that minimizes their surface contact with surrounding cells. The cells within this group, in both normal and experimentally manipulated conditions, pack together in the same way as soap bubbles do. The shaping of the cone cell group and packing of its components precisely imitate the physical tendency for surfaces to be minimized. Thus, simple patterned expression of N-cadherin results in a complex spatial pattern of cells owing to cellular surface mechanics. PMID:15470418

  1. 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

  2. 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

  3. 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

  4. 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.

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

    PubMed Central

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

    2015-01-01

    Abstract 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

  6. Rotations and pattern formation in granular materials under loading

    NASA Astrophysics Data System (ADS)

    Pasternak, Elena; Dyskin, Arcady V.; Esin, Maxim; Hassan, Ghulam M.; MacNish, Cara

    2015-10-01

    Shear band formation and evolution is a predominant mechanism of deformation patterning in granular materials. Independent rotations of separate particles can affect the pattern formation by adding the effect of rotational degrees of freedom to the mechanism of instability. We conducted 2D physical modelling where the particles are represented by smooth steel discs. We use the digital image correlation in order to recover both displacement and independent rotation fields in the model. We performed model calibration and determine the values of mechanical parameters needed for a DEM numerical modelling. Both mono- and polydisperse particle assemblies are used. During the loading, the deformation pattern undergoes stages of shear band formation followed by its dissolution due to recompaction and particle rearrangement with the subsequent formation of multiple shear bands merging into a single one and the final dissolution. We show that while the average (over the assembly) values of the angles of disc rotations are insignificantly different from zero, the particle rotations exhibit clustering at the mesoscale (sizes larger than the particles but smaller than the whole assembly): monodisperse assemblies produce vertical columns of particles rotating the same direction; polydisperse assemblies 2D form clusters of particles with alternating rotations. Thus, particle rotations produce a structure on their own, a structure different form the ones formed by particle displacements and force chains. This can give a rise to moment chains. These emerging mesoscopic structures - not observable at the macroscale - indicate hidden aspects of 'Cosserat behaviour' of the particles.

  7. 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.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Fast solvers for optimal control problems from pattern formation

    NASA Astrophysics Data System (ADS)

    Stoll, Martin; Pearson, John W.; Maini, Philip K.

    2016-01-01

    The modeling of pattern formation in biological systems using various models of reaction-diffusion type has been an active research topic for many years. We here look at a parameter identification (or PDE-constrained optimization) problem where the Schnakenberg and Gierer-Meinhardt equations, two well-known pattern formation models, form the constraints to an objective function. Our main focus is on the efficient solution of the associated nonlinear programming problems via a Lagrange-Newton scheme. In particular we focus on the fast and robust solution of the resulting large linear systems, which are of saddle point form. We illustrate this by considering several two- and three-dimensional setups for both models. Additionally, we discuss an image-driven formulation that allows us to identify parameters of the model to match an observed quantity obtained from an image.

  16. Formation of Interfacial Patterns in Aggregation and Viscous Flows

    NASA Astrophysics Data System (ADS)

    Vicsek, Tamás

    1987-01-01

    Computer simulations and experiments on viscous fingering are used to investigate the effects of fluctuations, driving force and anisotropy on the growth of two dimensional unstable interfaces. It is demonstrated that variations of the diffusion-limited aggregation model capture many of the most important features of Laplacian pattern formation. In the viscous fingering experiments carried out in a radial Hele-Shaw cell with nematic or smectic liquid crystals a number of unexpected morphological phase transitions can be observed including crossovers from tip splitting to dendritic growth and from fractal to homogeneous structures. The investigations reviewed here suggest that the role of noise, driving force and anisotropy is crucial in the formation of patterns and it is the complex interplay of these factors which produces the great variety of morphologies found in nature.

  17. 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

  18. 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

  19. 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

  20. Nonlinear dynamics of pattern formation and pattern recognition in the rabbit olfactory bulb

    NASA Astrophysics Data System (ADS)

    Baird, Bill

    1986-10-01

    A mathematical model of the process of pattern recognition in the first olfactory sensory cortex of the rabbit is presented. It explains the formation and alteration of spatial patterns in neural activity observed experimentally during classical Pavlovian conditioning. On each inspiration of the animal, a surge of receptor input enters the olfactory bulb. EEG activity recorded at the surface of the bulb undergoes a transition from a low amplitude background state of temporal disorder to coherent oscillation. There is a distinctive spatial pattern of rms amplitude in this oscillation which changes reliably to a second pattern during each successful recognition by the animal of a conditioned stimulus odor. When a new odor is paired as conditioned stimulus, these patterns are replaced by new patterns that stabilize as the animal adapts to the new environment. I will argue that a unification of the theories of pattern formation and associative memory is required to account for these observations. This is achieved in a model of the bulb as a discrete excitable medium with spatially inhomogeneous coupling expressed by a connection matrix. The theory of multiple Hopf bifurcations is employed to find coupled equations for the amplitudes of competing unstable oscillatory modes. These may be created in the system by proper coupling and selectively evoked by specific classes of inputs. This allows a view of limit cycle attractors as “stored” fixed points of a gradient vector field and thereby recovers the more familiar dynamical systems picture of associative memory.

  1. 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.

  2. 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.

  3. Modification of Blend Film Pattern Formation with Block Copolymer Additives

    NASA Astrophysics Data System (ADS)

    Sung, L.; Satija, S. K.; Karim, A.; Douglas, J. F.; Han, C. C.

    1997-03-01

    The kinetics of phase separation and morphology of polymer blend films of polystyrene(PS) and polybutadiene(PB) with and without diblock copolymer(PS-b-PB) is examined by optical and atomic force microscropy. The thicker PS/PB binary blend film (2000 Åexhibited essentially no surface pattern formation while spinodal decomposition-like patterns were exhibited by thinner films (<= 1000 ÅThis change is interpreted in terms of a suppression of surface-directed spinodal decomposition in the thinner films. A change in the coarsening kinetics was also observed in the thin films as the thickness was varied from 1000 Åto 200 Åand was interpreted as a crossover from three (bulk-like) to two-dimensional kinetics(Sung et al., Phys. Rev. Lett. 76), 4368 (1996).. The addition of diblock copolymer changed the characteristic dimension at which the surface patterning occurred and the surface pattern formation required thinner film. Neutron reflectivity measurements were carried out to study the density profile of diblcok copolymer on phase separation transverse to the silicon surface to understand this effect.

  4. 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.

  5. Evaluation of IVOCT imaging of coronary artery metallic stents with neointimal coverage.

    PubMed

    Elahi, Sahar; Ho, Derek; Feldman, Marc D; Dijkstra, Jouke; Milner, Thomas E

    2015-03-01

    Accuracy of IVOCT for measurement of neointimal thickness and effect of neointima in the appearance of metallic struts in IVOCT images was investigated. Phantom vessels were constructed and coronary stents were deployed and covered with thick (250-400 μm) and thin (30-70 μm) phantom neointima. High resolution Micro-CT images of the stent struts were recorded as a gold standard. IVOCT images of the phantom vessels were acquired with various luminal blood scattering strengths and measured neointimal thicknesses from IVOCT and Micro-CT images were compared. In transparent lumen, comparison of IVOCT and Micro-CT neointima thickness measurements found no significant difference (p > 0.05) in the thick neointima phantom but a significant difference (p < 0.05) in the thin neointima phantom. For both thick and thin neointima, IVOCT neointimal thickness measurements varied from Micro-CT values by as much as ±35%. Increased luminal scattering due to presence of blood at concentrations <5% did not interfere with measurement of thin neointimas and was validated by ANOVA analysis (p = 0.95). IV-OCT measurement of strut feature size with an overlying thin neointima match true values determined with Micro-CT (p = 0.82). Presence of a thick neointima resulted in lateral elongation or merry-go-rounding of stent strut features in IVOCT images. Phantom IVOCT images suggest that thick neointimal layers can result in more than 40 % lateral elongation of stent strut features. Simulated IVOCT images of metallic stent struts with varying neointimal thickness suggest that neointimal light scattering can introduce the merry-go-round effect. PMID:25395364

  6. 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

  7. Evaluation of IVOCT imaging of coronary artery metallic stents with neointimal coverage.

    PubMed

    Elahi, Sahar; Ho, Derek; Feldman, Marc D; Dijkstra, Jouke; Milner, Thomas E

    2015-03-01

    Accuracy of IVOCT for measurement of neointimal thickness and effect of neointima in the appearance of metallic struts in IVOCT images was investigated. Phantom vessels were constructed and coronary stents were deployed and covered with thick (250-400 μm) and thin (30-70 μm) phantom neointima. High resolution Micro-CT images of the stent struts were recorded as a gold standard. IVOCT images of the phantom vessels were acquired with various luminal blood scattering strengths and measured neointimal thicknesses from IVOCT and Micro-CT images were compared. In transparent lumen, comparison of IVOCT and Micro-CT neointima thickness measurements found no significant difference (p > 0.05) in the thick neointima phantom but a significant difference (p < 0.05) in the thin neointima phantom. For both thick and thin neointima, IVOCT neointimal thickness measurements varied from Micro-CT values by as much as ±35%. Increased luminal scattering due to presence of blood at concentrations <5% did not interfere with measurement of thin neointimas and was validated by ANOVA analysis (p = 0.95). IV-OCT measurement of strut feature size with an overlying thin neointima match true values determined with Micro-CT (p = 0.82). Presence of a thick neointima resulted in lateral elongation or merry-go-rounding of stent strut features in IVOCT images. Phantom IVOCT images suggest that thick neointimal layers can result in more than 40 % lateral elongation of stent strut features. Simulated IVOCT images of metallic stent struts with varying neointimal thickness suggest that neointimal light scattering can introduce the merry-go-round effect.

  8. 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

  9. 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.

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

    PubMed

    Dumais, J; Harrison, L G

    2000-02-29

    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.

  11. Singular Solutions and Pattern Formation in Aggregation Equations

    NASA Astrophysics Data System (ADS)

    Sun, Hui

    In this work, we study singular solutions and pattern formation in aggregation equations and more general active scalar problems. We derive a generalization of the Birkhoff-Rott equation to the case of active scalar problems with both gradient and divergence free structures. We present numerical simulations of this model demonstrating how the gradient part and the divergence free part of K influence each other and cause some nonlinear effects. Examples include superfluids, classical fluids and swarming models. The rest of this thesis focuses on aggregation models with gradient flow structure. The discrete version of the continuum aggregation equation is the kinematic equation x˙i = -mi sumj≠i ▿ U(|xi - x j|), ∀ 1 ≤ i ≤ N. For both discrete and continuum versions, we use linear stability analysis of a ring equilibrium to classify the morphology of patterns in two dimensions. Conditions are identified that assure the linear well-posedness of the ring. In addition, weakly nonlinear theory and numerical simulations demonstrate how a ring can bifurcate to more complex equilibria. Moreover, linear stability analysis of clusters equilibrium patterns are also investigated in both two-dimensional and higher-dimensional cases. We then apply our stability results of ring patterns and clusters patterns to a family of exact collapsing similarity solutions to the aggregation equation with pairwise potential U(r) = rgamma/gamma. It was previously observed that radially symmetric solutions are attracted to a self-similar collapsing shell profile in infinite time for gamma > 2 in all dimensions. The stability analysis for ring patterns and clusters patterns shows that the collapsing shell solution is stable for 2 < gamma < 4, while always unstable and destabilizes into clusters that form a simplex for gamma > 4. This holds in all spatial dimensions.

  12. Inhibition of allograft inflammatory factor-1 expression reduces development of neointimal hyperplasia and p38 kinase activity

    PubMed Central

    Sommerville, Laura J.; Xing, Chen; Kelemen, Sheri E.; Eguchi, Satoru; Autieri, Michael V.

    2009-01-01

    Aims Allograft inflammatory factor-1 (AIF-1) is a calcium-binding, scaffold-signalling protein expressed in vascular smooth muscle cells (VSMCs) in response to injury. The effects of AIF-1 attenuation on development of intimal hyperplasia are unknown, and the molecular mechanisms of these effects remain uncharacterized. The goals of the present study were to determine whether AIF-1 knockdown reduced VSMC proliferation, migration, and intimal hyperplasia, and determine AIF-1 effects on signal transduction in VSMCs. Methods and results Balloon angioplasty-injured rat carotid arteries transduced with adenovirus to overexpress AIF-1 (AdAIF-1) significantly increased, and adenovirus to knock down AIF-1 (AdsiRNA) expression significantly decreased neointimal formation compared with green fluorescent protein (AdGFP) and Adscrambled controls (P < 0.05 and P < 0.01, n = 6). Primary rat VSMCs transduced with AdAIF-1 displayed a significant increase in proliferation, and AdsiRNA-transduced VSMCs proliferated significantly more slowly than controls (P < 0.05). VSMCs transduced with AdAIF-1 show increased migration when compared with control VSMCs (P < 0.01). Rat VSMCs transduced with AdAIF-1 showed constitutive and prolonged activation of the mitogen-activated protein kinase p38, whereas AdsiRNA-treated VSMCs showed decreased p38 activation compared with AdGFP (P < 0.05). Immunohistochemical analysis of AdAIF-1-transduced carotid arteries showed increased staining with a phospho-specific p38 antibody compared with AdGFP-transduced arteries. A specific p38 inhibitor abrogated AIF-1-induced VSMC proliferation, but not AIF-1-induced migration. Conclusion Taken together, AIF-1 expression plays a key role in the development of neointimal hyperplasia. AIF-1 expression enhances the activation of p38 MAP kinase. AIF-1-enhanced proliferation is p38 kinase dependent, but AIF-1-enhanced VSMC migration is p38 independent. PMID:18779232

  13. Succinobucol-Eluting Stents Increase Neointimal Thickening and Peri-Strut Inflammation in a Porcine Coronary Model

    PubMed Central

    Watt, Jonathan; Kennedy, Simon; McCormick, Christopher; Agbani, Ejaife O; McPhaden, Allan; Mullen, Alexander; Czudaj, Peter; Behnisch, Boris; Wadsworth, Roger M; Oldroyd, Keith G

    2013-01-01

    Objective The aim of this study was to assess the efficacy of stent-based delivery of succinobucol alone and in combination with rapamycin in a porcine coronary model. Background: Current drugs and polymers used to coat coronary stents remain suboptimal in terms of long term efficacy and safety. Succinobucol is a novel derivative of probucol with improved antioxidant and anti-inflammatory properties. Methods Polymer-free Yukon stents were coated with 1% succinobucol (SucES), 2% rapamycin (RES), or 1% succinobucol plus 2% rapamycin solutions (SucRES) and compared with a bare metal stent (BMS). Results The in vivo release profile of SucES indicated drug release up to 28 days (60% drug released at 7 days); 41 stents (BMS, n = 11; SucES, n =10; RES, n = 10; SucRES, n = 10) were implanted in the coronary arteries of 17 pigs. After 28 days, mean neointimal thickness was 0.31 ± 0.14 mm for BMS, 0.51 ± 0.14 mm for SucES, 0.19 ± 0.11 mm for RES, and 0.36 ± 0.17 mm for SucRES (P < 0.05 for SucES vs. BMS). SucES increased inflammation and fibrin deposition compared with BMS (P < 0.05), whereas RES reduced inflammation compared with BMS (P < 0.05). Conclusion In this model, stent-based delivery of 1% succinobucol using a polymer-free stent platform increased neointimal formation and inflammation following coronary stenting. © 2012 Wiley Periodicals, Inc. PMID:22581717

  14. 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.

  15. 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.

  16. Evolutionary aspects of pattern formation during clitellate muscle development.

    PubMed

    Bergter, Annette; Hunnekuhl, Vera S; Schniederjans, Monika; Paululat, Achim

    2007-01-01

    As a taxon of the lophotrochozoans, annelids have re-entered scientific investigations focusing on plesiomorphic bilaterian features and the evolutionary changes therein. The view of a clitellate-like plesiomorphic muscle arrangement in annelids has been challenged by recent investigations of polychaete muscle organization. However, there are few investigations of muscle formation in clitellate species that address this problem. Direct comparison of potential homologous muscles between these annelid groups is thus hampered. Somatic muscle formation during embryogenesis of two clitellates-the oligochaete Limnodrilus sp. and the hirudinean Erpobdella octoculata-occurs by distinct processes in each species, even though they share a closed outer layer of circular and an inner layer of longitudinal muscles characteristic of clitellates. In E. octoculata, the first emerging longitudinal muscles are distributed irregularly on the body surface of the embryo whereas the circular muscles appear in an orderly repetitive pattern along the anterioposterior axis. Both primary muscle types consist of fiber-bundles that branch at both their ends. This way the circular muscle bundles divide into a fine muscle-grid. The primary longitudinal muscles are incorporated into a second type of longitudinal muscles, the latter starting to differentiate adjacent to the ventral nerve cord. Those secondary muscles emerge in a ventral to dorsal manner, enclosing the embryo of E. octoculata. In Limnodrilus sp., one dorsal and one ventral bilateral pair of primary longitudinal muscles are established initially, elongating toward posterior. Initial circular muscles are emerging in a segmental pattern. Both muscle layers are completed later in development by the addition of secondary longitudinal and circular muscles. Some features of embryonic longitudinal muscle patterns in Limnodrilus sp. are comparable to structures found in adult polychaete muscle systems. Our findings show that comparative

  17. Pattern Formation by Electrostatic Self-Organization of Membrane Proteins

    NASA Astrophysics Data System (ADS)

    Boedec, G.; Jaeger, M.; Homble, F.; Leonetti, M.

    2012-07-01

    The electric activity of biological cells and organs such as heart for example is at the origin of various phenomena of pattern formation. The electric membrane potential appears as the order parameter to characterize these spatiotemporal dynamics. A kind of patterns is characterized by a stationary spatial modulation of membrane potential along the cell, breaking a symmetry of the system. They are associated to transcellular currents. A mechanism proposed in literature is based on the coupling of the electric current produced by membrane proteins and their electrophoretic mobilities. Beyond its classical linear stability analysis, the numerical and theoretical analysis of this model offers a variety of spatiotemporal dynamics. Firstly, the background in the modelization of electric phenomena is recalled. Secondly, the analysis is focused on two nonlinear dynamics.

  18. 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.

  19. The role of auxin signaling in early embryo pattern formation.

    PubMed

    Smit, Margot E; Weijers, Dolf

    2015-12-01

    Pattern formation of the early Arabidopsis embryo generates precursors to all major cell types, and is profoundly controlled by the signaling molecule auxin. Here we discuss recent milestones in our understanding of auxin-dependent embryo patterning. Auxin biosynthesis, transport and response mechanisms interact to generate local auxin accumulation in the early embryo. New auxin-dependent reporters help identifying these sites, while atomic structures of transcriptional response mediators help explain the diverse outputs of auxin signaling. Key auxin outputs are control of cell identity and cell division orientation, and progress has been made towards understanding the cellular basis of each. Importantly, a number of studies have combined computational modeling and experiments to analyze the developmental role, genetic circuitry and molecular mechanisms of auxin-dependent cell division control.

  20. 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.

  1. 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

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Pattern formation during mixing and segregation of flowing granular materials

    NASA Astrophysics Data System (ADS)

    Metcalfe, Guy; Shattuck, Mark

    1996-02-01

    Powder mixing plays an important role in a number of industries ranging from pharmaceuticals and food to ceramics and mining. Avalanches provide a mechanism for the stretching and folding needed to mix granular solids. However, unlike fluids, when particles dissimilar in size, density, or shape flow, they can spontaneously demix or segregate. Using magnetic resonance imaging, we track the transport of granular solids in a slowly rotating tube both with and without segregation effects. Compared with experiments in a 2-dimensional rotating disk partially filled with colored particles, the mixing kinematics and the granular pattern formation in a tube are changed by an axial flow instability. From simple physical principles we argue how size and density segregation mechanisms can be made to cancel, allowing good mixing of dissimilar particles, and we show experiments verifying this. Further experiments isolate the axial transport in the slowly rotating tube. Axial transport can appear faster with segregation than without.

  14. 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

  15. Mixing dynamics and pattern formation around flow stagnation points

    NASA Astrophysics Data System (ADS)

    Hidalgo, Juan J.; Dentz, Marco

    2016-04-01

    We study the mixing of two reactive fluids in the presence of convective instabilities. Such system is characterized by the formation of unique porosity patterns and mixing dynamics linked to the evolution of vortices and stagnation points. Around them, the fluid-fluid interface is stretched and compressed, which enhances mixing and triggers chemical reactions, and the system can be analyzed using fluid deformation model. We consider velocity fields generated by a double gyre synthetic velocity field and Rayleigh-Bénard and Rayleigh-Taylor instabilities. The different flow structures can be visualized by the strain rate and the finite time Lyapunov exponents. We show that the mixing enhancement given by the scalar dissipation rate is controlled by the equilibrium between interface compression and diffusion, which depends on the velocity field configuration. Furthermore, we establish a quantitative relation between the mixing rate and the evolution of the potential energy of the fluid when convection is driven by density instabilities.

  16. Stochastic Simulations of Pattern Formation in Excitable Media

    PubMed Central

    Vigelius, Matthias; Meyer, Bernd

    2012-01-01

    We present a method for mesoscopic, dynamic Monte Carlo simulations of pattern formation in excitable reaction–diffusion systems. Using a two-level parallelization approach, our simulations cover the whole range of the parameter space, from the noise-dominated low-particle number regime to the quasi-deterministic high-particle number limit. Three qualitatively different case studies are performed that stand exemplary for the wide variety of excitable systems. We present mesoscopic stochastic simulations of the Gray-Scott model, of a simplified model for intracellular Ca oscillations and, for the first time, of the Oregonator model. We achieve simulations with up to particles. The software and the model files are freely available and researchers can use the models to reproduce our results or adapt and refine them for further exploration. PMID:22900025

  17. 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.

  18. Spontaneous pattern formation and pinning in the visual cortex

    NASA Astrophysics Data System (ADS)

    Baker, Tanya I.

    Bifurcation theory and perturbation theory can be combined with a knowledge of the underlying circuitry of the visual cortex to produce an elegant story explaining the phenomenon of visual hallucinations. A key insight is the application of an important set of ideas concerning spontaneous pattern formation introduced by Turing in 1952. The basic mechanism is a diffusion driven linear instability favoring a particular wavelength that determines the size of the ensuing stripe or spot periodicity of the emerging spatial pattern. Competition between short range excitation and longer range inhibition in the connectivity profile of cortical neurons provides the difference in diffusion length scales necessary for the Turing mechanism to occur and has been proven by Ermentrout and Cowan to be sufficient to explain the generation of a subset of reported geometric hallucinations. Incorporating further details of the cortical circuitry, namely that neurons are also weakly connected to other neurons sharing a particular stimulus orientation or spatial frequency preference at even longer ranges and the resulting shift-twist symmetry of the neuronal connectivity, improves the story. We expand this approach in order to be able to include the tuned responses of cortical neurons to additional visual stimulus features such as motion, color and disparity. We apply a study of nonlinear dynamics similar to the analysis of wave propagation in a crystalline lattice to demonstrate how a spatial pattern formed through the Turing instability can be pinned to the geometric layout of various feature preferences. The perturbation analysis is analogous to solving the Schrodinger equation in a weak periodic potential. Competition between the local isotropic connections which produce patterns of activity via the Turing mechanism and the weaker patchy lateral connections that depend on a neuron's particular set of feature preferences create long wavelength affects analogous to commensurate

  19. 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.

  20. 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.

  1. 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

  2. Cleavage pattern and mesentoblast formation in Acanthochiton crinitus (Polyplacophora, Mollusca).

    PubMed

    van den Biggelaar, J A

    1996-03-15

    In characteristic spiralian embryos the mesentoblast is the stem cell of the mesodermal bands. It is a derivative of the dorsal quadrant. At least in gastropod molluscs, the ancestral form for the specification of the dorsal quadrant out of four initially equal quadrants is by centralization of one of the four macromeres after the separation of the presumptive ecto- and entoblast cells. Then this macromere is induced by the animal micromeres to produce the mesentoblast. In this paper it is shown that in the embryo of the polyplacophoran Acanthochiton crinitus, specification of the dorsal quadrant and formation of the mesentoblast exactly follow the same pattern. After deletion of the first quartet of micromeres none of the macromeres is centralized, no mesentoblast is formed, and the embryo remains radially symmetrical. Apparently, the mechanism for the specification of the dorsal quadrant and the formation of the mesentoblast has been conserved during the evolution of the main molluscan taxa. It has been discussed whether this mechanism might be a plesiomorphous property, characteristic of less derived spiralian phyla.

  3. 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.

  4. Cleavage pattern and mesentoblast formation in Acanthochiton crinitus (Polyplacophora, Mollusca).

    PubMed

    van den Biggelaar, J A

    1996-03-15

    In characteristic spiralian embryos the mesentoblast is the stem cell of the mesodermal bands. It is a derivative of the dorsal quadrant. At least in gastropod molluscs, the ancestral form for the specification of the dorsal quadrant out of four initially equal quadrants is by centralization of one of the four macromeres after the separation of the presumptive ecto- and entoblast cells. Then this macromere is induced by the animal micromeres to produce the mesentoblast. In this paper it is shown that in the embryo of the polyplacophoran Acanthochiton crinitus, specification of the dorsal quadrant and formation of the mesentoblast exactly follow the same pattern. After deletion of the first quartet of micromeres none of the macromeres is centralized, no mesentoblast is formed, and the embryo remains radially symmetrical. Apparently, the mechanism for the specification of the dorsal quadrant and the formation of the mesentoblast has been conserved during the evolution of the main molluscan taxa. It has been discussed whether this mechanism might be a plesiomorphous property, characteristic of less derived spiralian phyla. PMID:8631512

  5. Reptile scale paradigm: Evo-Devo, pattern formation and regeneration.

    PubMed

    Chang, Cheng; Wu, Ping; Baker, Ruth E; Maini, Philip K; Alibardi, Lorenzo; Chuong, Cheng-Ming

    2009-01-01

    The purpose of this perspective is to highlight the merit of the reptile integument as an experimental model. Reptiles represent the first amniotes. From stem reptiles, extant reptiles, birds and mammals have evolved. Mammal hairs and feathers evolved from Therapsid and Sauropsid reptiles, respectively. The early reptilian integument had to adapt to the challenges of terrestrial life, developing a multi-layered stratum corneum capable of barrier function and ultraviolet protection. For better mechanical protection, diverse reptilian scale types have evolved. The evolution of endothermy has driven the convergent evolution of hair and feather follicles: both form multiple localized growth units with stem cells and transient amplifying cells protected in the proximal follicle. This topological arrangement allows them to elongate, molt and regenerate without structural constraints. Another unique feature of reptile skin is the exquisite arrangement of scales and pigment patterns, making them testable models for mechanisms of pattern formation. Since they face the constant threat of damage on land, different strategies were developed to accommodate skin homeostasis and regeneration. Temporally, they can be under continuous renewal or sloughing cycles. Spatially, they can be diffuse or form discrete localized growth units (follicles). To understand how gene regulatory networks evolved to produce increasingly complex ectodermal organs, we have to study how prototypic scale-forming pathways in reptiles are modulated to produce appendage novelties. Despite the fact that there are numerous studies of reptile scales, molecular analyses have lagged behind. Here, we underscore how further development of this novel experimental model will be valuable in filling the gaps of our understanding of the Evo-Devo of amniote integuments.

  6. Reptile scale paradigm: Evo-Devo, pattern formation and regeneration

    PubMed Central

    Chang, Cheng; Wu, Ping; Baker, Ruth E.; Maini, Philip K.; Alibardi, Lorenzo; Chuong, Cheng-Ming

    2010-01-01

    The purpose of this perspective is to highlight the merit of the reptile integument as an experimental model. Reptiles represent the first amniotes. From stem reptiles, extant reptiles, birds and mammals have evolved. Mammal hairs and feathers evolved from Therapsid and Sauropsid reptiles, respectively. The early reptilian integument had to adapt to the challenges of terrestrial life, developing a multi-layered stratum corneum capable of barrier function and ultraviolet protection. For better mechanical protection, diverse reptilian scale types have evolved. The evolution of endothermy has driven the convergent evolution of hair and feather follicles: both form multiple localized growth units with stem cells and transient amplifying cells protected in the proximal follicle. This topological arrangement allows them to elongate, molt and regenerate without structural constraints. Another unique feature of reptile skin is the exquisite arrangement of scales and pigment patterns, making them testable models for mechanisms of pattern formation. Since they face the constant threat of damage on land, different strategies were developed to accommodate skin homeostasis and regeneration. Temporally, they can be under continuous renewal or sloughing cycles. Spatially, they can be diffuse or form discrete localized growth units (follicles). To understand how gene regulatory networks evolved to produce increasingly complex ectodermal organs, we have to study how prototypic scale-forming pathways in reptiles are modulated to produce appendage novelties. Despite the fact that there are numerous studies of reptile scales, molecular analyses have lagged behind. Here, we underscore how further development of this novel experimental model will be valuable in filling the gaps of our understanding of the Evo-Devo of amniote integuments. PMID:19557687

  7. Patterns of Glide Formation in Niger-Congo: An Optimality Account.

    ERIC Educational Resources Information Center

    Casali, Roderic F.

    A study examined the pattern of formation of glides in a sample of 18 Niger-Congo languages that have substantial glide formation. It is noted first that four basic pattern dualities exist, with language-specific variations, determine by whether or not: (1) glide formation applies to both front and round first vowels or round first vowels only;…

  8. 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.

  9. Scaling and pattern formation in condensed matter systems

    NASA Astrophysics Data System (ADS)

    Chan, Pak Yuen

    In this dissertation, I present analytical and numerical work regarding the scaling behavior of three physical systems. I begin by analyzing the scaling behavior of Griffiths ferromagnets near the Griffiths-paramagnetic transition point. By deriving the asymptotic behavior of the magnetization of the system using an ansatz for the Yang-Lee zero density, I find that the scaling behavior of Griffiths ferromagnet is dominated by an essential singularity in the external magnetic field. Excellent agreement is found by comparing this prediction to the experimental data on La 0.7Ca0.3MnO3, from which I also extract the critical exponents. Next I report on a mathematical framework to describe landscape formation due to carbonate precipitation near geothermal hot springs. I derive analytically the shape and stability of the spherically symmetric domes. The solution agrees with field observations and simulation results. In addition, I apply a similar conceptual framework to study the formation and stability of stalactites in limestone caves. The shape of stalactites is calculated and the solution is found to be unconditionally stable, as opposite to the unstable dome solutions. By studying the linear stability of a uniform sheet of fluid flowing down a constant slope, moreover, I show that our theory gives results that are consistent with the scale-free terraced landscapes observed. Finally, I study multiscale patterns in polycrystalline materials, with the phase field crystal (PFC) model. I first show that the complex amplitudes representation incorporates the correct form of nonlinear elasticity. I then analyze the plastic properties of the model by applying a shearing force. Dislocation avalanches, which resembling the scaling behavior in driven ferromagnetic, are observed. Critical exponents are extracted from power laws extending over 5 decades. I extend the PFC model to accommodate actual atomic configurations and vacancies. I use the extended PFC model to simulate a

  10. 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.

  11. A small molecule PAI-1 functional inhibitor attenuates neointimal hyperplasia and vascular smooth muscle cell survival by promoting PAI-1 cleavage.

    PubMed

    Simone, Tessa M; Higgins, Stephen P; Archambeault, Jaclyn; Higgins, Craig E; Ginnan, Roman G; Singer, Harold; Higgins, Paul J

    2015-05-01

    Plasminogen activator inhibitor-1 (PAI-1), the primary inhibitor of urokinase-and tissue-type plasminogen activators (uPA and tPA), is an injury-response gene implicated in the development of tissue fibrosis and cardiovascular disease. PAI-1 mRNA and protein levels were elevated in the balloon catheter-injured carotid and in the vascular smooth muscle cell (VSMC)-enriched neointima of ligated arteries. PAI-1/uPA complex formation and PAI-1 antiproteolytic activity can be inhibited, via proteolytic cleavage, by the small molecule antagonist tiplaxtinin which effectively increased the VSMC apoptotic index in vitro and attenuated carotid artery neointimal formation in vivo. In contrast to the active full-length serine protease inhibitor (SERPIN), elastase-cleaved PAI-1 (similar to tiplaxtinin) also promoted VSMC apoptosis in vitro and similarly reduced neointimal formation in vivo. The mechanism through which cleaved PAI-1 (CL-PAI-1) stimulates apoptosis appears to involve the TNF-α family member TWEAK (TNF-α weak inducer of apoptosis) and it's cognate receptor, fibroblast growth factor (FGF)-inducible 14 (FN14). CL-PAI-1 sensitizes cells to TWEAK-stimulated apoptosis while full-length PAI-1 did not, presumably due to its ability to down-regulate FN14 in a low density lipoprotein receptor-related protein 1 (LRP1)-dependent mechanism. It appears that prolonged exposure of VSMCs to CL-PAI-1 induces apoptosis by augmenting TWEAK/FN14 pro-apoptotic signaling. This work identifies a critical, anti-stenotic, role for a functionally-inactive (at least with regard to its protease inhibitory function) cleaved SERPIN. Therapies that promote the conversion of full-length to cleaved PAI-1 may have translational implications.

  12. Improving arteriovenous fistula patency: Transdermal delivery of diclofenac reduces cannulation-dependent neointimal hyperplasia via AMPK activation

    PubMed Central

    MacAskill, Mark G.; Watson, David G.; Ewart, Marie-Ann; Wadsworth, Roger; Jackson, Andrew; Aitken, Emma; MacKenzie, Graeme; Kingsmore, David; Currie, Susan; Coats, Paul

    2015-01-01

    Creation of an autologous arteriovenous fistula (AVF) for vascular access in haemodialysis is the modality of choice. However neointimal hyperplasia and loss of the luminal compartment result in AVF patency rates of ~ 60% at 12 months. The exact cause of neointimal hyperplasia in the AVF is poorly understood. Vascular trauma has long been associated with hyperplasia. With this in mind in our rabbit model of AVF we simulated cannulation autologous to that undertaken in vascular access procedures and observed significant neointimal hyperplasia as a direct consequence of cannulation. The neointimal hyperplasia was completely inhibited by topical transdermal delivery of the non-steroidal anti-inflammatory (NSAID) diclofenac. In addition to the well documented anti-inflammatory properties we have identified novel anti-proliferative mechanisms demonstrating diclofenac increases AMPK-dependent signalling and reduced expression of the cell cycle protein cyclin D1. In summary prophylactic transdermal delivery of diclofenac to the sight of AVF cannulation prevents adverse neointimal hyperplasic remodelling and potentially offers a novel treatment option that may help prolong AVF patency and flow rates. PMID:25866325

  13. Hydrodynamic coarsening in striped pattern formation with a conservation law.

    PubMed

    Shiwa, Y

    2005-07-01

    We observed in numerical simulations that the interaction of striped-pattern-forming instability and a neutrally stable zero mode induces patterns of domains of upflow hexagons coexisting with domains of downflow hexagons. They appear only when hydrodynamic flow is present.

  14. 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

  15. 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.

  16. Pattern formation: a focus on notch in butterfly eyespots.

    PubMed

    French, Vernon; Brakefield, Paul M

    2004-08-24

    New observations of early and dynamic expression of Notch in developing lepidopteran wings suggests that this signalling pathway may function in defining the central focus that will specify the butterfly eyespot colour pattern. PMID:15324685

  17. Pattern formation: a focus on notch in butterfly eyespots.

    PubMed

    French, Vernon; Brakefield, Paul M

    2004-08-24

    New observations of early and dynamic expression of Notch in developing lepidopteran wings suggests that this signalling pathway may function in defining the central focus that will specify the butterfly eyespot colour pattern.

  18. 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.

  19. The role of hydrological transience in peatland pattern formation

    NASA Astrophysics Data System (ADS)

    Morris, P. J.; Baird, A. J.; Belyea, L. R.

    2013-10-01

    The sloping flanks of peatlands are commonly patterned with non-random, contour-parallel stripes of distinct micro-habitats such as hummocks, lawns and hollows. Patterning seems to be governed by feedbacks among peatland hydrological processes, plant micro-succession, plant litter production and peat decomposition. An improved understanding of peatland patterning may provide important insights into broader aspects of the long-term development of peatlands and their likely response to future climate change. We recreated a cellular simulation model from the literature, as well as three subtle variants of the model, to explore the controls on peatland patterning. Our models each consist of three submodels, which simulate: peatland water tables in a gridded landscape, micro-habitat dynamics in response to water-table depths, and changes in peat hydraulic properties. We found that the strength and nature of simulated patterning was highly dependent on the degree to which water tables had reached a steady state in response to hydrological inputs. Contrary to previous studies, we found that under a true steady state the models predict largely unpatterned landscapes that cycle rapidly between contrasting dry and wet states, dominated by hummocks and hollows, respectively. Realistic patterning only developed when simulated water tables were still transient. Literal interpretation of the degree of hydrological transience required for patterning suggests that the model should be discarded; however, the transient water tables appear to have inadvertently replicated an ecological memory effect that may be important to peatland patterning. Recently buried peat layers may remain hydrologically active despite no longer reflecting current vegetation patterns, thereby highlighting the potential importance of three-dimensional structural complexity in peatlands to understanding the two-dimensional surface-patterning phenomenon. The models were highly sensitive to the assumed values

  20. Modular genetic regulatory networks increase organization during pattern formation.

    PubMed

    Mohamadlou, Hamid; Podgorski, Gregory J; Flann, Nicholas S

    2016-08-01

    Studies have shown that genetic regulatory networks (GRNs) consist of modules that are densely connected subnetworks that function quasi-autonomously. Modules may be recognized motifs that comprise of two or three genes with particular regulatory functions and connectivity or be purely structural and identified through connection density. It is unclear what evolutionary and developmental advantages modular structure and in particular motifs provide that have led to this enrichment. This study seeks to understand how modules within developmental GRNs influence the complexity of multicellular patterns that emerge from the dynamics of the regulatory networks. We apply an algorithmic complexity to measure the organization of the patterns. A computational study was performed by creating Boolean intracellular networks within a simulated epithelial field of embryonic cells, where each cell contains the same network and communicates with adjacent cells using contact-mediated signaling. Intracellular networks with random connectivity were compared to those with modular connectivity and with motifs. Results show that modularity effects network dynamics and pattern organization significantly. In particular: (1) modular connectivity alone increases complexity in network dynamics and patterns; (2) bistable switch motifs simplify both the pattern and network dynamics; (3) all other motifs with feedback loops increase multicellular pattern complexity while simplifying the network dynamics; (4) negative feedback loops affect the dynamics complexity more significantly than positive feedback loops.

  1. 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

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

    NASA Astrophysics Data System (ADS)

    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 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.

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. Turing's model for biological pattern formation and the robustness problem

    PubMed Central

    Maini, Philip K.; Woolley, Thomas E.; Baker, Ruth E.; Gaffney, Eamonn A.; Lee, S. Seirin

    2012-01-01

    One of the fundamental questions in developmental biology is how the vast range of pattern and structure we observe in nature emerges from an almost uniformly homogeneous fertilized egg. In particular, the mechanisms by which biological systems maintain robustness, despite being subject to numerous sources of noise, are shrouded in mystery. Postulating plausible theoretical models of biological heterogeneity is not only difficult, but it is also further complicated by the problem of generating robustness, i.e. once we can generate a pattern, how do we ensure that this pattern is consistently reproducible in the face of perturbations to the domain, reaction time scale, boundary conditions and so forth. In this paper, not only do we review the basic properties of Turing's theory, we highlight the successes and pitfalls of using it as a model for biological systems, and discuss emerging developments in the area. PMID:23919129

  8. 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

  9. 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

  10. Resonant Chemical Oscillations: Pattern Formation in Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Lin, Anna L.

    2003-03-01

    Using the Belousov-Zhabotinsky (BZ) chemical system we explore the resonant response of spatially-extended oscillatory and excitable media to periodic perturbation. Resonance in excitable media is particularly relevant to biological systems, where excitable dynamics (threshold response to stimulus and refractoriness) are common. Methods to quantify spatio-temporal patterns will be discussed and the resonant patterns in excitable and oscillatory media will be compared. Experimental observations are compared to the results from numerical simulations of the Brusselator and FitzHugh-Nagumo models and from a forced complex Ginzburg-Landau amplitude equation.

  11. [Determination of type and spatial pattern formation of flower organs: dynamic model of development].

    PubMed

    Skriabin, K G; Alekseev, D V; Ezhova, T A; Kozlov, V N; Kudriavtsev, V B; Nosov, M V; Penin, A A; Chub, V V; Shestakov, S V; Shul'ga, O A

    2006-01-01

    The mathematical model imitating floral organ spatial pattern formation (positioning) was developed. Computer experiments performed on its basis demonstrated that organ spatial pattern formation in typical crucifer flower occurred in successive order: medial sepals, carpels, lateral sepals, long stamens, petals and short stamens. The positioning was advanced in two directions, acropetally in the perianth and basipetally in the stamens and carpels. The organ type specifying and positioning take place non-simultaneously in different floral areas. The organ type specifying passed ahead of organ primordial spatial pattern formation. The modeling of flower development of several mutants demonstrated that arabidopsis genes AP2 and AG in addition to specifying floral organ types also determine the particular zones in the floral meristem for futur organ development. The AG gene controls the formation of basipetal patterning zones where the reproductive organs develop, AP2 maintains the proliferative activity in the floral meristem that form acropetal patterning zones where perianth organ develop.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. On Pattern Formation Mechanisms for Lepidopteran Wing Patterns and Mammalian Coat Markings

    NASA Astrophysics Data System (ADS)

    Murray, J. D.

    1981-10-01

    The patterns on wings of Lepidoptera can be generated with a few pattern elements, but no mechanism has been suggested for producing them. I consider two of the basic patterns, namely, central symmetry and dependent patterns. A biochemically plausible model mechanism is proposed for generating major aspects of these patterns, based on a diffusing morphogen that activates a gene or colour-specific enzyme in a threshold manner to generate a stable heterogeneous spatial pattern. The model is applied to the determination stream hypothesis of Kuhn & von Engelhardt (Wilhelm Roux Arch. Entw Mech. Org. 130, 660 (1933)), and results from the model compared with their microcautery experiments on the pupal wing of Ephestia kuhniella. In the case of dependent patterns, results are compared with patterns on specific Papilionidae. For the same mechanism and a fixed set of parameters I demonstrate the important roles of geometry and scale on the spatial patterns obtained. The results and evidence presented here suggest the existence of diffusion fields of the order of several millimetres, which are very much larger than most embryonic fields. The existence of zones of polarizing activity is also indicated. Colour patterns on animals are considered to be genetically determined, but the mechanism is not known. I have previously suggested that a single mechanism that can exhibit an infinite variety of patterns is a candidate for that mechanism, and proposed that a reaction-diffusion system that can be diffusively driven unstable could be responsible for the laying down of the spacing patterns that generates the prepattern for animal coat markings. For illustrative purposes I consider a practical reaction mechanism, which exhibits substrate inhibition, and show that the geometry and scale of the domain (part of the epidermis) play a crucial role in the structural patterns that result. Patterns are obtained for a selection of geometries, and general features are related to the coat

  19. 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

  20. 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

  1. A simplified memory network model based on pattern formations

    NASA Astrophysics Data System (ADS)

    Xu, Kesheng; Zhang, Xiyun; Wang, Chaoqing; Liu, Zonghua

    2014-12-01

    Many experiments have evidenced the transition with different time scales from short-term memory (STM) to long-term memory (LTM) in mammalian brains, while its theoretical understanding is still under debate. To understand its underlying mechanism, it has recently been shown that it is possible to have a long-period rhythmic synchronous firing in a scale-free network, provided the existence of both the high-degree hubs and the loops formed by low-degree nodes. We here present a simplified memory network model to show that the self-sustained synchronous firing can be observed even without these two necessary conditions. This simplified network consists of two loops of coupled excitable neurons with different synaptic conductance and with one node being the sensory neuron to receive an external stimulus signal. This model can be further used to show how the diversity of firing patterns can be selectively formed by varying the signal frequency, duration of the stimulus and network topology, which corresponds to the patterns of STM and LTM with different time scales. A theoretical analysis is presented to explain the underlying mechanism of firing patterns.

  2. 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''.

  3. 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.

  4. Vegetation pattern formation due to interactions between water availability and toxicity in plant-soil feedback.

    PubMed

    Marasco, Addolorata; Iuorio, Annalisa; Cartení, Fabrizio; Bonanomi, Giuliano; Tartakovsky, Daniel M; Mazzoleni, Stefano; Giannino, Francesco

    2014-11-01

    Development of a comprehensive theory of the formation of vegetation patterns is still in progress. A prevailing view is to treat water availability as the main causal factor for the emergence of vegetation patterns. While successful in capturing the occurrence of multiple vegetation patterns in arid and semiarid regions, this hypothesis fails to explain the presence of vegetation patterns in humid environments. We explore the rich structure of a toxicity-mediated model of the vegetation pattern formation. This model consists of three PDEs accounting for a dynamic balance between biomass, water, and toxic compounds. Different (ecologically feasible) regions of the model's parameter space give rise to stable spatial vegetation patterns in Turing and non-Turing regimes. Strong negative feedback gives rise to dynamic spatial patterns that continuously move in space while retaining their stable topology.

  5. Butterfly wing pattern evolution is associated with changes in a Notch/Distal-less temporal pattern formation process.

    PubMed

    Reed, Robert D; Serfas, Michael S

    2004-07-13

    In butterflies there is a class of "intervein" wing patterns that have lines of symmetry halfway between wing veins. These patterns occur in a range of shapes, including eyespots, ellipses, and midlines, and were proposed to have evolved through developmental shifts along a midline-to-eyespot continuum. Here we show that Notch (N) upregulation, followed by activation of the transcription factor Distal-less (Dll), is an early event in the development of eyespot and intervein midline patterns across multiple species of butterflies. A relationship between eyespot phenotype and N and Dll expression is demonstrated in a loss-of-eyespot mutant in which N and Dll expression is reduced at missing eyespot sites. A phylogenetic comparison of expression time series from eight moth and butterfly species suggests that intervein N and Dll patterns are a derived characteristic of the butterfly lineage. Furthermore, prior to eyespot determination in eyespot-bearing butterflies, N and Dll are transiently expressed in a pattern that resembles ancestral intervein midline patterns. In this study we establish N upregulation as the earliest known event in eyespot determination, demonstrate gene expression associated with intervein midline color patterns, and provide molecular evidence that wing patterns evolved through addition to and truncation of a conserved midline-to-eyespot pattern formation sequence. PMID:15242612

  6. Butterfly wing pattern evolution is associated with changes in a Notch/Distal-less temporal pattern formation process.

    PubMed

    Reed, Robert D; Serfas, Michael S

    2004-07-13

    In butterflies there is a class of "intervein" wing patterns that have lines of symmetry halfway between wing veins. These patterns occur in a range of shapes, including eyespots, ellipses, and midlines, and were proposed to have evolved through developmental shifts along a midline-to-eyespot continuum. Here we show that Notch (N) upregulation, followed by activation of the transcription factor Distal-less (Dll), is an early event in the development of eyespot and intervein midline patterns across multiple species of butterflies. A relationship between eyespot phenotype and N and Dll expression is demonstrated in a loss-of-eyespot mutant in which N and Dll expression is reduced at missing eyespot sites. A phylogenetic comparison of expression time series from eight moth and butterfly species suggests that intervein N and Dll patterns are a derived characteristic of the butterfly lineage. Furthermore, prior to eyespot determination in eyespot-bearing butterflies, N and Dll are transiently expressed in a pattern that resembles ancestral intervein midline patterns. In this study we establish N upregulation as the earliest known event in eyespot determination, demonstrate gene expression associated with intervein midline color patterns, and provide molecular evidence that wing patterns evolved through addition to and truncation of a conserved midline-to-eyespot pattern formation sequence.

  7. A mechanistic description of the formation and evolution of vegetation patterns

    NASA Astrophysics Data System (ADS)

    Foti, R.; Ramírez, J. A.

    2013-01-01

    Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on the hillslope thermodynamics, runoff production and run-on infiltration, root density, surface albedo and soil moisture content are analyzed. In particular, we: (1) present a physically based mechanistic description of processes leading to vegetation pattern formation; (2) quantify the relative impact of each process on pattern formation; and (3) describe the relationships between vegetation patterns and the climatic, hydraulic and topographic characteristics of the system. We validate the model by comparing simulations with observed natural patterns in the areas of Niger near Niamey and Somalia near Garoowe. Our analyses suggest that the phenomenon of pattern formation is primarily driven by run-on infiltration and mechanisms of facilitation/inhibition among adjacent vegetation groups, mediated by vegetation effects on soil properties and controls on soil moisture and albedo. Nonetheless, even in presence of those mechanisms, patterns arise only when the climatic conditions, particularly annual precipitation and net radiation, are favorable.

  8. A mechanistic description of the formation and evolution of vegetation patterns

    NASA Astrophysics Data System (ADS)

    Foti, R.; Ramírez, J. A.

    2012-07-01

    Vegetation patterns are a common and well-defined characteristic of many landscapes. In this paper we explore some of the physical mechanisms responsible for the establishment of self-organized, non-random vegetation patterns that arise at the hillslope scale in many areas of the world, especially in arid and semi-arid regions. In doing so, we provide a fundamental mechanistic understanding of the dynamics of vegetation pattern formation and development. Reciprocal effects of vegetation on the hillslope thermodynamics, runoff production and run-on infiltration, root density, surface albedo and soil moisture content are analyzed. In particular, we: (1) present a physically based mechanistic description of processes leading to vegetation pattern formation; (2) quantify the relative impact of each process on pattern formation; and (3) describe the relationships between vegetation patterns and the climatic, hydraulic and topographic characteristics of the system. We validate the model by comparing simulations with observed natural patterns in the areas of Niger near Niamey and Somalia near Garoowe. Our analyses suggest that the phenomenon of pattern formation is primarily driven by run-on infiltration and mechanisms of facilitation/inhibition among adjacent vegetation groups mediated by vegetation effects on soil properties and controls on soil moisture and albedo. Nonetheless, even in presence of those mechanisms, patterns arise only when the climatic conditions, particularly annual precipitation and net radiation, are favorable.

  9. 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

  10. Pattern Formation in a Complex Plasma in High Magnetic Fields

    SciTech Connect

    Schwabe, M.; Konopka, U.; Bandyopadhyay, P.; Morfill, G. E.

    2011-05-27

    Low-pressure room-temperature neon, argon, krypton, and air plasmas were studied in magnetic fields up to flux densities of 2.3 T. Filaments appeared parallel to the magnetic field lines, and patterns such as spirals and concentric circles formed in the perpendicular direction. We link these effects to the magnetization of the ions. We also used a layer of embedded microparticles as probes in the plasma. Their motion changed dramatically from a collective rotation of the whole ensemble in moderate magnetic fields to a rotation in several small vortices centered at the filaments.

  11. 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

  12. 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.

  13. Vitamin K antagonism aggravates chronic kidney disease-induced neointimal hyperplasia and calcification in arterialized veins: role of vitamin K treatment?

    PubMed

    Zaragatski, Emma; Grommes, Jochen; Schurgers, Leon J; Langer, Stephan; Kennes, Lieven; Tamm, Miriam; Koeppel, Thomas A; Kranz, Jennifer; Hackhofer, Tina; Arakelyan, Karen; Jacobs, Michael J; Kokozidou, Maria

    2016-03-01

    Arteriovenous fistula (AVF) is the common vascular access type for a hemodialysis patient. Its failure is due to neointimal hyperplasia. Vitamin K antagonists are given to lower thrombosis tendency, but have side effects that enhance arterial calcifications. Here, we investigated the effects of vitamin K antagonists and vitamin K2 (K2) treatment on neointimal hyperplasia development and calcification in rats and in arterialized human veins. AVF was generated in female rats while chronic kidney disease (CKD) was induced using an adenine-enriched diet. Arterialization, CKD, and vitamin K antagonists all significantly enhanced venous neointimal hyperplasia. K2 treatment, additional to vitamin K antagonists, significantly reduced neointimal hyperplasia in arterialized veins in healthy rats but not in rats with CKD. Arterialization, CKD, and vitamin K antagonism all significantly increased, whereas K2 supplementation attenuated calcification in healthy rats and rats with CKD. K2 significantly enhanced matrix Gla protein carboxylation in control rats and rats with CKD. Arterialized human vein samples contained inactive matrix Gla protein at calcification and neointimal hyperplasia sites, indicating local vitamin K deficiency. Thus, vitamin K antagonists have detrimental effects on AVF remodeling, whereas K2 reduced neointimal hyperplasia and calcification indicating vasoprotective effects. Hence, K2 administration may be useful to prevent neointimal hyperplasia and calcification in arterialized veins

  14. [Certain patterns in the formation of optical illusions].

    PubMed

    Vertogradova, O P; Voĭtsekh, V F; Krasnov, V N

    1979-01-01

    A structural dynamic analysis of productive disorders in visual perception was attempted on the basis of psychological study of 344 patients. These disorders were studied according to the increasing degree of inadequacy (anisomorphia) of pathological images in respect to real stimula. Considering the differences of such phenomena according to the degree of discrepancy of their perceptive characteristics with the traits of real objects, some successively complicated pathological images were examined, including traditional false recognition, illusions and hallucinations, as well as interlapping intermediate structures. Some pathogenetical mechanisms in the formations of visual illusions are suggested. Clinico-psychopathological parallels are made between disorders of visual perception and disease entities.

  15. 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.

  16. [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.

  17. [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.

  18. Wetting and Roughness: Pattern Formation in a Rough Fracture

    NASA Astrophysics Data System (ADS)

    Pahlavan, A. A.; Cueto-Felgueroso, L.; McKinley, G. H.; Juanes, R.

    2015-12-01

    Wetting phenomena are inherently multiscale; owing to the complex nature of porous and fractured media, immiscible flows in this setting continue to challenge our microscopic and macroscopic descriptions. To gain some insight into the interplay between wettability and roughness of the medium, here we study experimentally the immiscible displacement of one fluid by another in a Hele-Shaw cell (two glass plates separated by a thin gap) with rough surfaces. We use a radial Hele-Shaw cell and saturate it with highly viscous silicone oil; we then inject a less viscous liquid at the center of the cell. Displacement of a more viscous liquid by a less viscous one leads to a hydrodynamic instability, known as viscous fingering. Wettability of the medium, however, has a profound influence on the displacement patterns and can lead to a complete suppression of the viscous fingering instability. Roughness, on the other hand, amplifies the wettability of the medium, making a wetting surface even more wetting and a non-wetting surface even more non-wetting. Roughness can also lead to contact-line pinning and intermittent avalanche-like behavior in the flow. We study the interplay between roughness and wettability of the medium by isolating each effect. We then propose a phase diagram that classifies the different displacement patterns, elucidating the underlying physics at play across scales.

  19. Novel short-duration heating balloon dilatation with uniform temperature distribution: the heating conditions to suppress neo-intimal hyperplasia.

    PubMed

    Kunio, M; Shimazaki, N; Arai, T; Sakurada, M

    2011-01-01

    We investigate the relation between the influences on smooth muscle cells and the chronic performances of our novel short-duration heating balloon dilatation to reveal the heating conditions which can suppress the neo-intimal hyperplasia after our heating dilatations. The temperature of prototype balloon catheter surface was measured during short-duration heating balloon dilatation ex vivo. There existed 2 °C temperature variations in the long direction of prototype balloon catheter at a maximum. The neo-intimal hyperplasia occupancy rate after our short-duration heating dilatations were measured in vivo porcine study. The neo-intimal hyperplasia was suppressed most at 75 °C in balloon peak temperature in vivo. The estimated dead rate of smooth muscle cells at this condition was about 13% by the Arrhenius equation. We think that the suppression of neo-intimal hyperplasia was obtained after our short-duration heating dilatation due to the proper decrease of smooth muscle cells by heating and no thermal damages to the adventitia and surrounding tissues.

  20. Formation of longitudinal patterns and dimensionality crossover of nonlinear spin waves in ferromagnetic stripes

    NASA Astrophysics Data System (ADS)

    Demidov, V. E.; Hansen, U.-F.; Dzyapko, O.; Koulev, N.; Demokritov, S. O.; Slavin, A. N.

    2006-09-01

    Formation of stationary longitudinal amplitude patterns by propagating nonlinear spin waves has been discovered and studied experimentally by means of space-resolved Brillouin light scattering spectroscopy. The pattern formation is observed for spin waves propagating in narrow, longitudinally magnetized yttrium iron garnet stripes, characterized by attractive nonlinearity in both the longitudinal and transverse directions. A clear crossover of the effective dimensionality describing the propagation of spin waves in the stripe is observed with increase of the wave amplitude.

  1. 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

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. Time rescaling and pattern formation in biological evolution.

    PubMed

    Igamberdiev, Abir U

    2014-09-01

    Biological evolution is analyzed as a process of continuous measurement in which biosystems interpret themselves in the environment resulting in changes of both. This leads to rescaling of internal time (heterochrony) followed by spatial reconstructions of morphology (heterotopy). The logical precondition of evolution is the incompleteness of biosystem's internal description, while the physical precondition is the uncertainty of quantum measurement. The process of evolution is based on perpetual changes in interpretation of information in the changing world. In this interpretation the external biospheric gradients are used for establishment of new features of organization. It is concluded that biological evolution involves the anticipatory epigenetic changes in the interpretation of genetic symbolism which cannot generally be forecasted but can provide canalization of structural transformations defined by the existing organization and leading to predictable patterns of form generation.

  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. Laser-based techniques for living cell pattern formation

    NASA Astrophysics Data System (ADS)

    Hopp, Béla; Smausz, Tomi; Papdi, Bence; Bor, Zsolt; Szabó, András; Kolozsvári, Lajos; Fotakis, Costas; Nógrádi, Antal

    2008-10-01

    In the production of biosensors or artificial tissues a basic step is the immobilization of living cells along the required pattern. In this paper the ability of some promising laser-based methods to influence the interaction between cells and various surfaces is presented. In the first set of experiments laser-induced patterned photochemical modification of polymer foils was used to achieve guided adherence and growth of cells to the modified areas: (a) Polytetrafluoroethylene was irradiated with ArF excimer laser ( λ=193 nm, FWHM=20 ns, F=9 mJ/cm2) in presence of triethylene tetramine liquid photoreagent; (b) a thin carbon layer was produced by KrF excimer laser ( λ=248 nm, FWHM=30 ns, F=35 mJ/cm2) irradiation on polyimide surface to influence the cell adherence. It was found that the incorporation of amine groups in the PTFE polymer chain instead of the fluorine atoms can both promote and prevent the adherence of living cells (depending on the applied cell types) on the treated surfaces, while the laser generated carbon layer on polyimide surface did not effectively improve adherence. Our attempts to influence the cell adherence by morphological modifications created by ArF laser irradiation onto polyethylene terephtalate surface showed a surface roughness dependence. This method was effective only when the Ra roughness parameter of the developed structure did not exceed the 0.1 micrometer value. Pulsed laser deposition with femtosecond KrF excimer lasers ( F=2.2 J/cm2) was effectively used to deposit structured thin films from biomaterials (endothelial cell growth supplement and collagen embedded in starch matrix) to promote the adherence and growth of cells. These results present evidence that some surface can be successfully altered to induce guided cell growth.

  13. 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.

  14. 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

  15. Pattern formation in skyrmionic materials with anisotropic environments

    NASA Astrophysics Data System (ADS)

    Hagemeister, Julian; Vedmedenko, Elena Y.; Wiesendanger, Roland

    2016-09-01

    Magnetic Skyrmions have attracted broad attention during recent years because they are regarded as promising candidates as bits of information in novel data storage devices. A broad range of theoretical and experimental investigations have been conducted with the consideration of axisymmetric Skyrmions in isotropic environments. However, one naturally observes a huge variety of anisotropic behavior in many experimentally relevant materials. In the present work, we investigate the influence of anisotropic environments onto the formation and behavior of the noncollinear spin states of skyrmionic materials by means of Monte Carlo calculations. We find skyrmionic textures which are far from having an axisymmetric shape. Furthermore, we show the possibility to employ periodic modulations of the environment to create skyrmionic tracks.

  16. 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

  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. 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.

  19. 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

  20. 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

  1. 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.

  2. 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…

  3. Robust dynamical pattern formation from a multifunctional minimal genetic circuit

    PubMed Central

    2010-01-01

    Background A practical problem during the analysis of natural networks is their complexity, thus the use of synthetic circuits would allow to unveil the natural mechanisms of operation. Autocatalytic gene regulatory networks play an important role in shaping the development of multicellular organisms, whereas oscillatory circuits are used to control gene expression under variable environments such as the light-dark cycle. Results We propose a new mechanism to generate developmental patterns and oscillations using a minimal number of genes. For this, we design a synthetic gene circuit with an antagonistic self-regulation to study the spatio-temporal control of protein expression. Here, we show that our minimal system can behave as a biological clock or memory, and it exhibites an inherent robustness due to a quorum sensing mechanism. We analyze this property by accounting for molecular noise in an heterogeneous population. We also show how the period of the oscillations is tunable by environmental signals, and we study the bifurcations of the system by constructing different phase diagrams. Conclusions As this minimal circuit is based on a single transcriptional unit, it provides a new mechanism based on post-translational interactions to generate targeted spatio-temporal behavior. PMID:20412565

  4. 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.

  5. 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.

  6. 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

  7. Physical schemata underlying biological pattern formation-examples, issues and strategies.

    PubMed

    Levine, Herbert; Ben-Jacob, Eshel

    2004-06-01

    Biological systems excel at building spatial structures on scales ranging from nanometers to kilometers and exhibit temporal patterning from milliseconds to years. One approach that nature has taken to accomplish this relies on the harnessing of pattern-forming processes of non-equilibrium physics and chemistry. For these systems, the study of biological pattern formation starts with placing a biological phenomenon of interest within the context of the proper pattern-formation schema and then focusing on the ways in which control is exerted to adapt the pattern to the needs of the organism. This approach is illustrated by several examples, notably bacterial colonies (diffusive-growth schema) and intracellular calcium waves (excitable-media schema). PMID:16204813

  8. 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.

  9. 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

  10. 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

  11. 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

  12. 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

  13. Novel nanocomposite stent coating releasing resveratrol and quercetin reduces neointimal hyperplasia and promotes re-endothelialization.

    PubMed

    Kleinedler, James J; Foley, John D; Orchard, Elysse A; Dugas, Tammy R

    2012-04-10

    Late-term thrombosis associated with drug-eluting stents may be due to the non-selective actions of antimitogenic drugs on endothelial cells, leading to delayed vascular healing after stenting angioplasty. Currently, there is a need for stent-based therapies that can both attenuate neointimal hyperplasia and promote re-endothelialization. The aim of this study was to compare the effects of a resveratrol (R)- and quercetin (Q)-eluting stent with that of a bare metal stent (BMS) on neointimal hyperplasia and re-endothelialization in a rat model of arterial angioplasty and stenting. Miniature stents (2.5×1.25mm) were sprayed with nanocomposite coatings containing two concentrations of R:Q (50:25μg/cm(2) (RQ1) or 150:75μg/cm(2) (RQ2)). The stents were deployed into the common carotid artery of rats and their impact on vascular remodeling was compared to that of BMS. Luminal stenosis in arteries stented with RQ2-eluting stents was reduced by 64.6% (p<0.05) compared to arteries stented with BMS. Accompanying this effect was a 59.8% reduction in macrophage infiltration (p<0.05). There were no differences found between RQ1 and BMS. Finally, the RQ2-coated stent accelerated re-endothelialization by 50% compared with BMS (p<0.05). Thus, compared with BMS, local delivery of R and Q from a stent platform significantly reduced in-stent stenosis, while promoting re-endothelialization. These data suggest that R and Q may be favorable candidates for novel stent coatings, potentially reducing the risk of late thrombosis associated with drug-eluting stents.

  14. 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

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

    PubMed Central

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

    2015-01-01

    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 co-localize 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

  16. Pattern formation and self-organization in plasmas interacting with surfaces

    NASA Astrophysics Data System (ADS)

    Trelles, Juan Pablo

    2016-10-01

    Pattern formation and self-organization are fascinating phenomena commonly observed in diverse types of biological, chemical and physical systems, including plasmas. These phenomena are often responsible for the occurrence of coherent structures found in nature, such as recirculation cells and spot arrangements; and their understanding and control can have important implications in technology, e.g. from determining the uniformity of plasma surface treatments to electrode erosion rates. This review comprises theoretical, computational and experimental investigations of the formation of spatiotemporal patterns that result from self-organization events due to the interaction of low-temperature plasmas in contact with confining or intervening surfaces, particularly electrodes. The basic definitions associated to pattern formation and self-organization are provided, as well as some of the characteristics of these phenomena within natural and technological contexts, especially those specific to plasmas. Phenomenological aspects of pattern formation include the competition between production/forcing and dissipation/transport processes, as well as nonequilibrium, stability, bifurcation and nonlinear interactions. The mathematical modeling of pattern formation in plasmas has encompassed from theoretical approaches and canonical models, such as reaction-diffusion systems, to drift-diffusion and nonequilibrium fluid flow models. The computational simulation of pattern formation phenomena imposes distinct challenges to numerical methods, such as high sensitivity to numerical approximations and the occurrence of multiple solutions. Representative experimental and numerical investigations of pattern formation and self-organization in diverse types of low-temperature electrical discharges (low and high pressure glow, dielectric barrier and arc discharges, etc) in contact with solid and liquid electrodes are reviewed. Notably, plasmas in contact with liquids, found in diverse

  17. Pattern formation in directional solidification under shear flow. I. Linear stability analysis and basic patterns.

    PubMed

    Marietti, Y; Debierre, J M; Bock, T M; Kassner, K

    2001-06-01

    An asymptotic interface equation for directional solidification near the absolute stability limit is extended by a nonlocal term describing a shear flow parallel to the interface. In the long-wave limit considered, the flow acts destabilizing on a planar interface. Moreover, linear stability analysis suggests that the morphology diagram is modified by the flow near onset of the Mullins-Sekerka instability. Via numerical analysis, the bifurcation structure of the system is shown to change. Besides the known hexagonal cells, structures consisting of stripes arise. Due to its symmetry-breaking properties, the flow term induces a lateral drift of the whole pattern, once the instability has become active. The drift velocity is measured numerically and described analytically in the framework of a linear analysis. At large flow strength, the linear description breaks down, which is accompanied by a transition to flow-dominated morphologies which is described in the following paper. Small and intermediate flows lead to increased order in the lattice structure of the pattern, facilitating the elimination of defects. Locally oscillating structures appear closer to the instability threshold with flow than without.

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Pattern formation in a spatial plant-wrack model with tide effect on the wrack.

    PubMed

    Sun, Gui-Quan; Li, Li; Jin, Zhen; Li, Bai-Lian

    2010-03-01

    Spatial patterns are a subfield of spatial ecology, and these patterns modify the temporal dynamics and stability properties of population densities at a range of spatial scales. Localized ecological interactions can generate striking large-scale spatial patterns in ecosystems through spatial self-organization. Possible mechanisms include oscillating consumer-resource interactions, localized disturbance-recovery processes, and scale-dependent feedback. However, in this paper, our main aim is to study the effect of tide on the pattern formation of a spatial plant-wrack model. We discuss the changes of the wavelength, wave speed, and the conditions of the spatial pattern formation, according to the dispersion relation formula. Both the mathematical analysis and numerical simulations reveal that the tide has great influence on the spatial pattern. More specifically, typical traveling spatial patterns can be obtained. Our obtained results are consistent with the previous observation that wracks exhibit traveling patterns, which is useful to help us better understand the dynamics of the real ecosystems.

  5. Beyond transmission: intergenerational patterns of family formation among middle-class American families.

    PubMed

    Fasang, Anette Eva; Raab, Marcel

    2014-10-01

    Research about parental effects on family behavior focuses on intergenerational transmission: that is, whether children show the same family behavior as their parents. This focus potentially over emphasizes similarity and obscures heterogeneity in parental effects on family behavior. In this study, we make two contributions. First, instead of focusing on isolated focal events, we conceptualize parents' and their children's family formation holistically as the process of union formation and childbearing between ages 15 and 40. We then discuss mechanisms likely to shape these intergenerational patterns. Second, beyond estimating average transmission effects, we innovatively apply multichannel sequence analysis to dyadic sequence data on middle-class American families from the Longitudinal Study of Generations (LSOG; N = 461 parent-child dyads). The results show three salient intergenerational family formation patterns among this population: a strong transmission, a moderated transmission, and an intergenerational contrast pattern. We examine what determines parents' and children's likelihood to sort into a specific intergenerational pattern. For middle-class American families, educational upward mobility is a strong predictor of moderated intergenerational transmission, whereas close emotional bonds between parents and children foster strong intergenerational transmission. We conclude that intergenerational patterns of family formation are generated at the intersection of macro-structural change and family internal psychological dynamics.

  6. 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.

  7. Nonlinear waves and pattern formation in multiphase flows in porous media

    NASA Astrophysics Data System (ADS)

    Elperin, T.; Kleeorin, N.; Rogachevskii, I.

    The paper analyzes pattern formation in initially homogeneous one-dimensional two-phase flows in porous medium. It is shown that generally these flows are unstable. The mechanism of the instabilities is associated with inertial effects. Such instabilities are of explosive type and are probably important in various engineering applications and natural phenomena. In small-amplitude finite approximation the evolution of patterns is governed by the Korteweg-de Vries-Burgers equation. Pattern formation occurs when the coefficient multiplying the Burgers term becomes negative. During nonlinear evolution a soliton with a tail is formed. The amplitude of the soliton increases while the tail decreases. These results can be regarded as a generalization of results by Harris and Crighton (1994) to the case of two-phase flows in porous medium. The obtained solution in form of soliton with a tail can be interpreted as initial phase of formation of the phase composition inhomogeneities in porous media. In the case of fluidized beds this pattern can be regarded as initial phase of bubble formation in a fluidized bed of granular material. The characteristic size of bubbles and time of its formation are estimated.

  8. Insular dentin formation pattern in human odontogenesis in relation to the scalloped dentino-enamel junction.

    PubMed

    Radlanski, Ralf J; Renz, Herbert

    2007-01-01

    This study is a first report on the modality of early dentin formation in respect to the scalloped pattern of the dentino-enamel junction (DEJ). We applied scanning electron microscopy (SEM), transmission electron microscopy (TEM), histological serial sections, and three-dimensional (3D) reconstructions. TEM and SEM showed scallops and secondary scallops on the DEJ of deciduous dental primordia and on deciduous teeth with the enamel cap removed. This peculiar outline of the DEJ requires a specific dentin formation pattern; histological sections showed that dentin formation began at the brims of the scallops, seen as triangular spikes in serial sections. The dentin formation front was not uniform; instead, it was characterized by multiple, insular forming centers, as revealed by our 3D reconstructions. As thicker dentin layers formed, the islands became confluent. Factors are discussed, which may lead to crimpling of the inner enamel epithelium, and maintained as the scalloped pattern of the DEJ develops. Signaling patterns in accordance with the insular dentin formation are unknown so far.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. On the dynamics of a forced reaction-diffusion model for biological pattern formation.

    PubMed Central

    Tsonis, A A; Elsner, J B; Tsonis, P A

    1989-01-01

    Ideas from the theory of dynamical systems are applied in biological pattern formation. By considering a simple reaction-diffusion model subjected to an external excitation, we find that the system can give rise to a great variety of periodic, quasiperiodic, and chaotic evolutions. PMID:2740333

  15. 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.

  16. Pattern formation in a model for mountain pine beetle dispersal: linking model predictions to data.

    PubMed

    Strohm, S; Tyson, R C; Powell, J A

    2013-10-01

    Pattern formation occurs in a wide range of biological systems. This pattern formation can occur in mathematical models because of diffusion-driven instability or due to the interaction between reaction, diffusion, and chemotaxis. In this paper, we investigate the spatial pattern formation of attack clusters in a system for Mountain Pine Beetle. The pattern formation (aggregation) of the Mountain Pine Beetle in order to attack susceptible trees is crucial for their survival and reproduction. We use a reaction-diffusion equation with chemotaxis to model the interaction between Mountain Pine Beetle, Mountain Pine Beetle pheromones, and susceptible trees. Mathematical analysis is utilized to discover the spacing in-between beetle attacks on the susceptible landscape. The model predictions are verified by analysing aerial detection survey data of Mountain Pine Beetle Attack from the Sawtooth National Recreation Area. We find that the distance between Mountain Pine Beetle attack clusters predicted by our model closely corresponds to the observed attack data in the Sawtooth National Recreation Area. These results clarify the spatial mechanisms controlling the transition from incipient to epidemic populations and may lead to control measures which protect forests from Mountain Pine Beetle outbreak.

  17. Category Formation in Autism: Can Individuals with Autism Form Categories and Prototypes of Dot Patterns?

    ERIC Educational Resources Information Center

    Gastgeb, Holly Zajac; Dundas, Eva M.; Minshew, Nancy J.; Strauss, Mark S.

    2012-01-01

    There is a growing amount of evidence suggesting that individuals with autism have difficulty with categorization. One basic cognitive ability that may underlie this difficulty is the ability to abstract a prototype. The current study examined prototype and category formation with dot patterns in high-functioning adults with autism and matched…

  18. 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.

  19. 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

  20. 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

  1. 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

  2. Spontaneous formation of dual stratification patterns in a large quasi-two-dimensional sand pile

    NASA Astrophysics Data System (ADS)

    Shimokawa, Michiko; Ohta, Shonosuke

    2008-01-01

    By pouring a mixture of two types of grains into a large vertical cell with a narrow space, we discovered a dual stratification pattern consisting of two different wavelengths at the upper and lower regions of the resulting sand pile. In the formation of this pattern, we also observed an additional type of kink—a wave that moves toward the top of the sand pile along the slope. The kink, herein called a trapped kink, is essential for the formation of dual stratification patterns. Asymmetric probability distributions are obtained from measurement of the position where the kinks are generated. We proposed a phenomenological model to describe the kink generation process. The results analyzed by this model agree with experimental distributions.

  3. Formation mechanism and ordered patterns in Cu films deposited on silicone oil surfaces

    NASA Astrophysics Data System (ADS)

    Chen, Miao-Gen; Xie, Jian-Ping; Ye, Gao-Xiang

    2006-12-01

    A copper (Cu) film system, deposited on silicone oil surfaces by vapor phase deposition method, has been fabricated and its formation mechanism as well as ordered patterns has been studied. The formation mechanism of the films obeys the two-stage growth model. The ordered patterns, which are composed of a large number of parallel keys with different width w but nearly uniform length L, are observed in the continuous Cu films. It is noted that, if the nominal film thickness d=120.0 nm, the value of α=L/(4w) reaches its maximum at the deposition rate f=0.05 nm/s. The experiment indicates that the ordered patterns mainly result from the ordered material aggregation, which depends closely on the internal stress in the nearly free sustained Cu film system.

  4. 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

  5. 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.

  6. Characterising the dynamics of expirated bloodstain pattern formation using high-speed digital video imaging.

    PubMed

    Donaldson, Andrea E; Walker, Nicole K; Lamont, Iain L; Cordiner, Stephen J; Taylor, Michael C

    2011-11-01

    During forensic investigations, it is often important to be able to distinguish between impact spatter patterns (blood from gunshots, explosives, blunt force trauma and/or machinery accidents) and bloodstain patterns generated by expiration (blood from the mouth, nose or lungs). These patterns can be difficult to distinguish on the basis of the size of the bloodstains. In this study, high-speed digital video imaging has been used to investigate the formation of expirated bloodstain patterns generated by breathing, spitting and coughing mechanisms. Bloodstain patterns from all three expiration mechanisms were dominated by the presence of stains less than 0.5 mm in diameter. Video analysis showed that in the process of coughing blood, high-velocity, very small blood droplets were ejected first. These were followed by lower velocity, larger droplets, strands and plumes of liquid held together in part by saliva. The video images showed the formation of bubble rings and beaded stains, traditional markers for classifying expirated patterns. However, the expulsion mechanism, the distance travelled by the blood droplets, and the type of surface the blood was deposited on were all factors determining whether beaded stains were generated.

  7. 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

  8. 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.

  9. 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.

  10. The role of localized recoil in the formation of Kikuchi patterns.

    PubMed

    Winkelmann, Aimo; Vos, Maarten

    2013-02-01

    In electron scattering from crystals, diffraction spots are replaced by Kikuchi patterns at high momentum transfer. Kikuchi pattern formation is based on the concept of effective incoherent electron sources (or detectors) inside a crystal. The resulting incoherence is a consequence of energy transfer connected with the momentum transfer in large-angle scattering events. We identify atomic recoil as a key incoherent process giving rise to electron Kikuchi patterns in the scope of the "channeling-in and channeling-out" model of electron backscatter diffraction (EBSD) and electron channeling patterns (ECP) in the scanning electron microscope (SEM). Using model calculations, we explore the characteristic role of the localization of the incoherent scattering event at specific places within the unit cell. In this way, we explain why sometimes inelastic losses do cause Kikuchi-type contrast, and sometimes inelastic losses result in the disappearance of this contrast in the SEM.

  11. 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

  12. 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

  13. Mathematical study of pattern formation accompanied by heterocyst differentiation in multicellular cyanobacterium.

    PubMed

    Ishihara, Jun-ichi; Tachikawa, Masashi; Iwasaki, Hideo; Mochizuki, Atsushi

    2015-04-21

    The filamentous cyanobacterium, Anabaena sp. PCC 7120, is one of the simplest models of a multicellular system showing cellular differentiation. In nitrogen-deprived culture, undifferentiated vegetative cells differentiate into heterocysts at ~10-cell intervals along the cellular filament. As undifferentiated cells divide, the number of cells between heterocysts (segment length) increases, and a new heterocyst appears in the intermediate region. To understand how the heterocyst pattern is formed and maintained, we constructed a one-dimensional cellular automaton (CA) model of the heterocyst pattern formation. The dynamics of vegetative cells is modeled by a stochastic transition process including cell division, differentiation and increase of cell age (maturation). Cell division and differentiation depend on the time elapsed after the last cell division, the "cell age". The model dynamics was mathematically analyzed by a two-step Markov approximation. In the first step, we determined steady state of cell age distribution among vegetative cell population. In the second step, we determined steady state distribution of segment length among segment population. The analytical solution was consistent with the results of numerical simulations. We then compared the analytical solution with the experimental data, and quantitatively estimated the immeasurable intercellular kinetics. We found that differentiation is initially independent of cellular maturation, but becomes dependent on maturation as the pattern formation evolves. Our mathematical model and analysis enabled us to quantify the internal cellular dynamics at various stages of the heterocyst pattern formation. PMID:25665721

  14. Modeling parr-mark pattern formation during the early development of Amago trout

    NASA Astrophysics Data System (ADS)

    Venkataraman, Chandrasekhar; Sekimura, Toshio; Gaffney, Eamonn A.; Maini, Philip K.; Madzvamuse, Anotida

    2011-10-01

    This paper studies the formation of the large dark patterns, known as parr marks, that form on the Amago trout as it grows from the early larval stages to adulthood. The Amago trout, known as Oncorhynchus masou ishikawa, exhibits stripes during the early stages of development that in turn evolve (through reorientation and peak insertion) to form zigzag spot patterns as the fish grows to adulthood. By considering a standard representation of the Turing model for biological self-organization via interacting and diffusing morphogens, we illustrate that a diffusively driven instability can generate transient patterns consistent with those experimentally observed during the process of parr-mark formation in the early development of the Amago trout. Surface evolution is modeled through an experimentally driven growth function. Our studies conclude that the surface evolution profile, the surface geometry, and the curvature are key factors that play a pivotal role in reaction-diffusion systems in a study motivated by observations of Amago trout parr-mark pattern formation.

  15. Experimental investigation on flame pattern formations of DME-air mixtures in a radial microchannel

    SciTech Connect

    Fan, Aiwu; Maruta, Kaoru; Nakamura, Hisashi; Kumar, Sudarshan; Liu, Wei

    2010-09-15

    Flame pattern formations of premixed DME-air mixture in a heated radial channel with a gap distance of 2.5 mm were experimentally investigated. The DME-air mixture was introduced into the radial channel through a delivery tube which connected with the center of the top disk. With an image-intensified high-speed video camera, rich flame pattern formations were identified in this configuration. Regime diagram of all these flame patterns was drawn based on the experimental findings in the equivalence ratio range of 0.6-2.0 and inlet velocity range of 1.0-5.0 m/s. Compared with our previous study on premixed methane-air flames, there are several distinct characteristics for the present study. First, Pelton-wheel-like rotary flames and traveling flames with kink-like structures were observed for the first time. Second, in most cases, flames can be stabilized near the inlet port of the channel, exhibiting a conical or cup-like shape, while the conventional circular flame was only observed under limited conditions. Thirdly, an oscillating flame phenomenon occurred under certain conditions. During the oscillation process, a target appearance was seen at some instance. These pattern formation characteristics are considered to be associated with the low-temperature oxidation of DME. (author)

  16. 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.

  17. Symmetries and pattern formation in hyperbolic versus parabolic models of self-organised aggregation.

    PubMed

    Buono, Pietro-Luciano; Eftimie, Raluca

    2015-10-01

    The study of self-organised collective animal behaviour, such as swarms of insects or schools of fish, has become over the last decade a very active research area in mathematical biology. Parabolic and hyperbolic models have been used intensively to describe the formation and movement of various aggregative behaviours. While both types of models can exhibit aggregation-type patterns, studies on hyperbolic models suggest that these models can display a larger variety of spatial and spatio-temporal patterns compared to their parabolic counterparts. Here we use stability, symmetry and bifurcation theory to investigate this observation more rigorously, an approach not attempted before to compare and contrast aggregation patterns in models for collective animal behaviors. To this end, we consider a class of nonlocal hyperbolic models for self-organised aggregations that incorporate various inter-individual communication mechanisms, and take the formal parabolic limit to transform them into nonlocal parabolic models. We then discuss the symmetry of these nonlocal hyperbolic and parabolic models, and the types of bifurcations present or lost when taking the parabolic limit. We show that the parabolic limit leads to a homogenisation of the inter-individual communication, and to a loss of bifurcation dynamics (in particular loss of Hopf bifurcations). This explains the less rich patterns exhibited by the nonlocal parabolic models. However, for multiple interacting populations, by breaking the population interchange symmetry of the model, one can preserve the Hopf bifurcations that lead to the formation of complex spatio-temporal patterns that describe moving aggregations.

  18. Differential patterns of altered bone formation in different bone compartments in established osteoporosis.

    PubMed Central

    Byers, R J; Denton, J; Hoyland, J A; Freemont, A J

    1999-01-01

    AIM: To investigate the level of bone formation in the different bone compartments in cases of established osteoporosis, as previous work has concentrated on trabecular bone alone. METHODS: Bone formation rates were measured histomorphometrically, in the periosteal (P), cortical (C), subcortical (SC), and trabecular (T) compartments in iliac crest biopsies from 159 patients with established osteoporosis. The values were standardised using age and sex matched control data and patterns of differential change determined by analysis of parametric status (increased, normal, reduced). RESULTS: Mean bone formation was reduced in all four compartments. This was more marked (4.4/4.1 standard deviations below the mean in C/T, v 2.3/0.9 in P/SC) and more frequent (reduced in 81.5%/78.3% in T/C, v 43.3%/44% in P/SC) in the trabecular and cortical compartments than in the periosteal or subcortical bone. Parametric status was equal in trabecular and cortical bone in 85.4% of cases, and in periosteal and subcortical bone in 65.7%, but in all four compartments in only 35.1%, indicating differential alteration of bone formation in the two sets of compartments (T/C v P/SC). CONCLUSIONS: Altered trabecular bone formation is important in osteoporosis, but there are differential patterns of alteration in the other three compartments, emphasising the presence of different microenvironments in bone; thus the effect on the cortical compartment was similar to that on the trabecular, while the subcortical and periosteal compartments also showed linkage. The linkage between the two pairs was divergent, indicating different control of bone formation, with resultant different patterns of perturbation in osteoporosis. Images PMID:10343608

  19. 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.

  20. 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.

  1. Regulative feedback in pattern formation: towards a general relativistic theory of positional information.

    PubMed

    Jaeger, Johannes; Irons, David; Monk, Nick

    2008-10-01

    Positional specification by morphogen gradients is traditionally viewed as a two-step process. A gradient is formed and then interpreted, providing a spatial metric independent of the target tissue, similar to the concept of space in classical mechanics. However, the formation and interpretation of gradients are coupled, dynamic processes. We introduce a conceptual framework for positional specification in which cellular activity feeds back on positional information encoded by gradients, analogous to the feedback between mass-energy distribution and the geometry of space-time in Einstein's general theory of relativity. We discuss how such general relativistic positional information (GRPI) can guide systems-level approaches to pattern formation.

  2. Buckling patterns of gold thin films on silicon substrates: Formation of superimposed blisters

    NASA Astrophysics Data System (ADS)

    Colin, J.; Coupeau, C.; Durinck, J.; Grilhé, J.

    2009-06-01

    Buckling phenomena leading to the formation of superimposed blisters have been experimentally observed with the help of a confocal interferometric microscope onto the surface of gold thin films deposited on silicon substrates. Assuming that residual folding effects resulting from plastic deformation mechanisms take place in the film during its morphological evolution, different probable scenarios for the formation of the observed buckling patterns are elaborated in the framework of the Föppl-von Karman's theory of thin plates. Multi-step buckling with growing interface delamination is considered for the first scenario while a single or multi-step buckling at a given delamination width is assumed for the other ones.

  3. Pattern formation in spatially extended nonlinear systems: Toward a foundation for meaning in symbolic forms

    NASA Astrophysics Data System (ADS)

    DeMaris, David

    1998-07-01

    This paper brings together observations from a variety of fields to point toward what the author believes to be the most promising computational approach to the modeling of brain-like symbol formation, unifying perceptual and linguistic domains under a common computational physics. It brings Cassirer's Gestalt era evolutionary theory of language and symbolic thought to the attention of the situated cognition community, and describes how recent observations in experimental brain dynamics and computational approaches can be brought to bear on the problem. Research by the author and others in oscillatory network models of ambiguous perception with an attentional component is emphasised as a starting point for exploring increasingly complex pattern formation processes leading to simple forms of linguistic performance. These forms occupy a space between iconic representations and grammar. The dynamic pattern network framework suggests that to separate perception, representation or models and action in a realistic biophysics of situated organisms may be problematic.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. ARGONAUTE1 acts in Arabidopsis root radial pattern formation independently of the SHR/SCR pathway.

    PubMed

    Miyashima, Shunsuke; Hashimoto, Takashi; Nakajima, Keiji

    2009-03-01

    The formation of radially symmetric tissue patterns is one of the most basic processes in the development of vascular plants. In Arabidopsis thaliana, plant-specific GRAS-type transcription factors, SHORT-ROOT (SHR) and SCARECROW (SCR), are required for asymmetric cell divisions that separate two ground tissue cell layers, the endodermis and cortex, as well as for endodermal cell fate specification. While loss of SHR or SCR results in a single-layered ground tissue, radially symmetric cellular patterns are still maintained, suggesting that unknown regulatory mechanisms act independently of the SHR/SCR-dependent pathway. In this study, we identified a novel root radial pattern mutant and found that it is a new argonaute1 (ago1) allele. Multiple ago1 mutant alleles contained supernumerary ground tissue cell layers lacking a concentric organization, while expression patterns of SHR and SCR were not affected, revealing a previously unreported role for AGO1 in root ground tissue patterning. Analyses of ago1 scr double mutants demonstrated that the simultaneous loss of the two pathways caused a dramatic reduction in cellular organization and ground tissue identity as compared with the single mutants. Based on these results, we propose that highly symmetric root ground tissue patterns are maintained by the actions of two independent pathways, one using post-transcriptional regulation mediated by AGO1 and the other using the SHR/SCR transcriptional regulator.

  10. AUXIN RESPONSE FACTOR17 is essential for pollen wall pattern formation in Arabidopsis.

    PubMed

    Yang, Jun; Tian, Lei; Sun, Ming-Xi; Huang, Xue-Yong; Zhu, Jun; Guan, Yue-Feng; Jia, Qi-Shi; Yang, Zhong-Nan

    2013-06-01

    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.

  11. Steady states and linear stability analysis of precipitation pattern formation at geothermal hot springs.

    PubMed

    Chan, Pak Yuen; Goldenfeld, Nigel

    2007-10-01

    A dynamical theory of geophysical precipitation pattern formation is presented and applied to irreversible calcium carbonate (travertine) deposition. Specific systems studied here are the terraces and domes observed at geothermal hot springs, such as those at Yellowstone National Park, and speleothems, particularly stalactites and stalagmites. The theory couples the precipitation front dynamics with shallow water flow, including corrections for turbulent drag and curvature effects. In the absence of capillarity and with a laminar flow profile, the theory predicts a one-parameter family of steady state solutions to the moving boundary problem describing the precipitation front. These shapes match the measured shapes near the vent at the top of observed travertine domes well. Closer to the base of the dome, the solutions deviate from observations and circular symmetry is broken by a fluting pattern, which we show is associated with capillary forces causing thin film break-up. We relate our model to that recently proposed for stalactite growth, and calculate the linear stability spectrum of both travertine domes and stalactites. Lastly, we apply the theory to the problem of precipitation pattern formation arising from turbulent flow down an inclined plane and identify a linear instability that underlies scale-invariant travertine terrace formation at geothermal hot springs. PMID:17995057

  12. Stochastic model explains formation of cell arrays on H/O-diamond patterns.

    PubMed

    Ukraintsev, Egor; Broz, Antonin; Hubalek Kalbacova, Marie; Kromka, Alexander; Rezek, Bohuslav

    2015-01-01

    Cell migration plays an important role in many biological systems. A relatively simple stochastic model is developed and used to describe cell behavior on chemically patterned substrates. The model is based on three parameters: the speed of cell movement (own and external), the probability of cell adhesion, and the probability of cell division on the substrate. The model is calibrated and validated by experimental data obtained on hydrogen- and oxygen-terminated patterns on diamond. Thereby, the simulations reveal that: (1) the difference in the cell movement speed on these surfaces (about 1.5×) is the key factor behind the formation of cell arrays on the patterns, (2) this difference is provided by the presence of fetal bovine serum (validated by experiments), and (3) the directional cell flow promotes the array formation. The model also predicts that the array formation requires mean distance of cell travel at least 10% of intended stripe width. The model is generally applicable for biosensors using diverse cells, materials, and structures.

  13. 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

  14. Steady states and linear stability analysis of precipitation pattern formation at geothermal hot springs.

    PubMed

    Chan, Pak Yuen; Goldenfeld, Nigel

    2007-10-01

    A dynamical theory of geophysical precipitation pattern formation is presented and applied to irreversible calcium carbonate (travertine) deposition. Specific systems studied here are the terraces and domes observed at geothermal hot springs, such as those at Yellowstone National Park, and speleothems, particularly stalactites and stalagmites. The theory couples the precipitation front dynamics with shallow water flow, including corrections for turbulent drag and curvature effects. In the absence of capillarity and with a laminar flow profile, the theory predicts a one-parameter family of steady state solutions to the moving boundary problem describing the precipitation front. These shapes match the measured shapes near the vent at the top of observed travertine domes well. Closer to the base of the dome, the solutions deviate from observations and circular symmetry is broken by a fluting pattern, which we show is associated with capillary forces causing thin film break-up. We relate our model to that recently proposed for stalactite growth, and calculate the linear stability spectrum of both travertine domes and stalactites. Lastly, we apply the theory to the problem of precipitation pattern formation arising from turbulent flow down an inclined plane and identify a linear instability that underlies scale-invariant travertine terrace formation at geothermal hot springs.

  15. 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.

  16. Steady states and linear stability analysis of precipitation pattern formation at geothermal hot springs

    NASA Astrophysics Data System (ADS)

    Chan, Pak Yuen; Goldenfeld, Nigel

    2007-10-01

    A dynamical theory of geophysical precipitation pattern formation is presented and applied to irreversible calcium carbonate (travertine) deposition. Specific systems studied here are the terraces and domes observed at geothermal hot springs, such as those at Yellowstone National Park, and speleothems, particularly stalactites and stalagmites. The theory couples the precipitation front dynamics with shallow water flow, including corrections for turbulent drag and curvature effects. In the absence of capillarity and with a laminar flow profile, the theory predicts a one-parameter family of steady state solutions to the moving boundary problem describing the precipitation front. These shapes match the measured shapes near the vent at the top of observed travertine domes well. Closer to the base of the dome, the solutions deviate from observations and circular symmetry is broken by a fluting pattern, which we show is associated with capillary forces causing thin film break-up. We relate our model to that recently proposed for stalactite growth, and calculate the linear stability spectrum of both travertine domes and stalactites. Lastly, we apply the theory to the problem of precipitation pattern formation arising from turbulent flow down an inclined plane and identify a linear instability that underlies scale-invariant travertine terrace formation at geothermal hot springs.

  17. 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.

  18. Nonlinear stability analyses of vegetative pattern formation in an arid environment

    PubMed Central

    Boonkorkuea, N.; Lenbury, Y.; Alvarado, F.J.; Wollkind, D.J.

    2009-01-01

    The development of spontaneous stationary vegetative patterns in an arid isotropic homogeneous environment is investigated by means of various weakly nonlinear stability analyses applied to the appropriate governing equation for this phenomenon. In particular, that process can be represented by a fourth-order partial differential time-evolution logistic equation for the total plant biomass per unit area divided by the carrying capacity of its territory and defined on an unbounded flat spatial domain. Those patterns that consist of parallel stripes, labyrinth-like mazes, rhombic arrays of rectangular patches, and hexagonal distributions of spots or gaps are generated by the balance between the effects of short-range facilitation and long-range competition. Then those theoretical predictions are compared with both relevant observational evidence and existing numerical simulations as well as placed in the context of the results from some recent nonlinear pattern formation studies. PMID:22881129

  19. 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

  20. Matter-wave interference versus spontaneous pattern formation in spinor Bose-Einstein condensates

    NASA Astrophysics Data System (ADS)

    Witkowski, Marcin; Gartman, Rafał; Nagórny, Bartłomiej; Piotrowski, Marcin; Płodzień, Marcin; Sacha, Krzysztof; Szczepkowski, Jacek; Zachorowski, Jerzy; Zawada, Michał; Gawlik, Wojciech

    2013-08-01

    We describe effects of matter-wave interference of spinor states in the 87Rb Bose-Einstein condensate. The components of the F=2 manifold are populated by forced Majorana transitions and then fall freely due to gravity in an applied magnetic field. Weak inhomogeneities of the magnetic field, present in the experiment, impose relative velocities onto different mF components, which show up as interference patterns upon measurement of atomic density distributions with a Stern-Gerlach imaging method. We show that interference effects may appear in experiments even if gradients of the magnetic field components are eliminated but higher-order inhomogeneity is present and the duration of the interaction is long enough. In particular, we show that the resulting matter-wave interference patterns can mimic spontaneous pattern formation in the quantum gas.

  1. 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

  2. Endothelin signalling in iridophore development and stripe pattern formation of zebrafish

    PubMed Central

    Krauss, Jana; Frohnhöfer, Hans Georg; Walderich, Brigitte; Maischein, Hans-Martin; Weiler, Christian; Irion, Uwe; Nüsslein-Volhard, Christiane

    2014-01-01

    ABSTRACT Colour patterns of adult fish are composed of several different types of pigment cells distributing in the skin during juvenile development. The zebrafish, Danio rerio, displays a striking pattern of dark stripes of melanophores interspersed with light stripes of xanthophores. A third cell type, silvery iridophores, contributes to both stripes and plays a crucial role in adult pigment pattern formation. Several mutants deficient in iridophore development display similar adult phenotypes with reduced numbers of melanophores and defects in stripe formation. This indicates a supporting role of iridophores for melanophore development and maintenance. One of these mutants, rose (rse), encodes the Endothelin receptor b1a. Here we describe a new mutant in zebrafish, karneol (kar), which has a phenotype similar to weak alleles of rse with a reduction in iridophore numbers and defects of adult pigment patterning. We show that, unlike rse, kar is not required in iridophores. The gene defective in the kar mutant codes for an endothelin-converting enzyme, Ece2, which activates endothelin ligands by proteolytic cleavage. By morpholino-mediated knockdown, we identify Endothelin 3b (Edn3b) as the ligand for endothelin receptor signalling in larval iridophores. Thus, Endothelin signalling is involved in iridophore development, proliferation and stripe morphogenesis in larvae as well as adult zebrafish. In mammals the pathway is required for melanocyte development; therefore, our results indicate a previously unrecognized close evolutionary relationship between iridophores in zebrafish and melanocytes in mammals. PMID:24857848

  3. An integrative approach for modeling and simulation of heterocyst pattern formation in cyanobacteria filaments.

    PubMed

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

    2015-03-01

    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

  4. 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

  5. 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.

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

    PubMed

    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=4m. The other is based on a lattice with Moore neighborhood and expanses along eight directions, generating networks with degree of K=8m. 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.

  7. Resonant-pattern formation induced by additive noise in periodically forced reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Wang, Hongli; Zhang, Ke; Ouyang, Qi

    2006-09-01

    We report frequency-locked resonant patterns induced by additive noise in periodically forced reaction-diffusion Brusselator model. In the regime of 2:1 frequency-locking and homogeneous oscillation, the introduction of additive noise, which is colored in time and white in space, generates and sustains resonant patterns of hexagons, stripes, and labyrinths which oscillate at half of the forcing frequency. Both the noise strength and the correlation time control the pattern formation. The system transits from homogeneous to hexagons, stripes, and to labyrinths successively as the noise strength is adjusted. Good frequency-locked patterns are only sustained by the colored noise and a finite time correlation is necessary. At the limit of white noise with zero temporal correlation, irregular patterns which are only nearly resonant come out as the noise strength is adjusted. The phenomenon induced by colored noise in the forced reaction-diffusion system is demonstrated to correspond to noise-induced Turing instability in the corresponding forced complex Ginzburg-Landau equation.

  8. Resonant-pattern formation induced by additive noise in periodically forced reaction-diffusion systems.

    PubMed

    Wang, Hongli; Zhang, Ke; Ouyang, Qi

    2006-09-01

    We report frequency-locked resonant patterns induced by additive noise in periodically forced reaction-diffusion Brusselator model. In the regime of 2:1 frequency-locking and homogeneous oscillation, the introduction of additive noise, which is colored in time and white in space, generates and sustains resonant patterns of hexagons, stripes, and labyrinths which oscillate at half of the forcing frequency. Both the noise strength and the correlation time control the pattern formation. The system transits from homogeneous to hexagons, stripes, and to labyrinths successively as the noise strength is adjusted. Good frequency-locked patterns are only sustained by the colored noise and a finite time correlation is necessary. At the limit of white noise with zero temporal correlation, irregular patterns which are only nearly resonant come out as the noise strength is adjusted. The phenomenon induced by colored noise in the forced reaction-diffusion system is demonstrated to correspond to noise-induced Turing instability in the corresponding forced complex Ginzburg-Landau equation. PMID:17025732

  9. 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.

  10. 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.

  11. 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.

  12. On the formation mechanisms, spatial resolution and intensity of backscatter Kikuchi patterns.

    PubMed

    Zaefferer, S

    2007-01-01

    The present paper is divided into two main sections. In the first, the formation mechanisms of backscatter Kikuchi patterns (BKP) are discussed on the basis of measurements on the sharpness of Kikuchi lines and on the spatial, that means the lateral and depth resolution of the technique. We propose that thermal diffuse scattering is the important incoherent scattering mechanism involved in pattern formation. This mechanism is not considered in the classical description of the origin of backscattered electrons in the scanning electron microscope (SEM) which is why there is in some important points no agreement between classical Monte-Carlo-type electron trajectory simulations and experimental results. We assume that the energy spectrum of the backscattered electrons shows, similar to the spectra in transmission electron microscopy, a sharp zero-loss peak. In the second section, we discuss the intensity of Kikuchi bands in BKP. It is shown that the kinematical theory gives-of course-not the correct intensities, but that these intensities are, on the other hand, not too far off the experimental ones. We subsequently introduce a simple intensity correction procedure that is based on the two-beam dynamical theory, originally proposed by Blackman for transmission electron diffraction patterns. It is shown by examples of diffraction patterns of niobium and silicon that this procedure leads to satisfying results, once two unknown variables (a universal constant and the exit depth of the electrons) have been empirically fit. It is assumed that in the future, this correction will improve the possibilities of phase identification by backscatter Kikuchi diffraction patterns.

  13. Dissipative parametric modulation instability and pattern formation in nonlinear optical systems

    NASA Astrophysics Data System (ADS)

    Perego, A. M.; Tarasov, N.; Churkin, D. V.; Turitsyn, S. K.; Staliunas, K.

    2016-04-01

    We present the essential features of the dissipative parametric instability, in the universal complex Ginzburg- Landau equation. Dissipative parametric instability is excited through a parametric modulation of frequency dependent losses in a zig-zag fashion in the spectral domain. Such damping is introduced respectively for spectral components in the +ΔF and in the -ΔF region in alternating fashion, where F can represent wavenumber or temporal frequency depending on the applications. Such a spectral modulation can destabilize the homogeneous stationary solution of the system leading to growth of spectral sidebands and to the consequent pattern formation: both stable and unstable patterns in one- and in two-dimensional systems can be excited. The dissipative parametric instability provides an useful and interesting tool for the control of pattern formation in nonlinear optical systems with potentially interesting applications in technological applications, like the design of mode- locked lasers emitting pulse trains with tunable repetition rate; but it could also find realizations in nanophotonics circuits or in dissipative polaritonic Bose-Einstein condensates.

  14. 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

  15. Gain-of-function screen for genes that affect Drosophila muscle pattern formation.

    PubMed

    Staudt, Nicole; Molitor, Andreas; Somogyi, Kalman; Mata, Juan; Curado, Silvia; Eulenberg, Karsten; Meise, Martin; Siegmund, Thomas; Häder, Thomas; Hilfiker, Andres; Brönner, Günter; Ephrussi, Anne; Rørth, Pernille; Cohen, Stephen M; Fellert, Sonja; Chung, Ho-Ryun; Piepenburg, Olaf; Schäfer, Ulrich; Jäckle, Herbert; Vorbrüggen, Gerd

    2005-10-01

    This article reports the production of an EP-element insertion library with more than 3,700 unique target sites within the Drosophila melanogaster genome and its use to systematically identify genes that affect embryonic muscle pattern formation. We designed a UAS/GAL4 system to drive GAL4-responsive expression of the EP-targeted genes in developing apodeme cells to which migrating myotubes finally attach and in an intrasegmental pattern of cells that serve myotubes as a migration substrate on their way towards the apodemes. The results suggest that misexpression of more than 1.5% of the Drosophila genes can interfere with proper myotube guidance and/or muscle attachment. In addition to factors already known to participate in these processes, we identified a number of enzymes that participate in the synthesis or modification of protein carbohydrate side chains and in Ubiquitin modifications and/or the Ubiquitin-dependent degradation of proteins, suggesting that these processes are relevant for muscle pattern formation.

  16. 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.

  17. Flow Field and Nutrient Dynamics Control Over Formation of Parallel Vegetation Patterns in the Florida Everglades

    NASA Astrophysics Data System (ADS)

    Engel, V.; Cheng, Y.; Stieglitz, M.

    2009-12-01

    Pattern formation in vegetated communities reflects the underlying mechanisms governing resource utilization and distribution across the landscape. An example of a patterned ecosystem is the Florida Everglades, which is characterized by parallel and slightly elevated peat "ridges" separated by deeper water "slough" communities (R&S). Ridges are dominated by sawgrass (Cladium jamaiscence). These patterns are thought to be aligned with and develop in response to the historic surface water flow direction, though the precise mechanisms which lead to their formation are poorly understood. Over the years this R&S habitat has degraded in areas where the natural flow regime, hydroperiod, and water depths have been impacted by human development. Managing and restoring this habitat has been an objective of the U.S. Federal and Florida State governments since the Comprehensive Everglades Restoration Plan (CERP) was authorized in 2000. It is imperative, however, to develop a mechanistic understanding of ridge-slough formation before the potential benefits of hydrologic forecasts associated with CERP can be evaluated. Recently, Cheng et al (see Cheng et al, session NG14) employed a simple 2D advection-diffusion model developed by Rietkerk et al (2004) to describe for the first time, the formation of parallel stripes from hydrologic interactions. To simulate parallel stripes, Cheng et al retained the basic equations of the Rietkerk model but allowed for constant advection of water and nutrient in one direction to simulate slope conditions, with evapotranspiration driven advection of water and nutrient perpendicular to the downhill flow direction. We employ this modeling framework and parameterize the model with Everglades field data to simulate ridge-slough formation. In this model, the relatively higher rates of evapotranspiration on the ridges compared to the sloughs create hydraulic gradients which carry dissolved nutrients from the sloughs to the faster growing ridges. With

  18. 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.

  19. Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation.

    PubMed

    Tseng, Aisun; Levin, Michael

    2013-01-01

    Patterns of resting potential in non-excitable cells of living tissue are now known to be instructive signals for pattern formation during embryogenesis, regeneration and cancer suppression. The development of molecular-level techniques for tracking ion flows and functionally manipulating the activity of ion channels and pumps has begun to reveal the mechanisms by which voltage gradients regulate cell behaviors and the assembly of complex large-scale structures. A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. This Addendum summarizes the current state of knowledge in developmental bioelectricity, proposes three possible interpretations of the bioelectric code that functionally maps physiological states to anatomical outcomes, and highlights the biggest open questions in this field. We also suggest a speculative hypothesis at the intersection of cognitive science and developmental biology: that bioelectrical signaling among non-excitable cells coupled by gap junctions simulates neural network-like dynamics, and underlies the information processing functions required by complex pattern formation in vivo. Understanding and learning to control the information stored in physiological networks will have transformative implications for developmental biology, regenerative medicine and synthetic bioengineering. PMID:23802040

  20. Pattern Formation in Populations with Density-Dependent Movement and Two Interaction Scales

    PubMed Central

    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

  1. Patterns formations in a diffusive ratio-dependent predator-prey model of interacting populations

    NASA Astrophysics Data System (ADS)

    Camara, B. I.; Haque, M.; Mokrani, H.

    2016-11-01

    The present investigation deals with the analysis of the spatial pattern formation of a diffusive predator-prey system with ratio-dependent functional response involving the influence of intra-species competition among predators within two-dimensional space. The appropriate condition of Turing instability around the interior equilibrium point of the present model has been determined. The emergence of complex patterns in the diffusive predator-prey model is illustrated through numerical simulations. These results are based on the existence of bifurcations of higher codimension such as Turing-Hopf, Turing-Saddle-node, Turing-Transcritical bifurcation, and the codimension- 3 ​Turing-Takens-Bogdanov bifurcation. The paper concludes with discussions of our results in ecology.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. Pattern formation during vapor deposition of organic films on inorganic substrates-continuum modeling vs experiments

    NASA Astrophysics Data System (ADS)

    Vree, C.; Mayr, S. G.

    2009-03-01

    The early stages during low temperature vapor deposition of organic materials onto inorganic substrates are frequently characterized by surface pattern formation on a characteristic length scale, accompanied by dramatic roughening, while these structures level at higher film thicknesses. Unexplainable by traditional liquid-state dewetting scenarios, we employ a combined experimental/modeling study to track down the underlying physics using poly(bisphenol A carbonate) (PC) on GaAs (100) as a model system. We present a minimum continuum model, which incorporates only material deposition and chemical potential driven surface diffusion as material processes, whose numerical solution is capable of reproducing key experimental features.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Delayed frost formation on hybrid nanostructured surfaces with patterned high wetting contrast

    NASA Astrophysics Data System (ADS)

    Hou, Youmin; Zhou, Peng; Yao, Shuhuai

    2014-11-01

    Engineering icephobic surfaces that can retard the frost formation and accumulation are important to vehicles, wind turbines, power lines, and HVAC systems. For condensation frosting, superhydrophobic surfaces promote self-removal of condensed droplets before freezing and consequently delay the frost growth. However, a small thermal fluctuation may lead to a Cassie-to-Wenzel transition, and thus dramatically enhance the frost formation and adhesion. In this work, we investigated the heterogeneous ice nucleation on hybrid nanostructured surfaces with patterned high wetting contrast. By judiciously introducing hydrophilic micro-patches into superhydrophobic nanostructured surface, we demonstrated that such a novel hybrid structure can efficiently defer the ice nucleation as compared to a superhydrophobic surface with nanostructures only. We observed efficient droplet jumping and higher coverage of droplets with diameter smaller than 10 μm, both of which suppress frost formation. The hybrid surface avoids the formation of liquid-bridges for Cassie-to-Wenzel transition, therefore eliminating the `bottom-up' droplet freezing from the cold substrate. These findings provide new insights to improve anti-frosting and anti-icing by using heterogeneous wettability in multiscale structures.

  16. 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

  17. Adenovirus-mediated gene transfer into normal rabbit arteries results in prolonged vascular cell activation, inflammation, and neointimal hyperplasia.

    PubMed Central

    Newman, K D; Dunn, P F; Owens, J W; Schulick, A H; Virmani, R; Sukhova, G; Libby, P; Dichek, D A

    1995-01-01

    Adenovirus vectors are capable of high efficiency in vivo arterial gene transfer, and are currently in use as therapeutic agents in animal models of vascular disease. However, despite substantial data on the ability of viruses to cause vascular inflammation and proliferation, and the presence in current adenovirus vectors of viral open reading frames that are translated in vivo, no study has examined the effect of adenovirus vectors alone on the arterial phenotype. In a rabbit model of gene transfer into a normal artery, we examined potential vascular cell activation, inflammation, and neointimal proliferation resulting from exposure to replication-defective adenovirus. Exposure of normal arteries to adenovirus vectors resulted in: (a) pronounced infiltration of T cells throughout the artery wall; (b) upregulation of intercellular adhesion molecule-1 and vascular cell adhesion molecule-1 in arterial smooth muscle cells; (c) neointimal hyperplasia. These findings were present both 10 and 30 d after gene transfer, with no evidence of a decline in severity over time. Adenovirus vectors have pleiotropic effects on the arterial wall and cause significant pathology. Interpretation of experimental protocols that use adenovirus vectors to address either biological or therapeutic issues should take these observations into account. These observations should also prompt the design of more inert gene transfer vectors. Images PMID:8675667

  18. Super diffraction lithography (SDL): fine random line pattern formation by single-exposure with binary mask

    NASA Astrophysics Data System (ADS)

    Nakao, S.; Abe, J.; Nakae, A.; Imai, A.; Narimatsu, K.; Suko, K.

    2005-05-01

    A novel RET named Super Diffraction Lithography (SDL), which enables 90~80 nm random line by single exposure in KrF wavelength, has been developed. A pair of bright lines, which sandwiches binary or Atten-PSM line and is surrounded by attenuating non-phase-shifting (Atten-NPS) area, is formed on a mask. The Atten-NPS area of the mask is composed with a small pad array whose pitch is finer than the resolution limit of projection optics. Then, this mask can be fabricated with a single layer patterning. When this mask is illuminated by an obliquely incident light with a specific incident angle, very sharp dark line image is formed at center of the bright lines. Because the outside of the pair is Atten-NPS area, image intensity for this area can become much higher than a slice level of the central dark line image, resulting in no resist pattern at the outside of the pair. By application of a sub-resolution assist feature (SRAF) for semi-dense pattern, fine line can be imaged throughout pattern pitch. Then, utilizing SDL, very fine random line can be formed by SINGLE EXPOSURE of SIMPLE STRUCTURE MASK. In KrF exposure at NA=0.82, 90 nm line with pitch of down to 240 nm can be achieved by a binary mask. Using 6% transmission Atten-PSM, 80 nm becomes possible. Moreover, 50 nm isolated line becomes feasible in KrF exposure by application of high transmission Atten-PSM. We believe that SDL is the most cost-effective and easily applicable RET for gate pattern formation in advanced logic devices.

  19. 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

  20. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    PubMed

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-01

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  1. Patterns formation in ferrofluids and solid dissolutions using stochastic models with dissipative dynamics

    NASA Astrophysics Data System (ADS)

    Morales, Marco A.; Fernández-Cervantes, Irving; Agustín-Serrano, Ricardo; Anzo, Andrés; Sampedro, Mercedes P.

    2016-08-01

    A functional with interactions short-range and long-range low coarse-grained approximation is proposed. This functional satisfies models with dissipative dynamics A, B and the stochastic Swift-Hohenberg equation. Furthermore, terms associated with multiplicative noise source are added in these models. These models are solved numerically using the method known as fast Fourier transform. Results of the spatio-temporal dynamic show similarity with respect to patterns behaviour in ferrofluids phases subject to external fields (magnetic, electric and temperature), as well as with the nucleation and growth phenomena present in some solid dissolutions. As a result of the multiplicative noise effect over the dynamic, some microstructures formed by changing solid phase and composed by binary alloys of Pb-Sn, Fe-C and Cu-Ni, as well as a NiAl-Cr(Mo) eutectic composite material. The model A for active-particles with a non-potential term in form of quadratic gradient explain the formation of nanostructured particles of silver phosphate. With these models is shown that the underlying mechanisms in the patterns formation in all these systems depends of: (a) dissipative dynamics; (b) the short-range and long-range interactions and (c) the appropiate combination of quadratic and multiplicative noise terms.

  2. 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

  3. The tomato SlSHINE3 transcription factor regulates fruit cuticle formation and epidermal patterning.

    PubMed

    Shi, Jian Xin; Adato, Avital; Alkan, Noam; He, Yonghua; Lashbrooke, Justin; Matas, Antonio J; Meir, Sagit; Malitsky, Sergey; Isaacson, Tal; Prusky, Dov; Leshkowitz, Dena; Schreiber, Lukas; Granell, Antonio R; Widemann, Emilie; Grausem, Bernard; Pinot, Franck; Rose, Jocelyn K C; Rogachev, Ilana; Rothan, Christophe; Aharoni, Asaph

    2013-01-01

    Fleshy tomato fruit typically lacks stomata; therefore, a proper cuticle is particularly vital for fruit development and interaction with the surroundings. Here, we characterized the tomato SlSHINE3 (SlSHN3) transcription factor to extend our limited knowledge regarding the regulation of cuticle formation in fleshy fruits. We created SlSHN3 overexpressing and silenced plants, and used them for detailed analysis of cuticular lipid compositions, phenotypic characterization, and the study on the mode of SlSHN3 action. Heterologous expression of SlSHN3 in Arabidopsis phenocopied overexpression of the Arabidopsis SHNs. Silencing of SlSHN3 results in profound morphological alterations of the fruit epidermis and significant reduction in cuticular lipids. We demonstrated that SlSHN3 activity is mediated by control of genes associated with cutin metabolism and epidermal cell patterning. As with SlSHN3 RNAi lines, mutation in the SlSHN3 target gene, SlCYP86A69, resulted in severe cutin deficiency and altered fruit surface architecture. In vitro activity assays demonstrated that SlCYP86A69 possesses NADPH-dependent ω-hydroxylation activity, particularly of C18:1 fatty acid to the 18-hydroxyoleic acid cutin monomer. This study provided insights into transcriptional mechanisms mediating fleshy fruit cuticle formation and highlighted the link between cutin metabolism and the process of fruit epidermal cell patterning.

  4. 13C Tracking after 13CO2 Supply Revealed Diurnal Patterns of Wood Formation in Aspen.

    PubMed

    Mahboubi, Amir; Linden, Pernilla; Hedenström, Mattias; Moritz, Thomas; Niittylä, Totte

    2015-06-01

    Wood of trees is formed from carbon assimilated in the photosynthetic tissues. Determining the temporal dynamics of carbon assimilation, subsequent transport into developing wood, and incorporation to cell walls would further our understanding of wood formation in particular and tree growth in general. To investigate these questions, we designed a (13)CO2 labeling system to study carbon transport and incorporation to developing wood of hybrid aspen (Populus tremula × tremuloides). Tracking of (13)C incorporation to wood over a time course using nuclear magnetic resonance spectroscopy revealed diurnal patterns in wood cell wall biosynthesis. The dark period had a differential effect on (13)C incorporation to lignin and cell wall carbohydrates. No (13)C was incorporated into aromatic amino acids of cell wall proteins in the dark, suggesting that cell wall protein biosynthesis ceased during the night. The results show previously unrecognized temporal patterns in wood cell wall biosynthesis, suggest diurnal cycle as a possible cue in the regulation of carbon incorporation to wood, and establish a unique (13)C labeling method for the analysis of wood formation and secondary growth in trees.

  5. 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.

  6. Pattern formation in fiber-reinforced tubular tissues: Folding and segmentation during epithelial growth

    NASA Astrophysics Data System (ADS)

    Ciarletta, P.; Ben Amar, M.

    2012-03-01

    Constrained growth processes in living materials result in a complex distribution of residual strains, which in certain geometries may induce a bifurcation in the elastic stability. In this work, we investigate the combined effects of growth and material anisotropy in the epithelial pattern formation of tubular tissues. In order to represent the structural organization of most organs, we adopt a strain energy density which accounts for the presence of a nonlinear reinforcement made of cross-ply fibers distributed inside a ground matrix. Using a canonical transformation in mixed polar coordinates, we transform the nonlinear elastic boundary value problem into a variational formulation, performing a straightforward derivation of the Euler-Lagrange equations for perturbations in circumferential and longitudinal directions. The corresponding curves of marginal stability are obtained numerically: the results demonstrate that both the three-dimensional distribution of residual strains and the mechanical properties of fiber reinforcements within the tissue are fundamental to determine the emergence of a specific instability pattern. In particular, different proportions of axial and circumferential residual strains can model the epithelial formation of mucosal folds in the esophagus and of plicae circulares in the small intestine. The theoretical predictions are compared with morphological data for embryonic intestinal tissues, suggesting that the volumetric growth of the epithelium can also drive the early stages of villi morphogenesis.

  7. 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.

  8. Entropy Reduction and Regular Pattern Formation in a Nonlinear Non-equilibrium System: An Energetic Approach

    NASA Astrophysics Data System (ADS)

    Ozawa, H.; Shimokawa, S.

    2005-12-01

    Regular pattern formation in a nonlinear non-equilibrium system is investigated from an energetic viewpoint. A nonlinear system is driven by available energy (energy available for conversion to kinetic energy) supplied from its non-equilibrium surroundings, and this energy is dissipated through small-scale dissipation processes in the system (i.e., entropy production). A power balance equation is formulated for the change rate of the total available energy of a system: C = G - D, where G is the generation rate of the available energy and D is the dissipation rate due to thermal and viscous dissipation (entropy production). The change rate C is zero when the concerned system is in a steady state, whereas it is positive (acceleration) or negative (deceleration) in non-steady transitional periods. A fluctuation in a macroscopic physical variable, such as fluid velocity, can change the value G, while it does not change the value D immediately when the scale of the fluctuation is larger than the dissipation scale. The large-scale fluctuation that increases G can therefore grow by the positive gain in the available energy (C > 0) through a nonlinear feedback process. This feedback process can thus drive the system towards a state with the maximum G, which also corresponds to the maximum D in the steady state (C = 0). It follows from mathematical manipulation that the change rate C is proportional to the decrease rate of entropy of a concerned system - the system's entropy must decrease during the acceleration period (C > 0). This result is consistent with our observations that regular patterns or orderly structures emerge spontaneously in the developing stages of the nonlinear non-equilibrium systems. Some examples (e.g., Benard convection, ocean circulation and granular pattern formation) are discussed in this respect.

  9. 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

  10. 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

  11. 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.

  12. Accelerated fluctuation analysis by graphic cards and complex pattern formation in financial markets

    NASA Astrophysics Data System (ADS)

    Preis, Tobias; Virnau, Peter; Paul, Wolfgang; Schneider, Johannes J.

    2009-09-01

    The compute unified device architecture is an almost conventional programming approach for managing computations on a graphics processing unit (GPU) as a data-parallel computing device. With a maximum number of 240 cores in combination with a high memory bandwidth, a recent GPU offers resources for computational physics. We apply this technology to methods of fluctuation analysis, which includes determination of the scaling behavior of a stochastic process and the equilibrium autocorrelation function. Additionally, the recently introduced pattern formation conformity (Preis T et al 2008 Europhys. Lett. 82 68005), which quantifies pattern-based complex short-time correlations of a time series, is calculated on a GPU and analyzed in detail. Results are obtained up to 84 times faster than on a current central processing unit core. When we apply this method to high-frequency time series of the German BUND future, we find significant pattern-based correlations on short time scales. Furthermore, an anti-persistent behavior can be found on short time scales. Additionally, we compare the recent GPU generation, which provides a theoretical peak performance of up to roughly 1012 floating point operations per second with the previous one. .

  13. 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

  14. 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.

  15. 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.

  16. 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

  17. Chemo-Marangoni convection driven by an interfacial reaction: Pattern formation and kinetics

    NASA Astrophysics Data System (ADS)

    Eckert, K.; Acker, M.; Tadmouri, R.; Pimienta, V.

    2012-09-01

    A combined study devoted to chemo-Marangoni convection and the underlying kinetics is presented for a biphasic system in which surfactants are produced in situ by an interfacial reaction. The pattern formation studied in a Hele-Shaw cell in both microgravity and terrestrial environments initially shows an ensemble of chemo-Marangoni cells along a nearly planar interface. Soon, a crossover occurs to periodic large-scale interfacial deformations which coexist with the Marangoni cells. This crossover can be correlated with the autocatalytic nature of the interfacial reaction identified in the kinetic studies. The drastic increase in the product concentration is associated with an enhanced aggregate-assisted transfer after the critical micellar concentration is approached. In this context, it was possible to conclusively explain the changes in the periodicity of the interfacial deformations depending on the reactant concentration ratio.

  18. 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.

  19. Chemo-Marangoni convection driven by an interfacial reaction: pattern formation and kinetics.

    PubMed

    Eckert, K; Acker, M; Tadmouri, R; Pimienta, V

    2012-09-01

    A combined study devoted to chemo-Marangoni convection and the underlying kinetics is presented for a biphasic system in which surfactants are produced in situ by an interfacial reaction. The pattern formation studied in a Hele-Shaw cell in both microgravity and terrestrial environments initially shows an ensemble of chemo-Marangoni cells along a nearly planar interface. Soon, a crossover occurs to periodic large-scale interfacial deformations which coexist with the Marangoni cells. This crossover can be correlated with the autocatalytic nature of the interfacial reaction identified in the kinetic studies. The drastic increase in the product concentration is associated with an enhanced aggregate-assisted transfer after the critical micellar concentration is approached. In this context, it was possible to conclusively explain the changes in the periodicity of the interfacial deformations depending on the reactant concentration ratio.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. Formation of colorimetric fingerprints on nano-patterned deterministic aperiodic surfaces.

    PubMed

    Boriskina, Svetlana V; Lee, Sylvanus Y K; Amsden, Jason J; Omenetto, Fiorenzo G; Dal Negro, Luca

    2010-07-01

    Periodic gratings and photonic bandgap structures have been studied for decades in optical technologies. The translational invariance of periodic gratings gives rise to well-known angular and frequency filtering of the incident radiation resulting in well-defined scattered colors in response to broadband illumination. Here, we demonstrate the formation of highly complex structural color patterns, or colorimetric fingerprints, in two-dimensional (2D) deterministic aperiodic gratings using dark field scattering microscopy. The origin of colorimetric fingerprints is explained by rigorous full-wave numerical simulations based on the generalized Mie theory. We show that unlike periodic gratings, aperiodic nanopatterned surfaces feature a broadband frequency response with wide angular intensity distributions governed by the distinctive Fourier properties of the aperiodic structures. Finally, we will discuss a range of potential applications of colorimetric fingerprints for optical sensing and spectroscopy. PMID:20639942

  5. 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

  6. Nonconstant Positive Steady States and Pattern Formation of 1D Prey-Taxis Systems

    NASA Astrophysics Data System (ADS)

    Wang, Qi; Song, Yang; Shao, Lingjie

    2016-08-01

    Prey-taxis is the process that predators move preferentially toward patches with highest density of prey. It is well known to have an important role in biological control and the maintenance of biodiversity. To model the coexistence and spatial distributions of predator and prey species, this paper concerns nonconstant positive steady states of a wide class of prey-taxis systems with general functional responses over 1D domain. Linearized stability of the positive equilibrium is analyzed to show that prey-taxis destabilizes prey-predator homogeneity when prey repulsion (e.g., due to volume-filling effect in predator species or group defense in prey species) is present, and prey-taxis stabilizes the homogeneity otherwise. Then, we investigate the existence and stability of nonconstant positive steady states to the system through rigorous bifurcation analysis. Moreover, we provide detailed and thorough calculations to determine properties such as pitchfork and turning direction of the local branches. Our stability results also provide a stable wave mode selection mechanism for thee reaction-advection-diffusion systems including prey-taxis models considered in this paper. Finally, we provide numerical studies of prey-taxis systems with Holling-Tanner kinetics to illustrate and support our theoretical findings. Our numerical simulations demonstrate that the 2× 2 prey-taxis system is able to model the formation and evolution of various striking patterns, such as spikes, periodic oscillations, and coarsening even when the domain is one-dimensional. These dynamics can model the coexistence and spatial distributions of interacting prey and predator species. We also give some insights on how system parameters influence pattern formation in these models.

  7. Mathematics and biology: a Kantian view on the history of pattern formation theory.

    PubMed

    Roth, Siegfried

    2011-12-01

    Driesch's statement, made around 1900, that the physics and chemistry of his day were unable to explain self-regulation during embryogenesis was correct and could be extended until the year 1972. The emergence of theories of self-organisation required progress in several areas including chemistry, physics, computing and cybernetics. Two parallel lines of development can be distinguished which both culminated in the early 1970s. Firstly, physicochemical theories of self-organisation arose from theoretical (Lotka 1910-1920) and experimental work (Bray 1920; Belousov 1951) on chemical oscillations. However, this research area gained broader acceptance only after thermodynamics was extended to systems far from equilibrium (1922-1967) and the mechanism of the prime example for a chemical oscillator, the Belousov-Zhabotinski reaction, was deciphered in the early 1970s. Secondly, biological theories of self-organisation were rooted in the intellectual environment of artificial intelligence and cybernetics. Turing wrote his The chemical basis of morphogenesis (1952) after working on the construction of one of the first electronic computers. Likewise, Gierer and Meinhardt's theory of local activation and lateral inhibition (1972) was influenced by ideas from cybernetics. The Gierer-Meinhardt theory provided an explanation for the first time of both spontaneous formation of spatial order and of self-regulation that proved to be extremely successful in elucidating a wide range of patterning processes. With the advent of developmental genetics in the 1980s, detailed molecular and functional data became available for complex developmental processes, allowing a new generation of data-driven theoretical approaches. Three examples of such approaches will be discussed. The successes and limitations of mathematical pattern formation theory throughout its history suggest a picture of the organism, which has structural similarity to views of the organic world held by the philosopher

  8. Pattern formation in discrete cell tissues under long range filopodia-based direct cell to cell contact.

    PubMed

    Vasilopoulos, Georgios; Painter, Kevin J

    2016-03-01

    Pattern formation via direct cell to cell contact has received considerable attention over the years. In particular the lateral-inhibition mechanism observed in the Notch signalling pathway can generate a regular periodic pattern of differential cell activity, and has been proposed to explain the emergence of patterns in various tissues and organs. The majority of models of this system have focussed on short-range contacts: a cell signals only to its nearest neighbours and the resulting patterns tend to be of fine-scale "salt and pepper" nature. The capacity of certain cells to extend signalling filopodia (cytonemes) over multiple cell lengths, however, inserts a long-range or non-local component into this process. Here we explore how long range signalling can impact on pattern formation. Specifically, we extend a standard model for Notch-like lateral inhibition to include cytoneme-mediated signalling, and investigate how pattern formation depends on the spatial distribution of signal from the signalling cell. We show that a variety of patterns can be obtained, ranging from a sparse pattern of single isolated cells to larger clusters or stripes.

  9. Suture pattern formation in ammonites and the unknown rear mantle structure

    PubMed Central

    Inoue, Shinya; Kondo, Shigeru

    2016-01-01

    Ammonite shells have complex patterns of suture lines that vary across species. The lines are formed at the intersection of the outer shell wall and the septa. The wavy septa can form if the rear mantle of the ammonite, which functions as the template, has a complex shape. Previous hypotheses assumed that the rear mantle is like a flexible membrane that can be folded by some physical force. The elucidation of the mechanism of septa formation requires that the detailed shape of the septa should be known. We developed a new protocol of X-ray micro-computed tomography (CT) and obtained high-resolution three-dimensional (3D) images of the septa of the Upper Cretaceous ammonite Damesites cf. damesi. The obtained image suggested that the wavy and branched structures of the rear mantle grew autonomously. We found that some extant sea slugs have branched structures and showed similar shape and growth sequence as those in fossils, suggesting that the mantle of molluscs basically has the potential to form branched projections. Based on the characteristics of the obtained 3D structure, we explain how ammonites might have formed the complex suture patterns. PMID:27640361

  10. 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

  11. Si micropyramid patterned anodes that can suppress fracture and solid electrolyte interface formation during electrochemical cycling

    NASA Astrophysics Data System (ADS)

    Deng, Haokun; Chu, Geng; Luo, Fei; Li, Hong; Chen, Liquan; Aifantis, Katerina E.

    2016-10-01

    Two new types of Si patterned surfaces are presented that have either a solid micropyramid structure or a double microstructure in which nanopores are induced on the pyramid surface. The pyramid diameter ranges between 1 and 6 μm, while the pores are 50-100 nm in diameter and ∼100-400 nm deep. It is illustrated that when they are employed as anodes, in Li-ion batteries, these patterned anodes, at high current densities of 1C, can (i) retain their initial morphology intact, despite the ∼400% expansion that Si experiences upon lithiation, and (ii) minimize the formation of the solid electrolyte interface (SEI) that forms upon decomposition of the electrolyte. Furthermore, for the nanoporous-micropyramids, scanning electron microscopy after twenty-five electrochemical cycles reveals that no fracture occurs in either high (1 C) or low (0.1 C) current densities. This is a unique and significant observation as similar experiments, at 0.1 C, on the solid micropyramid surfaces indicate severe fracture from the first Li-insertion. It is therefore concluded that introducing a nanostructure on micropyramids significantly enhances their structural stability. This suggests that microscale Si with induced nanopores is an alternative anode candidate to nanoscale Si.

  12. 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.

  13. Network inference of AP pattern formation system in D.melanogaster by structural equation modeling

    NASA Astrophysics Data System (ADS)

    Aburatani, S.; Toh, H.

    2014-03-01

    Within the field of systems biology, revealing the control systems functioning during embryogenesis is an important task. To clarify the mechanisms controlling sequential events, the relationships between various factors and the expression of specific genes should be determined. In this study, we applied a method based on Structural Equation Modeling (SEM), combined with factor analysis. SEM can include the latent variables within the constructed model and infer the relationships among the latent and observed variables, as a network model. We improved a method for the construction of initial models for the SEM calculation, and applied our approach to estimate the regulatory network for Antero-Posterior (AP) pattern formation in D. melanogaster embryogenesis. In this new approach, we combined cross-correlation and partial correlation to summarize the temporal information and to extract the direct interactions from the gene expression profiles. In the inferred model, 18 transcription factor genes were regulated by not only the expression of other genes, but also the estimated factors. Since each factor regulated the same type of genes, these factors were considered to be involved in maternal effects or spatial morphogen distributions. The interpretation of the inferred network model allowed us to reveal the regulatory mechanism for the patterning along the head to tail axis in D. melanogaster.

  14. Facets formation mechanism of GaN hexagonal pyramids on dot-patterns via selective MOVPE

    SciTech Connect

    Hiramatsu, Kazumasa; Kitamura, Shota; Sawaki, Nobuhiko

    1996-11-01

    Three-dimensional GaN pyramids have been successfully obtained on dot-patterned GaN(0001)/sapphire substrates by using the selective MOVPE technique. The dot-pattern is a hexagon arranged with a 5{micro}m width and a 10{micro}m spacing. The GaN structure comprises a hexagonal pyramid covered with six {l_brace}1{bar 1}01{r_brace} pyramidal facets on the side or a frustum of a hexagonal pyramid having a (0001) facet on the top. The facet formation mechanism has been investigated by observing the facet structure with the growth time. The {l_brace}1{bar 1}01{r_brace} facets are very stable during the growth. The (0001) facet growth is dominant at the initial growth but almost stops at a certain growth time and then the facet structure is maintained. The appearance of the self-limited (0001) facet is attributed to the balance of flux between incoming Ga atoms from the vapor phase to the (0001) surface and outgoing Ga atoms from the (0001) surface to the {l_brace}1{bar 1}01{r_brace} surface via migration. The longer the diffusion length of the Ga atoms on the (0001) surface is, the more the surface migration is enhanced, resulting in the appearance of the wider (0001) facet on the top.

  15. Drivers of emergent vegetation pattern formation at hillslope scales in a central Kenya dryland

    NASA Astrophysics Data System (ADS)

    Caylor, K. K.; Franz, T. E.; King, E.; Robinson, D.

    2010-12-01

    The natural state of vegetation in dryland ecosystems is a complex interaction between climate, soils, vegetation, and topography. Using an optimality tradeoff hypothesis of plant water use and plant water stress, we investigate the the dynamics of vegetation spatial pattern within topographically complex semi-arid landscapes of central Kenya. Gradual increases in grazing pressure over the last five decades has led to the loss of inter-canopy herbaceous vegetation and the proliferation of a previously rare native invasive succulent, Sansevieria volkensii. In order to determine if shifts in surface hydrological process have facilitated the expansion of S. volkensii, we use electromagnetic-induction (EMI) imaging, combined with soil moisture sensors to monitor event-scale infiltration/recharge dynamics in individual S. volkensii patches across an invaded hillslope. Coupling our field observations to a numerical subsurface flow model suggests the presence of positive hydrological feedbacks which may be encouraging the proliferation of S. volkensii. We incorporate these spatial feedbacks into a relatively simple spatially explicit ecohydrologic hillslope model. The model suggests that differences in canopy to root ratios have a substantial impact on optimal pattern formation, with succulent plants becoming highly clustered and reduced clustering predicted in trees.

  16. 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.

  17. Suture pattern formation in ammonites and the unknown rear mantle structure.

    PubMed

    Inoue, Shinya; Kondo, Shigeru

    2016-01-01

    Ammonite shells have complex patterns of suture lines that vary across species. The lines are formed at the intersection of the outer shell wall and the septa. The wavy septa can form if the rear mantle of the ammonite, which functions as the template, has a complex shape. Previous hypotheses assumed that the rear mantle is like a flexible membrane that can be folded by some physical force. The elucidation of the mechanism of septa formation requires that the detailed shape of the septa should be known. We developed a new protocol of X-ray micro-computed tomography (CT) and obtained high-resolution three-dimensional (3D) images of the septa of the Upper Cretaceous ammonite Damesites cf. damesi. The obtained image suggested that the wavy and branched structures of the rear mantle grew autonomously. We found that some extant sea slugs have branched structures and showed similar shape and growth sequence as those in fossils, suggesting that the mantle of molluscs basically has the potential to form branched projections. Based on the characteristics of the obtained 3D structure, we explain how ammonites might have formed the complex suture patterns. PMID:27640361

  18. 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

  19. Formation of ordered microphase-separated pattern during spin coating of ABC triblock copolymer

    NASA Astrophysics Data System (ADS)

    Huang, Weihuan; Luo, Chunxia; Zhang, Jilin; Han, Yanchun

    2007-03-01

    In this paper, the authors have systematically studied the microphase separation and crystallization during spin coating of an ABC triblock copolymer, polystyrene-b-poly(2-vinylpyridine)-b-poly(ethylene oxide) (PS-b-P2VP-b-PEO). The microphase separation of PS-b-P2VP-b-PEO and the crystallization of PEO blocks can be modulated by the types of the solvent and the substrate, the spinning speed, and the copolymer concentration. Ordered microphase-separated pattern, where PEO and P2VP blocks adsorbed to the substrate and PS blocks protrusions formed hexagonal dots above the P2VP domains, can only be obtained when PS-b-P2VP-b-PEO is dissolved in N,N-dimethylformamide and the films are spin coated onto the polar substrate, silicon wafers or mica. The mechanism of the formation of regular pattern by microphase separation is found to be mainly related to the inducement of the substrate (middle block P2VP wetting the polar substrate), the quick vanishment of the solvent during the early stage of the spin coating, and the slow evaporation of the remaining solvent during the subsequent stage. On the other hand, the probability of the crystallization of PEO blocks during spin coating decreases with the reduced film thickness. When the film thickness reaches a certain value (3.0nm), the extensive crystallization of PEO is effectively prohibited and ordered microphase-separated pattern over large areas can be routinely prepared. When the film thickness exceeds another definite value (12.0nm), the crystallization of PEO dominates the surface morphology. For films with thickness between these two values, microphase separation and crystallization can simultaneously occur.

  20. 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.

  1. Pattern formation arising from condensation of a homogeneous gas into a binary, phase-separating liquid.

    PubMed

    Pooley, C M; Balazs, Anna C; Yeomans, J M

    2005-08-01

    We examine the nucleated growth of a binary, immiscible liquid drop within a homogeneous gas. The system couples the growth of the liquid drop with the phase separation of the immiscible components and, thus, can potentially reveal novel pattern formation. To carry out this study, we first characterize the thermodynamic properties of the system in terms of an appropriate Ginzburg-Landau free energy density. By minimizing this free energy, we construct the equilibrium phase diagram for the system. We then use a lattice Boltzmann algorithm to solve the hydrodynamic equations describing the dynamical evolution of the fluid. We observe intriguing tentaclelike structures within the nucleation and growth regime and explore how the formation of these structures depends on the thermodynamic and transport properties of the system. We give scaling laws describing domain growth in both the diffusion- and flow-limited regimes. The results highlight the novel physics that can emerge when there is interplay between the ordering of a density and a concentration field.

  2. [Recombinant genome of cereals: the pattern of formation and the role in evolution of polyploid species].

    PubMed

    Dubovets, N I; Sycheva, E A; Soloveĭ, L A; Styk, T I; Bondarevich, E B

    2008-01-01

    The pivotal-differential model of evolution of polyploid species of cereals has been experimentally reproduced, and the pattern of the formation of a recombinant genome has been analyzed. It has been found that mutual substitution of chromosomes of the original genomes is subjected to selection pressure and, hence, is nonrandom. The selection occurs at the level of homeologs, whose selective advantages are determined by interactions between the genotype and the environment. If a homeolog has distinct selective advantages, the chromosomal composition of the corresponding homeologous group is completed rapidly, which leads to the formation of intergenomic recombination at the level of whole chromosomes. If homeologs have the same competitiveness, the composition of the group is stabilized more slowly. Domination of the genetic systems of the basic genome ensures a high rate of pairing of homeologous chromosomes of the recombinant genome during meiosis, which leads to recombinations at the level of chromosomal segments. It has been demonstrated that different combinations of chromosomes from original genomes are selected at different conditions of plant growth. PMID:18409387

  3. Cobalt (II) chloride promoted formation of honeycomb patterned cellulose acetate films.

    PubMed

    Naboka, Olga; Sanz-Velasco, Anke; Lundgren, Per; Enoksson, Peter; Gatenholm, Paul

    2012-02-01

    CoCl(2) containing honeycomb patterned films were prepared from cellulose acetate (CA)/CoCl(2)/acetone solutions by the breath figure method in a wide range of humidities. Size and pore regularity depend on the CA/CoCl(2) molar ratio and humidity. When replacing CoCl(2) with Co(NO(3))(2) or CoBr(2), no formation of ordered porosity in the cellulose acetate films is observed. According to data from scanning electron microscopy (SEM), Energy Dispersive X-ray Microanalysis (EDX), X-ray Diffraction (XRD) and Fourier transform infrared (FTIR) spectroscopy, the key role in the formation of honeycomb structures can be attributed to the physical and chemical properties of CoCl(2) - hygroscopicity, low interaction with CA, and extraction from CA/CoCl(2)/acetone solution by water droplets condensed on the surface of the CA/CoCl(2) solution. Obtained films are prospective for using in catalysis, hydrogen fuel cells, and optical sensing materials.

  4. 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.

  5. 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.

  6. Inhibition of neointimal proliferation in rabbits after vascular injury by a single treatment with a protein adduct of nitric oxide.

    PubMed Central

    Marks, D S; Vita, J A; Folts, J D; Keaney, J F; Welch, G N; Loscalzo, J

    1995-01-01

    Endothelium-derived relaxing factor is important for vascular homeostasis and possesses qualities that may modulate vascular injury, including vasodilation, platelet inhibition, and inhibition of smooth muscle proliferation. S-nitrososerum albumin is a naturally occurring adduct of nitric oxide (NO) with a prolonged biologic half-life and is a potent vasodilator and platelet inhibitor. Given the avidity of serum albumin for subendothelial matrix and the antiproliferative effects of NO, we investigated the effects of locally delivered S-nitroso-bovine serum albumin (S-NO-BSA) and a polythiolated form of bovine serum albumin (pS-BSA) modified to carry several S-nitrosothiol groups (pS-NO-BSA) on neointimal responses in an animal model of vascular injury. Locally delivered S-NO-BSA bound preferentially to denuded rabbit femoral vessels producing a 26-fold increase in local concentration compared with uninjured vessels (P = 0.029). pS-NO-BSA significantly reduced the intimal/medial ratio (P = 0.038) and did so in conjunction with elevations in platelet (P < 0.001) and vascular cGMP content (P < or = 0.001). pS-NO-BSA treatment also inhibited platelet deposition (P = 0.031) after denuding injury. Comparison of BSA, S-NO-BSA, pS-NO-BSA, and control revealed a dose-response relationship between the amount of displaceable NO delivered and the extent of inhibition of neointimal proliferation at 2 wk (P < or = 0.001). Local administration of a stable protein S-nitrosothiol inhibits intimal proliferation and platelet deposition after vascular arterial balloon injury. This strategy for the local delivery of a long-lived NO adduct has potential for preventing restenosis after angioplasty. Images PMID:8675628

  7. 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

  8. 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

  9. 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.

  10. Metolachlor and alachlor breakdown product formation patterns in aquatic field mesocosms

    USGS Publications Warehouse

    Graham, W.H.; Graham, D.W.; DeNoyelles, F.; 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

  11. [Modeling of hysteresis in pH pattern formation along the cell membrane of algae Chara corallina].

    PubMed

    Lavrova, A I; Pliusnina, T Iu; Bulychev, A A; Riznichenko, G Iu; Rubin, A B

    2005-01-01

    It is known that illumination of the algae Chara corallina results in the formation along the membrane of regions with inhomogeneous distribution of pH. It was shown that, in a particular range of illumination intensities, two states with different pH distribution are realized at one and the same value of light intensity: an entirely homogeneous state and completely formed structures (pattern). The transition from the homogeneous state to the pattern formation takes place at one value of light intensity, and the back transition, at another light intensity, i.e., the hysteresis is observed. This phenomenon was studied by mathematical modeling. The mechanism of hysteresis is discussed.

  12. 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.

  13. 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.

  14. Individual Rules for Trail Pattern Formation in Argentine Ants (Linepithema humile)

    PubMed Central

    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

  15. 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

  16. Pattern formation and coarse-graining in two-dimensional colloids driven by multiaxial magnetic fields.

    PubMed

    Müller, Kathrin; Osterman, Natan; Babič, Dušan; Likos, Christos N; Dobnikar, Jure; Nikoubashman, Arash

    2014-05-13

    We study the pattern formation in a two-dimensional system of superparamagnetic colloids interacting via spatially coherent induced interactions driven by an external precessing magnetic field. On the pair level, upon changing the opening angle of the external field, the interactions smoothly vary from purely repulsive (opening angle equal to zero) to purely attractive (time-averaged pair interactions at an opening angle of 90°). In the experiments, we observed ordered hexagonal crystals at the repulsive end and coarsening frothlike structures for purely attractive interactions. In both of these limiting cases, the dense colloidal systems can be sufficiently accurately described by assuming pairwise additivity of the interaction potentials. However, for a range of intermediate angles, pronounced many-body depolarization effects compete with the direct induced interactions, resulting in inherently anisotropic effective interactions. Under such conditions, we observed the decay of hexagonal order with the concomitant formation of short chains and percolated networks of chains coexisting with free colloids. In order to describe and investigate these systems theoretically, we developed a coarse-grained model of a binary mixture of patchy and nonpatchy particles with the ratio of patchy and nonpatchy colloids as the order parameter. Combining genetic algorithms with Monte Carlo simulations, we optimized the model parameters and quantitatively reproduced the experimentally observed sequence of colloidal structures. The results offer new insight into the anisotropy induced by the many-body effects. At the same time, they allow for a very efficient description of the system by means of a pairwise-additive Hamiltonian, whereupon the original, one-component system features a two-component mixture of isotropic and patchy colloids.

  17. 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.

  18. 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

  19. 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

    2013-06-04

    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.

  20. 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

  1. Parametric and nonparametric analysis of life courses: an application to family formation patterns.

    PubMed

    Bonetti, Marco; Piccarreta, Raffaella; Salford, Gaia

    2013-06-01

    We discuss a unified approach to the description and explanation of life course patterns represented as sequences of states observed in discrete time. In particular, we study life course data collected as part of the Dutch Fertility and Family Surveys (FFS) to learn about the family formation behavior of 1,897 women born between 1953 and 1962. Retrospective monthly data were available on each 18- to 30-year-old woman living either with or without children as single, married, or cohabiting. We first study via a nonparametric approach which factors explain the pairwise dissimilarities observed between life courses. Permutation distribution inference allows for the study of the statistical significance of the effect of a set of covariates of interest. We then develop a parametric model for the sequence-generating process that can be used to describe state transitions and durations conditional on covariates and conditional on having observed an initial segment of the trajectory. Fitting of the proposed model and the corresponding model selection process are based on the observed data likelihood. We discuss the application of the methods to the FFS.

  2. 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.

  3. Polar Pattern Formation in Driven Filament Systems Require Non-Binary Particle Collisions

    PubMed Central

    Suzuki, Ryo; Weber, Christoph A.; Frey, Erwin; Bausch, Andreas R.

    2016-01-01

    Living matter has the extraordinary ability to behave in a concerted manner, which is exemplified throughout nature ranging from the self-organisation of the cytoskeleton to flocks of animals [1–4]. The microscopic dynamics of constituents have been linked to the system’s meso- or macroscopic behaviour in silico via the Boltzmann equation for propelled particles [5–10]. Thereby, simplified binary collision rules between the constituents had to be assumed due to the lack of experimental data. We report here experimentally determined binary collision statistics by studying the recently introduced molecular system, the high density actomyosin motility assay [11–13]. We demonstrate that the alignment effect of the binary collision statistics is too weak to account for the observed ordering transition. The transition density for polar pattern formation decreases quadratically with filament length, which indicates 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. The presented findings demonstrate that the unique properties of biological active matter systems require a description that goes well beyond a gas-like picture developed in the framework of kinetic theories.

  4. Polar Pattern Formation in Driven Filament Systems Require Non-Binary Particle Collisions

    PubMed Central

    Suzuki, Ryo; Weber, Christoph A.; Frey, Erwin; Bausch, Andreas R.

    2016-01-01

    Living matter has the extraordinary ability to behave in a concerted manner, which is exemplified throughout nature ranging from the self-organisation of the cytoskeleton to flocks of animals [1–4]. The microscopic dynamics of constituents have been linked to the system’s meso- or macroscopic behaviour in silico via the Boltzmann equation for propelled particles [5–10]. Thereby, simplified binary collision rules between the constituents had to be assumed due to the lack of experimental data. We report here experimentally determined binary collision statistics by studying the recently introduced molecular system, the high density actomyosin motility assay [11–13]. We demonstrate that the alignment effect of the binary collision statistics is too weak to account for the observed ordering transition. The transition density for polar pattern formation decreases quadratically with filament length, which indicates 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. The presented findings demonstrate that the unique properties of biological active matter systems require a description that goes well beyond a gas-like picture developed in the framework of kinetic theories. PMID:27656244

  5. 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.

  6. Pattern formation, social forces, and diffusion instability in games with success-driven motion

    NASA Astrophysics Data System (ADS)

    Helbing, Dirk

    2009-02-01

    A local agglomeration of cooperators can support the survival or spreading of cooperation, even when cooperation is predicted to die out according to the replicator equation, which is often used in evolutionary game theory to study the spreading and disappearance of strategies. In this paper, it is shown that success-driven motion can trigger such local agglomeration and may, therefore, be used to supplement other mechanisms supporting cooperation, like reputation or punishment. Success-driven motion is formulated here as a function of the game-theoretical payoffs. It can change the outcome and dynamics of spatial games dramatically, in particular as it causes attractive or repulsive interaction forces. These forces act when the spatial distributions of strategies are inhomogeneous. However, even when starting with homogeneous initial conditions, small perturbations can trigger large inhomogeneities by a pattern-formation instability, when certain conditions are fulfilled. Here, these instability conditions are studied for the prisoner’s dilemma and the snowdrift game. Furthermore, it is demonstrated that asymmetrical diffusion can drive social, economic, and biological systems into the unstable regime, if these would be stable without diffusion.

  7. 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.

  8. 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.

  9. Peptide Induced Crystallization of Calcium Carbonate on Wrinkle Patterned Substrate: Implications for Chitin Formation in Molluscs

    PubMed Central

    Sengupta Ghatak, Anindita; 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

  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. 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.

  12. Pattern formation during healing of fluid-filled cracks: an analog experiment

    SciTech Connect

    F. Renard; D. K. Dysthe; J. G. Feder; Paul Meakin; S.J.S. Morris; B. Jamtveit

    2009-11-01

    The formation and subsequent healing of cracks and crack networks may control such diverse phenomena as the strengthening of fault zones between earthquakes, fluid migrations in the Earth's crust, or the transport of radioactive materials in nuclear waste disposal. An intriguing pattern-forming process can develop during healing of fluid-filled cracks, where pockets of fluid remain permanently trapped in the solid as the crack tip is displaced driven by surface energy. Here, we present the results of analog experiments in which a liquid was injected into a colloidal inorganic gel to obtain penny-shaped cracks that were subsequently allowed to close and heal under the driving effect of interfacial tension. Depending on the properties of the gel and the injected liquid, two modes of healing were obtained. In the first mode, the crack healed completely through a continuous process. The second mode of healing was discontinuous and was characterized by a 'zipper-like' closure of a front that moved along the crack perimeter, trapping fluid that may eventually form inclusions trapped in the solid. This instability occurred only when the velocity of the crack tip decreased to zero. Our experiments provide a cheap and simple analog to reveal how aligned arrays of fluid inclusions may be captured along preexisting fracture planes and how small amounts of fluids can be permanently trapped in solids, modifying irreversibly their material properties.

  13. 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

  14. 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

  15. 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.

  16. Neointimal coverage and late apposition of everolimus-eluting bioresorbable scaffolds implanted in the acute phase of myocardial infarction: OCT data from the PRAGUE-19 study.

    PubMed

    Toušek, Petr; Kočka, Viktor; Malý, Martin; Lisa, Libor; Buděšínský, Tomáš; Widimský, Petr

    2016-06-01

    Incomplete stent apposition and uncovered struts are associated with a higher risk of stent thrombosis. No data exist on the process of neointimal coverage and late apposition status of the bioresorbable vascular scaffold (BVS) when implanted in the highly thrombogenic setting of ST-segment elevation acute myocardial infarction (STEMI). The aim of this study was to assess the serial changes in strut apposition and early neointimal coverage of the BVS using optical coherence tomography (OCT) in selected patients enrolled in the PRAGUE-19 study. Intracoronary OCT was performed in 50 patients at the end of primary percutaneous coronary intervention for acute STEMI. Repeated OCT of the implanted BVS was performed in 10 patients. Scaffold area, scaffold mean diameter and incomplete strut apposition (ISA) were compared between baseline and control OCT. Furthermore, strut neointimal coverage was assessed during the control OCT. Mean scaffold area and diameter did not change between the baseline and control OCT (8.59 vs. 9.06 mm(2); p = 0.129 and 3.31 vs. 3.37 mm; p = 0.202, respectively). Differences were observed in ISA between the baseline and control OCT (0.63 vs. 1.47 %; p < 0.05). We observed 83.1 % covered struts in eight patients in whom the control OCT was performed 4-6 weeks after BVS implantation, and 100 % covered struts in two patients 6 months after BVS implantation. Persistent strut apposition and early neointimal coverage were observed after biodegradable vascular scaffold implantation in patients with acute ST-segment elevation myocardial infarction.

  17. 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.

  18. Impact of optical coherence tomography- and coronary angioscopy-assessed neointimal tissue characteristics on occurrence of periprocedural myonecrosis in patients with in-stent restenosis.

    PubMed

    Kimura, Shigeki; Sugiyama, Tomoyo; Hishikari, Keiichi; Nakamura, Shun; Nakagama, Shun; Misawa, Toru; Mizusawa, Masafumi; Hayasaka, Kazuto; Yamakami, Yosuke; Sagawa, Yuichiro; Kojima, Keisuke; Ohtani, Hirofumi; Hikita, Hiroyuki; Takahashi, Atsushi; Isobe, Mitsuaki

    2016-10-01

    Several characteristics of neointimal tissues, including neoatherosclerotic progression, have been reported in lesions with in-stent restenosis (ISR). However, the effects of these characteristics on outcomes after percutaneous coronary intervention (PCI) for ISR lesions remain unclear. We assessed the relationships between neointimal tissue characteristics and the occurrence of periprocedural myonecrosis (PMN) after PCI in ISR lesions. We investigated 72 ISR lesions in 72 patients with stable angina pectoris (SAP) who underwent pre- and post-revascularization optical coherence tomography (OCT) and coronary angioscopy (CAS). All lesions were classified as with PMN, defined by an elevated peak high-sensitivity cardiac troponin-T level during the 24-h post-PCI period, and without PMN. PMN was observed in 23 (31.9 %) lesions. PMN lesions had higher frequencies of OCT-derived thin-cap fibroatheroma (26.1 vs. 6.1 %, P = 0.03), CAS-derived intensive yellow neointima (30.4 vs. 10.2 %, P = 0.04), neointima with complex surface (60.9 vs. 28.6 %, P = 0.01), and CAS-derived atheromatous appearance (CAS-AAP), defined as yellow plaque including complex thrombi underneath disrupted neointimal coverage after ballooning (47.8 vs. 16.3 %, P = 0.008) at the most stenotic sites inside stents, compared to lesions without PMN. Multivariate logistic regression analysis identified CAS-AAP (odds ratio: 3.568, 95 % confidence interval: 1.109-11.475, P = 0.033) as an independent predictor of PMN. For ISR lesions in SAP patients, an OCT- and CAS-based assessment of neointimal tissue characteristics might help to predict the occurrence of PMN. PMID:27423209

  19. 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.

  20. Polychlorinated dibenzo-p-dioxin (PCDD) and dibenzofuran (PCDF) isomer patterns from municipal waste combustion: formation mechanism fingerprints.

    PubMed

    Ryu, Jae-Yong; Choi, Kum-Chan; Mulholland, James A

    2006-11-01

    Polychlorinated dibenzo-p-dioxin (PCDD) and dibenzofuran (PCDF) byproducts can be formed in combustion systems by a variety of mechanisms. While total PCDD/F emissions and, to a lesser extent, homologue distributions from incinerators have been found to vary widely depending on combustion conditions, PCDD/F isomer distributions do not. Formation mechanisms can be grouped into two general categories: condensation of precursors, such as chlorinated phenols, and formation from particulate carbon, termed de novo synthesis. In addition to these mechanisms, chlorination and dechlorination reactions may affect isomer patterns. In this work, isomer patterns from field and laboratory municipal waste combustion samples are compared with computed thermodynamic distributions and those from the following experimental investigations: both gas-phase and metal-catalyzed condensation of chlorinated phenols, chlorination of dibenzo-p-dioxin and dibenzofuran, and dechlorination of octachlorodibenzo-p-dioxin and octachlorodibenzofuran. PCDD/F isomer patterns produced by different formation mechanisms in controlled experiments are distinct and robust, largely unaffected by combustion conditions. PCDD isomer patterns from municipal waste combustion are most similar to those produced by CuCl(2)-catalyzed phenol condensation from 10 chlorinated phenols. PCDF isomer patterns are most similar to those produced by chlorination and dechlorination.

  1. Perivascular adipose tissue-secreted angiopoietin-like protein 2 (Angptl2) accelerates neointimal hyperplasia after endovascular injury.

    PubMed

    Tian, Zhe; Miyata, Keishi; Tazume, Hirokazu; Sakaguchi, Hisashi; Kadomatsu, Tsuyoshi; Horio, Eiji; Takahashi, Otowa; Komohara, Yoshihiro; Araki, Kimi; Hirata, Yoichiro; Tabata, Minoru; Takanashi, Shuichiro; Takeya, Motohiro; Hao, Hiroyuki; Shimabukuro, Michio; Sata, Masataka; Kawasuji, Michio; Oike, Yuichi

    2013-04-01

    Much attention is currently focused on the role of perivascular adipose tissue in development of cardiovascular disease (CVD). Some researchers view it as promoting CVD through secretion of cytokines and growth factors called adipokines, while recent reports reveal that perivascular adipose tissue can exert a protective effect on CVD development. Furthermore, adiponectin, an anti-inflammatory adipokine, reportedly suppresses neointimal hyperplasia after endovascular injury, whereas such vascular remodeling is enhanced by pro-inflammatory adipokines secreted by perivascular adipose, such as tumor necrosis factor-α (TNF-α). These findings suggest that extent of vascular remodeling, a pathological process associated with CVD development, depends on the balance between pro- and anti-inflammatory adipokines secreted from perivascular adipose tissue. We previously demonstrated that angiopoietin-like protein 2 (Angptl2), a pro-inflammatory factor secreted by adipose tissue, promotes adipose tissue inflammation and subsequent systemic insulin resistance in obesity. Here, we examined whether Angptl2 secreted by perivascular adipose tissue contributes to vascular remodeling after endovascular injury in studies of transgenic mice expressing Angptl2 in adipose tissue (aP2-Angptl2 transgenic mice) and Angptl2 knockout mice (Angptl2(-/-) mice). To assess the role of Angptl2 secreted by perivascular adipose tissue on vascular remodeling after endovascular injury, we performed adipose tissue transplantation experiments using these mice. Wild-type mice with perivascular adipose tissue derived from aP2-Angptl2 mice exhibited accelerated neointimal hyperplasia after endovascular injury compared to wild-type mice transplanted with wild-type tissue. Conversely, vascular inflammation and neointimal hyperplasia after endovascular injury were significantly attenuated in wild-type mice transplanted with Angptl2(-/-) mouse-derived perivascular adipose tissue compared to wild-type mice

  2. 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

  3. Developer molecular size dependence of pattern formation of polymer type electron beam resists with various molecular weights

    NASA Astrophysics Data System (ADS)

    Takayama, Tomohiro; Asada, Hironori; Kishimura, Yukiko; Ochiai, Shunsuke; Hoshino, Ryoichi; Kawata, Atsushi

    2016-05-01

    The sensitivity and the resolution are affected by not only the nature of the resist such as a chemical structure and a molecular weight but also the developing process such as a developer molecular size. Exposure characteristics of positive-tone polymer resists having various molecular weights (Mw's) ranging from 60 k to 500 k are investigated using different ester solvents as a developer. The line-and-space (L/S) patterns are exposed by the electron beam writing system with an acceleration voltage of 50 kV and the samples are developed by amyl acetate, hexyl acetate and heptyl acetate. The pattern shape becomes better and the surface of the resist also becomes smoother with increasing developer molecular size, though the exposure dose required for the formation of the L/S pattern increases. The dose margin of pattern formation is also wider in all the resists having the different molecular weights. The dissolution in the unexposed portions of the 60k-Mw resist for heptyl acetate is reduced significantly compared with those for amyl acetate and hexyl acetate. The improvement of the pattern shape and the increasing of dose margin are remarkable in the low molecular weight resist. The 3σ of line width roughness tends to be smaller in the higher molecular weight resist and with the larger molecular size developer. Exposure experiment of the 35 nm pitch pattern using the 500k-Mw resist developed at the room temperature is presented.

  4. Pigment pattern formation in the guppy, Poecilia reticulata, involves the Kita and Csf1ra receptor tyrosine kinases.

    PubMed

    Kottler, Verena A; Fadeev, Andrey; Weigel, Detlef; Dreyer, Christine

    2013-07-01

    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.

  5. 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

  6. Ancestral patterning of tergite formation in a centipede suggests derived mode of trunk segmentation in trilobites.

    PubMed

    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

  7. Cross-correlation patterns in social opinion formation with sequential data

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Anindya S.

    2016-11-01

    Recent research on large-scale internet data suggests existence of patterns in the collective behavior of billions of people even though each of them may pursue own activities. In this paper, we interpret online rating activity as a process of forming social opinion about individual items, where people sequentially choose a rating based on the current information set comprising all previous ratings and own preferences. We construct an opinion index from the sequence of ratings and we show that (1) movie-specific opinion converges much slower than an independent and identically distributed (i.i.d.) sequence of ratings, (2) rating sequence for individual movies shows lesser variation compared to an i.i.d. sequence of ratings, (3) the probability density function of the asymptotic opinions has more spread than that defined over opinion arising from i.i.d. sequence of ratings, (4) opinion sequences across movies are correlated with significantly higher and lower correlation compared to opinion constructed from i.i.d. sequence of ratings, creating a bimodal cross-correlation structure. By decomposing the temporal correlation structures from panel data of movie ratings, we show that the social effects are very prominent whereas group effects cannot be differentiated from those of surrogate data and individual effects are quite small. The former explains a large part of extreme positive or negative correlations between sequences of opinions. In general, this method can be applied to any rating data to extract social or group-specific effects in correlation structures. We conclude that in this particular case, social effects are important in opinion formation process.

  8. 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

  9. Statistical-mechanical analysis of self-organization and pattern formation during the development of visual maps

    NASA Astrophysics Data System (ADS)

    Obermayer, K.; Blasdel, G. G.; Schulten, K.

    1992-05-01

    We report a detailed analytical and numerical model study of pattern formation during the development of visual maps, namely, the formation of topographic maps and orientation and ocular dominance columns in the striate cortex. Pattern formation is described by a stimulus-driven Markovian process, the self-organizing feature map. This algorithm generates topologically correct maps between a space of (visual) input signals and an array of formal ``neurons,'' which in our model represents the cortex. We define order parameters that are a function of the set of visual stimuli an animal perceives, and we demonstrate that the formation of orientation and ocular dominance columns is the result of a global instability of the retinoptic projection above a critical value of these order parameters. We characterize the spatial structure of the emerging patterns by power spectra, correlation functions, and Gabor transforms, and we compare model predictions with experimental data obtained from the striate cortex of the macaque monkey with optical imaging. Above the critical value of the order parameters the model predicts a lateral segregation of the striate cortex into (i) binocular regions with linear changes in orientation preference, where iso-orientation slabs run perpendicular to the ocular dominance bands, and (ii) monocular regions with low orientation specificity, which contain the singularities of the orientation map. Some of these predictions have already been verified by experiments.

  10. Turing Instability and Pattern Formation in a Semi-Discrete Brusselator Model

    NASA Astrophysics Data System (ADS)

    Xu, L.; Zhao, L. J.; Chang, Z. X.; Feng, J. T.; Zhang, G.

    2013-01-01

    In this paper, a semi-discrete Brusselator system is considered. The Turing instability theory analysis will be given for the model, then Turing instability conditions can be deduced combining linearization method and inner product technique. A series of numerical simulations of the system are performed in the Turing instability region, various patterns such as square, labyrinthine, spotlike patterns, can be exhibited. The impact of the system parameters and diffusion coefficients on patterns can also observed visually.

  11. 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.

  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.

  13. Physical mechanisms of self-organization and formation of current patterns in gas discharges of the Townsend and glow types

    NASA Astrophysics Data System (ADS)

    Raizer, Yu. P.; Mokrov, M. S.

    2013-10-01

    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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. Kolmogorov complexity of epithelial pattern formation: the role of regulatory network configuration.

    PubMed

    Flann, Nicholas S; Mohamadlou, Hamid; Podgorski, Gregory J

    2013-05-01

    The tissues of multicellular organisms are made of differentiated cells arranged in organized patterns. This organization emerges during development from the coupling of dynamic intra- and intercellular regulatory networks. This work applies the methods of information theory to understand how regulatory network structure both within and between cells relates to the complexity of spatial patterns that emerge as a consequence of network operation. A computational study was performed in which undifferentiated cells were arranged in a two dimensional lattice, with gene expression in each cell regulated by identical intracellular randomly generated Boolean networks. Cell-cell contact signalling between embryonic cells is modeled as coupling among intracellular networks so that gene expression in one cell can influence the expression of genes in adjacent cells. In this system, the initially identical cells differentiate and form patterns of different cell types. The complexity of network structure, temporal dynamics and spatial organization is quantified through the Kolmogorov-based measures of normalized compression distance and set complexity. Results over sets of random networks that operate in the ordered, critical and chaotic domains demonstrate that: (1) ordered and critical networks tend to create the most information-rich patterns; (2) signalling configurations in which cell-to-cell communication is non-directional mostly produce simple patterns irrespective of the internal network domain; and (3) directional signalling configurations, similar to those that function in planar cell polarity, produce the most complex patterns, but only when the intracellular networks function in non-chaotic domains.

  3. Modeling reaction--diffusion pattern formation in the Couette flow reactor

    SciTech Connect

    Elezgaray, J. ); Arneodo, A. )

    1991-07-01

    We report on a numerical and theoretical study of spatio--temporal pattern forming phenomena in a one-dimensional reaction--diffusion system with equal diffusion coefficients. When imposing a concentration gradient through the system, this model mimics the sustained stationary and periodically oscillating front structures'' observed in a recent experiment conducted in the Couette flow reactor. Conditions are also found under which oscillations of the nontrivial spatial patterns become chaotic. Singular perturbation techniques are used to study the existence and the linear stability of single-front and multi-front patterns. A nonlinear analysis of bifurcating patterns is carried out using a center manifold/normal form approach. The theoretical predictions of the normal form calculations are found in quantitative agreement with direct simulations of the Hopf bifurcation from steady to oscillating front patterns. The remarkable feature of these sustained spatio--temporal phenomena is the fact that they organize due to the interaction of the diffusion process with a chemical reaction which itself would proceed in a stationary manner if diffusion was negligible. This study clearly demonstrates that complex spatio--temporal patterns do not necessarily result from the coupling of oscillators or nonlinear transport.

  4. The Self-Made Puzzle: Integrating Self-Assembly and Pattern Formation Under Non-Random Genetic Regulation

    NASA Astrophysics Data System (ADS)

    Doursat, René

    On the one hand, research in self-assembling systems, whether natural or artificial, has traditionally focused on pre-existing components endowed with fixed shapes. Biological development, by contrast, dynamically creates new cells that acquire selective adhesion properties through differentiation induced by their neighborhood. On the other hand, pattern formation phenomena are generally construed as orderly states of activity on top of a continuous 2-D or 3-D substrate. Yet, again, the spontaneous patterning of an organism into domains of gene expression arises within a multicellular medium in perpetual expansion and reshaping. Finally, both phenomena are often thought in terms of stochastic events, whether mixed components that randomly collide in self-assembly, or spots and stripes that occur unpredictably from instabilities in pattern formation. Here too, these notions need significant revision if they are to be extended and applied to embryogenesis. Cells are not randomly mixed but pre-positioned where cell division occurs. Genetic identity domains are not randomly distributed but highly regulated in number and position. In this work, I present a computational model of program-mable and reproducible artificial morphogenesis that integrates self-assembly and pattern formation under the control of a nonrandom gene regulatory network. The specialized properties of cells (division, adhesion, migration) are determined by the gene expression domains to which they belong, while at the same time these domains further expand and segment into subdomains due to the self-assembly of specialized cells. Through this model, I also promote a new discipline, embryomorphic engineering to solve the paradox of "meta-designing" decentralized, autonomous systems.

  5. Pattern formation in directional solidification under shear flow. II. Morphologies and their characterization.

    PubMed

    Marietti, Y; Debierre, J M; Bock, T M; Kassner, K

    2001-06-01

    In the preceding paper, we have established an interface equation for directional solidification under the influence of a shear flow parallel to the interface. This equation is asymptotically valid near the absolute stability limit. The flow, described by a nonlocal term, induces a lateral drift of the whole pattern due to its symmetry-breaking properties. We find that at not-too-large flow strengths, the transcritical nature of the transition to hexagonal patterns shows up via a hexagonal modulation of the stripe pattern even when the linear instability threshold of the flowless case has not yet been attained. When the flow term is large, the linear description of the drift velocity breaks down and transitions to flow-dominated morphologies take place. The competition between flow-induced and diffusion-induced patterns (controlled by the temperature gradient) leads to new phenomena such as the transition to a different lattice structure in an array of hexagonal cells. Several methods to characterize the morphologies and their transitions are investigated and compared. In particular, we consider two different ways of defining topological defects useful in the description of patterns and we discuss how they are related to each other.

  6. 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.

  7. Impact of Insulin Resistance on Neointimal Tissue Proliferation after 2nd-Generation Drug-Eluting Stent Implantation.

    PubMed

    Komatsu, Takaaki; Yaguchi, Isao; Komatsu, Sachiko; Nakahara, Shiro; Kobayashi, Sayuki; Sakai, Yoshihiko; Taguchi, Isao

    2015-08-01

    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

  8. Internal noise induced pattern formation and spatial coherence resonance for calcium signals of diffusively coupled cells

    NASA Astrophysics Data System (ADS)

    Wang, Maosheng; Sun, Runzhi; Huang, Wanxia; Tu, Yubing

    2014-01-01

    The effects of internal noise in a square-lattice Höfer calcium oscillation system have been studied numerically in the context of chemical Langevin equations. It was found that spatial pattern can be induced by internal noise and, interestingly, an optimal internal noise strength (or optimal cell size) exists which maximizes the spatial coherence of pattern, indicating the occurrence of spatial coherence resonance. The effects of control parameter and coupling strength on system’s spatial coherence have also been investigated. We found that larger internal noise strength is needed to induce spatial pattern for a small control parameter or a stronger coupling strength, and spatial coherence can be enhanced by coupling.

  9. 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.

  10. 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

  11. 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